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Donczew R.,Polish Academy of Sciences | Weigel C.,HTW Berlin University of Applied Sciences | Lurz R.,Max Planck Institute for Molecular Genetics | Zakrzewska-Czerwinska J.,Polish Academy of Sciences | And 2 more authors.
Nucleic Acids Research | Year: 2012

Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affinity. However, no unwinding within the oriC sequence has been detected. Comprehensive in silico analysis presented in this work allowed us to identify an additional region (oriC2), separated from the original one (oriC1) by the dnaA gene. DnaA specifically binds both regions, but DnaA-dependent DNA unwinding occurs only within oriC2. Surprisingly, oriC2 is bound exclusively as supercoiled DNA, which directly shows the importance of the DNA topology in DnaA-oriC interactions, similarly as previously presented only for initiator-origin interactions in Archaea and some Eukaryota. We conclude that H. pylori oriC exhibits bipartite structure, being the first such origin discovered in a Gram-negative bacterium. The H. pylori mode of initiator-oriC interactions, with the loop formation between the subcomplexes of the discontinuous origin, resembles those discovered in Bacillus subtilis chromosome and in many plasmids, which might suggest a similar way of controlling initiation of replication. © 2012 The Author(s).

Carvalho M.,Aragon Institute of Engineering Research | Lozano M.A.,Aragon Institute of Engineering Research | Serra L.M.,Aragon Institute of Engineering Research | Wohlgemuth V.,HTW Berlin University of Applied Sciences
Environmental Modelling and Software | Year: 2012

Integration of thermoeconomics and Life Cycle Analysis was carried out within the framework of an Environmental Management Information System. This combined approach identified where environmental loads were generated and tracked environmental loads throughout the system, allowing for a more precise understanding of operational activities. A trigeneration system was modeled, providing electricity, heat, and cooling to a building. The trigeneration system consists of a cogeneration module, auxiliary boiler, absorption chiller and electrical chiller. The trigeneration system model is flexible, as it allows electricity from/to the electric grid to be purchased/sold, and part of the cogenerated heat to be wasted. Umberto software is specifically designed to analyze the distribution of material and energy resources throughout a productive system. The software is based on Petri networks, double-entry bookkeeping and cost accounting, allowing the setup of complex systems and also a combined material, energy and inventory calculation. An assistant was built to include the tracking of emissions through the application of algebra and rules similar to those used in thermoeconomic analysis. It is possible to evaluate the environmental impact in terms of the consumption of natural resources and generation of emissions in the system, from the input of natural resources to the output of the final products. Network parameters were used to calculate the emissions associated with the operation of the system. The issue of allocating environmental loads was introduced and two scenarios for each operational mode were compared: the trigeneration system vs. a conventional energy supply system in which electricity was produced in a representative coal power plant. In this case the trigeneration system operated with significant reduction of the CO 2 emitted into the atmosphere. © 2011 Elsevier Ltd.

Mutterer J.,French National Center for Scientific Research | Zinck E.,HTW Berlin University of Applied Sciences
Journal of Microscopy | Year: 2013

We created FigureJ a new ImageJ plugin dedicated to scientific article figures preparation. Building a convincing figure is a demanding task that covers different steps ranging from content acquisition to figure assembly in editing software. Notions of image processing are required when it comes to even simple tasks such as cropping or resizing images and assembling them in a single figure. Scientific images are typically well handled in dedicated software but poorly supported in software used for laying out the final version of a figure for submission to review process. © 2013 Royal Microscopical Society.

Waldminghaus T.,University of Oslo | Waldminghaus T.,University of Marburg | Weigel C.,HTW Berlin University of Applied Sciences | Skarstad K.,University of Oslo
Nucleic Acids Research | Year: 2012

In Escherichia coli, the SeqA protein binds specifically to GATC sequences which are methylated on the A of the old strand but not on the new strand. Such hemimethylated DNA is produced by progression of the replication forks and lasts until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemimethylated DNA covered by SeqA follows the replication fork. We show that this is, indeed, the case by using global ChIP on Chip analysis of SeqA in cells synchronized regarding DNA replication. To assess hemimethylation, we developed the first genome-wide method for methylation analysis in bacteria. Since loss of the SeqA protein affects growth rate only during rapid growth when cells contain multiple replication forks, a comparison of rapid and slow growth was performed. In cells with six replication forks per chromosome, the two old forks were found to bind surprisingly little SeqA protein. Cell cycle analysis showed that loss of SeqA from the old forks did not occur at initiation of the new forks, but instead occurs at a time point coinciding with the end of SeqA-dependent origin sequestration. The finding suggests simultaneous origin de-sequestration and loss of SeqA from old replication forks. © The Author(s) 2012. Published by Oxford University Press.

Jung K.,HTW Berlin University of Applied Sciences
IEEE International Conference on Consumer Electronics - Berlin, ICCE-Berlin | Year: 2012

An image classification approach is presented that uses a combination of low-level image features with features obtained from interest point detection. A support vector machine is used for classification. The approach focuses on the recognition of three-dimensional objects captured with the camera of a smartphone under different perspectives. Recognition as well as the training of new objects can be performed by the smartphone within reasonable processing time. © 2012 IEEE.

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