Improved De Novo Peptide Sequencing using LC Retention Time Information

Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) is an important tool in proteomics for identifying the peptides in a sample. Liquid chromatography temporally separates the peptides and tandem mass spectrometry analyzes the peptides, that elute one after another, by measuring their mass-to-charge ratios and the mass-to-charge ratios of their prefix and suffix fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of the analyzed peptide from this measurement data. While previous approaches solely consider the mass spectrum of the fragments for reconstructing a sequence, we propose to also exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the retention time of the separation by liquid chromatography. We consider three models for predicting the retention time of a peptide and develop algorithms for de novo sequencing for each model. An evaluation on experimental data from synthesized peptides for two of these models shows an improved performance compared to not using the chromatographic information.ISSN:1868-896

Constraining the evolution of young radio-loud AGN

GPS and CSS radio sources are the objects of choice to investigate the evolution of young radio-loud AGN. Previous investigations, mainly based on number counts and source size distributions, indicate that GPS/CSS sources decrease significantly in radio power when evolving into old, extended objects. We suggest this is preceded by a period of increase in radio luminosity, which lasts as long as the radio source is confined within the core-radius of its host galaxy. We have selected a sample of nearby compact radio sources, unbiased by radio spectrum, to determine their radio luminosity function, size distribution, dynamical ages, and emission line properties in a complete and homogeneous way. First results indicate that the large majority of objects (>80%) exhibit classical GPS/CSS radio spectra, and show structures consistent with the being compact double, or compact symmetric objects. This sample provides and ideal basis to further test and constrain possible evolution scenarios, and to investigate the relation between radio spectra and morphologies, orientation and Doppler boosting in samples of young radio-loud AGN, in an unbiased way.Comment: LaTeX, 8 pages, 3 figs: Accepted by Publications of the Astronomical Society of Australia, as part of the proceedings of the 3rd GPS/CSS workshop, eds. T. Tzioumis et a

Nanoscopic compartmentalization of membrane protein motion at the axon initial segment

The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single-particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton. We observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of ∼190-nm-spaced segments along the AIS axis as early as day in vitro 4, and this pattern alternates with actin rings. Mathematical modeling shows that diffusion barriers between the segments significantly reduce lateral diffusion along the axon

Parsec-scale morphology and spectral index distribution in faint high frequency peakers

We investigate the parsec-scale structure of 17 high frequency peaking radio sources from the faint HFP sample. VLBA observations were carried out at two adjacent frequencies, 8.4 and 15.3 GHz, both in the optically-thin part of the spectrum, to obtain the spectral index information. We found that 64% of the sources are resolved into subcomponents, while 36% are unresolved even at the highest frequency. Among the resolved sources, 7 have a morphology and a spectral index distribution typical of young radio sources, while in other 4 sources, all optically associated with quasars, the radio properties resemble those of the blazar population. The equipartition magnetic field of the single components are a few tens milliGauss, similar to the values found in the hotspots of young sources with larger sizes. Such high magnetic fields cause severe radiative losses, precluding the formation of extended lobe structures emitting at centimeter wavelengths. The magnetic fields derived in the various components of individual source are usually very different, indicating a non self-similar source evolution, at least during the very first stages of the source growth.Comment: 14 pages, 5 figures, accepted for publication in MNRA

Chandra Discovery of a 300 kpc X-ray Jet in the GPS Quasar PKS1127-145

We have discovered an X-ray jet with Chandra imaging of the z=1.187 radio-loud quasar PKS1127-145. In this paper we present the Chandra X-ray data, follow-up VLA observations, and optical imaging using the HST WFPC2. The X-ray jet contains 273+/-5 net counts in 27ksec and extends ~30 arcsec, from the quasar core, corresponding to a minimum projected linear size of ~330/h_50 kpc. The evaluation of the X-ray emission processes is complicated by the observed offsets between X-ray and radio brightness peaks. We discuss the problems posed by these observations to jet models. In addition, PKS1127-145 is a Giga-Hertz Peaked Spectrum radio source, a member of the class of radio sources suspected to be young or ``frustrated'' versions of FRI radio galaxies. However the discovery of an X-ray and radio jet extending well outside the host galaxy of PKS1127-145 suggests that activity in this and other GPS sources may be long-lived and complex.Comment: 22 pages, 11 ps figures, 1 figure in a JPG file, 3 tables. AASTEX. Accepted by The Astrophysical Journa

Proper Motions in Compact Symmetric Objects

We discuss recent measurements of proper motions of the hotspots of Compact Symmetric Objects. Source expansion has been detected in ten CSOs so far and all these objects are very young (<3000 years). In a few sources ages have also been estimated from energy supply and spectral ageing arguments and these estimates are comparable. This argues that these sources are close to equipartition and that standard spectral ageing models apply. Proper motions studies are now constraining hotspot accelerations, side-to-side motions and differences in hotspot advance speeds between the two hotspots within sources. Although most CSOs are young sources their evolution is unclear. There is increasing evidence that in some objects the CSO structure represents a new phase of activity within a recurrent source.Comment: 10 pages, 3 figures, Accepted by Publications of the Astronomical Society of Australia (Vol. 20), as part of the proceedings of the 3rd GPS/CSS workshop, eds. T. Tzioumis, W. de Vries, I. Snellen, A. Koekemoe