Protein–DNA binding specificity predictions with structural models

Protein–DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein–DNA complexes is thus an important goal. Here we develop a simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence by the bound protein. The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases. Both models are used to carry out predictions of protein–DNA binding affinities which are then compared with experimental measurements. The nearly additive nature of protein–DNA interaction energies in our model allows us to construct position-specific weight matrices by computing base pair probabilities independently for each position in the binding site. Our approach is less data intensive than knowledge-based models of protein–DNA interactions, and is not limited to any specific family of transcription factors. However, native structures of protein–DNA complexes or their close homologs are required as input to the model. Use of homology modeling can significantly increase the extent of our approach, making it a useful tool for studying regulatory pathways in many organisms and cell types

Production and characterization of micro-size pores for ion track etching applications

For many years the applications of ion track etch materials have increased considerably, like charged particles detection, molecular identification with nanopores, ion track filters, magnetic studies with nanowires and so on. Over the materials generally used as track detector, the Poly-Allyl-Diglycol Carbonate (PADC), offers many advantages, like its nearly 100 % detection efficiency for charged particle, a high resistance to harsh environment, the lowest detection threshold, a high abrasion resistance and a low production costs. All of these properties have made it particularly attractive material, even if due to its brittleness, obtaining a thin film (less than 500 μm) is still a challenge. In this work, PADC foils have been exposed to a-particles emitted by a thin radioactive source of 241Am and to C ions from the Tandetron 4130 MC accelerator. The latent tracks generated in the polymer have been developed using a standard etching procedure in 6.25 NaOH solution. The dependence of the ion tracks' geometry on the ion beam energy and fluence has been evaluated combining the information obtained through a semiautomatic computer script that selects the etched ion tracks according to their diameter and mean grey value and nanometric resolution images by atomic force microscopy

Performance and application of heavy ion nuclear microbeam facility at the Nuclear Physics Institute in Řež, Czech Republic

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RBS, PIXE, Ion-Microbeam and SR-FTIR Analyses of Pottery Fragments from Azerbaijan

The present work is aimed at the investigation of the ceramic bulk and pigmented glazed surfaces of ancient potteries dating back to XIX century A.D. and coming from the charming archeological site located in the Medieval Agsu town (Azerbaijan), a geographic area of special interest due to the ancient commercial routes between China, Asia Minor, and Europe. For the purpose of the study, complementary investigation tools have been exploited: non-destructive or micro-destructive investigation at elemental level by ion beam analysis (IBA) techniques, by using Rutherford Backscattering Spectrometry (RBS), Proton-Induced X-ray Emission (PIXE) spectroscopy and ion-microbeam analysis, and chemical characterization at microscopic level, by means of synchrotron radiation (SR) Fourier transform infrared (FTIR) microspectroscopy. The acquired information reveals useful for the identification of the provenance, the reconstruction of the firing technology, and finally, the identification of the pigment was used as a colorant of the glaze

Technical note: Lessons from and best practices for the deployment of the Soil Water Isotope Storage System

Soil water isotope datasets are useful for understanding connections between the hydrosphere, atmosphere, biosphere, and geosphere. However, they have been underproduced because of the technical challenges associated with collecting those datasets. Here, we present the results of testing and automation of the Soil Water Isotope Storage System (SWISS). The unique innovation of the SWISS is that we are able to automatically collect water vapor from the critical zone at a regular time interval and then store that water vapor until it can be measured back in a laboratory setting. Through a series of quality assurance and quality control tests, we tested whether the SWISS is resistant to both atmospheric intrusion and leaking in both laboratory and field settings. We assessed the accuracy and precision of the SWISS through a series of experiments in which water vapor of known composition was introduced into the flasks, stored for 14 d, and then measured. From these experiments, after applying an offset correction to report our values relative to Vienna Standard Mean Ocean Water (VSMOW), we assess the precision of the SWISS to be ±0.9 ‰ and ±3.7 ‰ for δ18O and δ2H, respectively. We deployed three SWISS units at three different field sites to demonstrate that the SWISS stores water vapor reliably enough that we are able to differentiate dynamics both between the sites as well within a single soil column. Overall, we demonstrate that the SWISS retains the stable isotope composition of soil water vapor for long enough to allow researchers to address a wide range of ecohydrologic questions.</p

Performance of the first prototype of the CALICE scintillator strip electromagnetic calorimeter

A first prototype of a scintillator strip-based electromagnetic calorimeter was built, consisting of 26 layers of tungsten absorber plates interleaved with planes of 45x10x3 mm3 plastic scintillator strips. Data were collected using a positron test beam at DESY with momenta between 1 and 6 GeV/c. The prototype's performance is presented in terms of the linearity and resolution of the energy measurement. These results represent an important milestone in the development of highly granular calorimeters using scintillator strip technology. This technology is being developed for a future linear collider experiment, aiming at the precise measurement of jet energies using particle flow techniques

Shower development of particles with momenta from 15 GeV to 150 GeV in the CALICE scintillator-tungsten hadronic calorimeter

We present a study of showers initiated by electrons, pions, kaons, and protons with momenta from 15 GeV to 150 GeV in the highly granular CALICE scintillator-tungsten analogue hadronic calorimeter. The data were recorded at the CERN Super Proton Synchrotron in 2011. The analysis includes measurements of the calorimeter response to each particle type as well as measurements of the energy resolution and studies of the longitudinal and radial shower development for selected particles. The results are compared to Geant4 simulations (version 9.6.p02). In the study of the energy resolution we include previously published data with beam momenta from 1 GeV to 10 GeV recorded at the CERN Proton Synchrotron in 2010.Comment: 35 pages, 21 figures, 8 table