A Computational Pipeline for the Development of Comparative Anchor Tagged Sequence (CATS) Markers

Key points: Molecular markers that allow the transfer of map information from one species to another are vital in comparative genetics. To identify potential anchor marker sequences more efficiently, we have established a bioinformatic pipeline that combines multi-species EST- and genome- sequence data. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionary conserved sequences in less well-characterised species in the same family. Alignment of evolutionary conserved EST sequences with corresponding genomic sequences defines sets of PCR primer sites flanking introns. Markers identified by this procedure will be readily transferable to other species since they are selected on the basis of their common evolutionary origin. We exemplify our procedure on legumes and grasses, where model plant studies and the genome- and EST-sequence data available have a potential impact on breeding crop species

Colour superconductivity in finite systems

In this paper we study the effect of finite size on the two-flavour colour superconducting state. As well as restricting the quarks to a box, we project onto states of good baryon number and onto colour singlets, these being necessary restrictions on any observable ``quark nuggets''. We find that whereas finite size alone has a significant effect for very small boxes, with the superconducting state often being destroyed, the effect of projection is to restore it again. The infinite-volume limit is a good approximation even for quite small systems.Comment: 14 pages RevTeX4, 12 eps figure

Calibration of the NuSTAR High Energy Focusing X-ray Telescope

We present the calibration of the \textit{Nuclear Spectroscopic Telescope Array} (\nustar) X-ray satellite. We used the Crab as the primary effective area calibrator and constructed a piece-wise linear spline function to modify the vignetting response. The achieved residuals for all off-axis angles and energies, compared to the assumed spectrum, are typically better than $\pm 2$\% up to 40\,keV and 5--10\,\% above due to limited counting statistics. An empirical adjustment to the theoretical 2D point spread function (PSF) was found using several strong point sources, and no increase of the PSF half power diameter (HPD) has been observed since the beginning of the mission. We report on the detector gain calibration, good to 60\,eV for all grades, and discuss the timing capabilities of the observatory, which has an absolute timing of $\pm$ 3\,ms. Finally we present cross-calibration results from two campaigns between all the major concurrent X-ray observatories (\textit{Chandra}, \textit{Swift}, \textit{Suzaku} and \textit{XMM-Newton}), conducted in 2012 and 2013 on the sources 3C\,273 and PKS\,2155-304, and show that the differences in measured flux is within $\sim$10\% for all instruments with respect to \nustar

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide–oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design