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- ItemDNA and RNA extraction and quantitative real-time PCR-based assays for biogas biocenoses in an interlaboratory comparison(Basel : MDPI, 2016) Lebuhn, Michael; Derenkó, Jaqueline; Rademacher, Antje; Helbig, Susanne; Munk, Bernhard; Pechtl, Alexander; Stolze, Yvonne; Prowe, Steffen; Schwarz, Wolfgang H.; Schlüter, Andreas; Liebl, Wolfgang; Klocke, MichaelFive 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.
- ItemSwitchable Adhesion Surfaces with Enhanced Performance Against Rough Counterfaces(Basel : MDPI, 2016) Prieto-López, Lizbeth; Williams, JohnIn 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.
- ItemA Review on Passive and Integrated Near-Field Microwave Biosensors(Basel : MDPI, 2017) Guha, Subhajit; Jamal, Farabi Ibne; Wenger, ChristianIn 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.
- ItemMechanically reinforced catechol-containing hydrogels with improved tissue gluing performance(Basel : MDPI, 2017) Feng, Jun; Ton, Xuan-Anh; Zhao, Shifang; Paez, Julieta I.; del Campo, AránzazuIn situ forming hydrogels with catechol groups as tissue reactive functionalities are interesting bioinspired materials for tissue adhesion. Poly(ethylene glycol) (PEG)–catechol tissue glues have been intensively investigated for this purpose. Different cross-linking mechanisms (oxidative or metal complexation) and cross-linking conditions (pH, oxidant concentration, etc.) have been studied in order to optimize the curing kinetics and final cross-linking degree of the system. However, reported systems still show limited mechanical stability, as expected from a PEG network, and this fact limits their potential application to load bearing tissues. Here, we describe mechanically reinforced PEG–catechol adhesives showing excellent and tunable cohesive properties and adhesive performance to tissue in the presence of blood. We used collagen/PEG mixtures, eventually filled with hydroxyapatite nanoparticles. The composite hydrogels show far better mechanical performance than the individual components. It is noteworthy that the adhesion strength measured on skin covered with blood was >40 kPa, largely surpassing (>6 fold) the performance of cyanoacrylate, fibrin, and PEG–catechol systems. Moreover, the mechanical and interfacial properties could be easily tuned by slight changes in the composition of the glue to adapt them to the particular properties of the tissue. The reported adhesive compositions can tune and improve cohesive and adhesive properties of PEG–catechol-based tissue glues for load-bearing surgery applications.
- ItemThe role of bioenergy in enhancing energy, food and ecosystem sustainability based on societal perceptions and preferences in Asia(Basel : MDPI, 2016) Acosta, Lilibeth A.; Magcale-Macandog, Damasa B.; Kavi Kumar, K.S.; Cui, Xuefeng; Eugenio, Elena A.; Macandog, Paula Beatrice M.; Salvacion, Arnold R.; Eugenio, Jemimah Mae A.This paper discussed the analysis of the survey on sustainability of bioenergy conducted in the Philippines, India and China. It acquired general perceptions of the people by asking them (a) specific questions about their level of familiarity with bioenergy; (b) relationship of their work to bioenergy; and (c) their opinion on contribution of various feedstock on the economy and impact of bioenergy production on food security. In addition to these questions, we estimated preference weights of various feedstock based on the conjoint choices on bioenergy’s contribution to social stability, social welfare and ecological balance. The estimates revealed significant trade-offs not only among these three dimensions of sustainability but also the relative importance of energy security, food security and ecosystem capacity to other economic, social and environmental objectives. The types of first generation feedstock that are currently used for biofuel production in the respective countries and those that offer alternative household use are perceived as important to the economy and preferred bioenergy feedstock. Based on the results of the study, the preferred role of bioenergy for sustainable development reflects the social and economic concerns in the respective Asian countries, e.g., energy security in China, food security in India, and ecosystem degradation in the Philippines.
- ItemAre Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic Cosolvents?(Basel : MDPI, 2017) Markel, Ulrich; Zhu, Leilei; Frauenkron-Machedjou, Victorine; Zhao, Jing; Bocola, Marco; Davari, Mehdi; Jaeger, Karl-Erich; Schwaneberg, UlrichDespite the significant advances in the field of protein engineering, general design principles to improve organic cosolvent resistance of enzymes still remain undiscovered. Previous studies drew conclusions to engineer enzymes for their use in water-miscible organic solvents based on few amino acid substitutions. In this study, we conduct a comparison of a Bacillus subtilis lipase A (BSLA) library—covering the full natural diversity of single amino acid substitutions at all 181 positions of BSLA—with three state of the art random mutagenesis methods: error-prone PCR (epPCR) with low and high mutagenesis frequency (epPCR-low and high) as well as a transversion-enriched Sequence Saturation Mutagenesis (SeSaM-Tv P/P) method. Libraries were searched for amino acid substitutions that increase the enzyme’s resistance to the water-miscible organic cosolvents 1,4-dioxane (DOX), 2,2,2-trifluoroethanol (TFE), and dimethyl sulfoxide (DMSO). Our analysis revealed that 5%–11% of all possible single substitutions (BSLA site-saturation mutagenesis (SSM) library) contribute to improved cosolvent resistance. However, only a fraction of these substitutions (7%–12%) could be detected in the three random mutagenesis libraries. To our knowledge, this is the first study that quantifies the capability of these diversity generation methods generally employed in directed evolution campaigns and compares them to the entire natural diversity with a single substitution. Additionally, the investigation of the BSLA SSM library revealed only few common beneficial substitutions for all three cosolvents as well as the importance of introducing surface charges for organic cosolvent resistance—most likely due to a stronger attraction of water molecules. © 2017 by the authors.
- ItemCatalytic Performance of Lanthanum Vanadate Catalysts in Ammoxidation of 2-Methylpyrazine(Basel : MDPI, 2016) Kalevaru, Venkata; Dhachapally, Naresh; Martin, AndreasThe influence of reaction conditions on the catalytic performance of lanthanum vanadate (La0.1V0.9Ox) catalyst in the ammoxidation of 2-methylpyrazine (MP) to 2-cyanopyarazine (CP) has been investigated. This novel catalytic material exhibited remarkably good performance with very high space-time-yields (STY) of CP. The reaction parameters such as the effect of temperature, gas hourly space velocity (GHSV) and all other reaction variables (e.g., NH3, air, and MP feed rates) on the catalytic performance were explored and optimized. For example, an increase in MP feed rate from 2 to >16 mmol/h led to decreased conversion of MP but increased the STY of CP significantly. Optimal performance was achieved when the reaction temperature was 420 °C and the molar ratio of 2-MP, ammonia, air, H2O and N2 in the feed gas was set to 1:7:26:13:22. Under these optimal reaction conditions, the catalyst showed a MP conversion of ~100%, CP selectivity of 86%, and STY of >500 gCP/(kgcat∙h). On the other hand, the formation of pyrazine (Py) as a by-product was found to be high when the NH3:MP ratio was lower at increased contact time. This suggests possible differences in the reaction mechanism pathways with respect to feed composition over La0.1V0.9Ox catalysts.
- ItemBimetallic Catalysts Containing Gold and Palladium for Environmentally Important Reactions(Basel : MDPI, 2016) Alshammari, Ahmad; Kalevaru, Venkata Narayana; Martin, AndreasSupported bimetallic nanoparticles (SBN) are extensively used as efficient redox catalysts. This kind of catalysis particularly using SBN has attracted immense research interest compared to their parent metals due to their unique physico-chemical properties. The primary objective of this contribution is to provide comprehensive overview about SBN and their application as promising catalysts. The present review contains four sections in total. Section 1 starts with a general introduction, recent progress, and brief summary of the application of SBN as promising catalysts for different applications. Section 2 reviews the preparation and characterization methods of SBN for a wide range of catalytic reactions. Section 3 concentrates on our own results related to the application of SBN in heterogeneous catalysis. In this section, the oxidation of cyclohexane to adipic acid (an eco-friendly and novel approach) will be discussed. In addition, the application of bimetallic Pd catalysts for vapor phase toluene acetoxylation in a fixed bed reactor will also be highlighted. Acetoxylation of toluene to benzyl acetate is another green route to synthesize benzyl acetate in one step. Finally, Section 4 describes the summary of the main points and also presents an outlook on the application of SBN as promising catalysts for the production of valuable products.
- ItemClimate change in Afghanistan deduced from reanalysis and coordinated regional climate downscaling experiment (CORDEX)-South Asia simulations(Basel : MDPI, 2017) Aich, Valentin; Akhundzadah, Noor Ahmad; Knuerr, Alec; Khoshbeen, Ahmad Jamshed; Hattermann, Fred; Paeth, Heiko; Scanlon, Andrew; Paton, Eva NoraPast and the projected future climate change in Afghanistan has been analyzed systematically and differentiated with respect to its different climate regions to gain some first quantitative insights into Afghanistan’s vulnerability to ongoing and future climate changes. For this purpose, temperature, precipitation and five additional climate indices for extremes and agriculture assessments (heavy precipitation; spring precipitation; growing season length (GSL), the Heat Wave Magnitude Index (HWMI); and the Standardized Precipitation Evapotranspiration Index (SPEI)) from the reanalysis data were examined for their consistency to identify changes in the past (data since 1950). For future changes (up to the year 2100), the same parameters were extracted from an ensemble of 12 downscaled regional climate models (RCM) of the Coordinated Regional Climate Downscaling Experiment (CORDEX)-South Asia simulations for low and high emission scenarios (Representative Concentration Pathways 4.5 and 8.5). In the past, the climatic changes were mainly characterized by a mean temperature increase above global level of 1.8 °C from 1950 to 2010; uncertainty with regard to reanalyzed rainfall data limited a thorough analysis of past changes. Climate models projected the temperature trend to accelerate in the future, depending strongly on the global carbon emissions (2006–2050 Representative Concentration Pathways 4.5/8.5: 1.7/2.3 °C; 2006–2099: 2.7/6.4 °C, respectively). Despite the high uncertainty with regard to precipitation projections, it became apparent that the increasing evapotranspiration is likely to exacerbate Afghanistan’s already existing water stress, including a very strong increase of frequency and magnitude of heat waves. Overall, the results show that in addition to the already extensive deficiency in adaptation to current climate conditions, the situation will be aggravated in the future, particularly in regard to water management and agriculture. Thus, the results of this study underline the importance of adequate adaptation to climate change in Afghanistan. This is even truer taking into account that GSL is projected to increase substantially by around 20 days on average until 2050, which might open the opportunity for extended agricultural husbandry or even additional harvests when water resources are properly managed.
- ItemCHASE-PL—Future Hydrology Data Set: Projections of Water Balance and Streamflow for the Vistula and Odra Basins, Poland(Basel : MDPI, 2017) Piniewski, Mikołaj; Szcześniak, Mateusz; Kardel, IgnacyThere is considerable concern that the water resources of Central and Eastern Europe region can be adversely affected by climate change. Projections of future water balance and streamflow conditions can be obtained by forcing hydrological models with the output from climate models. In this study, we employed the SWAT hydrological model driven with an ensemble of nine bias-corrected EURO-CORDEX climate simulations to generate future hydrological projections for the Vistula and Odra basins in two future horizons (2024–2050 and 2074–2100) under two Representative Concentration Pathways (RCPs). The data set consists of three parts: (1) model inputs; (2) raw model outputs; (3) aggregated model outputs. The first one allows the users to reproduce the outputs or to create the new ones. The second one contains the simulated time series of 10 variables simulated by SWAT: precipitation, snow melt, potential evapotranspiration, actual evapotranspiration, soil water content, percolation, surface runoff, baseflow, water yield and streamflow. The third one consists of the multi-model ensemble statistics of the relative changes in mean seasonal and annual variables developed in a GIS format. The data set should be of interest of climate impact scientists, water managers and water-sector policy makers. In any case, it should be noted that projections included in this data set are associated with high uncertainties explained in this data descriptor paper.