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DNA and RNA extraction and quantitative real-time PCR-based assays for biogas biocenoses in an interlaboratory comparison
Five 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.
Design and Fabrication of a BiCMOS Dielectric Sensor for Viscosity Measurements: A Possible Solution for Early Detection of COPD
The 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.
Interaction of proteins identified in human thyroid cells
Influence 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.
Morphology, Optical Properties and Photocatalytic Activity of Photo- and Plasma-Deposited Au and Au/Ag Core/Shell Nanoparticles on Titania Layers
Titania is a promising material for numerous photocatalytic reactions such as water splitting and the degradation of organic compounds (e.g., methanol, phenol). Its catalytic performance can be significantly increased by the addition of co-catalysts. In this study, Au and Au/Ag nanoparticles were deposited onto mesoporous titania thin films using photo-deposition (Au) and magnetron-sputtering (Au and Au/Ag). All samples underwent comprehensive structural characterization by grazing incidence X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Nanoparticle distributions and nanoparticle size distributions were correlated to the deposition methods. Light absorption measurements showed features related to diffuse scattering, the band gap of titania and the local surface plasmon resonance of the noble metal nanoparticles. Further, the photocatalytic activities were measured using methanol as a hole scavenger. All nanoparticle-decorated thin films showed significant performance increases in hydrogen evolution under UV illumination compared to pure titania, with an evolution rate of up to 372 μL H2 h−1 cm−2 representing a promising approximately 12-fold increase compared to pure titania.
Switchable Adhesion Surfaces with Enhanced Performance Against Rough Counterfaces
In 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.
Vimentin levels and serine 71 phosphorylation in the control of cell-matrix adhesions, migration speed, and shape of transformed human fibroblasts
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.
Peptide induced crystallization of calcium carbonate on wrinkle patterned substrate: implications for chitin formation in molluscs
We 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.
A Review on Passive and Integrated Near-Field Microwave Biosensors
In 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.
Preparation of Polymer Electrolyte Membranes via Radiation-Induced Graft Copolymerization on Poly(ethylene-alt-tetrafluoroethylene) (ETFE) Using the Crosslinker N,N′-Methylenebis(acrylamide)
Polymer 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.
Recent developments in peptide-based nucleic acid delivery
Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cellpenetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10-30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisenseoligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls.