High Energetic Resolution Research Articles

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding

Transcription factors (TFs) are primary regulators of gene expression in cells, where they bind specific genomic target sites to control transcription. Quantitative measurements of TF-DNA binding energies can improve the accuracy of predictions of TF occupancy and downstream gene expression in vivo and shed light on how transcriptional networks are rewired throughout evolution. Here, we present a sequencing-based TF binding assay and analysis pipeline (BET-seq, for Binding Energy Topography by sequencing) capable of providing quantitative estimates of binding energies for more than one million DNA sequences in parallel at high energetic resolution. Using this platform, we measured the binding energies associated with all possible combinations of 10 nucleotides flanking the known consensus DNA target interacting with two model yeast TFs, Pho4 and Cbf1. A large fraction of these flanking mutations change overall binding energies by an amount equal to or greater than consensus site mutations, suggesting that current definitions of TF binding sites may be too restrictive. By systematically comparing estimates of binding energies output by deep neural networks (NNs) and biophysical models trained on these data, we establish that dinucleotide (DN) specificities are sufficient to explain essentially all variance in observed binding behavior, with Cbf1 binding exhibiting significantly more nonadditivity than Pho4. NN-derived binding energies agree with orthogonal biochemical measurements and reveal that dynamically occupied sites in vivo are both energetically and mutationally distant from the highest affinity sites.

Impedance spectroscopy for high resolution measurements of energetic distributions of localized states in organic semiconductors

A method has been proposed for the determination of energetic distributions of localized states in organic semiconductors by the analysis of the impedance spectra (T. Okachi, T. Nagase, T. Kobayashi, and H. Naito, Appl. Phys. Lett. 94 (2009) 043301). High energetic resolution of the method is demonstrated experimentally in organic semiconductor diodes using a polyfluorene derivative, poly(9,9-dioctyl-fluorene-co-N-(4-butylphenyl)-diphenylamine), by detecting a structured localized-state distribution. The method is a powerful tool for the determination of energetic distributions of localized states with high energetic resolution in organic thin film devices such as organic light-emitting diodes and organic solar cells.

Nieinwazyjna metoda identyfikacji pigmentów in situ – badania przenośnym spektroskopem XRF obrazów olejnych Józefa Pankiewicza

The elementary composition of selected pigments in 39 oil paintings by Jozef Pankiewicz, dating back to the years 1888 –1938, has been determined with the use of a portable XRF - spectrometer built in the Institute of Fluid-Flow Machinery, Polish Academy of Sciences in Gdańsk. The analysis was preceded by tests on samples of modern paints. To compare with the tests results obtained on the paint layers from paintings also the samples of pure historical paints from Jan Matejko palette from 1888 have been tested as well as paints form tubes preserved in a cassette of anonymous painter, sated back to early 20th century. The detection range of the spectrometer covers the elements of the atomic number 50 > Z > 18. A high-energy source of excitation has been employed (IS601.5, Italstructures) producing a collimated beam of 4 mm diameter and a detector (AXAS, Ketek) of high energetic resolution (FWHM <= 155 eV for the MnKα line) and high sensitivity, which allowed for detecting even trace amounts of elements in paint layer. Basing on the measurements the average volume of the lines of elements present in particular pigments has been established, as well as the factors infl uencing their value. Detection of the elements: Pb, Zn, Cr, Cd, Cu, As, Co, Fe, Hg, Sr, Ba, Sn, Sb, Ti, Ca, Se, Mn in the paint layer of paintings allowed to identify led-, zinc- and titanium-white, ochre, chrome -, strontium-, zinc, Neapolitan and cadmium-yellow, vermilion, cadmium- and iron-red, cerulean- and Prussian blue, cobalt-violet, emerald-, Schweinfurter and vermilion-green, green earth, sienna, umber, iron-, bone and cobalt-black. Apart from the above the composition of primings, extenders added to paints and in cases where it was not based on light elements – the base of organic red. Some pigments turned out to be dating ones (the fi rst use of cobalt-violet – 1908, of cadmium-red – 1919, titanium-white – ca. 1938). The advantages of this method, in relation with the methods of determining the elementary composition of paints used so far are: complete non-invasiveness, testing in situ, high sensibility (of energetic resolution), introducing a quasiquantitative analysis next to the qualitative one, easiness of use and short time of measurements. Besides, this technique allows also for obtaining information on the elementary composition of lower strata, depending on the permeability of upper ones.

Comprehensive high resolution photoelectron spectra of metal carbonyls using synchrotron radiation

High resolution photoelectron spectra of transition element carbonyls using synchrotron radiation are reported. The high energetic resolution of this technique and the variable nature of the excitation radiation allow far more detailed characterization of the energy levels of these complexes than observed previously.