Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms

Baumbach J, Rahmann S, Tauch A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Systems Biology. 2009;3(1):8.Background: Transcriptional regulation of gene activity is essential for any living organism. Transcription factors therefore recognize specific binding sites within the DNA to regulate the expression of particular target genes. The genome-scale reconstruction of the emerging regulatory networks is important for biotechnology and human medicine but cost-intensive, time-consuming, and impossible to perform for any species separately. By using bioinformatics methods one can partially transfer networks from well-studied model organisms to closely related species. However, the prediction quality is limited by the low level of evolutionary conservation of the transcription factor binding sites, even within organisms of the same genus. Results: Here we present an integrated bioinformatics workflow that assures the reliability of transferred gene regulatory networks. Our approach combines three methods that can be applied on a large-scale: re-assessment of annotated binding sites, subsequent binding site prediction, and homology detection. A gene regulatory interaction is considered to be conserved if (1) the transcription factor, (2) the adjusted binding site, and (3) the target gene are conserved. The power of the approach is demonstrated by transferring gene regulations from the model organism Corynebacterium glutamicum to the human pathogens C. diphtheriae, C. jeikeium, and the biotechnologically relevant C. efficiens. For these three organisms we identified reliable transcriptional regulations for similar to 40% of the common transcription factors, compared to similar to 5% for which knowledge was available before. Conclusion: Our results suggest that trustworthy genome-scale transfer of gene regulatory networks between organisms is feasible in general but still limited by the level of evolutionary conservation

Determination of Benzene, Toluene, and Xylene by means of an ion mobility spectrometer device using photoionization

The continuous monitoring of changes on the quality of ambient air is a field of advantage of ion mobility spectrometry. Benzene, Toluene, and Xylene are substances of special interest because of their toxicity. We present an optimized drift tube for ion mobility spectrometers, which uses photo-ionization tubes to produce the ions to be analyzed. The actual version of this drift tube has a length of 45 mm, an electric field strength established within the drift tube of about 180 V/cm and a shutter-opening-time of 400 mus. With the hydrogen tube used for ionisation a mean flux of 10(exp 12) photons/sq cm s was established for the experiments described. We discuss the results of investigations on Benzene, Toluene, and Xylene in normal used gasoline SUPER. The detection limits obtained with the ion mobility spectrometer developed in co-operation are in the range of 10 ppbv in this case. Normally, charge transfer from Benzene ions to Toluene takes place. Nevertheless the simultaneous determination in mixtures is possible by a data evaluation procedure developed for this case. The interferences found between Xylene and others are rather weak. The ion mobility spectra of different concentrations of gasoline SUPER are attached as an example for the resolution and the detection limit of the instrument developed. Resolution and sensitivity of the system are well demonstrated. A hand-held portable device produced just now is to be tested for special environmental analytical problems in some industrial and scientific laboratories in Germany

Ab initio and nuclear inelastic scattering studies of Fe3_3Si/GaAs heterostructures

The structure and dynamical properties of the Fe$_3$Si/GaAs(001) interface are investigated by density functional theory and nuclear inelastic scattering measurements. The stability of four different atomic configurations of the Fe$_3$Si/GaAs multilayers is analyzed by calculating the formation energies and phonon dispersion curves. The differences in charge density, magnetization, and electronic density of states between the configurations are examined. Our calculations unveil that magnetic moments of the Fe atoms tend to align in a plane parallel to the interface, along the [110] direction of the Fe$_3$Si crystallographic unit cell. In some configurations, the spin polarization of interface layers is larger than that of bulk Fe$_3$Si. The effect of the interface on element-specific and layer-resolved phonon density of states is discussed. The Fe-partial phonon density of states measured for the Fe$_3$Si layer thickness of three monolayers is compared with theoretical results obtained for each interface atomic configuration. The best agreement is found for one of the configurations with a mixed Fe-Si interface layer, which reproduces the anomalous enhancement of the phonon density of states below 10 meVComment: 14 pages, 9 figures, 4 table

A Twisted Ladder: relating the Fe superconductors to the high TcT_c cuprates

We construct a 2-leg ladder model of an Fe-pnictide superconductor and discuss its properties and relationship with the familiar 2-leg cuprate model. Our results suggest that the underlying pairing mechanism for the Fe-pnictide superconductors is similar to that for the cuprates.Comment: 5 pages, 4 figure

Status of COLDDIAG: A Cold Vacuum Chamber for Diagnostics

One of the still open issues for the development of superconducting insertion devices is the understanding of the beam heat load. With the aim of measuring the beam heat load to a cold bore and the hope to gain a deeper understanding in the beam heat load mechanisms, a cold vacuum chamber for diagnostics is under construction. The following diagnostics will be implemented: i) retarding field analyzers to measure the electron energy and flux, ii) temperature sensors to measure the total heat load, iii) pressure gauges, iv) and mass spectrometers to measure the gas content. The inner vacuum chamber will be removable in order to test different geometries and materials. This will allow the installation of the cryostat in different synchrotron light sources. COLDDIAG will be built to fit in a short straight section at ANKA. A first installation at the synchrotron light source Diamond is foreseen in June 2011. Here we describe the technical design report of this device and the planned measurements with beam.Comment: Presented at First International Particle Accelerator Conference, IPAC'10, Kyoto, Japan, from 23 to 28 May 201