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- ItemAn extended hybrid input-output model applied to fossil- and bio-based plastics(Amsterdam [u.a.] : Elsevier, 2021) Jander, WiebkeMatrix augmentation method is developed further and described transparently for enabling more specific input-output analyses of bio- vs. fossil-based sectors. A number of economic and environmental effects of substitution can be estimated, compared, and managed. While the model was applied for the first time to the German plastics industry, it can be well integrated into existing bioeconomy monitorings to represent substitution in sectors and countries. • Original matrix augmentation method is described in much detail for the first time considering available data for bio- and fossil-based industries. • Particular attention is paid to balancing cost and benefit in model building so that indicators can be integrated in a continuous monitoring of the bioeconomy. Hence, industry data is prefered to process data whenever possible. • Input structures of bio-based imports are considered in single-region input-output analysis.
- ItemRevealing the Chemical Composition of Birch Pollen Grains by Raman Spectroscopic Imaging(Basel : Molecular Diversity Preservation International (MDPI), 2022) Stiebing, Clara; Post, Nele; Schindler, Claudia; Göhrig, Bianca; Lux, Harald; Popp, Jürgen; Heutelbeck, Astrid; Schie, Iwan W.The investigation of the biochemical composition of pollen grains is of the utmost interest for several environmental aspects, such as their allergenic potential and their changes in growth conditions due to climatic factors. In order to fully understand the composition of pollen grains, not only is an in-depth analysis of their molecular components necessary but also spatial information of, e.g., the thickness of the outer shell, should be recorded. However, there is a lack of studies using molecular imaging methods for a spatially resolved biochemical composition on a single-grain level. In this study, Raman spectroscopy was implemented as an analytical tool to investigate birch pollen by imaging single pollen grains and analyzing their spectral profiles. The imaging modality allowed us to reveal the layered structure of pollen grains based on the biochemical information of the recorded Raman spectra. Seven different birch pollen species collected at two different locations in Germany were investigated and compared. Using chemometric algorithms such as hierarchical cluster analysis and multiple-curve resolution, several components of the grain wall, such as sporopollenin, as well as the inner core presenting high starch concentrations, were identified and quantified. Differences in the concentrations of, e.g., sporopollenin, lipids and proteins in the pollen species at the two different collection sites were found, and are discussed in connection with germination and other growth processes.
- ItemConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design(Basel : MDPI, 2022) Collatz, Maximilian; Braun, Sascha D.; Monecke, Stefan; Ehricht, RalfBackground: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated. Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays. Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.
- ItemParticulate Matter Dispersion Modeling in Agricultural Applications: Investigation of a Transient Open Source Solver(Basel : MDPI, 2021) Janke, David; Swaminathan, Senthilathiban; Hempel, Sabrina; Kasper, Robert; Amon, ThomasAgriculture is a major emitter of particulate matter (PM), which causes health problems and can act as a carrier of the pathogen material that spreads diseases. The aim of this study was to investigate an open-source solver that simulates the transport and dispersion of PM for typical agricultural applications. We investigated a coupled Eulerian–Lagrangian solver within the open source software package OpenFOAM. The continuous phase was solved using transient large eddy simulations, where four different subgrid-scale turbulence models and an inflow turbulence generator were tested. The discrete phase was simulated using two different Lagrangian solvers. For the validation case of a turbulent flow of a street canyon, the flowfield could be recaptured very well, with errors of around 5% for the non-equilibrium turbulence models (WALE and dynamicKeq) in the main regions. The inflow turbulence generator could create a stable and accurate boundary layer for the mean vertical velocity and vertical profile of the turbulent Reynolds stresses R11. The validation of the Lagrangian solver showed mixed results, with partly good agreements (simulation results within the measurement uncertainty), and partly high deviations of up to 80% for the concentration of particles. The higher deviations were attributed to an insufficient turbulence regime of the used validation case, which was an experimental chamber. For the simulation case of PM dispersion from manure application on a field, the solver could capture the influence of features such as size and density on the dispersion. The investigated solver is especially useful for further investigations into time-dependent processes in the near-source area of PM sources.
- ItemThe Effect of Diet and Farm Management on N2O Emissions from Dairy Farms Estimated from Farm Data(Basel : MDPI, 2021) Menardo, Simona; Lanza, Giacomo; Berg, WernerThe N2O emissions of 21 dairy farms in Germany were evaluated to determine the feasi-bility of an estimation of emissions from farm data and the effects of the farm management, along with possible mitigation strategies. Emissions due to the application of different fertilisers, manure storage and grazing were calculated based on equations from the IPCC (Intergovernmental Panel of Climate Change) and German emission inventory. The dependence of the N2O emissions on fertiliser type and quantity, cultivated crops and diet composition was assessed via correlation analysis and linear regression. The N2O emissions ranged between 0.11 and 0.29 kg CO2eq per kilogram energy-corrected milk, with on average 60% resulting from fertilisation and less than 30% from fertiliser storage and field applications. The total emissions had a high dependence on the diet composition; in particular, on the grass/maize ratio and the protein content of the animal diet, as well as from the manure management. A linear model for the prediction of the N2O emissions based on the diet composition and the fertilisation reached a predictive power of R2 = 0.89. As a possible mitigation strategy, the substitution of slurry for solid manure would reduce N2O emissions by 40%. Feeding cows maize-based diets instead of grass-based diets could reduce them by 14%. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemDNA-Biofunctionalization of CTAC-Capped Gold Nanocubes(Basel : MDPI, 2020) Slesiona, Nicole; Thamm, Sophie; Stolle, H. Lisa K.S.; Weißenborn, Viktor; Müller, Philipp; Csáki, Andrea; Fritzsche, WolfgangClinical diagnostics and disease control are fields that strongly depend on technologies for rapid, sensitive, and selective detection of biological or chemical analytes. Nanoparticles have become an integral part in various biomedical detection devices and nanotherapeutics. An increasing focus is laid on gold nanoparticles as they express less cytotoxicity, high stability, and hold unique optical properties with the ability of signal transduction of biological recognition events with enhanced analytical performance. Strong electromagnetic field enhancements can be found in close proximity to the nanoparticle that can be exploited to enhance signals for e.g., metal-enhanced fluorescence or Raman spectroscopy. Even stronger field enhancements can be achieved with sharp-edged nanoparticles, which are synthesized with the help of facet blocking agents, such as cetyltrimethylammonium bromide/chloride (CTAB/CTAC). However, chemical modification of the nanoparticle surface is necessary to reduce the particle’s cytotoxicity, stabilize it against aggregation, and to bioconjugate it with biomolecules to increase its biocompatibility and/or specificity for analytical applications. Here, a reliable two-step protocol following a ligand exchange with bis (p-sulfonatophenyl) phenyl phosphine (BSPP) as the intermediate capping-agent is demonstrated, which results in the reliable biofunctionalization of CTAC-capped gold nanocubes with thiol-modified DNA. The functionalized nanocubes have been characterized regarding their electric potential, plasmonic properties, and stability against high concentrations of NaCl and MgCl2.
- ItemTime Optimization of Seed-Mediated Gold Nanotriangle Synthesis Based on Kinetic Studies(Basel : MDPI, 2021) Podlesnaia, Ekaterina; Csáki, Andrea; Fritzsche, WolfgangThe synthesis of shape-anisotropic plasmonic nanoparticles such as gold nanotriangles is of increasing interest. These particles have a high potential for applications due to their notable optical properties. A key challenge of the synthesis is usually the low reproducibility. Even the optimized seed-based methods often lack in the synthesis yield or are labor- and time-consuming. In this work, a seed-mediated synthesis with high reproducibility is replicated in order to determine the necessary reaction time for each step. Online monitoring of the reaction mixtures by UV–VIS spectroscopy is used as a powerful tool to track the evolution of the synthesis. The kinetics of the individual stages is elucidated by real-time investigations. As a consequence, the complete synthesis could be optimized and can now be realized in a single day instead of three without any loss in the resulting sample quality.
- ItemSurface-Enhanced Raman Spectroscopy to Characterize Different Fractions of Extracellular Vesicles from Control and Prostate Cancer Patients(Basel : MDPI, 2021) Osei, Eric Boateng; Paniushkina, Liliia; Wilhelm, Konrad; Popp, Jürgen; Nazarenko, Irina; Krafft, ChristophExtracellular vesicles (EVs) are membrane-enclosed structures ranging in size from about 60 to 800 nm that are released by the cells into the extracellular space; they have attracted interest as easily available biomarkers for cancer diagnostics. In this study, EVs from plasma of control and prostate cancer patients were fractionated by differential centrifugation at 5000× g, 12,000× g and 120,000× g. The remaining supernatants were purified by ultrafiltration to produce EV-depleted free-circulating (fc) fractions. Spontaneous Raman and surface-enhanced Raman spectroscopy (SERS) at 785 nm excitation using silver nanoparticles (AgNPs) were employed as label-free techniques to collect fingerprint spectra and identify the fractions that best discriminate between control and cancer patients. SERS spectra from 10 µL droplets showed an enhanced Raman signature of EV-enriched fractions that were much more intense for cancer patients than controls. The Raman spectra of dehydrated pellets of EV-enriched fractions without AgNPs were dominated by spectral contributions of proteins and showed variations in S-S stretch, tryptophan and protein secondary structure bands between control and cancer fractions. We conclude that the AgNPs-mediated SERS effect strongly enhances Raman bands in EV-enriched fractions, and the fractions, EV12 and EV120 provide the best separation of cancer and control patients by Raman and SERS spectra.
- ItemMulti-Product Lactic Acid Bacteria Fermentations: A Review(Basel : MDPI AG, 2020) Mora-Villalobos, JosĂ© AnĂbal; Montero-Zamora, JĂ©ssica; Barboza, Natalia; Rojas-Garbanzo, Carolina; Usaga, Jessie; Redondo-Solano, Mauricio; Schroedter, Linda; Olszewska-Widdrat, Agata; LĂłpez-GĂłmez, JosĂ© PabloIndustrial biotechnology is a continuously expanding field focused on the application of microorganisms to produce chemicals using renewable sources as substrates. Currently, an increasing interest in new versatile processes, able to utilize a variety of substrates to obtain diverse products, can be observed. A robust microbial strain is critical in the creation of such processes. Lactic acid bacteria (LAB) are used to produce a wide variety of chemicals with high commercial interest. Lactic acid (LA) is the most predominant industrial product obtained from LAB fermentations, and its production is forecasted to rise as the result of the increasing demand of polylactic acid. Hence, the creation of new ways to revalorize LA production processes is of high interest and could further enhance its economic value. Therefore, this review explores some co-products of LA fermentations, derived from LAB, with special focus on bacteriocins, lipoteichoic acid, and probiotics. Finally, a multi-product process involving LA and the other compounds of interest is proposed.
- ItemEstablishment of a Laboratory Scale Set-Up with Controlled Temperature and High Humidity to Investigate Dry Matter Losses of Wood Chips from Poplar during Storage(Basel : MDPI, 2022) Hernandez-Estrada, Albert; Pecenka, Ralf; Dumfort, Sabrina; Ascher-Jenull, Judith; Lenz, Hannes; Idler, Christine; Hoffmann, ThomasThe aim of this work was to improve the understanding of dry matter losses (DML) that occur in wood chips during the initial phase of storage in outdoor piles. For this purpose, a laboratory scale storage chamber was developed and investigated regarding its ability to recreate the conditions that chips undergo during the initial phase of outdoor storage. Three trials with poplar Max-4 (Populus maximowiczii Henry Populus nigra L.) chips were performed for 6–10 weeks in the storage chamber under controlled temperature and assisted humidity. Two different setups were investigated to maintain a high relative humidity (RH) inside the storage chamber; one using water containers, and one assisted with a humidifier. Moisture content (MC) and DML of the chips were measured at different storage times to evaluate their storage behaviour in the chamber. Additionally, microbiological analyses of the culturable fraction of saproxylic microbiota were performed, with a focus on mesophilic fungi, but discriminating also xerophilic fungi, and mesophilic bacteria, with focus on actinobacteria, in two trials, to gain a view on the poplar wood chip-inhabiting microorganisms as a function of storage conditions (moisture, temperature) and time. Results show that DML up to 8.8–13.7% occurred in the chips within 6–10 storage weeks. The maximum DML were reached in the trial using the humidifier, which seemed a suitable technique to keep a high RH in the testing chamber, and thus, to analyse the wood chips in conditions comparable to those in outdoor piles during the initial storage phase.