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Biomedical subjects

Pengyuan Yang

Publications and source records attributed to Pengyuan Yang.

At least 19 recordsLinked to original sources
PubMed2006

Investigation on glycosylation patterns of proteins from human liver cancer cell lines based on the multiplexed proteomics technology.

Glycosylation, a very important post-translational modification of proteins, is increasingly coming into notice. However, large-scale, throughput investigations on glycosylated proteins are few. We applied a sensitive and fast fluorescence-based multiplexed proteomics (MP) technology which included two-dimensional gel electrophoresis (2-DE) followed by the fluorescence staining of glycoprotein and mass spectrometry identification for the purpose of constructing glycoprotein databases of the typical human hepatocellular carcinoma cell lines including Hep3B cell line without metastasis and MHCC97H with highly metastatic potential as well as the control non-tumor Chang liver cell. 74+/-2 (n=3), 78+/-3 (n=3) and 72+/-5 (n=3) glycoprotein spots were detected on 2-DE gels from Chang liver, Hep3B and MHCC97H cell sample using this MP technique, respectively. In all, 80 glycoproteins from three cell lines were successfully identified via peptide mass profiling using MALDI-TOF-MS/MS and the identified glycoproteins were annotated to our databases. In addition, we also found the glycosylation pattern differences among these three cell lines. The protein glycosylation alteration would be have great significance for the diagnosis of HCC and prediction of its metastasis. This study described the construction of glycosylation patterns of proteins and glycoproteome databases of human liver cells by the novel technological platform. The glycoproteome databases also provide essential basis for following study.

Animals↗
PubMed2006

Subproteomic study of hepatitis C virus replicon reveals Ras-GTPase-activating protein binding protein 1 as potential HCV RC component.

Hepatitis C virus (HCV) RNA synthesis takes place on a detergent resistant membrane (DRM) structure. To identify potential cellular proteins related to HCV replication complexes (RC), we purified DRMs from HCV subgenomic replicon cells and its parental Huh7 cells. The proteins of DRM fractions were separated by two-dimensional gel electrophoresis and identified by mass spectrometry. Comparing with parental Huh7 cells, 60 proteins were up-regulated while 14 proteins were down-regulated in HCV replicon cells. Ras-GTPase-activating protein binding protein 1 (G3BP1), one of the elevated proteins, was found to be associated with HCV NS5B and knockdown of G3BP1 by siRNA in HCV replicon cells significantly reduced HCV replication, which may indicate it a potential component of HCV RC. These results suggest that HCV viral gene and proteins may regulate the presence of host cellular proteins in DRM, ensure appropriate concentrations of replication components, and hence control the rates or efficiencies of HCV replication.

Amino Acid Sequence↗
PubMed2006

Assembly-controlled biocompatible interface on a microchip: strategy to highly efficient proteolysis.

A biocompatible interface was constructed on a microchip by using the layer-by-layer (LBL) assembly of charged polysaccharides incorporating proteases for highly efficient proteolysis. The controlled assembly of natural polyelectrolytes and the enzyme-adsorption step were monitored by using a quartz-crystal microbalance and atomic force microscopy (AFM). Such a multilayer-assembled membrane provides a biocompatible interconnected network with high enzyme-loading capacity. The maximum digestion rate of the adsorbed trypsin in a microchannel was significantly accelerated to 1600 mM min(-1) microg(-1), compared with the tryptic digestion in solution. Based on the Langmuir isotherm model, the thermodynamic constant of adsorption K was calculated to be 1.6 x 10(5) M(-1) and the maximum adsorption loading Gammamax was 3.6 x 10(-6) mol m(-2), 30 times more than a monolayer of trypsin on the native surface. The tunable interface containing trypsin was employed to construct a microchip reactor for digestion of femtomoles of proteins and the produced peptides were analyzed by MALDI-TOF mass spectroscopy. The efficient on-chip proteolysis was obtained within a few seconds, and the identification of biological samples was feasible.

Biocompatible Materials↗
PubMed2006

Nanopore-based proteolytic reactor for sensitive and comprehensive proteomic analyses.

Various silica-based microreactors have been designed that use enzyme immobilization to address technical concerns in proteolysis including inefficient and incomplete protein digestion. Most of current designs for proteolytic reactors can improve either protease stability or proteolysis efficiency of individual protein(s). However, the desired features such as rapid digestion, larger sequence coverage, and high sensitivity have not been achieved by a single microreactor design for broad range proteins with diverse physical properties. Here, unlike conventional enzyme immobilization strategies, we describe a novel proteolytic nanoreactor based on the unique three-dimensional nanopore structure of our newly synthesized mesoporous silica (MPS), FDU-12, which integrates substrate enrichment, "reagent-free" protein denaturation, and efficient proteolytic digestion. In our design, protein substrates were first captured by MPS nanopore structure and were concentrated from the solution. Following the pH change and applying trypsin, the denaturation and concurrent proteolysis of broad-range proteins were efficiently achieved. In minutes, many more sample peptides from the in-nanopore digestion of protein mixtures were detected by mass spectrometry, resulting in the identifications of a broad range of diverse proteins with high sequence coverage. The unique features of FDU-12 nanostructure that allow rapid, complete proteolysis and resulting enhanced sequence coverage of individual proteins were investigated by using Raman spectroscopy and comparative studies with respect to other MPSs.

Animals↗
PubMed2006

Determination of honokiol and magnolol in cortex Magnoliae Officinalis by capillary electrophoresis with electrochemical detection.

Capillary electrophoresis with electrochemical detection has been employed for the determination of honokiol and magnolol in Cortex Magnoliae Officinalis (i.e. Magnolia Bark) for the first time. Effects of several important factors such as the concentration and the acidity of the running buffer, separation voltage, injection time, and detection potential were investigated to acquire the optimum conditions. The detection electrode was a 300 microm diameter carbon disc electrode at a working potential of +0.90 V (versus saturated calomel electrode (SCE)). The two analytes can be well separated within 6 min in a 40 cm length fused silica capillary at a separation voltage of 18 kV in a 50mM borate buffer (pH 9.2). The relation between peak current and analyte concentration was linear over about three orders of magnitude with the detection limits (S/N=3) of 0.38 and 0.51 microM for honokiol and magnolol, respectively. The proposed method has been successfully applied to monitor the two bioactive constituents in the real plant samples with satisfactory assay results.

Anti-Arrhythmia Agents↗
PubMed2006

Construction of a biomimetic surface on microfluidic chips for biofouling resistance.

A biomimetic surface has been formed on the poly(methyl methacrylate) (PMMA) microfluidic chips for biofouling resistance on the basis of a simple modification. Accordingly, an amphiphilic phospholipid copolymer of 2-methacryloyloxyethyl phosphorylcholine and n-butyl methacrylate (PMB) was developed to introduce the phosphorylcholine functional groups onto the PMMA surface via the anchoring of hydrophobic n-butyl methacrylate units. The 2-methacryloyloxyethyl phosphorylcholine segments could form hydrophilic domains, considered to be located on the surface, to provide a biocompatible surface. X-ray photoelectron spectroscopy and Fourier transform infrared spectra confirmed the success of surface functionalization. The PMB-modified microchips containing phosphorylcholine moieties exhibited more stable electroosmotic mobility compared with the untreated one. In addition to being characterized for minimized nonspecific adhesion of serum proteins and plasma platelets, the PMB-functionalized microchannels have been exemplified by electrophoresis of proteins. This one-step procedure offers an effective approach for a biomimetic surface design on microfluidic chips, which is promising in high-throughput and complex biological analysis.

Biomimetics↗
PubMed2006

Deposition of PEG onto PMMA microchannel surface to minimize nonspecific adsorption.

A protein-resistant surface has been constructed on the poly(methyl methacrylate) (PMMA) microfluidic chips based on a one-step modification. The copolymer of butyl methacrylate (BMA) and poly(ethylene glycol) methyl ether methacrylate (PEGMA) is synthesized to introduce a dense PEG molecular brush-like coating on the PMMA microchannel surfaces via the anchoring effect of the hydrophobic BMA units. The PEGMA segments could produce hydrophilic domains formed on the interface so as to achieve stable electroosmotic flow, and less nonspecific adsorption toward biomolecules. The modification procedure and the properties of the poly(BMA-co-PEGMA)-coated surface have been characterized by FT-IR spectroscopy, confocal fluorescence microscopy, X-ray photoelectron spectroscopy and scanning electron microscopy. The water contact angle and electroosmotic flow of PEG-modified PMMA microchip are measured to be 36 degrees and 5.4 x 10(-4) cm(2) V(-1) s(-1), while those of 73 degrees and 1.9 x 10(-4) cm(2) V(-1) s(-1) for native one, respectively. The PEG-modified microchip has been applied for the electrophoresis separation of proteins, corresponding to the theoretical efficiencies about 16 300 and 412 300 plates m(-1). In the interest of achieving efficient separation while minimizing biofoulings from the serum and plasma, the fabrication of PEG-coated microfluidic chips would provide a biocompatible platform for complex biological analysis.

Adsorption↗
PubMed2006

Zeolite nanoparticle modified microchip reactor for efficient protein digestion.

An enzymatic microreactor has been fabricated based on the poly(methyl methacrylate) (PMMA) microchchip surface-modified with zeolite nanoparticles. By introducing the silanol functional groups, the surface of PMMA microchannel has been successfully modified with silicalite-1 nanoparticle for the first time due to its large external surface area and high dispersibility in solutions. Trypsin can be stably immobilized in the microchannel to form a bioreactor using silica sol-gel matrix. The immobilization of enzyme can be realized with a stable gel network through a silicon-oxygen-silicon bridge via tethering to those silanol groups, which has been investigated by scanning electron microscopy and microchip capillary electrophoresis with laser-induced fluorescence detection. The maximum proteolytic rate constant of the immobilized trypsin is measured to be about 6.6 mM s(-1). Using matrix assisted laser desorption and ionization time-of-flight mass spectrometry, the proposed microreactor provides an efficient digestion of cytochrome c and bovine serum albumin at a fast flow rate of 4.0 microL min(-1), which affords a very short reaction time of less than 5 s.

Amino Acid Sequence↗
PubMed2006

Multilayer-assembled microchip for enzyme immobilization as reactor toward low-level protein identification.

A microchip reactor has been developed on the basis of a layer-by-layer approach for fast and sensitive digestion of proteins. The resulting peptide analysis has been carried out by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Natural polysaccharides, positively charged chitosan (CS), and negatively charged hyaluronic acid (HA) were multilayer-assembled onto the surface of a poly(ethylene terephthalate) (PET) microfluidic chip to form a microstructured and biocompatible network for enzyme immobilization. The construction of CS/HA assembled multilayers on the PET substrate was characterized by AFM imaging, ATR-IR, and contact angle measurements. The controlled adsorption of trypsin in the multilayer membrane was monitored using a quartz crystal microbalance and an enzymatic activity assay. The maximum proteolytic velocity of the adsorbed trypsin was approximately 600 mM/min mug, thousands of times faster than that in solution. BSA, myoglobin, and cytochrome c were used as model substrates for the tryptic digestion. The standard proteins were identified at a low femtomole per analysis at a concentration of 0.5 ng/muL with the digestion time <5s. This simple technique may offer a potential solution for low-level protein analysis.

Adsorption↗
PubMed2006

Rapid separation and determination of carbamate insecticides using isocratic elution pressurized capillary electrochromatography.

An isocratic elution pressurized CEC (pCEC) system was used to separate and determine ten carbamate insecticides. It was found that introduction of the electrical field, supplementary pressure, and SDS in the proposed method greatly improved the speed, column efficiency, selectivity, and repeatability for separation and determination of carbamates. On a capillary column of 75 microm ID packed with 3 microm octadecyl silica, baseline separation and detection of ten analytes was performed by using a mobile phase consisting of 30% v/v ACN and 70% v/v of 5 mmol/L ammonium acetate (pH 6.5) containing 1 mmol/L SDS and 0.01% triethylamine (TEA). Under the optimum conditions ten carbamate insecticides could be completely separated within 20 min. For the real vegetable samples, an SPE procedure for the cleanup of matrices was carried out prior to pCEC analysis. The detection limits of 0.05-1.6 mg/kg for ten carbamates and mean recoveries of 51.3-109.2% for eight kinds of vegetable samples at different concentrations of carbamates with RSD less than 11.4% were obtained, respectively. The proposed method has been proved to be effective in the rapid analysis of carbamate residues in vegetables.

Buffers↗
PubMed2006

Carbon nanotube/poly(methyl methacrylate) composite electrode for capillary electrophoretic measurement of honokiol and magnolol in Cortex Magnoliae Officinalis.

This paper describes the development and the application of a novel carbon nanotube/poly(methyl methacrylate) (CNT/PMMA) composite electrode as a sensitive amperometric detector of CE. The composite electrode was fabricated on the basis of the in situ polymerization of a mixture of CNT and prepolymerized methylmethacrylate in the microchannel of a piece of fused-silica capillary under heat. The performance of this unique system has been demonstrated by separating and detecting honokiol and magnolol in traditional Chinese medicine, Cortex Magnoliae Officinalis. Factors influencing their separation and detection processes were examined and optimized. Honokiol and magnolol were well separated within 7 min in a 40 cm long capillary at a separation voltage of 15 kV using a 50 mM borate buffer (pH 9.2). The new CNT-based CE detector offered significantly lower operating potentials, yielded substantially enhanced S/N characteristics, and exhibited resistance to surface fouling and hence enhanced stability. It demonstrated long-term stability and reproducibility with RSDs of less than 5% for the peak current (n = 9) and should also find a wide range of applications in microchip CE, flowing injection analysis, and other microfluidic analysis systems.

Biphenyl Compounds↗
PubMed2006

Expressed proteome analysis of human hepatocellular carcinoma in nude mice (LCI-D20) with high metastasis potential.

We report for the first time an expressed proteome for human hepatocellular carcinoma (HCC) in nude mice model. Most cases of human liver cancer are HCC with highly metastatic ability. Therefore, the early prediction or diagnosis and effective treatment are the key points of research. We have previously successfully established a human HCC nude mice model (LCI-D20) with high metastasis potential. To understand better the tumor biology of HCC it is worth to explore the relativity of all expressed protein profiles in the LCI-D20 HCC nude mice model. With advanced proteomics technologies, we have carried out a proteomic analysis with following stages: protein sample preparation of cancer tissue, including total cellular extraction and sequential fractionation, 2-DE and 2-D LC separation, ESI/MALDI-MS/MS identification, as well as data-dependent bioinformatics. The identified proteins were classified bioinformatically respective to their function, biological process and intracellular localization. Some important proteins found in HCC, e.g. metabolism enzymes, proteins regulating cell motility, signaling proteins, and heat shock proteins, are discussed in terms of their metastasis.

Animals↗
PubMed2006

Proteome analysis of human liver carcinoma Huh7 cells harboring hepatitis C virus subgenomic replicon.

Chronic infection by hepatitis C virus (HCV) is closely correlated with serious liver diseases. Although considerable progress has been made during recent years, the mechanism of replication and pathogenesis of HCV infection are still elusive. We have applied proteomic techniques in this work to globally analyze the protein expression profiles of a human liver cell lines Huh7 in absence and presence of HCV replication, aiming at elucidating the components of HCV replication and the cellular responses to HCV replication. The protein mixtures of three subcellular fractions from Huh7 and Huh7-HCV were separated by 2-DE under various pH gradients. Differentially expressed spots were identified by MALDI-TOF MS, followed by database searching. A total of 179 comparative proteins were identified unambiguously, including proteins associated with host cytoskeleton, intracellular traffic, oxidative and ER stress, proteasome degradation, translation, apoptosis, proliferation, etc. Host proteins known to interact with HCV proteins, such as HSP27, alpha-actinin, nucleolin and eukaryotic initiation factor 4A-I, were elevated in Huh7-HCV cells. Our study provides the global information of proteomic alteration of Huh7 cells in the presence of HCV replication and the clues for further understanding of the mechanism of HCV replication and pathogenesis.

Carcinoma, Hepatocellular↗
PubMed2006

Highly efficient enrichment and subsequent digestion of proteins in the mesoporous molecular sieve silicate SBA-15 for matrix-assisted laser desorption/ionization mass spectrometry with time-of-flight/time-of-flight analyzer peptide mapping.

Based on a previous study of protein digestion inside the nanoreactor channels of the mesoporous molecular sieve silicate SBA-15 (Chem. Eur. J. 2005, 11: 5391), we have developed a highly efficient enrichment and subsequent tryptic digestion of proteins in SBA-15 for matrix-assisted laser desorption/ionization mass spectrometry with time-of-flight/time-of-flight analyzer (MALDI-TOF/TOF) peptide mapping. The performance of the method is exemplified with myoglobin and cytochrome c. First, protein adsorption isotherms for two standard proteins with a range of initial concentration of proteins were investigated at room temperature. The results revealed that the kinetic adsorption rate of a protein within SBA-15 was independent of initial protein concentration, and a 15-min protein enrichment within SBA-15 could be enough for protein identification in biological samples. It was noticed that no washing steps were needed to avoid protein loss due to desorption from the mesochannels into solution. Second, protein digestion inside the channels of SBA-15 was also optimized. After adsorption of proteins into SBA-15 in 15 min, the trypsin solution (pH 8) was directly added to the SBA-15 beads with immobilized proteins by centrifugation, and then the digestion was performed for 15 min at 37 degrees C. It was observed that a higher peptide sequence covering of 98% for myoglobin was obtained by MALDI-TOF/TOF analysis, compared to in-solution digestion. So the protein digestion inside SBA-15 was proved to be significantly faster and yielded a better sequence coverage. The new procedure allows for rapid protein enrichment and digestion inside SBA-15, and has great potential for protein analysis.

Adsorption↗
PubMed2006

Novel strategy of high-abundance protein depletion using multidimensional liquid chromatography.

In this study, for the first time, a comprehensive two-dimensional (2D) liquid-phase separation system, coupling strong cation exchange chromatography (SCX) to reversed-phase high performance liquid chromatography (RPLC), instead of specificity depletion method, was developed at the intact protein level for depletion of high-abundance proteins from rat liver. Proteins were prefractionated by SCX in the first dimensional separation, followed by RPLC with high resolution separation. UV absorption intensity was used to differentiate high-abundance proteins. The proteins with the absorbance intensity above 0.1 AU were defined as high abundance proteins and depleted. After removal of high-abundance proteins; other proteins were pooled, digested, and subsequently separated by capillary liquid chromatography coupled with MALDI-TOF/TOF mass spectrometry analysis. The high efficiency of the strategy was demonstrated by analyzing the soluble protein extracted from rat liver tissue. In total, 77 high-abundance proteins were depleted in one experiment flow. The ratio of depleted content of high-abundance proteins to that of total proteins was about 34.5%. In total, 1530 proteins were identified using the depletion strategy. Quantitative estimation of high-abundance proteins through liquid chromatography combined with UV absorption spectra was achieved. On the basis of the reproducible experimental results, a rapid and high-throughput depletion protocol was put forward. Along with depletion of the most (79.1%) high-abundance proteins and the separation of digested peptides, the total separation time could be less than 30 h. This strategy has no bias for depleting high-abundance proteins and enhances the number of identified proteins; therefore, it can be widely used in the global proteins analysis.

Animals↗
PubMed2006

Proteomic analysis of rat aorta during atherosclerosis induced by high cholesterol diet and injection of vitamin D3.

1. Atherosclerosis (AS) in rats displays important clinical similarities to human AS. 2. After the experimental model of AS in rat was established and using a proteomic approach, we compared the protein profiling of aorta tissues from healthy and AS rats. 3. Using two-dimensional electrophoresis (2-DE), over 1878 protein species were separated; among them, 1239 protein spots were matched between different gels with average matching rate of approximately 66%. Gel analysis and protein characterization have identified 58 protein spots whose abundance is significantly altered in AS rats. 4. By using matrix-associated laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS) and NCBInr database, 46 proteins were successfully identified. Among them, 18 proteins were of increased abundance in diseased tissues including a group of oxidization-related enzymes such as peroxiredoxin2 and NADH dehydrogenase Fe-S protein 6, components of inflammatory pathways such as lamin A, while 28 proteins were of decreased abundance in the diseased state, including CaM-KII inhibitory protein, transferring, fructose-bisphosphate aldolase. 5. We believe that these results would give insights into the cellular and molecular mechanisms involved in AS development and might lead to the discovery of novel diagnostic markers and new therapeutic opportunities.

Animals↗