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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.
Our goal was to provide a comprehensive overview of the antibody response to Staphylococcus aureus antigens in the general population as a basis for defining disease-specific profiles and diagnostic signatures. We tested the specific IgG and IgA responses to 79 staphylococcal antigens in 996 individuals from the population-based Study of Health in Pomerania. Using a dilution-based multiplex suspension array, we extended the dynamic range of specific antibody detection to seven orders of magnitude, allowing the precise quantification of high and low abundant antibody specificities in the same sample. The observed IgG and IgA antibody responses were highly heterogeneous with differences between individuals as well as between bacterial antigens that spanned several orders of magnitude. Some antigens elicited significantly more IgG than IgA and vice versa. We confirmed a strong influence of colonization on the antibody response and quantified the influence of sex, smoking, age, body mass index, and serum glucose on anti-staphylococcal IgG and IgA. However, all host parameters tested explain only a small part of the extensive variability in individual response to the different antigens of S. aureus.
A lot of research data has become available since the outbreak of the COVID-19
pandemic in 2019. Connecting this data is essential for the understanding of the
SARS-CoV-2 virus and the fight against the pandemic.
Amongst biological and biomedical research data, computational models targeting
COVID-19 have been emerging and their number is growing constantly. They are a
central part of the field of Systems Biology, which aims to understand the mechanisms
and behaviour of biological systems. Model predictions help to understand the
mechanisms of the novel coronavirus and the life-threatening disease it is causing.
Both biomedical research data and modelling data regarding COVID-19 have
previously been stored in separated domain-specific graph databases. MaSyMoS,
short for Management System for Models and Simulations, is a graph database for
storing simulation studies of biological and biochemical systems. The CovidGraph
project integrates research data regarding COVID-19 and the coronavirus family
from various data resources in a knowledge graph.
In this thesis, we integrate simulation models from MaSyMoS, including models
targeting COVID-19, into the CovidGraph. Therefore, we present a concept for
the integration of simulation studies and the linkage through ontology terms and
reference publications in the CovidGraph. Ultimately, we connect data from the field
of systems biology and biomedical research data in a graph database.
Dengue virus (DV) is a positive-strand RNA virus of the Flavivirus genus. It is one of the most prevalent mosquito-borne viruses, infecting globally 390 million individuals per year. The clinical spectrum of DV infection ranges from an asymptomatic course to severe complications such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS), the latter because of severe plasma leakage. Given that the outcome of infection is likely determined by the kinetics of viral replication and the antiviral host cell immune response (HIR) it is of importance to understand the interaction between these two parameters. In this study, we use mathematical modeling to characterize and understand the complex interplay between intracellular DV replication and the host cells' defense mechanisms. We first measured viral RNA, viral protein, and virus particle production in Huh7 cells, which exhibit a notoriously weak intrinsic antiviral response. Based on these measurements, we developed a detailed intracellular DV replication model. We then measured replication in IFN competent A549 cells and used this data to couple the replication model with a model describing IFN activation and production of IFN stimulated genes (ISGs), as well as their interplay with DV replication. By comparing the cell line specific DV replication, we found that host factors involved in replication complex formation and virus particle production are crucial for replication efficiency. Regarding possible modes of action of the HIR, our model fits suggest that the HIR mainly affects DV RNA translation initiation, cytosolic DV RNA degradation, and naïve cell infection. We further analyzed the potential of direct acting antiviral drugs targeting different processes of the DV lifecycle in silico and found that targeting RNA synthesis and virus assembly and release are the most promising anti-DV drug targets.
Background: Previous studies suggest that blood donation impacts blood donors’ psychological state, with either positive or negative effects, such as feeling more energetic or more exhausted. It has not yet been described how long these effects last. Materials and Methods: This prospective cohort study consisted of a qualitative and a quantitative part: (1) Psychological characteristics which changed after blood donation were identified by structured interviews of regular whole blood donors (n = 42). Based on this, a questionnaire addressing 7 psychological dimensions was established. (2) The psychological state of 100 blood donors was assessed after blood donation by applying the questionnaire 15–30 min before and during donation, as well as 15–30 min, 6 h, 24 h, 72 h, 1 week, and 8 weeks after donation. The resulting changes were summarized to a score. Furthermore, potential correlations of the score with pre-donation blood pressure, hemoglobin, or body mass index were calculated. Results: Seven items were identified which changed in at least 25% of blood donors (mood, concentration, satisfaction, resilience, spirit of initiative, physical well-being, energy level). In the 100 blood donors, the well-being score increased (positive effects, n = 23), showed minor changes (n = 53), or decreased (negative effects, n = 24). The positive effects lasted for about 1 week and the negative effects for 3 days. Conclusion: While the frequency of psychological effects following blood donation identified by our study was comparable to others, the changes of the psychological state in our donors were traceable for a longer period than previously acknowledged.
We introduce PVSC-DTM (Parallel Vectorized Stencil Code for Dirac and Topological Materials), a library and code generator based on a domain-specific language tailored to implement the specific stencil-like algorithms that can describe Dirac and topological materials such as graphene and topological insulators in a matrix-free way. The generated hybrid-parallel (MPI+OpenMP) code is fully vectorized using Single Instruction Multiple Data (SIMD) extensions. It is significantly faster than matrix-based approaches on the node level and performs in accordance with the roofline model. We demonstrate the chip-level performance and distributed-memory scalability of basic building blocks such as sparse matrix-(multiple-) vector multiplication on modern multicore CPUs. As an application example, we use the PVSC-DTM scheme to (i) explore the scattering of a Dirac wave on an array of gate-defined quantum dots, to (ii) calculate a bunch of interior eigenvalues for strong topological insulators, and to (iii) discuss the photoemission spectra of a disordered Weyl semimetal.
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.
Background
The Federal Ministry of Education and Research of Germany (BMBF) funds a network of university medicines (NUM) to support COVID-19 and pandemic research at national level. The “COVID-19 Data Exchange Platform” (CODEX) as part of NUM establishes a harmonised infrastructure that supports research use of COVID-19 datasets. The broad consent (BC) of the Medical Informatics Initiative (MII) is agreed by all German federal states and forms the legal base for data processing. All 34 participating university hospitals (NUM sites) work upon a harmonised infrastructural as well as legal basis for their data protection-compliant collection and transfer of their research dataset to the central CODEX platform. Each NUM site ensures that the exchanged consent information conforms to the already-balloted HL7 FHIR consent profiles and the interoperability concept of the MII Task Force “Consent Implementation” (TFCI). The Independent Trusted Third-Party (TTP) of the University Medicine Greifswald supports data protection-compliant data processing and provides the consent management solutions gICS.
Methods
Based on a stakeholder dialogue a required set of FHIR-functionalities was identified and technically specified supported by official FHIR experts. Next, a “TTP-FHIR Gateway” for the HL7 FHIR-compliant exchange of consent information using gICS was implemented. A last step included external integration tests and the development of a pre-configured consent template for the BC for the NUM sites.
Results
A FHIR-compliant gICS-release and a corresponding consent template for the BC were provided to all NUM sites in June 2021. All FHIR functionalities comply with the already-balloted FHIR consent profiles of the HL7 Working Group Consent Management. The consent template simplifies the technical BC rollout and the corresponding implementation of the TFCI interoperability concept at the NUM sites.
Conclusions
This article shows that a HL7 FHIR-compliant and interoperable nationwide exchange of consent information could be built using of the consent management software gICS and the provided TTP-FHIR Gateway. The initial functional scope of the solution covers the requirements identified in the NUM-CODEX setting. The semantic correctness of these functionalities was validated by project-partners from the Ludwig-Maximilian University in Munich. The production rollout of the solution package to all NUM sites has started successfully.
Diagenetic illite growth in porous sandstones leads to significant modifications of the initial pore system which result in tight reservoirs. Understanding and quantifying these changes provides insight into the porosity-permeability history of the reservoir and improves predictions on petrophysical behavior. To characterize the various stages of diagenetic alteration, a focused ion beam – scanning electron microscopy (FIB-SEM) study was undertaken on aeolian sandstones from the Bebertal outcrop of the Parchim Formation (Early Permian Upper Rotliegend group). Based on 3D microscopic reconstructions, three different textural types of illite crystals occur, common to many tight Rotliegend sandstones, namely (1) feldspar grain alterations and associated illite meshworks, (2) tangential grain coats, and (3) pore-filling laths and fibers. Reaction textures, pore structure quantifications, and numerical simulations of fluid transport have revealed that different generations of nano-porosity are connected to the diagenetic alteration of feldspars and the authigenic growth of pore-filling illites. The latter leads to the formation of microstructures that range from authigenic compact tangential grain coatings to highly porous, pore-filling structures. K-feldspar replacement and initial grain coatings of illite are composed primarily of disordered 1Md illite whereas the epitaxially grown illite lath- and fiber-shaped crystals occurring as pore-filling structures are of the trans-vacant 1Mtv polytype. Although all analyzed 3D structures offer connected pathways, the largest reduction in sandstone permeability occurred during the initial formation of the tangential illite coatings that sealed altered feldspars and the subsequent growth of pore-filling laths and fibrous illites. Analyses of both illite pore-size and crystallite-size distributions indicate that crystal growth occurred by a continuous nucleation and growth mechanism probably controlled by the multiple influx of potassium-rich fluids during late Triassic and Jurassic times. The detailed insight into the textural varieties of illite crystal growth and its calculated permeabilities provides important constraints for understanding the complexities of fluid-flow in tight reservoir sandstones.
Lacewings (Neuroptera) have predatory larvae with highly specialised mouthparts. Larvae of many groups within Neuroptera are well represented as fossils preserved in ambers; however, larvae of some groups are less often reported in the literature. Here we report such a rare case, a larva of the group Hemerobiidae, an aphidlion, preserved in a piece of Eocene Baltic amber (about 40 million years old). It is preserved together with three possible prey items, wingless aphids, most likely representatives of Germaraphis (or at least closely related to this group). The aphidlion can be identified based on the morphology of the antennae, simple curved and toothless stylets, well developed labial palps, and the absence of other mouth-part structures such as a protruding labrum or maxillary palps. A long, club-shaped distal element of the labial palps identifies the specimen as a larva of Hemerobiidae. The aphids can be identified based on their very long, beak-like mouth parts. This find is, to our knowledge, the first example of a lacewing larva preserved together with its potential prey. We briefly discuss other cases in which fossils preserved in amber allow us to reconstruct aspects of behaviour and interactions of fossil lacewing larvae.
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.
For the characterization of Kv7.2/3 channel activators, several analytical methods are available that vary in effort and cost. In addition to the technically elaborate patch-clamp method, which serves as a reference method, there exist several medium to high-throughput screening methods including a rubidium efflux flame-atomic absorption spectrometry (F-AAS) assay and a commercial thallium uptake fluorescence-based assay. In this study, the general suitability of a graphite furnace atomic absorption spectrometry (GF-AAS)-based rubidium efflux assay as a screening method for Kv7.2/3 channel activators was demonstrated. With flupirtine serving as a reference compound, 16 newly synthesizedcompounds and the known Kv7.2/3 activator retigabine were first classified as either active or inactive by using the GF-AAS-based rubidium (Rb) efflux assay. Then, the results were compared with a thallium (Tl) uptake fluorescence-based fluorometric imaging plate reader (FLIPR) potassium assay. Overall, 16 of 17 compounds were classified by the GF-AAS-based assay in agreement with their channel-activating properties determined by the more expensive Tl uptake, fluorescence-based assay. Thus, the performance of the GF-AAS-based Rb assay for primary drug screening of Kv7.2/3-activating compounds was clearly demonstrated, as documented by the calculated Z’-factor of the GF-AAS-based method. Moreover, method development included optimization of the coating of the microtiter plates and the washing procedure, which extended the range of this assay to poorly adherent cells such as the HEK293 cells used in this study.
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.
Fast screening of enzyme variants is crucial for tailoring biocatalysts for the asymmetric synthesis of non-natural chiral chemicals, such as amines. However, most existing screening methods either are limited by the throughput or require specialized equipment. Herein, we report a simple, high-throughput, low-equipment dependent, and generally applicable growth selection system for engineering amine-forming or converting enzymes and apply it to improve biocatalysts belonging to three different enzyme classes. This results in (i) an amine transaminase variant with 110-fold increased specific activity for the asymmetric synthesis of the chiral amine intermediate of Linagliptin; (ii) a 270-fold improved monoamine oxidase to prepare the chiral amine intermediate of Cinacalcet by deracemization; and (iii) an ammonia lyase variant with a 26-fold increased activity in the asymmetric synthesis of a non-natural amino acid. Our growth selection system is adaptable to different enzyme classes, varying levels of enzyme activities, and thus a flexible tool for various stages of an engineering campaign.
The vast majority of RNA splicing in today‘s organisms is achieved by the highly regulated and precise removal of introns from pre-mRNAs via the spliceosome. Here we present a model of how RNA splicing may have occurred in earlier life forms. We have designed a hairpin ribozyme derived spliceozyme that mediates two RNA cleavages and one ligation event at specific positions and thus cuts a segment (intron) out of a parent RNA and ligates the remaining fragments (exons). The cut-out intron then performs a downstream function, acting as a positive regulator of the activity of a bipartite DNAzyme. This simple scenario shows how small RNAs can perform complex RNA processing dynamics, involving the generation of new phenotypes by restructuring segments of given RNA species, as well as delivering small RNAs that may play a functional role in downstream processes.
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.
The human brain is distinguished by its remarkable size, high energy consumption, and cognitive abilities compared to all other mammals and non-human primates. However, little is known about what has accelerated brain evolution in the human lineage. One possible explanation is that the appearance of advanced communication skills and language has been a driving force of human brain development. The phenotypic adaptations in brain structure and function which occurred on the way to modern humans may be associated with specific molecular signatures in today’s human genome and/or transcriptome. Genes that have been linked to language, reading, and/or autism spectrum disorders are prime candidates when searching for genes for human-specific communication abilities. The database and genome-wide expression analyses we present here revealed a clustering of such communication-associated genes (COAG) on human chromosomes X and 7, in particular chromosome 7q31-q36. Compared to the rest of the genome, we found a high number of COAG to be differentially expressed in the cortices of humans and non-human primates (chimpanzee, baboon, and/or marmoset). The role of X-linked genes for the development of human-specific cognitive abilities is well known. We now propose that chromosome 7q31-q36 also represents a hot spot for the evolution of human-specific communication abilities. Selective pressure on the T cell receptor beta locus on chromosome 7q34, which plays a pivotal role in the immune system, could have led to rapid dissemination of positive gene variants in hitchhiking COAG.
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.
Target proteins in biotechnological applications are highly diverse. Therefore, versatile flexible expression systems for their functional overproduction are required. In order to find the right heterologous gene expression strategy, suitable host-vector systems, which combine different genetic circuits, are useful. In this study, we designed a novel Bacillus subtilis expression toolbox, which allows the overproduction and secretion of potentially toxic enzymes. This toolbox comprises a set of 60 expression vectors, which combine two promoter variants, four strong secretion signals, a translation-enhancing downstream box, and three plasmid backbones. This B. subtilis toolbox is based on a tailor-made, clean deletion mutant strain, which is protease and sporulation deficient and exhibits reduced autolysis and secondary metabolism. The appropriateness of this alternative expression platform was tested for the overproduction of two difficult-to-produce eukaryotic model proteins. These included the sulfhydryl oxidase Sox from Saccharomyces cerevisiae, which forms reactive hydrogen peroxide and undesired cross-linking of functional proteins, and the human interleukin-1β, a pro-inflammatory cytokine. For the best performing Sox and interleukin, overproducing and secreting variants of these new B. subtilis toolbox fermentation strategies were developed and tested. This study demonstrates the suitability of the prokaryotic B. subtilis host-vector system for the extracellular production of two eukaryotic proteins with biotechnological relevance.