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- ItemDNA and RNA extraction and quantitative real-time PCR-based assays for biogas biocenoses in an interlaboratory comparison(Basel : MDPI, 2016) Lebuhn, Michael; Derenkó, Jaqueline; Rademacher, Antje; Helbig, Susanne; Munk, Bernhard; Pechtl, Alexander; Stolze, Yvonne; Prowe, Steffen; Schwarz, Wolfgang H.; Schlüter, Andreas; Liebl, Wolfgang; Klocke, MichaelFive institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on physical and chemical lysis with excellent extraction efficiency yielded highly reproducible results among the partners and clearly outperformed a traditional CTAB/chloroform/isoamylalcohol based method. Analytical purpose, sample texture, consistency and upstream pretreatment steps determine the modifications that should be applied to achieve maximum efficiency in the trade-off between extract purity and nucleic acid recovery rate. RNA extraction was much more variable, and the destination of the extract determines the method to be used. RNA stabilization with quaternary ammonium salts was an as satisfactory approach as flash freezing in liquid N2. Due to co-eluted impurities, spectrophotometry proved to be of limited value for nucleic acid qualification and quantification in extracts obtained with the kit, and picoGreen® based quantification was more trustworthy. Absorbance at 230 nm can be extremely high in the presence of certain chaotropic guanidine salts, but guanidinium isothiocyanate does not affect (q)PCR. Absolute quantification by qPCR requires application of a reliable internal standard for which correct PCR efficiency and Y-intercept values are important and must be reported.
- ItemTowards CMOS integrated microfluidics using dielectrophoretic immobilization(Basel : MDPI, 2019) Ettehad, Honeyeh Matbaechi; Yadav, Rahul Kumar; Guha, Subhajit; Wenger, ChristianDielectrophoresis (DEP) is a nondestructive and noninvasive method which is favorable for point-of-care medical diagnostic tests. This technique exhibits prominent relevance in a wide range of medical applications wherein the miniaturized platform for manipulation (immobilization, separation or rotation), and detection of biological particles (cells or molecules) can be conducted. DEP can be performed using advanced planar technologies, such as complementary metal-oxide-semiconductor (CMOS) through interdigitated capacitive biosensors. The dielectrophoretically immobilization of micron and submicron size particles using interdigitated electrode (IDE) arrays is studied by finite element simulations. The CMOS compatible IDEs have been placed into the silicon microfluidic channel. A rigorous study of the DEP force actuation, the IDE’s geometrical structure, and the fluid dynamics are crucial for enabling the complete platform for CMOS integrated microfluidics and detection of micron and submicron-sized particle ranges. The design of the IDEs is performed by robust finite element analyses to avoid time-consuming and costly fabrication processes. To analyze the preliminary microfluidic test vehicle, simulations were first performed with non-biological particles. To produce DEP force, an AC field in the range of 1 to 5 V (peak-to-peak) is applied to the IDE. The impact of the effective external and internal properties, such as actuating DEP frequency and voltage, fluid flow velocity, and IDE’s geometrical parameters are investigated. The IDE based system will be used to immobilize and sense particles simultaneously while flowing through the microfluidic channel. The sensed particles will be detected using the capacitive sensing feature of the biosensor. The sensing and detecting of the particles are not in the scope of this paper and will be described in details elsewhere. However, to provide a complete overview of this system, the working principles of the sensor, the readout detection circuit, and the integration process of the silicon microfluidic channel are briefly discussed. © 2019 by the authors.
- ItemSwitchable Adhesion Surfaces with Enhanced Performance Against Rough Counterfaces(Basel : MDPI, 2016) Prieto-López, Lizbeth; Williams, JohnIn a recent study, we demonstrated that the pressurization of micro-fluidic features introduced in the subsurface of a soft polymer can be used to actively modify the magnitude of the adhesion to a harder counterface by changing its waviness or long wavelength undulations. In that case, both contacting surfaces had very smooth finishes with root-mean-square roughnesses of less than 20 nm. These values are far from those of many engineering surfaces, which usually have a naturally occurring roughness of between ten and a hundred times this value. In this work, we demonstrate that appropriate surface features, specifically relatively slender “fibrils”, can enhance the ability of a such a soft surface to adhere to a hard, but macroscopically rough, counterface, while still maintaining the possibility of switching the adhesion force from one level to another. Conversely, stiffer more conical surface features can suppress adhesion even against a smooth counterface. Examples of each form of topography can be found in the natural world.
- ItemA Review on Passive and Integrated Near-Field Microwave Biosensors(Basel : MDPI, 2017) Guha, Subhajit; Jamal, Farabi Ibne; Wenger, ChristianIn this paper we review the advancement of passive and integrated microwave biosensors. The interaction of microwave with biological material is discussed in this paper. Passive microwave biosensors are microwave structures, which are fabricated on a substrate and are used for sensing biological materials. On the other hand, integrated biosensors are microwave structures fabricated in standard semiconductor technology platform (CMOS or BiCMOS). The CMOS or BiCMOS sensor technology offers a more compact sensing approach which has the potential in the future for point of care testing systems. Various applications of the passive and the integrated sensors have been discussed in this review paper.
- ItemDesign and Fabrication of a BiCMOS Dielectric Sensor for Viscosity Measurements: A Possible Solution for Early Detection of COPD(Basel : MDPI, 2018) Soltani Zarrin, Pouya; Jamal, Farabi Ibne; Guha, Subhajit; Wessel, Jan; Kissinger, Dietmar; Wenger, ChristianThe viscosity variation of sputum is a common symptom of the progression of Chronic Obstructive Pulmonary Disease (COPD). Since the hydration of the sputum defines its viscosity level, dielectric sensors could be used for the characterization of sputum samples collected from patients for early diagnosis of COPD. In this work, a CMOS-based dielectric sensor for the real-time monitoring of sputum viscosity was designed and fabricated. A proper packaging for the ESD-protection and short-circuit prevention of the sensor was developed. The performance evaluation results show that the radio frequency sensor is capable of measuring dielectric constant of biofluids with an accuracy of 4.17%. Integration of this sensor into a portable system will result in a hand-held device capable of measuring viscosity of sputum samples of COPD-patients for diagnostic purposes.
- ItemVimentin levels and serine 71 phosphorylation in the control of cell-matrix adhesions, migration speed, and shape of transformed human fibroblasts(Basel : MDPI, 2017) Terriac, Emmanuel; Coceano, Giovanna; Mavajian, Zahra; Hageman, Tijmen A.G.; Christ, Andreas F.; Testa, Ilaria; Lautenschläger, Franziska; Gad, Annica K.G.Metastasizing tumor cells show increased expression of the intermediate filament (IF) protein vimentin, which has been used to diagnose invasive tumors for decades. Recent observations indicate that vimentin is not only a passive marker for carcinoma, but may also induce tumor cell invasion. To clarify how vimentin IFs control cell adhesions and migration, we analyzed the nanoscale (30–50 nm) spatial organization of vimentin IFs and cell-matrix adhesions in metastatic fibroblast cells, using three-color stimulated emission depletion (STED) microscopy. We also studied whether wild-type and phospho-deficient or -mimicking mutants of vimentin changed the size and lifetime of focal adhesions (FAs), cell shape, and cell migration, using live-cell total internal reflection imaging and confocal microscopy. We observed that vimentin exists in fragments of different lengths. Short fragments were mostly the size of a unit-length filament and were mainly localized close to small cell-matrix adhesions. Long vimentin filaments were found in the proximity of large FAs. Vimentin expression in these cells caused a reduction in FAs size and an elongated cell shape, but did not affect FA lifetime, or the speed or directionality of cell migration. Expression of a phospho-mimicking mutant (S71D) of vimentin increased the speed of cell migration. Taken together, our results suggest that in highly migratory, transformed mesenchymal cells, vimentin levels control the cell shape and FA size, but not cell migration, which instead is linked to the phosphorylation status of S71 vimentin. These observations are consistent with the possibility that not only levels, but also the assembly status of vimentin control cell migration.
- ItemPreparation of Polymer Electrolyte Membranes via Radiation-Induced Graft Copolymerization on Poly(ethylene-alt-tetrafluoroethylene) (ETFE) Using the Crosslinker N,N′-Methylenebis(acrylamide)(Basel : MDPI, 2018) Ke, Xi; Drache, Marco; Gohs, Uwe; Kunz, Ulrich; Beuermann, SabinePolymer electrolyte membranes (PEM) prepared by radiation-induced graft copolymerization are investigated. For this purpose, commercial poly(ethylene-alt-tetrafluoroethylene) (ETFE) films were activated by electron beam treatment and subsequently grafted with the monomers glycidyl methacrylate (GMA), hydroxyethyl methacrylate (HEMA) and N,N′-methylenebis(acrylamide) (MBAA) as crosslinker. The target is to achieve a high degree of grafting (DG) and high proton conductivity. To evaluate the electrochemical performance, the PEMs were tested in a fuel cell and in a vanadium redox-flow battery (VRFB). High power densities of 134 mW∙cm−2 and 474 mW∙cm−2 were observed, respectively.
- ItemIn vitro entero-capillary barrier exhibits altered inflammatory and exosomal communication pattern after exposure to silica nanoparticles(Basel : MDPI, 2019) Kasper, J.Y.; Iris, Hermanns, M.; Kraegeloh, A.; Roth, W.; James, Kirkpatrick, C.; Unger, R.E.The intestinal microvasculature (iMV) plays multiple pathogenic roles during chronic inflammatory bowel disease (IBD). The iMV acts as a second line of defense and is, among other factors, crucial for the innate immunity in the gut. It is also the therapeutic location in IBD targeting aggravated leukocyte adhesion processes involving ICAM-1 and E-selectin. Specific targeting is stressed via nanoparticulate drug vehicles. Evaluating the iMV in enterocyte barrier models in vitro could shed light on inflammation and barrier-integrity processes during IBD. Therefore, we generated a barrier model by combining the enterocyte cell line Caco-2 with the microvascular endothelial cell line ISO-HAS-1 on opposite sides of a transwell filter-membrane under culture conditions which mimicked the physiological and inflamed conditions of IBD. The IBD model achieved a significant barrier-disruption, demonstrated via transepithelial-electrical resistance (TER), permeability-coefficient (Papp) and increase of sICAM sE-selectin and IL-8. In addition, the impact of a prospective model drug-vehicle (silica nanoparticles, aSNP) on ongoing inflammation was examined. A decrease of sICAM/sE-selectin was observed after aSNP-exposure to the inflamed endothelium. These findings correlated with a decreased secretion of ICAM/E-selectin bearing exosomes/microvesicles, as evaluated via ELISA. Our findings indicate that aSNP treatment of the inflamed endothelium during IBD may hamper exosomal/microvesicular systemic communication. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemInteraction of proteins identified in human thyroid cells(Basel : MDPI, 2013) Pietsch, Jessica; Riwaldt, Stefan; Bauer, Johann; Sickmann, Albert; Weber, Gerhard; Grosse, Jirka; Infanger, Manfred; Eilles, Christoph; Grimm, DanielaInfluence of gravity forces on the regulation of protein expression by healthy and malignant thyroid cells was studied with the aim to identify protein interactions. Western blot analyses of a limited number of proteins suggested a time-dependent regulation of protein expression by simulated microgravity. After applying free flow isoelectric focusing and mass spectrometry to search for differently expressed proteins by thyroid cells exposed to simulated microgravity for three days, a considerable number of candidates for gravi-sensitive proteins were detected. In order to show how proteins sensitive to microgravity could directly influence other proteins, we investigated all polypeptide chains identified with Mascot scores above 100, looking for groups of interacting proteins. Hence, UniProtKB entry numbers of all detected proteins were entered into the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and processed. The program indicated that we had detected various groups of interacting proteins in each of the three cell lines studied. The major groups of interacting proteins play a role in pathways of carbohydrate and protein metabolism, regulation of cell growth and cell membrane structuring. Analyzing these groups, networks of interaction could be established which show how a punctual influence of simulated microgravity may propagate via various members of interaction chains.
- ItemPeptide induced crystallization of calcium carbonate on wrinkle patterned substrate: implications for chitin formation in molluscs(Basel : MDPI, 2013) Weiss, Ingrid M.; Ghatak, Anindita Sengupta; Koch, Markus; Guth, ChristinaWe here present the nucleation and growth of calcium carbonate under the influence of synthetic peptides on topographically patterned poly(dimethylsiloxane) (PDMS) substrates, which have a controlled density of defects between the wrinkles. Experiments with two lysine-rich peptides derived from the extracellular conserved domain E22 of the mollusc chitin synthase Ar-CS1, AKKKKKAS (AS8) and EEKKKKKES (ES9) on these substrates showed their influence on the calcium carbonate morphology. A transition from polycrystalline composites to single crystalline phases was achieved with the peptide AS8 by changing the pH of the buffer solution. We analyzed three different pH values as previous experiments showed that E22 interacts with aragonite biominerals more strongly at pH 7.75 than at pH 9.0. At any given pH, crystals appeared in characteristic morphologies only on wrinkled substrates, and did not occur on the flat, wrinkle-free PDMS substrate. These results suggest that these wrinkled substrates could be useful for controlling the morphologies of other mineral/peptide and mineral/protein composites. In nature, these templates are formed enzymatically by glycosyltransferases containing pH-sensitive epitopes, similar to the peptides investigated here. Our in vitro test systems may be useful to gain understanding of the formation of distinct 3D morphologies in mollusc shells in response to local pH shifts during the mineralization of organic templates.