Site-specific identification and quantitation of endogenous SUMO modifications under native conditions.

Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. Proteome-wide detection of SUMOylation sites on target proteins typically requires ectopic expression of mutant SUMOs with introduced tryptic sites. Here, we report a method for proteome-wide, site-level detection of endogenous SUMOylation that uses α-lytic protease, WaLP. WaLP digestion of SUMOylated proteins generates peptides containing SUMO-remnant diglycyl-lysine (KGG) at the site of SUMO modification. Using previously developed immuno-affinity isolation of KGG-containing peptides followed by mass spectrometry, we identified 1209 unique endogenous SUMO modification sites. We also demonstrate the impact of proteasome inhibition on ubiquitin and SUMO-modified proteomes using parallel quantitation of ubiquitylated and SUMOylated peptides. This methodological advancement enables determination of endogenous SUMOylated proteins under completely native conditions

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes

Adversarial Sample Detection for Deep Neural Network through Model Mutation Testing

Deep neural networks (DNN) have been shown to be useful in a wide range of applications. However, they are also known to be vulnerable to adversarial samples. By transforming a normal sample with some carefully crafted human imperceptible perturbations, even highly accurate DNN make wrong decisions. Multiple defense mechanisms have been proposed which aim to hinder the generation of such adversarial samples. However, a recent work show that most of them are ineffective. In this work, we propose an alternative approach to detect adversarial samples at runtime. Our main observation is that adversarial samples are much more sensitive than normal samples if we impose random mutations on the DNN. We thus first propose a measure of `sensitivity' and show empirically that normal samples and adversarial samples have distinguishable sensitivity. We then integrate statistical hypothesis testing and model mutation testing to check whether an input sample is likely to be normal or adversarial at runtime by measuring its sensitivity. We evaluated our approach on the MNIST and CIFAR10 datasets. The results show that our approach detects adversarial samples generated by state-of-the-art attacking methods efficiently and accurately.Comment: Accepted by ICSE 201

Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen

The visualization of taxonomically diagnostic features of individual pollen grains can be a challenge for many ecologically and phylogenetically important pollen types. The resolution of traditional optical microscopy is limited by the diffraction of light (250 nm), while high resolution tools such as electron microscopy are limited by laborious preparation and imaging workflows. Airyscan confocal superresolution and structured illumination superresolution (SR-SIM) microscopy are powerful new tools for the study of nanoscale pollen morphology and three-dimensional structure that can overcome these basic limitations. This study demonstrates their utility in capturing morphological details below the diffraction limit of light. Using three distinct pollen morphotypes (Croton hirtus, Dactylis glomerata, and Helianthus sp.) and contrast-enhancing fluorescent staining, we were able to assess the effectiveness of the Airyscan and SR-SIM. We further demonstrate that these new superresolution methods can be easily applied to the study of fossil pollen material

Nuclear Matter in Intense Magnetic Field and Weak Processes

We study the effect of magnetic field on the dominant neutrino emission processes in neutron stars.The processes are first calculated for the case when the magnetic field does not exceed the critical value to confine electrons to the lowest Landau state.We then consider the more important case of intense magnetic field to evaluate the direct URCA and the neutronisation processes. In order to estimate the effect we derive the composition of cold nuclear matter at high densities and in beta equilibrium, a situation appropriate for neutron stars. The hadronic interactions are incorporated through the exchange of scalar and vector mesons in the frame work of relativistic mean field theory. In addition the effects of anomalous magnetic moments of nucleons are also considered.Comment: 29 pages (LaTeX) including 7 figure

A new window on Strange Quark Matter as the ground state of strongly interacting matter

If strange quark matter is the true ground state of matter, it must have lower energy than nuclear matter. Simultaneously, two-flavour quark matter must have higher energy than nuclear matter, for otherwise the latter would convert to the former. We show, using an effective chiral lagrangian, that the existence of a new lower energy ground state for two-flavour quark matter, the pion condensate, shrinks the window for strange quark matter to be the ground state of matter and sets new limits on the current strange quark mass

A Comparison between Horizontal and Vertical Interchannel Decorrelation

The perceptual effects of interchannel decorrelation on perceived image spread have been investigated subjectively in both horizontal and vertical stereophonic reproductions, looking specifically at the frequency dependency of decorrelation. Fourteen and thirteen subjects graded the horizontal and vertical image spreads of a pink noise sample, respectively. The pink noise signal had been decorrelated by a complementary comb-filter decorrelation algorithm, varying the frequency-band, time-delay and decorrelation factor for each sample. Results generally indicated that interchannel decorrelation had a significant effect on auditory image spread both horizontally and vertically, with spread increasing as correlation decreases. However, it was found that the effect of vertical decorrelation was less effective than that of horizontal decorrelation. The results also suggest that the decorrelation effect was frequency-dependent; changes in horizontal image spread were more apparent in the high frequency band, whereas those in vertical image spread were in the low band. Furthermore, objective analysis suggests that the perception of vertical image spread for the low and middle frequency bands could be associated with a floor reflection; whereas for the high band, the results appear to be related to spectral notches in the ear input signals

Higgs decay into photons through a spin-2 loop

A new particle with proprieties similar to those of the Higgs boson in the Standard Model (SM) has been recently discovered. The biggest discrepancy is related to its diphoton decay, whose branching ratio seems to be around two times larger with respect to the correspondent SM value; this evidence, even if still affected by large uncertainties, suggests that clues of new physics related to the spontaneous breaking of the electroweak symmetry could be hidden under this loop-induced process. A new strongly-coupled sector responsible for this breaking, for instance, could produce in analogy with QCD a charged massive spin-2 state. In light of these arguments we calculate and discuss the role of such a resonance in the diphoton decay width of the Higgs.Comment: 12 pages + appendices, 5 figures. v2: minor changes, references adde