Candida tropicalis, a diploid asporogenic yeast, is frequently utilized in industrial applications and research studies. However, the low efficiency of genetic transformation limits the strain improvement by metabolic engineering. A reliable transformation and efficient deletion of target gene are prerequisite for molecular improvement of C. tropicalis. In this study, an efficient approach for genetic transformation of C. tropicalis was developed based on the URA3 gene as a reusable selection marker and both of PDC allele genes encoding pyruvate decarboxylase were successfully deleted by this approach. Firstly, an auxotrophic mutant strain of C. tropicalis XZX which is defective in orotidine-5'-phosphate decarboxylase (URA3) was isolated by chemical mutagenesis combined with nystatin enrichment selection and 5-fluoro-orotic acid (5-FOA) resistance selection using C. tropicalis ATCC 20336 as the parent strain. Then, the first PDC deletion cassette PDC1-hisG-URA3-hisG- PDC1 (PHUHP) which contains a 1.6 kb URA3 marker gene, two copies of 1.1 kb Salmonella hisG fragments and homologous arms of target gene was constructed and transformed into C. tropicalis XZX cells. Transformants with a single copy of PDC deleted were isolated and identified by PCR and DNA sequencing, which was designated as C.tropicalis XZX02. The C.tropicalis XZX02 cells were spread on the minimal medium containing 5-FOA to generate mutant C. tropicalis XZX03 in which URA3 marker gene was excised from PHUHP fragment integrated into the PDC gene site. The second PDC gene deletion cassette PDCm-URA3-PDCm (MUM) was constructed and transformed into C. tropicalis XZX03 to generate C.tropicalis XZX04 in which both of PDC allele genes were deleted. All strains were confirmed by PCR and DNA sequencing. This efficient genetic transformation approach laid a foundation for further metabolic engineering of C. tropicalis.
Unlike other crystalline metal oxides amenable to templating by the combined assemblies of soft and hard chemistries (CASH) method, vanadium oxide nanostructures templated by poly(ethylene oxide-b-1,4-butadiene-b-ethylene oxide) (OBO) triblock copolymers are not preserved upon high temperature calcination in argon. Triconstituent cooperative assembly of a phenolic resin oligomer (resol) and an OBO triblock in a VOCl3 precursor solution enhances the carbon yield and can prevent breakout crystallization of the vanadia during calcination. However, the calcination environment significantly influences the observed mesoporous morphology in these composite thin films. Use of an argon atmosphere in this processing protocol leads to nearly complete loss of carbon-vanadium oxide thin film mesostructure, due to carbothermal reduction of vanadium oxide. This reduction mechanism also explains why the CASH method is not more generally successful for the fabrication of ordered mesoporous vanadia. Carbonization under a nitrogen atmosphere at temperatures up to 800 °C instead enables formation of a block copolymer-templated mesoporous structure, which apparently stems from the formation of a minor fraction of a stabilizing vanadium oxynitride. Thus, judicious selection of the inert gas for template removal is critical for the synthesis of well-defined, mesoporous vanadia-carbon composite films. This resol-assisted assembly method may generally apply to the fabrication of other mesoporous materials, wherein inorganic framework crystallization is problematic due to kinetically competitive carbothermal reduction processes.
We report high-yield room-temperature growth of vertical single-crystalline bismuth nanowire array by vacuum thermal evaporation of bismuth over a choice of arbitrary substrate coated with a thin interlayer of nanoporous vanadium. The nanowire growth is the result of spontaneous and continuous expulsion of nanometer-sized bismuth domains from the vanadium pores, driven by their excessive surface energy that suppresses the melting point of bismuth close to room temperature. The simplicity of the technique opens a new avenue for the growth of nanowire arrays of a variety of materials.
Nicotine has a broad impact on both the central and peripheral nervous systems. Over the past decades, an increasing number of genes potentially involved in nicotine addiction have been identified by different technical approaches. However, the molecular mechanisms underlying nicotine addiction remain largely unknown. Under such situation, prioritizing the candidate genes for further investigation is becoming increasingly important. In this study, we presented a multi-source-based gene prioritization approach for nicotine addiction by utilizing the vast amounts of information generated from for nicotine addiction study during the past years. In this approach, we first collected and curated genes from studies in four categories, i.e., genetic association analysis, genetic linkage analysis, high-throughput gene/protein expression analysis, and literature search of single gene/protein-based studies. Based on these resources, the genes were scored and a weight value was determined for each category. Finally, the genes were ranked by their combined scores, and 220 genes were selected as the prioritized nicotine addiction-related genes. Evaluation suggested the prioritized genes were promising targets for further analysis and replication study.
In this work, an ampholine-functionalized hybrid organic-inorganic silica sorbent was successfully used to extract melamine from a milk formula sample via a hydrophilic interaction chromatography solid-phase extraction protocol. Primary factors affecting the extraction efficiency of the material such as extraction solvent, elution solvent, sample loading volume and elution volume have been thoroughly optimized. Under the optimized hydrophilic solid-phase extraction conditions, the recoveries of melamine spiked in milk formula samples were ranged from 86.2-101.8% with relative standard deviations of 4.1-9.4% (n = 3). The limit of detection (signal/noise = 3) was 0.32 ?g.g(-1) . The adsorption capacity toward melamine was 30 ?g of melamine/g of sorbent. Due to its simplicity, rapidity and cost effectiveness, the newly developed hydrophilic solid-phase extraction method should provide a promising tool for daily monitoring of doped melamine in milk formula. This article is protected by copyright. All rights reserved.
Abstract Mitochondrial DNA of velvet antler was amplified with random amplified polymorphic DNA (RAPD) technique and the PCR products were detected with non-gel sieving capillary electrophoresis to establish a RAPD-HPCE method used for identifying the authenticity of velvet antler or it counterfeits. Factors that could affect the PCR amplification and capillary electrophoresis were optimized. Under the optimized conditions, namely, 20?mmol?L(-1) NaH2PO4-Na2HPO4-2?mmolL(-1) EDTA buffer solution [0.8% (W/V) HPMC, 15?mmol?L(-1) TBAP and pH 7.3], -10?kV injection voltage and -8?kV separation voltage, Cervus nippon Temminck antler, Cervus elaphus Linnaeus antler, Rangifer tarandus antler, Cervus canadensis antler and Elaphurus davidianus antler were analyzed. The analysis on the similarity of obtained elctrophoretograms showed that there were significant differences in similarities of different velvet antlers, which could be used for the quick identification of the authenticity of velvet antler samples. It can be found that the technique of RAPD combined with HPCE is advantageous in rich polymorphism, high detection rate, simple and convenient performance, high efficiency, rapidness and sensitivity, indicating that it should be suitable for the quick identification of the authenticity of velvet antler samples.
We investigated the interface between hexagonal ZnO films and cubic MgO (001) substrates, fabricated via molecular beam epitaxy. X-ray diffraction and (scanning) transmission electron microscopy revealed that growth follows the single  direction when the temperature of the substrate is above 200 °C, while when the substrate temperature is below 150 °C, growth initially is along  and then mainly changes to [0-332] variants beyond a thickness of ?10 nm. Interestingly, a double-domain feature with a rotational angle of 30° appears during growth along  regardless of the temperature, experimentally demonstrating the theoretical predictions for the occurrence of double rotational domains in such a heteroepitaxy [Grundmann et al., Phys. Rev. Lett. 105, 146102 (2010)]. We also found that the optical properties of the ZnO film are influenced greatly by the mutation of growth directions, stimulated by the bond-length modulations, as we determined from X-ray absorption spectra at Zn K edge. These results also showed the evolution of the 4p(xy) and 4p(z) states in the conduction band with the rise in the temperature for growth. We consider that our findings may well promote the applications of ZnO in advanced optoelectronics for which its integration with other materials of different phases is desirable.
To improve the accuracy, throughput and automation of proteome quantification analysis, an integrated platform including a microflow mixed-bed ion exchange column, a hydrophilic immobilized enzymatic reactor (hIMER) and nanoRPLC-electrospray ionization (ESI)-MS/MS system was established. Online separation and digestion of dimethylated proteins, followed by peptide separation, identification and quantification can be realized automat ically by this platform. High and light dimethyl-labeled (H/L) proteins with the mass ratio of 1:1 were used to evaluate the quantification performance of the platform. The results showed that the dimethyl labeling efficiency at protein level was 90%. The incomplete digestion resulting from 10 min online digestion by the hIMER column and the non-specific adsorption of protein digests on the column had little adverse effect on the accuracy of protein quantification results. The mean value of H/L (mass ratio) of all the quantified proteins was 1.01. This platform was finally applied to analyze the different protein expression levels of two mice hepatocarcinoma ascites cell lines with high and low lymph node metastasis rates (Hca-F and Hca-P cell lines). Finally 15 up-regulated and 12 down-regulated proteins (Hca-F/Hca-P) were successfully obtained. All these results demonstrated that the integrated platform can be used for proteome quantification with the advantages of high accuracy and high throughput.
As an important technology for targeted protein analysis, selective reaction monitoring technology (SRM) improves the detection sensitivity and quantification accuracy by eliminating the interference of impurities and co-eluting peptides by selective detection of specific mother ions and daughter ions. It has been widely applied to the quantitative proteomics study due to the advantages of high selectivity, excellent reproducibility, high sensitivity and wide dynamic range and plays an important role in the area of life science. For the quantitative analysis of the complex samples with wide dynamic range, the throughput of analysis and detection sensitivity still need to be improved. Moreover, van quantification strategies have been proposed to improve the accuracy and precision of quantification. Furthermore, data processing becomes more and more important with the application of SRM technology to the analysis of complex samples. In this work, the recent development of SRM technology is reviewed from the above mentioned aspects. Since SRM technology gains wider applications along with the technological development, its applications in the area of proteomics quantitative study including biomarker validation, post-translational proteomics study (phosphorylation, glycosation, acetylation and so on), biotechnology and signaling pathway analysis are briefly described. Finally, the future developments, applications and outlook of SRM technology are described.
Polymer self-assembly was developed as an epitope imprinting strategy involving facile processes and high recognition site density. As a model, transferrin epitope imprinted polyethersulfone (PES) beads were successfully fabricated using this technique. The imprinted beads demonstrated excellent selectivity toward the transferrin epitope and transferrin even in the real sample.
Due to their extremely hydrophobic nature, the analysis of integral membrane proteins (IMPs) is of great challenge. Although various additives have been applied to improve the solubility of IMPs, they still suffer from low solubilization efficiency, incompatibility with trypsin digestion, or interference with MS detection. Herein, the systematic study on the effect of ionic liquid structure on membrane protein solubilization and trypsin biocompatibility was performed, based on which 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was selected for the sample preparation of IMPs. Compared with other commonly used additives, such as sodium dodecyl sulfate (SDS), Rapigest, and methanol, C12Im-Cl showed the best performance. In addition, with a strong cation exchange trap column, it could be easily removed after trypsin digestion, which not only was beneficial to avoid protein precipitation during digestion but also had no adverse effect on LC-MS-based separation and detection. Such a C12Im-Cl-assisted sample preparation method was further applied to the membrane proteome analysis of rat brain. Compared with the SDS-assisted method, 1.4 and 3.5 times improvement on the identified IMP and hydrophobic peptide number were achieved (251 vs 178, and 982 vs 279). All these results demonstrated that the C12Im-Cl-assisted sample preparation method is of great promise to promote the large-scale membrane proteome profiling.
One challenge existing since the invention of electron-beam lithography (EBL) is understanding the exposure mechanisms that limit the resolution of EBL. To overcome this challenge, we need to understand the spatial distribution of energy density deposited in the resist, that is, the point-spread function (PSF). During EBL exposure, the processes of electron scattering, phonon, photon, plasmon, and electron emission in the resist are combined, which complicates the analysis of the EBL PSF. Here, we show the measurement of delocalized energy transfer in EBL exposure by using chromatic aberration-corrected energy-filtered transmission electron microscopy (EFTEM) at the sub-10 nm scale. We have defined the role of spot size, electron scattering, secondary electrons, and volume plasmons in the lithographic PSF by performing EFTEM, momentum-resolved electron energy loss spectroscopy (EELS), sub-10 nm EBL, and Monte Carlo simulations. We expect that these results will enable alternative ways to improve the resolution limit of EBL. Furthermore, our approach to study the resolution limits of EBL may be applied to other lithographic techniques where electrons also play a key role in resist exposure, such as ion-beam-, X-ray-, and extreme-ultraviolet lithography.
Mutations in KRAS, BRAF and PIK3CA are the most common somatic alterations found in the colorectal cancer (CRC) patients from Western countries; but their prevalence and prognostic value have not been adequately assessed in Asian patients. The aim of this study was to determine the mutation frequencies of these genes in Chinese CRC patients and to investigate their impact on prognosis.
We have compared mutation analysis by Amplification Refractory Mutation System (ARMS) and epidermal growth factor receptor (EGFR) mutant-specific antibodies for their ability to detect two common activating EGFR mutations in a cohort of 115 advanced non-small cell lung cancer (NSCLC), including cytology material, core biopsy, and bronchoscopic biopsies. Assessment of EGFR mutation status was performed by using antibodies and ARMS assay specific to the two major forms of mutant EGFR, exon 19 deletion E746-A750 (c.2235_2249del15 or c.2236_2250del15, p. Glu746_Ala750 del) and exon 21 L858R point mutation (c.2573T>G, p.Leu858Arg). In this study the optimal buffer for antigen retrieval was sodium citrate (pH 6.0). Q score was used to evaluate the specific mutant EGFR proteins expression. Validation using clinical material showed deletions in exon 19 were detected in 19.1% and L858R mutation in 20% of all cases by ARMS assay. A cutoff value of score 1 was used as positive by IHC. No wild type cases were immuno-reactive. The antibodies performed well in cytology, core biopsies and bronchoscopic biopsies. There were only one false positive case using L858R IHC (sensitivity 100%, specificity 98.5%, positive predictive value 96%, negative predictive value 100%). All 23 E746-A750 exon 19 deletions identified by mutation analysis were positive by IHC. The sensitivity of exon 19 IHC for E746-A750 was 100%, specificity 100%, positive predictive value 100% and negative predictive value 100%. The result of the IHC stains was finely correlated with mutations status determined by ARMS assay. Although inferior to molecular genetic analysis of the EGFR gene, IHC is highly specific and sensitive for the targeted EGFR mutations. The antibodies are likely to be of clinical value in cases especially where limited tumor material is available, or in situations where molecular genetic analysis is not readily available.
Lithium iron borate (LiFeBO3) has a high theoretical specific capacity (220 mAh/g), which is competitive with leading cathode candidates for next-generation lithium-ion batteries. However, a major factor making it difficult to fully access this capacity is a competing oxidative process that leads to degradation of the LiFeBO3 structure. The pristine, delithiated, and degraded phases of LiFeBO3 share a common framework with a cell volume that varies by less than 2%, making it difficult to resolve the nature of the delithiation and degradation mechanisms by conventional X-ray powder diffraction studies. A comprehensive study of the structural evolution of LiFeBO3 during (de)lithiation and degradation was therefore carried out using a wide array of bulk and local structural characterization techniques, both in situ and ex situ, with complementary electrochemical studies. Delithiation of LiFeBO3 starts with the production of LitFeBO3 (t ? 0.5) through a two-phase reaction, and the subsequent delithiation of this phase to form Lit-xFeBO3 (x < 0.5). However, the large overpotential needed to drive the initial two-phase delithiation reaction results in the simultaneous observation of further delithiated solid-solution products of Lit-xFeBO3 under normal conditions of electrochemical cycling. The degradation of LiFeBO3 also results in oxidation to produce a Li-deficient phase D-LidFeBO3 (d ? 0.5, based on the observed Fe valence of ?2.5+). However, it is shown through synchrotron X-ray diffraction, neutron diffraction, and high-resolution transmission electron microscopy studies that the degradation process results in an irreversible disordering of Fe onto the Li site, resulting in the formation of a distinct degraded phase, which cannot be electrochemically converted back to LiFeBO3 at room temperature. The Li-containing degraded phase cannot be fully delithiated, but it can reversibly cycle Li (D-Lid+yFeBO3) at a thermodynamic potential of ?1.8 V that is substantially reduced relative to the pristine phase (?2.8 V).
Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests demonstrated that the introduction of PEG brushes greatly improved the anti-fouling properties of the pristine low-density polyethylene (LDPE), for which the absorption to bovine serum albumin was reduced by 83.3%. Moreover, the 3D protein microarrays exhibited a higher protein capacity than the controls to which were attached the same protein on PGMA brushes and monolayer epoxy functional groups. The 3D protein microarrays were used to test the immunoglobulin G (IgG) concentration in human serum, suggesting that they could be used for biomedical diagnosis, which indicates that more potential bio-applications could be developed for these protein microarrays in the future.
Fluorescent silver nanoclusters (Ag NCs) as novel fluorophores have received much attention because of their high brightness, good photostability and widely tunable emissions from the visible to the near-infrared range as a result of their size and existing environment. However, efforts are still needed to find the factors that tune the emission of Ag NCs. In this work, Ag NCs that were size-selectively grown on DNA were used to investigate the effect of the electronic properties of coordinating ligands. Halogen anions were used as the paradigm because of their periodicity in element properties. We found that addition of halogen anions did not alter the emission wavelength of Ag NCs, but the fluorescence intensity showed an initial increase at low concentrations of Cl(-), Br(-) and I(-) followed by a gradual decrease at high concentrations. No increase in fluorescence was observed for F(-) at either low or high concentration. Such specific halogen-anion sensitization of the fluorescence of Ag NCs suggests that the binding strength/manner and dipole polarizability of these anions synergistically tune the emission behavior of Ag NCs. Less fluorescence sensitization occurred for the anion having high enough polarizability to form a covalent bond with Ag NCs. The anion polarizability-sensitized fluorescence indicates the role of anion electronic properties in tuning the emission behavior of Ag NCs, which should be seriously considered in designing Ag NC-based sensors and devices.
Experimental evidence has shown significant cardioprotective effects of insulin, whereas clinical trials produced mixed results without valid explanations. This study was designed to examine the effect of hyperglycaemia on insulin cardioprotective action in a preclinical large animal model of myocardial ischaemia/reperfusion (MI/R).
Over the last decade, Clostridium difficile infection (CDI) has emerged as a significant nosocomial infection, yet little has been reported from China. This study aimed to characterize the clinical and microbiological features of CDI from a hospital in Shanghai.
The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected.
Peimisine, the common ingredient of "zhebeimu" groups and "chuanbeimu" groups, is responsible for the expectorant and cough relieving effects. The aim of this study was to investigate the pharmacokinetics, tissue distribution and excretion of peimisine in male and female SD (Sprague-Dawley) rats by a rapid and sensitive LC-MS/MS (liquid chromatography-tandem mass spectrometry) method used carbamazepine as the internal standard after oral administration, carbamazepine was stated as an IS. The results showed that peimisine was slowly distributed, and eliminated from rat plasma and manifested linear dynamics in a dose range of 0.26-6.5 mg/kg. Tested by ANOVA, there were gender differences in the pharmacokinetic parameters of AUC0-t, AUC0-? among a single dose of 0.26, 1.3, 6.5 mg/kg (P < 0.05). Drug blood and tissue levels in male rats were significantly higher than the female counterparts after oral administration, while both the males and the females showed high drug levels in spleen, kidney, lung, liver and heart. On the other hand, the peimisine levels that can be reached in uterus, ovary, testis and brain is low. The excretion study showed that little administered peimisine (<0.7 %) was recovered in the male and female bile. Approximately 13.46 and 15.05 % were recovered in female urine and feces, while 43.07 and 7.49 % were recovered in male urine and feces, respectively, which indicated that the major elimination route of male rats was urine excretion. In addition, there was significant differences in total cumulative excretive ratio of peimisine in feces (P < 0.05) and no significant differences in the urine (P > 0.05) at a dose of 1.3 mg/kg.
GO-PEI-Au-L-Cys composites were synthesized via loading gold nanoparticles on a GO surface using polyethylenimine as reducing and stabilizing reagents, followed by L-cysteine immobilization through an Au-S bond. The composites were applied as a kind of novel ZIC-HILIC material to achieve highly selective enrichment of glycopeptides from biological samples.
Parkinson disease (PD) is a progressive neurodegenerative disorder in which the nigrostriatal pathway, consisting of dopaminergic neuronal projections from the substantia nigra to the striatum, degenerates. Viral transduction is currently the most promising in vivo strategy for delivery of therapeutic proteins into the brain for treatment of PD. Sonic hedgehog (Shh) is necessary for cell proliferation, differentiation and neuroprotection in the central nervous system. In this study, we investigated the effects of overexpressed N-terminal product of SHH (SHH-N) in a PD model rat. A lentiviral vector containing SHH-N was stereotactically injected into the striatum 24 h after a striatal 6-OHDA lesion. We found that overexpressed SHH-N attenuated behavioral deficits and reduced the loss of dopamine neurons in the substantia nigra and the loss of dopamine fibers in the striatum. In addition, fluoro-ruby-labeled nigrostriatal projections were also repaired. Together, our results demonstrate the feasibility and efficacy of using the strategy of lentivirus-mediated Shh-N delivery to delay nigrostriatal pathway degeneration. This strategy holds the potential for therapeutic application in the treatment of PD.
In this work, 1.9 ?m reversed-phase packing materials with superficially porous structure were prepared to achieve the rapid and high efficient separation of peptides and proteins. The silica particles were synthesized via three steps, nonporous silica particle preparation by a modified seeded growth method, mesoporous shell formation by a one pot templated dissolution and redeposition strategy, and pore size expansion via acid-refluxing. By such a method, 1.9 ?m superficially porous materials with 0.18 ?m shell thickness and tailored pore diameter (10 nm, 15 nm) were obtained. After pore enlargement, the formerly dense arrays of mesoporous structure changed, the radially oriented pores dominated the superficially porous structure. The chromatographic performance of such particles was investigated after C18 derivatization. For packing materials with 1.9 ?m diameter and 10 nm pore size, the column efficiency could reach 211,300 plates per m for naphthalene. To achieve the high resolution separation of peptides and proteins, particles with pore diameter of 15 nm were tailored, by which the baseline separation of 5 peptides and 5 intact proteins could be respectively achieved within 1 min, demonstrating the superiority in the high efficiency and high throughput analysis of biomolecules. Furthermore, BSA digests were well separated with peak capacity of 120 in 30 min on a 15 cm-long column. Finally, we compared our columns with a 1.7 ?m Kinetex C18 column under the same conditions, our particles with 10nm pore size demonstrated similar performance for separation of the large intact proteins. Moreover, the particles with 15 nm pore size showed more symmetrical peaks for the separation of large proteins (BSA, OVA and IgG) and provided rapid separation of protein extracts from Escherichia coli in 5 min. All these results indicated that the synthesized 1.9 ?m superficially porous silica packing materials would be promising in the ultra-fast and high-resolution separation of biomolecules.
The normal cellular prion protein, PrP(C) is a highly conserved and widely expressed cell surface glycoprotein in all mammals. The expression of PrP is pivotal in the pathogenesis of prion diseases; however, the normal physiological functions of PrP(C) remain incompletely understood. Based on the studies in cell models, a plethora of functions have been attributed to PrP(C). In this paper, we reviewed the potential roles that PrP(C) plays in cell physiology and focused on its contribution to tumorigenesis.
A neutral polysaccharide fraction (CGPP) was extracted from Gynostemma pentaphyllum by water extraction and ethanol precipitation. Gas chromatography (GC) analysis showed that the CGPP was mainly composed of mannose, glucose, arabinose, rhamnose, galactose and glucuronic acid in molar ratios of 2.0:2.2:1.3:2.2:1.2:2.5. The present study aimed at evaluating the antitumor potentials of CGPP on the growth of H22 tumor transplanted in mice and the underlying mechanism. The results showed that CGPP (50 and 200mg/kg) could effectively inhibit the solid tumor growth of H22 hepatocarcinoma transplanted in ICR mice. Besides, the body weight, spleen/thymus indexes and splenocytes proliferation of H22 tumor bearing mice were also improved in CGPP-treated groups. Furthermore, the level of the cytokines, such as IL-2, TNF-? and IFN-?, as well as the activity of natural killer (NK) cells and cytotoxic T lymphocytes (CTL) in tumor-bearing mice were markedly promoted by CGPP oral administration. In addition, CGPP treatment greatly prolonged the survival period in H22 ascites tumor-bearing mice. Taken together, these findings indicate that CGPP has antitumor activity in vivo at least partly via improving immune responses of host organism, and seems to be a safe and effective supplementary agent for the treatment of hepatocellular carcinoma (HCC).
As low abundance is the great obstacle for glycoprotein analysis, the development of materials with high efficiency and selectivity for glycoprotein enrichment is a prerequisite in glycoproteome research. Herein, we report a new kind of hydrophilic boronate affinity monolith by attaching 4-mercaptophenylboronic acid (MPBA) with 2-mercaptoethylamine (MPA) on the gold nanoparticle-modified poly(glycidyl methacrylate-co-poly(ethylene glycol) diacrylate)) monolith for glycoprotein enrichment. With poly(ethylene glycol) diacrylate as the cross-linker and the further modification of gold nanoparticles, the matrix has advantages of good hydrophilicity and enhanced surface area, which are beneficial to improve the enrichment selectivity and efficiency for glycoproteins. The attachment of MPBA and MPA provide intramolecular B?N coordination, which could further enhance the specificity of glycoprotein capture. Such a boronate affinity monolith was applied to enrich horseradish peroxidase (HRP) from the mixture of HRP and bovine serum albumin (BSA), and high selectivity was obtained even at a mass ratio of 1:1000. In addition, the binding capacity of ovalbumin on such monolith reached 390??g?g(-1) . Furthermore, the average recovery of HRP on the prepared affinity monoliths was (84.8±1.9)?%, obtained in three times enrichment with the same column. Finally, the boronate affinity monolith was successfully applied for the human-plasma glycoproteome analysis. As a result, 160 glycoproteins were credibly identified from 9??g of human plasma, demonstrating the great potential of such a monolith for large-scale glycoproteome research.
Hierarchical imprinting was developed to prepare the protein imprinted materials, as the artificial antibody, for the selective depletion of HSA from the human serum proteome. Porcine serum albumin (PSA) was employed as the dummy template for the fabrication of the recognition sites. To demonstrate the advantages of the hierarchical imprinting, molecularly imprinted polymers prepared by hierarchical imprinting technique (h-MIPs) were compared with those obtained by bulk imprinting (b-MIPs), in terms of the binding capacity, adsorption kinetics, selectivity and synthesis reproducibility. The binding capacity of h-MIPs could reach 12 mg g(-1). And saturation binding could be reached in less than 20 min for the h-MIPs. In the protein mixture, h-MIPs exhibit excellent selectivity for PSA, with imprinting factors as about 3.6, much higher than those for non-template proteins. For the proteomic application, the identified protein group number in serum treated by h-MIPs was increased to 422, which is 21% higher than that obtained from the original serum, meanwhile the identified protein group number for the Albumin Removal kit was only 376. The results demonstrate that protein imprinted polymers prepared by hierarchical imprinting technique, might become the artificial antibodies for the selective depletion of high abundance proteins in proteome study.
Relative quantification of N-glycoproteomes shows great promise for the discovery of candidate biomarkers and therapeutic targets. The traditional protocol for quantitative analysis of glycoproteomes is usually off-line performed, and suffers from long sample preparation time, and the risk of sample loss or contamination due to manual manipulation. In this study, a novel integrated sample preparation platform for quantitative N-glycoproteome analysis was established, with combination of online N-glycopeptide capture by a HILIC column, sample buffer exchange by a N2-assisted HILIC-RPLC interface, deglycosylation by a hydrophilic PNGase F immobilized enzymatic reactor (hIMER) and solid dimethyl labeling on a C18 precolumn. To evaluate the performance of such a platform, two equal aliquots of immunoglobulin G (IgG) digests were sequentially pretreated, followed by MALDI-TOF MS analysis. The signal intensity ratio of heavy/light (H/L) labeled deglycosylated peptides with the equal aliquots was 1.00 (RSD=6.2%, n=3), much better than those obtained by the offline protocol, with H/L ratio as 0.76 (RSD=11.6%, n=3). Additionally, the total on-line sample preparation time was greatly shortened to 160 min, much faster than that of offline approach (24h). Furthermore, such an integrated pretreatment platform was successfully applied to analyze the two kinds of hepatocarcinoma ascites syngeneic cell lines with high (Hca-F) and low (Hca-P) lymph node metastasis rates. For H/L labeled Hca-P lysates with the equal aliquots, 99.6% of log2 ratios (H/L) of quantified glycopeptides ranged from -1 to 1, demonstrating high accuracy of the developed sample preparation strategy. By triplicated analysis of glycopeptides and non-glycopeptides of Hca-F and Hca-P lysates, 43 up-regulated and 30 down-regulated (Hca-F/P) N-glycosylation sites, and 11 significantly changed N-glycoproteins were successfully quantified, and most of them were related to tumorigenesis and tumor metastasis. All these results demonstrate the developed integrated N-glycoprotein pretreatment platform is of great power for the accurate, precise and high-throughput analysis of N-glycoproteomes.
Chemical derivatization is a very promising technique for improving analysis of peptides by mass spectrometry (MS). Thereinto, development of novel tags compatible with MS and/or MS/MS has always been the focus point of study. In this review, the recent reported tags for derivatization of thiol groups of cysteine, carboxyl groups, and amino groups on peptides as well as peptides with post-translational modifications (PTMs) are summarized. Moreover, the tags used for derivatization of glycans or oligosaccharides released from glycoproteins are also reviewed.
Substantial evidence suggests that inflammation is an important contributor to many neurodegenerative disorders. Activated microglial cells play an important role in releasing pro-inflammatory factors, including tumor necrosis factor-? (TNF-?) and interleukin-1? (IL-1?) for inducing inflammation. Recently, some reports have suggested that glycoprotein nonmetastatic melanoma B (GPNMB) is highly expressed in microglia after LPS treatment. However, the role of GPNMB in activated microglia is not clearly understood. In this study, we used RT-PCR and Western blotting to detect GPNMB and matrix metalloproteinase-3 (MMP-3) expressions in activated microglia. GPNMB small interfering RNA (siRNA) or MMP-3 inhibitor was applied on microglial BV2 cells, and ELISA was performed to measure the expressions of TNF-? and IL-1? in BV2 cells. Levels of iNOS and NO in BV2 cells were also determined. We found that the levels of GPNMB and MMP-3 were significantly increased in BV2 cells after LPS treatment. Moreover, we found that GPNMB significantly upregulated the expression of MMP-3 in BV2 cells, and high expression of MMP-3 was dependent on the level of GPNMB. Inhibition of GPNMB or MMP-3 expression by GPNMB siRNA or MMP-3 inhibitor dramatically suppressed the expressions of TNF-?, IL-1?, iNOS, and NO in activated microglia. All of these results suggest that GPNMB is involved in the inflammatory responses of microglia.
Smooth muscle cell (SMC) proliferation and migration are known to play a critical role in the development of atherosclerosis. Oxidized low-density lipoprotein (oxLDL) is involved in the generation of atherosclerotic lesions. Recent studies have indicated that oxLDL is a well-established risk factor for atherosclerosis that induces vascular smooth muscle cell (VSMC) proliferation and migration; however, the exact mechanisms involved have not been fully elucidated. In this study, the proliferation of human coronary artery smooth muscle cells (HCASMCs) was detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Cell migration was determined by Transwell assay. Osteopontin (OPN), matrix metaloproteinase-9 (MMP-9) and ?v?3 integrin expression were measured by mRNA and western blot analysis. OPN and MMP-9 knockdown cells were established through transfection with OPN siRNA or MMP-9 siRNA, respectively. Our results revealed that oxLDL makredly promoted HCASMC proliferation and migration in a dose-dependent manner. Further experiments demonstrated that oxLDL upregulated the expression of OPN and oxLDL. Cell proliferation and migration were markedly reduced following the knockdown of the OPN gene in the HCASMCs. We then found that treatment with oxLDL induced a concentration-dependent increase in MMP-9 mRNA and protein levels in the HCASMCs. These effects were partially abrogated by silencing OPN expression or blocking the ?v?3 integrin pathway. Moreover, cells treated with MMP-9 siRNA or ?v?3 antibody showed lower proliferation and migration rates. This study provides direct in vitro evidence that the exposure of HCASMCs to oxLDL induces the activation of OPN, leading to higher protein levels of MMP-9, and to an increased proliferation and migration of HCASMCs.
To assess the value of detecting silent myocardial ischemia (SMI) by single photon emission computed tomography (SPECT) in predicting risk of cardiac events among patients with type 2 diabetes mellitus (T2DM) who do not have overt cardiac symptoms.
c-Jun N-terminal kinase (JNK) is a stress-activated mitogen-activated protein kinase that plays a central role in initiating apoptosis in disease conditions. Recent studies have shown that mitochondrial JNK signaling is partly responsible for ischemic myocardial dysfunction; however, the underlying mechanism remains unclear. Here we report for the first time that activation of mitochondrial JNK, rather than JNK localization on mitochondria, induces autophagy and apoptosis and aggravates myocardial ischemia/reperfusion injury. Myocardial ischemia/reperfusion induced a dominant increase of mitochondrial JNK phosphorylation, while JNK mitochondrial localization was reduced. Treatment with Tat-SabKIM1, a retro-inverso peptide which blocks JNK interaction with mitochondria, decreased mitochondrial JNK activation without affecting JNK mitochondrial localization following reperfusion. Tat-SabKIM1 treatment reduced Bcl2-regulated autophagy, cytochrome c-mediated apoptosis and myocardial infarct size. Notably, selective inhibition of mitochondrial JNK activation using Tat-SabKIM1 produced a similar infarct size-reducing effect as inhibiting universal JNK activation with JNK inhibitor SP600125. Moreover, insulin-treated animals exhibited significantly dampened mitochondrial JNK activation accompanied by reduced infarct size and diminished autophagy and apoptosis following reperfusion. Taken together, these findings demonstrate that mitochondrial JNK activation, rather than JNK mitochondrial localization, induces autophagy and apoptosis and exacerbates myocardial ischemia/reperfusion injury. Insulin selectively inhibits mitochondrial JNK activation, contributing to insulin cardioprotection against myocardial ischemic/reperfusion injury. This article is part of a Special Issue entitled: Autophagy and protein quality control in cardiometabolic diseases.
Pancreatic carcinoma is the most common pancreatic malignancy and is associated with a very poor prognosis. Therefore, new prognostic factors and new treatment strategies are clearly needed. In this study, we retrospectively studied the levels of phosphorylated ezrin in 19 patients with pancreatic carcinoma by immunohistochemical analysis and determined the correlation between protein expression, clinicopathological characteristics and prognosis in pancreatic adenocarcinoma. We also characterized the phenotype of the overexpression of wild-type and phosphorylated ezrin and merlin in human pancreatic cancer cell lines. A significant correlation between the levels of phosphorylated ezrin 353 and ezrin 567 and the stage of pancreatic cancer was observed. Moreover, Kaplan-Meier analysis revealed that patients with high levels of phosphorylated ezrin had a significantly poorer survival rate (P<0.05). In addition, the overexpression of wild-type merlin or ezrin inhibited cell proliferation, migration and adhesion. However, the overexpression of T567D ezrin, a mutant that mimics permanent phosphorylation, promoted the proliferation, adhesion and migration of the pancreatic adenocarcinoma cell line SW1990. The overexpression of S518D merlin inhibited the growth of SW1990 and did not affect migration or adhesion. These results suggest that the phosphorylation of ezrin may contribute to the progression of pancreatic carcinoma and that the level of phosphorylated ezrin may serve as an adverse prognostic factor for pancreatic carcinoma.
Gaining experimental insight into the intrinsic properties of nanoparticles (NPs) represents a scientific challenge due to the difficulty of deconvoluting these properties from various environmental effects such as the presence of adsorbates or a support. A synergistic combination of experimental and theoretical tools, including X-ray absorption fine-structure spectroscopy, scanning transmission electron microscopy, atomic force microscopy, and density functional theory was used in this study to investigate the structure and electronic properties of small (?1-4 nm) Au NPs synthesized by an inverse micelle encapsulation method. Metallic Au NPs encapsulated by polystyrene 2-vinylpiridine (PS-P2VP) were studied in the solution phase (dispersed in toluene) as well as after deposition on ?-Al2O3. Our experimental data revealed a size-dependent contraction of the interatomic distances of the ligand-protected NPs with decreasing NP size. These findings are in good agreement with the results from DFT calculations of unsupported Au NPs surrounded by P2VP, as well as those obtained for pure (ligand-free) Au clusters of analogous sizes. A comparison of the experimental and theoretical results supports the conclusion that the P2VP ligands employed to stabilize the gold NPs do not lead to strong distortions in the average interatomic spacing. The changes in the electronic structure of the Au-P2VP NPs were found to originate mainly from finite size effects and not from charge transfer between the NPs and their environment (e.g., Au-ligand interactions). In addition, the isolated ligand-protected experimental NPs only display a weak interaction with the support, making them an ideal model system for the investigation of size-dependent physical and chemical properties of structurally well-defined nanomaterials.
In this study, dendrimer grafted graphene oxide nanosheets (dGO) were prepared by covalent reaction. The successful synthesis of dGO was confirmed by Fourier-transform infrared spectra, Raman spectra, Thermo gravimetric analysis and Zeta potential. Taking advantages of large surface area, excellent biocompatibility and abundant functional groups, dGO provided an ideal substrate for trypsin immobilization. Trypsin-linked dGO was synthesized through covalent bonding using glutaraldehyde as coupling agents. The amount of trypsin immobilized on dGO nanosheets was calculated to be about 649 ± 20 mg/g. The activity of immobilized trypsin could be maintained for over 10 days at 4 °C. On-plate proteolysis could be performed without removing trypsin-linked dGO, because dGO did not interfere with matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry analysis. By such an immobilized enzymatic reactor, standard proteins could be efficiently digested within 15 min, with sequence coverages comparable or better than those obtained by conventional over-night in-solution digestion. Furthermore, trypsin-linked dGO showed high sensitivity when applied to trace samples analysis. All these results demonstrated that the developed dGO based enzymatic reactor might provide a promising tool for high throughput proteome identification.
The development of a highly specific recognition system for glycoprotein capture from complex biological samples is a prerequisite to the success of mass spectra-based glycoproteomics analysis. To achieve this purpose, a one-pot precipitation polymerization (PP) strategy with a novel solvent system composed of water/ethanol (4:1, v/v) is described for preparing boronate-affinity polymeric micro/nano particles using 4-vinylphenylboronic acid (VPBA) as the functional monomer and N,N'-methylenebis(acrylamide) (MBA) alone or together with divinylbenzene (DVB) as the cross-linker(s). The proposed polymerization strategy not only affords monodisperse polymeric submicrometer particles with a smooth surface and controllable size, ranging from 300 to 700 nm, but also increases the loading capacity of boronic acid, which could hardly be achieved by other polymerization methods, thus leading to the specific recognition of glycoproteins. The effects of solvent systems and monomers on the morphology and boronate-affinity capacity of prepared materials were further investigated based on the Flory-Huggins model. It was proved that the reaction rate of various monomers during particle formation might be the key factor affecting the affinity capacity for glycoproteins. Our results demonstrated that under the theoretical guidance of the Flory-Huggins model the PP strategy with a selected monomer and solvent system might provide a good approach to prepare submicrometer polymer particles with plenty of boronic acid groups on the surface to achieve a highly selective enrichment of glycoproteins.
This work demonstrates the significant fluorescence enhancement of thioflavin T (ThT) when binding to G-quadruplexes possessing hybrid structures by using UV-vis absorption spectra, fluorescence spectra, and Tm experiments to confirm the binding events. ThT binding does not disturb native G-quadruplex structures preformed in Na(+) and K(+) solutions. The fluorescence enhancement is caused by the rotation restriction of benzothiazole (BZT) and dimethylaminobenzene (DMAB) rings in the ThT excited state upon its G-quadruplex binding. This molecular rotor mechanism as a means of fluorescence enhancement is confirmed using a nonrotor analogue of ThT. Hydroxylation and electrolyte experiments demonstrate that ThT stacks on the tetrad of the hybrid G-quadruplexes, whereas electrostatic forces contribute more to ThT binding for other G-quadruplex structures. By stacking on the tetrad, the ThT binding favors selective identification of DNA hybrid G-quadruplex structures with enhanced fluorescence and can serve as a conformation probe to monitor G-quadruplex structure conversion between hybrid and other structures. Using these properties, we developed a selective and label-free fluorescent K(+) sensor with a detection limit of 1 mM for K(+) in the presence of 100 mM Na(+). The coexistence of other metal ions produces a fluorescence response comparable to K(+) alone. We believe that ThT can potentially provide structure identification of hybrid G-quadruplexes and aid in the construction of G-quadruplex-based sensors.
Castration-resistant prostate cancer (CRPC), whose pathogenesis is known to be regulated by microRNAs (miRNAs), has a poor prognosis. In our present study, we found that the expression of miR-361-5p in CRPC was lower than in androgen-dependent prostate cancer (ADPC), indicating that miR-361-5p may play an important role in the progression of ADPC to CRPC. The role of miR-361-5p in prostate cancer (PCa) has not been evaluated until date. Our findings suggest that miR-361-5p is a suppressor in CRPC. Signal transducer and activator of transcription-6 (STAT6), a direct target of miR-361-5p, enhances the expression of B-cell lymphoma-extra large (Bcl-xL), while miR-361-5p inhibits its expression through STAT6. Therefore, miR-361-5p has great clinical significance in preventing the malignant progression of PCa.
A novel protein sample pretreatment method based on ampholine immobilized polymer microsphere (ampholine@PM) was developed for the fractionation of intact proteins prior to protein digestion and peptide analysis to reduce the dynamic range of human plasma proteome. After incubation with our prepared ampholine@PM, the captured plasma proteins were successively desorbed by 2M NaCl, 100mM glycine-hydrochloric acid, and 30% (v/v) acetonitrile with 0.1% (v/v) trifluoroacetic acid. The SDS-PAGE results showed the protein dynamic range in such three fractions was obviously reduced as compared with the native plasma. On-particle digestion was ultimately performed to release all proteins retained on ampholine@PM. Followed by MuPIT analysis, the number of identified proteins in plasma was improved by 75% after ampholine@PM treatment. Furthermore, the spectral count of 9 high abundance proteins was decreased by 37.6-97.2%, and the identified low abundance protein (<100ngmL(-1)) number was increased from 4 to 17. These results demonstrated that the fractionation by ampholine@PM could efficiently decrease the protein dynamic range in abundance, beneficial to achieve the deep coverage identification of human plasma proteome.
New types of imidazolium-based iodoacetamide tags were designed, synthesized and further exploited for cysteinyl-peptide analysis with superior labeling efficiency, high stability, improved ionization efficiency, and increased charge states by mass spectrometry. For the first time, the effects of these kinds of tags on the mass spectrometry performance of the derivatized peptides were investigated, which is of great importance to help us design more efficient tags for the analysis of peptides or proteins, especially for those with low abundance.
Ion channels have been suggested to be important in the development and progression of tumors, however, chloride channels have rarely been analyzed in tumorigenesis. More recently, transmembrane protein with unknown function 16A (TMEM16A), hypothesized to be a candidate calcium?activated Cl? channel, has been found to be overexpressed in a number of tumor types. Although several studies have implicated the overexpression of TMEM16A in certain tumor types, the exact role of TMEM16A in gliomas and the underlying mechanisms in tumorigenesis, remain poorly understood. In the present study, the role of TMEM16A in gliomas and the potential underlying mechanisms were analyzed. TMEM16A was highly abundant in various grades of gliomas and cultured glioma cells. Knockdown of TMEM16A suppressed cell proliferation, migration and invasion. Furthermore, nuclear factor??B (NF??B) was activated by overexpression of TMEM16A. In addition, TMEM16A regulated the expression of NF??B?mediated genes, including cyclin D1, cyclin E and c?myc, involved in cell proliferation, and matrix metalloproteinases (MMPs)?2 and MMP?9, which are associated with the migration and invasion of glioma cells. Collectively, results of the present study provide evidence for the involvement of TMEM16A in gliomas and the potential mechanism through which TMEM16A promotes glioma formation.
Cysteine-rich 61/connective tissue growth factor/nephroblastoma overexpressed (CCN) 3 has been recently reported to play a role in regulating inflammation of vascular endothelial cells. However, the role of CCN3 in atherosclerosis, which is characterized by vascular inflammation, remains unclear.
Chemical derivatization is a very promising technique for improving analysis of peptides by mass spectrometry (MS). In this study, a novel kind of imidazolium-based aromatic quaternary ammonium tag, 1-[3-[(2-iodo-1-oxoethyl)amino]propyl]-3-butylimidazolium bromide (IPBI), designed with strong gas-phase basicity and a permanent positive charge, was firstly synthesized and further used for derivatization of cysteinyl-peptides with improved ionization efficiency and higher charge states.
Proteome scale absolute quantification is fundamental for the quantitative understanding of an organism. The unsatisfactory accuracy for protein abundance estimation of current algorithms has been partially improved by the Absolute Protein EXpression profiling (APEX) algorithm, which implements the prior expectations of peptides appearances in the calculation of protein abundances. However, the abundance feature (AF) in APEX is the spectral count (SC); an AF suffers from a narrow dynamic range, thus, unsatisfactory accuracy. Therefore, we adopted another tandem mass spectrometric (MS/MS) level AF called Summed MS/MS Total ion current (SMT), which cumulates the MS/MS fragment intensities rather than simply counting the MS/MS spectra, to surmount this particular deficiency. The combination of APEX and SMT (abbreviated as APEX-SMT) is capable of improving the accuracy of absolute quantification by reducing the average relative deviation by ?55-85% compared to that of APEX, through a series of tests on the Universal Proteomics Standard sample with a dynamic range of 5 orders of magnitude (UPS2). The algorithm could also be used for relative quantification. When applied to the relative quantification of a publicly available benchmark dataset, APEX-SMT could provide comparable accuracy to APEX. All these results suggest that APEX-SMT is a promising alternative to APEX for proteome quantification.
Discovering differentially expressed proteins in various biological samples requires proteome quantification methods with accuracy, precision, and wide dynamic range. This study describes a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) method based on the subtle mass defect differences between (12)C/(13)C and (1)H/(2)H. Lys-C protein digests were labeled with CD2O/(13)CD2O and reduced with NaCNBD3/NaCNBH3 as heavy and light isotopologues, respectively. The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution tandem mass spectrometry (MS/MS) and used for quantification. The pIDL method described here resulted in highly accurate and precise quantification results with approximately 100-fold dynamic range. Furthermore, the pIDL method was extended to 4-plex proteome quantification and applied to the quantitative analysis of proteomes from Hca-P and Hca-F, two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates.
The effects of hepatocellular carcinoma on liver metabolism and circulating metabolites have been subjected to continuing investigation. This study compares the levels of selected metabolites in sera of hepatocellular carcinoma cases versus patients with liver cirrhosis and evaluates the influence of gender, race, and alcoholic cirrhosis on the performance of the metabolites as candidate biomarkers for hepatocellular carcinoma.
Epithelial ovarian cancer presents mostly with serous, endometrioid or mucinous histology but is treated as a single disease. The development of histotype-specific therapy has been challenging because of the relative lack of studies attributing disrupted pathways to a distinct histotype differentiation. mTOR activation is frequently associated with poor prognosis in serous ovarian cancer, which is the most common and most deadly histotype. However, the mechanisms dysregulating mTOR in the pathogenesis of ovarian cancer are unknown. We detected copy number loss and correlated lower expression levels of LKB1, TSC1, TSC2 and PTEN tumor suppressor genes for upstream regulators of mTOR activity in up to 80% in primary ovarian serous tumor databases, with LKB1 allelic loss-predominant. Reduced LKB1 protein was usually associated with increased mTOR activity in both serous ovarian cancer cell lines and primary tumors. Conditional deletion of Lkb1 in murine ovarian surface epithelial (OSE) cells caused papillary hyperplasia and shedding but not tumors. Simultaneous deletion of Lkb1 and Pten, however, led to development of high-grade ovarian serous histotype tumors with 100% penetrance that expressed WT1, ER?, PAX8, TP53 and cytokeratin 8, typical markers used in the differential diagnosis of serous ovarian cancer. Neither hysterectomy nor salpingectomy interfered with progression of ovarian tumorigenesis, suggesting that neither uterine nor Fallopian tube epithelial cells were contributing to tumorigenesis. These results implicate LKB1 loss in the OSE in the pathogenesis of serous ovarian cancer and provide a compelling rationale for investigating the therapeutic potential of targeting LKB1 signaling in patients with this deadly disease.
Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.
An SPE cartridge based on an ampholine-functionalized hybrid organic-inorganic silica sorbent has been adopted for the analysis of aromatic amines including 4-aminobiphenyl, benzidine, 2-naphthylamine, p-chloroaniline, 2,4,5-trimethylaniline, and 3,3-dichlorobenzidine. Crucial variables governing the extraction efficiency of the material such as the pH of sample, sample loading volume, solvent used for elution, and elution volume have been thoroughly optimized. The adsorption capacities for the six aromatic amines ranged from 0.17 to 1.82 ?g/mg. The recoveries of aromatic amines spiked in textile samples ranged from 78.9 to 103.0%, with RSDs of 1.1-11.9% (n = 3). Moreover, the extraction efficiency of the ampholine-functionalized hybrid organic-inorganic silica sorbent was at least comparable with that of Oasis WCX.
Combining good dissolving ability of formic acid (FA) for membrane proteins and excellent complementary retention behavior of proteins on strong cation exchange (SCX) and strong anion exchange (SAX) materials, a biphasic microreactor was established to pretreat membrane proteins at microgram and even nanogram levels. With membrane proteins solubilized by FA, all of the proteomics sample processing procedures, including protein preconcentration, pH adjustment, reduction, and alkylation, as well as tryptic digestion, were integrated into an "SCX-SAX" biphasic capillary column. To evaluate the performance of the developed microreactor, a mixture of bovine serum albumin, myoglobin, and cytochrome c was pretreated. Compared with the results obtained by the traditional in-solution process, the peptide recovery (93% vs 83%) and analysis throughput (3.5 vs 14 h) were obviously improved. The microreactor was further applied for the pretreatment of 14 ?g of membrane proteins extracted from rat cerebellums, and 416 integral membrane proteins (IMPs) (43% of total protein groups) and 103 transmembrane peptides were identified by two-dimensional nanoliquid chromatography-electrospray ionization tandem mass spectrometry (2D nano-LC-ESI-MS/MS) in triplicate analysis. With the starting sample preparation amount decreased to as low as 50 ng, 64 IMPs and 17 transmembrane peptides were identified confidently, while those obtained by the traditional in-solution method were 10 and 1, respectively. All these results demonstrated that such an "SCX-SAX" based biphasic microreactor could offer a promising tool for the pretreatment of trace membrane proteins with high efficiency and throughput.
The purpose of this research was to investigate the possibility of dexamethasone (DEX)-loaded PLGA-TPGS nanoparticles (NPs) in rabbits after intravitreal administration for the treatment of posterior segment diseases. The DEX-loaded PLGA-TPGS NPs were fabricated and characterized in terms of surface morphology, particle size and size distribution, entrapment efficiency, and in vitro drug release. The animals were classified randomly into two groups: experimental group with thirty rabbits, and control group with eighteen rabbits. Rabbits in the experimental group received intravitreal injections of 0.1 mL of DEX-loaded PLGA-TPGS NPs suspension and the control rabbits received intravitreal injection of 0.1 mL DEX (20 g/L in saline). The DEX concentrations in plasma and the ocular tissues such as the cornea, aqueous humor, lens, iris, vitreous humor, and chorioretina were determined by HPLC. The DEX-loaded PLGA-TPGS nanoparticle suspension were transparent and maintained a sustained release of DEX for about 45 days in vitreous and provided relatively constant DEX levels for more than 30 days with a mean concentration of 3.93 mg/L. Based on the area-under-the-curve (AUC), the bioavailability of DEX in the experimental group was significantly higher than that in the control group administrated with regular DEX. These results suggest that intravitreal administration of DEX-loaded PL.3A-TPGS NPs leads to a sustained release of DEX with a high bioavailability, providing a basis for a novel approach to treat posterior segment diseases.
Abstract The use of Martes zibellina L. heart as a famous kind of traditional Chinese medicine has been documented for many years in China. Identification of its authenticity as raw materials became a key in controlling of herbal preparations. In this study, the characteristics of mitochondrial cytochrome b (Cyt b) gene from four species of Martes were explored, and a specific molecular genetics technique for identifying the heart of M. zibellina L. in addition to some close relatives from their counterfeits was established. The bioinformatics was carried out to design the primers for the Cyt b gene based on the different species of Martes. PCR and sequencing technology were performed. The mt DNA was extracted from all of fresh M. zibellina L., Martes melampus. Martes flavigula. Martes martes heart samples and dry M. zibellina L. heart powder through the modified alkaline extracting method in addition to its counterfeits including the chicken heart, duck heart, goose heart, rabbit heart and Mustela vison. The complete mt DNA was separated from all samples used in the study, and the Cyt b gene with 310?bp segments was amplified only from M. zibellina L. heart as DNA template by the PCR technique. The sequencing indicated that the segment amplified by the PCR was homologous with the species of M. zibellina in GenBank. The data revealed that the primers and selected segment could be used as the genetic markers to identify M. zibellina L. heart from its counterfeits among different animal species.
Thioflavin T (ThT) has been widely utilized as a fluorescent marker for amyloid fibrils. However, the use of ThT as an efficient reporter for a specific DNA structure still remains in question. Here, we report that the fluorescence intensity of ThT is obviously enhancement in when it binds to ds-DNAs which contain cavity structures such as an abasic site, gap site or mismatch site. Such enhancement in fluorescence cannot be achieved for DNA without these cavity structures. The DNA cavities provide appropriate spaces to accommodate ThT and allow the occurrence of some specific interactions. The stacking interaction of the bound ThT with the cavity context bases is the main driving force for ThT binding to the cavities. This interaction restricts the excited states rapid torsional rotation around the single C-C bond between the benzothiazole and dimethylaminobenzene moieties and thus results in a decreased population of the nonradiative twisted internal charge-transfer (TICT) state. It is impossible for this stacking interaction to occur in DNA without these cavities. This property can be used to recognize DNA cavities with high selectivity and sensitivity. We expect that the ability of ThT to target these DNA structures has the potential to be developed into practical and functional biomaterials for DNA sensors or devices.
The hepatitis B virus (HBV) X protein (HBx) plays a key role in the molecular pathogenesis of HBV-related hepatocellular carcinoma (HCC). However, its critical gene targets remain largely unknown. RASSF1A gene (Ras-association domain family 1A, RASSF1A), a tumor-suppressor gene, is frequently found to be hypermethylated and downregulated in HCC. In the present study, we investigated whether HBx is involved in the hypermethylation and downregulation of RASSF1A and we examined the potential regulation mechanisms. RT-PCR analysis was used to determine RASSF1A and HBx expression in 9 liver cell lines and the results showed that RASSF1A expression was relatively low in HBx-positive cells. Notably, RASSF1A was downregulated in HepG2.2.15 cells, as compared to HepG2 cells. Further analysis revealed that HBx transfection suppressed RASSF1A expression and HBx knockdown induced its expression. Enforced HBx suppressed RASSF1A and meanwhile induced DNMT1 and DNMT3B expression. In addition, RASSF1A is negatively regulated by DNMT1. ChIP analysis using an antibody against DNMT1 revealed that HBx enhanced the binding of DNMT1 to the RASSF1A promoter but the inhibition of RASSF1A by HBx is DNA methylation-independent as detected by methylation-specific PCR (MSP). Further studies using MSP and bisulfite genomic sequencing (BGS) revealed that no significant methylation changes were observed for regional methylation levels of RASSF1A in DNMT1 knockdown cells, although methylation levels of specific CpG sites at the predicted binding sites for the Sp1 and USF transcription factors were reduced. Additionally, RASSF1A was downregulated in HBV-associated HCC (HBV-HCC) as detected by RT-PCR and immunohistochemistry suggesting RASSF1A expression may be related to HBx in HCC and the clinical relevance of our observations. Collectively, our data showed that HBx suppressed RASSF1A expression via DNMT1 and offered a new mechanism of RASSF1A inactive in HCC in addition to the widely known DNA methylation, enriching the epigenetic mechanism by which HBx contributes to the pathogenesis of HBV-HCC.
As an important clinically relevant pathogen, Clostridium difficile has a high multidrug resistance rate. Conjugative transposons play a vital role in its resistance phenotype. In the present study, 34 tetracycline-resistant clinical isolates of C. difficile were studied to detect tetracycline resistance genes and the presence of transposons. Thirty-two isolates were found to harbour Tn916-like elements carrying the tet(M) resistance gene, of which only one copy existed in the genome by Southern blot analysis. To characterise the genetic organisation of the Tn916-like elements, overlap PCR assays were performed with nine primer pairs, revealing three types of elements designated T1 to T3. The prevalent element T1 lacking PCRA (ORF23 to ORF21) and PCRB (ORF21 to ORF20) products, present in the epidemic ST37 clone, was further analysed by genome walking PCR in the left and right end sequences of the novel Tn916-like element. A gene coding for an FtsK/SpoIIIE family protein was found to replace the ORF24 to ORF21 region in Tn916. Moreover, the element could hardly conjugate between cells by filter mating experiments. These findings suggest that the dissemination of Tn916-like elements in epidemic ST37 strains in China was likely to have been conferred by clonal spread, signifying the importance of future surveillance and characterisation of conjugative transposons.
VO(x)/Pt(111), which was grown layer-by-layer and exhibited a well-defined structure, was used as a model catalytic surface to study the intrinsic catalytic activity of Pt, as well as the effect of VO(x) additive, for the oxidation of propane. A special sample system was designed to ensure a reliable analysis of the trace amount of model catalytic reaction products. The results show that the catalytic activities for the oxidation of C3H8 on the Pt(111) surface as adding VO(x) are suppressed apparently at temperatures below 400 K, but enhanced significantly at temperatures above 400 K. Maximum reaction rates are achieved at a VO(x) coverage of about 0.3 ML at the test temperatures of 423 and 473 K. The infrared reflection-absorption spectroscopy (IRAS) results show that the redox property of the VO(x)-Pt is much better than that of the bulklike VO(x). This is confirmed by CO poisoning tests, in that the oxidation of VO(x)/Pt(111) is significantly suppressed by the coadsorbed CO. The kinetic data demonstrate that there are at least two catalytically active sites, metallic Pt and VO(x)-Pt interface, for the activation and oxidation of C3H8. The promotion effects of VO(x) on Pt for the oxidation of C3H8 can be attributed to the synergy between VO(x) and Pt.
A key event during mammalian sexual development is regression of the Müllerian ducts (MDs) in the bipotential urogenital ridges (UGRs) of fetal males, which is caused by the expression of Müllerian inhibiting substance (MIS) in the Sertoli cells of the differentiating testes. The paracrine signaling mechanisms involved in MD regression are not completely understood, particularly since the receptor for MIS, MISR2, is expressed in the mesenchyme surrounding the MD, but regression occurs in both the epithelium and mesenchyme. Microarray analysis comparing MIS signaling competent and Misr2 knockout embryonic UGRs was performed to identify secreted factors that might be important for MIS-mediated regression of the MD. A seven-fold increase in the expression of Wif1, an inhibitor of WNT/?-catenin signaling, was observed in the Misr2-expressing UGRs. Whole mount in situ hybridization of Wif1 revealed a spatial and temporal pattern of expression consistent with Misr2 during the window of MD regression in the mesenchyme surrounding the MD epithelium that was absent in both female UGRs and UGRs knocked out for Misr2. Knockdown of Wif1 expression in male UGRs by Wif1-specific siRNAs beginning on embryonic day 13.5 resulted in MD retention in an organ culture assay, and exposure of female UGRs to added recombinant human MIS induced Wif1 expression in the MD mesenchyme. Knockdown of Wif1 led to increased expression of ?-catenin and its downstream targets TCF1/LEF1 in the MD mesenchyme and to decreased apoptosis, resulting in partial to complete retention of the MD. These results strongly suggest that WIF1 secretion by the MD mesenchyme plays a role in MD regression in fetal males.
To evaluate the oncologic safety of laparoscopic total mesorectal excision for rectal cancer. Methods and study design. Patients who underwent laparoscopic (n = 256) or open (n = 173) total mesorectal excision for rectal cancer between June 2005 and June 2011 were included. Long-term survival operative data and postoperative recovery were retrospectively reviewed from a prospectively collected database.
Vanadium oxide (VO(x)) has been extensively used in many oxidation and selective oxidation reactions. In this study, VO(x) thin films were prepared in an ultra-high vacuum (UHV) chamber by evaporating V onto a Pt(111) surface followed by subsequent oxidation at 623 K in 1 × 10(-7) Torr O2, and further oxidized in the high-pressure reaction cell with 1 Torr O2. The film quality and structure were investigated by high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED), low energy ion scattering spectroscopy (LEIS), Auger electron spectroscopy (AES), and in situ infrared reflection absorption spectroscopy (IRAS). On the Pt(111) surface, VO(x) forms isolated O=VO(x) (x = 0-3) species, surface two-dimensional (2D) (2 × 2)-V2O3 domains, a bi-layer structure with a (3?3 × 6) arrangement, and a complicated tri-layer structure as the coverage increases from submonolayer to multilayer. Under the UHV conditions, the oxidation state of V is mainly +3 and the stability was found to be surface V2O3 > bi-layer V2O3 > tri-layer one. After exposing to 0.3-1 Torr O2, VO(x) can be oxidized to higher oxidation states, mainly V2O5, as evidenced by the shifts of the core-level binding energies and presence of V=O. These results indicate that thorough oxidation of VO(x) requires sufficiently high O2 pressure, and that vanadium-based catalysts may possess higher oxidation states under most reaction conditions in the presence of O2.
We report a facile synthesis route to prepare high-quality Pt3 Co nanocubes with a concave structure, and further demonstrate that these concave Pt3 Co nanocubes are terminated with high-index crystal facets. The success of this preparation is highly dependent on an appropriate nucleation process with a successively anisotropic overgrowth and a preservation of the resultant high-index planes by control binding of oleyl-amine/oleic acid with a fine-tuned composition. Using a hydrogenation of styrene as a model reaction, these Pt3 Co concave nanocubes as a new class of nanocatalysts with more open structure and active atomic sites located on their high-index crystallographic planes exhibit an enhanced catalytic activity in comparison with low-indexed surface terminated Pt3 Co nanocubes in similar size.
Ataxia telangiectasia (AT) is a human genetic disease characterized by radiation sensitivity, impaired neuronal development and predisposition to cancer. Using a genetically defined model cell system consisting of cells expressing a kinase dead or a kinase proficient ATM gene product, we previously reported systemic alterations in major metabolic pathways that translate at the gene expression, protein and small molecule metabolite levels. Here, we report ionizing radiation induced stress response signaling arising from perturbations in the ATM gene, by employing a functional proteomics approach. Functional pathway analysis shows robust translational and post-translational responses under ATM proficient conditions, which include enrichment of proteins in the Ephrin receptor and axonal guidance signaling pathways. These molecular networks offer a hypothesis generating function for further investigations of cellular stress responses.
Velvet antler is one of the most important animal medicines, and has been used with a variety of functions, such as anti-fatigue, tissue repair and health promotion. In the past few years, the investigation on chemical compositions, bioactive components, and pharmacological effects has been performed, which demonstrates that velvet antlers could be used as an important health-promoting tonic with great nutritional and medicinal values. This review focuses on the recent advance in studying the bioactive components of velvet antlers.
Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1-like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.
The cationic reagent 1-(3-aminopropyl)-3-butylimidazolium bromide (BAPI) was exploited for the derivatization of carboxyl groups on peptides. Nearly 100% derivatization efficiency was achieved with the synthetic peptide RVYVHPI (RI-7). Furthermore, the peptide derivative was stable in a 0.1% TFA/water solution or a 0.1% (v/v) TFA/acetonitrile/water solution for at least one week. The effect of BAPI derivatization on the ionization of the peptide RI-7 was further investigated, and the detection sensitivity was improved >42-fold via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), thus outperforming the commercial piperazine derivatization approach. Moreover, the charge states of the peptide were largely increased via BAPI derivatization by electrospray ionization (ESI) MS. The results indicate the potential merits of BAPI derivatization for high sensitivity peptide analysis by MS.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.