BKM-react, an integrated biochemical reaction database

<p>Abstract</p> <p>Background</p> <p>The systematic, complete and correct reconstruction of genome-scale metabolic networks or metabolic pathways is one of the most challenging tasks in systems biology research. An essential requirement is the access to the complete biochemical knowledge - especially on the biochemical reactions. This knowledge is extracted from the scientific literature and collected in biological databases. Since the available databases differ in the number of biochemical reactions and the annotation of the reactions, an integrated knowledge resource would be of great value.</p> <p>Results</p> <p>We developed a comprehensive non-redundant reaction database containing known enzyme-catalyzed and spontaneous reactions. Currently, it comprises 18,172 unique biochemical reactions. As source databases the biochemical databases <it>BRENDA</it>, <it>KEGG</it>, and <it>MetaCyc </it>were used. Reactions of these databases were matched and integrated by aligning substrates and products. For the latter a two-step comparison using their structures (<it>via InChIs</it>) and names was performed. Each biochemical reaction given as a reaction equation occurring in at least one of the databases was included.</p> <p>Conclusions</p> <p>An integrated non-redundant reaction database has been developed and is made available to users. The database can significantly facilitate and accelerate the construction of accurate biochemical models.</p

Flexibilisierung von Studiengängen : Lernen im Zwischenraum von formellen und informellen Kontexten

Die School of Management and Law der ZHAW transformiert derzeit einen ganzen Studiengang in ein flexibilisiertes Lernformat. Die Studienform FLEX sieht vor, dass der Präsenzunterricht vor Ort um die Hälfte reduziert und durch dreiwöchige Online-Phasen ersetzt wird. Damit entsteht ein neuer Lernraum, der das formelle Lernen in informellen Kontexten stärkt. Der vorliegende Bericht beschreibt, wie die Transformation des Studienganges über alle 34 Module vollzogen und wie das Spannungsfeld zwischen informellen und formellen Kontext gestaltet wird

Microbial community and inorganic fluid analysis during CO2 storage within the frame of CO2SINK–Long-term experiments under in situ conditions

AbstractMicroorganisms play an important role in the transformation of material within the earth’s crust. The storage of CO2 could affect the composition of inorganic and organic components in the reservoir, consequently influencing microbial activities. To study the microbial induced processes together with geochemical, petrophysical and mineralogical changes, occurring during CO2 storage, long-term laboratory experiments under simulated reservoir P-T conditions were carried out. Clean inner core sections, obtained from the reservoir region at the CO2 storage site in Ketzin (Germany) from a depth of about 650 m, were incubated in high pressure vessels together with sterile synthetic formation brine under in situ P-T conditions of 5.5 MPa and 40 °C. A 16S rDNA based fingerprinting method was used to identify the dominant species in DNA extracts of pristine sandstone samples. Members of the α- and β-subdivisions of Proteobacteria and the Actinobacteria were identified. So far sequences belonging to facultative anaerobic, chemoheterotrophic bacteria (Burkholderia fungorum, Agrobacterium tumefaciens) gaining their energy from the oxidation of organic molecules and a genus also capable of chemolithoautotrophic growth (Hydrogenophaga) was identified.During CO2 incubation minor changes in the microbial community composition were observed. The majority of microbes were able to adapt to the changed conditions. During CO2 exposure increased concentrations of Ca2+, K+, Mg2+ and SO42− were observed. Partially, concentration rises are (i) due to equilibration between rock pore water and synthetic brine, and (ii) between rock and brine, and are thus independent on CO2 exposure. However, observed concentrations of Ca2+, K+, Mg2+ are even higher than in the original reservoir fluid and therefore indicate mineral dissolution due to CO2 exposure

Learning novel skills from iconic gestures : a developmental and evolutionary perspective

This research was supported by Horizon 2020 European Research Council Grant Nos. 609819 and 749229.Cumulative cultural learning has been argued to rely on high fidelity copying of others’ actions. Iconic gestures of actions have no physical effect on objects in the world but merely represent actions that would have an effect. Learning from iconic gestures thus requires paying close attention to the teacher’s precise bodily movements – a prerequisite for high fidelity copying. Three studies investigated whether 2- and 3-year-old children (N=122) and great apes (N=36) learn novel skills from iconic gestures. When faced with a novel apparatus, participants either watched an experimenter perform an iconic gesture depicting the action necessary to open the apparatus or a gesture depicting a different action. Children, but not great apes, profited from iconic gestures, with older children doing so to a larger extent. These results suggest that high fidelity copying abilities are firmly in place in humans by at least three years of age.PostprintPeer reviewe