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- 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.
- ItemPhenotypic, Morphological and Adhesive Differences of Human Hematopoietic Progenitor Cells Cultured on Murine versus Human Mesenchymal Stromal Cells([London] : Macmillan Publishers Limited, part of Springer Nature, 2015) Reichert, Doreen; Friedrichs, Jens; Ritter, Steffi; Käubler, Theresa; Werner, Carsten; Bornhäuser, Martin; Corbeil, DenisXenogenic transplantation models have been developed to study human hematopoiesis in immunocompromised murine recipients. They still have limitations and therefore it is important to delineate all players within the bone marrow that could account for species-specific differences. Here, we evaluated the proliferative capacity, morphological and physical characteristics of human CD34+ hematopoietic stem and progenitor cells (HSPCs) after co-culture on murine or human bone marrow-derived mesenchymal stromal cells (MSCs). After seven days, human CD34+CD133– HSPCs expanded to similar extents on both feeder layers while cellular subsets comprising primitive CD34+CD133+ and CD133+CD34– phenotypes are reduced fivefold on murine MSCs. The number of migrating HSPCs was also reduced on murine cells suggesting that MSC adhesion influences cellular polarization of HSPC. We used atomic force microscopy-based single-cell force spectroscopy to quantify their adhesive interactions. We found threefold higher detachment forces of human HSPCs from murine MSCs compared to human ones. This difference is related to the N-cadherin expression level on murine MSCs since its knockdown abolished their differential adhesion properties with human HSPCs. Our observations highlight phenotypic, morphological and adhesive differences of human HSPCs when cultured on murine or human MSCs, which raise some caution in data interpretation when xenogenic transplantation models are used.
- ItemGlobal data on earthworm abundance, biomass, diversity and corresponding environmental properties(London : Nature Publ. Group, 2021) Phillips, Helen R. P.; Bach, Elizabeth M.; Bartz, Marie L. C.; Bennett, Joanne M.; Beugnon, Rémy; Briones, Maria J. I.; Brown, George G.; Ferlian, Olga; Gongalsky, Konstantin B.; Guerra, Carlos A.; König-Ries, Birgitta; López-Hernández, Danilo; Loss, Scott R.; Marichal, Raphael; Matula, Radim; Minamiya, Yukio; Moos, Jan Hendrik; Moreno, Gerardo; Morón-Ríos, Alejandro; Motohiro, Hasegawa; Muys, Bart; Krebs, Julia J.; Neirynck, Johan; Norgrove, Lindsey; Novo, Marta; Nuutinen, Visa; Nuzzo, Victoria; Mujeeb Rahman, P.; Pansu, Johan; Paudel, Shishir; Pérès, Guénola; Pérez-Camacho, Lorenzo; Orgiazzi, Alberto; Ponge, Jean-François; Prietzel, Jörg; Rapoport, Irina B.; Rashid, Muhammad Imtiaz; Rebollo, Salvador; Rodríguez, Miguel Á.; Roth, Alexander M.; Rousseau, Guillaume X.; Rozen, Anna; Sayad, Ehsan; Ramirez, Kelly S.; van Schaik, Loes; Scharenbroch, Bryant; Schirrmann, Michael; Schmidt, Olaf; Schröder, Boris; Seeber, Julia; Shashkov, Maxim P.; Singh, Jaswinder; Smith, Sandy M.; Steinwandter, Michael; Russell, David J.; Szlavecz, Katalin; Talavera, José Antonio; Trigo, Dolores; Tsukamoto, Jiro; Uribe-López, Sheila; de Valença, Anne W.; Virto, Iñigo; Wackett, Adrian A.; Warren, Matthew W.; Webster, Emily R.; Schwarz, Benjamin; Wehr, Nathaniel H.; Whalen, Joann K.; Wironen, Michael B.; Wolters, Volkmar; Wu, Pengfei; Zenkova, Irina V.; Zhang, Weixin; Cameron, Erin K.; Eisenhauer, Nico; Wall, Diana H.; Brose, Ulrich; Decaëns, Thibaud; Lavelle, Patrick; Loreau, Michel; Mathieu, Jérôme; Mulder, Christian; van der Putten, Wim H.; Rillig, Matthias C.; Thakur, Madhav P.; de Vries, Franciska T.; Wardle, David A.; Ammer, Christian; Ammer, Sabine; Arai, Miwa; Ayuke, Fredrick O.; Baker, Geoff H.; Baretta, Dilmar; Barkusky, Dietmar; Beauséjour, Robin; Bedano, Jose C.; Birkhofer, Klaus; Blanchart, Eric; Blossey, Bernd; Bolger, Thomas; Bradley, Robert L.; Brossard, Michel; Burtis, James C.; Capowiez, Yvan; Cavagnaro, Timothy R.; Choi, Amy; Clause, Julia; Cluzeau, Daniel; Coors, Anja; Crotty, Felicity V.; Crumsey, Jasmine M.; Dávalos, Andrea; Cosín, Darío J. Díaz; Dobson, Annise M.; Domínguez, Anahí; Duhour, Andrés Esteban; van Eekeren, Nick; Emmerling, Christoph; Falco, Liliana B.; Fernández, Rosa; Fonte, Steven J.; Fragoso, Carlos; Franco, André L. C.; Fusilero, Abegail; Geraskina, Anna P.; Gholami, Shaieste; González, Grizelle; Gundale, Michael J.; López, Mónica Gutiérrez; Hackenberger, Branimir K.; Hackenberger, Davorka K.; Hernández, Luis M.; Hirth, Jeff R.; Hishi, Takuo; Holdsworth, Andrew R.; Holmstrup, Martin; Hopfensperger, Kristine N.; Lwanga, Esperanza Huerta; Huhta, Veikko; Hurisso, Tunsisa T.; Iannone, Basil V.; Iordache, Madalina; Irmler, Ulrich; Ivask, Mari; Jesús, Juan B.; Johnson-Maynard, Jodi L.; Joschko, Monika; Kaneko, Nobuhiro; Kanianska, Radoslava; Keith, Aidan M.; Kernecker, Maria L.; Koné, Armand W.; Kooch, Yahya; Kukkonen, Sanna T.; Lalthanzara, H.; Lammel, Daniel R.; Lebedev, Iurii M.; Le Cadre, Edith; Lincoln, Noa K.Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.
- ItemSimulations of Protein Adsorption on Nanostructured Surfaces([London] : Macmillan Publishers Limited, part of Springer Nature, 2019) Manzi, Berardo M.; Werner, Marco; Ivanova, Elena P.; Crawford, Russell J.; Baulin, Vladimir A.Recent technological advances have allowed the development of a new generation of nanostructured materials, such as those displaying both mechano-bactericidal activity and substrata that favor the growth of mammalian cells. Nanomaterials that come into contact with biological media such as blood first interact with proteins, hence understanding the process of adsorption of proteins onto these surfaces is highly important. The Random Sequential Adsorption (RSA) model for protein adsorption on flat surfaces was modified to account for nanostructured surfaces. Phenomena related to the nanofeature geometry have been revealed during the modelling process; e.g., convex geometries can lead to lower steric hindrance between particles, and hence higher degrees of surface coverage per unit area. These properties become more pronounced when a decrease in the size mismatch between the proteins and the surface nanostructures occurs. This model has been used to analyse the adsorption of human serum albumin (HSA) on a nano-structured black silicon (bSi) surface. This allowed the Blocking Function (the rate of adsorption) to be evaluated. The probability of the protein to adsorb as a function of the occupancy was also calculated.
- ItemPhysical plasma-treated saline promotes an immunogenic phenotype in CT26 colon cancer cells in vitro and in vivo([London] : Macmillan Publishers Limited, part of Springer Nature, 2019) Freund, Eric; Liedtke, Kim Rouven; van der Linde, Julia; Metelmann, Hans-Robert; Heidecke, Claus-Dieter; Partecke, Lars-Ivo; Bekeschus, SanderMetastatic colorectal cancer is the fourth most common cause of cancer death. Current options in palliation such as hyperthermic intraperitoneal chemotherapy (HIPEC) present severe side effects. Recent research efforts suggested the therapeutic use of oxidant-enriched liquid using cold physical plasma. To investigate a clinically accepted treatment regimen, we assessed the antitumor capacity of plasma-treated saline solution. In response to such liquid, CT26 murine colon cancer cells were readily oxidized and showed cell growth with subsequent apoptosis, cell cycle arrest, and upregulation of immunogenic cell death (ICD) markers in vitro. This was accompanied by marked morphological changes with re-arrangement of actin fibers and reduced motility. Induction of an epithelial-to-mesenchymal transition phenotype was not observed. Key results were confirmed in MC38 colon and PDA6606 pancreatic cancer cells. Compared to plasma-treated saline, hydrogen peroxide was inferiorly toxic in 3D tumor spheroids but of similar efficacy in 2D models. In vivo, plasma-treated saline decreased tumor burden in Balb/C mice. This was concomitant with elevated numbers of intratumoral macrophages and increased T cell activation following incubation with CT26 cells ex vivo. Being a potential adjuvant for HIPEC therapy, our results suggest oxidizing saline solutions to inactivate colon cancer cells while potentially stimulating antitumor immune responses.
- ItemMagnetically Controllable Polymer Nanotubes from a Cyclized Crosslinker for Site-Specific Delivery of Doxorubicin([London] : Macmillan Publishers Limited, part of Springer Nature, 2015) Newland, Ben; Leupelt, Daniel; Zheng, Yu; Thomas, Laurent S.V.; Werner, Carsten; Steinhart, Martin; Wang, WenxinExternally controlled site specific drug delivery could potentially provide a means of reducing drug related side effects whilst maintaining, or perhaps increasing therapeutic efficiency. The aim of this work was to develop a nanoscale drug carrier, which could be loaded with an anti-cancer drug and be directed by an external magnetic field. Using a single, commercially available monomer and a simple one-pot reaction process, a polymer was synthesized and crosslinked within the pores of an anodized aluminum oxide template. These polymer nanotubes (PNT) could be functionalized with iron oxide nanoparticles for magnetic manipulation, without affecting the large internal pore, or inherent low toxicity. Using an external magnetic field the nanotubes could be regionally concentrated, leaving areas devoid of nanotubes. Lastly, doxorubicin could be loaded to the PNTs, causing increased toxicity towards neuroblastoma cells, rendering a platform technology now ready for adaptation with different nanoparticles, degradable pre-polymers and various therapeutics.
- ItemHigh resolution spectroscopy reveals fibrillation inhibition pathways of insulin([London] : Macmillan Publishers Limited, part of Springer Nature, 2016) Deckert-Gaudig, Tanja; Deckert, VolkerFibril formation implies the conversion of a protein’s native secondary structure and is associated with several neurodegenerative diseases. A better understanding of fibrillation inhibition and fibril dissection requires nanoscale molecular characterization of amyloid structures involved. Tip-enhanced Raman scattering (TERS) has already been used to chemically analyze amyloid fibrils on a sub-protein unit basis. Here, TERS in combination with atomic force microscopy (AFM), and conventional Raman spectroscopy characterizes insulin assemblies generated during inhibition and dissection experiments in the presence of benzonitrile, dimethylsulfoxide, quercetin, and β-carotene. The AFM topography indicates formation of filamentous or bead-like insulin self-assemblies. Information on the secondary structure of bulk samples and of single aggregates is obtained from standard Raman and TERS measurements. In particular the high spatial resolution of TERS reveals the surface conformations associated with the specific agents. The insulin aggregates formed under different inhibition and dissection conditions can show a similar morphology but differ in their β-sheet structure content. This suggests different aggregation pathways where the prevention of the β-sheet stacking of the peptide chains plays a major role. The presented approach is not limited to amyloid-related reasearch but can be readily applied to systems requiring extremely surface-sensitive characterization without the need of labels.