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Find video protocols related to scientific articles indexed in Pubmed.
Flexible Single Crystal Silicon Nanomembrane Photonic Crystal Cavity.
ACS Nano
PUBLISHED: 11-20-2014
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Flexible inorganic electronic devices promise numerous applications, especially in fields that could not be covered satisfactorily by conventional rigid devices. Benefits on a similar scale are also foreseeable for silicon photonic components. However, the difficulty in transferring intricate silicon photonic devices has deterred widespread development. In this paper, we demonstrate a flexible single crystal silicon nanomembrane photonic crystal microcavity through a bonding and substrate removal approach. The transferred cavity shows a quality factor of 2.2×10^4, and could be bended to a curvature of 5 mm radius without deteriorating the performance compared to its counterparts on rigid substrates. A thorough characterization of the device reveals that the resonant wavelength is a linear function of the bending-induced strain. The device also shows a curvature-independent sensitivity to the ambient index variation.
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Correction: Rapidly improved determination of metabolites from biological data sets using the high-efficient TransOmics tool.
Mol Biosyst
PUBLISHED: 11-20-2014
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Correction for 'Rapidly improved determination of metabolites from biological data sets using the high-efficient TransOmics tool' by Aihua Zhang et al., Mol. BioSyst., 2014, 10, 2160-2165.
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Method for Transforming Alkynes into (E)-Dibromoalkenes.
J. Org. Chem.
PUBLISHED: 11-20-2014
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The highly stereoselective bromination of alkynes has been realized by using copper(II) bromide as both the reacting partner and the catalyst, offering a generally efficient synthesis of (E)-dibromoalkenes. The reaction conditions are exceptionally mild, and a wide range of functional groups are well tolerated.
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Evaluation of a 2-Channel Portable Device and a Predictive Model to Screen for Obstructive Sleep Apnea in a Laboratory Environment.
Respir Care
PUBLISHED: 11-20-2014
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Various portable monitors for identifying obstructive sleep apnea (OSA) have been investigated and reported to enable accurate recording of OSA severity. However, more information is needed from different populations. This study was conducted to evaluate the efficiency of a portable 2-channel sleep apnea device (SleepView) for screening OSA in the Chinese population.
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Whirlin and PDZ Domain Containing 7 (PDZD7) Proteins are Both Required to Form the Quaternary Protein Complex Associated with Usher Syndrome Type 2.
J. Biol. Chem.
PUBLISHED: 11-20-2014
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Usher syndrome (USH) is the leading genetic cause of combined hearing and vision loss. Among the three USH clinical types, type 2 (USH2) occurs most commonly. USH2A, GPR98 and WHRN are three known causative genes of USH2, while PDZD7 is a modifier gene found in USH2 patients. The proteins encoded by these four USH genes have been proposed to form a multiprotein complex, the USH2 complex, due to interactions found among some of these proteins in vitro, their colocalization in vivo, and mutual dependence of some of these proteins for their normal in vivo localizations. However, evidence showing the formation of the USH2 complex is missing, and details on how this complex is formed remain elusive. Here, we systematically investigated interactions among the intracellular regions of the four USH proteins using colocalization, yeast two-hybrid and pull-down assays. We show that multiple domains of the four USH proteins interact among one another. Importantly, both WHRN and PDZD7 are required for the complex formation with USH2A and GPR98. In this USH2 quaternary complex, WHRN prefers to bind to USH2A, while PDZD7 prefers to bind to GPR98. Interaction between WHRN and PDZD7 is the bridge between USH2A and GPR98. Additionally, the USH2 quaternary complex has a variable stoichiometry. These findings suggest that a non-obligate, short-term and dynamic USH2 quaternary protein complex may exist in vivo. Our work provides valuable insight into the physiological role of the USH2 complex in vivo and informs possible reconstruction of the USH2 complex for future therapy.
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Preparation of Monolithic Polymer Columns with Homogeneous Structure via Photo-initiated Thiol-yne Click Polymerization and Their Application in Separation of Small Molecules.
Anal. Chem.
PUBLISHED: 11-19-2014
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Two monolithic polymer columns were directly prepared in the UV-transparent fused-silica capillaries via photo-initiated thiol-yne click polymerization of 1,7-octadiyne (ODY) with a dithiol (1,6-hexanedithiol, 2SH) or a tetrathiol (pentaerythriol tetrakis(3-mercaptopropionate), 4SH) within 15 minutes. The rapid polymerization provided a time-saving approach to optimize preparation conditions. Then two porogenic systems of diethylene glycol diethyl ether (DEGDE)/tetrahydrofuran (THF) and DEGDE/PEG 200 were found to effectively control porous structure of two kinds of polymeric monoliths (O2SH and O4SH), respectively. The almost disappearance of thiol and alkynyl vibrations (2560 and 2115 cm-1, respectively) in infrared spectra and Raman spectra indicated high conversion of thiol-yne polymerization reaction. The thiol-yne polymerization was further proved by analyzing energy-dispersive X-ray spectrum (EDS), MALDI-TOF mass spectrum and elemental data. Scanning electron microscopy (SEM) images showed the monolithic polymer columns with homogeneous porous structure and macropore size of 0.5-1.0 ?m, which facilitated the minimum plate heights of 10.0-12.0 ?m for alkylbenzenes in reversed-phase liquid chromatography (RPLC). The low values of A and C terms (<1.0 ?m and <15.5 ms, respectively) in van Deemter equation were similar to those obtained by some monolithic silica columns. The BSA tryptic digest was also separated on the monolithic polymer column by cLC-MS/MS. The result with 85% protein coverage was better than those given by some hybrid monolithic columns. The monolithic polymer columns were further applied for separation of phenols, natural products and standard proteins, and demonstrated satisfactory separation ability.
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Effect of Laparoscopic Roux-en-Y Gastric Bypass Surgery on Obstructive Sleep Apnea in a Chinese Population with Obesity and T2DM.
Obes Surg
PUBLISHED: 11-14-2014
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Bariatric surgery has been reported to be an effective treatment for obstructive sleep apnea (OSA). However, this evidence was not enough for different populations. Thus, we conducted a follow-up study to evaluate the effect of bariatric surgery on OSA in a Chinese population with obesity and type 2 diabetes mellitus (T2DM).
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Investigation of drugs responsible for perioperative anaphylactic reactions using cellular allergen stimulation test.
Chin. Med. J.
PUBLISHED: 11-11-2014
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Anaphylactic reactions during anesthesia and operation are common and life threatening. Follow-up investigation is necessary for avoiding potential re-exposure of the patients to the offending drugs. The purpose of this study was to assess cellular allergen stimulation test (CAST) as a diagnostic instrument in immunoglobulin E (IgE)- and non-IgE-mediated anaphylactic reactions.
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Layer-by-Layer Films with Bioreducible and Nonbioreducible Polycations for Sequential DNA Release.
Biomacromolecules
PUBLISHED: 10-31-2014
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Layer-by-layer (LbL) films containing cationic polyelectrolytes and anionic bioactive molecules such as DNA are promising biomaterials for controlled and localized gene delivery for a number of biomedical applications including cancer DNA vaccine delivery. Bioreducible LbL films made of disulfide-containing poly(amido amine)s (PAAs) and plasmid DNA can be degraded by redox-active membrane proteins through the thiol-disulfide exchange reaction to release DNA exclusively into the extracellular microenvironment adjacent to the film. In order to better understand the film degradation mechanism and nature of the released species, the bioreducible film degradation is studied by atomic force microscopy, fluorescence, and dynamic light scattering in solutions containing a reducing agent. The PAA/DNA LbL film undergoes fast bulk degradation with micrometer-sized pieces breaking off from the substrate. This bulk degradation behavior is arrested by periodic insertions of a nonbioreducible poly(ethylenimine) (PEI) layer. The LbL films containing PAA/DNA and PEI/DNA bilayers display sequential film disassembly and are capable of continuously releasing DNA nanoparticles over a prolonged time. Insertion of the PEI layer enables the bioreducible LbL films to transfect human embryonic kidney 293 cells. The data conclude that the PEI layer is effective as a barrier layer against interlayer diffusion during LbL film assembly and more importantly during film disassembly. Without the barrier layer, the high mobility of cleaved PAA fragments is responsible for bulk degradation of bioreducible LbL films, which may prevent their ultimate gene-delivery applications. This work establishes a direct link among film internal structure, disassembly mechanism, and transfection efficiency. It provides a simple method to design bioreducible LbL films for sequential and long-time DNA release.
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Multiplex isotope dimethyl labeling of substrate peptides for high throughput kinase activity assay via quantitative MALDI MS.
Chem. Commun. (Camb.)
PUBLISHED: 10-01-2014
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A simple, cost-effective and high throughput method was developed for multiplexed kinase activity assay based on the multiplex isotope labeling of designed substrate peptides. This strategy was successfully applied to monitor the time-dependent consumption of substrates and generation of products in the single and multiple substrate systems.
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Interference in autophagosome fusion by rare Earth nanoparticles disrupts autophagic flux and regulation of an interleukin-1? producing inflammasome.
ACS Nano
PUBLISHED: 10-01-2014
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Engineered nanomaterials (ENMs) including multiwall carbon nanotubes (MWCNTs) and rare earth oxide (REO) nanoparticles, which are capable of activating the NLRP3 inflammasome and inducing IL-1? production, have the potential to cause chronic lung toxicity. Although it is known that lysosome damage is an upstream trigger in initiating this pro-inflammatory response, the same organelle is also an important homeostatic regulator of activated NLRP3 inflammasome complexes, which are engulfed by autophagosomes and then destroyed in lysosomes after fusion. Although a number of ENMs have been shown to induce autophagy, no definitive research has been done on the homeostatic regulation of the NLRP3 inflammasome during autophagic flux. We used a myeloid cell line (THP-1) and bone marrow derived macrophages (BMDM) to compare the role of autophagy in regulating inflammasome activation and IL-1? production by MWCNTs and REO nanoparticles. THP-1 cells express a constitutively active autophagy pathway and are also known to mimic NLRP3 activation in pulmonary macrophages. We demonstrate that, while activated NLRP3 complexes could be effectively removed by autophagosome fusion in cells exposed to MWCNTs, REO nanoparticles interfered in autophagosome fusion with lysosomes. This leads to the accumulation of the REO-activated inflammasomes, resulting in robust and sustained IL-1? production. The mechanism of REO nanoparticle interference in autophagic flux was clarified by showing that they disrupt lysosomal phosphoprotein function and interfere in the acidification that is necessary for lysosome fusion with autophagosomes. Binding of LaPO4 to the REO nanoparticle surfaces leads to urchin-shaped nanoparticles collecting in the lysosomes. All considered, these data demonstrate that in contradistinction to autophagy induction by some ENMs, specific materials such as REOs interfere in autophagic flux, thereby disrupting homeostatic regulation of activated NLRP3 complexes.
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Identification of phosphopeptides with unknown cleavage specificity by a de novo sequencing assisted database search strategy.
Proteomics
PUBLISHED: 09-25-2014
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In theory, proteases with broad cleavage specificity could be applied to digest protein samples to improve the phosphoproteomic analysis coverage. However, in practice this approach is seldom employed. This is because the identification of phosphopeptides without enzyme specificity by conventional database search strategy is extremely difficult due to the huge search space. In this study, we investigated the performance of a de novo sequencing assisted database search strategy for the identification of such phosphopeptides. Firstly, we compared the performance of conventional database search strategy and the de novo sequencing assisted database search strategy for the identification of peptides and phosphopeptides without stetting enzyme specificity. It was found that the identification sensitivity dropped significantly for the conventional one while it was only slightly decreased for the new approach. Then, this new search strategy was applied to identify phosphopeptides generated by Proteinase K digestion, which resulted in the identification of 717 phosphopeptides. Finally, this strategy was utilized for the identification of serum endogenous phosphopeptides, which were generated in vivo by different kinds of proteases and kinases, and the identification of 68 unique serum endogenous phosphopepitdes was successfully achieved.
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High-throughput determination of the site-specific N-sialoglycan occupancy rates by differential oxidation of glycoproteins followed with quantitative glycoproteomics analysis.
Anal. Chem.
PUBLISHED: 09-22-2014
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Sialylated glycoproteins, which play important roles in tumor progression, have been extensively analyzed for the discovery of potential biomarkers for cancer diagnosis and prognosis. The site-specific N-sialoglycan occupancy rates of glycoproteins reflect the activities of glycosyltransferases and glycosidases in vivo and could be novel disease biomarkers. However, a high-throughput method to determine the N-sialoglycan occupancy rates is not available. On the basis of the fact that dihydroxy of sialic acid of glycan chains in glycoproteins can be specifically oxidized to aldehyde in mild periodate concentration while all types of glycan chains can be oxidized in high periodate concentration, we developed a modified protein-level hydrazide chemistry method for the determination of the N-sialoglycan occupancy rates. This method was first applied to determine the N-sialoglycan occupancy rates of two glycosites on human transferrin. These two sites were found to be fully sialylated and the N-sialoglycan occupancy rates were found to under significant decrease after the neuraminidase treatment. This method was then applied to analyze N-sialoglycan occupancy rates in proteome samples. We determined 496 and 632 site-specific N-sialoglycan occupancy rates on 334 and 394 proteins from hepatocellular carcinoma (HCC) and normal human liver tissues, respectively. By comparing the N-sialoglycan occupancy rates between the above two samples, we determined 76 N-sialoglycosites with more than a 2-fold change. This method was demonstrated to be an effective and high-throughput method for the analysis of the N-sialoglycan occupancy rates.
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Comprehensive proteome quantification reveals NgBR as a new regulator for epithelial-mesenchymal transition of breast tumor cells.
J Proteomics
PUBLISHED: 08-27-2014
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Nogo-B receptor (NgBR) is a type I receptor and specifically binds to ligand Nogo-B. Our previous work has shown that NgBR is highly expressed in human breast invasive ductal carcinoma. Here, comprehensive proteome quantification was performed to examine the alteration of protein expression profile in MDA-MB-231 breast tumor cells after knocking down NgBR using lentivirus-mediated shRNA approach. Among a total of 1771 proteins feasibly quantified, 994 proteins were quantified in two biological replicates with RSD <50%. There are 122 proteins significantly down-regulated in NgBR knockdown MDA-MB-231 breast tumor cells, such as vimentin and S100A4, well-known markers for mesenchymal cells, and CD44, a stemness indicator. The decrease of vimentin, S100A4 and CD44 protein expression levels was further confirmed by Western blot analysis. MDA-MB-231 cells are typical breast invasive ductal carcinoma cells showing mesenchymal phenotype. Cell morphology analysis demonstrates NgBR knockdown in MDA-MB-231 cells results in reversibility of epithelial-mesenchymal transition (EMT), which is one of the major mechanisms involved in breast cancer metastasis. Furthermore, we demonstrated that NgBR knockdown in MCF-7 cells significantly prevented the TGF-?-induced EMT process as determined by the morphology change, and staining of E-cadherin intercellular junction as well as the decreased expression of vimentin.
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Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method.
J Proteomics
PUBLISHED: 08-23-2014
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The detailed characterization of site-specific glycosylation requires the identification of glycan composition and specific attachment sites on proteins, which need the identification of intact glycopeptides by mass spectrometry. In this study, we present an analytical and computational strategy for the high throughput characterization of intact N-glycopeptides derived from complex proteome samples. N-glycopeptides were identified using the spectra acquired for intact glycopeptides as well as de-glycopeptides. The Y1 ion (peptide+GlcNAc) was accurately determined from the spectra of intact glycopeptides, and the structure of glycan was then identified by searching a constructed glycan database with calculated molecular weight of glycans and their fragment ions. The peptide sequences of intact glycopeptides were identified by matching the molecular weight calculated from Y1 ion to that of deglycosylated peptides from the same HILIC enrichment and identified by a separated LC-MS/MS analysis. The fully automated software platform integrates all of the above processes involved in the identification of the intact N-glycopeptides. This platform was applied to detailed characterization of site-specific glycosylation in HEK 293T cells, which led to the identification of 2249 unique intact N-glycopeptides. These intact glycopeptides revealed 1769 site-specific N-glycans on 453 glycosylation sites which demonstrated the high heterogeneity of glycosylations.
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Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion.
Anal Bioanal Chem
PUBLISHED: 08-19-2014
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Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.
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Efficient enrichment of glycopeptides using metal-organic frameworks by hydrophilic interaction chromatography.
Analyst
PUBLISHED: 08-12-2014
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Selective enrichment of glycopeptides from complicated biological samples is critical for glycoproteomics to obtain the structure and glycosylation information of glycoproteins using mass spectrometry (MS), which still remains a great challenge. Hydrophilic interaction chromatography (HILIC)-based strategies have been proposed for selective isolation of glycopeptides via the interactions between the glycan of glycopeptides and the matrices. However, the application of these methods is limited by the medium selectivity of HILIC matrices. In this study, hydrophilic metal-organic frameworks (MOFs) were fabricated and used as a HILIC matrix. The cross-linked CD-MOFs (LCD-MOFs) were facilely prepared with ?-cyclodextrin as ligand and possessed nano-sized cubic structure, superior hydrophilicity, and bio-compatibility. The LCD-MOFs performance for the selective enrichment of glycopeptides from the complex biological samples were investigated with a digested mixture of human immunoglobulin G (IgG) that was used as standard samples. In the selectivity assessment, the non-glycopeptides causing ion suppression to the glycopeptides were effectively removed, the signal of glycopeptides were enhanced significantly by LCD-MOFs, and twenty glycopeptides were identified with 67 fmol of IgG digest. In addition, the resulting LCD-MOFs demonstrated the lower detection limit (3.3 fmol) with a satisfactory recovery yield (84-103%) for glycopeptide enrichment from a digest of IgG. Furthermore, a promising protocol was developed for the selective enrichment of glycopeptides from mouse liver, and 344 unique N-glycosylation sites that mapped to 290 different glycoproteins were identified in a single MS run. The results clearly demonstrated that when used in a HILIC matrix, LCD-MOFs have great potential for identifying and enriching low-abundant glycopeptides in complex biological samples.
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Chromatographic assessment of two hybrid monoliths prepared via epoxy-amine ring-opening polymerization and methacrylate-based free radical polymerization using methacrylate epoxy cyclosiloxane as functional monomer.
J Chromatogr A
PUBLISHED: 08-11-2014
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Two kinds of hybrid monolithic columns were prepared by using methacrylate epoxy cyclosiloxane (epoxy-MA) as functional monomer, containing three epoxy moieties and one methacrylate group. One column was in situ fabricated by ring-opening polymerization of epoxy-MA and 1,10-diaminodecane (DAD) using a porogenic system consisting of isopropanol (IPA), H2O and ethanol at 65°C for 12h. The other was prepared by free radical polymerization of epoxy-MA and ethylene dimethacrylate (EDMA) using 1-propanol and 1,4-butanediol as the porogenic solvents at 60°C for 12h. Two hybrid monoliths were investigated on the morphology and chromatographic assessment. Although two kinds of monolithic columns were prepared with epoxy-MA, their morphologies looked rather different. It could be found that the epoxy-MA-DAD monolith possessed higher column efficiencies (25,000-34,000plates/m) for the separation of alkylbenzenes than the epoxy-MA-EDMA monolith (12,000-13,000plates/m) in reversed-phase nano-liquid chromatography (nano-LC). Depending on the remaining epoxy or methacrylate groups on the surface of two pristine monoliths, the epoxy-MA-EDMA monolith could be easily modified with 1-octadecylamine (ODA) via ring-opening reaction, while the epoxy-MA-DAD monolith could be modified with stearyl methacrylate (SMA) via free radical reaction. The chromatographic performance for the separation of alkylbenzenes on SMA-modified epoxy-MA-DAD monolith was remarkably improved (42,000-54,000 plates/m) when compared with that on pristine epoxy-MA-DAD monolith, while it was not obviously enhanced on ODA-modified epoxy-MA-EDMA monolith when compared with that on pristine epoxy-MA-EDMA monolith. The enhancement of the column efficiency of epoxy-MA-DAD monolith after modification might be ascribed to the decreased mass-transfer resistence. The two kinds of hybrid monoliths were also applied for separations of six phenols and seven basic compounds in nano-LC.
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Proteomic analysis of protein methylation in the yeast Saccharomyces cerevisiae.
J Proteomics
PUBLISHED: 08-08-2014
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Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in many important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the yeast Saccharomyces cerevisiae based on the online multidimensional ?HPLC/MS/MS technology. We identified 43 methylated proteins, containing 68 methylation events associated with 64 methylation sites. More than 90% of these methylation events were previously unannotated in Uniprot database. Our results indicated, 1) over 2.6% of identified S. cerevisiae proteins are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys?Arg>Asp>Asn?Gln?His>Glu>Cys, and 3) the methylation state on nitrogen center is largely exclusive. As our dataset covers various types of methylation centers, it provides rich information about yeast methylproteome and should significantly contribute to the field of protein methylation.
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In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis.
J. Proteome Res.
PUBLISHED: 08-05-2014
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Current sample preparation protocols for quantitative phosphoproteome analysis are tedious and time-consuming. Here, a facile in situ sample processing approach (iSPA) is developed by using macroporous Ti(IV)-IMAC microspheres as the preparation "beds", where all sample preparation procedures including the enrichment of phosphoproteins, tryptic digestion of proteins, enrichment, and isotope labeling of phosphopeptides are performed in situ sequentially. As a result of the in situ processing design and the seamless procedures, extra steps for desalting and buffer exchanging, which are always required in conventional approaches, are avoided, and the sample loss and contamination could be greatly reduced. Thus, better sensitivity and accuracy for the quantitative phosphoproteome analysis were obtained. This strategy was further applied to differential phosphoproteome analysis of human liver tissues with or without hepatocellular carcinoma (HCC). In total, 8548 phosphorylation sites were confidently quantified from three replicate analyses of 0.5 mg of human liver protein extracts.
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[Effect of the lysine guanidination on proteomic analysis].
Se Pu
PUBLISHED: 07-30-2014
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The guanidination of lysine side chain was paid great attention in recent years. It plays an important role in qualitative and quantitative proteomics. In this study, based on the results of separated peptides extracted from HeLa cells before and after the guanidination by liquid chromatography-tandem mass spectrometry (LC-MS/MS), the effect of the guanidination of three different kinds of peptides was systematically analyzed. It was found that the selectivity of the guanidination of the lysine side chain was as high as 96.8%. The ratio of identified peptides with lysine at C-term to all peptides increased from 51.7% to 57.3% and more new peptides were identified, while the ratio of peptides with lysine in the middle or without lysine changed little. Further study on the ratio of b and y ions indicated that there were more y ions of peptides with lysine at C-term after the guanidination. The results proved that the selective conversion of lysine to homoarginine by the guanidination could increase the sensitivity and selectivity of mass spectrum. The increased basicity and ability to sequester proton of lysine produced more y ions fragmentation information, which contributed to more identified peptides. It concluded that the lysine guanidination can improve the coverage of proteomic analysis.
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Generation of CRISPR/Cas9-mediated gene-targeted pigs via somatic cell nuclear transfer.
Cell. Mol. Life Sci.
PUBLISHED: 07-20-2014
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The domestic pig has been widely used as an important large animal model. Precise and efficient genetic modification in pig provides a great promise in biomedical research. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has been successfully used to produce many gene-targeted animals. However, these animals have been generated by co-injection of Cas9 mRNA and single-guide RNA (sgRNA) into one-cell stage embryos, which mostly resulted in mosaicism of the modification. One or two rounds of further breeding should be performed to obtain homozygotes with identical genotype and phenotype. To address this issue, gene-targeted somatic cells can be used as donor for somatic cell nuclear transfer (SCNT) to produce gene-targeted animals with single and identical mutations. In this study, we applied Cas9/sgRNAs to effectively direct gene editing in porcine fetal fibroblasts and then mutant cell colonies were used as donor to generate homozygous gene-targeted pigs through single round of SCNT. As a result, we successfully obtained 15 tyrosinase (TYR) biallelic mutant pigs and 20 PARK2 and PINK1 double-gene knockout (KO) pigs. They were all homozygous and no off-target mutagenesis was detected by comprehensive analysis. TYR (-/-) pigs showed typical albinism and the expression of parkin and PINK1 were depleted in PARK2 (-/-)/PINK1 (-/-) pigs. The results demonstrated that single- or double-gene targeted pigs can be effectively achieved by using the CRISPR/Cas9 system combined with SCNT without mosaic mutation and detectable off-target effects. This gene-editing system provides an efficient, rapid, and less costly manner to generate genetically modified pigs or other large animals.
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Photoinduced thiol-ene polymerization reaction for fast preparation of macroporous hybrid monoliths and their application in capillary liquid chromatography.
Chem. Commun. (Camb.)
PUBLISHED: 07-08-2014
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Hybrid monoliths with a macroporous structure were prepared within a few minutes via a photoinduced thiol-ene polymerization reaction, the surfaces of which showed hydrophobic character. The monolithic column demonstrated good separation performance towards alkylbenzenes, peptides, proteins and BSA tryptic digest in cLC.
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Large-scale proteome quantification of hepatocellular carcinoma tissues by a three-dimensional liquid chromatography strategy integrated with sample preparation.
J. Proteome Res.
PUBLISHED: 07-07-2014
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Hepatocellular carcinoma is one of the most fatal cancers worldwide. In this study, a reversed-phase-strong cation exchange-reversed-phase three-dimensional liquid chromatography strategy was established and coupled with mass spectrometry to investigate the differential proteome expression of HCC and normal liver tissues. In total, 2759 proteins were reliably quantified, of which, 648 proteins were dysregulated more than 3-fold in HCC liver tissues. Some important proteins that relate to HCC pathology were significantly dysregulated, such as NAT2 and AKR1B10. Furthermore, 2307 phosphorylation sites from 1264 phosphoproteins were obtained in our previous phosphoproteome quantification, and the nonphosphorylated counterparts of 445 phosphoproteins with 983 phosphorylation sites were reliably quantified in this work. It was observed that 337 (34%) phosphorylation sites exhibit significantly different expression trends from that of their corresponding nonphosphoproteins. Some novel phosphorylation sites with important biological functions in the progression of HCC were reliably quantified, such as the significant downregulation of pT185 for ERK2 and pY204 for ERK1.
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Recent development of hybrid organic-silica monolithic columns in CEC and capillary LC.
Electrophoresis
PUBLISHED: 07-03-2014
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As an attractive alternative to organic and silica monoliths, hybrid organic-inorganic monolith somewhat combines the advantages of them, such as high surface area, excellent mechanical strength, and thermal stability. We have reviewed the preparation and application of hybrid monoliths in 2011 and 2013. The preparation approaches have been mainly summarized into three categories: (1) common sol-gel process using trialkoxysilanes and tetraalkoxysilanes as precursors; (2) "one-pot" process of alkoxysilanes and organic monomers simultaneously via sol-gel chemistry and free radical polymerization; and (3) other polymerization of silane-containing monomers. Herein, we would focus on the recent progress and development of preparation approaches, mainly covering the literatures since July of 2012. First, the direct synthesis approach of hybrid monoliths via sol-gel chemistry and following postmodification was an important route to fabricate various monolithic stationary phases, particularly, to modify the hybrid monoliths containing amino, epoxy, vinyl, and other groups. Second, "one-pot" process, as a novel preparation approach of hybrid monoliths, was further developed in the past 2 years, in which various organic functional monomers, not only water-soluble monomers, but also hydrophobic monomers could be added in the preparation system. Other polymerization techniques in the preparation of organic monolithic materials, particularly, free radical polymerization and ring-opening polymerization, were successfully transferred to fabricate the hybrid monoliths by using silane-containing monomers including POSS monomers or other self-synthesized monomers.
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Integration of cell lysis, protein extraction, and digestion into one step for ultrafast sample preparation for phosphoproteome analysis.
Anal. Chem.
PUBLISHED: 07-02-2014
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Conventional sample preparation protocols for phosphoproteome analysis require multiple time-consuming and labor-intensive steps, including cell lysis, protein extraction, protein digestion, and phosphopeptide enrichment. In this study, we found that the presence of a large amount of trypsin in the sample did not interfere with phosphopeptide enrichment and subsequent LC-MS/MS analysis. Taking advantage of fast digestion achieved with high trypsin-to-protein ratio, we developed a novel concurrent lysis-digestion method for phosphoproteome analysis. In this method, the harvested cells were first placed in a lysis buffer containing a huge amount of trypsin. After ultrasonication, the cells were lysed and the proteins were efficiently digested into peptides within one step. Thereafter, tryptic digest was subjected to phosphopeptide enrichment, in which unphosphorylated peptides, trypsin, and other components incompatible with LC-MS/MS analysis were removed. Compared with conventional methods, better phosphoproteome coverage was achieved in this new one-step method. Because protein solubilization and cell lysis were facilitated by fast protein digestion, the complete transformation of cell pellets into the peptide mixture could be finished within 25 min, while it would take at least 16 h for conventional methods. Hence, our method, which integrated cell lysis, protein extraction, and protein digestion into one step, is rapid and convenient. It is expected to have broad applications in phosphoproteomics analysis.
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Grating-coupled silicon-on-sapphire integrated slot waveguides operating at mid-infrared wavelengths.
Opt Lett
PUBLISHED: 07-01-2014
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We demonstrate subwavelength bidirectional grating (SWG) coupled slot waveguide fabricated in silicon-on-sapphire for transverse electric polarized wave operation at 3.4 ?m wavelength. Coupling efficiency of 29% for SWG coupler is experimentally achieved. Propagation loss of 11??dB/cm has been experimentally obtained for slot waveguides. Two-step taper mode converters with an insertion loss of 0.13 dB are used to gradually convert the strip waveguide mode into slot waveguide mode.
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Parasitic loss suppression in photonic and plasmonic photovoltaic light trapping structures.
Opt Express
PUBLISHED: 07-01-2014
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In this paper, we examine the optical loss mechanisms and mitigation strategies in classical photovoltaic light trapping structures consisting of diffractive gratings integrated with a backside reflector, which couple normal incident solar radiation into guided modes in solar cells to enhance optical absorption. Parasitic absorption from metal or dielectric backside reflectors is identified to be a major loss contributor in such light trapping structures. We elucidate the optical loss mechanism based on the classical coupled mode theory. Further, a spacer design is proposed and validated through numerical simulations to significantly suppress the parasitic loss and improve solar cell performance.
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Facile fabrication of a near-infrared responsive nanocarrier for spatiotemporally controlled chemo-photothermal synergistic cancer therapy.
Nanoscale
PUBLISHED: 06-24-2014
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Remote-controlled nanocarriers for drug delivery are of great promise to provide timely, sensitive and spatiotemporally selective treatments for cancer therapy. Due to convenient and precise manipulation, deep penetration through tissues and excellent biocompatibility, near-infrared (NIR) irradiation is a preferred external stimulus for triggering the release of loaded drugs. In this work, for spatiotemporally controlled chemo-photothermal synergistic cancer therapy, a NIR responsive nanocarrier was fabricated using reduced graphene oxide nanosheets (rNGO) decorated with mesoporous silica shell and the subsequent functionalization of the thermoresponsive polymer brushes (pNIPAM-co-pAAm) at the outlet of the silica pore channels. rNGO, which combined with the mesoporous silica shell provide a high loading capacity for anticancer drugs (doxorubicin, DOX), was assigned to sense NIR irradiation for the manipulation of pNIPAM-co-pAAm valve to control the diffusion of loaded DOX. Under NIR irradiation, rNGO would generate heat, which could not only elevate the surrounding temperature over the low critical solution temperature (LCST) of pNIPAM-co-pAAm to open the thermoresponsive polymer valve and promote the diffusion of DOX, but also kill the cancer cells through the hypothermia effect. By manipulating NIR irradiation, the nanocarrier exhibited efficiently controlled release of loaded DOX both in the buffer and in living HeLa cells (the model cancer cells), providing powerful and site-targeted treatments, which can be attributed to synergistic effects of chemo-photothermal therapy. To sum up, this novel nanocarrier is an excellent drug delivery platform in remote-controlled chemo-photothermal synergistic cancer therapy via NIR irradiation.
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Novel helper factors influencing recombinant protein production in Pichia pastoris based on proteomic analysis under simulated microgravity.
Appl. Microbiol. Biotechnol.
PUBLISHED: 06-09-2014
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Microgravity and simulated microgravity (SMG) have quite significant effects on numerous microbial cellular processes. The effects of SMG on the production of recombinant proteins and transcription profiling in prokaryotic and eukaryotic expression host have been investigated. The present study showed that SMG significantly enhanced the specific productivities and activities of the reporter enzymes PGUS and AtXYN that were expressed in recombinant Pichia pastoris. Proteomic profiling revealed that 21 proteins were significantly up-regulated and 35 proteins were drastically down-regulated at the stationary phase, when the recombinant P. pastoris responded to SMG. Six strongly up-regulated genes, TPX, FBA, PGAM, ENO, SBA1, and AKR-E, involved in the oxidative stress response, methanol metabolism, glycolytic pathway, and protein folding, were selected to analyze their impacts on recombinant protein production by co-overexpression in the shaker flask fermentation. The co-overexpressed strains, particularly TPX, FBA, and PGAM, demonstrated promising results with approximately 2.46-fold, 1.58-fold, and 1.33-fold increases in the specific yields of PGUS compared to the control after 48 h of methanol induction, respectively. In the meantime, the corresponding PGUS specific activities were increased by 2.33-fold, 2.09-fold, and 1.32-fold, respectively. Thiol peroxidase (TPX), which is involved in the oxidative stress response, significantly influenced the transcriptional levels of the reporter gene PGUS. The present study provides valuable information for further exploration of the molecular mechanism of P. pastoris response to SMG and facilitates simulated microgravity for finding novel helper factors to rationally engineer the strains in normal fermentation by using proteomic studies.
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One-pot synthesis of magnetic colloidal nanocrystal clusters coated with chitosan for selective enrichment of glycopeptides.
Anal. Chim. Acta
PUBLISHED: 05-28-2014
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Selective enrichment of glycopeptides prior to the mass spectrometry (MS) analysis is essential due to ion suppression effect during ionization caused by the co-presence of non-glycosylated peptides. Among the enrichment approaches, hydrophilic interaction liquid chromatography (HILIC) based on magnetic separation has become a popular method in recent years. As the conventional synthesis procedures of these materials are tedious and time-consuming with at least four steps. Herein, magnetic colloidal nanocrystal clusters coated with chitosan (Fe3O4@CS MCNCs) have been successfully prepared by a simple one-pot method. The resulting Fe3O4@CS MCNCs demonstrated an excellent ability for glycopeptide enrichment with high selectivity, low detection limit and high binding capacity. Furthermore, in the analysis of real complicated biological sample, 283 unique N-glycosylation sites corresponding to 175 glycosylated proteins were identified in three replicate analyses of 45?g protein sample extracted from HeLa cells, indicating the great potential in detection and identification of low abundant glycopeptides in glycoproteome analysis.
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Synthesis of novel perphenylcarbamated ?-cyclodextrin based chiral stationary phases via thiol-ene click chemistry.
Electrophoresis
PUBLISHED: 05-17-2014
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Novel cyclodextrin (CD) chiral stationary phases (CD-CSPs) with well-defined structure have been successfully synthesized by immobilization of mono/di(10-undecenoyl)-perphenylaminocarbonyl ?-CD on the 3-mercaptopropyl functionalized silica gel via thiol-ene click chemistry. The phenyl carbamate groups on the rims of CD extended the cavity of CD-CSPs, which facilitated the formation of inclusion complex with various types of racemic compounds under RP mode, and also improved the ?-? stacking interaction, dipole-dipole interaction, and hydrogen bonding interaction with racemic compounds under normal phase mode. Fifteen racemic compounds were successfully separated on this CD-CSP with HPLC, and the chromatographic results also demonstrated that thiol-ene click chemistry affords a facile approach for preparation of CSPs.
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Multiple systemic transplantations of human amniotic mesenchymal stem cells exert therapeutic effects in an ALS mouse model.
Cell Tissue Res.
PUBLISHED: 04-28-2014
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Amyotrophic lateral sclerosis (ALS) is an adult-onset progressive neurodegenerative disease involving degeneration of motor neurons in the central nervous system. Stem cell treatment is a potential therapy for this fatal disorder. The human amniotic membrane (HAM), an extremely rich and easily accessible tissue, has been proposed as an attractive material in cellular therapy and regenerative medicine because of its advantageous characteristics. In the present study, we evaluate the long-term effects of a cellular treatment by intravenous administration of human amniotic mesenchymal stem cells (hAMSCs) derived from HAM into a hSOD1(G93A) mouse model. The mice received systemic administration of hAMSCs or phosphate-buffered saline (PBS) at the onset, progression and symptomatic stages of the disease. hAMSCs were detected in the spinal cord at the final stage of the disease, in the form of isolates or clusters and were negative for ?-tubulin III and GFAP. Compared with the treatment with PBS, multiple hAMSC transplantations significantly retarded disease progression, extended survival, improved motor function, prevented motor neuron loss and decreased neuroinflammation in mice. These findings demonstrate that hAMSC transplantation is a promising cellular treatment for ALS.
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Quantitative proteomic study of myocardial mitochondria in urea transporter B knockout mice.
Proteomics
PUBLISHED: 04-04-2014
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In previous research, we showed that 16-week-old urea transporter B (UT-B) null mice have an atrial-ventricular conduction block, and hypothesized myocardial mitochondrial dysfunction. To investigate the mechanism of this block, we examined the proteomic differences in the myocardial mitochondria of UT-B null and wild-type mice with nanoscale LC-MS/MS. Of 26 proteins clearly downregulated in the UT-B null mice, 15 are involved in complexes I, III, IV, and V of the respiratory chain, which would strongly reduce the activity of the electron transport chain. Excess electrons from complexes I and III pass directly to O2 to generate ROS and deplete ROS-scavenging enzymes. Myocardial intracellular ROS were significantly higher in UT-B null mice than in wild-type mice (p < 0.01), constituting an important cause of oxidative stress injury in the myocardia of UT-B null mice. The mitochondrial membrane potential (??m) was also lower in UT-B null mice than in wild-type mice (p < 0.05), causing oxidative phosphorylation dysfunction of complex V and insufficient ATP in the myocardial cells of UT-B null mice. HADHA (a trifunctional protein) and HSP60 were also downregulated in the UT-B null myocardial mitochondria. These results confirm that mitochondrial dysfunction underlies the pathogenesis of the atrial-ventricular conduction block in UT-B null mice.
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Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC-MS/MS.
J Proteomics
PUBLISHED: 03-25-2014
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Glycosylation of membrane proteins plays an important role in cellular behaviors such as cell-cell interaction, immunologic recognition and cell signaling. However, the effective extraction of membrane proteins, the selective isolation of glycopeptides and the mass spectrometric characterization of glycosylation are challenging with current analytical techniques. In this study, a systematic approach was developed which combined: an integrated hydrophilic interaction chromatography solid phase interaction (HILIC SPE) for simultaneous detergent removal and glycopeptide enrichment, and mass spectrometric identification of both protein N-glycosylation sites and site-specific glycan composition. The HILIC SPE conditions were optimized to enable the use of a high concentration of strong detergents, such as SDS and Triton X-100 and to dissolve highly hydrophobic membrane proteins, thus increasing the yield of membrane protein extraction. We illustrated the performance of this approach for the study of membrane protein glycosylation from human embryonic kidney cell lines (HEK 293T). 200?g total protein digest was processed using this approach, leading to the identification of 811 N-glycosylation sites from 567 proteins within two experimental replicates. Furthermore, 177 glycopeptides representing 82 N-glycosites with both glycan composition and peptide sequence were identified by high energy collision dissociation.
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Analysis of ultra-high sensitivity configuration in chip-integrated photonic crystal microcavity bio-sensors.
Appl Phys Lett
PUBLISHED: 03-13-2014
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We analyze the contributions of quality factor, fill fraction, and group index of chip-integrated resonance microcavity devices, to the detection limit for bulk chemical sensing and the minimum detectable biomolecule concentration in biosensing. We analyze the contributions from analyte absorbance, as well as from temperature and spectral noise. Slow light in two-dimensional photonic crystals provide opportunities for significant reduction of the detection limit below 1?×?10(-7) RIU (refractive index unit) which can enable highly sensitive sensors in diverse application areas. We demonstrate experimentally detected concentration of 1 fM (67 fg/ml) for the binding between biotin and avidin, the lowest reported till date.
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Preparation of hydrazine functionalized polymer brushes hybrid magnetic nanoparticles for highly specific enrichment of glycopeptides.
Analyst
PUBLISHED: 03-12-2014
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Hydrazide chemistry is a powerful technique in glycopeptides enrichment. However, the low density of the monolayer hydrazine groups on the conventional hydrazine-functionalized magnetic nanoparticles limits the efficiency of glycopeptides enrichment. Herein, a novel magnetic nanoparticle grafted with poly(glycidyl methacrylate) (GMA) brushes was fabricated via reversible addition-fragmentation chain transfer (RAFT) polymerization, and a large amount of hydrazine groups were further introduced to the GMA brushes by ring-opening the epoxy groups with hydrazine hydrate. The resulting magnetic nanoparticles (denoted as Fe3O4@SiO2@GMA-NHNH2) demonstrated the high specificity of capturing glycopeptides from a tryptic digest of the sample comprising a standard non-glycosylated protein bovine serum albumin (BSA) and four standard glycoproteins with a weight ratio of 50?:?1, and the detection limit was as low as 130 fmol. In the analysis of a real complex biological sample, the tryptic digest of hepatocellular carcinoma, 179 glycosites were identified by the Fe3O4@SiO2@GMA-NHNH2 nanoparticles, surpassing that of 68 glycosites by Fe3O4@SiO2-single-NHNH2 (with monolayer hydrazine groups on the surface). It can be expected that the magnetic nanoparticles modified with hydrazine functionalized polymer brushes via RAFT technique will improve the specificity and the binding capacity of glycopeptides from complex samples, and show great potential in the analysis of protein glycosylation in biological samples.
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The role of group index engineering in series-connected photonic crystal microcavities for high density sensor microarrays.
Appl Phys Lett
PUBLISHED: 03-11-2014
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We experimentally demonstrate an efficient and robust method for series connection of photonic crystal microcavities that are coupled to photonic crystal waveguides in the slow light transmission regime. We demonstrate that group index taper engineering provides excellent optical impedance matching between the input and output strip waveguides and the photonic crystal waveguide, a nearly flat transmission over the entire guided mode spectrum and clear multi-resonance peaks corresponding to individual microcavities that are connected in series. Series connected photonic crystal microcavities are further multiplexed in parallel using cascaded multimode interference power splitters to generate a high density silicon nanophotonic microarray comprising 64 photonic crystal microcavity sensors, all of which are interrogated simultaneously at the same instant of time.
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Highly efficient N-glycoproteomic sample preparation by combining C(18) and graphitized carbon adsorbents.
Anal Bioanal Chem
PUBLISHED: 02-20-2014
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Conventional N-glycoproteome analysis usually applies C18 reversed-phase (RP) adsorbent for sample purification, which will lead to unavoidable sample loss due to the high hydrophilicity of N-glycopeptides. In this study, a porous graphitized carbon (PGC) absorbent was combined with a C18 adsorbent for N-glycopeptide purification in comprehensive N-glycoproteome analysis based on the hydrophobic and polar interactions between carbon and N-glycans. It was observed that the small hydrophilic N-glycopeptides that cannot retain onto C18 adsorbent can be captured by the graphitized carbon, while the large hydrophobic N-glycopeptides that cannot retain onto the graphitized carbon can be feasibly captured by the C18 adsorbent. Comparing with sample purification by using C18 adsorbent only, 28.5 % more N-glycopeptides were identified by combining both C18 and PGC adsorbents. The C18-PGC strategy was further applied for both sample purification and pre-fractionation of a complex protein sample from HeLa cell. After hydrophilic interaction chromatography enrichment, 1,484 unique N-glycopeptides with 1,759 unique N-glycosylation sites were finally identified.
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Nanoparticle size matters in the formation of plasma protein coronas on Fe3O4 nanoparticles.
Colloids Surf B Biointerfaces
PUBLISHED: 02-19-2014
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When nanoparticles (NPs) enter into biological systems, proteins would interact with NPs to form the protein corona that can critically impact the biological identity of the nanomaterial. Owing to their fundamental scientific interest and potential applications, Fe3O4 NPs of different sizes have been developed for applications in cell separation and protein separation and as contrast agents in magnetic resonance imaging (MRI), etc. Here, we investigated whether nanoparticle size affects the formation of protein coronas around Fe3O4 NPs. Both the identification and quantification results demonstrated that particle size does play an important role in the formation of plasma protein coronas on Fe3O4 NPs; it not only influenced the protein composition of the formed plasma protein corona but also affected the abundances of the plasma proteins within the coronas. Understanding the different binding profiles of human plasma proteins on Fe3O4 NPs of different sizes would facilitate the exploration of the bio-distributions and biological fates of Fe3O4 NPs in biological systems.
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Pubertal bisphenol A exposure alters murine mammary stem cell function leading to early neoplasia in regenerated glands.
Cancer Prev Res (Phila)
PUBLISHED: 02-11-2014
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Perinatal exposure to bisphenol A (BPA) has been shown to cause aberrant mammary gland morphogenesis and mammary neoplastic transformation. Yet, the underlying mechanism is poorly understood. We tested the hypothesis that mammary glands exposed to BPA during a susceptible window may lead to its susceptibility to tumorigenesis through a stem cell-mediated mechanism. We exposed 21-day-old Balb/c mice to BPA by gavage (25 ?g/kg/d) during puberty for 3 weeks, and a subset of animals were further challenged with one oral dose (30 mg/kg) of 7,12-dimethylbenz(a)anthracene (DMBA) at 2 months of age. Primary mammary cells were isolated at 6 weeks, and 2 and 4 months of age for murine mammary stem cell (MaSC) quantification and function analysis. Pubertal exposure to the low-dose BPA increased lateral branches and hyperplasia in adult mammary glands and caused an acute increase of MaSC in 6-week-old glands and a delayed increase of luminal progenitors in 4-month-old adult gland. Most importantly, pubertal BPA exposure altered the function of MaSC from different age groups, causing early neoplastic lesions in their regenerated glands similar to those induced by DMBA exposure, which indicates that MaSCs are susceptible to BPA-induced transformation. Deep sequencing analysis on MaSC-enriched mammospheres identified a set of aberrantly expressed genes associated with early neoplastic lesions in patients with human breast cancer. Thus, our study for the first time shows that pubertal BPA exposure altered MaSC gene expression and function such that they induced early neoplastic transformation.
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Developmental and activity-dependent expression of LanCL1 confers antioxidant activity required for neuronal survival.
Dev. Cell
PUBLISHED: 02-10-2014
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Production of reactive oxygen species (ROS) increases with neuronal activity that accompanies synaptic development and function. Transcription-related factors and metabolic enzymes that are expressed in all tissues have been described to counteract neuronal ROS to prevent oxidative damage. Here, we describe the antioxidant gene LanCL1 that is prominently enriched in brain neurons. Its expression is developmentally regulated and induced by neuronal activity, neurotrophic factors implicated in neuronal plasticity and survival, and oxidative stress. Genetic deletion of LanCL1 causes enhanced accumulation of ROS in brain, as well as development-related lipid, protein, and DNA damage; mitochondrial dysfunction; and apoptotic neurodegeneration. LanCL1 transgene protects neurons from ROS. LanCL1 protein purified from eukaryotic cells catalyzes the formation of thioether products similar to glutathione S-transferase. These studies reveal a neuron-specific glutathione defense mechanism that is essential for neuronal function and survival.
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Analysis of the human urine endogenous peptides by nanoparticle extraction and mass spectrometry identification.
Anal. Chim. Acta
PUBLISHED: 02-04-2014
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Peptides in urine are excreted by kidney from the blood and tissues, which are composed of a large amount of hormones, cytokines, regulatory factors and the metabolized fragments of proteins. The peptide distribution in urine will reflect the physiological and pathophysiological processes in body. In past, limited information was reported about the composition of the peptides in urine. One possible reason is that the peptides in urine are fairly low abundant and there are high concentrations of salts and organic metabolites in the urine. In this report, we extracted the peptides from human urine by highly ordered mesoporous silica particles with the pore size of 2 nm, which will exclude the high molecular weight proteins over 12 kDa. The extracted peptides were then separated into fractions according to their molecular weight by size exclusion chromatography. Each of the fractions was further analyzed by MALDI-TOF MS and ?RPLC-MS/MS. Totally, 193 peptides were identified by two-dimensional SEC/?RPLC-MS/MS analysis. By analyzing the progenitor protein of the peptides; we found that two-thirds of the proteins differed from the reported urine proteome database, and the high abundant proteins in urine proteome were less detected in the urine peptidome. The developed extraction and separation methods were efficient for the profiling of the endogenous peptides in human urine. The peptidome in human urine was complementary to the human urinary proteome and may provide an emerging field for biomarker discovery.
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The outer membrane protein P2 (OmpP2) of Haemophilus parasuis induces proinflammatory cytokine mRNA expression in porcine alveolar macrophages.
Vet. J.
PUBLISHED: 02-04-2014
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Porins, expressed by Gram-negative bacteria, have several biological effects on host tissues or cells. The outer membrane protein P2 (OmpP2), a member of the porin family, has been identified as a multifunctional protein involved in the pathogenicity of Haemophilus parasuis. In the present study, it was shown that OmpP2 (0.5-10 ?g/mL) from H. parasuis Nagasaki strain up-regulated mRNA expression of interleukin (IL)-1?, IL-1?, IL-6 and IL-8 in porcine alveolar macrophages (PAM, 3D4/31) in vitro, in a dose-dependent manner. Moreover, OmpP2 porin induced a more prolonged cytokine response in PAM than that of the lipooligosaccharide (LOS) from this microorganism. The data demonstrate that H. parasuis OmpP2 can stimulate proinflammatory cytokine mRNA expression, suggesting that this particular porin might play an important role in the pathogenesis of disease caused by H. parasuis.
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Facile preparation of core-shell magnetic metal-organic framework nanospheres for the selective enrichment of endogenous peptides.
Chemistry
PUBLISHED: 01-30-2014
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Facile preparation of core-shell magnetic metal-organic framework nanospheres by a layer-by-layer approach is presented. The nanospheres have high surface area (285.89?cm(2) ?g(-1)), large pore volume (0.18?cm(3) ?g(-1)), two kinds of mesopores (2.50 and 4.72?nm), excellent magnetic responsivity (55.65?emu?g(-1)), structural stability, and good dispersibility. The combination of porosity, hydrophobicity, and uniform magnetism was exploited for effective enrichment of peptides with simultaneous exclusion of high molecular weight proteins. The nanospheres were successfully applied in the selective enrichment of endogenous peptides in human serum.
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Analysis of the endogenous human serum peptides by on-line extraction with restricted-access material and HPLC-MS/MS identification.
Talanta
PUBLISHED: 01-29-2014
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The selective extraction of endogenous serum peptides has been a challenge due to the high abundant proteins present in serum. Here a simple on-line extraction of peptides from human serum using strong cation-exchange diol silica restricted-access materials (SCX-RAM) coupled with two-dimensional RP-RP liquid chromatography mass spectrometry was developed. The operation of the on-line extraction system is simple to use and does not need complex equipments. The two-dimensional RP-RP was proved to be orthogonal and efficient to separate peptides extracted from human serum.
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The on-bead digestion of protein corona on nanoparticles by trypsin immobilized on the magnetic nanoparticle.
J Chromatogr A
PUBLISHED: 01-23-2014
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Proteins interacting with nanoparticles would form the protein coronas on the surface of nanoparticles in biological systems, which would critically impact the biological identities of nanoparticles and/or result in the physiological and pathological consequences. The enzymatic digestion of protein corona was the primary step to achieve the identification of protein components of the protein corona for the bottom-up proteomic approaches. In this study, the investigation on the tryptic digestion of protein corona by the immobilized trypsin on a magnetic nanoparticle was carried out for the first time. As a comparison with the usual overnight long-time digestion and the severe self-digestion of free trypsin, the on-bead digestion of protein corona by the immobilized trypsin could be accomplished within 1h, along with the significantly reduced self-digestion of trypsin and the improved reproducibility on the identification of proteins by the mass spectrometry-based proteomic approach. It showed that the number of identified bovine serum (BS) proteins on the commercial Fe3O4 nanoparticles was increased by 13% for the immobilized trypsin with 1h digestion as compared to that of using free trypsin with even overnight digestion. In addition, the on-bead digestion of using the immobilized trypsin was further applied on the identification of human plasma protein corona on the commercial Fe3O4 nanoparticles, which leads the efficient digestion of the human plasma proteins and the identification of 149 human plasma proteins corresponding to putative critical pathways and biological processes.
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PELP1 oncogenic functions involve alternative splicing via PRMT6.
Mol Oncol
PUBLISHED: 01-23-2014
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Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) is a proto-oncogene that functions as coactivator of the estrogen receptor and is an independent prognostic predictor of shorter survival of breast cancer patients. The dysregulation of PELP1 in breast cancer has been implicated in oncogenesis, metastasis, and therapy resistance. Although several aspects of PELP1 have been studied, a complete list of PELP1 target genes remains unknown, and the molecular mechanisms of PELP1 mediated oncogenesis remain elusive. In this study, we have performed a whole genome analysis to profile the PELP1 transcriptome by RNA-sequencing and identified 318 genes as PELP1 regulated genes. Pathway analysis revealed that PELP1 modulates several pathways including the molecular mechanisms of cancer, estrogen signaling, and breast cancer progression. Interestingly, RNA-seq analysis also revealed that PELP1 regulates the expression of several genes involved in alternative splicing. Accordingly, the PELP1 regulated genome includes several uniquely spliced isoforms. Mechanistic studies show that PELP1 binds RNA with a preference to poly-C, co-localizes with the splicing factor SC35 at nuclear speckles, and participates in alternative splicing. Further, PELP1 interacts with the arginine methyltransferase PRMT6 and modifies PRMT6 functions. Inhibition of PRMT6 reduced PELP1-mediated estrogen receptor activation, cellular proliferation, and colony formation. PELP1 and PRMT6 are co-recruited to estrogen receptor target genes, PELP1 knockdown affects the enrichment of histone H3R2 di-methylation, and PELP1 and PRMT6 coordinate to regulate the alternative splicing of genes involved in cancer. Collectively, our data suggest that PELP1 oncogenic functions involve alternative splicing leading to the activation of unique pathways that support tumor progression and that the PELP1-PRMT6 axis may be a potential target for breast cancer therapy.
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Synthesis of zwitterionic polymer brushes hybrid silica nanoparticles via controlled polymerization for highly efficient enrichment of glycopeptides.
Anal. Chim. Acta
PUBLISHED: 01-15-2014
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Zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) materials have been increasingly attractive in glycopeptide enrichment. However, the traditional ZIC-HILIC materials are modified with monolayer zwitterionic molecules on the surface, therefore, the hydrophilicity, detection sensitivity and loading capacity are limited. In this work, we synthesized novel silica nanoparticles with uniform poly(2-(methacryloyloxy)ethyl)dimethyl-(3-sul-fopropyl)ammonium hydroxide (PMSA) brushes grafted onto the surface via reversible addition-fragmentation chain transfer (RAFT) polymerization (denoted as SiO2-RAFT@PMSA). The resulting SiO2-RAFT@PMSA nanoparticles demonstrated low detection limit (10 fmol) and high recovery yield (over 88%) for glycopeptide enrichment from tryptic digest of human IgG. The SiO2-RAFT@PMSA nanoparticles were further applied for the analysis of mouse liver glycoproteome, a total number of 303 unique N-glycosylation sites corresponding to 185 glycoproteins was reliably profiled in three replicate nano-LC-MS/MS runs. Significantly, more glycopeptides were identified than those of nanoparticles, monolayer MSA molecules modified SiO2@single-MSA and nonuniform multi-layer PMSA brushes coated SiO2@PMSA, as well as commercial ZIC@HILIC beads and Click Maltose beads. The excellent performance of SiO2-RAFT@PMSA nanoparticles results from the non-fouling property, a large quantity of functional molecules and suitable link arms provided by uniform PMSA brushes, as well as efficient interaction between glycopeptides and uniform PMSA brushes. It is concluded that the synthesized SiO2-RAFT@PMSA nanoparticles exhibit great potential in glycoproteome analysis. Moreover, this strategy to modify nanopaticles with uniform polymer brushes via RAFT polymerization can also be explored to design other types of materials for bioseparation application.
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Preparation of polyhedral oligomeric silsesquioxane-based hybrid monolith by ring-opening polymerization and post-functionalization via thiol-ene click reaction.
J Chromatogr A
PUBLISHED: 01-06-2014
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A polyhedral oligomeric silsesquioxane (POSS) hybrid monolith was simply prepared by using octaglycidyldimethylsilyl POSS (POSS-epoxy) and cystamine dihydrochloride as monomers via ring-opening polymerization. The effects of composition of prepolymerization solution and polycondensation temperature on the morphology and permeability of monolithic column were investigated in detail. The obtained POSS hybrid monolithic column showed 3D skeleton morphology and exhibited high column efficiency of ?71,000 plates per meter in reversed-phase mechanism. Owing to this POSS hybrid monolith essentially possessing a great number of disulfide bonds, the monolith surface would expose thiol groups after reduction with dithiothreitol (DTT), which supplied active sites to functionalize with various alkene monomers via thiol-ene click reaction. The results indicated that the reduction with DTT could not destroy the 3D skeleton of hybrid monolith. Both stearyl methylacrylate (SMA) and benzyl methacrylate (BMA) were selected to functionalize the hybrid monolithic columns for reversed-phase liquid chromatography (RPLC), while [2-(methacryloyloxy)ethyl]-dimethyl-(3-sulfopropyl)-ammonium hydroxide (MSA) was used to modify the hybrid monolithic column in hydrophilic interaction chromatography (HILIC). These modified hybrid monolithic columns could be successfully applied for separation of small molecules with high efficiency. It is demonstrated that thiol-ene click reaction supplies a facile way to introduce various functional groups to the hybrid monolith possessing thiol groups. Furthermore, due to good permeability of the resulting hybrid monoliths, we also prepared long hybrid monolithic columns in narrow-bore capillaries. The highest column efficiency reached to ?70,000 plates using a 1-m-long column of 75?m i.d. with a peak capacity of 147 for isocratic chromatography, indicating potential application in separation and analysis of complex biosamples.
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Direct conversion of human fibroblasts into neuronal restricted progenitors.
J. Biol. Chem.
PUBLISHED: 01-02-2014
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Neuronal restricted progenitors (NRPs) represent a type of transitional intermediate cells that lie between multipotent neural progenitors and terminal differentiated neurons during neurogenesis. These NRPs have the ability to self-renew and differentiate into neurons, but not into glial cells, which is considered an advantage for cellular therapy of human neurodegenerative diseases. However, difficulty in the extraction of highly purified NRPs from normal nervous tissue prevents further studies and applications. In this study, we report the conversion of human fetal fibroblasts into human induced NRPs (hiNRPs) in 11 days by using just three defined factors: Sox2, c-Myc, and either Brn2 or Brn4. The hiNRPs exhibited distinct neuronal characteristics, including cell morphology, multiple neuronal marker expression, self-renewal capacity, and a genome-wide transcriptional profile. Moreover, hiNRPs were able to differentiate into various terminal neurons with functional membrane properties but not glial cells. Direct generation of hiNRPs from somatic cells will provide a new source of cells for cellular replacement therapy of human neurodegenerative diseases.
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Generation of multi-gene knockout rabbits using the Cas9/gRNA system.
Cell Regen (Lond)
PUBLISHED: 01-01-2014
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The prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) is a simple, robust and efficient technique for gene targeting in model organisms such as zebrafish, mice and rats. In this report, we applied CRISPR technology to rabbits by microinjection of Cas9 mRNA and guided RNA (gRNA) into the cytoplasm of pronuclear-stage embryos. We achieved biallelic gene knockout (KO) rabbits by injection of 1 gene (IL2rg) or 2 gene (IL2rg and RAG1) Cas9 mRNA and gRNA with an efficiency of 100%. We also tested the efficiency of multiple gene KOs in early rabbit embryos and found that the efficiency of simultaneous gene mutation on target sites is as high as 100% for 3 genes (IL2rg, RAG1 and RAG2) and 33.3% for 5 genes (IL2rg, RAG1, RAG2, TIKI1 and ALB). Our results demonstrate that the Cas9/gRNA system is a highly efficient and fast tool not only for single-gene editing but also for multi-gene editing in rabbits.
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Establishment of a Rabbit Oct4 Promoter-Based EGFP Reporter System.
PLoS ONE
PUBLISHED: 01-01-2014
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Rabbits are commonly used as laboratory animal models to investigate human diseases and phylogenetic development. However, pluripotent stem cells that contribute to germline transmission have yet to be established in rabbits. The transcription factor Oct4, also known as Pou5f1, is considered essential for the maintenance of the pluripotency of stem cells. Hence, pluripotent cells can be identified by monitoring Oct4 expression using a well-established Oct4 promoter-based reporter system. This study developed a rabbit Oct4 promoter-based enhanced green fluorescent protein (EGFP) reporter system by transfecting pROP2-EGFP into rabbit fetal fibroblasts (RFFs). The transgenic RFFs were used as donor cells for somatic cell nuclear transfer (SCNT). The EGFP expression was detected in the blastocysts and genital ridges of SCNT fetuses. Fibroblasts and neural stem cells (NSCs) were derived from the SCNT fetuses. EGFP was also reactivated in blastocysts after the second SCNT, and induced pluripotent stem cells (iPSCs) were obtained after reprogramming using Yamanaka's factors. The results above indicated that a rabbit reporter system used to monitor the differentiating status of cells was successfully developed.
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Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling.
Clin Proteomics
PUBLISHED: 01-01-2014
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Dysregulation of glycoproteins is closely related with many diseases. Quantitative proteomics methods are powerful tools for the detection of glycoprotein alterations. However, in almost all quantitative glycoproteomics studies, trypsin is used as the only protease to digest proteins. This conventional method is unable to quantify N-glycosites in very short or long tryptic peptides and so comprehensive glycoproteomics analysis cannot be achieved.
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Evolution with reinforcement learning in negotiation.
PLoS ONE
PUBLISHED: 01-01-2014
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Adaptive behavior depends less on the details of the negotiation process and makes more robust predictions in the long term as compared to in the short term. However, the extant literature on population dynamics for behavior adjustment has only examined the current situation. To offset this limitation, we propose a synergy of evolutionary algorithm and reinforcement learning to investigate long-term collective performance and strategy evolution. The model adopts reinforcement learning with a tradeoff between historical and current information to make decisions when the strategies of agents evolve through repeated interactions. The results demonstrate that the strategies in populations converge to stable states, and the agents gradually form steady negotiation habits. Agents that adopt reinforcement learning perform better in payoff, fairness, and stableness than their counterparts using classic evolutionary algorithm.
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Structural insight into the tetramerization of an iterative ketoreductase siam through aromatic residues in the interfaces.
PLoS ONE
PUBLISHED: 01-01-2014
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In the biosynthesis of polyketides, ketoreductases (KRs) are an important group of enzymes that determine the chiralities of the carbon backbones. SiaM is a special member of this group that can recognize substrates with different lengths and can be used iteratively. Here we report the crystal structure of SiaM. Structural analysis indicates that the overall structure resembles those of other KRs. However, significant disparity can be found in the conserved LDD motif that is replaced with IRD motif in SiaM. The isoleucine and aspartic acid residues take similar orientations as leucine and aspartic acid in the conserved LDD motif, while the arginine residue points out towards the solvent. PISA analysis shows that SiaM forms a tetramer. Several aromatic residues are found in the interfaces, which have aromatic stacking interactions with the aromatic residues in the neighboring protomers. Mutagenesis studies performed on the aromatic residues show that these sites are important for maintaining the structural integrity of SiaM. However, the aromatic residues contribute differently to the enzymatic activity. In the N-terminal interface, the aromatic residues can be replaced with leucine without affecting the enzymatic activity while, in the other interface, such mutations abolish the enzymatic activity.
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[Apoptosis of A549 cells induced by cloned Noxa gene].
Sichuan Da Xue Xue Bao Yi Xue Ban
PUBLISHED: 12-12-2013
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To clone the Noxa gene and to observe the apoptosis of A549 cells transfected with the recombinant plasmid of pcDNA-Noxa.
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Deletion of PDZD7 Disrupts the Usher Syndrome Type 2 Protein Complex in Cochlear Hair Cells and Causes Hearing Loss in Mice.
Hum. Mol. Genet.
PUBLISHED: 12-11-2013
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Usher syndrome type 2 (USH2) is the predominant form of USH, a leading genetic cause of combined deafness and blindness. PDZD7, a paralog of two USH causative genes, USH1C and USH2D (WHRN), was recently reported to be implicated in USH2 and nonsyndromic deafness. It encodes a protein with multiple PDZ domains. To understand the biological function of PDZD7 and the pathogenic mechanism caused by PDZD7 mutations, we generated and thoroughly characterized a Pdzd7 knockout mouse model. The Pdzd7 knockout mice exhibit congenital profound deafness, as assessed by ABR, DPOAE and CM tests, and normal vestibular function, as assessed by their behaviors. Lack of PDZD7 leads to disorganization of stereocilia bundles and reduction in mechanotransduction currents and sensitivity in cochlear outer hair cells. At the molecular level, PDZD7 determines localization of the USH2 protein complex, composed of USH2A, GPR98, and WHRN, to ankle links in developing cochlear hair cells, likely through its direct interactions with these three proteins. The localization of PDZD7 to the ankle links of cochlear hair bundles also relies on USH2 proteins. In photoreceptors of Pdzd7 knockout mice, the three USH2 proteins largely remain unchanged at the periciliary membrane complex. The electroretinogram responses of both rod and cone photoreceptors are normal in knockout mice at one month of age. Therefore, although the organization of the USH2 complex appears different in photoreceptors, it is clear that PDZD7 plays an essential role in organizing the USH2 complex at ankle links in developing cochlear hair cells.
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Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy.
J. Proteome Res.
PUBLISHED: 11-25-2013
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Global quantification of the single amino-acid variations (SAAVs) is essential to investigate the roles of SAAVs in disease progression. However, few efforts have been made on this issue due to the lack of high -throughput approach. Here we presented a strategy by integration of the stable isotope dimethyl labeling with variation-associated database search to globally quantify the SAAVs at the first time. A protein database containing 87?745 amino acid variant sequences and 73?910 UniProtKB/Swiss-Prot canonical protein entries was constructed for database search, and higher energy collisional dissociation combined with collision-induced dissociation fragmentation modes were applied to improve the quantification coverage of SAAVs. Compared with target proteomics in which only a few sites could be quantified, as many as 282 unique SAAVs sites were quantified between hepatocellular carcinoma (HCC) and normal human liver tissues by our strategy. The variation rates in different samples were evaluated, and some interesting SAAVs with significant increase normalized quantification ratios, such as T1406N in CPS1 and S197R in HTATIP2, were observed to highly associate with HCC progression. Therefore, the newly developed strategy enables the large-scale comparative analysis of variations at the protein level and holds a promising future in the research related to variations.
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Multiplexed detection of xylene and trichloroethylene in water by photonic crystal absorption spectroscopy.
Opt Lett
PUBLISHED: 10-02-2013
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We experimentally demonstrate simultaneous selective detection of xylene and trichloroethylene (TCE) using multiplexed photonic crystal waveguides (PCWs) by near-infrared optical absorption spectroscopy on a chip. Based on the slow light effect of photonic crystal structure, the sensitivity of our device is enhanced to 1 ppb (v/v) for xylene and 10 ppb (v/v) for TCE in water. Multiplexing is enabled by multimode interference power splitters and Y-combiners that integrate multiple PCWs on a silicon chip in a silicon-on-insulator platform.
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Facile synthesis of yolk-shell magnetic mesoporous carbon microspheres for efficient enrichment of low abundance peptides.
Nanoscale
PUBLISHED: 09-23-2013
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Magnetic mesoporous carbon microspheres with a yolk-shell structure (YSMMCS) have been prepared via a new in situ carbon source strategy. The material was fabricated by two shells coated onto the Fe3O4 particles; the inner dense and thick silica shell could protect the magnetic core from harsh acidic solvents as well as induce the void between the core and the outer shell for the yolk-shell structure, while the outer organosilica shell was used as the template and carbon source for in situ preparation of a carbon shell with mesoporous structure. A C18-alkyl chain was incorporated in situ as the carbon precursor efficiently, avoiding the conventional infiltration step, which was very difficult to manipulate and time-consuming with the possibility of losing the carbon precursor. The resulting yolk-shell magnetic mesoporous carbon microspheres exhibited a high surface area (273.15 m(2) g(-1)), a large pore volume (0.31 cm(3) g(-1)), and a strong magnetic response (a saturation magnetization value of 34.57 emu g(-1)). As a result of the void between the core and the outer shell and the ?-? stacking effect, adsorption capacity reached 191.64 mg g(-1) by using Rhodamine B as a standard analyte, indicating the great potential application of the material as drug carriers. Owing to the inherent hydrophobicity and high surface area, the composite material showed better performance in the enrichment of peptides than a magnetic mesoporous silica material (Fe2O3@nSiO2@mSiO2). According to the LC-MS/MS results, about 51 and 29 nonredundant peptides were identified from tryptic digests of 5 nM BSA. Additionally, taking advantage of the mesoporous structure and strong magnetic response, the material was utilized to selectively extract low abundance endogenous peptides from human serum in the presence of high abundance proteins. Based on the LC-MS/MS results, 962 endogenous peptides were obtained by 2.5 mg YSMMCS relative to 539 endogenous peptides by 5 mg Fe2O3@nSiO2@mSiO2, confirming the outstanding performance of YSMMCS in peptidome analysis.
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Layer-by-layer assembly of multilayer polysaccharide coated magnetic nanoparticles for the selective enrichment of glycopeptides.
Chem. Commun. (Camb.)
PUBLISHED: 09-03-2013
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Magnetic nanoparticles (MNPs) coated with multilayer polysaccharide shells have been fabricated using a layer-by-layer approach via the alternate deposition of hyaluronan (HA) and chitosan (CS) onto the surface, and the hydrophilic materials were utilized for effective and selective enrichment of glycopeptides in biological samples.
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Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow.
Sci Rep
PUBLISHED: 08-19-2013
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Due to its constitutive activity and ubiquitous distribution, CK2 is the most pleiotropic kinase among the individual members of the protein kinase superfamily. Identification of CK2 substrates is vital to decipher its role in biological processes. However, only a limited number of CK2 substrates were identified so far. In this study, we developed an integrated phosphoproteomics workflow to identify the CK2 substrates in large scale. First, in vitro kinase reactions with immobilized proteomes were combined with quantitative phosphoproteomics to identify in vitro CK2 phosphorylation sites, which leaded to identification of 988 sites from 581 protein substrates. To reduce false positives, we proposed an approach by comparing these in vitro sites with the public databases that collect in vivo phosphorylation sites. After the removal of the sites that were excluded in the databases, 605 high confident CK2 sites corresponding to 356 proteins were retained. The CK2 substrates identified in this study were based on the discovery mode, in which an unbiased overview of CK2 substrates was provided. Our result revealed that CK2 substrates were significantly enriched in the spliceosomal proteins, indicating CK2 might regulate the functions of spliceosome.
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[Preparation and modification of polyhedral oligomeric silsesquioxane-containing hybrid monolithic capillary columns].
Se Pu
PUBLISHED: 08-01-2013
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Two kinds of hybrid monolithic capillary columns were prepared via free radical polymerization. First, the hybrid monolithic column was in situ fabricated by using two polyhedral oligomeric silsesquioxanes (POSS), POSS-methacryl substituted (cage mixture, n = 8, 10, 12) (POSS-MA) and POSS-(1-propylmethacrylate)-heptaisobutyl substituted (Bu-POSS), as crosslinker and monomer, respectively, in the presence of porogenic solvents (propanol/ PEG400) and initiator (azodisobutyronitrile). Second, the hybrid monolithic column was similarly prepared by using POSS-MA, as sole monomer under the same conditions. The resulting two kinds of hybrid monolithic columns, poly (Bu-POSS-co-POSS-MA) and poly (POSS-MA), were characterized and applied for the separation of alkylbenzenes by capillary liquid chromatography (cLC), showing good mechanical stability and reproducibility. Additionally, the poly (POSS-MA) monolith could be easily modified with other organic monomers, such as stearyl methacrylate (SMA) and benzyl metacrylate (BeMA), with the presence of methacryl groups on the surface of the poly(POSS-MA) monolith. Compared with the raw poly(POSS-MA) monolith, the post-modified poly(POSS-MA) monolith exhibited higher column efficiency and better selectivity. This simple process of using POSS reagents via free radical polymerization is providing a novel way for the preparation of the organic-silica hybrid monolithic columns.
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Polyacrylamide gel with switchable trypsin activity for analysis of proteins.
Anal. Chem.
PUBLISHED: 07-19-2013
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Trypsin was immobilized on a variety of materials to improve digestion efficiency. However, because the immobilized trypsin will digest proteins during electrophoresis, direct immobilization of active trypsin in polyacrylamide gel will compromise the protein separation. To overcome this problem, here we report a novel polyacrylamide gel with switchable trypsin activity. It was prepared by copolymerization of the PEG-trypsin-aprotinin complex during the gel-casting step. Because the inhibitor aprotinin binds strongly with trypsin at alkaline pH, this novel gel does not display hydrolytic activity during electrophoresis. After electrophoresis, the activity of trypsin embedded in gel could be recovered by simply washing away the bound inhibitor at a low pH. It was demonstrated that this unique switchable activity design allowed high resolution of the complex protein mixture during electrophoresis and highly efficient digestion of the separated proteins in situ in the gel after electrophoresis.
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Stereospecific Biosynthesis of ?-Methyltryptophan from L-Tryptophan Features a Stereochemical Switch.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 07-18-2013
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Make the switch: The three-enzyme cassette MarG/H/I is responsible for stereospecific biosynthesis of ?-methyltryptophan from L-tryptophan (1). MarG/I convert 1 into (2S,3R)-?-methyltryptophan, while MarG/I combined with MarH convert 1 into (2S,3S)-?-methyltryptophan. MarH serves as a stereochemical switch by catalyzing the stereoinversion of the ?-stereocenter.
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An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.
J Proteomics
PUBLISHED: 07-17-2013
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Protein phosphorylation is one of the most common post-translational modifications. It plays key roles in regulating diverse biological processes of liver tissues. To better understand the role of protein phosphorylation in liver functions, it is essential to perform in-depth phosphoproteome analysis of human liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid chromatography (RP-RPLC) approach with both RPLC separations operated with optimized acidic mobile phase was developed. High orthogonal separation was achieved by trypsin digestion of the Glu-C generated peptides in the fractions collected from the first RPLC separation. The phosphoproteome coverage was further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526 nonredundant phosphoproteins were finally identified from normal human liver tissues. Of these sites, 15,229 sites were confidently localized with Ascore?13. This dataset was the largest phosphoproteome dataset of human liver. It can be a public resource for the liver research community and holds promise for further biology studies.
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Cell nucleus targeting for living cell extraction of nucleic acid associated proteins with intracellular nanoprobes of magnetic carbon nanotubes.
Anal. Chem.
PUBLISHED: 07-12-2013
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Since nanoparticles could be ingested by cells naturally and target at a specific cellular location as designed, the extraction of intracellular proteins from living cells for large-scale analysis by nanoprobes seems to be ideally possible. Nucleic acid associated proteins (NAaP) take the crucial position during biological processes in maintaining and regulating gene structure and gene related behaviors, yet there are still challenges during the global investigation of intracellular NAaP, especially from living cells. In this work, a strategy to extract intracellular proteins from living cells with the magnetic carbon nanotube (oMWCNT@Fe3O4) as an intracellular probe is developed, to achieve the high throughput analysis of NAaP from living human hepatoma BEL-7402 cells with a mass spectrometry-based proteomic approach. Due to the specific intracellular localization of the magnetic carbon nanotubes around nuclei and its strong interaction with nucleic acids, the highly efficient extraction was realized for cellular NAaP from living cells, with the capability of identifying 2383 intracellular NAaP from only ca. 10,000 living cells. This method exhibited potential applications in dynamic and in situ analysis of intracellular proteins.
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Determination of CK2 specificity and substrates by proteome-derived peptide libraries.
J. Proteome Res.
PUBLISHED: 07-12-2013
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Understanding the specificity of kinases enables prediction of their substrates and uncovering kinase functions in signaling pathways. Traditionally synthesized peptide libraries are used to determine the kinase specificity. In this study, a proteomics-based method was developed to determine the specificity of kinase by taking the advantages of proteome-derived peptide libraries and quantitative proteomics. Proteome-derived peptide libraries were constructed by digesting proteins in total cell lysate followed with dephosphorylation of the resulting peptides. After incubating the peptide libraries with/without CK2 for in vitro kinase assay, stable isotopic labeling based quantitative phosphoproteomics was applied to distinguish the in vitro phosphosites generated by CK2. By using the above approach, 404 CK2 in vitro phosphosites were identified by 1D LC-MS/MS. Those sites allowed the statistic determination of the CK2 specificity. In addition to the easy construction of the proteome-derived peptide library, another significant advantage of this method over the method with synthesized peptide libraries is that the identified phosphosites could be directly mapped to proteins for the screening of putative kinase substrates. It was found that the confidence for substrate identification could be significantly improved by comparing the in vitro CK2 sites with the in vivo sites identified by phosphoproteomics analysis of the same cell lines. By applying this integrated strategy, 138 phosphosites from 105 putative CK2 substrates of high confidence were determined.
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