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1. "Sole or Whole" – Quilting the Racialized Subject Calgary feminist and scholar Aruna Srivastava tackles the complex question of what it means to be "mixed-race/mixedblood/halfbreed/mestizo/hybrid/hyphenated?" in her editorial to Hyphe Nation (1996). In response to her question, this study of contemporary African-Canadian literature suggests that mixed-race Canadians are often constructed as the Other in Canadian society. In consequence, constructions of "racial hybridity" in African-Canadian literature usually aim at carving out a space that doesnt marginalize "racial" mixing but eviscerates restrictive Manichean constructions of identity in order to promulgate concepts of wholeness and self-definition. In consequence, African-Canadian mixed-race writers create hybrid identities that are infinite, multilayered, fragmented and yet whole. They reflect the processes of shifting, overlapping and re-creation in the process of creating identity and can hence be read as representations of complex, de-central, non-hierarchical identities. They are quilting multidimensional racialized subjects. 2. Signifying the In-Between: "Race", "Racial Hybridity" and Questions of Belonging "Race" is not a biological category. Rather it represents a social construction predicated upon the interpretation of difference. It was designed to establish, justify or perpetuate hegemonic social structures and is adherent to the principle of white supremacy. Contemporary "race" theory often neglects the experiences of racially mixed individuals because it fails to offer flexible models of identity in which bi- and multiracial people find themselves represented. This thesis argues in favor of a poetics of difference that accepts and recognizes the heterogeneity of subjectivities while taking into consideration the various dimensions of class, gender, sexuality and ethnicity. Accordingly, constructions of racial hybridity in contemporary African-Canadian literature demonstrate that racism must be acknowledged as an ideology in which people believe and upon which people act. Thus identities often bear the stamp of various histories of resistance and domination, while tackling the question of belonging and re-defining Canadianness. 3. African-Canadian Borderlands References to interracial contacts and the existence of bi- and multiracial people have been omitted from the official founding narratives of the Canadian nation. African-Canadian writers have therefore been successful chroniclers of the past and filled blanks in Canadian historiography in order to shed light on hitherto repressed or erased knowledge. Part of this process is also the inscription of the mixed-race experience into Canadas past. Along this line, bi- and multiracial Canadians often criticize that the state-proclaimed policy of multiculturalism fails to take their manifold racial and ethnic subjectivities into account. 4. "From Sole to Whole" – African-Canadian Mixed-Race Poetics Mixed-race characters in US-American literature often appear in the literary motif of the "tragic mulatto" and it is often implicitly suggested that the bi- or multiracial protagonist is categorized as black. In contrast, African-Canadian constructions of racial hybridity less frequently adhere to the stereotype of the "tragic mulatto" and leave more space for employing alternative modes of racial and ethnic identification. Canadian writers of mixed descent have created a mixed-race poetics that calls attention to contexts, relationships, intersections and wholes. They encourage sites of inclusiveness, incessant shifting and discontinuity in the process of constructing identities. Nevertheless, modes of identification among racially hybrid writers in Canada vary, ranging from detesting whiteness to claiming a Black Nationalist stance. In general, however, they support the idea of fluid and flexible identities. The answer to the initial question of Srivastava is hence given by a vast variety of African-Canadian subject positions. An essentially "black" or "racially mixed" Canadian subject does not exist. Instead, constructions of racial hybridity in African-Canadian literature offer a holistic view of identity and aim at re-conceptualizing the various senses of self and community in Canada. This strategy provides a significant means of self-empowerment and self-reclamation – making racially mixed African-Canadians "whole" instead of "sole".
Until today most social, historical and cultural studies of the American postwar era have contributed to the myth of a relatively homogeneous society and culture. Even though they understood these years as a turning point for modern American society, they failed to encompass the polyvalence and heterogeneity of American society. Focussing mostly on white and middle class males, these studies formed a onedimensional picture of sociocultural conformity, a picture in which issues of gender, race and class were largely absent. Crossing the boundaries of feminist, cultural and historical studies this dissertation starts from identifying the gaps and problems in current academic research. Those sociopolitical structures that affected non-white women are then juxtaposed with the dominant postwar discourse of womanhood. The literary texts by women of color show them grappling with the conflicting demands of socioecnomic realities and pervasive role definitions. On the surface these literary interventions seemed to submit to dominant ideologies while opposing them at the same time. Thus they are both anticipatory and antagonistic. The dissent and criticism in writings by women of color seem to have become a catalyst for the deep social transformations in the following decades.
The thesis is about ideological change of political parties and the way parties gather information, learn by updating their beliefs and ultimately make "rational choices". Analyzing 1451 policy moves of 137 parties in 22 OECD-countries from 1950 to 2013 it is a story about rational learning, about emulating other parties abroad and chasing public opinion. Yet, the "internal life" of a party conditions the effects when activists have some influence over the formation of party policy. As volunteers facing a scarcity of time and resources, members of the party on the ground have a different information horizon, and may arrive at the opposite decision where to move than party elites which (can) rest their decision on a broader set of information resources. In some parties the party on the ground thus constitutes an "internal wall of resistance" to the strategy party elites would choose, if they were free from constraints.
Microbial infections can be either caused by a single species or complex multi-species consortia. One of the most prominent opportunistic human pathogens leading to mono- or mixed-species infections is the Gram-negative bacterium Pseudomonas aeruginosa. Understanding the molecular basis of its adaptation to infection-related stresses is an essential prerequisite for the prevention and treatment of P. aeruginosa infections. We therefore employed state-of-the-art proteomics approaches to elucidate the molecular adaptation mechanisms of P. aeruginosa to infection-related conditions. Moreover, structure, function and interaction of complex microbial consortia containing P. aeruginosa and causing catheter-associated urinary tract infections were investigated by metaproteomics analyses. Our investigations revealed that the adaptation of P. aeruginosa during infection is either based on gene expression changes caused by environmental signal integration or by gene mutations leading to a selective advantage in a particular host environment. In study I, investigating the proteome response of P. aeruginosa biofilms to the clinical relevant antibiotic ciprofloxacin, global changes in the protein profile were observed. Ciprofloxacin induced the expression of proteins involved in the Lex-induced SOS-response, drug efflux pumps and gene products of the ciprofloxacin-responsive prophage cluster and repressed the expression of porins and DNA-binding proteins. In study II the transcriptome and proteome of two clonal P. aeruginosa lineages during long-term colonization of cystic fibrosis (CF) patient’s lungs were analyzed. Point mutations in global regulator genes, i.e. retS, gacS, and gacA, were identified by genomic sequencing. Inactivation of RetS, found two years after the initial colonization, induced the expression of genes involved in chronic infections and coding for the type 6-secretion system (T6SS). Additional mutations in the GacS/GacA two-component regulatory system (TCS) were found to repress the expression of T6SS proteins and to induce the expression of proteins belonging to the type 3-secretion system (T3SS). In study III we elucidated the niche-specific adaptation of P. aeruginosa isolates from different infection sites by investigating their protein expression patterns and glucose metabolic fluxes. We could show that isolates from the urinary tract express a higher amount of proteins involved in the acquisition of micronutrients (i.e. iron) and carbohydrates compared to isolates from the CF lung. In study IV 16S rDNA sequencing and metaproteomics were employed to demonstrate that the investigated CAUTI-related biofilms consisted of two to five different species with one or two species dominating the mixed community. Following this line of research, we investigated in study V structure and function of a biofilm of a long-term catheterized patient, which was predominantly composed of P. aeruginosa and Morganella morganii, but also contained a minor proportion of the obligate anaerobe Bacteroides sp.. The comparison of in vivo and in vitro protein expression profiles of P. aeruginosa and M. morganii indicated that iron and carbohydrates are the major growth-limiting factors in the bladder. These results indicate different nutritional strategies of the two pathogens in the bladder environment. A comparison of urinary protein profiles of healthy persons and catheterized patients suggested that the human innate immune system is induced by CAUTIs. Moreover, numerous proteins involved in nutritional immunity, e.g. iron-, calcium- and magnesium-binding proteins, were found to be more abundant in the urine of catheterized patients. A follow-up (meta)proteomics study (study VI) aiming at the elucidation of interspecies interactions during multi-species infections indicated that the urease-positive uropathogen Proteus mirabilis induces the precipitation of metal ions by urine alkalization and thereby limits the availability of these important micronutrients for other co-infecting bacteria. This limitation seems to be sensed by the P. aeruginosa PhoP-PhoQ two-component system (TCS) leading to an increased resistance to antimicrobial peptides and biofilm-forming capacity of the pathogen. Also during co-cultivation of P. aeruginosa with Staphylococcus aureus a slight increase in the expression of the PhoP-PhoQ TCS and the alkaline protease could be observed (study VII). In study VIII a combined metagenomics and metaproteomics approach was employed to investigate structure and function of the lichen Lobaria pulmonaria, a complex consortium consisting of a fungus, an algal partner, cyanobacteria, and a highly diverse bacterial microbiome. The results presented in this work contribute to a better understanding of the manifold and complex bacterial adaptation mechanisms to infection-related and environmental stress and thereby foster the development of novel treatment and prevention strategies.
Manipulating and utilizing plasmas becomes a more and more important task in various research fields of physics and in industrial developments. Especially in nowadays spacerelevant applications there are different ideas to modify plasmas concerning particular tasks.
One major point of interest is the ability to influence plasmas using magnetic fields. To study the underlying physical effects that were achieved by these magnetic fields for both scenarios Particle-in-Cell simulations were done. Two examples are discussed in this thesis.
The first example originates from an experiment performed by the European Space Agency ESA in collaboration with the German Space Agency DLR. To verify the possibility of heat-flux reduction by magnetic fields onto the thermal protection system of a space vehicle a simplified experiment on earth was developed. Most of the heat that is created during re-entry comes from compression of the air ahead of the hypersonic vehicle, as a result of the basic thermodynamic relation between temperature and pressure. The shock front, which builds up in front of the vehicle deflects most of the heat and prohibits the surface of the space vehicle from direct contact with the maximum flux. State of the art spacecrafts use highly developed materials like ceramics to handle the enormous heat. An attractive approach to reduce costs is to use magnetic fields for heat-flux reduction. This would allow the use of cheaper materials and thus reduce costs for the whole space mission. A partially-ionized Argon beam was used to create a certain heat-flux onto a target. The main finding of the experimental campaign was a large mitigation of heat-flux by applying a dipole-like magnetic field. The Particle-in-Cell method was able to reproduce experimental observations like the heat-flux reduction. An additionally implemented optical diagnostics module allowed to confirm the results of the spectroscopy done during the experiment. The underlying effect that is responsible for the heat-flux reduction was identified as a coupling between the modified plasma and the dominating neutral flux component. The plasma, that is guided towards the target, act as a shield in front of the target surface for arriving neutrals. These neutrals are slowed down by charge-exchange collisions. Furthermore the magnetic field induces an increased turbulent transport that is also needed to reach a reduction in heat-ux. The turbulent transport was also obtained by three-dimensional Direct Simulation Monte Carlo simulations. Unfortunately, such source driven turbulence can not be expected in space, so that a heat flux reduction in real space applications is questionable. Nevertheless, other effects like the induced turbulence by the rotating vehicle can compensate the missing source driven effect.
The second scenario in which a magnetic field is used to modify the heat flux of a plasma is the operation of the pulsed cathodic arc thruster. The same Particle-in-Cell code was used to simulate a typical pulse of this newly developed thruster of Neumann Space Pty Ltd. The typical behavior of the thruster could be reproduced numerically. The thrust is mainly produced by fast electrons. These electrons are accelerated by electric fields as a result of a plasma-beam instability. This plasma-beam instability was verified by a phase space diagnostics for the electrons. To demonstrate the influence of the magnetic field a simulation of the cathodic arc thruster without magnetic field and one with magnetic field were compared. It was shown that the use of a magnetic field leads to a ten times larger thrust by directing the heat ux. The resulting narrow plume is an additional Advantage of the particle guiding magnetic field. This narrowness of the plume reduces the danger of interaction with other components of the space vehicle.
Both scenarios demonstrate the different capabilities for electromagnetic fields to manipulate plasmas and especially the corresponding heat-flux with respect to certain tasks. The possibilities range from reducing the heat-flux onto a target to maximizing the thrust by directing the heat-ux. This thesis demonstrates that simulations are a great tool to support experiments and to deliver an improved physics understanding. They help to identify the basic physics principles in the different systems, because they can deliver information not accessible to experiments.
In particular, a better understanding of the influence of electromagnetic fields on the heat-flux distribution in space-relevant applications was obtained. This can be the basis for further simulation-guided optimization, e.g. for the design of more effective cathodic arc thrusters. Here, the goal is to minimize costs for prototypes by replacing the hardware by virtual prototypes in the simulations. This allows to test basic design ideas in advance and get more highly-optimized designs at a fraction of time and costs.
Until today, more than 17% of the population in Mecklenburg Western-Pomerania suffer from chronic kidney disease (CKD) which was revealed by the SHIP study (Study of Health in Pomerania). 20% of CKD cases can be traced back to glomerulopathies. One common characteristic of glomerulopathies is the morphologic change of the glomerular filtration barrier which consists of endothelial cells, the glomerular basement membrane and podocytes. Under healthy conditions, the foot processes of the podocytes interdigitate with the foot processes of the neighboring podocytes with a filtration slit in between. Apart from the slit membrane protein nephrin, typical adherens junction proteins like occludin or JAM-A are also expressed at this cell-cell junction. This junction is therefore considered to be a specialized type of adherens junction, necessary to maintain the size-selectivity of the filtration barrier. During podocyte injury, podocyte foot processes lose their characteristic morphology and the typical meandering filtration slit becomes linearized, a process which is described as foot process effacement.
Since morphological change is directly linked to change or loss of function, ultrastructural analysis of the foot processes is necessary for diagnostics and research. By using 3D-structured illumination microscopy (3D-SIM), we quantified these morphological changes as well as studied a possible biomarker, the tight junction protein claudin 5 (CLDN5). Our study showed a spatially restricted up-regulation of CLDN5 in effaced filtration slit areas in biopsies of patients suffering from minimal change disease (MCD), focal and segmental glomerulosclerosis (FSGS) as well as in mice after NTS injection and in the uninephrectomy DOCA-salt mouse model. CLDN5/nephrin ratios of biopsies from patients with glomerulopathies and of tissue received from NTS-treated mice were significantly higher compared to controls. We found that in patients the CLDN5/nephrin ratios were negatively correlated with the filtration slit density. Since CLDN5 up-regulation was observed in several areas of high filtration slit density, we hypothesized that CDLN5 upregulation preceded visible foot process effacement. Taken together, we suggest that CLDN5 could be a helpful biomarker to identify an early change of the foot process morphology in addition to filtration slit density measurement. Additionally, correlation analysis of foot process effacement with patient data showed a significant negative correlation of the filtration slit density with proteinuria in MCD patients.
Nowadays, a challenge in wildlife management and nature conservation is to reach a state of human-wildlife coexistence, integrating wildlife into the human-dominated landscape. Achieving a state of coexistence is urgent as human-wildlife conflicts increase over time. Thus a "route guide" for researchers and conservation practitioners will be needed to identify if a human-wildlife interaction is heading towards conflict or coexistence, enabling them to conduct management activities, when possible, to achieve human-wildlife coexistence. Researchers have used different individual-based attributes as a proxy to measure support towards wildlife species by the general public. Different operationalizations from Environmental Economics and Environmental and Conservation Psychology research fields have been used to measure support. Examples of operationalization are the willingness-to-pay and Likert-type scale, or rating scale, from the first and second research fields. In the first, participants must indicate how much they would be willing to pay to protect a specific wildlife species population in a particular area and time. In the second, participants are asked to rate statements through, e.g., a five-point ordinal rating scale with opposite alternatives between, e.g., strongly agree and strongly disagree. In the human dimension of natural resources management research, variations of these methodologies have been used to measure support, not only for one wildlife species but for a set. For the willingness-to-pay variation, i.e., money allocation, participants must distribute a constant sum of money among a set of wildlife species. For the rating scale variation, each of the wildlife species in the set corresponds to a statement to be rated. The thesis aims to contrast these two variations, i.e., money allocation and rating scale, in their capacity to assess support changes towards a set of 12 native wildlife species from different taxa.
A survey was applied in 2018 (n: 368) and replicated in 2019 (n: 359) among urban dwellers who cohabit with the wildlife species set, in Valdivia, south of Chile. The surveys were applied before and after information disclosure and exposure in an experimental and longitudinal research design structure, respectively. As information disclosure, the threatened and endemic status of the wildlife species was presented to the participants. On the other hand, mass media coverage of a human-wildlife conflict involving one of the species included in study, the South American Sea Lion, was used for information exposure. The results indicate that the money allocation method identified support changes among the wildlife species to a greater extent than the rating scale for both types of information (Chapters 2, 3, and 4). The money allocation in the experimental design structure grouped the wildlife species based on their threatened and endemic status, while the rating scale did not come with the same results (Chapter 3). In the longitudinal design structure, the South American Sea Lion support decreased based on the average values of the money allocation and rating scale after the information exposure (Chapter 4). Differently, when the South American Sea Lion position support is compared with the other wildlife species, based on the money allocation, there was a descent, while the rating scale presented an ascent after the mass media coverage of the human-wildlife conflict (Chapter 4). This difference between the results of the two methods, in both research design structures, can be explained to a certain extent due to their scaling technique characteristics. The money allocation is a comparative scale; therefore, the support given to one wildlife species will affect the possible support given to the other species. In contrast, the rating scale is a non-comparative scale, i.e., the support given to a wildlife species is independent of the support given to the other wildlife species in the set. In the experimental research design structure (Chapters 2 and 3), to give or increase the support to a threatened or endemic wildlife species, a bill should be taken from another wildlife species, usually not threatened nor endemic. On the contrary, in the rating scale, there was no need to choose; the support could be increased for a wildlife species without decreasing the support for other wildlife species. In the longitudinal study design structure, the money allocation allows direct comparison between wildlife species from one year to another, while the rating scale does not. For the money allocation, the possible amount of support to be given to a wildlife species, i.e., 12 bills of 1,000 CLP each, did not vary from 2018 to 2019. For the rating scale, the values received among the wildlife species can vary within the rating scale from one year to another, misleading to incorrect interpretations. The money allocation method can be suitable for monitoring human-wildlife interactions, i.e., to position and visualize support shifts. The money allocation could be used as an overview of human-wildlife interactions in a specific area, working as a first assessment.
Pentathiepins are cyclic polysulfides that exert antiproliferative and cytotoxic activity in cancer cells, induce oxidative stress and apoptosis, and potently inhibit GPx1. These properties render this class of compounds promising candidates for the development of anticancer drugs. However, the biological effects and how they intertwine to promote high cytotoxicity have not been systematically assessed throughout a panel of cancer cell lines from distinct tissues of origin. In this thesis, six novel pentathiepins were analyzed and constitute the second generation of compounds with additional properties such as fluorescence or improved water solubility to facilitate cellular testing. All compounds underwent extensive biological evaluation in 14 human cancer cell lines. These studies included investigations of the inhibitory potential with regards to GPx1 and cell proliferation, examined the cytotoxicity in human cancer cell lines, as well as the induction of oxidative stress and DNA strand breaks. Furthermore, selected hallmarks of apoptosis, ferroptosis, and autophagy were studied. Experimental approaches regarding these cellular mechanisms included observing morphological changes, detecting phosphatidyl serine exposure and caspase activity, and quantifying cleaved PARP1 and levels of LC3B II. In addition, the analysis of the cell cycle aimed to identify aberrations or arrests in cell division.
Five of the six tested pentathiepins proved to be potent inhibitors of the GPx1, while all six exerted high cytotoxic and antiproliferative activity, although to different extents. There was a clear connection observed between the potential to provoke oxidative stress and damage to DNA in the form of single- and double-strand breaks both extra- and intracellularly. Furthermore, various experiments supported apoptosis but not ferroptosis as the mechanism of cell death in four different cell lines. In particular, the externalization of PS, the detection of activated caspases, and the cleavage of PARP1 corroborated this conclusion. Additionally, indications for autophagy were found, but more investigations are required to verify the current data. The findings of this dissertation are mainly in line with the postulated mechanism of action proposed for pentathiepins and a previous publication from our group that described their biological activity. However, the influence of modulators such as oxygen and GSH on the biological effects was ambiguous and dependent on the compound. The expression profile of the cell lines concerning GPx1 and CAT did not influence the cellular response toward the treatment, whereas the cell doubling time correlated with the cytotoxicity.
As the various pentathiepins give rise to different biological responses, modulation of the biological effects depends on the distinct chemical structures fused to the sulfur ring. This may allow for future optimization of the anticancer activity of pentathiepins. An analysis of the structure-activity relationships revealed that the piperazine scaffold was associated with superior biological activity compared to the pyrrolo-pyrazine backbone. Furthermore, substituents with electron-withdrawing properties or those providing a free electron pair, such as fluorine or morpholine, were advantageous. These findings should help design and synthesize the next generation of pentathiepins, thereby expanding the library of compounds, allowing for the further deduction of structure-activity relationships and an improved understanding of their mechanism of action.
The present experimental work investigates plasma turbulence in the edge region of magnetized high-temperature plasmas. A main topic is the turbulent dynamics parallel to the magnetic field, where hitherto only a small data basis existed, especially for very long scale lengths in the order of ten of meters. A second point of special interest is the coupling of the dynamics parallel and perpendicular to the magnetic field. This anisotropic turbulent dynamics is investigated by two different approaches. Firstly, spatially and temporally high-resolution measurements of fluctuating plasma parameters are investigated by means of two-point correlation analysis. Secondly, the propagation of signals externally imposed into the turbulent plasma background is studied. For both approaches, Langmuir probe arrays were utilized for diagnostic purposes. The main findings can be summarized as follows: Greatly elongated fluctuation structures exist in plasma edge turbulence. The structures are aligned along the confining magnetic field (k|| = 0). The correlation degree of fluctuations for a short connection length of 0.75m is greater than 80%. For much longer connection lengths of 23m and 66m, the correlation degree is reduced to approximately 40%. A conceptual interpretation of these observations is the coexistence of two different fluctuation components. One component has a correlation length parallel to the magnetic field below 20m and the other component a correlation length greater than 70m. Sine signals in the frequency range 1-100 kHz were injected into the turbulent plasma background. The propagation parallel and perpendicular to the magnetic field of the signals was studied. In poloidal direction, an asymmetry is observed, that can be explained by a copropagation of the signal with the background E × B-rotation of the plasma. The signal propagation parallel to the magnetic field shows no such asymmetry. As an advanced approach, spatio-temporal wave patters were injected into the edge plasma. The waves launched that way can be seen as test waves' in a turbulent background. The coupling strength of the imposed wave patterns to the background turbulence relies on the match of the imposed waves to the dynamics of turbulent structures. If the propagation direction of the imposed waves is parallel to the propagation direction of the background plasma, improved coupling is observed. This finding underlines the importance of the background plasma rotation for future attempts of controlling the plasma edge turbulence. Further optimization of frequency and wave vector of the imposed waves is probably a promising approach for achieving a significant and systematic influence of turbulence. Taking into account the present experimental state-of-the-art, for a deeper insight into the mechanism of the plasma edge turbulence of magnetized high-temperature plasmas a joint effort of numerical modeling and experimental results is a valuable approach. Such a cooperation should cover the explanation of the correlation observations as well as the experiments on signal injection into background turbulence. A quantitative comparison between the results presented in this work and a dedicated numerical drift wave simulation would be a significant step forward to a better understanding of plasma edge turbulence.
Serbian Tertiary ultrapotassic province is part of widespread but not voluminous basaltic magmatism in Serbia. Two principal groups of ultrapotassic rocks are recognized; the lamproite affinity group (LAG) and the kamafugite affinity group (KAG). My results demonstrate three dominant low-pressure evolutional processes: magma mixing and fractional crystallization, analcimization and heteromorphism. The two suites of ultrapotassic rocks show large ranges of Sr and Nd isotopic values but a restricted variation of Pb isotopes. LAG is characterized by wide ranges of Sr and Nd isotopes (87Sr/86Sri 0.70735- 0.71299, 143Nd/144Ndi 0.51251-0.51216). KAG is isotopically homogeneous with a limited range of Sr-Nd isotopes (87Sr/86Sri 0.70599-0.70674, 143Nd/144Ndi 0.51263-0.51256). The Pb isotope compositions of both groups are similar (206Pb/204Pb 18.581-18.832, 207Pb/204Pb 15.624-15.696 and 208Pb/204Pb 38.744-38.987), and fall within the pelagic sediment field resembling Mesozoic flysch sediments from the Vardar ophiolitic composite suture zone. Highly variable Sr and Nd isotopic signatures of primitive-LAG rocks correlate with REE fractionation and enrichment of the HFSE. I explain this correlation using vein+wall-rock melting model, invoking the presence of different metasomatic domains (veins with phlogopite, Cpx and F-apatite) that are out of isotopic equilibrium with the peridotite wall rock. Relatively uniform Sr and Nd isotopic data of KAG rocks, similar trace element patterns and small but regular variations of HFSE ratios, indicate different degrees of melting of a relatively homogeneously metasomatized mantle source. Geochemical modelling implies the role of phlogopite, apatite and Ti-oxide in their mantle source.
Forest ecosystems around the world and especially boreal forests, are facing
drastically changing climatic conditions. It is known that these changes could
challenge their functionality and vitality. Still, the exact impact is not fully
understood, as tree growth is a complex process and depends on countless
environmental and genetic factors. To estimate the effects of climate change
on tree growth and forest development precisely, we must learn more about
tree growth itself. A comprehensive approach is needed where trees and
forests are investigated on different scales and levels of detail, ranging from
global studies to studies on single individuals.
In this dissertation, I follow such a comprehensive approach, using the
North American conifer white spruce as an example. I present three papers
in the form of three chapters in which my co-authors and I studied the
growth and anatomy of white spruce (Picea glauca [Moench] Voss) and how
it is influenced by environmental, climatic, and genetic factors.
We used diverse approaches and methods on different spatial scales, ranging from
investigations on the landscape to the local scale. We established three paired
plots with forest and treeline sites (two cold-limited and one drought-limited).
as well as one additional forest site. In the first chapter, we concentrated
on the genetic diversity of white spruce within and between populations at
all study sites throughout Alaska. The genetic investigations were combined
with analyses on the individual growth response of trees to climatic conditions
to find whether genetic similarities or spatial proximity caused similarities
in growth and climatic sensitivity. In the second chapter, we studied the
direct and indirect effects of environmental conditions on the xylem tissue
of white spruce. We analyzed the impact of precipitation, temperature, and
tree height on four xylem anatomical traits in trees growing at the three
treelines. The investigated traits represented the main functions of xylem
tissue (i.e., water transport and structural support). In the third chapter,
we investigated similar xylem anatomical traits at one cold-limited treeline.
We compared xylem anatomy and annual increment between genetic groups
and individuals and between spatial groups to investigate whether spatial or
genetic grouping influenced the anatomy and growth of white spruce.
We found an overall high gene flow and high genetic diversity in white
spruce. However, the sensitivity of the growth and anatomical traits of white
spruce was driven mainly by spatial rather than genetic effects and differed
between study sites. Trees from the drought-limited site were more sensitive
towards precipitation and a moisture index, while trees from the cold-limited
sites were more sensitive towards temperature. A strong direct effect of tem-
perature was primarily found in latewood traits related to the structural sup-
port of the tree. Earlywood traits related to water transport, however, were
influenced mainly by tree height. Tree height itself was potentially affected
by diverse abiotic and biotic factors (e.g., (micro)climate, soil conditions,
and competition). Thus, traits related to water transport were indirectly
influenced by environmental conditions. Genetic effects in xylem anatomical
traits were found in the earlywood hydraulic diameter and latewood den-
sity, whereas in general, primarily spatial rather than genetic grouping was
influencing the anatomy of white spruce.
Overall, white spruce showed to be a genetically diverse species with a
high gene flow. The effects of spatial proximity and spatial grouping on the
sensitivity and anatomy of white spruce indicate high phenotypic plastic-
ity. This high phenotypic plasticity combined with the vast genetic diversity
translates into an immense potential for the species to adjust (phenotypically)
and possibly adapt (genetically) to changing conditions. Thus, in terms of
climate change, white spruce may be a rather persistent species that manages
to cope with the drastic changes. Though additional work might be needed to
draw a more solid conclusion, the presented work shows how a comprehensive
study approach can help to interpret and understand the growth and ecology
of a tree species. It may be an inspiration for future studies to broaden their
approaches and to use comprehensive methods on different levels of detail to
not only observe trees but to explore and understand them.
In the present work high density helicon plasma discharges are created and characterized as a promising concept towards the realization of plasma wakefield accelerators to build up electric fields in the order of GV/m to accelerate electrons to energies in the TeV range with proton driving bunches. For such a concept plasma sources are needed that are able to maintain discharges with plasma densities of n_e = 7E20 m^-3 over long distances with a low variation in plasma density. Measurements at the PROMETHEUS-A device are performed for variable parameters, like magnetic induction, RF heating power and filling gas pressure. A CO2 laser interferometer, a laser induced fluorescence (LIF) diagnostic and a reaction rate model are combined to give a full picture. It is shown that in most cases the plasma density is centrally peaked with a high density region +- 5 mm from the center. The peak plasma density increases with increasing filling gas pressure, RF heating power and magnetic induction, limited by the number of neutral particles in low pressure discharges, by the transferred heating power and the increasing recombination and electron quenching rates of argon ions in high filling pressure cases. The increase in plasma density with increasing magnetic induction correlates to the direct proportionality in the helicon dispersion relation. For all investigated operational parameters the time evolution of the helicon discharge shows the same characteristics and is reliably reproducable inside the error bars. The electron temperature is determined by combining the collisional radiative model with line ratio measurements of two spontaneously emitted LIF lines. The low electron temperature regime of 1.2 eV < T_e < 1.4 eV and the electron temperature profiles are consistent with helicon wave heating via collisional power dissipation. The maximum plasma density of n_e = (6 +- 1)E20 m^-3 is measured at high RF power of P_RF = 24 kW, p_0 = 9 Pa filling gas pressure and a magnetic induction of B = 105 mT with a maximum electron temperature at 1.4 eV. At these operational parameters the plasma density peaking time and width are determined to be 270E-6 s and 50E-6 s, respectively. This shows that specific plasma density requirements for the use of a wakefield accelerator are reachable and the duration of the peak plasma density is more than sufficient for a relativistic particle to pass a 1 km long plasma cell. Additionally time-resolved LIF profile measurements for neutral and singly ionized argon were conducted to complement the previously evaluated measurements. The time resolution of the LIF diagnostic was chosen in a way to adequately represent the evolution of densities and to allow full profile measurements over one day. A resolution of 200E-6 s was chosen. The time-resolved neutral and ion metastable densities show hollow profiles with high densities at the edges over the first ms indicating higher ionization levels and increasing electron quenching rates. The metastable densities are highly determined by electron temperature, RF heating power and filling neutral gas pressure and do not reflect the neutral argon evolution. To investigate the influence of neutral depletion on the density evolution and maximum plasma density, the argon neutral and ion ground state densities are determined. Both time-resolved density profiles show a hollow profile with highest densities at the edges over a longer time interval of 3-4 ms. The penetration depths (ionization mean-free paths) indicate increased ionization of neutral argon while dissipating inwards, corresponding well to the theoretical value of lambda = 20 mm. This results in a depletion of neutrals in the center of the discharge, leading to a limitation and a fast decrease of plasma density after the neutrals are partially ionized. The shown refilling effect of neutral argon is too slow to have an important impact. At operation parameters for highest plasma density, the calculated ground states also show a fast increase in density at the end of the discharge after the RF-heating is switched off. This indicates recombination effects to these atomic states and higher ionization levels than ArII in the helicon discharge.
A highly stereoselective recombinant alcohol dehydrogenase aus 'Pseudomonas fluorescens' DSM50106
(2005)
The alcohol dehydrogenase was biochemically characterized. A broad range of arylaliphatic ketones is efficiently reduced to the corresponding optically active (R)-alcohols by a recombinant alcohol dehydrogenase (PF-ADH) produced by overexpression in 'Escherichia coli'. PF-ADH shows high activity and stereoselectivity in the reduction of acetophenone and various derivatives (45-99%), as well as in the reduction of 3-oxy-butyric acid methyl ester and 3-oxy-butyric acid methyl ester and 3-oxy-hexanoic acid ethyl ester (>99%). The highest activity was observed between 10 and 20°C. The copfactor NADH can be efficiently recycled by the addition of 10-20% of iso-propanol. A flow-through-polarimetry-based assay to determine oxidoreductase activity and stereoselectivity is described.
A molecular approach to characterize the arbuscular mycorrhizal fungus, Glomus sp. AMykor isolate
(2012)
The arbuscular mycorrhizal fungi (AMF) interaction with plants has a major impact on the soil ecosystem. However, so far, only a few studies on AMF genetics have been performed and molecular information on the genetic diversity of AMF is limited. In this study a fundamental genetic characterization of the industrial isolate, Glomus sp. AMykor (AMykor GmbH, Bitterfeld, Germany) has been undertaken to increase the understanding of AMF genetic diversity. Based on phylogenetic analysis of partial rDNA sequences, Glomus sp. AMykor isolate was proposed to belong to the G. irregulare species together with the reference isolate, DAOM197198. To investigate if both isolates differ in their ploidy level, fluorescence in situ hybridization (FISH) was performed and mainly one or two hybridization signals per nucleus were observed in both isolates. It is suggested that they harbour at least two major rDNA sites and possibly two minor sites. The DNA content was estimated by means of flow cytometry (FC) and confirmed by Feulgen densitometry (FD). The calculated average DNA content per nucleus is 153.0 ± 3.6 Mb for the G. irregulare AMykor isolate and 154.8 ± 6.2 Mb for the DAOM197198 isolate. Since there are plenty criticisms coming recently of using rDNA sequence for fungal barcoding there is necessity of development other system for the identification to species level of Glomeromycotan fungi. The focus of this part of the study was the GiFRD gene encoding fumarate reductase enzyme for use as a potential candidate for AMP species determination. Unfortunately, observed sequence variations do not allow the discrimination of Glomeromycotan species. However, further analysis of enzyme encoded by GiFRD showed a possible role of fumarate reductase in AMF redox balance maintaining under oxygen deficient conditions. Using a yeast expression system, it has been demonstrated that the protein encoded by GiFRD has fumarate reductase activity. The functional expression of GiFRD in the S. cerevisiae fumarate reductase deletion mutant restored the ability of growth under anaerobiosis which indicated that Gifrdp is able to functionally complement the S. cerevisiae missing genes. The fact that GiFRD expression was present only in the asymbiotic stage confirmed existence of at least one metabolic pathway involved in anaerobic metabolism and suggested that AMF behave as a facultative anaerobe in asymbiotic stage.
Understanding the fundamental mechanisms in the extracellular matrix of cells (ECM) is crucial for the development of drugs and biomaterials. Therefore, an atomistic model of the extracellular matrix is a cost-efficient way to observe influences of drugs, test the effect of mutations or misfolds in proteins or study the properties of fibril or network-forming peptides.
With this thesis, a refined molecular model of an adhesion complex is proposed that contains collagen, fibronectin and the cell receptor integrin. During the building of the model, major new insights are given for each of these proteins and a powerful protein-folding algorithm is
developed.
This thesis describes experiments with clusters stored in an electrostatic ion trap called Multi-reflection time-of-flight (MR-ToF) analyzer. These devices are established as mass separators and analyzers with high resolving powers and fast processing times. The objective was to characterize an experiment that utilizes such analyzer for cluster research, to this end a laser-ablation ion source was combined with an MR-ToF analyzer.
In the first part, an experiment scheme that combines two operating modes, namely in-trap lift operation and mirror operation, is presented and characterized for the present setup. For ion capture in-trap lift switching was employed and exit-side mirror switching for ejection with higher information content. Measurements were performed with small lead clusters to illustrate individual advantages of both techniques and the gain of combining them with focus on the ions’ ToF ejection window.
In the second part, a recently introduced method of ion separation by transversal ejection of unwanted species inside the trap was studied for the present setup. The ejection is performed by appropriate pulses of the potentials of deflector electrodes located in the trap. The various parameters affecting the selection effectivity and resolving power are illustrated with tin-cluster measurements, with resolving powers of up to several tens of thousands.
The third part presents the experiment in detail, with the construction of each component and measurements for its various performance parameters. Because the heart of the setup is the MR-ToF analyzer the characterization focuses on the trap. In addition, cluster ions were mass selected in the MR-ToF device and photodissociated. The charged fragments were stored and mass analyzed in a proof-of principle MS/MS experiment where both MS steps were performed in the MR-ToF operation mode.
Background:
Microvascular decompression (MVD) success rates exceed 90% in hemifacial spasm (HFS).
However, postoperative recovery patterns and durations are variable.
Objective:
We aim to study factors that might influence the postoperative patterns and duration needed until
final recovery.
Method:
Only patients following de-novo MVD with a minimum follow-up of 6 months were included.
Overall trend of recovery was modeled. Patients were grouped according to recognizable clinical
recovery patterns. Uni- and multivariable analyses were used to identify the factors affecting
allocation to the identified patterns and time needed to final recovery.
Results:
323(92.6%) patients had >90% symptom improvement and 269(77.1%) patients had complete
resolution at the last follow–up. The overall trend of recovery showed steep remission within the
first 6 months, followed by relapse peaking around 8 months with a second remission ~16
months. Five main recovery patterns were identified.
Patterns analysis showed that evident proximal indentation of the facial nerve at REZ, males and
facial palsy are associated with earlier recovery at multivariable and univariable levels. AICA,
AICA/VA compressions and shorter disease durations are related to immediate resolution of the
symptoms only on the univariable level. Time analysis showed that proximal indentation (vs.
distal indentation), males and facial palsy witnessed significantly earlier recoveries.
Conclusion:
Our main finding is that in contrast to peripheral indentation, proximal indentation of the facial
nerve at REZ is associated with earlier recovery. Postoperative facial palsy and AICA
compressions are associated with earlier recoveries. We recommend a minimum of 1 year before
evaluating the final outcome of MVD for HFS.
This thesis revolves around a new concept of independence of algebras. The independence nicely fits into the framework of universal products, which have been introduced to classify independence relations in quantum probability theory; the associated product is called (r,s)-product and depends on two complex parameters r and s. Based on this product, we develop a theory which works without using involutive algebras or states. The following aspects are considered: 1. Classification: Universal products are defined on the free product of algebras (the coproduct in the category of algebras) and model notions of independence in quantum probability theory. We distinguish universal products according to their behaviour on elements of length two, calling them (r,s)-universal products with complex parameters r and s respectively. In case r and s equal 1, Muraki was able to show that there exist exactly five universal products (Muraki’s five). For r equals s nonzero we get five one parameter families (q-Muraki’s five). We prove that in the case r not equal to s the (r,s)-product, a two parameter deformation of the Boolean product, is the only universal product satisfying our set of axioms. The corresponding independence is called (r,s)-independence. 2. Dual pairs and GNS construction: By use of the GNS construction, one can associate a product of representations with every positive universal product. Since the (r,s)-product does not preserve positivity, we need a substitute for the usual GNS construction for states on involutive algebras. In joint work with M. Gerhold, the product of representations associated with the (r,s)-product was determined, whereby we considered representations on dual pairs instead of Hilbert spaces. This product of representations is - as we could show - essentially different from the Boolean product. 3. Reduction and quantum Lévy processes: U. Franz introduced a category theoretical concept which allows a reduction of the Boolean, monotone and antimonotone independence to the tensor independence. This existing reduction could be modified in order to apply to the (r,s)-independence. Quantum Lévy processes with (r,s)-independent increments can, in analogy with the tensor case, be realized as solutions of quantum stochastic differential equations. To prove this theorem, the previously mentioned reduction principle in the sense of U. Franz and a generalization of M. Schürmann’s theory for symmetric Fock spaces over dual pairs are used. As the main result, we obtain the realization of every (r,s)-Lévy process as solution of a quantum stochastic differential equation. When one, more generally, defines Lévy processes in a categorial way using U. Franz’s definition of independence for tensor categories with inclusions, compatibility of the inclusions with the tensor category structure plays an important role. For this thesis such a compatibility condition was formulated and proved to be equivalent to the characterization proposed by M. Gerhold. 4. Limit distributions: We work with so-called dual semigroups in the sense of D. V. Voiculescu (comonoids in the tensor category of algebras with free product). The polynomial algebra with primitive comultiplication is an example for such a dual semigroup. We use a "weakened" reduction which we call reduction of convolution and which essentially consists of a cotensor functor constructed from the symmetric tensor algebra. It turns dual semigroups into commutative bialgebras and also translates the convolution exponentials. This method, which can be nicely described in the categorial language, allows us to formulate central limit theorems for the (r,s)-independence and to calculate the correponding limit distributions (convergence in moments). We calculate the moments appearing in the central limit theorem for the (r,s)-product: The even moments are homogeneous polynomials in r and s with the Eulerian numbers as coefficients; the odd moments vanish. The moment sequence that we get from the central limit theorem for an arbitrary universal product is the moment sequence of a probability measure on the real line if and only if r equals s greater or equal to 1. In this case we present an explicit formula for the probability measure.
This work studies different alternatives for parallelization of ground-state DMRG, with a focus on shared memory multiprocessor systems. Exploiting the parallelism in the dominant part of a DMRG calculation (diagonalization of the superblock Hamiltonian), speedups of 5 to 6 on 8-CPU machines can be achieved. A performance analysis gives hints as to which machine is best siuted for the task. The parallelized DMRG code is then applied to current problems in theoretical solid state physics with electronics, bosonic and spin degrees of freedom. Stripe-like modulations of the hole density in the ground state of doped Hubbard with cylindrical boundary conditions are idenficied in the thermodynamic limit using extrapolation techniques. In the 1D Holstein model of spinless fermions at half filling, Luttinger parameters and the charge structure factor are determinde in order to derive the phase diagram that had previously been established only on small lattices. For the 1D half-filled Holstein-Hubbard model, a finite size analysisof spine and charge excitation gaps in the relevant sectors (Mott insulator, Peierls band insulator and bipolaronic Peierls insulator) is able to yield the phase diagram as well. Finally, is the Heisenberg spin chain with dynamical phonons is considered as a relevant model for a spin-Peierls transition in Copper Germanate. Using DMRG, the relation between singlet-triplet excitation gap and dynamical dimeriaztion is calculated for the first time.
The thesis develops a scholarly-artistic modular method of analysis for literary studies, film studies and comic studies. Artistic modules of analysis are combined with established research methods used by the humanities on order to deepen the level of understanding of the analysed comic/literary/cineastic work. Martin Rowson's comic adaptation of Laurence Sterne's novel "The Life and Opinions of Tristram Shandy, Gentleman" is analysed with the scholartistic method and treated as an addative literary adaptation.
Hyperoxia is a well-known cause of cerebral white matter injury in preterm infants with male sex being an independent and critical risk factor for poor neurodevelopmental outcome. We investigated the underlying mechanisms behind such a sex dependent difference in oligodendrocyte progenitor cells (OPCs). Our findings demonstrate that oxidative stress severely affects cellular functions related to energy metabolism, stress response, and maturation in male derived oligodendrocyte progenitor cells (OPCs) whereas the female cells remain largely unaffected. This impairment of maturation is accompanied by the downregulation of nucleoporin and nuclear lamina proteins. We identify Nup133, which regulates OPC maturation as a major target protein affected by hyperoxia in male cells and that this differential response is mediated by an inverse Nup133 regulation in the male and female cells. It also regulates mitochondrial function and oxidative stress response through its downstream target Nuclear respiratory factor 1 (Nrf1). Additionally, the presence of 17-β estradiol and higher amounts of fetal zone steroids (precursors for maternal estrogen synthesis during fetal development) confer resistance to the female cells mediated by the estrogen receptor alpha (ERα) along with Nup133. Both Nup133 and ERα regulate mitochondrial function and oxidative stress response by transcriptional regulation of Nrf1. These findings establish prominent sex based differences and the molecular mechanisms involved in differential response of OPCs towards oxidative stress and the important role of Nup133 in mediating a severe negative outcome in the male cells.
The present doctoral dissertation comprises new studies on the fossil vertebrate assemblage recovered from the late Early Jurassic marine “Green Series” clay deposits of Grimmen and Dobbertin in north-eastern Germany that contribute to fill the gap of knowledge regarding its faunal composition and its relevance for understanding Early Jurassic vertebrate life. The investigations led to the recognition of wide range of vertebrate taxa, including basal gravisaurian sauropods, secondarily marine reptiles, a diverse fauna of leptolepid fishes, and a new genus and species of pycnodontiform fishes. In addition, a taxonomic revision of the Early Jurassic saurichthyid fish Saurorhynchus was performed, leading to the identification of two new, previously unnamed species. The results provide new insights into the taxonomic, systematic, and ecological diversity of Early Jurassic vertebrates, and hence add significant new data to our knowledge on Lower Jurassic vertebrate palaeobiodiversity patterns.
Numerous signalling pathways orchestrate the development, the functions, and the survival of cells, mostly in response to external stimuli. An overwhelming amount of data supports the concept of specific, spatio-temporal redox signalling pathways that affect the redox state of protein cysteinyl side chains and thus the biological function of these proteins. Glutaredoxins (Grxs) and thioredoxins (Trxs) catalyse reversible thiol-disulphide exchange reactions. The cytosolic Grx2 isoform Grx2c is essential for brain development and axonal outgrowth. A reversible dithiol-disulphide switch of CRMP2 has been identified as one of the major targets regulated by Grx2c. This CRMP2 redox switch is toggled in neuronal differentiation. Reduction of CRMP2 thiols induces profound conformational changes, modifying interactions and downstream elements of this redox switch. In [article I] and [manuscript V], we identified the Cys504 of CRMP2 to be the redox regulated residue. We used various in vitro assays with recombinant protein and molecular dynamics simulations to characterise the conformational change. The changes involve the solvent accessible surface area of at least one known phosphorylation site at the C-terminus of the protein. In [article III], we analysed the function of Grx2 and Trx1 in a model for perinatal asphyxia. Trx family proteins exhibit a very complex, cell-type and tissue specific expression pattern following hypoxia/ischemia and reoxygenation, especially Trx1 and Grx2. The results imply the clinical relevance for both proteins in perinatal asphyxia as well as many other neurological disorders. In agreement with the results presented in [articleI], Grx2 may be required for the re-establishment of neuronal integrity and connectivity. Cell shape, all forms of intracellular transport, and cell movement depend on the cytoskeleton, particularly on the fine tuned complex regulation of the dynamic re-arrangement of actin filaments and microtubules. In [article IV], we discuss the redox regulation of this dynamic cytoskeletal remodelling. Taking recent discoveries into account, we focus on redox signalling mechanisms, e.g. reversible thiol and methionyl switches. These switches are specifically controlled by enzymes such as Trx1 and Grx2c, for instance, and not the result of random modification by unspecific oxidants. Methionyl sulphoxidation of actin can be reversed by methionyl sulphoxide reductase (MsrA), promoting actin polymerisation. Human cells express two different Msr enzymes (MsrA and MsrB), that can reduce S- and R-methionyl sulphoxide, respectively. In the gram-positive Streptococcus pneumoniae, on the other hand, both Msr genes and thus enzymes were fused during evolution. In [article II], we characterised the surface-exposed thioredoxin family lipoproteins Etrx1 and 2 and regulators of this Msr (SpMsrAB). A loss of function of both Etrx proteins or SpMsrAB dramatically reduced pneumococcal virulence, enhanced the bacterial uptake by macrophages, and accelerated pneumococcal killing by H2O2 or free methionine sulphoxide. Identification and characterisation of components of this redox regulated system may contribute to the design of new antimicrobials. In [manuscript VI], we investigated the effects of Grx2c expression on cell morphology, migration, and invasion behaviour of cancer cells. Grx2c expressing cancer cells developed dramatic changes in phenotype, including alterations in cytoskeletal dynamics and significantly increased motility and invasiveness. We used quantitative proteomics and phopshoproteomic approaches to characterise the underlying mechanisms. Proteins and pathways regulating cytoskeletal dynamics, cell adhesion, and receptor-mediated signal transduction were detected to be specifically altered. We started a clinical pilot study with patients suffering from clear cell renal cell carcinoma (ccRCC). Grx2c was expressed with significantly higher frequency in ccRCC compared to healthy kidney tissue, associated with a strong trend for locally more advanced tumour stages and a clear tendency for a decreased cancer-specific survival, compared to patients without detectable Grx2c. These results were supported by data from "The Cancer Genome Atlas". In synopsis, the results presented and discussed in these articles and manuscripts, support the concept of specific redox signalling in different models and model organisms. They also demonstrate the importance of the specific redox control of signalling pathways that, in the case of errors or misinterpretations, contribute to pathophysiological alterations. The regulation of the CRMP2 redox switch by Grx2c, for instance, is physiologically essential for brain development, but might lead to cancer progression, if "switched on" in adult tissue. Identification of further interaction partners as well as the development of compounds modulating this redox switch and CRMP2s conformations, will be part of our future research.
Liu–II coal pit is a typical example of China’s deep coal mines which is seriously threatened by groundwater inrush from the underlying carboniferous Taiyuan limestone formation. An exhaustive data set of this confined aquifer exists. The aquifer lies 45 m∼ 60 m below the major coal seam. A traditional artesian aquifer test has been performed in order to assess the hydraulic properties, e.g. transmissivity (T) and storage coefficient (S). This artesian aquifer test is conducted with four simultaneously operating production wells while the discharge of each production well varied with time. The results of this test suggest that the aquifer is heterogeneous. Therefore, the according problems are: (1) how to analyze the artesian aquifer test with linearly declining discharge; (2) how to deal with multiple production wells in an aquifer test; (3) how to adequately consider aquifer heterogeneity. Thus, the objective of this thesis is to solve these problems. 1) As opposed to classical above-ground pumping tests, it is difficult to control the discharge rate of the production well in a deep mine artesian aquifer test since the hydraulic pressure is extraordinary high. Moreover the discharge rate won’t descend rapidly to zero, thus the analytical solution of Jacob and Lohman (1952) type curve for the artesian aquifer test will not be applicable. It is more reasonable to analyze the test as a pumping test with variable discharge. It is considered to rebuild a hydrogeological conceptual model which is similar with Theis (1935) model but with the variable discharge. A general equation for any discharge variability is given. Its application for the linearly declining discharge is presented subsequently, and a type curve of this equation with linearly declining discharge is given as well. After that, a simple numerical model is built by FEFLOW to simulate an artificial pumping test with the linearly declining discharge by assigning different parameter sets for transmissivity and storage coefficient. The type curve method is applied to evaluate transmissivity and storage coefficient for the linearly declining discharge well. The deviation between the given values of transmissivity and storage coefficient in FEFLOW and the values of those calculated by matching point are sufficiently small. Thus, when the discharge of production well declines linearly, a type curve method as an empirical method is reasonable and gives satisfactory values of these hydrogeological parameters. 2) In some cases, it is necessary to conduct a pumping test (or an artesian aquifer test) with several pumping wells (or production wells) which work simultaneously in order to discharge maximum quantity of groundwater. Normally, the superposition method or numerical simulation is applied to analyze the test result. However, a new approach called “Well Generalization Method” is defined and analyzed in this thesis. It is an easy–to–use approach for hydrogeologist to estimate the aquifer parameters while conducting an aquifer test. Since the key point of this approach is using a generalization well to substitute the pumping (or production) wells, it is obvious that this approach will generate the estimated error of parameters. Accordingly, several scenarios are analyzed and discussed based on the artificial type aquifer designed in FEFLOW. A homogeneous aquifer and a heterogeneous aquifer which is generated by geostatistical stochastic simulation technique (see 3)) are discussed separately. As a result, this approach is feasible and applicable under some conditions when the calculated observation well is arranged more than about 2.5 times the scale of the multi–pumping–wells field away from the center of the multi–pumping–wells field, furthermore, the maximum deviation of drawdown resulting from these observation wells will be less than 0.5 m, and the estimated value of transmissivity will be 0.44% smaller than real value. 3) Finally aquifer heterogeneity is addressed, in order to check the introduced method for applicability under realistic conditions. It has been described that aquifer heterogeneity plays a major role in hydrodynamic processes (e.g. de Marsily et al., 1998). Geostatistics which is considered as a useful tool for characterizing the spatial variability of transmissivity is applied to solve this problem. Based on the results of the artesian aquifer test conducted in Liu–II coal pit, a model of spatial variability of transmissivity is developed. Sequentially, the variogram model is applied in ordinary kriging to interpolate the transmissivity distribution, and in sequential Gaussian simulation to simulate a random field of transmissivity data in order to reflect its small scale variability. A comparison of the results of estimation and simulation of transmissivity indicates that the simulated values better reflect the spatial variability, reversely, the estimated values are much smoother.
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.
Microbial cell factories have been largely exploited for the controlled production of recombinant proteins, including industrial enzymes and biopharmaceuticals. The advent of high-throughput ‘-omics’ techniques have boosted the design of these production systems due to their valuable contribution to the field of systems metabolic engineering, a discipline integrating metabolic engineering with systems and synthetic biology. In order to thrive, the field of systems metabolic engineering needs absolute proteomics data to be generated, as proteins are the central players in the complex metabolic and adaptational networks. Due to advent of mass spectrometry-based proteomics, a substantial amount of absolute proteomic data became available in the past decade. However, membrane proteins remained inaccessible to these efforts.
Nonetheless, comparative studies targeting the membrane proteome have been quite successful in characterizing physiological processes. Hence, label-free proteomics was used in a study (Quesada-Ganuza et al, 2019 – Article I) to identify and optimize PrsA in Bacillus subtilis, for improved yield of amylase. Amylase is one of the most relevant enzymes in the biotechnological sector. By employing a label-free mass spectrometry approach targeting the membrane proteome of this bacterium, relative changes in heterologous and native levels of PrsA could be quantified. The results of this study evidenced that each PrsA shows different relative abundancies, but with no relevant impact in the yield of amylase.
Even though relative protein quantification can already provide a good visualization of the physiological changes occurring between different conditions, they are not sufficient to understand how resources are allocated in the cell under certain physiological conditions. Therefore, a global method for absolute membrane protein quantification remains the biggest requirement for systems metabolic engineering.
Hence, with this work, we successfully developed a mass spectrometry-based approach enabling the absolute quantification of membrane proteins (Antelo-Varela et al, 2019 – Article II). This study was also performed in the Gram-positive model organism Bacillus subtilis, regarded as a prolific microbial cell factory. The method developed in this work combines the comprehensiveness of shotgun proteomics with the sensitivity and accuracy of targeted mass spectrometry. Fundamental to the method is that it relies on the application of a correction and an enrichment factor to calibrate absolute membrane protein abundances derived from shotgun mass spectrometry. This has permitted, for the first time reported, the calculation of absolute membrane protein abundances in a living organism.
The newly developed approach enabled to accurately quantify ~40% of the predicted proteome of this bacterium, offering a clear visualization of the physiological rearrangements occurring upon the onset of osmotic stress. In addition, this work also provides evidence for new membrane protein stoichiometries.
Overall, this study enabled the development of a straightforward methodology long-needed in the scientific and biotechnological community and, for the first time reported, providing absolute abundances of one of the most puzzling fractions of the cell – the membrane proteome.
The next step of the work summarized here was to implement the afore described method to a biotechnological relevant strain, as absolute membrane protein abundances are essential to understand the fundamental principles of protein secretion and production stress. Hence, this work was applied in a genome-reduced B. subtilis strain, ‘midiBacillus’, expressing the major staphylococcal antigen IsaA (Antelo-Varela et al, submitted – Article III). The employed absolute membrane protein quantification methodology enabled the analysis of physiological rearrangements occurring upon the induction of heterologous protein production. This work showed that, even though IsaA was successfully secreted into the growth medium, one of the main requirements for the biotechnological sector, it was still partly accumulated in the cell membrane of this bacterium. This led to an exacerbated physiological response where membrane proteins involved in the management of secretion stress were activated. In addition, this study also showed that a rearrangement of the cell’s translocation machinery occurs upon induction of production, where a ‘game’ of in- and decrease of transporters takes place.
Anticipating the impact of genetic and environmental insults, such as the ones caused by production stress, is essential for the field of systems metabolic engineering. Thus, the highly accurate and comprehensive dataset generated during this work can be implemented in predictive mathematical models, thereby contributing in the rational design of next-generation secretion systems.
In this work, spatial distributions for reactive stable and transient species that are involved
in the reaction cycle of H2O2, a key species for biomedical applications, were
determined directly in the effluent of a kINPen-sci plasma jet. The small diameter
of cold atmospheric pressure plasma jets and their operation at atmospheric pressure
that causes strong quenching reactions make diagnostics challenging. Here, various diagnostic
techniques have been employed and adapted for the use in the effluent of a
cold atmospheric pressure plasma jet, which were laser atomic absorption spectroscopy
(LAAS) at 811.5 nm for the detection of Ar(3P2), picosecond two-photon absorption
laser-induced fluorescence spectroscopy (ps-TALIF) at 225 nm and 205 nm for the
detection of O and H atoms, respectively, and continuous wave cavity ring-down spectroscopy
(cw-CRDS) at 1.506 µm for the detection of HO2, and cw-CRDS at 8000 µm
for the detection of H2O2. All these methods provide absolute number densities. In
this work, spatial distributions within the small diameter of the effluent of a CAPJ
were obtained, which have not been reported so far literature. In order to overcome the
line-of-sight limitations of CRDS, radial scans were performed and transformed into a
spatial distribution by using Abel inversion.
Based on the determined spatial density distributions for H atoms, O atoms, HO2
radicals, and H2O2 molecules, together with the investigated impact of humidity in the
feed gas on the excitation dynamics and the production of Ar(3P2), and finally on a
comparison of the experimental results to a plasma chemical and reacting flow model,
three different zones with varying reaction kinetics were identified. The densities close
to the nozzle of the kINPen-sci plasma jet were dominated by reactions within the
plasma zone including the dissociation of H2O added to the Ar feed gas and O2 that
was presumably transferred into the plasma zone by counter-propagating ionisation
waves. Notably, also the larger molecules, such as HO2 and H2O2 were mainly formed
within the plasma zone of the plasma jet. Between 1.5 mm and 5 mm below the nozzle,
the atomic species and molecular radicals generated in the plasma zone were consumed
by chemical reactions with the surrounding gas, whose composition was controlled by
applying a gas curtain. At further distances from the nozzle, where typically biological
samples are positioned, only H2O2 and HO2 were observed.
With this work, it is successfully demonstrated that even for the small diameters of
cold atmospheric pressure plasma jets the determination of spatial profiles for reactive
transient and stable species is possible within the effluent. By combining the experimental
results, important insights into the formation and consumption of H2O2 and its
precursors were gained, which are essential for the understanding of use of plasmas in
biomedical applications.
Tunable Diode Laser Absorption Spectroscopy in the mid InfraRed spectral range (IR-TDLAS) has been applied to investigate the behaviour of CF, CF2 and C2F4 species produced in pulsed CF4/H2 capacitively coupled radio frequency plasmas (13.56 MHz CCP). This experimental technique was shown to be suitable for temporally resolved measurements of the absolute number density of the target molecules in the studied fluorocarbon discharges. The temporal resolution of about 20…40 ms typically achieved in the standard data acquisition mode (“stream mode”) was sufficient for the real-time measurements of CF2 and C2F4, but not of CF whose kinetics was observed to be much faster. Therefore, a more sophisticated approach (“burst mode”) providing a temporal resolution of 0.94 ms was established and successfully applied to CF density measurements. In order to enable the TDLAS measurements of the target species, preliminary investigations on their spectroscopic data had been carried out. In particular, pure C2F4 has been produced in laboratory by means of vacuum thermal decomposition (pyrolysis) of polytetrafluoroethylene and used as a reference gas. Therefore, an absorption structure consisting of several overlapping C2F4 lines around 1337.11 cm-1 was selected and carefully calibrated, which provided the first absolute measurements of the species by means of the applied experimental technique. The absolute number density traces measured for CF, CF2 and C2F4 in the studied pulsed plasmas were then analysed, in which two differential balance equations were proposed for each of the species to describe their behaviour during both “plasma on” and “plasma off” phases. Analytical solutions of the balance equations were used to fit the experimental data and hence to deduce important information on the kinetics of the studied molecules. In particular, during the “plasma off” phase, the self-recombination of CF2 (CF2 + CF2 (+M) → C2F4 (+M)) was found to be dominant in the kinetics of the radical, but of minor importance for C2F4 production. A rapid consumption of CF observed within 7…25 ms after switching off the plasma was explained mainly by volume reaction with other species (most likely with CF3), whereas diffusion of the radical towards the reactor walls followed by sticking on the surfaces was found to contribute only at relatively low pressures (<10 Pa). Under certain discharge conditions, measured CF density traces exhibited significant overshoots in 50…150 ms after the plasma ignition, which had not been known from literature before. The electron impact fragmentation of C2F4 was shown to be essential for CF production at the beginning of the “plasma on” phase and therefore for formation of the observed CF density overshoots. Finally, the broad band FTIR spectroscopy was applied in order to better characterize the gas phase composition of the studied plasmas. Thus, absorption bands of CF4, C2F4, C2F6, C3F8, CHF3 and HF stable molecules were detected in the FTIR spectra recorded between 400 and 4000 cm-1. The spectra were then successfully deconvolved and the absolute concentration of the detected species was estimated. In particular, the absolute number density of C2F4 obtained from the FTIR measurements was in a good agreement with that achieved by means of the IR-TDLAS technique. The work was supported by the German Research Foundation (DFG) within the framework of the Collaborative Research Centre Transregio 24 “Fundamentals of Complex Plasmas” (SFB/TRR24, project section B5).
Turbulence is a state of a physical system characterized by a high degree of spatiotemporal disorder. Turbulent processes are driven by instabilities exhibiting complex nonlinear dynamics, which span over several spatial as well as temporal scales. Apart from fluids and gases, turbulence is observed in plasmas. While turbulent mixing of a system is sometimes a desired effect, often turbulence is an undesired state. In hot, magnetically confined plasmas, envisaged for energy generation by thermonuclear fusion, plasma turbulence is clearly a problem, since the magnetic confinement time is drastically deteriorated by turbulent transport. Hence, a control mechanism to influence and to suppress turbulence is of significance for future fusion power devices. An important area of plasma turbulence is drift wave turbulence. Drift waves are characterized by currents parallel to the ambient magnetic field, that are tightly coupled to a coherent mode structure rotating in the perpendicular plane. In the present work, the control of drift waves and drift wave turbulence is experimentally investigated in the linear magnetized helicon experiment VINETA. Two different open-loop control systems - electrostatic and electromagnetic - are used to drive dynamically parallel currents. It is observed that the dynamics of the drift waves can be significantly influenced by both control schemes. If the imposed mode number as well as the rotation direction match those of the drift waves, classical synchronization effects like, e.g., frequency locking, frequency pulling, and Arnold tongues are observed. These confirm the nonlinear interaction between the control signal and the drift wave dynamics. Finally, the broadband drift wave turbulence, and thereby turbulent transport, is considerably reduced if the applied control signal is sufficiently large in amplitude.
Despite a plethora of therapeutic approaches, the injection of local anaesthetics itself remains one of the most painful and dreadful procedures among children. Stimulation of acupoint LI4 is associated with analgesic effects in dentistry. Goal of the study To investigate whether stimulation of LI4, added to standard therapy (ST), reduces pain and distress during injection of local anaesthetic (LA) in comparison with ST alone. Materials and Methods Children, scheduled for dental treatment in local anaesthesia on 2 separate days were enrolled in this trial, approved by local ethics commission. On one day each child received bilateral acupuncture of LI4 point, using indwelling fixed “New Pyonex” needles (0.2 x 1.5 mm; Seirin, Japan). The parents of the children were asked to stimulate the needles by massage. Standardized injection of LA was performed 5 min following acupuncture. The needles were withdrawn at the end of dental treatment. On the other day of treatment children received LA injection without acupuncture. The order of treatment days (acupuncture first or vice versa) was randomised. Primary endpoint was the pain intensity during LA injection reported by children on Visual Rating Scale from 0=no pain to 10=maximal pain imaginable (VRS-11). Secondary endpoints were parent- and dentist-assessed pain intensity (measured on Numeric Rating Scale 1-10), patients’ heart rate before and during dental treatment and satisfaction with received therapy (measured on Numerical Rating Scale 1-5.) Side effects of LI4 stimulation were also recorded. Results and Discussion The data of 49 children (22 females; age 10 ± 4 yrs; mean ± SD), who completed both visits, were analysed. Children reported less pain with than without acupuncture: 2.2 ± 2.5 vs. 3.9 ± 2.7; mean ± SD, p<0.001. Heart rate decreased after LI4 stimulation compared to ST alone throughout the dental treatment (p<0.05). LI4 stimulation was safe and raised better satisfaction with the treatment among children and parents, than ST alone (p<0.05). Other secondary endpoints were comparable between both sessions. Conclusion Stimulation of acupuncture point LI4 reduces pain and autonomous stress during injection of local anaesthetics in paediatric dentistry.
Adaptation mechanisms within the B cell composition for successful human and murine pregnancies.
(2021)
Introduction
A well-balanced immune maternal status is essential for favourable outcome of pregnancy. Due to their complexities, not all immune adaptations that promote tolerance during pregnancy are known. To understand the adaptation of the B cell compartment, we analysed and compared B cell lymphopoiesis in different lymphoid tissues in a number of murine models.
Furthermore, we focused on the humoral immune response during pregnancy. We analysed immunoglobulin profiles in human subjects and mice during pregnancy.
These cellular alterations are subject to the influence of chemokines, among others. Therefore, we assessed serum levels of B cell activation factor to clarify its effects during pregnancy.
Methods
For analysis of the human peripheral B cell compartment, peripheral blood samples from age-matched non-pregnant and pregnant women without pregnancy complications, immunological disease or acute/chronic inflammation were collected and sub-classified into four different groups: non-pregnant, and first, second, or third trimester of pregnancy. The experiments, based on a mouse model, were performed with 8-week-old female mice: clinically healthy non-pregnant (CBA/J (H2k)), pregnant mice with normal gestation (BALB/c (H2d) x CBA/J (H2k)), and mice with pregnancy loss (DBA/2J (H2d) x CBA/J (H2k)). Subsequently, peripheral blood mononuclear cells from blood and lymphatic organs were isolated following standard protocols. The B cell analysis was performed by flow cytometry. The immunoglobulin serum levels of the human and murine subgroups were quantitated using Bio-Plex isotyping assay and analysed by a Bio-Plex reader. To quantify B cell activating factor (BAFF) in serum of pregnant and non-pregnant mice a BAFF enzyme-linked immunosorbent assay was used. The concentrations were determined by using a FLUOstar OPTIMA microplate reader. All statistical analyses were performed using the Kruskal–Wallis test with Dunn’s post-test in GraphPad Prism software. P values of < 0.05 were considered statistically significant.
Results
We were able to demonstrate B cell lymphopenia in mice bone marrow downstream of pre-pro B cells, irrespective of pregnancy outcome. The mature bone marrow B cells did not show this adjustment mechanism during normal gestation.
Closer inspection of the splenic tissue revealed expansion and activation of marginal zone B cells in mice with a normal pregnancy. However, this was not observed in mice suffering from pregnancy disturbances. Natural antibodies secreted from marginal zone B cells were also present at higher concentrations in serum of pregnant mice, compared to non-pregnant animals.
We also found significantly higher levels of natural antibodies in serum of pregnant women compared to non-pregnant age-matched controls. Analysis showed significantly lower levels of BAFF in mice with normal pregnancy as compared to non-pregnant mice.
Conclusions
We are able to show mechanisms within the B cell compartment as well as the change within the natural antibodies that might be crucial for successful pregnancy in both humans and mice. Furthermore, BAFF seems to play a central role as a mediator of peripheral B cell compartment and B cell lymphopoiesis in the bone marrow for successful pregnancy.
The toluene-degrading and solvent-tolerant strain Pseudomonas putida DOT-T1E was investigated with respect to its suitability and economic efficiency as biocatalyst in aqueous-organic two-phase systems with aliphatic solvents as organic phase (Rojas et al. 2004, chapter 4 and 5) and to its adaptive responses to the solvent decanol. The adaptive changes on the level of cell morphology (chapter 2), membrane fatty acids and permeability (chapter 3), as well as energetics and surface properties (chapter 5) of P. putida DOT-T1E have been investigated in order to ascertain information about the strain's suitability for two-phase biotransformation systems (chapter 4). The morphological adaptation to the presence of solvents was observable in changes of the cell size of P. putida DOT-T1E. Those changes were dependent on the cellular activity and occurred only after addition of non-lethal solvent concentrations. The cells reacted to the presence of organic solvents by decreasing the ratio between surface and volume of the cells and therefore reducing their relative surfaces (chapter 2). The cell surface and especially the cytoplasmic membrane are the major targets for toxic effects of membrane-active compounds like solvents. The mechanism of the cis-trans isomerisation of unsaturated fatty acids counteracts the fluidizing effect of solvents by increase the ordering of the membrane and therefore its rigidity. By comparing the responses of the cells to a series of stress factors (like solvents), a direct correlation between the activation of this mechanism and the well investigated K+-uptake pumps was observed (chapter 3). Huertas et al. (1998) reported that this strain tolerated concentrations of heptane, propylbenzene, octanol, and toluene of at least 10 % (vol/vol). 1-decanol is, in comparison to toluene, less hazardous and volatile, and it possesses good extraction properties for the desired fine chemical products. In further investigations of possible biotechnological processes, it was discovered that decanol is also a more suitable solvent as organic phase (chapter 4). Although the cells of P. putida DOT-T1E needed additional energy for their adaptation to the presence of the solvent decanol, they were able to maintain or activate their electron transport phosphorylation allowing homeostasis of ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities converging with more negative cell surface charges were observed in cells grown in the presence of 1-decanol (chapter 5). It is however important to note that all the cell’s properties observed are closely linked to each other since they are all part of the adaptive response of the cells. It can be concluded that the easy adaptability and good growth properties of Pseudomonas putida DOT-T1E in the presence of the organic solvent 1-decanol make this system an excellent candidate for two-phase fermentation processes. Moreover, the absence of differences in the energetics of the bacteria during exposure to 1-decanol as compared to bacteria that grew in the absence of 1-decanol, support that this organism can be used for the industrial production of fine chemicals in an economically sound manner.
Technological advances in light microscopy have always gone hand in hand with unprecedented biological insight. For microbiology, light microscopy even played a founding role in the conception of the entire discipline. The ability to observe pathogens that would otherwise evade human observation makes it a critical necessity and an indispensable tool to infectious disease research. Thus, the aim of this thesis was to optimize, extend, and functionally apply advanced light microscopy techniques to elucidate spatio-temporal and spatio-morphological components of bacterial and viral infection in vitro and in vivo.
Pathogens are in a constant arms race with the host’s immune system. By finding ways to circumvent host-mediated immune responses, they try to evade elimination and facilitate their own propagation. The first study (publication I) demonstrated that the obligate intracellular pathogen Coxiella burnetii is not just able to infect natural killer (NK) cells, but is actually capable of surviving the harsh degradative conditions in the cytotoxic lymphocyte’s granules. Using live-cell imaging of reporter-expressing Coxiella burnetii, the transient NK cell passage was closely monitored to provide detailed spatio-temporal information on this dynamic process in support of a range of static analyses. Bacterial release from NK cells was pinpointed to a time frame between 24 to 48 hours post-infection and the duration of release to about 15 minutes.
The second approach (publications II-V) aimed at shedding light on the greater spatio-morphological context of virus infection. Thus far, most studies investigating the distribution or tropism of viruses in vivo have used conventional immunohistochemistry in thin sections. Omitting the native spatial context of the infection site in vivo inherently bears the risk of incomplete description. While the microscopic tools and sample preparation protocols needed for volumetric 3D immunofluorescence imaging have recently been made available, they had not gained a foothold in virus research yet. An integral part of this thesis was concerned with the assessment and optimization of available tissue optical clearing protocols to develop an immunofluorescence-compatible 3D imaging pipeline for the investigation of virus infection inside its intact spatio-morphological environment (publication II). This formed the basis for all subsequent volumetric analyses of virus infection in vivo presented here. Consequently, this thesis provided a valuable proof of concept and blueprints for future virus research on the mesoscopic scale of host-pathogen interactions in vivo (publications II-V), using rabies virus (RABV; publications II-IV) and the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; publication V) as infection models for the nervous system and the respiratory tract, respectively.
Applying and further improving this volumetric 3D imaging workflow enabled unprecedented insights into the comprehensive in vivo cell tropism of RABV in the central (CNS) (publication III) and peripheral nervous system (PNS) (publication IV). Accordingly, differential infection of CNS-resident astrocytes by pathogenic and lab-attenuated RABV was demonstrated (publication III). While either virus variant showed equal capacity to infect neurons, as demonstrated by quantitative image analysis, only pathogenic field RABVs were able to establish non-abortive infection of astrocytes via the natural intramuscular inoculation route. A combined 3D LSFM-CLSM workflow further identified peripheral Schwann cells as a relevant target cell population of pathogenic RABV in the PNS (publication IV). This suggested that non-abortive infection of central and peripheral neuroglia by pathogenic RABV impairs their immunomodulatory function and thus represents a key step in RABV pathogenesis, which may contribute significantly to the establishment of lethal rabies disease.
Finally, utilizing the full volumetric acquisition power of LSFM, a further refined version of the established 3D imaging pipeline facilitated a detailed mesoscopic investigation of the distribution of SARS-CoV-2 in the respiratory tract of the ferret animal model (publication V). Particularly for this newly-emerged pathogen of global concern, in-depth knowledge of host-pathogen interactions is critical. By preserving the complete spatio-morphological context of virus infection in the ferret respiratory tract, this thesis provided the first specific 3D reconstruction of SARS-CoV-2 infection and the first report of 3D visualization of respiratory virus infection in nasal turbinates altogether. 3D object segmentation of SARS-CoV-2 infection in large tissue volumes identified and emphasized a distinct oligofocal infection pattern in the upper respiratory tract (URT) of ferrets. Furthermore, it corroborated a preferential replication of SARS-CoV-2 in the ferret URT, as only debris-associated virus antigen was detected in the lower respiratory tract of ferrets, thus providing crucial information on the spatial distribution of SARS-CoV-2.
Ion traps such as Paul traps and MR-ToF (multi-reflection time-of-flight) devices are indispensable tools at radioactive ion beam facilities for the preparation of high-quality radioactive ion beams for subsequent experiments or for precise measurements of the properties of radioactive ions, such as nuclear binding energies or nuclear charge radii.
Within the work of this thesis, Doppler- and sympathetic cooling is implemented in a linear Paul-trap cooler-buncher enabling a reduction of the longitudinal emittance of radioactive ion beams resulting in a significant improvement of the ion beam quality. Moreover, a next-generation MR-ToF device is conceptualized in order to achieve isobaric pure beams with a higher ion intensity than state-of-the-art MR-ToF devices can provide. Once fully constructed and commissioned, it will operate at an unprecedented ion beam energy of 30 keV. Both of these advances are expected to become important for a wide range of experimental programs pursued at low-energy branches of RIB facilities ranging from fundamental symmetry studies, nuclear structure, rare isotope studies with antimatter, searches of physics beyond the standard model to material science and the production of medical isotopes.
The next-generation MR-ToF mass separator is based on MIRACLS’ 30-keV MR-ToF device for highly sensitive and high-resolution collinear laser spectroscopy. By storing the ions in the Multi Ion Reflection Apparatus for Collinear Laser Spectroscopy (MIRACLS), the same ion bunch is probed by a spectroscopic laser for thousands of times compared to a single passage in traditional collinear laser spectroscopy (CLS). Dedicated simulation studies show that the accuracy and resolution will be close to traditional single-passage CLS while the sensitivity is significantly enhanced. Hence, measurements of nuclear properties via fluorescence-based CLS of very rare radionuclides as well as highly sensitive and high-precision measurements of electron affinities via laser-photodetachment-threshold spectroscopy of negatively-charged (radioactive) ions will become possible.
First measurement campaigns employing MIRACLS’ 1.5-keV MR-ToF device confirm the outstanding boost in signal sensitivity and provide confidence in the application of the MIRACLS technique for the measurement of scarcely produced radioactive ions that have been so far beyond the reach of conventional techniques. Furthermore, the electron affinity of 35Cl was measured, which is in perfect agreement with the literature value. These measurements will serve as important benchmarks for modern atomic and nuclear theory, especially in its description of nuclear charge radii.
In summary, the implementation of Doppler and sympathetic cooling at RIB facilities, the conceptualization of a 30-keV MR-ToF apparatus for highly selective and high-flux mass separation as well as for highly sensitive and high-resolution fluorescence-based laser spectroscopy and the expansion of the MIRACLS technique for the study of negatively-charged ions will enable unprecedented new measurement opportunities at RIB facilities.
A paradigm was developed to experimentally investigate the dysregulation of affective reactivity in clinical depression. The literature so far reported evidence for three directions of dysregulation - negative potentiation, positive attenuation, and emotion context insensitivity. Therefore a paradigm was designed to allow to test all three hypotheses simultaneously. Furthermore, to enable generalization across the specific stimuli used in the experiment, stimuli of two sensory modalities were used - pictures and sounds. Because it was hypothesized, that the specificity of affective reactivity of depressed patients will be especially prominent in long lasting affective situations, a categorically blocked presentation mode was chosen. Regarding the dependent variables, a multimethod approach was conducted. Besides self-report ratings of the feeling state, startle responses, skin conductance responses, heart rate, and the electromyogram of the corrugator and zygomatic muscle were recorded. In a separate session, BOLD-responses during picture viewing were collected by functional magnetic resonance imaging (fMRI). Both sessions were conducted with three samples: a healthy student sample, a depressed outpatient sample, and a healthy age and gender matched control sample. The results of the patient sample support an integration of the emotion context insensitivity and the negative potentiation hypothesis. Patients reported generally to feel more unpleasant and more aroused than healthy controls. Skin conductance and startle responses were modulated by valence to a smaller degree in the patients than in the controls. No group differences were found in the facial muscle activity. BOLD-responses were potentiated during unpleasant compared to neutral pictures in the patient but not in the control group in the amygdala, the insular cortex and the orbito frontal cortex. A model to integrate these results is developed. Its central assumption is, that the inability to respond to affective stimuli is an aversive experience and therefore leads to a negativity bias in attention and cognition. Direction of further research and implications for psychotherapies are discussed.
We consider Iterated Function Systems (IFS) on the real line and on the complex plane. Every IFS defines a self-similar measure supported on a self-similar set. We study the transfer operator (which acts on the space of continuous functions on the self-similar set) and the Hutchinson operator (which acts on the space of Borel regular measures on the self-similar set). We show that the transfer operator has an infinitely countable set of polynomial eigenfunctions. These eigenfunctions can be regarded as generalized Bernoulli polynomials. The polynomial eigenfuctions define a polynomial approximation of the self-similar measure. We also study the moments of the self-similar measure and give recursions for computing them. Further, we develop a numerical method based on Markov chains to study the spectrum of the Hutchinson and transfer operators. This method provides numerical approximations of the invariant measure for which we give error bounds in terms of the Wasserstein-distance. The standard example in this thesis is the parametric family of Bernoulli convolutions.
African swine fever virus (ASFV) is one of the most threatening animal viruses which has dramatically expanded its distribution range within the last years. ASFV was first described and is endemic in sub-Saharan Africa where it is transmitted in a sylvatic cycle between indigenous suids and Ornithodoros soft ticks. Therefore, ASFV is the only known DNA-arbovirus and, in addition to that, the only member of the genus Asfivirus within the family Asfarviridae. Being highly infectious to domestic pigs and wild boar, the virus was introduced into Georgia in 2007 and has subsequently spread throughout eastern Europe reaching the European Union in 2014. Despite almost 100 years of intensive research and the occurrence of African swine fever (ASF) on four continents including Europe, many aspects of its epidemiology, vector dynamics and virus evolution are unknown. In our study, first evidence is presented on endogenous ASFV-like (EASFL)- elements which are integrated into the genome of ASFV natural vectors, O. moubata soft ticks. Through a series of experiments including next-generation sequencing, infection experiments, phylogenetic and BEAST analyses as well as PCR-screening, evidence is provided that these elements belong to an ancestral ASFV strain that might have existed 50,000 to 30,000 years BCE. Further results suggest that the EASFL-elements are involved in protecting ticks against ASFV infection and might belong to a generalised tick defence mechanism. In order to evaluate factors influencing ASFV epidemiology in eastern Europe, experiments were conducted on possible indigenous vector species and circulating virus isolates. In the absence of the natural tick vector, blow fly larvae were considered as possible mechanical vectors involved in ASFV transmission and persistence. Results are presented that even after feeding on highly infectious wild boar tissue, fly larvae and pupae showed no contamination with infectious virus. On the contrary, the maggots appeared to have inactivated the virus in the organ tissue through their salivary secretions. Further experiments conducted on an ASFV-strain isolated from northeastern Estonia resulted in the first report of an ASFV-strain with attenuated phenotype isolated in Eastern Europe. Results from NGS-analyses provided evidence for a major genome reorganisation in that strain that included a large deletion and a duplication of multiple ASFV genes.
Taken together, this study provides novel insights into the epidemiology of ASF and evolution of ASFV one of the major threats to animal health worldwide and therefore does not only contribute significantly to basic research but possibly also to specific knowledge necessary for future disease management.
Abstract: Ischemic stroke is an aging disease and causes high mortality or long-term disability. The reduced neurological recovery in aging is possibly associated with impairment of angiogenesis and non-specific enhancement of inflammatory reaction. To check this hypotheses, those events were compared within young and elder animals brain at day 14 following focal ischemic stroke. Moreover, it is of importance to investigate also the potential therapies of indomethacin for prolonging the therapeutic window using aged animal models. The focus of present study was on neurobiological and neurological differences between young and old rats modulated by indomethacin daily treatment beginning at four hours post-ischemic episode. The effectiveness of indomethacin treatment in young and elder rats was probed using immunohistochemistry, oligonucleotide microarray, Real Time PCR and neurological evaluation. Our results provide insight of several age-independent positive consequences of Cox non-specific inhibition by indomethacin including increased NeuN positive surviving neurons, reduced infarct volume and enhanced neuroprotective response of innate immune system evidenced by increased Iba1 and Anx3 immunoreactivities in moderately activated microglia in periinfarction. From gene level we observed in both age groups downregulation of Mdk and Cxcl1 chemokines, and Id3 transcription factor which might modulate inflammatory response and facilitate repair. Other several findings showed age-dependent drug effect. Indomethacin had reduced efficacy in aged ischemic brain. From a total of 34 genes differential regulated, we observed 43% in young and only 28% of genes in aged have tendency toward age-matched sham expression level. In aged rats, indomethacin is ineffective in inhibiting phagocytic activity which is probably due to no expression changes of several cytokines like Tnfá and Cxcl4. Also, at protein level we observed no change of lysosomal ED1 immunoreactivity under treatment. On the other hand aging is characterized by no expression changes of Plau, Timp1, Timp2 and Col18a1 after treatment resulting in no improvement of angiogenesis. In young rats, conversely, drug administration decreased phagocytic activity by downregulating several cytotoxic cytokines such as Tnfá and Cxcl4. Moreover, the observable decrease of proteases like MMP10, Plau and MMP inhibitor Timp2 employed in matrix remodeling together with downregulation of Col18a1 expression after treatment might sustain angiogenesis in young rat ischemic brain. Indomethacin improves the motor-sensory performance in ischemic stroke rats as compared with age-matched untreated animals. Young rats fully recovered while aged showed important recuperation but did not achieve the preoperative level. In view of all this, indomethacin treatment might be consider as adjuvant therapy following ischemic stroke, even if aging blunts the positive effect of indomethacin on altered angiogenic-related gene expression. Because of the small number of rats, the results obtained from this study show only a tendency to significance and that further studies with more animals need to be statistically validated before firmly conclusions can be drawn. KEY WORDS: indomethacin; aging; microglia; angiogenesis; gene expression; microarray; neurological recovery; reversible middle cerebral artery occlusion.
External effects of agglomeration and human capital is a more than a century old research topic. Their theory and empirics have evolved over time to interact with more economic factors and to dig more deeply into heterogeneous effects, whose empirical evidence remains scarce, especially for developing countries. Furthermore, local human capital and agglomeration are often introduced in separate models rather than a single model in explaining productivity. These limitations motivate the implementation of this thesis. To achieve this, firm-level panel data from Vietnam is employed. This developing country provides an interesting case because its level of agglomeration and human capital is still low but its socio-economic conditions are highly dynamic with the high growth rates of urbanization and university-educated labor force (production inputs) as well as income (production output), in comparison with developed countries. The heart of this thesis lies on its chapter 2 and chapter 3, which are summarized as follows.
Chapter 2 aims at finding which agglomeration forces play the dominant role in affecting firms’ productivity and how agglomeration induces unequal influences across various firm characteristics. To achieve this, a six-year panel data set is employed, and the estimation is based on a production function that the left-hand side is firm’s total factor productivity while the righthand side is local technology which contains the agglomeration terms. In the first step of regression, consistent values of productivity are obtained following a strategy that combines the control function approach with the instrumental variables technique to tackle endogeneity caused by a possibility that firms choose their production inputs based on their productivity. In the second step, log of productivity is regressed on agglomeration proxies and controls, using multiple fixedeffects terms to control for unobserved factors and local shocks. Estimated results show that urbanization rather than specialization has a positive impact on productivity. Besides, the agglomeration effects are stronger for foreign-owned, small-sized, or young firms.
Chapter 3 shows attempts to find evidence of human capital externalities along with urbanization economies, given that the two external terms are rarely placed together in a single specification in literature. The estimation is implemented based on a production function whose context is an unique spatial equilibrium resulting from migration behaviors of entrepreneurs and workers. In this function, the externalities play the role of a region-specific productivity shifter. The model is regressed primarily with the instrumental variables technique to tackle possible identification problems. Between the two external terms, the resulting estimates confirm only the existence of urbanization economies. However, human capital externalities are found to be strong and significant in high-tech industries, implying that the effects of local human capital are very heterogeneous across different technological levels.
Background: Alcohol consumption accounts for a high burden of disease. The general population of West Pomerania has been characterized as a population at risk with a high prevalence of behavioural risk factors such as alcohol risk drinking. This is reflected by the high proportion of patients being admitted to general hospitals due to alcohol-attributable diseases. The aims of the present dissertation were (a) to analyze dose-response relations between volume of alcohol drinking and the risk of diseases with different alcohol-attributable fractions (AAF) in general hospital inpatients (study 1); (b) to assess motivation to change drinking behaviour and motivation to seek help for alcohol problems during their hospital stay as well as changes in motivation to change drinking behaviour, motivation to seek help and changes in daily alcohol consumption across time according to diseases with different AAFs (study 2); and (c) to investigate the association of fatty liver disease (FLD) with blood pressure and hypertension in a general population sample and to test for the specific contribution of alcohol consumption to this association (study 3). Methods: For studies 1 and 2, data from 'Early Intervention at General Hospitals', a randomized controlled trial to test the effectiveness of brief intervention for alcohol problem drinking in general hospitals, were used. Study 1 comprised data from 846 inpatients, study 2 comprised data from 294 inpatients aged 18 to 64 years with alcohol problem drinking and alcohol-attributable diseases from four general hospitals in West Pomerania. Hospital diagnoses were classified according to their AAF: (1) diseases wholly attributable to alcohol consumption by definition (AAF=1), (2) diseases partially attributable to alcohol consumption (AAF<1), and (3) diseases with no relation to alcohol consumption or where alcohol consumption has been found to be a protective factor (AAF=0). Study 3 encompassed data from the 'Study of Health in Pomerania', a general population sample of 3191 adults aged 20-79 years. FLD was defined using ultrasound in combination with increased serum alanine aminotransferase levels. Results: Analyses showed that 46.8% of the general hospital inpatients had a disease attributable to alcohol consumption. There was a dose-response relationship between volume of alcohol drinking and the risk of diseases with different AAFs. Inpatients consuming >120 g and inpatients consuming 61-120 g of pure alcohol per day revealed significantly higher odds for diseases with AAF=1 compared to inpatients consuming 31-60 g of pure alcohol per day with odds ratios (OR) of 6.3 (95% CI 3.6-11.3) and 2.9 (95% CI 1.6-5.1), respectively. Regarding diseases with AAF<1, inpatients consuming >120 g of pure alcohol per day had significantly higher odds compared to inpatients consuming 31-60 g of pure alcohol per day (OR 2.0, CI 1.2-3.4). Analyses on motivation to change drinking behaviour and on motivation to seek help at hospitalization revealed that motivation to change drinking behaviour was higher among inpatients with alcohol-attributable diseases than among inpatients without alcohol-attributable diseases (p<.001). Among inpatients with AAF=1, motivation to seek help was higher than among inpatients with AAF<1 and AAF=0 (p<.001). While motivation to change drinking behaviour remained stable within one year after hospitalization in all three AAF groups, motivation to seek help decreased in this time period. The volume of alcohol consumed decreased in all three AAF groups within one year after hospitalization. Data from the general population study revealed that FLD was associated with blood pressure and hypertension at baseline and at five-year examination follow-up. For example, the chance of hypertension at both time points was threefold higher in individuals with FLD (OR 2.8, CI 1.3-6.2; OR 3.1, CI 1.7-5.8, respectively) compared to individuals without FLD. Analyses further revealed that the association of FLD with blood pressure and hypertension was independent of alcohol consumption. Conclusion: The results of the present dissertation provide relevant implications for public health. In view of the high proportion of general hospital inpatients with alcohol-attributable diseases, a screening procedure for problem drinking is needed. Furthermore, appropriate interventions considering the inpatient’s motivational level have to be implemented. The concept of AAFs to classify disease conditions according to their causal relationship with alcohol consumption might be a tool to detect inpatients with problem drinking. The results regarding FLD and its association with blood pressure and hypertension demonstrate that it is important to pay attention to alcohol-attributable diseases in the general population and that alcohol-attributable diseases are associated with subsequent serious sequelae. The results of the present work further indicate that the concept to distinguish between alcoholic and non-alcoholic origin of FLD might be obsolete and should be replaced by a concept that regards FLD as a multifactorial disease condition.
Alcohol dehydrogenases as biocatalysts for the production of enantiomerically pure chiral alcohols
(2016)
Summary Enantiomerically pure chiral alcohols are key compounds in the production of certain chemicals including pharmaceuticals. Chemical synthesis allows to obtain maximal yield of 50% for one enantiomer ( >50% yield is achievable with chiral catalysts used in chemical synthesis), whereas biosynthesis leads to nearly 100% yield. Hence, expensive and time consuming resolution of racemic mixture can be avoided. Alcohol dehydrogenases are the most popular enzymes used in the chiral alcohols synthesis due to high activity with appropriate aldehydes or ketones. ADHs require a cofactor which has to be regenerated after the conversion of aldehyde/ketone to the respective alcohol. Thereby, different regeneration methods were used in the practical work to compare and choose the better one. R. erythropolis and C. hydrogenoformans alcohol dehydrogenases were chosen based on the literature screening. Each gene was cloned into Xplor2 vector and pFPMT vector. Xplor2 vector was used for the transformation of A. adeninivorans and pFPMT vector was used for the transformation of H. polymorpha. Chemically synthesized alcohol dehydrogenase sequences from R. erythropolis (ReADH) and C. hydrogenoformans (ChADH) were cloned between TEF1 promoter and PHO5 terminator which are components of Xplor2 vector or between FMD promoter and MOX terminator which are genetic elements of pFPMT vector. Moreover, ChADH and ReADH sequences with His-tag encoding sequence at the 5’ or 3’ end were constructed and the most active form of the protein was selected for further studies. ReADH-6H was used for the synthesis of 1-(S)-phenylethanol and ethyl (R)-4-chloro-3-hydroxybutanoate whereas ChADH-6H was used for the production of ethyl (R)-mandelate. ReADH-6H synthesized in A. adeninivorans and H. polymorpha was fully biochemically characterized. The enzymes from the two yeast species showed some differences in their pH and temperature optima, thermostability and activity levels. A-ReADH (A. adeninivorans) and H-ReADH (H. polymorpha) were highly active with the same substrates which were: acetophenone, 4-hydroxy-3-butanone and ethyl 4-chloroacetoacetate for reduction reaction along with 1-phenylethanol and 1,6-hexanediol for oxidation reaction. Recombinant A-ReADH-6H and H-ReADH-6H were synthesized in A. adeninivorans and H. polymorpha, respectively. Both enzymes were used for the synthesis of 1-(S)-phenylethanol and ethyl (R)-4-chloro-3-hydroxybutanoate with the use of substrate-coupled cofactor regeneration system. The enantiopurity of the products was >99%. Moreover, A. adeninivorans whole cell catalyst was also used for the synthesis of both chiral alcohols. BmGDH (Bacillus megaterium glucose dehydrogenase) was co-expressed with ReADH-6H for NADH cofactor regeneration. Comparison between isolated enzymes and permeabilized whole cell catalysts indicate that cell biocatalysts are more suitable for the production of 1-(S)-phenylethanol with 92% of acetophenone being converted in 60 min. However, cells did not show any significant advantage over isolated enzymes in the synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate although the velocity of the synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate was slightly improved using whole-cell catalysts, giving an 80% substrate conversion in 120 min. Recombinant C. hydrogenoformans alcohol dehydrogenase was synthesized in A. adeninivorans and biochemically characterized. Enzyme showed high activity only with one substrate, ethyl benzoylformate. The A. adeninivorans and H. polymorpha cell catalysts synthesizing ChADH and BmGDH (Bacillus megaterium glucose dehydrogenase) were constructed and used in the synthesis of ethyl (R)-mandelate (reduction product of ethyl benzoylformate) with the enantiopurity of the reaction product being >98%. H. polymorpha catalysts were more effective in the synthesis than A. adeninivorans cells. The first were able to convert 93% of ethyl benzoylformate within 180 min and the latter were converting 94% of the substrate within 360 min. Re-use of non-immobilized cells and catalysts entrapped in Lentikat® was performed and the improvement of the stability of immobilized catalysts was reported. Space time yield of 3.07 mmol l-1 h-1 and 6.07 mmol l-1 h-1 was achieved with A. adeninivorans and H. polymorpha cell catalysts, respectively. Alcohol dehydrogenase 1 from A. adeninivorans was analyzed concerning the synthesis of enantiomerically pure chiral alcohols. The enzyme did not synthesize industrially attractive products. However, based on biochemical characterization enzyme plays a role in the synthesis of 1-butanol or ethanol and thereby it is of biotechnological interest.
Alcohol-related somatic disorders are highly prevalent among general hospital inpatients. Alcohol problem drinking can be differentiated into alcohol use disorders (alcohol dependence and alcohol abuse) and three subtypes of drinking above recommended levels (at-risk drinking only [AR], heavy episodic drinking only [HE], at-risk and heavy episodic drinking [ARHE]). The aims of this study were threefold. First, proportions of alcohol problem drinking among general hospital inpatients in a region of north-eastern Germany were estimated (study 1). Second, among individuals with alcohol problem drinking the association between beverage preference and alcohol-related diseases was tested (study 2). Third, subtype differences regarding demographics, alcohol-related variables, motivation to change drinking behaviors, and the risk to develop short-term alcohol dependence among the three subtypes of drinking above recommended levels were analyzed (study 3). The data presented in this dissertation are based on the randomized controlled trial “Early Intervention at General Hospitals”, which is part of the Research Collaboration Early Substance Use Intervention (EARLINT). Study 1 includes a sample of consecutively admitted general hospital inpatients between 18 and 64 years old (n = 14,332). The study adopted a two-stage-sampling approach: (a) screening and (b) ascertainment of alcohol problem drinking. Those who were identified with alcohol problem drinking were asked for written consent for further study participation. This included further baseline assessment, the consent to use routine treatment diagnoses and participation in a follow-up interview 12 months after hospitalization. For study 2, routine treatment diagnoses were provided by hospital physicians for a total of 1,011 men with problem drinking. These diagnoses were classified into three categories according to their alcohol-attributable fractions (AAF): diseases totally attributable to alcohol by definition (AAF=1), diseases partially attributable to alcohol (AAF<1) and diseases with no empirical relationship to alcohol or with a possibly protective effect associated with alcohol (AAF=0). Study 3 was restricted to study participants with drinking above recommended levels (n=425). Study 1: Among all general hospital inpatients, 8.9% were identified with current problem drinking in the following descending order: 5.3% exhibited alcohol use disorders and 3.6% drinking above recommended levels. Higher proportions of problem drinking were found at rural sites compared to urban sites (13.7 vs. 7.5%, p<.001). Study 2: Because of the low proportion of women with alcohol problem drinking the following analyses were restricted to males. Multinomial regression analyses revealed different risks for alcohol-related diseases in relation to beverage preference while controlling for alcohol-associated and demographic confounders. Compared to all other groups, spirits only drinkers had the highest risk for having a disease with AAF>0; e.g., beer only drinkers had lower odds of having a disease with AAF<1 (odds ratio, OR=0.50, 95% confidence interval, CI: 0.27-0.92). Study 3: Men with alcohol use disorder were excluded from the following analysis. At baseline, multinomial logistic regression revealed differences between individuals with AR, HE and ARHE while controlling for age. ARHE was associated with higher odds of having a more severe alcohol problem (OR=2.06, CI: 1.23-3.45), using formal help (OR=2.21, CI: 1.02-4.79), and having a disease with AAF=1 (OR=3.43, CI: 1.58-7.43), compared with AR. In addition, individuals with ARHE had higher odds of taking action to change drinking behaviors (i.e., beginning to implement change) than individuals with HE (OR=2.29, CI: 1.21-4.34) or AR (OR=2.11, CI: 1.15-3.86). At follow-up, individuals with ARHE had higher odds of having alcohol dependence according to the DSM-IV (OR=4.73, CI: 1.01–22.20) compared to individuals with AR. In addition to alcohol use disorders, drinking above recommended levels is a common problem among general hospital inpatients. Thus, the implementation of systematic alcohol screening and brief interventions should be considered. These data suggest an association between beverage preference and alcohol-related diseases. Among hospitalized problem drinkers, spirits only drinkers had the greatest risk of having diseases with AAF>0. Of the three subtypes of drinking above recommended levels, ARHE seems to be particularly problematic because there appears to be an indication of a subclinical diagnosis. To provide adequate intervention, clinical practice should distinguish between the three groups of drinking above recommended levels. Brief alcohol intervention should be tailored to the individual’s motivation to change and to the type of alcohol problem drinking. The effectiveness of such a procedure remains to be evaluated in further studies.
In their idealized forms, enzymes can facilitate complex reactions with extreme specificity and selectivity. Additionally, in this imaginative form, they only require mild reaction conditions, resulting in low energy consumption, and they are biodegradable, efficient, reusable, and sustainable. Unfortunately, this idealized form often deviates significantly from reality, where enzymes are more likely to be associated with marginal stability and low reaction rates, leaving them less than desirable for many industrial applications. As such, if we could master the process of engineering the configuration of a protein towards a given task, the implications could be staggering.
This thesis aims to contribute to the process of protein engineering, mainly how computational tools can be used to make the protein engineering process more efficient and accessible.
Article I explores the current state of the art in machine learning-guided directed evolution and serves as a foundation for Article II, which is a concrete application of these techniques to an engineering campaign. Despite successfully improving overall activity and selectivity, we also observe limitations and constraints within the methodology. Article III then delves into these drawbacks and attempts to lay the foundation for a more generalizable and, more importantly, efficient engineering workflow, balancing the strengths and weaknesses of computational techniques with advances in gene synthesis. We then validated this novel pipeline in Article IV, where we show the potential of this methodology. Article V describes a more standard protein engineering campaign on squalene-hopene cyclases for potentially interesting products in the flavor and fragrance industry. Lastly, Article VI outlines a PyMol plugin for molecular docking.
Humans are exposed to a plethora of microorganisms that reside on outer and inner body surfaces. These are collectively referred to as the human microbiome. The evolutionary relationship between humans and their microbiome is very complex. It is now widely accepted that these microorganisms are not just passive spectators but play an important role in health. The presence or absence of certain microbes is also linked to various diseases, including inflammatory bowel disease, cardiovascular disease, obesity, cancer, and allergies.
Allergies are several conditions caused by a misguided immune response to foreign antigens that are typically harmless. Common allergic diseases include atopic dermatitis (AD), allergic asthma, hay fever, and anaphylaxis. The incidences of allergic diseases are continuously rising, with up to 40% of the human population thought to be sensitised to environmental antigens. This increased incidence is not simply the result of societies becoming more aware and better at diagnosing these diseases. It is believed that the increases in allergies and sensitisation have environmental causes and are related to Western lifestyles. It is known that the rate of allergies is less frequent in developing countries. They are also more likely to occur in urban than rural areas. The prevailing view of the involvement of bacteria in allergies is described by the hygiene hypothesis. The hypothesis claims that decreased exposure to diverse microbial communities early in life increases the risk of developing allergic diseases. There are numerous examples to support this claim. For example, children born and raised in close contact to farm animals or in the presence of pets, and who are thus in direct and constant contact with a complex microbial environment, are protected from allergic diseases. On the other hand, colonisation or infection with certain bacteria increases allergic disease risks. This seems to contradict the hygiene hypothesis.
It appears that the members of the microbiome have different effects on allergy, and the hygiene hypothesis may not apply to every player in the complex microbial diversity that humans are in contact with. Therefore, a better understanding of the host bacterial interaction is required on the level of bacterial species.
This work studies the interplay between bacteria and the immune system to identify and characterise bacterial components with allergenic properties. In this quest, Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis) were investigated for their allergenic properties and involvement in different allergic diseases. In the case of S. aureus, evidence is presented on allergic implications for two different components; serine protease-like proteins (Spls) and superantigens (SAg). Furthermore, experimental support is provided on the allergenic properties of the extracellular serine protease (Esp) from S. epidermidis. We argue that stimulating allergic reactions by staphylococci is an immune evasion mechanism that increases the survival chances of the bacteria within the host.
In chapter 1, an introduction is given to both S. aureus and S. epidermidis and their interactions with the immune system. Also, the bacterial components with allergenic properties and allergic diseases with known bacterial involvement are presented. Finally, the question of why bacteria cause allergy is discussed.
Chapter 2 describes allergic reactions to the Spls of S. aureus in a cohort of cystic fibrosis patients. Chapter 3 focuses on the SAgs of S. aureus. SAgs were discovered more than 30 years ago, but their physiological function is still under discussion. In this chapter, the allergenic properties of SAgs and their possible immunological mechanisms are reviewed, and a possible link between SAgs and allergic diseases is discussed. In chapter 4, the focus shifts to S. epidermidis and its involvement in AD. The human immune response to the Esp from S. epidermidis is characterised in healthy and AD individuals. The allergenic properties of Esp imply a detrimental role of S. epidermidis in AD. Finally, chapter 5 summarises and discusses the results of this thesis. In this section, the pieces are put together, and attention is brought back to the question of why bacteria cause allergies.
The experience of abuse in the period of childhood and youth is a key stressor that has con-sequences on the developing brain and is associated with the genesis of mental disorders. Childhood abuse and depression often cooccur together and have both been associated with cortical thickness resulting in a difficulty to detangle the influence of each factor. In prior studies, childhood abuse and depression were inconsistently related to whole-brain cortical thickness. Thus, this thesis aims to investigate the link between childhood abuse, depres-sive symptoms, and alterations of the cortex.
Therefore, this study analyses 1,551 individuals of the general population. A significant in-teraction effect of childhood abuse and depressive symptoms is observed for whole-brain cortical thickness. Yet, the results indicate no influence of childhood abuse or depression alone. A thinner cortex was associated with more severe depressive symptoms in the abused, but not in the non-abused group. In non-depressed participants, an increased whole-brain cortex was found in the abused, compared to the non-abused group. Similar interaction effects were observed in 12 out of 34 cortical regions.
The results suggest, in line with prior findings, that depressed individuals with a history of childhood abuse are a specific ecophenotype which is also reflected in specific brain altera-tions. Cortical regions that are distinct associated with the interaction of depressive symp-toms and childhood abuse are involved in various fields such as sensory processing, self-conception, and memory. Greater cortical thickness in subjects with childhood abuse and without depressive symptoms might act compensatory and thus reflect resilience against depressive symptoms.
Practical implications concern the treatment and diagnostic system as well as the im-portance of early prevention programs. An individualised treatment is necessary as various studies found a less favourable outcome in depressive patients with a history of maltreat-ment. Therefore, it seems urgent to assess experiences of childhood abuse at the beginning of psychiatric and psychotherapeutic treatment. In addition, early prevention programs are in need to support vulnerable family systems and thereby strengthening the economic, health and social system.
The widespread use of natural and synthetic estrogens or chemicals with estrogenic activities is causing an increasing accumulation of estrogenic compounds in the environment. Already at very low concentrations these estrogenics can severely affect the wildlife, particularly in an aquatic environment. For these reasons measuring devices for detecting estrogen contaminations are in great demand. The majority of the analytical methods and bioassays on the market so far, lack semi-online adaptability, and usually cannot be used for automatic and continuous determination. Therefore, we have embarked on the development of new systems, which are able to fulfil those demands. The EstraMonitor combines recombinant A. adeninivorans G1212/YRC102-hERa-phyK yeast cells as the microbial component with an amperometric detection method to analyze estrogenic contaminations. A. adeninivorans G1212/YRC102-hERa-phyK was constructed by Kaiser et al. (2010). These cells were engineered to co-express the human estrogen receptor (hERa) gene and the inducible phytase (phyK, derived from Klebsiella sp. ASR1) reporter gene under control of a promoter with estrogen response elements (EREs). In the presence of estrogenic substances, such as 17ß -estradiol (E2), the phyK gene is expressed and recombinant phytase is secreted into the media. The level of phytase is quantified by amperometric detection using substrate p-aminophenyl phosphate (p-APP). Phytase dephosphorylates p-aminophenyl phosphate (p-APP) into an intermediate product p-aminophenol (p-AP). p-AP is electroactive and oxidized at the electrode. This generates electrons and produces a current which is proportional to the level of phytase activity. Since phytase activity is directly correlated to the E2 concentration, the estrogenic activity can thus be calculated from the current measured. The microbial component of the EstraMonitor, the non-immobilized A. adeninivorans G1212/YRC102-hERa-phyK, works well with the amperometric method in a quantitative manner. The optimal applied potential determined for amperometric measurements was 150 mV and provided a low background signal for the amperometric detection. The half maximal effective concentration (EC50) and limit of detection (LoD) values for E2 obtained from amperometric measurements with the EstraMonitor were 69.9 ng L-1 and 44.5 ng L-1, respectively. The measuring procedure of the EstraMonitor system including incubation of A. adeninivorans G1212/YRC102-hERa-phyK cells with E2, subsequently incubation with electrochemical substrate (p-APP), and signal recordation is completed within only 4 h and 10 min. Out of this total time, amperometric detection including substrate incubation and signals recordation takes only 10 min out of total time. The use of immobilized cells for a microbial biosensor is an essential advantage of the EstraMonitor system because it allows easy-handiness next to long-term stability and reusability. Immobilized A. adeninivorans G1212/YRC102-hERa-phyK cells revealed excellent properties which make them very suitable for semi-online, automatic and continuous monitoring. They were stable up to 30 days when stored at 4 °C. Furthermore, they could be reused up to 15 times. The EC50 and LoD values achieved for E2 using immobilized cells in combination with amperometric detection were 20.9 and 8.3 ng L-1, respectively. Furthermore, this application also removes the need to separate cells by centrifugation, to sterilize the samples as well as to cultivate repeatly. Additionally, both immobilized and non-immobilized A. adeninivorans G1212/YRC102-hERa-phyK cells remain fully functional in a wide range of untreated wastewater samples and in environments containing up to 5% NaCl. To enhance the sensitivity and reduce the time for estrogenic determination, an alternative A. adeninivorans G1214/YRC103-hERa-phyK strain was developed. This strain can produce a detectable amount of phytase within 2 h after induction with E2. It offers an improved microbial component in terms of sensitivity and time-effectiveness. In addition, to reduce the cost for estrogenic detection an alternative substrate, ascorbic acid 2-phosphate (AA2P), was tested. AA2P, which is both cheap and widely available, performed better than p-APP. The EC50 and LoD values for E2 obtained with AA2P were 15.69 and 0.92 ng L-1 versus 20.09 and 8.3 ng L-1 when examined with p-APP, respectively. Taken together, the EstraMonitor is an automated system with respect to sample cycling, sample measuring and calibration supplemented with an alarm function. This system makes it possible to control estrogenic activity semi-online, automatically and continuously. These are advantages of the EstraMonitor compared to other estrogenic detection systems. It can thus be concluded that, the EstraMonitor is a powerful and feasible semi-online device for monitoring estrogenic activity especially adapted for the use in sewage treatment plants.
Self-affine tiles and fractals are known as examples in analysis and topology, as models of quasicrystals and biological growth, as unit intervals of generalized number systems, and as attractors of dynamical systems. The author has implemented a software which can find new examples and handle big databases of self-affine fractals. This thesis establishes the algebraic foundation of the algorithms of the IFStile package. Lifting and projection of algebraic and rational iterated function systems and many properties of the resulting attractors are discussed.
In this thesis an artificial enzyme cascade consisting of an ADH from Lactobacillus kefir, a CHMO from Acinetobacter sp. NCIMB 9871 and lipase A from Candida antarctica has been investigated for the biocatalytic synthesis of the bulk chemical ε-caprolactone as well as several derivatives for their direct utilization as polymer building blocks. Due to major limitations, which hamper such a biocatalytic route, the first addressed demand in this work was the improvement of the stability of the CHMO. By structure-guided engineering, distinctively improved variants concerning the resistance against oxidation as well as temperature stability without compromising the catalytic activity were successfully created. Due to the incomplete knowledge of the mechanisms that lead to thermal and/or oxidative inactivation of enzymes, this study illustrates that the selection of mutations for increased protein stability is still hard to predict. Thus, these results can serve as a basis for further stability studies on this enzyme class to give better insights into the underlying mechanisms, which determine the stability of an enzyme. Such a highly stabilized biocatalyst will pave the way for the successful use of flavin-dependent enzymes for industrial applications. A further aim of this thesis was dedicated to the second major hurdle en route to polyester precursors represented by the product inhibition and enzyme deactivation caused by ε-caprolactone, particularly at higher concentrations. To overcome this limitation, we developed an elegant solution in which the ε-caprolactone produced by the one-pot two-step enzymatic method is directly subjected to ring-opening polymerization using the unique lipase A from Candida antarctica. Applying this enzyme cascade in a whole cell biocatalysis in combination with an improved cofactor regeneration approach, the problem of product inhibition problem was efficiently solved leading to the formation of oligo-ε-caprolactone at more than 20 g/L when starting from 200 mM cyclohexanol. By a process development approach through solvent engineering it was found that biotransformations proceed much faster in an isooctane-containing biphasic solvent system when using free enzymes. Finally, the improved enzyme cascade was applied for the synthesis of chiral substrates and provided access to functionalized chiral compounds in high yields (up to >99%) and optical purities (up to >99%ee). By subsequent enzymatic enantioselective ring-opening of the enantiopure monomers, oligomeric lactones were successfully synthesized, which can be directly serve as building blocks for the polymer industry.
Objectives:
This study investigates the effectiveness of the Cold AP on the alteration of the enamel surface
without using acid etchant by using Conventional photo-activated resin bond to bond the
orthodontic brackets.
Materials and Methods:
One hundred and twenty-five Enamel specimens are prepared from disinfected bovine
mandibular incisors are divided into five groups. Group I: brackets are attached on the enamel
surface with the standard adhesive technique (etch + primer +bond). Group II: the brackets are
attached with the Standard Orthodontic adhesive technique without etching. Group III: the
enamel surface is conditioned with pure Argon Cold atmospheric plasma before the application
of the primer without using an acid etchant. Group IV: the enamel surface is conditioned with
the admixture of Argon Cold atmospheric plasma with 0.5 % Oxygen before the application of
the primer without using acid etchant Group V: after the application of Argon Cold atmospheric
plasma with 0.5 % Oxygen the surface is rewetted by deionized water before the application
of the primer and adhesive. After that, the samples are exposed to thermal cycling. The shear
bond strength of the samples is tested by the universal testing machine which measured the
maximum force at which the brackets are deboned from the tooth surface at a speed of
1mm/minute is measured.
Results:
Significant intergroup differences were found. Group V showed the highest shear bond
strength followed by Group I, VI, III, II respectively. There isn’t a statistical difference in the
values of The Shear bond strength values between Group III and IV.
Conclusions:
this study implies that Cold Atmospheric Plasma is a safe method to change the chemical
surface characteristics of the enamel surface.in addition to the significant importance of plasma
treatment followed by water rewetting, which could enhance adhesion between the orthodontic
attachments and the enamel layer
In the framework of the current work has been the plasma initiated and surface catalysed species conversion studied in low pressure and atmospheric plasmas. The aim of the work is to improve the understanding of the internal processes in order to increase the energy efficiency as well as the selectivity of the reaction products of future plasma devices. Beside many technical applications of plasmas, air purification shows great potential. Over the last decades, plasma based pollution control has proofed its ability to remove harmful contaminants or annoying odours from an air stream. However, the energy efficiency and the selectivity of the products are a remaining challenge.
Motivated by these issues, a multi stage packed-bed reactor has been used to remove admixed ethylene and toluene from an air stream. It has been found that the maximum toluene destruction has been 60%, whereas ethylene has been nearly completely removed. The specific energy β has been between 120 and 1600 JL-1. Fourier Transform Infrared spectroscopy, FTIR spectroscopy, has been used to identify and quantify the species H2O, CO2, CO, O3, HNO3, HCN, CH2O, CH2O2, N2O and NO2. However, none of these experiments led to the detection of NO.
The embedment of packing material into a plasma volume leads to increased surface effects. In order to study them, the inner side of a tube reactor, made of Pyrex, served as the surface under study and has been exposed to a rf plasma for 1h. The surface effects of the plasma treatment have been investigated indirectly by studying the oxidation of NO into NO2. After the plasma exposure, the reactor has been evacuated and filled with a gas mixture of 1% NO in N2 / Ar. Both species have been measured using quantum cascade laser absorption spectroscopy, QCLAS. It has been found that, using oxygen containing plasmas, the NO concentration decreased whereas the NO2 concentration increased. Therefore, oxygen containing plasmas are able to deposit oxygen on the surface. The filling with NO leads to the oxidation via the Eley-Rideal mechanism. A simplified model calculation supports these assumptions.
For a more comfortable application of the QCLAS, a compact multi channel spectrometer has been developed, TRIPLE Q. It combines the high time resolution with the possibility to measure the concentration of at least three infrared active species simultaneously. Due to the high time resolution, a huge number of spectra have to be analysed. In order to calculate absolute number densities, an algorithm has been developed which automatically treats typical phenomena like pulse jitter, rapid passage effect or variations of the intensity of the laser pulses.
The gas temperature is an important parameter in plasma physics. Using the TRIPLE Q system, the gas temperature has been determined for pulsed dc plasmas. For this case, NO has been used as a probe gas. From the spectra, the temperature has been calculated using the line ratio method. The relative intensity of the absorption structures of NO at 1900.5cm-1 and 1900.08cm-1 depend on the temperature. Therefore, the ratio has been used to calculate the gas temperature with a time resolution in the μs range.
Vibrationally excited nitrogen can be an energy reservoir that plays an important role in plasma chemistry. In N2 / N2O plasmas, vibrationally excited N2 can undergo relaxation via a resonant vibration vibration coupling between vibrationally excited N2 and N2O. Due to such an efficient energy transfer, the method allows one to study the relaxation of vibrationally excited N2. Using this method, molecules, which are not infrared active, can be monitored. This approach has extended the field of scientific and commercial applications of the QCLAS.
In this thesis, it was the subject to build a setup to study the interaction of clusters with intense laser light. A magnetron sputter cluster ion source was built to create metal clusters for the planned investigations. Furthermore, a linear Paul trap setup was built in order to allow the investigation of the mentioned interaction at one specific cluster size. The whole apparatus was characterized and first experiments were performed.
Genomics is the field of modern biology that studies the genome as the sum of all genes of a given organism. Genomics includes the analysis of genomic variations in order to identify genetic susceptibility loci for various human diseases. Besides genomics, there are related fields summarized by the term "Omics" such as transcriptomics and proteomics, studying the sum of all transcripts and proteins in a defined biological system, respectively. Genetic variants, namely single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are used to identify genomic loci associated with human traits and diseases. Genome-wide association studies (GWASs) based on SNP data have been performed for a wide range of human traits and diseases. In the population-based Study of Health in Pomerania (SHIP) and the independent SHIP-TREND study, whole-genome genotyping data were available for 4081 and 986 individuals, respectively. In contrast to the widely used GWAS based on SNPs, association studies using CNV data are difficult to implement and thus less common. Therefore, one aim of this work was to detect CNVs using the whole-genome genotyping data available for 4081 individuals from SHIP. Another aim was to develop an efficient workflow for the analysis of these CNVs. As most common genetic variants exhibit only relatively small effects on phenotypic variability, large sample sizes are needed to maximize the statistical power to detect such effects. Therefore, the integration of data from multiple collaborating studies is indispensable. In this context, several CNV studies with the SHIP data have been performed and published, for example on body mass index (BMI) phenotypes where the SHIP cohort was used as a population-based control. Trait-associated genetic markers identified through GWASs are often intergenic or synonymous coding, and those loci identified through whole-genome CNV analyses often contain multiple genes, making it difficult to identify the causal variants. In this context, the functional analysis of identified loci aids in determining causal variant(s). One possibility to conduct functional analysis is the expression quantitative trait loci (eQTL) analysis, defined as the association of genome-wide genotyping data with genome-wide gene expression data based on measured transcriptomes. This allows the identification of genetic variants influencing the expression levels of defined genes. A further example are transcriptome-wide association analysis (TWAS), defined as the association of phenotype data with whole-genome expression data. Thus, another aim of this work was to establish an analysis pipeline for processing such expression data, which were available for about 1000 individuals from the SHIP-TREND study. Here, array-based gene expression data were generated using RNA prepared from whole-blood. Interpretation of TWAS results is often difficult, because of possible reverse causation on gene expression data. Furthermore, technical errors of measurement may bias the results. In a comprehensive work, biological and technical factors influencing measured gene expression data have been identified and were subsequently taken into account to improve the association analyses. To further elucidate the molecular mechanisms underlying the relationship of gene expression levels with human traits or diseases, pathway analyses using the Ingenuity Pathway Analysis (IPA) tool have been performed in connection with the TWAS. As for GWASs, the associations identified in TWAS usually exhibit only small effect sizes, highlighting the need for larger studies or meta-analysis to identify all susceptibility variants. In this context several eQTL- and TWAS meta-analyses using the SHIP-TREND data have been performed, for example on the phenotypes age, sex, BMI, smoking status and serum lipid traits. The results of these analyses are in preparation for publication and the most advanced example, the correlation of expression data with BMI, is presented here. The integration of whole-genome genotyping and expression data provides new functional information of the underlying biological mechanisms of complex human traits and diseases. Within the frame of this work, this could be demonstrated for the example of susceptibility to Helicobacter pylori infection.
Analysis and Reduction of Cellular Heterogeneity in Strain Optimization of Bacillus licheniformis
(2021)
Bacillus species invest substantial resources in inherent cellular processes for pre-adaptation to environmental changes, many of which are dispensable in the controlled environment of industrial bioprocesses. The underlying physiological mechanisms are well characterized in B. subtilis, but only little is known about these processes in the closely related B. licheniformis. Moreover, experimental conditions in previous studies differ from industrial settings in most parameters, foremost in batch cultures or plate-based analysis over fed-batch processes. In this thesis, cellular heterogeneity was analyzed in B. licheniformis in optimized, nutrient-rich media in batch and fed-batch cultivations. Systematic inactivation of genes involved in biofilm formation and synthesis of the flagellar apparatus or global regulators thereof resulted in higher protein production and provided new insights into biofilm formation and cellular heterogeneity in this strain.
Analysis of bioactive lipids from different infection models during bacterial and viral infections
(2021)
Bioactive lipids or lipid mediators influence numerous processes like the reproduction, the bone turnover, the pain perception, the cardiovascular function and the immune system. Eicosanoids and oxylipins are parts of the immunomodulatory lipid mediators, which can be synthesized from polyunsaturated fatty acids (PUFAs) by enzymatic and non-enzymatic reactions. Typical members of eicosanoids are prostaglandins and leukotrienes. The properties of bioactive lipids include the activation of inflammatory reactions as well as the support of resolution. Like hormones, they act locally restricted and in low concentrations. Further bioactive lipids exist i.e. intermediates of the sphingolipid class. The biosynthesis of some of these compounds like the prostaglandins can be influenced by different drugs whereas for other groups of lipid selective inhibitors are still missing. Their impact on inflammatory processes and against chronic diseases has already been analyzed, while studies in context with infection are largely limited. Infection of the upper respiratory tract caused by viral and bacterial pathogens constitute a huge burden for the human healthcare. The main pathogens are the Influenza A virus (IAV), Staphylococcus aureus (S. aureus), Streptococcus pneumoniae (S. pneumoniae) and Streptococcus pyogenes (S. pyogenes). Besides mono-infection with one of these pathogens, frequently occurring bacto-viral co-infections exist, which negatively influence the etiopathology. The main task of the immune system is the detection and the elimination of pathogens, which can essentially be affected by lipid mediators. Their instability due to oxidizability, the existence of regioisomers and the low abundance of eicosanoids and other oxylipins are the main problems for their analytical measurement.
The mayor objective of this dissertation was the establishment of a suitable analytical method for selected lipid mediators and the detection of infection-related changes. The separation and detection was performed by using high-performance liquid chromatography (HPLC) coupled with triple quad mass spectrometry. This combination is called tandem mass spectrometry (MS/MS). The MS parameters were optimized for approximately 30 lipid mediators by use of chemical standards and the detection was achieved by dynamic multiple reaction monitoring (MRM). Furthermore, the spatial resolution of selected sphingolipids was analyzed in tissue samples using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MS-Imaging). Concerning the HPLC-MS/MS detection, an MS method was established and optimized with standard compounds. Another crucial part of the establishment was the extraction of bioactive lipids from the different sampling materials. Whereas well tested protocols exist for the extraction and detection of lipid mediators, such protocols for MALDI-MS-Imaging are still limited due to the novelty of this measurement. Ultimately, robust and reproducible protocols for both techniques that were used for the analysis of a broad array of samples from infection experiments were established for both techniques. The analyses of infected cell culture, mice and pigs revealed infection-related perturbations of host lipid mediator levels. Depending on the scientific issue, the sample types cell pellets, lungs, spleens, livers, blood plasmas, pawns including bones or bronchoalveolar lavages were analyzed. For MALDI-MS-Imaging, the spatial distribution of sphingolipids in lung and spleen was detected.
The present dissertation includes four coherent research scopes, in which the pathogen impact on host-derived lipid mediators was detected with the above mentioned analytical methods. The infection models epithelial cells (article II), mouse (article III and IV) and pig (article I) – the latter as the most human like model - showed different aspects of the host-pathogen interaction. The analysis of samples from IAV infection for all three hosts revealed a couple of similarities for some oxylipins that were also described in human infections. Additionally, cell culture and mouse samples from mono-infections as well as co-infections with the pathogens S. aureus and S. pneumoniae were measured. In particular for the bacterial mono- and co-infections, these are the first published results with aspects of infection related changes of lipid mediators. The additional spatial resolution of the sphingolipid intermediates sphingosine 1-phosphate and ceramide 1-phosphate revealed important new insights into their tissue distribution and changes during co-infection.
Article I describes the IAV-specific oxylipin changes in the pig (german landrace) as infection model. Therefore, the sample types lung, spleen, blood plasma, and bronchoalveolar lavage from infected animals at different time points after infection were analyzed and compared with samples from uninfected pigs. Mainly in the lung and the spleen, increased amounts of certain lipid mediators were observed. These changes coincide well with already described alterations in humans and mice. Furthermore, the analysis of different sample material provided an overview about appropriate sample types. Surprisingly, many perturbations were detected in the spleen, which itself was uninfected. Based on the local reaction of lipid mediators, most studies concentrate on sample material with close contact to side of infection. Therefore, this dissertation reveals new insights into a form of systemic immune response. Besides the use of animals with a complex immune system for infection experiments, human bronchial epithelial cells (16HBE) were mono- and co-infected with the pathogens S. aureus, S. pneumoniae and IAV as described in article II. Such cells are the initial barrier for and first contact site with pathogens and thus the comprehension of this host-pathogen interaction is of essential importance. Most changes were detected during pneumococcal infection. Furthermore, the analyzed infections with bacterial pathogens differed from IAV infection by an increased synthesis of 5-hydroxyeicosatetraenoic acid (HETE). For further infections with the above mentioned pathogens, the mouse was used as an infection model. Besides infections affecting the respiratory tract, also the impact of an S. pyogenes infection in different mice strains was analyzed and described in article III. Infection-related changes in prostaglandins, which are involved in bone turnover in swollen pawns as well as enhanced amounts of sepsis- and arthritis-associated lipid mediators were detected, in case arthritis had been induced prior to infection. Furthermore, increased amounts of 20-HETE could be observed for such severe infections. An enhanced biosynthesis of 20-HETE was further confirmed in a high-pathogenic S. aureus LUG2012 infection in article IV for all examined sample types. In this last article of this dissertation, bacterial and viral infections in mice were analyzed similar to those described in article II. Mainly IAV-specific lipid mediator alterations were detected, which are in accordance with the findings of the infected pigs. The additional MALDI-MS-Imaging measurements revealed so far unknown accumulation of ceramide 1-phosphate in lung and spleen as well as enrichment in the red pulp of the spleen.
In summary, this dissertation provides substantial lipid mediator profiles for infections in three different model systems with selected bacterial and viral pathogens. The obtained data constitute a suitable basis for continuative research projects, in which the influence of single bioactive lipids on the course of infection could be examined in more detail.
Analysis of partial migration strategies of Central European raptors based on ring re-encounter data
(2018)
The phenomenon of partial migration in birds in
which some individuals of a population are migratory while others stay in the breeding area is of increasing scientific interest. The strategies of partial migratory raptors from Central Europe are, however, unclear for most species. We analysed ring re-encounter data of Common Kestrels Falco tinnunculus, Eurasian Sparrowhawks Accipter nisus and Common Buzzards Buteo buteo ringed in Germany in terms of distances and directions between ringing and re-encounter sites. We investigated possible differences between sexes and age classes, as well as effects of ringing region, seasonal weather (in the form of North Atlantic Oscillation indices) and long-term temporal changes (including climate change) on migratory strategies by means of generalized linear models. We found that migration is mostly conducted by juveniles, although migratory adults were also found. In general, males tend to migrate less than females and juveniles less than adults.
Kestrels showed differences between age classes and sexes and they responded to weather in summer and autumn. The migration activities of Kestrels decreased over years. Sparrowhawks from different regions showed no differences in migration activity and no responses to long-term temporal changes. They did not respond to seasonal weather either. Buzzards showed strong responses to winter weather (‘winter escapes’) predominantly in highland regions, and a reduction of migratory intensity probably due to global warming.
The explanatory power of ringing data, however, is limited by low re-encounter rates and temporal and spatial heterogeneity in re-encounter probability. Spatial heterogeneity mainly depends on the distribution of observers as well as on their willingness to report a re-encountered ring to the corresponding ringing scheme. We analyzed a data set of ringing and re-encounter data of Kestrels, Buzzards and Sparrowhawks provided by the EURING Data Bank. We calculated monthly re-encounter rates across Europe and, for different time periods, we predicted re-encounters for individuals of these species ringed in Germany, on the assumption that re-encounter probabilities are evenly distributed at the highest value observed within the respective home ranges. Subsequently, we tested for correlation between re-encounter rates and human population density. The number of predicted re-encounters exceed the observed by 50-300 %. We found differences between monthly re-encounter rates and between different prediction periods. Distances (between ringing and re-encounter sites) differ significantly between observations and predicted re-encounters, with higher distances in predictions. Correlation between re-encounter rates and human population density is significant, but correlation coefficients are low (ρ = 0.291-0.511). Correcting for observer heterogeneity can help to analyze ring re-encounter data e.g. in terms of dispersal and migration. However, a comprehensive data collection and a digitalization of possible prior data records by the respective ringing schemes may allow advances in this method even further.
Severe trauma results in alterations in immune functions, correlated with a dysbalanced cytokine synthesis. This imbalance endangers severely injured patients for post-traumatic complications such as MODS, liver failure, renal dysfunction and ARDS. IL-10, a powerful immunosuppressive cytokine, plays a central role in the immune response after severe trauma. The relevance of IL-10 for single and multiple organ failure was studied in a prospective study at a level I trauma center. Blood was systematically obtained from a total of 118 severely injured [median (IQR) ISS=34 (27-34)] patients. IL-10 plasma levels were measured by ELISA. Patients showed elevated IL-10 levels throughout the whole observation period of 5 days. IL-10 plasma levels rose rapidly after trauma and gradually declined towards day 5. Patients who developed complications demonstrated significantly elevated IL-10 levels compared with patients who did not. The odds of developing MODS were 9.6 times greater in patients with IL-10 plasma levels higher than 124 pg/mL 6 hours after arrival at the ICU. Multivariate analysis showed that IL-10 plasma levels >124 pg/mL at time-point 6h, severe head injury and an arterial pH <7.34 were simultaneously significant predictors of the development of MODS in severely injured patients. The dynamic with rapid increase and gradual decline in IL-10 plasma levels indicated that IL-10 is a marker of the initial damage to the organism caused by trauma, rather than a marker of somatic dysregulations.
This work presents the first experimental investigation of the gas balance on the optimized modular stellarator Wendelstein 7-X (W7-X). A balance of all injected and removed particles and a measurement of internal particle reservoirs allows inference of the bound particle reservoir in the wall, which is of interest due to its effects on plasma density control and fuel retention. Different scenarios of the gas balance are presented with data from the operation campaign 1.2 with an inertially cooled graphite divertor. Both net outgassing and net retention scenarios are presented and W7-X is found to operate stable in a wide range of scenarios with varying wall conditions.
Since fusion experiments are conducted in ultra-high vacuum, suitable gauges are required for total and partial pressure measurement. The challenges and opportunities of the operation of pressure gauges in the steady magnetic field extending beyond plasma pulses are discussed. The performance of newly improved neutral pressure gauges, based on crystal cathode emitters is quantified. These provide improved operational robustness since they can be operated for long periods of time in strong magnetic fields. A crystal cathode setup and and its operation performance is presented along with a fast calibration scheme.
Partial pressure measurements provide additional important information complementing the total neutral pressure measurements, and allowing additional physics insights. As part of this thesis work, a new diagnostic of this kind was implemented on W7-X, the so-called diagnostic residual gas analyzer (DRGA). It provides a wealth of information on various neutral gas species, with a relatively high time resolution - of order a few seconds. The diagnostic setup and its first results are presented in this thesis.
In phylogenetics, evolutionary relationships of different species are represented by phylogenetic trees.
In this thesis, we are mainly concerned with the reconstruction of ancestral sequences and the accuracy of this reconstruction given a rooted binary phylogenetic tree.
For example, we wish to estimate the DNA sequences of the ancestors given the observed DNA sequences of today living species.
In particular, we are interested in reconstructing the DNA sequence of the last common ancestor of all species under consideration. Note that this last common ancestor corresponds to the root of the tree.
There exist various methods for the reconstruction of ancestral sequences.
A widely used principle for ancestral sequence reconstruction is the principle of parsimony (Maximum Parsimony).
This principle means that the simplest explanation it the best.
Applied to the reconstruction of ancestral sequences this means that a sequence which requires the fewest evolutionary changes along the tree is reconstructed.
Thus, the number of changes is minimized, which explains the name of Maximum Parsimony.
Instead of estimating a whole DNA sequence, Maximum Parsimony considers each position in the sequence separately. Thus in the following, each sequence position is regarded separately, and we call a single position in a sequence state.
It can happen that the state of the last common ancestor is reconstructed unambiguously, for example as A. On the other hand, Maximum Parsimony might be indecisive between two DNA nucleotides, say for example A and C.
In this case, the last common ancestor will be reconstructed as {A,C}.
Therefore we consider, after an introduction and some preliminary definitions, the following question in Section 3: how many present-day species need to be in a certain state, for example A, such that the Maximum Parsimony estimate of the last common ancestor is also {A}?
The answer of this question depends on the tree topology as well as on the number of different states.
In Section 4, we provide a sufficient condition for Maximum Parsimony to recover the ancestral state at the root correctly from the observed states at the leaves.
The so-called reconstruction accuracy for the reconstruction of ancestral states is introduced in Section 5. The reconstruction accuracy is the probability that the true root state is indeed reconstructed and always takes two processes into account: on the one hand the approach to reconstruct ancestral states, and on the other hand the way how the states evolve along the edges of the tree. The latter is given by an evolutionary model.
In the present thesis, we focus on a simple symmetric model, the Neyman model.
The symmetry of the model means for example that a change from A to C is equally likely than a change from C to A.
Intuitively, one could expect that the reconstruction accuracy it the highest when all present-day species are taken into account. However, it has long been known that the reconstruction accuracy improves when some taxa are disregarded for the estimation.
Therefore, the question if there exits at least a lower bound for the reconstruction accuracy arises, i.e. if it is best to consider all today living species instead of just one for the reconstruction.
This is bad news for Maximum Parsimony as a criterion for ancestral state reconstruction, and therefore the question if there exists at least a lower bound for the reconstruction accuracy arises.
In Section 5, we start with considering ultrametric trees, which are trees where the expected number of substitutions from the root to each leaf is the same.
For such trees, we investigate a lower bound for the reconstruction accuracy, when the number of different states at the leaves of the tree is 3 or 4.
Subsequently in Section 6, in order to generalize this result, we introduce a new method for ancestral state reconstruction: the coin-toss method.
We obtain new results for the reconstruction accuracy of Maximum Parsimony by relating Maximum Parsimony to the coin-toss method.
Some of these results do not require the underlying tree to be ultrametric.
Then, in Section 7 we investigate the influence of specific tree topologies on the reconstruction accuracy of Maximum Parsimony. In particular, we consider balanced and imbalanced trees as the balance of a tree may have an influence on the reconstruction accuracy.
We end by introducing the Colless index in Section 8, an index which measures the degree of balance a rooted binary tree can have, and analyze its extremal properties.
Protamine is administered as protamine sulfate to reverse the anticoagulant effect of heparin following cardiopulmonary bypass surgery. Immunogenicity of protamine has been recognized for decades in several patient groups including vasectomized men, diabetic patients on protamine-containing insulin and patients undergoing cardiopulmonary bypass surgery. Anti-protamine/heparin antibodies are a newly described class of heparin-dependent antibodies found in about 30% of patients exposed to protamine and heparin during cardiac surgery. A subset of seropositive patients especially who tested positive for platelet-activating anti-protamine/heparin immunoglobulin G (IgG) antibodies before surgery have prolonged postoperative thrombocytopenia with an increased risk for arterial occlusions. Studies presented in this thesis shed light on potential approaches that may prevent antibody-mediated platelet activation by anti-protamine/heparin antibodies. Two approaches are presented in this thesis, partially desulfated heparin (ODSH) and low molecular weight protamine (LMWP). Our studies demonstrated the ability of ODSH to inhibit anti-protamine/heparin antibody-mediated platelet destruction in the NOD/SCID mouse model by: i) reduction of antibody binding to preformed protamine/heparin complexes, as shown by enzyme immunoassay, ii) interfering with the binding of protamine/heparin complexes to platelets as shown by flow cytometry and fluorescence microscopy, and iii) inhibition of antibody-mediated platelet activation. Interestingly, ODSH was also able to block ongoing platelet destruction by displacing pre-bound complexes from the platelet surface. In addition, our data suggest the use of synthesized LMWP as a substitute for protamine in heparin reversal. The in vitro investigations showed that synthesized LMWP efficiently neutralizes heparin using the activated partial thromboplastin time. Anti-protamine/heparin antibodies have low binding properties to LMWP/heparin complexes as indicated in enzyme immunoassay. The ability of platelet-activating anti-protamine/heparin antibodies to induce platelet activation in the functional assay was significantly reduced in the presence of LMWP/heparin compared to protamine/heparin complexes. Owing to findings obtained in our studies, both approaches might be a promising future option to reduce anti-protamine/heparin antibody-mediated adverse effects.
Protamine (PRT) is a positively charged protein, which is widely used in medicine as an adjunct to certain preparations of insulin and as a rapidly-acting antidote for heparin, particularly to neutralize the effects of high heparin concentrations needed for anticoagulation during cardiac surgical procedures using cardiopulmonary bypass. It has been demonstrated that PRT and heparin form multimolecular complexes and that these complexes have high immunogenicity in a mouse model. Studies in this thesis provide new insights into the pathophysiology of anti-PRT/heparin antibodies. The results of study I showed that the administration of PRT combined with heparin is responsible for high immunoglobulin G (IgG) immunization after cardiac surgery. A subset of these antibodies was able to induce platelet activation in a way similar to that observed by heparin-induced thrombocytopenia (HIT). Using an animal model, we demonstrated that anti-PRT/heparin antibodies are capable of platelet destruction in the presence of PRT and heparin. Moreover, our data suggests that platelet-activating anti-PRT/heparin antibodies at surgery are potentially associated with postoperative thrombocytopenia and an increased risk for thromboembolic events. In study II, the immune response against PRT/heparin complexes was investigated. This study showed a relatively fast development of IgG with no general preceding IgM formation. In addition, patients undergoing liver transplantation developed anti-PRT/heparin antibodies without previous exposure to PRT. These results suggest that a previous contact with the antigen(s) itself or other antigens with molecular mimicry induced this immune response. In fact, we were able to identify Neutral Protamine Hagedorn (NPH) insulin and core histones (DNA-binding proteins) as potentially antigenic candidates for a previous immunization. Furthermore, the findings of study III demonstrate the ability of anti-PRT/heparin antibodies to activate platelets in the presence of NPH insulin in a heparin-dependent way suggesting that diabetic patients may have an enhanced risk for thromboembolic complications if treated with NPH insulin and possibly while receiving prophylactic heparin. These observations justify further clinical investigations to assess the impact of the interaction between anti-PRT/heparin antibodies and PRT-mimicking antigens, such as NPH insulin or histones.
This dissertation focuses on the characterization of novel enzymes and metabolic pathways that fulfill crucial functions during marine carbohydrate degradation by Bacteroidetes and thus contributes to an advanced understanding of the global carbon cycle. Depolymerization and utilization of marine polysaccharides by Bacteroidetes requires a tremendous repertoire of enzymes with a wide range of functions. For instance, during the breakdown of the marine red algal polysaccharide porphyran, an oxidative demethylation of the methoxy sugar 6-O-methyl-D-galactose (G6Me) by cytochrome P450 monooxygenases occurs. This reaction produces huge amounts of cytotoxic formaldehyde, marine bacteria capable of degrading porphyran must therefore possess suitable formaldehyde detoxification pathways. Consequently, Article I focus on the identification of possible formaldehyde detoxification pathways in marine
Flavobacteriia, which led to the discovery of the ribulose monophosphate pathway as specific pathway for the detoxification of formaldehyde in certain Bacteroidetes like Zobellia galactanivorans. Furthermore, it was demonstrated in Article II that alcohol dehydrogenases play an essential role in the microbial utilization of G6Me and therefore possess a function in porphyran degradation. Discovering novel enzymes, entire enzymatic cascades or biotechnologically important microorganisms that can metabolize these marine carbohydrates also contributes to the utilization of marine polysaccharides as feedstock for potential biotechnological applications. A prospective biorefinery process was proposed in Article III by the identification of Bacillus licheniformis as promising utilizer of marine carbohydrate-derived monosaccharides and the creation of a microbial cell factory capable of growing on ulvan, a marine carbohydrate obtainable from algal bloom-dominating green algae, enabling an industrial use of the renewable and abundant algal biomass in future.
The focus of the first two articles was the engineering and application of enzymes for the conversion of the bio-based resources glycerol and its oxidation product glyceraldehyde for the production of the value added product glyceric acid. Article III focuses on the cloning, exploration and engineering of a polyol dehydrogenase, which later on was used as cofactor recycling system in order to produce ε-caprolactone from cyclohexanol as presented in arti-cle IV. The following paragraphs will give a short outline of each article. ARTICLE I: ASYMMETRIC SYNTHESIS OF D-GLYCERIC ACID BY AN ALDITOL OXIDASE AND DIRECTED EVOLUTION FOR ENHANCED OXIDATIVE ACTIVITY TOWARDS GLYCEROL. GERSTENBRUCH, S., WULF, H., MUßMANN, N., O’CONNELL, T., MAURER, K.-H. & BORNSCHEUER, U. T. (2012). Appl. Microbiol. Biotechnol. 96, 1243-1252. The alditol oxidase of Streptomyces coelicolor A3(2) (AldO) was used to catalyze the oxida-tion of glycerol to glyceraldehyde and glyceric acid. The enantioselectivity for the FAD-de-pendent glycerol oxidation was elucidated and different strategies were used to enhance the substrate specificity towards glycerol. Directed evolution by error-prone PCR led to an AldO double mutant with 1.5-fold improved activity for glycerol. Further improvement of activity was achieved by combination of mutations, leading to a quadruple mutant with 2.4-fold higher specific activity towards glycerol compared to the wild-type enzyme. In small-scale biotransformation concentrations up to 2.0 g•l-1 D-glyceric acid could be reached using whole cells. Investi¬gation of the effects of the introduced mutations led to a further identification of es¬sential amino acids with respect to enzyme functionality and structural stability. ARTICLE II: KINETIC RESOLUTION OF GLYCERALDEHYDE USING AN ALDEHYDE DEHYDROGENASE FROM DEINOCOCCUS GEOTHERMALIS DSM 11300 COMBINED WITH ELECTROCHEMICAL COFACTOR RECYCLING. WULF, H., PERZBORN, M., SIEVERS, G., SCHOLZ, F. & BORNSCHEUER, U. T. (2012). J. Mol. Catal. B Enzym. 74, 144-150. Two aldehyde dehydrogenases (ALDH) from Escherichia coli BL21 and Deinococcus geother-malis were cloned, characterized and evaluated according to their applicability for a bio-catalysis setup with electrolytic cofactor recycling. Both ALDHs turned out to have a sim¬ilar substrate scope and favor short to medium chain aldehydes and both oxidize glyceralde¬hyde to D-glyceric acid. The ALDH variant of D. geothermalis shows higher specific activity towards glyceraldehyde and has an elevated optimum temperature compared to the BL21 enzyme. Due to the higher specific activity of the ALDH of D. geothermalis, this enzyme was used to conduct a kinetic resolution of glyceraldehyde with electrolytic NAD+ recycling at a glassy carbon foam electrode with ABTS as redox mediator yielding in 1.8 g•l-1 glyceric acid. ARTICLE III: PROTEIN ENGINEERING OF A THERMOSTABLE POLYOL DEHYDROGENASE. WULF, H.*, MALLIN, H.*, BORNSCHEUER U.T. (2012). Enzyme Microb. Technol. 51, 217-224 (*equally contributed). The new enzyme polyol dehydrogenase PDH-11300 from D. geothermalis was extensively characterized regarding its temperature optimum and thermostability. A peptide stretch responsible for substrate recognition from the PDH-11300 was substituted by this particular stretch of a homolog enzyme, the galactitol dehydrogenase from Rhodobacter sphaeroides (PDH-158), resulting in a chimeric enzyme (PDH-loop). The substrate scopes were deter-mined and basically the chimeric enzyme represented the average of both wild-type en-zymes. A rather unexpected finding was the notably increased T5060, by 7°C to 55.3°C, and an increased specific activity against cyclohexanol. Finally, the cofactor specificity was suc¬cess-fully altered from NADH to NADPH by an Asp55Asn mutation, which is located at the NAD+ binding cleft, without influencing the catalytic properties of the dehydrogenase. ARTICLE IV: A SELF-SUFFICIENT BAEYER-VILLIGER BIOCATALYSIS SYSTEM FOR THE SYNTHESIS OF Ɛ-CAPROLACTONE FROM CYCLOHEXANOL. MALLIN, H. *, WULF, H. *, BORNSCHEUER U.T. (2013). Enzyme Microb. Technol., online, DOI: 10.1016/j.enzmictec.2013.01.007 (*equally contributed). The application of the engineered PDH-loopN mutant [1] (Article III) for the production of ε-caprolactone from cyclohexanol was investigated in a co-immobilization approach with the cyclohexanone monooxygenase from Acinetobacter calcoaceticus. Biotransformation with solubilized enzymes led to an isolated yield of 55% pure ε-caprolactone with no residual cy-clohexanol to be detected. During the immobilization experiments a higher enzyme ratio in favor of the CHMO led to higher reaction velocities. Similarly, the addition of soluble fresh CHMO during reuse of co-immobilization batches significantly increased the activity identi-fying the CHMO as the bottleneck in this reaction setup.
Amine transaminases are versatile biocatalysts for the production of pharmaceutically and agrochemically relevant chiral amines. They represent an environmentally benign alternative to waste intensive transition metal catalysed synthesis strategies, especially because of their high stereoselectivity and robustness. Therefore, they have been frequently used in the (chemo)enzymatic synthesis of amines and/or became attractive targets for enzyme engineering especially in the last decade, mainly in order to enlarge their substrate scope. Certainly, one of the most notable examples of amine transaminase engineering is the
manufacturing of the anti-diabetic drug Sitagliptin in large scale after several rounds of protein engineering. Thereby, the target amine was produced in asymmetric synthesis mode which is the most convenient and favored route to a target chiral amine, starting from the corresponding ketone. The choice of the amine donor is highly relevant for reaction design in terms of economical and thermodynamic considerations. For instance, the use of alanine as the natural amine donor is one of the most common strategies for the amination of target ketones but needs the involvement of auxiliary enzymes to shift the reaction equilibrium towards product formation. In fact, isopropylamine is probably one of the most favored donor molecules since it is cheap and achiral but it is supposed to be accepted only by a limited number of amine transaminases.
This thesis focusses on the optimization and application of amine transaminases for asymmetric synthesis reactions en route to novel target chiral amines using isopropylamine as the preferred amine donor.
The biomechanical (Young's modulus, adhesion force, deformability) properties of platelets depend on the cytoskeleton and have an undisputed influence on physiological and pathological processes such as hemostasis and thrombosis. The alterations of these biomechanical properties can be used as label-free diagnostic markers in initiation or progressive diseases such as MYH9-inherited disease. Therefore, the focus of my thesis was to investigate the relationship between the changes in platelet cytoskeleton proteins and the resulting biomechanical properties using biophysical methods.
In the first chapter of my thesis I focused on my review of the biophysical methods that are most commonly used to assess and quantify the biomechanical properties of platelets. In this review, I provide an in-depth insight into the governing principles and instrumentation setup and discuss relevant examples applied to platelet mechanics. In addition, my review also summarizes the limitations of these biophysical methods and highlight latest improvements. The review covers the following techniques: micropipette aspiration, atomic force microscopy (AFM), scanning ion conductance microscopy (SICM), tensile force microscopy on hydrogel substrates, microcolumns, and deformable 3D substrates, and real-time deformability cytometry (RT-DC). This review is directed toward clinician scientists who are interested in exploring applications of single-cell based biophysical approaches in unraveling the role of platelet biomechanics in hemostasis and thrombosis research.
In the second chapter of my thesis, I present my research paper on the influence of commonly used ex vivo anticoagulants on the intrinsic biomechanical properties and functional parameters (e.g. activation profils) of human platelets. To comprehensively assess this, platelets obtained in different ex vivo anticoagulants such as ACD-A, Na-Citrate, K2-EDTA, Li-Heparin, and r-Hirudin were used, and their biomechanical properties were determined by real-time fluorescence and deformability cytometry (RT-FDC). Flow cytometry, and confocal laser scanning fluorescence microscopy were used to determine platelet function properties. K2-EDTA and Li-Heparin were found to affect platelet biomechanics by increasing actin polymerization of non-stimulated human platelets. This increased actin polymerization results in decreased platelet deformation. It is recommended that an ex vivo anticoagulant such as ACD-A, Na-Citrate, or r-Hirudin be chosen for the study of the cytoskeleton of human platelets and, if possible, that it not be exchanged, because comparability of results is not assured. Furthermore, I demonstrate the significance of choosing correct ex vivo anticoagulants in RT-FDC by showing that platelets from a healthy donor and a MYH9 patient with the E1841K point mutation differ in their deformation. This paper is the first comprehensive investigation at the single platelet level to establish the relevance of preanalytical standardization in platelet sample preparation for biomechanical studies.
The third chapter of my thesis is focused on the biomechanical analyses of platelets and thrombi from MYH9-related disease. Here I studied three Myh9 mouse lines with a point mutation in the Myh9 gene at positions 702, 1424, or 1841. Furthermore, two MYH9 patients (MYH9 p.D1424N, MYH9 p.E1841K) were examined. MYH9-related disease (MYH9-RD) presents with macrothrombocytopenia with a moderate bleeding tendency. It is caused by mutations in the MYH9 gene that lead to alteration of non-muscle myosin heavy chains type IIA (NMMHC IIA), resulting in disruption of the platelet cytoskeleton. Western blot analysis, flow cytometry, in vitro aggregometry, and transmission electron microscopy demonstrated that Myh9 point mutant mice have comparable primary function compared to the control group. The heterozygous point mutations in the Myh9 gene resulted in decreased platelet deformation (RT-FDC), decreased platelet adhesion to collagen (single platelet force spectroscopy-SPFS), and decreased platelet-platelet interaction forces (SPFS). Decreased platelet force (Micropost Arrays) results in softer thrombi (colloidal probe Spectroscopy), impaired clot retraction, and thus prolonged bleeding time. The R702C, D1424N, and E1841K mutations have a similar effect on platelet biomechanical functions, although the E1841K mutation had less impact on thrombus formation and stiffness. MYH9-RD patients have an increased risk of bleeding, and the antifibrinolytic drug tranexamic acid (TXA) is one way to control bleeding complications in these patients. It was shown that TXA treatment significantly reduced bleeding time in the three Myh9 mouse models, confirming that the enhanced bleeding phenotype due to decreased platelet forces in Myh9 mutant mice can be compensated by the addition of TXA.
With the biophysical methods and research results presented in my thesis, it is clear that it is essential to study the altered response of the platelet cytoskeleton by cytoskeletal mutations, biochemical, physical stimuli, or by pharmacological aspects. This will provide us with an opportunity to better understand the underlying mechanisms and thus contribute to better clinical treatment.
Metabolomics is the scientific study of metabolites of an organism, cell, or tissue. Metabolomics makes use of different analytical approaches. In this thesis, an analytical platform consisting of proton nuclear magnetic resonance spectroscopy (1H-NMR), gas chromatography-mass spectrometry (GC-MS, EI/quadrupol) and liquid chromatography-mass spectrometry (LC-MS, ESI/TOF) was used for metabolite analysis. Due to the high physicochemical diversity of metabolites, the usage of different analytics is profitable. Focusing on metabolome analysis of microorganisms, the development of viable protocols was prerequisite. To ensure metabolome samples of best possible quality, particularly the sampling procedure has to be optimized for each microorganism to be analyzed individually. In microbial metabolomics, the energy charge value is a commonly used parameter to assure high sample quality (Atkinson 1968). The pathogenic bacterium Staphylococcus aureus and the biotechnical relevant bacterium Bacillus subtilis were main target of research. The sampling protocol development “A protocol for the investigation of the intracellular Staphylococcus aureus metabolome” (Meyer et al. 2010) and “Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis”s (Meyer et al. 2013) confirmed the need for development and verification of viable protocols. It was observed, that minor differences in the sampling procedure can cause major differences in sample quality. Using the validated analytical platform and the optimized protocols, we were able to investigate the metabolome of S. aureus and B. subtilis under different conditions. Investigations of the pathogenic bacterium S. aureus are of major interest due to its increasing resistance to antibiotics. Methicillin (multi)-resistant S. aureus (MRSA) strains are responsible for several difficult-to-treat infections. The cell wall of bacteria is the target of an array of antibiotics, like the beta-lactam antibiotics. Our study “A metabolomic view of Staphylococcus aureus and Its Ser/Thr kinase and phosphatase deletion mutants: Involvement in cell wall biosynthesis” (Liebeke et al. 2010) revealed the influence of the serine-threonine kinase on cell wall biosynthesis of S. aureus. LC-MS based metabolome data uncovered prevalent wall teichoic acid precursors in the serine-threonine kinase deletion mutant (ΔpknB), and predominantly peptidoglycan precursors in the phosphatase deletion mutant (Δstp), compared to the S. aureus wild type strain 8325. This uncovered a so far undescribed importance of the serine-threonine kinase on the cell wall metabolism and provides new insights into its regulation. The nasopharynx and the human skin are often the ecological niche of S. aureus. Furthermore, S. aureus exists outside its host, for example on catheters. Depending on its niche, S. aureus is exposed to several stress factors and limitation conditions, such as carbon source limitation and starvation. To cope with the latter, a number of regulatory cellular processes take place. In “Life and death of proteins: a case study of glucose-starved Staphylococcus aureus” (Michalik et al. 2012) protein degradation during glucose starvation was monitored. An intriguing observation was that proteins involved in branch chain amino acid biosynthesis and purine nucleotide biosynthesis were distinctly down-regulated in the clpP mutant. This lead to the assumption of a stronger repression of CodY-dependent genes in the clpP mutant. Intracellular metabolome data revealed higher GTP concentrations in the clpP mutant. This may explain the higher CodY activity and thereby stronger repression of CodY-dependent genes in the clpP mutant. Since different S. aureus strains are known to colonize different niches, global carbon source (glucose, glucose 6-phosphate, glycerol, lactate, lactose and a mixture of all) and carbon source limitation dependent exo-metabolome analyses were performed using three different S. aureus strains (HG001: laboratory strain, EN493: human endocarditis isolate and RF122: bovine mastitis strain). The most apparent observation was that RF122 can utilize lactose best, while EN493 and HG001 are better at utilizing glucose-6-phosphate compared to the bovine RF122 strain. Bacillus subtilis is an extensively studied Gram-positive and non-pathogenic bacterium. In the functional genomics approach “System-wide temporal proteomics profiling in glucose-starved Bacillus subtilis” (Otto et al. 2010) growth phase dependent changes in the proteome, transcriptome and extracellular metabolome were monitored. By mass spectrometric analysis of five different cellular subfractions, ~ 52% of the predicted proteins could be identified. To confirm and complete the proteomic data transcriptome and extracellular metabolome analyses were performed. The extracellular metabolome data ensured that cells were glucose-starved and revealed growth phase dependent metabolic footprints. In “A time resolved metabolomics study: The influence of different carbon sources during growth and starvation of Bacillus subtilis” ((Meyer et al. 2013) submitted) four different compounded cultivation media were investigated as only glucose, glucose and malate, glucose and fumarate and glucose and citrate as carbon source. It could be shown, that B. subtilis is able to maintain an intracellular metabolite homeostasis independent of the available carbon source. On the other hand, in the exo-metabolome, carbon source as well as growth phase dependent differences were detected. Furthermore, in this study the influence of ATP and GTP on the activation of the alternative RNA polymerase sigma factor B (σB) was discussed. The concentration of ATP and GTP decreased for all conditions, as cells entered the stationary growth phase. While cell growth on solely glucose and during growth on glucose and additional malate, the ATP and GTP concentrations increased slightly when the consumption of the second carbon source was initiated. Only under these conditions, a considerable σB activity increase during the transition from exponential to stationary growth phase was observed. Furthermore, the developed sampling protocol for metabolome analysis of B. subtilis enabled us to be part of a “multi omics” system biological approach to study the physiological adjustment of B. subtilis to cope with osmotic stress under chemostat conditions.
Approaches to the Analysis of Proteomics and Transcriptomics Data based on Statistical Methodology
(2014)
Recent developments in genomics and molecular biology led to the generation of an enormous amount of complex data of different origin. This is demonstrated by a number of published results from microarray experiments in Gene Expression Omnibus. The number was growing in exponential pace over the last decade. The challenge of interpreting these vast amounts of data from different technologies led to the development of new methods in the fields of computational biology and bioinformatics. Researchers often want to represent biological phenomena in the most detailed and comprehensive way. However, due to the technological limitations and other factors like limited resources this is not always possible. On one hand, more detailed and comprehensive research generates data of high complexity that is very often difficult to approach analytically, however, giving bioinformatics a chance to draw more precise and deeper conclusions. On the other hand, for low-complexity tasks the data distribution is known and we can fit a mathematical model. Then, to infer from this mathematical model, researchers can use well-known and standard methodologies. In return for using standard methodologies, the biological questions we are answering might not be unveiling the whole complexity of the biological meaning. Nowadays it is a standard that a biological study involves generation of large amounts of data that needs to be analyzed with a statistical inference. Sometimes data challenge researchers with low complexity task that can be performed with standard and popular methodologies as in Proteomic analysis of mouse oocytes reveals 28 candidate factors of the "reprogrammome". There, we established a protocol for proteomics data that involves preprocessing of the raw data and conducting Gene Ontology overrepresentation analysis utilizing hypergeometric distribution. In cases, where the data complexity is high and there are no published frameworks a researcher could follow, randomization can be an approach to exploit. In two studies by The mouse oocyte proteome escapes maternal aging and CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction we showed how randomization can be performed for distinct complex tasks. In The mouse oocyte proteome escapes maternal aging we constructed a random sample of semantic similarity score between oocyte transcriptome and random transcriptome subset of oocyte proteome size. Therefore, we could calculate whether the proteome is representative of the trancriptome. Further, we established a novel framework for Gene Ontology overrepresentation that involves randomization testing. Every Gene Ontology term is tested whether randomly reassigning all gene labels of belonging to or not belonging to this term will decrease the overall expression level in this term. In CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction we validated CellFateScout against other well-known bioinformatics tools. We stated the question whether our plugin is able to predict small molecule effects better in terms of expression signatures. For this, we constructed a protocol that uses randomization testing. We assess here if the small molecule effect described as a (set of) active signaling pathways, as detected by our plugin or other bioinformatics tools, is significantly closer to known small molecule targets than a random path.
Decades after international guidelines to approach Universal Health Coverage and Access for All to essential health care services have been formulated by the global community, social protection in health remains a major global challenge. This implies the devastating situation of having less than 15% of the global population benefiting of any kind of social protection in health, while more than 70% of the world population lacks any type of social protection coverage. 36 years after the famous and often-cited Alma-Ata Declaration proclaimed that „the promotion and protection of the health of the people is essential to sustained economic and social development and contributes to a better quality of life and to world peace”, people of the informal sector – which forms up to 90% of the population in many countries of sub-Saharan Africa – are still forced to take out loans or sell their assets to settle their hospital bills and in the end fall into poverty because of unbearable health care costs. While private health insurance schemes are mainly serving people living in urban areas and offer products and services that are not tailored to the needs of people of low-income from rural and/or remote areas, public social health insurance schemes are usually designed to serve the formal sector or are exclusively catering for public servants. At the same time, social protection in health is increasingly regarded to be a guarantor for development and economic growth of the national economy. In this context, some authors are convinced that community-based health financing is to be seen as a promising approach to insure parts of the population, which are normally excluded from any type of social protection in health, against catastrophic health care costs. With a focus on low-income people, Community-based Health Financing (CBHF) schemes offer products, processes and institutions that are tailored to the specific needs of their low-income target group, usually situated in the informal sector. In the aim to meet international standards and comply with the global development agenda, governments in sub-Saharan Africa are increasingly acknowledging the need to include the informal sector and people of low-income into their public health financing systems. As a result, innovative health systems evolved, which often comprise of hybrid sub-systems to cover various target groups of the society. While some governments – such as the governments of Rwanda, Ghana and Tanzania – have already implemented integrated national Social Health Insurance (SHI) systems that consider CBHF schemes to cover the informal sector, others are aiming at implementing this innovative idea in the near future, e.g. Burkina Faso and Togo. Given the above-illustrated situation, the overall research objective of this thesis is to explore the potential contribution of CBHF schemes towards Universal Health Coverage (UHC) in low- income countries of sub-Saharan Africa. Furthermore, the specific research objectives are set as follows; (1) To establish common lessons learnt from low-income countries in sub-Saharan Africa which implemented integrative SHI systems by combining efforts of national SHI schemes and CBHF schemes, or which are in an advanced stage of designing and implementing the same. (2) To comprehensively analyze the Kenyan health financing system and design adequate interventions towards the design and implementation of an integrative national SHI scheme in Kenya which is favoring UHC. (3) To develop a standard model for implementing integrative SHI systems in low-income countries of sub-Saharan Africa and the world. This thesis will at first provide a comprehensive topical background containing evidence about different relevant concepts such as Development, Universal Health Coverage, Social Protection, Health Financing and Micro Health Insurance. On this basis, the potential of combining community-based and national efforts towards tailored health care financing at national level will be explored by analyzing strengths and weaknesses of both approaches and providing brief insights from low-income countries of sub-Sahara Africa in this area. Furthermore, a comprehensive background to common development initiatives as well as the social protection and health care financing sectors in Kenya is provided to introduce the case study of chapter four. In the third chapter, common efforts of governments and other stakeholders involved in health care financing in sub-Saharan African countries to integrate CBHI schemes into public SHI schemes will be reviewed and analyzed. In the scope of this review, Tanzania, Rwanda, Burkina Faso and Ghana will serve as practical country case examples. Based on this extensive cross-country analysis, common lessons learnt regarding the complex process of designing integrative SHI systems in low-income countries of sub-Saharan Africa will be presented. In chapter four, through a comprehensive country case study, the Kenyan health and health financing sector and its stakeholders will be analyzed regarding its potential towards UHC, aiming at the development of most promising interventions towards the design and implementation of an integrated SHI scheme in Kenya, considering CBHF schemes as one building block of the system. A multi-stage model as well as a multi-level structure of a national SHI system to approach UHC in Kenya will be outlined and presented. The thesis will be concluded in chapter five by transferring the Kenyan experience to a global level and suggesting a standard model for implementing integrated SHI schemes in similar contexts as given in Kenya and the presented case examples. In the conclusion, common opportunities and limitations of community-based approaches towards UHC are highlighted and a way forward for the Kenyan context is suggested.
The development of the two main types of diabetes mellitus, type 1 and type 2 (T1D, T2D), is closely associated with the formation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in insulin-secreting pancreatic β-cells. In T1D, β-cell death
is triggered by proinflammatory cytokines, which mainly lead to the formation of ROS
in mitochondria and RNS in the cytosol. Pancreatic β-cells are extraordinarily sensitive
to oxidative stress due to their low glutathione peroxidase and catalase expression.
Thus, hydrogen peroxide (H2O2) cannot be detoxified, neither sufficiently, nor rapidly.
H2O2 itself is a rather weakly reactive ROS but can react in the Fenton reaction to form
highly reactive hydroxyl radicals (●OH), that can damage cells in a variety of ways and
induce cell death. The cell and its organelles are bounded by biological membranes
that differ in their permeability to H2O2. Aquaporins (AQPs) are water-transporting
transmembrane proteins, and some isoforms have been shown to facilitate a bidirectional transport of H2O2 across cellular membranes in addition to water. The role of
AQP8 was investigated in an insulin-producing cell model by stably overexpressing
AQP8 (AQP8↑) and by a CRISPR/Cas9-mediated AQP8 knockout. However, AQP8
proved to be an essential protein for the viability of the insulin-producing RINm5F cells, and so we established a tet-on-regulated AQP8 knockdown (AQP8 KD). Our results highlight that AQP8 is involved in H2O2 transport across the plasma and mitochondrial membranes, and that AQP8 expression gets upregulated by proinflammatory cytokines (in vitro) and in an acutely diabetic rat model (in vivo). Furthermore, it was shown that the increased proinflammatory cytokine toxicity is due to enhanced mitochondrial oxidative stress, because H2O2 cannot be efficiently transported in AQP8 KD cells and ●OH
are increasingly generated. Caspase activity then raises, and apoptosis is increasingly
induced coupled with a proportion of ferroptosis-mediated cell death because of a concomitant decrease in nitric oxide (NO●) concentration. In conclusion, AQP8 is localized in the plasma and mitochondrial membrane of insulin-producing RINm5F cells, where it is involved in H2O2 transport. In T1D, AQP8 plays an important role in the transport of H2O2 from the mitochondrial matrix to the cytosol so that the concentration is lowered in the mitochondria. This wider distribution of H2O2 may ease the inactivation of H2O2.
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: Cardiovascular disease (CVD) remains the major cause of mortality and morbidity worldwide and produces large productivity loss. The majority of CVD mortality could be prevented with changes in modifiable risk factors including tobacco use, physical inactivity, unhealthy diet and harmful use of alcohol. Successful behavioral prevention of CVD requires the identification of relevant target behaviors and reach of populations at risk. Presenteeism i.e. attending work while ill is discussed as a work-related risk factor for CVD. However, little is known about the interplay of presenteeism with established health risk behaviors. The first aim of this dissertation was to examine the association of presenteeism with health behaviors (study 1). The second aim was to examine factors that can enhance the public health impact of CVD prevention efforts. Therefore, the effect of recruitment strategy used on reach (study 2) and of communication channel used on intervention usage (study 3) was examined. Methods: Study 1 comprised data from 710 Australian employees aged 18 years and older who completed an online-survey. Linear regression analysis was used to examine the association of health behaviors (physical activity, work and non-work-related sitting time, sleep duration and sleep quality) with presenteeism. For study 2 individuals aged 40-65 years were invited to a two-stage cardio-preventive program including an on-site health screening and a cardiovascular examination program (CEP) using face-to-face recruitment in general practices (n = 671) and job centers (n = 1,049), and mail invitations from a health insurance company (n = 894). Recruitment strategies were compared regarding three aspects of reach: (1) participation rate, (2) participants’ characteristics i.e. socio-demographics, self-reported health and CVD risk factors, and (3) predictors of program participation. Study 3 compromised 16,948 users (aged 18 years and older) of the feely available physical activity promotion program 10,000 Steps. Users were grouped based on which platform (website, app) they logged their physical activity: Web-only, App-only, or Web-and-app. Groups were compared on socio-demographics, engagement parameters and logged physical activity. Non-usage attrition i.e. discontinued program usage over the first three months was examined using Kaplan-Meier survival curves. A Cox regression model was used to determine predictors of non-usage attrition. Results: Analyses from study 1 revealed that presenteeism was associated with poor sleep quality and suboptimal sleep duration after controlling for socio-demographics, work and health-related variables. Engaging in three health risk behaviors was associated with higher presenteeism compared with engaging in none or one. Study 2 showed screening participation rates of 56.0%, 32.8%, 23.5% for general practices, job centers and the health insurance company, respectively. Participation rate for the CEP among eligible individuals was 80.3%, 65.5%, and 96.1%, respectively. Job center clients showed the lowest socio-economic status and the most adverse CVD risk pattern. Whereas being female predicted screening participation across all strategies, higher age predicted screening participation only within individuals recruited via the health insurance company. Within general practices and job centers CEP participants were less likely to be smokers than non-participants. Study 3 revealed that engagement with the program was highest for Web-and-app users. Cox regression showed that user group predicted non-usage attrition: Web-and-app users (hazard ratio = 0.86; P < .001) and App-only users (hazard ratio = 0.63; P < .001) showed a reduced attrition risk compared to Web-only users. Further, older age, being male, being non-Australian, higher program engagement and higher number of steps logged were associated with reduced non-usage attrition risk. Conclusion: The results of this dissertation have three implications for designing CVD behavioral interventions with a high public health impact. First, employees suffering from presenteeism may require interventions addressing health risk behaviors including suboptimal sleep behaviors. Second, implementing prevention efforts in job centers may be especially useful to reduce health inequalities induced by social gradient. Third, the population impact of web-based interventions may be increased when using mobile delivery channels.
The Institute of German Dentists [Institut der Deutschen Zahnärzte (IDZ)] conducted four national cross-sectional surveys of oral health in the German resident population [German Oral Health Studies, "Deutsche Mundgesundheitsstudien", (DMS)]: in 1989 (DMS I, only West Germany), 1992 (DMS II, only East Germany), 1997 (DMS III), and 2005 (DMS IV). In this study, the first two surveys (1989/92) were merged to achieve comparability with the last two studies. The Studies of Health in Pomerania (SHIP) are two independent regional cross-sectional population-based studies conducted during 1997-2001 (SHIP-0) and 2008-2012 (SHIP-Trend) in northeast Germany. In this thesis, we addressed three main questions: First, we aimed to explore the relative contributions of clinical oral health variables assessing caries, periodontal status, and prosthetic status to self-perceived oral health by means of an age-specific approach in DMS IV. Second, we aimed to assess the changes of dental health in West and East Germany between 1989 and 2005 in DMS I-IV. Third, we aimed to evaluate the changes of periodontal status and number of teeth within the last decade based on data from the DMS and the SHIP studies. To explore the associations of self-perceived oral health with clinical oral health variables, we developed separate multinomial logistic regression models for adults and seniors in DMS IV by using stepwise methods. To assess the changes of dental health in West and East Germany between 1989 and 2005, we applied regression models and assessed associations between region, survey year, their interactions and variables assessing dental disease status (number of missing, filled, decayed and sound teeth, the DMFT-index and the probability of having ≤20 teeth), adjusting for potential risk factors for caries. To assess changes of periodontal status in Germany, prevalences, percentages and numbers of teeth affected were defined. In summary, the number of unreplaced teeth showed the strongest association with self-perceived oral health in adults and was the second variable to enter the model for seniors during the stepwise selection process. Between 1997 and 2005, the number of missing teeth considerably decreased in DMS but East Germans had consistently more missing teeth than West Germans in each survey year. Further, during the last decade, the periodontal status significantly improved in SHIP and in West German adults, which might translate into a even higher tooth retention in the future.
This thesis aims at improving the current representation of adaptation in economic frameworks of climate change by a) accounting for the time-dependent evolution of the adaptive capacities of countries and b) quantifying unwelcome feedbacks of the adaptation process. In this context, it is proposed that economic assessments of climate change incorporate adaptation as a cyclic and phase-dependent process while devising their cost methodologies. A phase-dependent process acknowledges the existence of adaptation barriers while a cyclic process accounts for potential unwanted feedbacks of adaptation. By analyzing economic assessments against this framework, it is shown that dependencies between phases of adaptation and phases altogether are often disregarded. Furthermore, potential negative consequences associated with adaptation are rarely considered and adaptation is generally assumed to be unconstrained. The assumption of unconstrained adaptation is only acceptable in the context of high adaptive capacity. This concept was further investigated through a review of vulnerability assessments regarding their operation of the adaptive capacity component. It was found that adaptive capacity is mostly equated to proxies that reflect the knowledge, financial and livelihood capacities of the system under analysis. With this theoretical considerations in mind, a dynamic representation of adaptive capacity was elaborated at a country-level. The Human Development Index (HDI) was used as a proxy of the adaptive capacity of countries and its evolution in time extrapolated. The time required for countries to achieve developed world standards of human development was then estimated. The results indicate that between 2005 and 2020, half of the world population will live in countries with low adaptive capacity. This percentage is then progressively reduced to 15% in the year 2050, with marked regional differences. The time required for a country to achieve an appropriate level of development sets a clear constraint on when, and to what extent, the country can engage on climate change adaptation. This does not imply that adaptation will not take place before development occurs. Rather, it calls for adaptation options to be tailored in order to t the current and future adaptive capacities of countries. Obtaining higher levels of adaptive capacity is likely to be associated with negative consequences for the climatic system. The statistical relation between HDI and per-capita emissions of countries was established and future projections made. Between 2010 and 2050 approx. 300 Gt of CO2 are estimated to be associated with the increase of adaptive capacities of current developing countries. This value represents about 30% of the allowed CO2-budgets to restrict global temperatures to an increase of 2 degrees by 2100 compared to pre-industrial times - conditional to a 25% risk of failing to meet the target. For the case of sea-level rise, the modelling framework DIVA (Dynamic Interactive Vulnerability Assessment) was used in order to illustrate the drawbacks of a simplistic representation of adaptation. The results show that adaptation via the construction of protective infrastructure might be economically feasible for particular countries. For others, modeled results fail to provide a clear choice between adaptation or inaction. The assumption of unconstrained adaptation resulted in the valuation of costly protection options whose financial and knowledge requirements can be at odds with the capacities of some coastal countries - namely developing countries. Further, infrastructural protection as adaptive measure to prevent coastal damages can have the counter-productive effect of raising the amount and value of assets at risk. This is a direct result of DIVA disregarding the potential unwelcome feedbacks of adaptation itself. In conclusion, the full potential of economic assessments of climate adaptation is likely to remain unlocked as long as adaptation continues to be misrepresented. The methodologies discussed in this work provide a way forward to alleviate this deficiency in forthcoming assessments. For the case of sea-level rise, the modeling framework DIVA (Dynamic Interactive Vulnerability Assessment) was used in order to illustrate the drawbacks of a simplistic representation of adaptation. The results show that adaptation via the construction of protective infrastructure might be economically feasible for particular countries. For others, modeled results fail to provide a clear choice between adaptation or inaction. The assumption of unconstrained adaptation resulted in the valuation of costly protection options whose financial and knowledge requirements can be at odds with the capacities of some coastal countries - namely developing countries. Further, infrastructural protection as adaptive measure to prevent coastal damages can have the counter-productive effect of raising the amount and value of assets at risk. This is a direct result of DIVA disregarding the potential unwelcome feedbacks of adaptation itself. In conclusion, the full potential of economic assessments of climate adaptation is likely to remain unlocked as long as adaptation continues to be misrepresented. The methodologies discussed in this work provide a way forward to alleviate this deficiency in forthcoming assessments.
In terms of climate change and climate change mitigation, the quantitative knowledge of global carbon pools is important information. On the one hand, knowledge on the amount of carbon cycling among – and stored in – global pools (i.e. Atmosphere, Biosphere, Cryosphere, Hydrosphere, and Lithosphere) may improve the reliability of models predicting atmospheric CO2 concentrations in terms of fossil fuel combustion. On the other hand, the carbon sequestration potential of specific ecosystems allows for estimating their feasibility regarding carbon trade mechanisms such as the Clean Development Mechanism or the Reducing Emissions from Deforestation and Degradation Program (REDD+). However, up to date, the majority of terrestrial carbon assessments have focused on forests and peatlands, leaving a data gap open regarding the remaining ecosystems. This data gap is likely to be explained by the relatively high carbon densities and/or productivities of forests and peatlands. Nevertheless, to get a precise as possible global picture, information on carbon pools and sequestration of other ecosystems is needed. Although desert ecosystems generally express low carbon densities, they may absolutely store a remarkable amount of carbon due to their large areal extent. In this context, Central Asian Deserts (in particular within the Turanian Deserts, i.e. Karakum, Kysylkum, Muyunkum) likely inhibit comparably high carbon pools as they express a sparse vegetation cover due to an exceptionally high annual precipitation if compared to the World’s deserts. In this dissertation, three important woody plant species – Populus euphratica and Haloxylon aphyllum and Haloxylon persicum – of Central Asian Deserts were investigated for their carbon pools and carbon sequestration potential. These species were chosen as they I) locally express high carbon densities, II) are dominant species, III) have a rather large spatial distribution, and IV) have experienced a strong degradation throughout the 20th century. Thus, they likely show a remarkable potential for carbon re-sequestration through restoration and thus for an application of carbon trade mechanisms (CHAPTER I). P. euphratica was investigated in the nature reserve Kabakly at the Amu Darya, Turkmenistan and in Iminqak at the Tarim He, Xinjiang, China. The assessment of Haloxylon species was restricted to the Turanian deserts west of the Tain Shan. To achieve a first scientific basis for large scale estimates, different methodologies, ranging from allometric formulas, over dendrochronology to remote sensing were combined (CHAPTERS II-V). In CHAPTER II allometric formulas were successfully developed for Haloxylon aphyllum and Haloxylon persicum and applied to six study sites distributed over the Turanian Deserts to represent the allometric variability of Haloxylon species in Central Asia. CHAPTER III derives another allometric formula (only based on canopy area) for H. aphyllum and combines it with a remote sensing analysis from the nature reserve Repetek. Thereby, a first large scale estimate covering the Northeastern Karakum Desert of carbon pools related to mono specific H. aphyllum stands is achieved. CHAPTER IV describes the wood structure of Populus euphratica forests in the nature reserve Kabakly (Turkmenistan) and in Iminqak (Xinjiang, China). In CHAPTER V a dendrochronological approach derives models for predicting the Net Primary Productivity (NPP) and the age of P. euphratica in the nature reserve Kabakly. Thereby, a first feasibility assessment regarding remote sensing analyses and the upscaling of the obtained NPP results is carried out. First estimates based on these local studies (CHAPTER VI), reveal carbon densities ranging from 0.1 – 26.3 t C ha 1 for the three investigated species. Highest maximum and median carbon densities were found for P. euphratica, but Haloxylon aphyllum expressed remarkable maximum carbon densities (13.1 t C ha-1), too. The total carbon pools were estimated at 6480 kt C for P. euphratica, 520 kt C for H. aphyllum stands and 6900 kt C for Haloxylon persicum shrubland. Accounting for the extent of degraded areas, the total re-sequestration potentials of the respective species were estimated at 4320 kt C, 1620 kt C and 21900 kt C, this highlighting the remarkable absolute re-sequestration potential of H. persicum shrubland despite its low average carbon densities. In the end, the main results were put into a broader context (CHAPTER VI), discussing the general feasibility of reforestations both in ecological terms as well as in terms of carbon trade mechanisms. A short example highlights the strong connection between the feasibility of reforestations and the global carbon market. Finally, open research questions are brought forth revealing the yet large research potential of Central Asian Desert ecosystems in general and in terms of carbon sequestration.
Objective: The purpose of this study was to determine the accuracy and reliability of Frankfort horizontal plane identification using displays of multi-planar reconstructed MRI images, and propose it as a sufficiently stable and standardized reference plane for craniofacial structures Materials and Methods: MRI images of 43 adolescent randomly selected subjects were obtained from the longitudinal population based cohort study SHIP-2 using a T1-weighted 3D sequence. Five examiners independently identified the three landmarks that form FH plane. Intra-examiner reproducibility and inter-examiner reliability, correlation coefficients (ICC), coefficient of variability and Bland-Altman plots were obtained for all landmarks coordinates to assess reproducibility. Intra-examiner reproducibility and inter-examiner reliability in terms of location and plane angulation were also assessed. Results: Intra- and inter-examiner reliabilities for X, Y and Z coordinates of all three landmarks were excellent with ICC values ranging from 0.914 to 0.998. Differences among examiners were more in X and Z than in Y dimensions. The Bland–Altman analysis demonstrated excellent intra- as well as inter-examiner agreement between examiners in all coordinates for all landmarks. Intra-examiner reproducibility and inter-examiner reliability of the three landmarks in terms of distance showed mean differences between 1.3 to 2.9 mm, Mean differences in plane angulation were between 1.0° to 1.5° among examiners. Conclusion: This study revealed excellent intra-examiner and inter-examiner reproducibility of Frankfort Horizontal plane through 3D landmark identification in MRI. Sufficiently stable landmark-based reference plane could be used for different treatments and studies.
Chronic infections, including periodontal infections, may reduce lung function. To date, there are hardly any population-based studies evaluating the association between periodontitis and lung function. However, there are some studies that used variables associated with obstructive pulmonary diseases (FEV1, FEV1/FVC). Thus, we aimed to assess the potential association of periodontal diseases with lung volumes and airflow limitation in the population-based Study of Health in Pomerania (SHIP). Of 3300 participants aged 25-85 years of the 5-year follow-up (SHIP-1), 1809 subjects participated in lung function examinations. 1465 subjects were included in the analyses. Lung function was measured using spirometry, body plethysmography, helium dilution, and diffusing capacity for carbon monoxide. Periodontal status was assessed by clinical attachment loss, probing depth, and number of missing teeth. Linear regression models using fractional polynomials were used to assess linear and non-linear associations between periodontal disease and lung function adjusting for confounders. Adjusting for age, sex, waist circumference, physical activity, diabetes, asthma, and time between core and pulmonary examination, mean attachment loss was significantly associated with variables of dynamic and static lung volumes, airflow limitation and hyperinflation. Total lung capacity and diffusing capacity for carbon monoxide were not associated with mean attachment loss. Adjustment for smoking and height considerably changed coefficients indicating profound confounding. Including fibrinogen and high sensitive CRP into fully adjusted models did not change coefficients of mean attachment loss. Restricted to never smokers, mean attachment loss was significantly associated with FEV1, FVC, and RV/TLC. Relations with lung function were confirmed for mean probing depth, extent measures of attachment loss/probing depth, and number of missing teeth. Periodontal disease was significantly associated with decreased lung function. Systemic inflammation did not provide a mechanism linking both diseases. However, cohort studies evaluating lung function in the current manner are needed to confirm results from this study and to assess a causal relationship. Furthermore, it needs to be investigated with the help of randomized clinical trials whether prevention or treatment of periodontitis might have a beneficial impact on lung function.
Aim: To evaluate the association of Insulin-like Growth Factor (IGF) I related variables with periodontitis in the population-based Study of Health in Pomerania (SHIP). Material and Methods: From the cross-sectional SHIP, 2293 subjects with clinical attachment loss (CAL) data and 2398 subjects with tooth count data aged 20-59 years were analysed. Serum IGF-I and IGF binding protein (BP)-3 levels were determined by chemiluminescence immunoassays. Linear and logistic regressions with fractional polynomials were used to study associations between IGF-related variables and mean CAL or high tooth loss. For non-linear relations between IGFBP-3 and mean CAL, graphical presentations of fractional polynomials were used to deduce knots for linear splines. Results: In fully adjusted models, for serum IGFBP-3 values ≤1200 ng/mL, mean CAL increased significantly for decreasing serum IGFBP-3 levels (B=-0.027 (95% CI, -0.049; -0.005), p=0.02). The odds for high tooth loss decreased significantly for high serum IGFBP-3 values (OR=0.97 (0.95; 0.99), p=0.02). Serum IGF-I levels and the IGF-I/IGFBP-3 ratio were not related to mean CAL or tooth loss after full adjustment. Conclusions: Low serum IGFBP-3 levels might be associated with higher levels of periodontal disease. Neither serum IGF-I nor IGF-I/IGFBP-3 ratios were associated with periodontitis.
Diabetes mellitus has been linked with an increased risk for oral diseases, especially periodontitis. However, studies results were not consistent. The present study was conducted to evaluate whether both type 1 (T1DM) and type 2 diabetes mellitus (T2DM) are associated with increased prevalence and extent of periodontal disease and tooth loss compared with non-diabetic subjects within a homogeneous adult study population. T1DM, T2DM and non-diabetic subjects were recruited from the population-based Study of Health in Pomerania (SHIP). Additionally, T1DM subjects were retrieved from a Diabetes Centre in the same region. The total study population comprised 145 T1DM and 2,647 non-diabetic subjects aged 20-59 years, and 182 T2DM and 1,314 non-diabetic subjects aged 50-81 years. Multivariable regression revealed an association between T1DM and mean attachment loss (B=0.40 [95% CI; 0.19, 0.61], adjusted). Also, T1DM was positively associated with increased number of missing teeth after full adjustment (p<0.001). The association between T1DM and tooth loss was enhanced in subjects aged 40-49 and 50-59 years (p for interaction=0.01). In T2DM subjects, mean attachment loss was significantly higher compared with non-diabetic subjects (B=0.47 [95% CI; 0.21, 0.73], adjusted). The effect of T2DM was significantly enhanced in 60-69-years-old subjects (p for interaction=0.04). The association between T2DM and number of missing teeth was not statistically significant after adjustment (p=0.25). Analyses showed that the effect of T2DM on tooth loss was pronounced in females compared with males (p for interaction=0.01). In accordance with previous literature, present results suggested that periodontal diseases and tooth loss can been seen as a complication of both types of diabetes. Generally, periodontal diseases are preventable and treatable. Therefore, appropriate goals and strategies for improving periodontal health in subjects with diabetes need to be developed. Further, early detection and careful managed therapeutics with the physician and dentist working hand-in-hand may prove beneficial to the patient–s general health.
Brain aging even in healthy older adults is characterized by a decline in cognitive functions including memory, learning and attention. Among others, memory is one of the major cognitive functions affected by aging. Understanding the mechanisms underlying age-related memory decline may help pave the road for novel treatment strategies. Here, we tried to elucidate the neural correlates associated with memory decline using structural and functional neuroimaging and neuromodulation with transcranial direct current stimulation (tDCS).
Over the course of three studies, we investigated 1) the influence of white matter integrity and grey matter volume on memory performance in healthy older adults, 2) the role of functional coupling within the memory network in predicting memory performance and the impact of tDCS in modulating retrieval performance in healthy older adults, 3) the effect of tDCS over the sensorimotor cortex on cognitive performance in young adults.
MRI was used to study associations of cognitive performance with white matter integrity and grey matter volume, and examine their causal relationship in the course of aging. White matter integrity was assessed by acquiring diffusion tensor imaging (DTI) and performing deterministic tractography based on constrained spherical deconvolution. Grey matter volume was estimated using fully automated segmentation. Both white matter integrity and grey matter volume were correlated with behavioral data of a verbal episodic memory task. Percentage of correct answers at retrieval was used to measure memory performance (Manuscript 1). In addition, anodal tDCS (atDCS) (1 mA, 20 min) was applied over CP5 (left temporoparietal cortex) to modulate memory formation in healthy older adults. Participants underwent resting-state fMRI before the stimulation. Functional connectivity analysis was performed to determine whether functional coupling within the memory network predicted initial memory performance, and to examine its association to tDCS-induced enhancement effect (Manuscript 2). Finally, atDCS (1 mA, 20 min) was applied over C3 (left sensorimotor cortex) to explore the effect of tDCS over the sensorimotor cortex on cognitive performance in young adults. During the stimulation, participants performed three tasks; gestural task, attentional load task and simple reaction time task (Manuscript 3).
Results showed that volumes of the left dentate gyrus (DG) and tractography-based fractional anisotropy (FA) of individual fornix pathways were positively related to memory retrieval in older adults. Brain-behavior associations were observed for correct rejections rather than hits of memory performance, indicating specificity of memory network functioning for detecting false associations. Thus, the data suggested a particular role of neural integrity that promotes successful memory retrieval in older adults. Subsequent mediation analysis showed that left DG volume mediated the effect of fornix FA on memory performance (48%), corrected for age, revealing a crucial role of hippocampal pathway microstructure in modulating memory performance in older adults (Manuscript 1). tDCS results showed that atDCS led to better retrieval performance and increasing learning curves, indicating that brain stimulation can induce plasticity of episodic memory processes in older adults. Combining tDCS and fMRI, hippocampo-temporoparietal functional connectivity was positively associated with initial memory performance in healthy older adults and was positively correlated with the magnitude of individual tDCS-induced enhancement, suggesting that individual tDCS responsiveness may be determined by intrinsic network coupling (Manuscript 2). Finally, our findings suggested that atDCS over left sensorimotor cortex reduced reaction times in the gestural-verbal integration task, specifically for incongruent pairs of gestures and verbal expressions, indicating the role of sensorimotor cortex in gestural-verbal integration in young adults (Manuscript 3).
The results of all three studies may help to elucidate age-related structural deterioration and functional coupling network underlying cognitive processes in healthy adults. Furthermore, these studies emphasized the importance of interventions like tDCS in modulating cognitive performance, specifically episodic verbal memory and gestural-verbal integration. By unveiling the specific role of brain structures and functional network coupling as well as the role of tDCS in modulating cognitive performance, our results contribute to a better understanding of brain-behavior associations, and may help to develop clinical interventional approaches, tailored for specific cognitive functions in aging.
Liver dysfunctions are commonly associated with diabetes and mortality in the general
population. However, previous studies lack to define these disorders with hepatic markers from
MRI, which have been shown to be more accurate and sensitive than hepatic ultrasound and
laboratory markers. Further, previous studies defining different categories of prediabetes by oral
glucose tolerance states revealed controversial findings. Hence, this dissertation contributed to
understand the associations of liver dysfunctions with glucose intolerance states and all-cause
mortality in the general population.
In the first part of the dissertation, the associations of MRI-related hepatic steatosis and hepatic
iron overload with prediabetes were investigated. Prediabetes was categorized into IFG, IGT,
(alone or in combination) or previously unknown type 2 diabetes mellitus using OGGT data, as
suggested by the ADA. For analyses, we included 1632 subjects with MRI who participated in
an OGTT and reported no type 2 diabetes mellitus. We found that hepatic steatosis was
positively associated with continuous markers of glucose metabolism. Similarly, subjects with
hepatic steatosis as defined by MRI had a higher relative risk ratio to be in the prediabetes
groups (i-IFG, i-IGT and IFG + IGT) or having undiagnosed diabetes than individuals without
this condition. The observed associations were more obvious for MRI-derived hepatic steatosis
compared to ultrasound. In comparison to hepatic steatosis, we found that MRI-assessed hepatic
iron overload was positively associated only with both 2-hour plasma glucose and the combined
IFG + IGT category. There were no significant associations between hepatic iron overload and
other glucose tolerance states or biomarkers of glucose metabolism, regardless of possible
confounding factors.
In the second part, the associations of liver volume and other markers of hepatic steatosis with
all-cause mortality in the general population were investigated. We included 2769 middle-aged
German subjects with a median follow-up of 8.9 years (23,898 person-years). Serum liver
enzymes and FIB-4 score were used as quantitative markers, while MRI measurements of liver
fat content and total liver volume included as qualitative markers of hepatic steatosis. Compared
to other markers of hepatic steatosis, larger liver volumes were significantly associated with a
nearly three-fold increase in the long-term risk of all-cause mortality. Furthermore, this
association was consistent across all subgroups considered (men vs. women; presence or absence
of metabolic syndrome or type 2 diabetes at baseline). A positive association between FIB-4
score and all-cause mortality was found both in the entire cohort and in women. Likewise,
positive associations of higher serum AST and GGT levels with all-cause mortality were found
in the entire cohort and in men.
To conclude, this dissertation acknowledges the fact that prevention and early intervention of
liver dysfunction has major impact to reduce the burden of public health problems. Thus, our
findings suggest that hepatic markers contributes to an increased risk of prediabetes and all-cause
mortality, which might be helpful to identify high risk groups who need closer attention with
respect to prevention of liver disorders and diabetes.
Abstract Atmospheric Pressure Discharges have attracted much interest in recent years. The development of a new processes based on this discharge needs a clear understanding of plasma and discharge physics and chemistry. At the present time much attention is paid to the chemical processes in barrier discharge plasma in various gas mixtures, since the understanding of these processes is necessary for the development of industrial reactors. Besides these, hydrocarbons are being used for the formation of diamond like or amorphous carbon (DLC) films. Specially, hydrogenated amorphous carbon (a-C: H) and plasma polymerization. In this work we have used Dielectric Barrier Discharge (DBD) a plasma device used to investigate simple hydrocarbon reactions in a plasma phase. Our aim of plasma phase chemical reaction studies is to form molecular hydrogen, higher order hydrocarbons CnHm up to n ≥ 12 series and nitrogen - containing organic complexes using simple hydrocarbons. Deposition of thin organic films or DLC films were carried out using the DBD. In this study we have chosen certain combination of gases such as C2Hm/N2 (m = 2, 4, 6) and C2Hm/Ar (m = 2, 4, 6); the purpose of using N2 and Ar gases are to dilute and stabilize the hydrocarbon plasma and to investigate plasma chemical reactions with nitrogen gas. All reactions were carried out under an atmospheric pressure (300 mbar) with gas ratio 1:2; Experiments were performed by applying high voltage with a frequency 5.5 kHz. The plasma phase diagnostics have been investigated using mass spectrometry and FTIR spectroscopy. Formation of molecular hydrogen, N-containing organic complexes and higher order hydrocarbons with C ≥ 12, have been investigated with mass spectrometry. FTIR spectroscopy reveals the formation of substituted alkanes (sp3), alkenes (sp2) and alkynes (sp) and nitrogen containing functional groups from the individual gases which are used in this work. Abundant formation of acetylene occurs with C2H6 and C2H4 as precursor gases. Amorphous hydrogenated carbon nitride (a-CNx:H) films have been deposited on Si (100) and glass substrates using gas mixtures C2Hm/N2 (m = 2, 4, 6). Surface chemical compositions have been derived from Fourier Transform Infrared Reflection Absorption Spectroscopy (FT-IRRAS) and X-ray Photo electron Spectroscopy (XPS). FT-IRRAS and XPS show the presence of sp, sp2 and sp3 bonds of carbon and nitrogen for C2Hm/N2 thin films. Various functional groups such as amines, saturated and unsaturated alkyl groups have been identified. Thin films obtained from C2H2/N2 and C2H4/N2 gas mixture had a larger N/C ratio when compared to the film obtained from C2H6/N2. Thickness, refractive index and extinction co-efficient were investigated by ellipsometry. Rate of deposition have been investigated. Different surface morphology has been derived using Scanning Electron Microscopy. Amorphous hydrogenated carbon (a-C:H) films or diamond like carbon (DLC) films have been deposited on Si (100) and glass substrates using gas mixtures C2Hm/Ar (m = 2, 4, 6). Diagnostics for the deposited films have been done using different spectroscopic techniques. Surface chemical compositions have been derived from Fourier Transform Infrared Reflection Absorption Spectroscopy (FT-IRRAS) and X-ray Photo electron Spectroscopy (XPS). FT-IRRAS show the presence of sp, sp2 and sp3 bonds of carbon and hydrogen for C2Hm/Ar (m = 2, 4, 6) thin films. The characteristic peak for C1s has been observed from XPS. Thickness, refractive index and extinction co-efficient were investigated by ellipsometry. Rate of deposition have been investigated.
The dentate gyrus (DG) of the hippocampus is one of the stem cell housing niches in the adult mammalian brain. Canonical Wingless-type (Wnt) signals provided by the microenvironment are one of the major niche factors that regulate the differentiation of adult neural stem cells (aNSCs) towards the neuronal lineage. Wnts are part of a complex and diverse set of signaling pathways with a wide range of possible interactions. It remains unknown whether different canonical and non-canonical Wnt signals act in a stage-specific manner to regulate distinctive steps of adult hippocampal neurogenesis. Using in vitro assays on adult hippocampal NSCs, we identified an attenuation of canonical Wnt/ß-Catenin signaling responsiveness in the course of neuronal differentiation, while non-canonical Wnt/Planar Cell Polarity (PCP) signaling events progressively increased. Single-cell genetic manipulations were performed by using retroviral vectors to target dividing progenitor cells in the murine hippocampus. Retrovirus-mediated knockdown of ATP6AP2, a recently discovered core protein involved in both Wnt signaling pathways, revealed that the dual role of this adaptor protein is dependent on the signaling context that is present. We were able to confirm its dual role in neurogenic Wnt signaling in cultured adult hippocampal progenitors (AHPs) for both canonical Wnt signaling in proliferating AHPs and non-canonical Wnt signaling in differentiating AHPs. Specific knockdown of ATP6AP2 in neural progenitor cells in vivo resulted in a decreased induction of neuronal cell fate and severe morphological defects of newborn neurons, likely via altering both canonical and non-canonical Wnt signaling. Furthermore, in vivo knockdown of PCP core proteins CELSR1-3 and FZD3 mimicked the maturational defects of ATP6AP2-deficient neuroblasts but did not affect granule cell fate. In summary, the data presented here characterize a transition of Wnt signaling responsiveness from Wnt/ß-Catenin signaling to non-canonical Wnt/PCP signaling in the course of granule cell fate that was confirmed in a human pluripotent stem cell (hPSC)-based model of dentate granule neurogenesis. Our findings suggest that these pathways show stage-dependent activities and regulate distinct steps of adult dentate granule cell neurogenesis. Conclusively, we provide evidence for a stage-specific regulation of fate determination through the Wnt/ß-Catenin pathway and granule cell morphogenesis through the Wnt/PCP signaling pathway, including the FZD3-CELSR1-3 system. Additionally, the Wnt adaptor protein ATP6AP2 is involved in earlier and later stages of adult neurogenesis and its knockdown in vivo resembles all phenotypic features of both canonical and Wnt/PCP signaling mutants.
Introduction:
The amniotic fluid – as the medium surrounding the fetus, it is holding a crucial role in the maintenance and development of a successful pregnancy. While providing mechanical protection to the fetus, it also offers considerable immunological defense. In fact, it is known that the amniotic fluid plays a significant role in the innate immune system, as many of its corresponding substances show substantial antimicrobial function. Also, components of the adaptive immune system, including B cells, have been described within the amniotic fluid. An increase of immune cells in the amniotic fluid in cases of intra-amniotic infection indicates their involvement in inflammation-related pathologies of pregnancy. However, especially B cells in the amniotic fluid have not yet been thoroughly investigated.
The aim of this work is a deeper examination of the B-lymphocytes within the amniotic fluid. Based on the analysis of surface molecules this includes their phenotype, origin and func-tion. In the long term this could substantiate our understanding of intraamniotic inflammation and or infection, which are casually linked with preterm birth, fetal inflammatory response syndrome and fetal morbidity.
This, in turn, could pave the way for potential diagnostic methods and treatments.
Methods:
For all experiments 8-12-weeks-old pregnant mice were sacrificed at day 14 of pregnancy. The amniotic fluid was collected and specific cell subsets were isolated using MACS cell separation. Cells were then co-cultured with a bone marrow stromal cell line and stimulated in vitro.
The analysis of the population distribution and cytokine production was performed by flow cytometry. To analyze IgM-levels in the supernatant of the co culture, ELISA was used. Statistical analysis was performed using GraphPad Prism software.
Results:
The amniotic fluid contains different developmental stages of B cells, which most likely are of fetal origin. This is supported by the expression of paternal surface markers. An extensive proliferation and switch towards a more mature phenotype upon co-culture shows that the immature subsets of amniotic fluid B cells are able to expand and mature in vitro. Amniotic
fluid B cells spontaneously produce IgM and show functional adaption upon in vitro stimula-tion as evidenced by the increase of cell activation markers.
Conclusion:
For the first time a deep investigation of B-cells within the amniotic fluid was performed, covering phenotype and cell functionality. This work shows that there is a B cell compartment within the amniotic fluid, which, to a certain extent, is able to mature and gain functionality when exposed to external stimuli. This supports the hypothesis of the amniotic fluid as crucial immunological line of defense against inflammatory and infectious challenges during pregnancy.
In this thesis, all three BVMOs from Pseudomonas putida NCIMB10007, that were known to be responsible for the ability of this strain to degrade camphor since the 1950s were successfully made available as recombinant biocatalysts. While the genomic sequence of 2,5-DKCMO was available from the database, the genes encoding 3,6-DKCMO and OTEMO had to be identified using certain PCR-techniques first. All three enzymes were cloned into standard plasmids enabling convenient expression in E. coli facilitating the application of the enzymes in organic chemistry. Their synthetic potential was already reported during the 1990s, but at that time their efficient application was limited due to difficulties with respect to low production levels and insufficient purity and separation of enzyme fractions. These drawbacks are now overcome. Furthermore, biochemical characterization of the camphor-degrading BVMOs was performed including the substrate spectra of these enzymes. Thereby OTEMO turned out not only to have a broad substrate scope accepting mono- and bicyclic aliphatic and arylaliphatic ketones, but also to efficiently convert alpha/beta-unsaturated cycloalkanones due to the similarity of these compounds to OTEMOs natural substrate. Finally, the major limitation in the synthetic application of Type II BVMOs was addressed by searching a flavin-reductase suitable for coupling to these two-component oxygenases. Putative candidates from the respective P. putida strain were identified by the use of amino acid motifs conserved in other representatives of two-component systems. While these enzymes failed, flavin-reductase Fre from E. coli - that also contained the motifs - was shown to enhance the activity of the DKCMOs when applied as crude cell extract as well as pure enzyme. This finding represents a key step for future application of Type II BVMOs.
In this thesis, we elaborate upon Bayesian changepoint analysis, whereby our focus is on three big topics: approximate sampling via MCMC, exact inference and uncertainty quantification. Besides, modeling matters are discussed in an ongoing fashion. Our findings are underpinned through several changepoint examples with a focus on a well-log drilling data.
Staphylococcus aureus is one of the commonly encountered bacteria of the human microbiome. Although mostly a seemingly harmless commensal microbe, S. aureus can act as an invasive pathogen with seriously devastating effects on its host’s health and wellbeing. A wide range of infections caused by this bacterium has been reported to affect diverse parts of the human body, including the skin, soft tissues and bones, as well as important organs like the heart, kidneys and lungs. Particularly, S. aureus is infamous for being a major causative agent of respiratory tract infections that may escalate up to necrotizing pneumonia. Due to its clinical relevance, this pathogen has been intensively studied for many years. Nonetheless, further research in this field is still needed, because of the high capacity of S. aureus to evolve drug resistance, its high genomic plasticity and adaptability and, not in the last place, the plethora of niches within the human body where it can thrive and survive. In this regard, there are still many uncertainties concerning the specific adaptations carried out by S. aureus during colonization and infection of the human body, the transition between both stages, and upon the invasion of different types of host cells. To shed more light on some of these adaptations, the research described in this thesis has employed in vitro models of infection that mimic particular conditions during the infectious process with special focus on the lung epithelium. The adaptations displayed by S. aureus were monitored using advanced proteomics. Furthermore, the analyses documented in this thesis included S. aureus strains with diverse backgrounds and epidemiology to take into account the genetic diversity encountered in this species.
This thesis focuses on the establishment of biocatalytic cascade reactions for the production and detection of industrially relevant flavor and fragrance compounds for food and cosmetic products. To meet the consumer’s demand for those products to be natural, environmentally friendly biocatalytic manufacturing processes that operate GMO-free must be established. Thus, this thesis presents such pathways for the production of an industrially relevant long-chain hydroxy fatty acid and the important flavor and aroma compound raspberry ketone. Furthermore, a biosensor for aldehyde detection was implemented to facilitate screening for suitable biocatalysts that produce industrially relevant aldehydes that are widely applied in the flavor and fragrance industry.
This thesis investigates the biocatalytic synthesis of amines and amino alcohols. The applicability and economic feasibility of biocatalysis for chiral amine synthesis is reviewed and the findings were compared to established chemical processes using relevant process parameters (TON, TOF and STY). This review clearly showcases the potential of biocatalysis for the synthesis of chiral amines and provides a valuable guide for synthetic chemists who want to benefit from these new opportunities. Next, biocatalysis is applied for the synthesis of an amino alcohol with two stereocentres: A novel route for the synthesis of all four stereoisomers of 4-amino-1-phenylpentane-2-ol is presented. Enzymes were applied to install both stereocentres successively, which allowed the selective synthesis with high yields and optical purities. A small scale preparative asymmetric transamination yielded one amino alcohol stereoisomer selectively. The approach presented in this thesis provides a valuable option for the synthesis of this compound class as it is highly selective, step efficient and circumvents the need for protecting groups as well as transition-metal catalysis. The substrate scope of an (S)-selective amine transaminase (ATA) was altered in order to expand the applicability for amino alcohol synthesis. Protein engineering was conducted to enlarge the small binding pocket. Small scale preparative synthesis of the 1,2-amino alcohol (R)-phenylglycinol exemplifies the applicability of the evolved variants for the asymmetric synthesis of this compound. The designed variants expand the collection of ATAs that are suitable for the synthesis of amino alcohols with bulkier substituents. To deepen the understanding of ATAs further, a class III TA family wide analysis (which includes (S)-selective ATAs) is presented. After comparing the active site architectures and performing literature research amino acids were identified that correlate with the reaction- and substrate specificity of the enzymes within this family. This information is compiled in a sequence-function matrix, which allows the prediction of the main activity of biochemically uncharacterised enzymes from their sequence. These insights provide a better understanding of the activity determining residues in (S)-ATAs and class III TAs in general.
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.
Free radicals are known to induce significant structural and functional modifications to the cell membrane and its components. Biophysical quantification of such changes using single molecule studies highlight the role of these individual biomolecules. In this PhD work, we focus on nitric oxide radical and try to understand how they influence interaction of different biomolecules with lipid membranes by using biomimetic systems. In specific we try to answer how cell membrane permeability and bilayer thickness would be influenced by the nitric oxide radical with different phospholipids compositions (i.e. on planar supported lipid bilayers). Later we tested, interaction of transmembrane protein integrin αiibβ3 incorporated into the bilayer (i.e. nanodiscs) with nitric oxide. Finally, how to overcome the negative effects encountered by the phospholipids and proteins using biopolymer coated gold nanoparticles as delivery system. The study involved use of atomic force microscopy and quartz-crystal microbalance with dissipation as primary investigation tools complemented with other relevant biophysical and biochemical techniques.
Deflected by the barrier function of topographical structures such as high mountain ranges, open water bodies or desert, migrating birds concentrate at certain points or corridors referred to as ‘bottlenecks’. An area like this was discovered at Mount Besh Barmag (Azerbaijan) in autumn 2007, but the data gathered during a four-week survey was insufficient to do more than hint at the existence of a major bird migration bottleneck. Therefore, a comprehensive bird migration study was conducted to analyse the magnitude of this potential bottleneck site. The study covers the periods from August to mid-November 2011 and from March to the end of May 2012 and includes daily counts at three observation points focusing on three different migrant types: passerine, waterbirds and soaring birds. In addition, a sound recorder with an omnidirectional microphone collected bird migration calls by both day and night. In total, 278 bird species were observed in an estimated passage of 1,239,369–1,514,267 diurnally migrating individuals in autumn 2011 and 646,733–817,183 individuals in spring 2012. Fifteen species passed through the study area in numbers exceeding 1% of their world populations and 34 species in more than 1% of their flyway populations in at least one of the observation periods. 84% of the observed migrating birds in autumn 2011 and 95% of them in spring 2012 passed through at heights below 50 m above ground exposing them imminently to the danger of collision with obstacles. In the analysis of nocturnal sound recordings, 119 bird species were identified of which 106 were expected to occur as migrants, and calculated estimates revealed the occurrence of 108,986 calls in autumn 2011 and 33,348 calls in spring 2012. The volume of diurnal bird migration emerging from the data with respect to species number and number of individuals is certainly a strong indication of the existence of a major bird migration bottleneck at Besh Barmag. On account of methodological constraints, the high number of night flight calls can only hint at a nocturnal bird migration bottleneck and confirmatory research aided by visual methods (radar, thermal imaging) is necessary to back up the acoustic results. The Besh Barmag bottleneck offers a great opportunity to establish a standardised long-term monitoring programme to investigate avian population dynamics in the vast and little known Eurasian landmass. Acoustic-based monitoring might be a cost-effective method, but it is limited to a few vocally prolific species only. The aim should rather be the establishment of a bird observatory as already successfully installed in a number of European bird migration bottlenecks.
Midges are small mosquitoes that can transmit pathogens to susceptible hosts through their blood-sucking act. They are known as biological vectors that can transmit the bluetongue virus (BTV) and the Schmallenberg virus (SBV) to ruminants, among others. Various vector control measures can be used to curtail the spread of the virus during an epidemic. However, for effective vector measures, it is essential to have profound knowledge of the role of biting midges as vectors, as well as their biology and phenology. For several years, midges were not in the focus of research and there are still considerable gaps in knowledge. Therefore, the present work examines various aspects of biting midges of the genus Culicoides, whose function as vectors of the Schmallenberg virus was already proven at the beginning of the project.
The aim of the first part of this work was to determine the percentage of infected midges in various German areas in order to determine the influence of Culicoides midges within the virus epidemic. For this purpose, samples, collected during 2011 and 2012 as part of monitoring projects, were analysed. Additionally, in early 2013, various farms in southern and eastern regions of Germany, where SBV was considered to be largely absent, were equipped with UV traps. The small number of virus-positive samples did not allow a more precise assessment of the viral spread in culicoid midges. Instead, it revealed the importance to conduct targeted samplings of its vectors during an acute outbreak. Additionally, the presented results and statements made by several animal owners, gave reason to believe, that SBV must have affected the southern and eastern parts of Germany earlier than actually assumed. This would consequently have led to an increased immunity in host animals, which provides a reasonable explanation for the low positive values and is in agrement with the statements made by various farmers.
The second part of this work identifies the conditions and surrounding factors under which acute SBV diseases emerged in ruminants in the cold winter months of 2012/2013. After the diagnosis of several acute SBV infections of sheep in a sheep pen in Mecklenburg-Western Pomerania, culicoid midge activity could be proven. This demonstrates that, suitable conditions for its vectors given, an infection of SBV can also take place during wintertime. A more detailed analysis of the surrounding conditions revealed, that the outdoor temperatures during infection were consistently at values of at least 5-9 ° C for several consecutive days, which enabled the flight and blood-sucking activity of the midges within
the shelter.
Midge activity during wintertime represents a crucial component in understanding how the virus can outlast the cold season. A constant midge presence could lead to a low but permanent infection rate throughout the cold months, enabling a recurrence of the pathogen the following year. Instead, a longer vector-free timeperiod would point to other mechanisms that allow the virus to re-occur in Germany on a yearly basis. Thus, the acute cases of SBV infections in sheep rose the question of critical threshold temperatures, representing the beginning of midge activity. The investigation of several stables sheltering cattle, horse or sheep addressed potential differences between indoor and outdoor activity and whether the type of host animal has an influence on the beginning of the flight. In the third part of this work, a long vector-free period and several differences in the onset of midge activity between different types of host animals could be detected. It could also be illustrated that the progression of the flight began differently depending on the present type of host animal/type of stable. For all cattle stables and the sheep barn the first midge activity was measured indoors, whereas for horses, culicoid midges were found to become active either at the same time or almost simultaneously inside and outside the animal shelters. This suggests that the horse stables do not represent good breeding sites for midges, which might be attributed to husbandry practices. In addition, it was possible to determine specific threshold temperatures for the different types of host animals and for various midge species. Altogether, the late beginning of flight, measured at the beginning of March, was surprising. This raises more questions of alternative mechanisms enabling the virus to outlast the winter months. The documentation of species-specific threshold temperatures can be a useful tool f.i. within automated large stables to keep indoor temperatures under the threshold value in order to postpone the onset of culicoid activity of various vector species. This may help to prevent virus transmissions during winter or to evoke a delay in spring, making it more difficult for the virus to overwinter.
To be able to start instant defense measures during an ongoing virus epidemic, which is transmitted by Culicoides midges, reducing the ground-living midge larvae offers a promising option during the warm season. For targeted vector control measures, it is important to know the breeding sites of culicoid midge species. Therefore, four agriculturally used biotopes were sampled and compared to four biotopes of a forest-dominated area. The results clearly show that meadows per se are not suitable breeding habitats for Culicoides
spp. Only the influence of livestock animals induces their potential as developmental sites. The various biotopes of the forest-dominated region were less subject to anthropogenic influences. Although fewer individual midges were found here, it displayed a higher biodiversity than the agricultural habitats. These results demonstrate once more the potential of forests in regards to the preservation of biodiversity. In Particular, the alder on fen site revealed most midge species and also the highest number of collected specimens among the studied biotopes. That illustrates the high impact of this specific humid type of habitat in respect to species diversity and the need of its perpetuation.
As part of this work, new breeding sites for a variety of culicoid species were identified and assigned to the usually rather short profiles of known Culicoides species. For one part, previous observations of chosen substrates could be consolidated. Furthermore, new breeding substrates were identified. Additionally, information of abiotic factors such as ph-value, soil moisture or organic compound of all sampled breeding substrates obtained from a soil analysis, extended the knowledge about the species-specific choice of breeding habitats and their characteristical traits. The additional knowledge about potential breeding substrates and their soil factors might be useful for future epidemiological modelling approaches. It can also raise the effectiveness and accuracy of targeted vector control measurements during an epidemic outbreak. Therefore, it may indirectly contribute to the preservation of endangered rare species. However, there is still an enormous need for more research before this goal can be fully achieved.
The thesis contains 6 studies and mentions the validation and comparison of several methods for measuring body composition and assessing nutritional status in different groups of pediatric patients. It also deals with the effects of infant formulas supplemented with nucleotides on the growth and body composition of healthy term and preterm babies. The first study shows that BMI-standard deviation score and %BF have a moderate agreement in classifying the nutritional status. The second study done in preterm neonates points out that bioelectrical impedance provides only insignificant information on fat-free mass (FFM) compared to anthropometry. The third study validates published prediction equations and develops a new equation in a group of children with Crohn's disease. The equation of Schaefer et al. is the best to predict FFM. The accuracy of a prediction equation is influenced by weight, height and age other than impedance index alone. The fourth study indicates that impedance index is better than weight, height squared as the predictor for estimating FFM. Addition of weight improves the predictive accuracy of prediction equations. The fifth study shows that birth weight centiles gives a rough estimation of nutritional status. Weight-for-length ratio shows the best correlation with fat mass. The last study shows that weight gain and gain in lean mass are higher in the standard formula group than in the groups nourished with nucleotides or breast milk.
The hairpin ribozyme is a small Mg2+-dependent catalytic RNA molecule able to catalyze the trans-cleavage of an RNA substrate via a reversible trans-esterification mechanism. In this study, the cleavage activities of several fragmented hairpin ribozyme systems were examined. Due to the complex catalytic structure of the hairpin ribozyme, a new boronic acid ester was used as a covalent linkage to hold the folding of the functional system. It has been demonstrated the possibility of replacing the phosphodiester linkage, at specific positions, with a boronic acid ester to restore or improve the catalytic activity of fragmented hairpin ribozyme.
A slice is an intersection of a hyperplane and a self-similar set. The main purpose of this work is the mathematical description of slices. A suitable tool to describe slices are branching dynamical systems. Such systems are a generalisation of ordinary discrete dynamical systems for multivalued maps. Simple examples are systems arising from Bernoulli convolutions and beta-representations. The connection between orbits of branching dynamical systems and slices is demsonstrated and conditions are derived under which the geometry of a slice can be computed. A number of interesting 2-d and 3-d slices through 3-d and 4-d fractals is discussed.
The dissertation aims at developing means to integrate conservation and development in biosphere reserves in Madagascar. Despite a multitude of concepts such as UNESCO biosphere reserves, Integrated Conservation and Development Projects and community-based natural resource management, gaps between conservation and development remain to exist. In a qualitative case study in Mananara-Nord and Sahamalaza Iles-Radama Biosphere Reserves in Madagascar data was collected on biosphere reserve management, local use of natural resources and socio-cultural aspects that influence natural resource use. Furthermore, natural values local people associate with the forest were investigated. Analysis revealed that management capacities constitute a limiting factor in biosphere reserve management. Collaboration between management, local people and international organisations fosters the achievement of both conservation and development. However, collaboration is only possible if (i) clear rules are formulated and (ii) partners have a vision in common. Based on the theory of social capital, newly introduced and locally existent rules/institutions having an influence on the use of natural resource were categorized in bonding, linking and bridging social capital. Furthermore, the perception of natural values was classified in instrumental and non-instrumental values and assigned to ecosystem services identifying the importance of nature for human well-being. With the capabilities approach Amartya Sen defined human well-being as the achievement of those capabilities a person considers valuable. This includes aspects that assure livelihoods on the one hand and aspects that are conducive to well-being on the other, thus both being relevant for development. In the dissertation capabilities are based on both instrumental and non-instrumental natural values and consequently offer an opportunity to demonstrate and characterise the relationship between nature and human well-being. Social and natural values provide orientation for a biosphere reserve management. The category bonding social capital (social values) describes local socio-cultural aspects in communities and their importance for collaborative processes. Natural values provide the management with guiding principles to foster nature conservation and to integrate locally existent capabilities. Supporting and furthering these capabilities enables the development of new capabilities of all concerned persons. The dissertation demonstrates various possibilities to build bridges between (i) nature conservation and development, (ii) natural and social sciences, (iii) formal regulations and local socio-cultural aspects and (iv) diverse actors. Implementation of a social monitoring is recommended together with local stewards and Malagasy students to collect information about the perception of natural and social values and use them as guiding principles for biosphere reserves. Collaboration with national and international scientific institutions can foster this process.
Frontotemporal lobar degeneration (FTLD) is likely to be the second-most common cause of dementia in individuals under 65 years of age. Pathognomonic changes in personality, behavior and motivation are known to lead to high caregiver stress and burden, with little support being available. The aim of this work is to present the current state of knowledge on the characteristics, challenges and unmet needs of caregivers as well as on possible interventions.
Two scoping reviews on caregiver burden using the PRISMA checklist for scoping reviews were conducted using PubMed, Web of Science and ScienceDirect in April 2017 and November 2019, respectively. A total of 107 articles were considered eligible and were analyzed qualitatively and summarized.
Our results show that caregivers of patients with FTLD are often female, spouses of the PwD, younger in age, have underage children and provide care at home. Behavioral and motivational disturbances in the PwD are perceived to be the most burdensome aspects of caregiving. Those caring for an individual with the bvFTD subtype thus report higher levels of burden than caregivers of an individual with a form of PPA. With rising dementia severity, caregivers report higher levels of burden. Many caregivers experience a decline in their own physical and mental health as well as a significant financial burden resulting from care duties. The deterioration of the relationship between the PwD and their caregivers is a main burdensome aspect. Only few interventions were conducted so far, and none of those that were identified were designed as an RCT. The most efficacious interventions were those aimed directly at caregivers, whereas interventions aiming at the amelioration of symptoms in the PwD showed little effect.
Further research should reproduce and validate efficacious interventions and establish new interventional approaches. Another focus should be set on the situation of underage children of individuals with FTLD and relatives of a person with hereditary FTD. More research from non-Western countries is needed in order to identify culture-specific factors of caregiver burden. Along those lines, support structures for FTLD caregivers should be assessed on a local basis and extended accordingly. So far, no study has assessed the relationship between caregiver burden and possible consequences for the quality of care provided to the PwD in FTLD specifically. Awareness both in the wider population and among healthcare professionals is an urgent need for the future since FTLD is often misdiagnosed, leading to a delay in obtaining the correct diagnosis and access to suitable support.
The worldwide distribution and prevalence of melioidosis, an infectious disease caused by the soil-dwelling Gram-negative bacterium Burkholderia pseudomallei, is unknown. In Vietnam, sporadic cases of melioidosis have been reported for decades, but clinical and epidemiological data for the indigenous population are still scarce. In this study, we reviewed clinical and demographic data of patients with culture-proven melioidosis diagnosed at a single large referral hospital in Hanoi between November 1997 and December 2005. The clinical manifestations of melioidosis with fatal septicaemia as the most common presentation, a high rate of underlying diseases and a peak of cases admitted during the wet season were similar to studies from other endemic areas. The geographical origin of melioidosis patients shows that melioidosis exists in at least 18 northern provinces. The characterization of clinical B. pseudomallei strains by multilocus sequence typing identified 17 different sequence types (STs), ten of which have (as yet) not been found outside Vietnam. Several of these STs presumably were generated through recent evolutionary events in this rapidly diversifying bacterial species, and thus restricted geographic distribution may be a consequence of limited time passed since emergence. In order to define the distribution of the bacterium in the environment, our study also aimed to develop a more sensitive culture method for the detection of B. pseudomallei from soil samples in endemic areas compared to the currently used culture method based on soil dispersion in water. Our newly developed protocol involving soil dispersion in a polyethylene glycol and sodium deoxycholate solution increased the yield of viable B. pseudomallei from soil samples. Comparative testing of soil samples from Northeast Thailand covering a wide range of B. pseudomallei concentrations demonstrated a significantly higher recovery (p < 0.0001) of B. pseudomallei colony forming units by the new method compared to the conventional method. Our data indicate that using the detergents polyethylene glycol and sodium deoxycholate not only results in a higher recovery of viable B. pseudomallei, but also results in a shift in the bacterial species recovered from soil samples. Molecular methods based on direct bacterial nucleic acid extraction from environmental samples and subsequent amplification have the potential to overcome many restrictions of traditional microbiological approaches. Moreover, culture-dependent methods require special expertise in recognizing B. pseudomallei colony morphologies. Thus, a highly sensitive culture-independent DNA-based method that allows direct quantification of B. pseudomallei from soil is needed, particularly in diagnostic laboratories outside endemic areas. We therefore aimed to establish a protocol for B. pseudomallei soil DNA isolation, purification and quantification by qPCR targeting a type three secretion system 1 single copy gene. This assay was validated using 40 soil samples from Northeast Thailand that underwent parallel bacteriological culture. All 26 samples that were B. pseudomallei-positive by direct culture were B. pseudomallei qPCR-positive, with a median of 1.84 x 104 genome equivalents (range 3.65 x 102 to 7.85 x 105) per gram of soil. This was 10.6 fold (geometric mean; range 1.1 to 151.3) higher than the bacterial count as defined by culture. Moreover, the qPCR detected B. pseudomallei in seven samples (median 36.9 genome equivalents per g soil; range 9.4 to 47.3), which were negative on direct culture. These seven positives were reproduced using a nested PCR targeting a second, independent B. pseudomallei-specific sequence. Two samples were direct culture and qPCR negative but nested PCR positive. Five samples were negative by both PCR methods and culture. In conclusion, this is the first report on a series of cases describing clinical and epidemiological features of melioidosis and corresponding Burkholderia pseudomallei strains from northern Vietnam. Moreover, our newly developed culture-based and PCR-based methods provide highly specific and sensitive tools for the quantitative environmental surveillance of B. pseudomallei.
What shapes the prospect for democracy in the aftermath of civil conflicts? Some authors claim a successful transition from violence to elections mainly depends on the ability of political institutions, such as power-sharing arrangements, to mitigate the security dilemma among former battlefield adversaries. Drawing on a broader literature, others point to potential effects of foreign aid on democratic development.
This predominant focus on elections and the security dilemma, however, limits our understanding in a number of ways. We do not know how the choice of post-conflict elites to hold elections is strategically intertwined with their willingness to reform other state institutions. We also have only begun to understand how post-conflict power-sharing governments function as revenue source for elites. Knowing how this economic function drives or obstructs post-conflict democratic development is particularly helpful if we shift our attention to a major source of income for post-conflict elites: foreign aid, and the democratic conditions donors attach to it.
Addressing these gaps, I argue that both the economic utility from office as well as political conditionalities give rise to a rent-seeking/democracy dilemma for post-conflict elites: they can either hold elections and face uncertainty over their access to power, but secure economic rents from aid. Or they refuse to democratize, secure their hold on power, but risk losing revenues when donors withdraw aid. In this situation, their optimal strategy is to agree to democratic reforms in the area on which donors place most value, elections. But to maximize their chances of electoral victory and continued access to rents from office, elites simultaneously restrain an independent rule of law and narrowly distribute private goods to their supporters.
This rent-seeking/democracy dilemma is particularly prevalent in one of the most popular forms of post-conflict institutions: power-sharing governments. Including rebel groups in post-conflict cabinets increases the number of constituencies that need to be sustained from the government budget. In addition, the interim nature of transitional power-sharing cabinets leads elites to steeply discount the future and increase rent-seeking in the short term. My main hypothesis is therefore that large aid flows to extensive power-sharing governments should be associated with improved elections, but limits in the rule of law and more provision of private instead of public goods.
To test this prediction quantitatively, I combine data on aid flows and rebel participation in post-conflict cabinets between 1990 and 2010 with indicators for democratic development, election quality, rule of law, and public goods provision. Results from a wide range of regression models provide empirical support for my argument. Individually, extensive power-sharing governments and large aid flows do not seem to have strong effects. Models that introduce an interaction term between aid and power-sharing, however, yield strong evidence of a rent-seeking/democracy dilemma: Power-sharing and foreign aid jointly predict a positive, but small change in democracy scores as well as cleaner elections. At the same time, they are jointly associated with a limited rule of law and stronger distribution of private goods. For each indicator, I document evidence for mechanisms and changes in the effect over time.
The theory and empirical results presented in this dissertation have a number of implications for future research. They highlight the importance of moving away from a singular focus on post-conflict elections and looking also at other institutional dimensions of post-conflict politics. My political economy model of power-sharing also demonstrates the utility of explicitly including economic functions of post-conflict institutions into power-sharing and broader peacebuilding research. And I introduce novel evidence into research and practice of aid delivery; this helps not only to clarify academic debates under which conditions aid can be effective, but also informs practitioners who help conflict-affected countries in their transition from war to democracy.
All types of muscles use Ca2+ as their main intracellular messenger. In skeletal muscle fibers abnormal levels of intracellular calcium result in altered contractile properties, altered energy metabolism, and altered gene expression. Moreover, long term failure of normal Ca2+ homeostasis can lead to cell death of muscle fibers by necrosis and apoptosis. Elevations of intracellular Ca2+ levels are more and more regarded as the reason for pathological changes and muscle fiber damage in Duchenne Muscular Dystrophy (DMD). DMD is a severe recessive x-linked muscle disease caused by mutations in the dystrophin gene. The characteristics of DMD are muscle tissue wasting and fibrosis. Both muscle wasting and intracellular Ca2+ are to be reflected in changes of muscle force. Several Ca2+ conducting channels including transient receptor potential (TRP) channels are supposed to account for the abnormal Ca2+ homeostasis in DMD. Gene expressions of TRP channels have been studied in human and mouse skeletal muscle and among others TRPC3, TRPC6 and TRPV4 channels were found to occur in skeletal muscles. The present study followed the hypothesis that TRPC3, TRPC6 and TRPV4 are functional in skeletal muscle fibers and that they contribute to muscular Ca2+ homeostasis. Further, it was assumed that dysfunction of the mentioned TRP channels contributes to abnormal contractile properties and pathology and of dystrophin-deficient muscle. To study Ca2+ changes in mouse skeletal muscle fibers the fluorescent calcium indicator Fura-2 was used. Further, the technique of Mn2+ quench of Fura-2 fluorescence was applied. Muscle force measurements of mouse soleus and diaphragm strips were performed. To elucidate abnormalities of TRP channel function in dystrophin-deficient muscle, muscles and muscle fibers of mdx mice were studied. Hyperforin, an activator of TRPC6 channels elicited increases of calcium levels in wildtype muscle fibers. These increases were partly inhibited by the TRPC6 inhibitor 1-(5-chloronaphthalenesulfonyl) homopiperazine hydrochloride (ML-9). The TRPC3/TPRC6 activator 1-oleoyl-2-acetyl-sn-glycerol (OAG) resulted in increased calcium entry, which was attenuated by ML-9. 2-aminoethoxydiphenylborane (2-APB), an unspecific TRP channel inhibitor, suppressed calcium entry in muscle fibers under basal conditions. In addition, the specific TRPC3 inhibitor Pyr3, strongly inhibited background calcium entry. The TRPV4 activator 4α-phorbol 12,13-didecanoate (4α-PDD) induced significant increased calcium entry and this increase could be inhibited by the TRPV4 inhibitor HC 067047. During muscle force recordings ML-9 significantly inhibited twitches and tetani and accelerated muscle fatigue during sustained repetitive stimulation. The results indicate that TRPC3, TRPC6 and TRPV4 are functionally expressed in mouse muscle fibers. TRPC3 stays active under the basal conditions and contributes to background calcium entry. In contrast, TRPC6 and TRPV4 did not seem to be active at resting conditions, but could be pharmacologically activated. TRPC6 may play a role to counteract the calcium loss under long-term muscle fatigue. Though TRPC3 and C6 play a role for muscular Ca2+ homeostasis, it is unclear whether and how the two channels associate and cross-talk with each other in skeletal muscle cells. In mdx fibers Pyr3 inhibited background calcium influx stronger that in WT fibers, implying a possible over-activation of TRPC3 channels in mdx muscle fibers. At later stages mdx muscle showed marked decrease in force reflecting muscle wasting. Soleus showed moderate decrease and diaphragm showed severe decrease (more than 60%) in force. Resistance to muscle fatigue was shown in mdx soleus muscle when compared with WT soleus muscle. Diaphragm segments of mdx mice showed very strong resistance to muscle fatigue. The results indicate a substantial loss of muscle mass, an increase in oxidative fiber types and a reduction of fast fatigable muscle fibers. It is concluded that the hypothesis of functional expression of TRPC3, TRPC6 and TRPV4 in mouse skeletal muscle has been confirmed. The results give improved knowledge about the relation of Ca2+ homeostasis, mdx pathology and TRP channels. Diaphragms of old mdx mice show severe muscle weakness but the remaining fibers of the diaphragm showed strong fatigue-resistance. The application of a TRPC3 inhibitor may be a promising treatment to prevent high Ca2+ mediated muscle damage in muscular dystrophy.
Low risk prostate cancer does not always necessitate aggressive or invasive intervention and is best monitored through active surveillance, but in daily practice a majority of men seek a more proactive approach. Therefore, tertiary chemoprevention is an attractive option for men seeking a way to slow disease progression. Several natural anti-carcinogens have been identified in soy beans, especially isoflavones. Case series have been published, demonstrating a positive influence of isoflavones on PSA serum levels in prostate cancer.
Therefore, a systematic review of the effect of isoflavones versus placebo on PSA levels in localized prostate cancer was conducted, following the recommendations of the Cochrane Handbook of systematic Reviews. On the whole, the primary aim of this review is to summarize the evidence for the use of isoflavones in localized prostate cancer in terms of PSA response. In total, we identified four relevant RCTs involving 298 treated men. The result of this synopsis was that none of the studies showed a significant effect on serum PSA levels, suggesting that isoflavone intake has no effect on biochemical progression. The influence of isoflavones on overall survival in localized prostate cancer remains unclear.
Nevertheless, there are indications that isoflavones may be clinically beneficial, for example regarding lipid metabolism and cholesterol. Isoflavones represent a safe therapeutic option with few side effects, where further interdisciplinary research is needed.