Prediction of β-barrel membrane proteins by searching for restricted domains

BACKGROUND: The identification of beta-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses. RESULTS: For the prediction of beta-barrel membrane proteins within prokaryotic proteomes a set of parameters was developed. We have focused on a procedure with a low false positive rate beside a procedure with lowest false prediction rate to obtain a high certainty for the predicted sequences. We demonstrate that the discrimination between beta-barrel membrane proteins and other proteins is improved by analyzing a length limited region. The developed set of parameters is applied to the proteome of E. coli and the results are compared to four other described procedures. CONCLUSION: Analyzing the beta-barrel membrane proteins revealed the presence of a defined membrane inserted beta-barrel region. This information can now be used to refine other prediction programs as well. So far, all tested programs fail to predict outer membrane proteins in the proteome of the prokaryote E. coli with high reliability. However, the reliability of the prediction is improved significantly by a combinatory approach of several programs. The consequences and usability of the developed scores are discussed

Optimization of the geometric dimensions of vertical electrolyzers with gas-generating electrodes

A study is made to determine whether, under the conditions of electrolyte circulation induced by evolved gases, it is possible to increase the vertical scale without a great increase in cell voltage. The mathematical modeling used is discussed, and a comparison is made with experimental results and conclusions. It is found that it is possible to increase the vertical scale without producing a cell voltage increase

Concerning the electrosynthesis of hydrogen peroxide and peroxodisulfates. Section 2: Optimization of electrolysis cells using an electrolyzer for peroxodisulfuric acid as an example

The model is presented of an electrolyzer for peroxodisulfuric acid, and it is analyzed mathematically. Its application for engineering and economic optimization is investigated in detail. The mathematical analysis leads to conclusions concerning the change in position of the optimum with respect to the various target functions due to changes of the individual design-caused and economic parameters

Der Weg zum grünen Kraftwerk : oder: Wie ein Kamel durch ein Nadelöhr passt

Wer hat nicht angesichts rauchender Schlote und verschmutzter Luft von Kraftwerken geträumt, die reinen Sauerstoff produzieren? Die Natur erbaut solche Kraftwerke täglich neu – in Pflanzen. Darin verwandelt der grüne Blattfarbstoff Chlorophyll Sonnenlicht und Kohlendioxid in Sauerstoff und Energie. Die komplexen Reaktionen laufen in mikroskopisch kleinen Maschinen – den Photosystemen – ab. Aber was haben Kraftwerke mit Kamelen zu tun? Wie auch bei den uns bekannten Kraftwerken gibt es in Pflanzen ein »Werksgelände«, die Chloroplasten. Sie besitzen einen Eingang, durch den zuweilen Moleküle passieren müssen, die so groß sind wie das sprichwörtliche Kamel, das durch ein Nadelöhr gehen soll

Mechanistic Approach to Understand Crop Salt Tolerance under Brackish Irrigation

The build-up of lateral salinity gradients around roots irrigated with brackish waters in conjunction with root traits is considered as an important link to understand crop salt tolerance

Mooncakes and Marshmallows

Hannah Jones awoke on the morning of her first day of school in a cold sweat. All summer she had dreamed the same dream. It was about her first day of 10th grade, her first day of high school. Her dream first day was fine. Nothing went wrong. It was a normal first day. Normal day. Normal Dream. Normal Hannah. But then why djd it freak her out

Conceptual approach to lateral salinity gradients around roots of salt-sensitive and salt-tolerant crops under irrigation conditions

Under controlled crop irrigation with brackish water, a vertical soil salinity gradient develops in the rooted soil layer. Furthermore, in periods of soil water depletion, due to ion exclusion by roots, a transpiration-driven, lateral build-up of a salinity gradient between the soil fraction adjacent to roots and distant, occurs. Root morphological traits determine the volume of the soil fraction, in which salt accumulation occurs (rhizospheric soil volume). The increase of soil salinity near roots is greater, when plant roots form a small rhizospheric soil volume (e.g. leek). When roots form a larger rhizospheric soil volume, salts are distributed throughout a larger soil volume, which improves conditions for root water uptake and crop salt tolerance (e.g. rape)

Modeling and technical use of gas evolving electrodes. Part 2: Modeling of gas-evolving electrolyzers with free electrolyte circulation

In an electrochemical reactor with gas-evolving electrodes, the transporting action of the gas bubbles can be used to move the electrolyte in a cycle flow, when the structure of the flow channels is suitable. For an electrolysis cell with such a circulation system a mathematic model was set up and evaluated. It is shown that in this manner, a rapid flow through the electrode gap can be achieved without additional energy consumption, in addition to a low gas fraction and a low cell voltage. The cell voltage and the attainable cycle spread are investigated as a function of the geometric parameters for their optimum values

Phosphorylation regulates the assembly of chloroplast import machinery

Chloroplast function depends on the translocation of cytosolically synthesized precursor proteins into the organelle. The recognition and transfer of most precursor proteins across the outer membrane depend on a membrane inserted complex. Two receptor components of this complex, Toc34 and Toc159, are GTPases, which can be phosphorylated by kinases present in the hosting membrane. However, the physiological function of phosphorylation is not yet understood in detail. It is demonstrated that both receptors are phosphorylated within their G-domains. In vitro, the phosphorylation of Toc34 disrupts both homo- and heterodimerization of the G-domains as determined using a phospho-mimicking mutant. In endogenous membranes this mutation or phosphorylation of the wild-type receptor disturbs the association of Toc34, but not of Toc159 with the translocation pore. Therefore, phosphorylation serves as an inhibitor for the association of Toc34 with other components of the complex and phosphorylation can now be discussed as a mechanism to exchange different isoforms of Toc34 within this ensemble