TY - GEN A1 - Hoffmann, Mathias A1 - Schulz-Hanke, Maximilian A1 - Alba, Juana Garcia A1 - Jurisch, Nicole A1 - Hagemann, Ulrike A1 - Sachs, Torsten A1 - Sommer, Michael A1 - Augustin, Jürgen T1 - A simple calculation algorithm to separate high-resolution CH4 flux measurements into ebullition- and diffusion-derived components T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Processes driving the production, transformation and transport of methane (CH4) in wetland ecosystems are highly complex. We present a simple calculation algorithm to separate open-water CH4 fluxes measured with automatic chambers into diffusion- and ebullition-derived components. This helps to reveal underlying dynamics, to identify potential environmental drivers and, thus, to calculate reliable CH4 emission estimates. The flux separation is based on identification of ebullition-related sudden concentration changes during single measurements. Therefore, a variable ebullition filter is applied, using the lower and upper quartile and the interquartile range (IQR). Automation of data processing is achieved by using an established R script, adjusted for the purpose of CH4 flux calculation. The algorithm was validated by performing a laboratory experiment and tested using flux measurement data (July to September 2013) from a former fen grassland site, which converted into a shallow lake as a result of rewetting. Ebullition and diffusion contributed equally (46 and 55 %) to total CH4 emissions, which is comparable to ratios given in the literature. Moreover, the separation algorithm revealed a concealed shift in the diurnal trend of diffusive fluxes throughout the measurement period. The water temperature gradient was identified as one of the major drivers of diffusive CH4 emissions, whereas no significant driver was found in the case of erratic CH4 ebullition events. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 604 KW - water methane emissions KW - chamber system KW - CO2 KW - lake KW - fen KW - exchange KW - mechanism KW - turbulence KW - transport KW - reservior Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416659 SN - 1866-8372 IS - 604 SP - 109 EP - 118 ER - TY - GEN A1 - Riedelsberger, Janin A1 - Dreyer, Ingo A1 - Gonzalez, Wendy T1 - Outward rectification of voltage-gated K+ channels evolved at least twice in life history T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories-hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 521 KW - multiple sequence alignment KW - potassium channel KW - Arabidopsis thaliana KW - inward rectification KW - pacemaker channels KW - S4-S5 linker KW - sensor KW - expression KW - mechanism KW - activation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409594 SN - 1866-8372 IS - 521 ER - TY - GEN A1 - Hess, Anne-Katrin A1 - Saffert, Paul A1 - Liebeton, Klaus A1 - Ignatova, Zoya T1 - Optimization of translation profiles enhances protein expression and solubility T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 518 KW - transfer-RNA genes KW - codon usage KW - Escherichia coli KW - Epoxide hydrolases KW - messenger-RNA KW - sequence KW - elongation KW - Ribosome KW - mechanism KW - Membrane Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409574 SN - 1866-8372 IS - 518 ER -