Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody

BACKGROUND: Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examined with the application of histone PTM-specific antibodies. In spite of their central role in chromatin research, polyclonal antibodies suffer from disadvantages like batch-to-batch variability and insufficient documentation of their quality and specificity. RESULTS: To mitigate some of the pitfalls of using polyclonal antibodies against H3K4me3, we successfully validated the application of a recombinant TAF3 PHD domain as anti-H3K4me3 affinity reagent in peptide array, western blot and ChIP-like experiments coupled with qPCR and deep sequencing. CONCLUSIONS: The successful addition of the TAF3 PHD domain to the growing catalog of recombinant affinity reagents for histone PTMs could help to improve the reproducibility, interpretation and cross-laboratory validation of chromatin data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0061-9) contains supplementary material, which is available to authorized users

Coarse-scale representations and smoothed Wigner transforms

Smoothed Wigner transforms have been used in signal processing, as a regularized version of the Wigner transform, and have been proposed as an alternative to it in the homogenization and / or semiclassical limits of wave equations. We derive explicit, closed formulations for the coarse-scale representation of the action of pseudodifferential operators. The resulting ``smoothed operators'' are in general of infinite order. The formulation of an appropriate framework, resembling the Gelfand-Shilov spaces, is necessary. Similarly we treat the ``smoothed Wigner calculus''. In particular this allows us to reformulate any linear equation, as well as certain nonlinear ones (e.g. Hartree and cubic non-linear Schr\"odinger), as coarse-scale phase-space equations (e.g. smoothed Vlasov), with spatial and spectral resolutions controlled by two free parameters. Finally, it is seen that the smoothed Wigner calculus can be approximated, uniformly on phase-space, by differential operators in the semiclassical regime. This improves the respective weak-topology approximation result for the Wigner calculus.Comment: 58 pages, plain Te

Use of remote sensing for hydrological parameterisation of Alpine catchments

International audiencePhysically-based water balance models require a realistic parameterisation of land surface characteristics of a catchment. Alpine areas are very complex with strong topographically-induced gradients of environmental conditions, which makes the hydrological parameterisation of Alpine catchments difficult. Within a few kilometres the water balance of a region (mountain peak or valley) can differ completely. Hence, remote sensing is invaluable for retrieving hydrologically relevant land surface parameters. The assimilation of the retrieved information into the water balance model PROMET is demonstrated for the Toce basin in Piemonte/Northern Italy. In addition to land use, albedos and leaf area indices were derived from LANDSAT-TM imagery. Runoff, modelled by a water balance approach, agreed well with observations without calibration of the hydrological model. Keywords: PROMET, fuzzy logic based land use classification, albedo, leaf area inde

O(αs) O(\alpha_s) corrections to polarized top decay into a charged Higgs t(↑)→H++b t(\uparrow) \to H^+ + b

We calculate the $O(\alpha_s)$ radiative corrections to polarized top quark decay into a charged Higgs boson and a massive bottom quark in two variants of the two-Higgs-doublet model. The radiative corrections to the polarization asymmetry of the decay may become as large as $25$. We provide analytical formulae for the unpolarized and polarized rates for $m_b \neq 0$ and for $m_b = 0$. For $m_b = 0$ our closed-form expressions for the unpolarized and polarized rates become rather compact.Comment: 24 pages, 5 figures in the text, content modified, comments added, appendices added, references updated, replaced with published versio

Electroweak and finite width corrections to top quark decays into transverse and longitudinal W W -bosons

We calculate the electroweak and finite width corrections to the decay of an unpolarized top quark into a bottom quark and a $W$-gauge boson where the helicities of the $W$ are specified as longitudinal, transverse-plus and transverse-minus. Together with the $O(\alpha_s)$ corrections these corrections may become relevant for the determination of the mass of the top quark through angular decay measurements.Comment: 4 pages, 7 postscript figures adde