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Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring.
In a recent paper, the Lefschetz number for endomorphisms (modulo trace class operators) of sequences of trace class curvature was introduced. We show that this is a well defined, canonical extension of the classical Lefschetz number and establish the homotopy invariance of this number. Moreover, we apply the results to show that the Lefschetz fixed point formula holds for geometric quasiendomorphisms of elliptic quasicomplexes.
Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. In response to specific environmental stresses the cell activates several stress-specific molecules such as sigma factors. They reversibly bind the RNA polymerase to form the so-called holoenzyme and direct it towards the appropriate stress response genes. In exponentially growing E. coli cells, the majority of the transcriptional activity is carried out by the housekeeping sigma factor, while stress responses are often under the control of alternative sigma factors. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross talk between genes or gene classes via the sharing of expression machinery. To quantitatively analyze the contribution of sigma factor competition to global changes in gene expression, we develop a thermodynamic model that describes binding between sigma factors and core RNAP at equilibrium, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components.
Association of housekeeping sigma factor to RNAP is generally favored by its abundance and higher binding affinity to the core. In order to promote transcription by alternative sigma subunits, the bacterial cell modulates the transcriptional efficiency in a reversible manner through several strategies such as anti-sigma factors, 6S RNA and generally any kind of transcriptional regulators (e.g. activators or inhibitors). By shifting the outcome of sigma factor competition for the core, these modulators bias the transcriptional program of the cell. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. We observe that transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected.
Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross talk effects and raising the question of how their in vitro measure is relevant in the cell. We also estimate that sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors, and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program and gives new insights into RNAP partitioning in the cell.
A feasible approach to construct multilayer films of sulfonated polyanilines – PMSA1 and PABMSA1 – containing different ratios of aniline, 2-methoxyaniline-5-sulfonic acid (MAS) and 3-aminobenzoic acid (AB), with the entrapped redox enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) on Au and ITO electrode surfaces, is described. The formation of layers has been followed and confirmed by electrochemical impedance spectroscopy (EIS), which demonstrates that the multilayer assembly can be achieved in a progressive and uniform manner. The gold and ITO electrodes subsequently modified with PMSA1:PQQ-GDH and PABMSA1 films are studied by cyclic voltammetry (CV) and UV-Vis spectroscopy which show a significant direct bioelectrocatalytical response to the oxidation of the substrate glucose without any additional mediator. This response correlates linearly with the number of deposited layers. Furthermore, the constructed polymer/enzyme multilayer system exhibits a rather good long-term stability, since the catalytic current response is maintained for more than 60% of the initial value even after two weeks of storage. This verifies that a productive interaction of the enzyme embedded in the film of substituted polyaniline can be used as a basis for the construction of bioelectronic units, which are useful as indicators for processes liberating glucose and allowing optical and electrochemical transduction.
Potentiality of nanosized materials has been largely proved but a closer look shows that a significant percentage of this research is related to oxides and metals, while the number drastically drops for metallic ceramics, namely transition metal nitrides and metal carbides. The lack of related publications do not reflect their potential but rather the difficulties related to their synthesis as dense and defect-free structures, fundamental prerequisites for advanced mechanical applications.
The present habilitation work aims to close the gap between preparation and processing, indicating novel synthetic pathways for a simpler and sustainable synthesis of transition metal nitride (MN) and carbide (MC) based nanostructures and easier processing thereafter. In spite of simplicity and reliability, the designed synthetic processes allow the production of functional materials, with the demanded size and morphology.
The goal was achieved exploiting classical and less-classical precursors, ranging from common metal salts and molecules (e.g. urea, gelatin, agar, etc), to more exotic materials, such as leafs, filter paper and even wood. It was found that the choice of precursors and reaction conditions makes it possible to control chemical composition (going for instance from metal oxides to metal oxy-nitrides to metal nitrides, or from metal nitrides to metal carbides, up to quaternary systems), size (from 5 to 50 nm) and morphology (going from mere spherical nanoparticles to rod-like shapes, fibers, layers, meso-porous and hierarchical structures, etc). The nature of the mixed precursors also allows the preparation of metal nitrides/carbides based nanocomposites, thus leading to multifunctional materials (e.g. MN/MC@C, MN/MC@PILs, etc) but also allowing dispersion in liquid media. Control over composition, size and morphology is obtained with simple adjustment of the main route, but also coupling it with processes such as electrospin, aerosol spray, bio-templating, etc. Last but not least, the nature of the precursor materials also allows easy processing, including printing, coating, casting, film and thin layers preparation, etc).
The designed routes are, concept-wise, similar and they all start by building up a secondary metal ion-N/C precursor network, which converts, upon heat treatment, into an intermediate “glass”. This glass stabilizes the nascent nanoparticles during their nucleation and impairs their uncontrolled growth during the heat treatment (scheme 1). This way, one of the main problems related to the synthesis of MN/MC, i.e. the need of very high temperature, could also be overcome (from up to 2000°C, for classical synthesis, down to 700°C in the present cases). The designed synthetic pathways are also conceived to allow usage of non-toxic compounds and to minimize (or even avoid) post-synthesis purification, still bringing to phase pure and well-defined (crystalline) nanoparticles.
This research aids to simplify the preparation of MN/MC, making these systems now readily available in suitable amounts both for fundamental and applied science. The prepared systems have been tested (in some cases for the first time) in many different fields, e.g. battery (MnN0.43@C shown a capacity stabilized at a value of 230 mAh/g, with coulombic efficiencies close to 100%), as alternative magnetic materials (Fe3C nanoparticles were prepared with different size and therefore different magnetic behavior, superparamagnetic or ferromagnetic, showing a saturation magnetization value up to 130 emu/g, i.e. similar to the value expected for the bulk material), as filters and for the degradation of organic dyes (outmatching the performance of carbon), as catalysts (both as active phase but also as active support, leading to high turnover rate and, more interesting, to tunable selectivity). Furthermore, with this route, it was possible to prepare for the first time, to the best of our knowledge, well-defined and crystalline MnN0.43, Fe3C and Zn1.7GeN1.8O nanoparticles via bottom-up approaches.
Once the synthesis of these materials can be made straightforward, any further modification, combination, manipulation, is in principle possible and new systems can be purposely conceived (e.g. hybrids, nanocomposites, ferrofluids, etc).
Extreme weather events are likely to occur more often under climate change and the resulting effects on ecosystems could lead to a further acceleration of climate change. But not all extreme weather events lead to extreme ecosystem response. Here, we focus on hazardous ecosystem behaviour and identify coinciding weather conditions. We use a simple probabilistic risk assessment based on time series of ecosystem behaviour and climate conditions. Given the risk assessment terminology, vulnerability and risk for the previously defined hazard are estimated on the basis of observed hazardous ecosystem behaviour.
We apply this approach to extreme responses of terrestrial ecosystems to drought, defining the hazard as a negative net biome productivity over a 12-month period. We show an application for two selected sites using data for 1981-2010 and then apply the method to the pan-European scale for the same period, based on numerical modelling results (LPJmL for ecosystem behaviour; ERA-Interim data for climate).
Our site-specific results demonstrate the applicability of the proposed method, using the SPEI to describe the climate condition. The site in Spain provides an example of vulnerability to drought because the expected value of the SPEI is 0.4 lower for hazardous than for non-hazardous ecosystem behaviour. In northern Germany, on the contrary, the site is not vulnerable to drought because the SPEI expectation values imply wetter conditions in the hazard case than in the non-hazard case.
At the pan-European scale, ecosystem vulnerability to drought is calculated in the Mediterranean and temperate region, whereas Scandinavian ecosystems are vulnerable under conditions without water shortages. These first model- based applications indicate the conceptual advantages of the proposed method by focusing on the identification of critical weather conditions for which we observe hazardous ecosystem behaviour in the analysed data set. Application of the method to empirical time series and to future climate would be important next steps to test the approach.
Modern 3D geovisualization systems (3DGeoVSs) are complex and evolving systems that are required to be adaptable and leverage distributed resources, including massive geodata. This article focuses on 3DGeoVSs built based on the principles of service-oriented architectures, standards and image-based representations (SSI) to address practically relevant challenges and potentials. Such systems facilitate resource sharing and agile and efficient system construction and change in an interoperable manner, while exploiting images as efficient, decoupled and interoperable representations. The software architecture of a 3DGeoVS and its underlying visualization model have strong effects on the system's quality attributes and support various system life cycle activities. This article contributes a software reference architecture (SRA) for 3DGeoVSs based on SSI that can be used to design, describe and analyze concrete software architectures with the intended primary benefit of an increase in effectiveness and efficiency in such activities. The SRA integrates existing, proven technology and novel contributions in a unique manner. As the foundation for the SRA, we propose the generalized visualization pipeline model that generalizes and overcomes expressiveness limitations of the prevalent visualization pipeline model. To facilitate exploiting image-based representations (IReps), the SRA integrates approaches for the representation, provisioning and styling of and interaction with IReps. Five applications of the SRA provide proofs of concept for the general applicability and utility of the SRA. A qualitative evaluation indicates the overall suitability of the SRA, its applications and the general approach of building 3DGeoVSs based on SSI.
The zero-noise limit of differential equations with singular coefficients is investigated for the first time in the case when the noise is a general alpha-stable process. It is proved that extremal solutions are selected and the probability of selection is computed. Detailed analysis of the characteristic function of an exit time form on the half-line is performed, with a suitable decomposition in small and large jumps adapted to the singular drift.
Today, it is well known that galaxies like the Milky Way consist not only of stars but also of gas and dust. The galactic halo, a sphere of gas that surrounds the stellar disk of a galaxy, is especially interesting. It provides a wealth of information about in and outflowing gaseous material towards and away from galaxies and their hierarchical evolution. For the Milky Way, the so-called high-velocity clouds (HVCs), fast moving neutral gas complexes in the halo that can be traced by absorption-line measurements, are believed to play a crucial role in the overall matter cycle in our Galaxy. Over the last decades, the properties of these halo structures and their connection to the local circumgalactic and intergalactic medium (CGM and IGM, respectively) have been investigated in great detail by many different groups. So far it remains unclear, however, to what extent the results of these studies can be transferred to other galaxies in the local Universe. In this thesis, we study the absorption properties of Galactic HVCs and compare the HVC absorption characteristics with those of intervening QSO absorption-line systems at low redshift. The goal of this project is to improve our understanding of the spatial extent and physical conditions of gaseous galaxy halos in the local Universe. In the first part of the thesis we use HST /STIS ultraviolet spectra of more than 40 extragalactic background sources to statistically analyze the absorption properties of the HVCs in the Galactic halo. We determine fundamental absorption line parameters including covering fractions of different weakly/intermediately/highly ionized metals with a particular focus on SiII and MgII. Due to the similarity in the ionization properties of SiII and MgII, we are able to estimate the contribution of HVC-like halo structures to the cross section of intervening strong MgII absorbers at z = 0. Our study implies that only the most massive HVCs would be regarded as strong MgII absorbers, if the Milky Way halo would be seen as a QSO absorption line system from an exterior vantage point. Combining the observed absorption-cross section of Galactic HVCs with the well-known number density of intervening strong MgII absorbers at z = 0, we conclude that the contribution of infalling gas clouds (i.e., HVC analogs) in the halos of Milky Way-type galaxies to the cross section of strong MgII absorbers is 34%. This result indicates that only about one third of the strong MgII absorption can be associated with HVC analogs around other galaxies, while the majority of the strong MgII systems possibly is related to galaxy outflows and winds. The second part of this thesis focuses on the properties of intervening metal absorbers at low redshift. The analysis of the frequency and physical conditions of intervening metal systems in QSO spectra and their relation to nearby galaxies offers new insights into the typical conditions of gaseous galaxy halos. One major aspect in our study was to regard intervening metal systems as possible HVC analogs. We perform a detailed analysis of absorption line properties and line statistics for 57 metal absorbers along 78 QSO sightlines using newly-obtained ultraviolet spectra obtained with HST /COS. We find clear evidence for bimodal distribution in the HI column density in the absorbers, a trend that we interpret as sign for two different classes of absorption systems (with HVC analogs at the high-column density end). With the help of the strong transitions of SiII λ1260, SiIII λ1206, and CIII λ977 we have set up Cloudy photoionization models to estimate the local ionization conditions, gas densities, and metallicities. We find that the intervening absorption systems studied by us have, on average, similar physical conditions as Galactic HVC absorbers, providing evidence that many of them represent HVC analogs in the vicinity of other galaxies. We therefore determine typical halo sizes for SiII, SiIII, and CIII for L = 0.01L∗ and L = 0.05L∗ galaxies. Based on the covering fractions of the different ions in the Galactic halo, we find that, for example, the typical halo size for SiIII is ∼ 160 kpc for L = 0.05L∗ galaxies. We test the plausibility of this result by searching for known galaxies close to the QSO sightlines and at similar redshifts as the absorbers. We find that more than 34% of the measured SiIII absorbers have galaxies associated with them, with the majority of the absorbers indeed being at impact parameters ρ ≤160 kpc.