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- ItemThe Global Gridded Crop Model Intercomparison phase 1 simulation dataset(London : Nature Publ. Group, 2019) MĆ¼ller, Christoph; Elliott, Joshua; Kelly, David; Arneth, Almut; Balkovic, Juraj; Ciais, Philippe; Deryng, Delphine; Folberth, Christian; Hoek, Steven; Izaurralde, Roberto C.; Jones, Curtis D.; Khabarov, Nikolay; Lawrence, Peter; Liu, Wenfeng; Olin, Stefan; Pugh, Thomas A. M.; Reddy, Ashwan; Rosenzweig, Cynthia; Ruane, Alex C.; Sakurai, Gen; Schmid, Erwin; Skalsky, Rastislav; Wang, Xuhui; de Wit, Allard; Yang, HongThe Global Gridded Crop Model Intercomparison (GGCMI) phase 1 dataset of the Agricultural Model Intercomparison and Improvement Project (AgMIP) provides an unprecedentedly large dataset of crop model simulations covering the global ice-free land surface. The dataset consists of annual data fields at a spatial resolution of 0.5 arc-degree longitude and latitude. Fourteen crop modeling groups provided output for up to 11 historical input datasets spanning 1901 to 2012, and for up to three different management harmonization levels. Each group submitted data for up to 15 different crops and for up to 14 output variables. All simulations were conducted for purely rainfed and near-perfectly irrigated conditions on all land areas irrespective of whether the crop or irrigation system is currently used there. With the publication of the GGCMI phase 1 dataset we aim to promote further analyses and understanding of crop model performance, potential relationships between productivity and environmental impacts, and insights on how to further improve global gridded crop model frameworks. We describe dataset characteristics and individual model setup narratives. Ā© 2019, The Author(s).
- ItemNanocarriers in photodynamic therapyāin vitro and in vivo studies(Malden, MA : Wiley-Blackwell, 2019) Sztandera, Krzysztof; Gorzkiewicz, MichaÅ; KlajnertāMaculewicz, BarbaraPhotodynamic therapy (PDT) is a minimally invasive technique which has proven to be successful in the treatment of several types of tumors. This relatively simple method exploits three inseparable elements: phototoxic compound (photosensitizer [PS]), light source, and oxygen. Upon irradiation by light with specified wavelength, PS generates reactive oxygen species, which starts the cascade of reactions leading to cell death. The positive therapeutic outcome of PDT may be limited due to several aspects, including low water solubility of PSs, hampering their effective administration and blood circulation, as well as low tumor specificity, inefficient cellular uptake and activation energies requiring prolonged illumination times. One of the promising approaches to overcome these obstacles involves the use of carrier systems modulating pharmacokinetics and pharmacodynamics of the PSs. In the present review, we summarized current in vitro and in vivo studies regarding the use of nanoparticles as potential delivery devices for PSs to enhance their cellular uptake and cytotoxic properties, and thusāthe therapeutic outcome of PDT.
- ItemComplete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis(Washington, DC : American Soc. for Microbiology, 2018) Hahnke, Sarah; Abendroth, Christian; Langer, Thomas; CodoƱer, Francisco M.; Ramm, Patrice; Porcar, Manuel; Luschnig, Olaf; Klocke, MichaelA new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratoryscale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5- B5C with the family Ruminococcaceae outside recently described genera. Ā© 2018 Hahnke et al.
- ItemFast, economic and simultaneous identification of clinically relevant Gram-negative species with multiplex real-time PCR(London : Future Medicine Ltd, 2019) Weiss, Daniel; Gawlik, Darius; Hotzel, Helmut; Engelmann, Ines; Mueller, Elke; Slickers, Peter; Braun, Sascha D.; Monecke, Stefan; Ehricht, RalfAim: A newly designed multiplex real-time PCR (rt-PCR) was validated to detect four clinically relevant Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa). Materials & methods: Serial dilutions of genomic DNA were used to determine the limit of detection. Colony PCR was performed with isolates of the four selected species and other species as negative controls. Isolates were characterized genotypically and phenotypically to evaluate the assay. Results: Specific signals of all target genes were detected with diluted templates comprising ten genomic equivalents. Using colony rt-PCR, all isolates of the target species were identified correctly. All negative control isolates were negative. Conclusion: The genes gad, basC, khe and ecfX can reliably identify these four species via multiplex colony rt-PCR. Ā© 2018 Daniel Weiss.
- ItemComplete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis(Washington, DC : American Soc. for Microbiology, 2017) Abendroth, Christian; Hahnke, Sarah; CodoƱer, Francisco M.; Klocke, Michael; Luschnig, Olaf; Porcar, ManuelA new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism. Ā© 2017 Abendroth et al.
- ItemTowards a Biohybrid Lung: Endothelial Cells Promote Oxygen Transfer through Gas Permeable Membranes(New York, NY [u.a.] : Hindawi Publ. Corp., 2017) Menzel, Sarah; Finocchiaro, Nicole; Donay, Christine; Thiebes, Anja Lena; Hesselmann, Felix; Arens, Jutta; Djeljadini, Suzana; Wessling, Matthias; Schmitz-Rode, Thomas; Jockenhoevel, Stefan; Cornelissen, Christian GabrielIn patients with respiratory failure, extracorporeal lung support can ensure the vital gas exchange via gas permeable membranes but its application is restricted by limited long-term stability and hemocompatibility of the gas permeable membranes, which are in contact with the blood. Endothelial cells lining these membranes promise physiological hemocompatibility and should enable prolonged application. However, the endothelial cells increase the diffusion barrier of the blood-gas interface and thus affect gas transfer. In this study, we evaluated how the endothelial cells affect the gas exchange to optimize performance while maintaining an integral cell layer. Human umbilical vein endothelial cells were seeded on gas permeable cell culture membranes and cultivated in a custom-made bioreactor. Oxygen transfer rates of blank and endothelialized membranes in endothelial culture medium were determined. Cell morphology was assessed by microscopy and immunohistochemistry. Both setups provided oxygenation of the test fluid featuring small standard deviations of the measurements. Throughout the measuring range, the endothelial cells seem to promote gas transfer to a certain extent exceeding the blank membranes gas transfer performance by up to 120%. Although the underlying principles hereof still need to be clarified, the results represent a significant step towards the development of a biohybrid lung.
- ItemFunctionalization of Ti-40Nb implant material with strontium by reactive sputtering(London : BioMed Central, 2017-10-10) Gƶttlicher, Markus; Rohnke, Marcus; Moryson, Yannik; Thomas, JĆ¼rgen; Sann, Joachim; Lode, Anja; Schumacher, Matthias; Schmidt, Romy; Pilz, Stefan; Gebert, Annett; Gemming, Thomas; Janek, JĆ¼rgenBackground: Surface functionalization of orthopedic implants with pharmaceutically active agents is a modern approach to enhance osseointegration in systemically altered bone. A local release of strontium, a verified bone building therapeutic agent, at the fracture site would diminish side effects, which could occur otherwise by oral administration. Strontium surface functionalization of specially designed titanium-niobium (Ti-40Nb) implant alloy would provide an advanced implant system that is mechanically adapted to altered bone with the ability to stimulate bone formation. Methods: Strontium-containing coatings were prepared by reactive sputtering of strontium chloride (SrCl2) in a self-constructed capacitively coupled radio frequency (RF) plasma reactor. Film morphology, structure and composition were investigated by scanning electron microscopy (SEM), time of flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS). High-resolution transmission electron microscopy (HR-TEM) was used for the investigation of thickness and growth direction of the product layer. TEM lamellae were prepared using the focused ion beam (FIB) technique. Bioactivity of the surface coatings was tested by cultivation of primary human osteoblasts and subsequent analysis of cell morphology, viability, proliferation and differentiation. The results are correlated with the amount of strontium that is released from the coating in biomedical buffer solution, quantified by inductively coupled plasma mass spectrometry (ICP-MS). Results: Dense coatings, consisting of SrOxCly, of more than 100 nm thickness and columnar structure, were prepared. TEM images of cross sections clearly show an incoherent but well-structured interface between coating and substrate without any cracks. Sr2+ is released from the SrOxCly coating into physiological solution as proven by ICP-MS analysis. Cell culture studies showed excellent biocompatibility of the functionalized alloy. Conclusions: Ti-40Nb alloy, a potential orthopedic implant material for osteoporosis patients, could be successfully plasma coated with a dense SrOxCly film. The material performed well in in vitro tests. Nevertheless, the Sr2+ release must be optimized in future work to meet the requirements of an effective drug delivery system.
- ItemThermo-responsive cell culture carrier: Effects on macrophage functionality and detachment efficiency(London : Sage, 2017) Rennert, Knut; Nitschke, Mirko; Wallert, Maria; Keune, Natalie; Raasch, Martin; Lorkowski, Stefan; Mosig, Alexander S.Harvesting cultivated macrophages for tissue engineering purposes by enzymatic digestion of cell adhesion molecules can potentially result in unintended activation, altered function, or behavior of these cells. Thermo-responsive polymer is a promising tool that allows for gentle macrophage detachment without artificial activation prior to subculture within engineered tissue constructs. We therefore characterized different species of thermo-responsive polymers for their suitability as cell substrate and to mediate gentle macrophage detachment by temperature shift. Primary human monocyte- and THP-1-derived macrophages were cultured on thermo-responsive polymers and characterized for phagocytosis and cytokine secretion in response to lipopolysaccharide stimulation. We found that both cell types differentially respond in dependence of culture and stimulation on thermo-responsive polymers. In contrast to THP-1 macrophages, primary monocyteāderived macrophages showed no signs of impaired viability, artificial activation, or altered functionality due to culture on thermo-responsive polymers compared to conventional cell culture. Our study demonstrates that along with commercially available UpCell carriers, two other thermo-responsive polymers based on poly(vinyl methyl ether) blends are attractive candidates for differentiation and gentle detachment of primary monocyteāderived macrophages. In summary, we observed similar functionality and viability of primary monocyteāderived macrophages cultured on thermo-responsive polymers compared to standard cell culture surfaces. While this first generation of custom-made thermo-responsive polymers does not yet outperform standard culture approaches, our results are very promising and provide the basis for exploiting the unique advantages offered by custom-made thermo-responsive polymers to further improve macrophage culture and recovery in the future, including the covalent binding of signaling molecules and the reduction of centrifugation and washing steps. Optimizing these and other benefits of thermo-responsive polymers could greatly improve the culture of macrophages for tissue engineering applications.
- ItemDecreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress(Washington, DC : Soc., 2019) Liu, Boqun; Hasrat, Zarief; Poolman, Bert; Boersma, Arnold J.; Mullineaux, Conrad W.Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that the diffusion of green fluorescent protein (GFP) in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with fluorescence resonance energy transfer (FRET)-based sensors. We apply an osmotic upshift and find that after an initial increase, the apparent crowding decreases over the course of hours to arrive at a value lower than that before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation, and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and it could apply to other species or conditions as well.IMPORTANCE Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.
- ItemThe synergistic effect of chlorotoxin-mApoE in boosting drug-loaded liposomes across the BBB(London : BioMed Central, 2019) Formicola, Beatrice; Dal, Magro, Roberta; Montefusco-Pereira, Carlos V.; Lehr, ClausāMichael; Koch, Marcus; Russo, Laura; Grasso, Gianvito; Deriu, Marco A.; Danani, Andrea; Bourdoulous, Sandrine; Re, FrancescaWe designed liposomes dually functionalized with ApoE-derived peptide (mApoE) and chlorotoxin (ClTx) to improve their blood-brain barrier (BBB) crossing. Our results demonstrated the synergistic activity of ClTx-mApoE in boosting doxorubicin-loaded liposomes across the BBB, keeping the anti-tumour activity of the drug loaded: mApoE acts promoting cellular uptake, while ClTx promotes exocytosis of liposomes. Ā© 2019 The Author(s).