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- ItemNitrosylation vs. oxidation – How to modulate cold physical plasmas for biological applications(San Francisco, California, US : PLOS, 2019) Lackmann, Jan-Wilm; Bruno, Giuliana; Jablonowski, Helena; Kogelheide, Friederike; Offerhaus, Björn; Held, Julian; Schulz-von der Gathen, Volker; Stapelmann, Katharina; von Woedtke, Thomas; Wende, KristianThiol moieties are major targets for cold plasma-derived nitrogen and oxygen species, making CAPs convenient tools to modulate redox-signaling pathways in cells and tissues. The underlying biochemical pathways are currently under investigation but especially the role of CAP derived RNS is barely understood. Their potential role in protein thiol nitrosylation would be relevant in inflammatory processes such as wound healing and improving their specific production by CAP would allow for enhanced treatment options beyond the current application. The impact of a modified kINPen 09 argon plasma jet with nitrogen shielding on cysteine as a thiol-carrying model substance was investigated by FTIR spectroscopy and high-resolution mass spectrometry. The deposition of short-lived radical species was measured by electron paramagnetic resonance spectroscopy, long-lived species were quantified by ion chromatography (NO2-, NO3-) and xylenol orange assay (H2O2). Product profiles were compared to samples treated with the so-called COST jet, being introduced by a European COST initiative as a reference device, using both reference conditions as well as conditions adjusted to kINPen gas mixtures. While thiol oxidation was dominant under all tested conditions, an Ar + N2/O2 gas compositions combined with a nitrogen curtain fostered nitric oxide deposition and the desired generation of S-nitrosocysteine. Interestingly, the COST-jet revealed significant differences in its chemical properties in comparison to the kINPen by showing a more stable production of RNS with different gas admixtures, indicating a different •NO production pathway. Taken together, results indicate various chemical properties of kINPen and COST-jet as well as highlight the potential of plasma tuning not only by gas admixtures alone but by adjusting the surrounding atmosphere as well.
- ItemImproving Accuracy and Temporal Resolution of Learning Curve Estimation for within- and across-Session Analysis(San Francisco, California, US : PLOS, 2016) Deliano, Matthias; Tabelow, Karsten; König, Reinhard; Polzehl, JörgEstimation of learning curves is ubiquitously based on proportions of correct responses within moving trial windows. Thereby, it is tacitly assumed that learning performance is constant within the moving windows, which, however, is often not the case. In the present study we demonstrate that violations of this assumption lead to systematic errors in the analysis of learning curves, and we explored the dependency of these errors on window size, different statistical models, and learning phase. To reduce these errors in the analysis of single-subject data as well as on the population level, we propose adequate statistical methods for the estimation of learning curves and the construction of confidence intervals, trial by trial. Applied to data from an avoidance learning experiment with rodents, these methods revealed performance changes occurring at multiple time scales within and across training sessions which were otherwise obscured in the conventional analysis. Our work shows that the proper assessment of the behavioral dynamics of learning at high temporal resolution can shed new light on specific learning processes, and, thus, allows to refine existing learning concepts. It further disambiguates the interpretation of neurophysiological signal changes recorded during training in relation to learning.
- ItemMonoclonal Antibodies 13A4 and AC133 Do Not Recognize the Canine Ortholog of Mouse and Human Stem Cell Antigen Prominin-1 (CD133)(San Francisco, California, US : PLOS, 2016) Thamm, Kristina; Graupner, Sylvi; Werner, Carsten; Huttner, Wieland B.; Corbeil, Denis; Nabi, Ivan RThe pentaspan membrane glycoprotein prominin-1 (CD133) is widely used in medicine as a cell surface marker of stem and cancer stem cells. It has opened new avenues in stem cell-based regenerative therapy and oncology. This molecule is largely used with human samples or the mouse model, and consequently most biological tools including antibodies are directed against human and murine prominin-1. Although the general structure of prominin-1 including its membrane topology is conserved throughout the animal kingdom, its primary sequence is poorly conserved. Thus, it is unclear if anti-human and -mouse prominin-1 antibodies cross-react with their orthologs in other species, especially dog. Answering this issue is imperative in light of the growing number of studies using canine prominin-1 as an antigenic marker. Here, we address this issue by cloning the canine prominin-1 and use its overexpression as a green fluorescent protein fusion protein in Madin-Darby canine kidney cells to determine its immunoreactivity with antibodies against human or mouse prominin-1. We used immunocytochemistry, flow cytometry and immunoblotting techniques and surprisingly found no cross-species immunoreactivity. These results raise some caution in data interpretation when anti-prominin-1 antibodies are used in interspecies studies.
- ItemProximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?(San Francisco, California, US : PLOS, 2016) Schirrmann, Michael; Joschko, Monika; Gebbers, Robin; Kramer, Eckart; Zörner, Mirjam; Barkusky, Dietmar; Timmer, JensBackground: Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS) provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils. Methodology/Principal Findings: Proximal soil sensing data, e.g., soil electrical conductivity (EC), pH, and near infrared absorbance (NIR), were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage) and sandy to loam soils. PSS was related to observations from a long-term (11 years) earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species. Conclusions/Significance: Our findings suggest that PSS contributes to the spatial modelling of earthworm abundances at field scale and that it will support species distribution modelling in the attempt to understand the soil-earthworm relationships in agroecosystems.
- ItemInvestigating the Mutagenicity of a Cold Argon-Plasma Jet in an HET-MN Model(San Francisco, California, US : PLOS, 2016) Kluge, Susanne; Bekeschus, Sander; Bender, Claudia; Benkhai, Hicham; Sckell, Axel; Below, Harald; Stope, Matthias B.; Kramer, Axel; Yousfi, MohammedObjective: So-called cold physical plasmas for biomedical applications generate reactive oxygen and nitrogen species and the latter can trigger DNA damage at high concentrations. Therefore, the mutagenic risks of a certified atmospheric pressure argon plasma jet (kINPen MED) and its predecessor model (kINPen 09) were assessed. Methods: Inner egg membranes of fertilized chicken eggs received a single treatment with either the kINPen 09 (1.5, 2.0, or 2.5 min) or the kINPen MED (3, 4, 5, or 10 min). After three days of incubation, blood smears (panoptic May-Grünwald-Giemsa stain) were performed, and 1000 erythrocytes per egg were evaluated for the presence of polychromatic and normochromic nuclear staining as well as nuclear aberrations and binucleated cells (hen’s egg test for micronuclei induction, HET-MN). At the same time, the embryo mortality was documented. For each experiment, positive controls (cyclophosphamide and methotrexate) and negative controls (NaCl-solution, argon gas) were included. Additionally, the antioxidant potential of the blood plasma was assessed by ascorbic acid oxidation assay after treatment. Results: For both plasma sources, there was no evidence of genotoxicity, although at the longest plasma exposure time of 10 min the mortality of the embryos exceeded 40%. The antioxidant potential in the egg’s blood plasma was not significantly reduced immediately (p = 0.32) or 1 h (p = 0.19) post exposure to cold plasma. Conclusion: The longest plasma treatment time with the kINPen MED was 5–10 fold above the recommended limit for treatment of chronic wounds in clinics. We did not find mutagenic effects for any plasma treatment time using the either kINPen 09 or kINPen MED. The data provided with the current study seem to confirm the lack of a genotoxic potential suggesting that a veterinary or clinical application of these argon plasma jets does not pose mutagenic risks.
- ItemGuidance of mesenchymal stem cells on fibronectin structured hydrogel films(San Francisco, California, US : PLOS, 2014) Kasten, Annika; Naser, Tamara; Brüllhoff, Kristina; Fiedler, Jörg; Müller, Petra; Möller, Martin; Rychly, Joachim; Groll, Jürgen; Brenner, Rolf E.; Engler, Adam J.Designing of implant surfaces using a suitable ligand for cell adhesion to stimulate specific biological responses of stem cells will boost the application of regenerative implants. For example, materials that facilitate rapid and guided migration of stem cells would promote tissue regeneration. When seeded on fibronectin (FN) that was homogeneously immmobilized to NCO-sP(EO-stat-PO), which otherwise prevents protein binding and cell adhesion, human mesenchymal stem cells (MSC) revealed a faster migration, increased spreading and a more rapid organization of different cellular components for cell adhesion on fibronectin than on a glass surface. To further explore, how a structural organization of FN controls the behavior of MSC, adhesive lines of FN with varying width between 10 µm and 80 µm and spacings between 5 µm and 20 µm that did not allow cell adhesion were generated. In dependance on both line width and gaps, cells formed adjacent cell contacts, were individually organized in lines, or bridged the lines. With decreasing sizes of FN lines, speed and directionality of cell migration increased, which correlated with organization of the actin cytoskeleton, size and shape of the nuclei as well as of focal adhesions. Together, defined FN lines and gaps enabled a fine tuning of the structural organization of cellular components and migration. Microstructured adhesive substrates can mimic the extracellular matrix in vivo and stimulate cellular mechanisms which play a role in tissue regeneration.
- ItemFemtosecond laser induced step-like structures inside transparent hydrogel due to laser induced threshold reduction(San Francisco, California, US : PLOS, 2019) Saerchen, Emanuel; Liedtke-Gruener, Susann; Kopp, Maximilian; Heisterkamp, Alexander; Lubatschowski, Holger; Ripken, TammoIn the area of laser material processing, versatile applications for cutting glasses and transparent polymers exist. However, parasitic effects such as the creation of step-like structures appear when laser cutting inside a transparent material. To date, these structures were only described empirically. This work establishes the physical and chemical mechanisms behind the observed effects and describes the influence of process and material parameters onto the creation of step-like structures in hydrogel, Dihydroxyethylmethacrylat (HEMA). By focusing laser pulses in HEMA, reduced pulse separation distance below 50 nm and rise in pulse energy enhances the creation of unintended step-like structures. Spatial resolved Raman-spectroscopy was used to measure the laser induced chemical modification, which results into a reduced breakdown threshold. The reduction in threshold influences the position of optical breakdown for the succeeding laser pulses and consequently leads to the step-like structures. Additionally, the experimental findings were supplemented with numerical simulations of the influence of reduced damage threshold onto the position of optical breakdown.
- ItemColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data(San Francisco, California, US : PLOS, 2019) Smit, Jochem H.; Li, Yichen; Warszawik, Eliza M.; Herrmann, Andreas; Cordes, Thorben; Gilestro, Giorgio FSingle-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique. With the cost of microscopes dropping and the availability of fully automated microscopes, the volume of microscopy data produced has increased tremendously. These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis. Furthermore, requirements for analysis procedures have become more stringent given the demand of various journals to make data and analysis procedures available. To address these issues we have developed a new data analysis package for analysis of fluorescence microscopy data from rod-like cells. Our software ColiCoords structures microscopy data at the single-cell level and implements a coordinate system describing each cell. This allows for the transformation of Cartesian coordinates from transmission light and fluorescence images and single-molecule localization microscopy (SMLM) data to cellular coordinates. Using this transformation, many cells can be combined to increase the statistical power of fluorescence microscopy datasets of any kind. ColiCoords is open source, implemented in the programming language Python, and is extensively documented. This allows for modifications for specific needs or to inspect and publish data analysis procedures. By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research. The source code and documentation can be found via the project’s GitHub page.
- ItemBiogas residue parameterization for soil organic matter modeling(San Francisco, California, US : PLOS, 2018-10-12) Prays, Nadia; Dominik, Peter; Sänger, Anja; Franko, UweA variety of biogas residues (BGRs) have been used as organic fertilizer in agriculture. The use of these residues affects the storage of soil organic matter (SOM). In most cases, SOM changes can only be determined in long-term observations. Therefore, predictive modeling can be an efficient alternative, provided that the parameters required by the model are known for the considered BGRs. This study was conducted as a first approach to estimating the organic matter (OM) turnover parameters of BGRs for process modeling. We used carbon mineralization data from six BGRs from an incubation experiment, representing a range of substrate inputs, to calculate a turnover coefficient k controlling the velocity of fresh organic matter (FOM) decay and a synthesis coefficient describing the SOM creation from FOM. An SOM turnover model was applied in inverse mode to identify both parameters. In a second step, we related the parameters k and to chemical properties of the corresponding BGRs using a linear regression model and applied them to a long-term scenario simulation. According to the results of the incubation experiment, the k values ranged between 0.28 and 0.58 d-1 depending on the chemical composition of the FOM. The estimated values ranged between 0.8 and 0.89. The best linear relationship of k was found to occur with pH (R2 = 0.863). Parameter is related to the Ct/Norg ratio (R2 = 0.696). Long-term scenario simulations emphasized the necessity of specific k and values related to the chemical properties for each BGR. However, further research is needed to validate and improve these preliminary results. © 2018 Prays et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- ItemOptical Sectioning and High Resolution in Single-Slice Structured Illumination Microscopy by Thick Slice Blind-SIM Reconstruction(San Francisco, California, US : PLOS, 2015) Jost, Aurélie; Tolstik, Elen; Feldmann, Polina; Wicker, Kai; Sentenac, Anne; Heintzmann, Rainer; Degtyar, Vadim E.The microscope image of a thick fluorescent sample taken at a given focal plane is plagued by out-of-focus fluorescence and diffraction limited resolution. In this work, we show that a single slice of Structured Illumination Microscopy (two or three beam SIM) data can be processed to provide an image exhibiting tight sectioning and high transverse resolution. Our reconstruction algorithm is adapted from the blind-SIM technique which requires very little knowledge of the illumination patterns. It is thus able to deal with illumination distortions induced by the sample or illumination optics. We named this new algorithm thick slice blind-SIM because it models a three-dimensional sample even though only a single two-dimensional plane of focus was measured.