sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Unlabelled: Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data.

Integrated care: a comprehensive bibliometric analysis and literature review.

Introduction: Integrated care could not only fix up fragmented health care but also improve the continuity of care and the quality of life. Despite the volume and variety of publications, little is known about how 'integrated care' has developed. There is a need for a systematic bibliometric analysis on studying the important features of the integrated care literature.

Expansion of the ion library for mining SWATH-MS data through fractionation proteomics.

The strategy of sequential window acquisition of all theoretical fragment ion spectra (SWATH) is emerging in the field of label-free proteomics. A critical consideration for the processing of SWATH data is the quality of the ion library (or mass spectrometric reference map). As the availability of open spectral libraries that can be used to process SWATH data is limited, most users currently create their libraries in-house.

Simultaneous determination of four volatile compounds in rat plasma after oral administration of Shexiang Baoxin Pill (SBP) by HS-SPDE-GC-MS/MS and its application to pharmacokinetic studies.

In this study, a headspace, solid-phase dynamic extraction method coupled to gas chromatography-tandem mass spectrometry (HS-SPDE-GC-MS/MS) method was developed for the simultaneous determination of four volatile compounds, namely, isoborneol, borneol, muscone and cinnamaldehyde, in rat plasma after oral administration of Shexiang Baoxin Pill (SBP) using naphthalene as an internal standard (IS). The target compounds were extracted using an SPDE needle device coated with a poly (dimethylsiloxane) (PDMS) phase. The detection was achieved by GC-MS/MS in multiple reaction monitoring (MRM) mode.

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community.

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes.

A novel suppressive effect of alcohol dehydrogenase 5 in neuronal differentiation.

Alcohol dehydrogenase 5 (ADH5) is a conserved enzyme for alcohol and aldehyde metabolism in mammals. Despite dynamic expression throughout neurogenesis, its role in neuronal development remains unknown. Here we present the first evidence that ADH5 is a negative regulator of neuronal differentiation.

Voltage-independent sodium channels emerge for an expression of activity-induced spontaneous spikes in GABAergic neurons.

Background: Cerebral overexcitation needs inhibitory neurons be functionally upregulated to rebalance excitation vs. inhibition. For example, the intensive activities of GABAergic neurons induce spontaneous spikes, i.

Physisorption of molecular hydrogen on carbon nanotube with vacant defects.

Physisorption of molecular hydrogen on single-walled carbon nanotubes (SWCNTs) is important for its engineering applications and hydrogen energy storage. Using molecular dynamics simulation, we study the physisorption of molecular hydrogen on a SWCNT with a vacant defect, focusing on the effect of the vacant defect size and external parameters such as temperature and pressure. We find that hydrogen can be physisorbed inside a SWCNT through a vacant defect when the defect size is above a threshold.

Investigation of metabolism and disposition of GSK1322322, a peptidase deformylase inhibitor, in healthy humans using the entero-test for biliary sampling.

GSK1322322 (N-((R)-2-(cyclopentylmethyl)-3-(2-(5-fluoro-6-((S)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl)-2-methylpyrimidin-4-yl)hydrazinyl)-3-oxopropyl)-N-hydroxy-formamide) is an antibiotic in development by GlaxoSmithKline. In this study, we investigated the metabolism and disposition of [(14)C]GSK1322322 in healthy humans and demonstrated the utility of the Entero-Test in a human radiolabel study. We successfully collected bile from five men using this easy-to-use device after single i.

Suv39h1 mediates AP-2α-dependent inhibition of C/EBPα expression during adipogenesis.

Previous studies have shown that CCAAT/enhancer-binding protein α (C/EBPα) plays a very important role during adipocyte terminal differentiation and that AP-2α (activator protein 2α) acts as a repressor to delay the expression of C/EBPα. However, the mechanisms by which AP-2α prevents the expression of C/EBPα are not fully understood. Here, we present evidence that Suv39h1, a histone H3 lysine 9 (H3K9)-specific trimethyltransferase, and G9a, a euchromatic methyltransferase, both interact with AP-2α and enhance AP-2α-mediated transcriptional repression of C/EBPα.

Metabolic activation of the indoloquinazoline alkaloids evodiamine and rutaecarpine by human liver microsomes: dehydrogenation and inactivation of cytochrome P450 3A4.

Evodiamine and rutaecarpine are the main active indoloquinazoline alkaloids of the herbal medicine Evodia rutaecarpa, which is widely used for the treatment of hypertension, abdominal pain, angina pectoris, gastrointestinal disorder, and headache. Immunosuppressive effects and acute toxicity were reported in mice treated with evodiamine and rutaecarpine. Although the mechanism remains unknown, it is proposed that metabolic activation of the indoloquinazoline alkaloids and subsequent covalent binding of reactive metabolites to cellular proteins play a causative role.

Reduced graphene oxides: light-weight and high-efficiency electromagnetic interference shielding at elevated temperatures.

Chemical graphitized r-GOs, as the thinnest and lightest material in the carbon family, exhibit high-efficiency electromagnetic interference (EMI) shielding at elevated temperature, attributed to the cooperation of dipole polarization and hopping conductivity. The r-GO composites show different temperature-dependent imaginary permittivities and EMI shielding performances with changing mass ratio.

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization.

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.

Fabrication of Reduced Graphene Oxide (RGO)/Co O Nanohybrid Particles and a RGO/Co O /Poly(vinylidene fluoride) Composite with Enhanced Wave-Absorption Properties.

Reduced graphene oxide (RGO)/Co O nanohybrid particles, composed of reduced graphite oxide and Co O particles, have been fabricated by an in situ growth method under mild wet-chemical conditions (140 °C). A series of characterization results indicate that the as-prepared Co O particles with relatively uniform sizes are embedded in RGO layers to form unique core-shell nanostructures. The RGO/Co O /poly(vinylidene fluoride) composite was found to possess excellent absorption properties.

The OMSSAPercolator: an automated tool to validate OMSSA results.

Protein identification by MS/MS is an important technique in proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) is an open-source search engine that can be used to identify MS/MS spectra acquired in these experiments. Here, we present a software tool, termed OMSSAPercolator, which interfaces OMSSA with Percolator, a post-search machine learning method for rescoring database search results.

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications.

We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535).

Uterine myomas treated with microwave ablation: the agreement between ablation volumes obtained from contrast-enhanced sonography and enhanced MRI.

Purpose: This study explores the agreement between ablated uterine myoma volumes obtained from contrast-enhanced sonography and enhanced magnetic resonance imaging (MRI) after microwave ablation therapy.

Materials And Methods: Twenty uterine myomas in 18 patients (average size: 5.56 ± 1.

Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines.

Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence.

Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1.

Our first proteomic exploration of human chromosome 1 began in 2012 (CCPD 1.0), and the genome-wide characterization of the human proteome through public resources revealed that 32-39% of proteins on chromosome 1 remain unidentified. To characterize all of the missing proteins, we applied an OMICS-integrated analysis of three human liver cell lines (Hep3B, MHCC97H, and HCCLM3) using mRNA and ribosome nascent-chain complex-bound mRNA deep sequencing and proteome profiling, contributing mass spectrometric evidence of 60 additional chromosome 1 gene products.

Lentiviral backbone-based hepatitis B virus replicon-mediated transfer favours the establishment of persistent hepatitis B virus infection in mice after hydrodynamic injection.

Establishment of a non-transgenic mouse model of persistent hepatitis B virus (HBV) infection is urgently needed. In this study, we constructed novel lentiviral-transfer plasmids containing HBV replicon DNA (pCS-HBV1.3, containing a 1.

p300-dependent acetylation of activating transcription factor 5 enhances C/EBPβ transactivation of C/EBPα during 3T3-L1 differentiation.

Adipogenesis is a multistep process by which 3T3-L1 preadipocytes differentiate into mature adipocytes through mitotic clonal expansion (MCE) and terminal differentiation. The CCAAT/enhancer-binding protein β (C/EBPβ) is an important transcription factor that takes part in both of these processes. C/EBPβ not only transactivates C/EBPα and the peroxisome proliferator-activated receptor γ (PPARγ), which cause 3T3-L1 preadipocytes to enter terminal adipocyte differentiation, but also is required to activate cell cycle genes necessary for MCE.

Decreased thalamocortical functional connectivity after 36 hours of total sleep deprivation: evidence from resting state FMRI.

Objectives: The thalamus and cerebral cortex are connected via topographically organized, reciprocal connections, which hold a key function in segregating internally and externally directed awareness information. Previous task-related studies have revealed altered activities of the thalamus after total sleep deprivation (TSD). However, it is still unclear how TSD impacts on the communication between the thalamus and cerebral cortex.

Quantitative evaluation of the mitochondrial proteomes of Drosophila melanogaster adapted to extreme oxygen conditions.

Mitochondria are the primary organelles that consume oxygen and provide energy for cellular activities. To investigate the mitochondrial mechanisms underlying adaptation to extreme oxygen conditions, we generated Drosophila strains that could survive in low- or high-oxygen environments (LOF or HOF, respectively), examined their mitochondria at the ultrastructural level via transmission electron microscopy, studied the activity of their respiratory chain complexes, and quantitatively analyzed the protein abundance responses of the mitochondrial proteomes using Isobaric tag for relative and absolute quantitation (iTRAQ). A total of 718 proteins were identified with high confidence, and 55 and 75 mitochondrial proteins displayed significant differences in abundance in LOF and HOF, respectively, compared with the control flies.