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

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

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

Association of different antiplatelet therapies with mortality after primary percutaneous coronary intervention.

OBJECTIVES: Prasugrel and ticagrelor both reduce ischaemic endpoints in high-risk acute coronary syndromes, compared with clopidogrel. However, comparative outcomes of these two newer drugs in the context of primary percutaneous coronary intervention (PCI) for ST-elevation myocardial infarction (STEMI) remains unclear. We sought to examine this question using the British Cardiovascular Interventional Society national database in patients undergoing primary PCI for STEMI. METHODS: Data from January 2007 to December 2014 were used to compare use of P2Y12 antiplatelet drugs in primary PCI in >89 000 patients. Statistical modelling, involving propensity matching, multivariate logistic regression (MLR) and proportional hazards modelling, was used to study the association of different antiplatelet drug use with all-cause mortality. RESULTS: In our main MLR analysis, prasugrel was associated with significantly lower mortality than clopidogrel at both 30 days (OR 0.87, 95% CI 0.78 to 0.97, P=0.014) and 1 year (OR 0.89, 95% CI 0.82 to 0.97, P=0.011) post PCI. Ticagrelor was not associated with any significant differences in mortality compared with clopidogrel at either 30 days (OR 1.07, 95% CI 0.95 to 1.21, P=0.237) or 1 year (OR 1.058, 95% CI 0.96 to 1.16, P=0.247). Finally, ticagrelor was associated with significantly higher mortality than prasugrel at both time points (30 days OR 1.22, 95% CI 1.03 to 1.44, P=0.020; 1 year OR 1.19 95% CI 1.04 to 1.35, P=0.01). CONCLUSIONS: In a cohort of over 89 000 patients undergoing primary PCI for STEMI in the UK, prasugrel is associated with a lower 30-day and 1-year mortality than clopidogrel and ticagrelor. Given that an adequately powered comparative randomised trial is unlikely to be performed, these data may have implications for routine care

Lattice dynamics of endotaxial silicide nanowires

Self-organized silicide nanowires are considered as main building blocks of future nanoelectronics and have been intensively investigated. In nanostructures, the lattice vibrational waves (phonons) deviate drastically from those in bulk crystals, which gives rise to anomalies in thermodynamic, elastic, electronic, and magnetic properties. Hence, a thorough understanding of the physical properties of these materials requires a comprehensive investigation of the lattice dynamics as a function of the nanowire size. We performed a systematic lattice dynamics study of endotaxial FeSi$_2$ nanowires, forming the metastable, surface-stabilized $\alpha$-phase, which are in-plane embedded into the Si(110) surface. The average widths of the nanowires ranged from 24 to 3 nm, their lengths ranged from several $\mu$m to about 100 nm. The Fe-partial phonon density of states, obtained by nuclear inelastic scattering, exhibits a broadening of the spectral features with decreasing nanowire width. The experimental data obtained along and across the nanowires unveiled a pronounced vibrational anisotropy that originates from the specific orientation of the tetragonal $\alpha$-FeSi$_2$ unit cell on the Si(110) surface. The results from first-principles calculations are fully consistent with the experimental data and allow for a comprehensive understanding of the lattice dynamics of endotaxial silicide nanowires.Comment: 9 pages, 7 figures, 3 table

Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery

Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns. (C) 2016 Optical Society of Americ