Fully Automatable Two-dimensional HILIC–RP Liquid Chromatography with Online Tandem Mass Spectrometry for Shotgun Proteomics

Poster PresentationConference theme: Proteomics: Better for lifeMultidimensional liquid chromatography (MDLC) which multiples the resolution power of individual dimension with high orthogonality is a very efficient front-end separation method for analyzing the digests of complex biological samples. Among the existing two dimensional liquid chromatography (2DLC) systems, the combination of hydrophilic interaction liquid chromatography (HILIC) followed by low-pH reversed-phase (RP)LC (HILIC-RP) has very high orthogonality and is a very promising 2DLC method. Herein, a fully automatable two-dimensional (2D) liquid chromatography system was developed for shotgun proteomics analyses, which coupling the hydrophilic interaction liquid chromatography (HILIC) TSKgel Amide 80 (a non-ionic type) with the low-pH reversedphase (RP) chromatography. The performance of the 2D HILIC-RP LC platform was investigated at both pH 6.8 (neutral pH) and pH 2.7 (acidic pH) of the first dimension HILIC column by duplicate analyses of a Rat pheochromocytoma lysates.Online coupling of the neutral-pH HILIC and RP systems outperformedthe acidic HILIC–RP combination,resulting in 18.4% (1914 versus 1617 nonredundant proteins) and 41.6% (12,989 versus 9172unique peptides) increases in the number of identified proteins and peptides. To further test the established 2D HILIC-RP platform, we identified 2648 non-redundant proteins from triplicate analyses of a Saccharomyces cerevisiae lysate, with the detected protein abundances spanning from approximately41 to 106 copies per cell, which contained up to 2164 different validated protein species with a dynamic range of concentrations up to approximately 104. Herein, this studyestablished a fully automated 2D liquid chromatography platform to enable onlinecoupling of different HILIC and RP chromatography systems, thereby expanding the choice and application of multidimensional liquid chromatography for shotgun proteomics.published_or_final_versio

And the winner is: galaxy mass

The environment is known to affect the formation and evolution of galaxies considerably best visible through the well-known morphology-density relationship. We study the effect of environment on the evolution of early-type galaxies for a sample of 3,360 galaxies morphologically selected by visual inspection from the SDSS in the redshift range 0.05<z<0.06, and analyse luminosity-weighted age, metallicity, and alpha/Fe ratio as function of environment and galaxy mass. We find that on average 10 per cent of early-type galaxies are rejuvenated through minor recent star formation. This fraction increases with both decreasing galaxy mass and decreasing environmental density. However, the bulk of the population obeys a well-defined scaling of age, metallicity, and alpha/Fe ratio with galaxy mass that is independent of environment. Our results contribute to the growing evidence in the recent literature that galaxy mass is the major driver of galaxy formation. Even the morphology-density relationship may actually be mass-driven, as the consequence of an environment dependent characteristic galaxy mass coupled with the fact that late-type galaxy morphologies are more prevalent in low-mass galaxies.Comment: 5 pages, proceedings of JENAM 2010, Symposium 2: "Environment and the formation of galaxies: 30 years later

Open-Label Observational Study for Evaluating the Short-term Benefits of Rabeprazole Medication on Laryngopharyngeal Reflux

ObjectivesThe aims of this study were to determine the benefits of short-term empirical proton pump inhibitor (PPI) medication on laryngopharyngeal reflux (LPR) and to determine whether scores on the reflux symptom index (RSI) and the reflux finding score (RFS) could be combined to identify subgroups of patients that will more likely to improve with this medication.MethodsFifty-one Korean Otolaryngology Board-certified specialists joined this prospective, multi-center, and open-label observational study. A total of 1,142 adult patients with LPR was enrolled for 12 weeks of rabeprazol medication. According to pre-treatment scores on RSI and RFS, patients were divided into 4 subgroups. RFS and RSI were measured repeatedly with a month interval along the treatment period. Changes of RSI and RFS were analyzed in an overall study cohort as well as in each subgroup.ResultsApproximately 40% (n=455) of enrolled patients were followed up until 12 weeks of PPI treatment. Significant improvement in RSI was obtained in 29%, 58%, and 75% of patients after 4, 8, and 12 weeks of PPI medication. RFS was improved in 16%, 42%, and 57% of the patients with 4, 8, and 12 weeks of PPI medication. All subgroups showed improvement regardless of their pre-treatment scores on the RSI and RFS.ConclusionEven though RSI and RFS may be used as a general guideline for LPR management, pre-treatment RSI and RFS are not useful in predicting the patients' response to short-term PPI medication in the usual pattern of practice for LPR, which is mostly based on the physical evaluation and history taking

Integration of decision support systems to improve decision support performance

Decision support system (DSS) is a well-established research and development area. Traditional isolated, stand-alone DSS has been recently facing new challenges. In order to improve the performance of DSS to meet the challenges, research has been actively carried out to develop integrated decision support systems (IDSS). This paper reviews the current research efforts with regard to the development of IDSS. The focus of the paper is on the integration aspect for IDSS through multiple perspectives, and the technologies that support this integration. More than 100 papers and software systems are discussed. Current research efforts and the development status of IDSS are explained, compared and classified. In addition, future trends and challenges in integration are outlined. The paper concludes that by addressing integration, better support will be provided to decision makers, with the expectation of both better decisions and improved decision making processes

Novel Cβ–Cγ Bond Cleavages of Tryptophan-Containing Peptide Radical Cations

In this study, we observed unprecedented cleavages of the Cβ–Cγ bonds of tryptophan residue side chains in a series of hydrogen-deficient tryptophan-containing peptide radical cations (M•+) during low-energy collision-induced dissociation (CID). We used CID experiments and theoretical density functional theory (DFT) calculations to study the mechanism of this bond cleavage, which forms [M – 116]+ ions. The formation of an α-carbon radical intermediate at the tryptophan residue for the subsequent Cβ–Cγ bond cleavage is analogous to that occurring at leucine residues, producing the same product ions; this hypothesis was supported by the identical product ion spectra of [LGGGH – 43]+ and [WGGGH – 116]+, obtained from the CID of [LGGGH]•+ and [WGGGH]•+, respectively. Elimination of the neutral 116-Da radical requires inevitable dehydrogenation of the indole nitrogen atom, leaving the radical centered formally on the indole nitrogen atom ([Ind]•-2), in agreement with the CID data for [WGGGH]•+ and [W1-CH3GGGH]•+; replacing the tryptophan residue with a 1-methyltryptophan residue results in a change of the base peak from that arising from a neutral radical loss (116 Da) to that arising from a molecule loss (131 Da), both originating from Cβ–Cγ bond cleavage. Hydrogen atom transfer or proton transfer to the γ-carbon atom of the tryptophan residue weakens the Cβ–Cγ bond and, therefore, decreases the dissociation energy barrier dramatically

Quantum state preparation and macroscopic entanglement in gravitational-wave detectors

Long-baseline laser-interferometer gravitational-wave detectors are operating at a factor of 10 (in amplitude) above the standard quantum limit (SQL) within a broad frequency band. Such a low classical noise budget has already allowed the creation of a controlled 2.7 kg macroscopic oscillator with an effective eigenfrequency of 150 Hz and an occupation number of 200. This result, along with the prospect for further improvements, heralds the new possibility of experimentally probing macroscopic quantum mechanics (MQM) - quantum mechanical behavior of objects in the realm of everyday experience - using gravitational-wave detectors. In this paper, we provide the mathematical foundation for the first step of a MQM experiment: the preparation of a macroscopic test mass into a nearly minimum-Heisenberg-limited Gaussian quantum state, which is possible if the interferometer's classical noise beats the SQL in a broad frequency band. Our formalism, based on Wiener filtering, allows a straightforward conversion from the classical noise budget of a laser interferometer, in terms of noise spectra, into the strategy for quantum state preparation, and the quality of the prepared state. Using this formalism, we consider how Gaussian entanglement can be built among two macroscopic test masses, and the performance of the planned Advanced LIGO interferometers in quantum-state preparation

Searching for a Stochastic Background of Gravitational Waves with LIGO

The Laser Interferometer Gravitational-wave Observatory (LIGO) has performed the fourth science run, S4, with significantly improved interferometer sensitivities with respect to previous runs. Using data acquired during this science run, we place a limit on the amplitude of a stochastic background of gravitational waves. For a frequency independent spectrum, the new limit is $\Omega_{\rm GW} < 6.5 \times 10^{-5}$. This is currently the most sensitive result in the frequency range 51-150 Hz, with a factor of 13 improvement over the previous LIGO result. We discuss complementarity of the new result with other constraints on a stochastic background of gravitational waves, and we investigate implications of the new result for different models of this background.Comment: 37 pages, 16 figure

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex

Dosage compensation in male Drosophila relies on the X chromosome–specific recruitment of a chromatin-modifying machinery, the dosage compensation complex (DCC). The principles that assure selective targeting of the DCC are unknown. According to a prevalent model, X chromosome targeting is initiated by recruitment of the DCC core components, MSL1 and MSL2, to a limited number of so-called “high-affinity sites” (HAS). Only very few such sites are known at the DNA sequence level, which has precluded the definition of DCC targeting principles. Combining RNA interference against DCC subunits, limited crosslinking, and chromatin immunoprecipitation coupled to probing high-resolution DNA microarrays, we identified a set of 131 HAS for MSL1 and MSL2 and confirmed their properties by various means. The HAS sites are distributed all over the X chromosome and are functionally important, since the extent of dosage compensation of a given gene and its proximity to a HAS are positively correlated. The sites are mainly located on non-coding parts of genes and predominantly map to regions that are devoid of nucleosomes. In contrast, the bulk of DCC binding is in coding regions and is marked by histone H3K36 methylation. Within the HAS, repetitive DNA sequences mainly based on GA and CA dinucleotides are enriched. Interestingly, DCC subcomplexes bind a small number of autosomal locations with similar features