[Clinical analysis and electroneurophysiology of chronic normal hexane poisoning in 11 patients].
Explore the source record for details and available documents.
Adult↗
Biomedical subjects
Xiao-jun Li
Publications and source records attributed to Xiao-jun Li.
[Investigation on mercury baseline level in urine in healthy population].
Explore the source record for details and available documents.
Adolescent↗
[Associations between periodontal status and delivery outcomes in pregnant women with a diagnosis of threatened premature labor].
OBJECTIVE: To evaluate the association between periodontal conditions and delivery outcomes in pregnant women with a diagnosis of threatened premature labor (TPL). METHODS: Eighty systemically healthy pregnant women were enrolled in the study. Forty of these were pregnant women hospitalized with the diagnosis of TPL, and 40 normal pregnant women served. TPL was control clarified as TPL-PB (14 women) and TPL-TB (26 women) based on the delivery outcomes. No infants were delivered as PB in the control with non-TPL. Periodontal examinations included assessments of plaque index (PLI), clinical attachment loss (CAL), probing depth (PD), bleeding index (BI) and the percentage of periodontitis sites (PD > 3 mm, CAL >or= 2 mm). The serum level of TNF-alpha was determined using commercially available enzyme-linked immunoassays (ELISA). RESULTS: The mean PLI (0.94 +/- 0.05), percentage of periodontitis sites (2.93%) and TNF-alpha levels [14.81 ng/L (13.40 - 15.64 ng/L)] were significantly higher in the TPL group than in the non-TPL group [0.59 +/- 0.03, 1.32% and 11.47 ng/L (10.82 - 12.86) ng/L] (P < 0.001). The mean PLI (0.96 +/- 0.06), BI (2.99 +/- 0.14), percentage of periodontitis sites (3.61%) and TNF-alpha levels [18.35 ng/L (15.47 - 31.94) ng/L] were significantly higher in the TPL-PB group than in the TPL-TB group [0.66 +/- 0.04, 2.76 +/- 0.12, 2.25% and 13.70 ng/L (12.64 - 14.80 ng/L)]. Significant negative correlations were observed between the gestational age at delivery and percentage of periodontitis sites as well as serum TNF-alpha levels (P < 0.05). And significant positive correlations were observed between percentage of periodontitis site and serum TNF-alpha levels (P < 0.05). CONCLUSIONS: Periodontal inflammation might be involved in the pathogenesis of preterm birth.
Adult↗
A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Archaeal Proteins↗
A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry.
There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited reproducibility and low throughput make this a challenging task. A new LC-MS-based platform is able to generate complex peptide patterns from the analysis of proteolyzed protein samples at high throughput and represents a promising approach for quantitative proteomics. A crucial component of the LC-MS approach is the accurate evaluation of the abundance of detected peptides over many samples and the identification of peptide features that can stratify samples with respect to their genetic, physiological, or environmental origins. We present here a new software suite, SpecArray, that generates a peptide versus sample array from a set of LC-MS data. A peptide array stores the relative abundance of thousands of peptide features in many samples and is in a format identical to that of a gene expression microarray. A peptide array can be subjected to an unsupervised clustering analysis to stratify samples or to a discriminant analysis to identify discriminatory peptide features. We applied the SpecArray to analyze two sets of LC-MS data: one was from four repeat LC-MS analyses of the same glycopeptide sample, and another was from LC-MS analysis of serum samples of five male and five female mice. We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics.
Amino Acid Sequence↗
ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer.
In MS/MS experiments with automated precursor ion, selection only a fraction of sequencing attempts lead to the successful identification of a peptide. A number of reasons may contribute to this situation. They include poor fragmentation of the selected precursor ion, the presence of modified residues in the peptide, mismatches with sequence databases, and frequently, the concurrent fragmentation of multiple precursors in the same CID attempt. Current database search engines are incapable of correctly assigning the sequences of multiple precursors to such spectra. We have developed a search engine, ProbIDtree, which can identify multiple peptides from a CID spectrum generated by the concurrent fragmentation of multiple precursor ions. This is achieved by iterative database searching in which the submitted spectra are generated by subtracting the fragment ions assigned to a tentatively matched peptide from the acquired spectrum and in which each match is assigned a tentative probability score. Tentatively matched peptides are organized in a tree structure from which their adjusted probability scores are calculated and used to determine the correct identifications. The results using MALDI-TOF-TOF MS/MS data demonstrate that multiple peptides can be effectively identified simultaneously with high confidence using ProbIDtree.
Algorithms↗
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.
We present a robust and general method for the identification and relative quantification of phosphorylation sites in complex protein mixtures. It is based on a new chemical derivatization strategy using a dendrimer as a soluble polymer support and tandem mass spectrometry (MS/MS). In a single step, phosphorylated peptides are covalently conjugated to a dendrimer in a reaction catalyzed by carbodiimide and imidazole. Modified phosphopeptides are released from the dendrimer via acid hydrolysis and analyzed by MS/MS. When coupled with an initial antiphosphotyrosine protein immunoprecipitation step and stable-isotope labeling, in a single experiment, we identified all known tyrosine phosphorylation sites within the immunoreceptor tyrosine-based activation motifs (ITAM) of the T-cell receptor (TCR) CD3 chains, and previously unknown phosphorylation sites on total 97 tyrosine phosphoproteins and their interacting partners in human T cells. The dynamic changes in phosphorylation were quantified in these proteins.
Cells, Cultured↗
Engagement of membrane immunoglobulin enhances Id3 promoter activity in WEHI-231 B lymphoma cells.
AIM: We have recently shown that engagement of membrane immunoglobulin (mIg) induced upregulation of inhibitor of differentiation 3 (Id3) mRNA, resulting in growth arrest at G1 phase in WEHI-231 cells. In the present study, we examined whether engagement of mIg will affect promoter activity of the Id3 gene in WEHI-231 cells. METHODS: DNA fragments corresponding to the 5'-flanking region of mId3 gene were amplified by polymerase chain reaction (PCR) using genomic DNA as the template. Three DNA fragments upstream of the transcription start site (+1) of the mId3 gene were subcloned into the luciferase reporter vector PGV-B2. The recombinant constructs were transiently transfected into WEHI-231 cells by an electroporation method. After incubation for 24 h, WEHI-231 cells were stimulated with 10 mg/L anti-IgM or irradiated CD40L-expressing NIH3T3 cells or control NIH3T3 cells for further 24 h, followed by assay for luciferase activity. RESULTS: The luciferase analysis demonstrated that basal promoter activity of the Id3 gene was found in the region between -200 and +54. The Id3 promoter activity was increased 2-fold following stimulation with anti-IgM, but not CD40L, compared with medium alone. CONCLUSION: The mIg-mediated upregulation of Id3 expression is controlled, at least in part, through transcriptional regulation, as assessed by luciferase assay.
Animals↗
High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry.
It is expected that the composition of the serum proteome can provide valuable information about the state of the human body in health and disease and that this information can be extracted via quantitative proteomic measurements. Suitable proteomic techniques need to be sensitive, reproducible, and robust to detect potential biomarkers below the level of highly expressed proteins, generate data sets that are comparable between experiments and laboratories, and have high throughput to support statistical studies. Here we report a method for high throughput quantitative analysis of serum proteins. It consists of the selective isolation of peptides that are N-linked glycosylated in the intact protein, the analysis of these now deglycosylated peptides by liquid chromatography electrospray ionization mass spectrometry, and the comparative analysis of the resulting patterns. By focusing selectively on a few formerly N-linked glycopeptides per serum protein, the complexity of the analyte sample is significantly reduced and the sensitivity and throughput of serum proteome analysis are increased compared with the analysis of total tryptic peptides from unfractionated samples. We provide data that document the performance of the method and show that sera from untreated normal mice and genetically identical mice with carcinogen-induced skin cancer can be unambiguously discriminated using unsupervised clustering of the resulting peptide patterns. We further identify, by tandem mass spectrometry, some of the peptides that were consistently elevated in cancer mice compared with their control littermates.
Animals↗
System-based proteomic analysis of the interferon response in human liver cells.
BACKGROUND: Interferons (IFNs) play a critical role in the host antiviral defense and are an essential component of current therapies against hepatitis C virus (HCV), a major cause of liver disease worldwide. To examine liver-specific responses to IFN and begin to elucidate the mechanisms of IFN inhibition of virus replication, we performed a global quantitative proteomic analysis in a human hepatoma cell line (Huh7) in the presence and absence of IFN treatment using the isotope-coded affinity tag (ICAT) method and tandem mass spectrometry (MS/MS). RESULTS: In three subcellular fractions from the Huh7 cells treated with IFN (400 IU/ml, 16 h) or mock-treated, we identified more than 1,364 proteins at a threshold that corresponds to less than 5% false-positive error rate. Among these, 54 were induced by IFN and 24 were repressed by more than two-fold, respectively. These IFN-regulated proteins represented multiple cellular functions including antiviral defense, immune response, cell metabolism, signal transduction, cell growth and cellular organization. To analyze this proteomics dataset, we utilized several systems-biology data-mining tools, including Gene Ontology via the GoMiner program and the Cytoscape bioinformatics platform. CONCLUSIONS: Integration of the quantitative proteomics with global protein interaction data using the Cytoscape platform led to the identification of several novel and liver-specific key regulatory components of the IFN response, which may be important in regulating the interplay between HCV, interferon and the host response to virus infection.
Cell Line, Tumor↗
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.
We present a software tool for visualizing data obtained from analyzing complex peptide mixtures by liquid chromatography (LC) electrospray ionization (ESI) mass spectrometry (MS). The data are represented as a two-dimensional density plot. For experiments employing collision-induced dissociation (CID), links are embedded in the image to the CID spectra and the corresponding peptide sequences that are represented by the respective feature. The image provides an intuitive method to evaluate sample quality and the performance of an LC-ESI-MS system and can be used to optimize experimental conditions. Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics.
Chromatography, Liquid↗
Identification of TFB5, a new component of general transcription and DNA repair factor IIH.
We previously described the use of quantitative proteomics to study macromolecular complexes. Applying the method to analyze a yeast RNA polymerase II preinitiation complex, we identified a new 8-kDa protein, encoded by the uncharacterized open reading frame YDR079c-a, as a potential new component of the preinitiation complex. Here we show that YDR079c-a is a bona fide component of polymerase II preinitiation complexes and investigate its role in transcription. YDR079c-a is recruited to promoters both in vivo and in vitro and is required for efficient transcription in vitro and for normal induction of GAL genes. In addition, YDR079c-a is a core component of general transcription and DNA repair factor IIH and is required for efficient recruitment of TFIIH to a promoter. Yeast lacking YDR079c-a grow slowly, and, like strains carrying mutations in core TFIIH subunits, are sensitive to ultraviolet radiation. YDR079c-a is conserved throughout evolution, and mutations in the human ortholog account for a DNA repair-deficient form of the tricothiodystrophy disorder called TTD-A(2). The identification of a new, evolutionarily conserved, core TFIIH subunit is essential for our understanding of TFIIH function in transcription, DNA repair and human disease.
DNA Polymerase II↗
Lipid raft proteins and their identification in T lymphocytes.
This review focuses on how membrane lipid rafts have been detected and isolated, mostly from lymphocytes, and their associated proteins identified. These proteins include transmembrane antigens/receptors, GPI-anchored proteins, cytoskeletal proteins, Src-family protein kinases, G-proteins, and other proteins involved in signal transduction. To further understand the biology of lipid rafts, new methodological approaches are needed to help characterize the raft protein component, and changes that occur in this component as a result of cell perturbation. We describe the application of new proteomic approaches to the identification and quantification of raft proteins in T-lymphocytes. Similar approaches, applied to other model cell systems, will provide valuable new insights into both cellular signal transduction and lipid raft biology.
Animals↗
[The effect of casting techniques on the accuracy of titanium crown and bridge].
OBJECTIVE: To investigate the method of enhancing the accuracy of titanium crowns by improving the casting method. METHODS: A self-assembled die was used to fabricate 48 standardized wax crowns. The dies were averagely divided into two groups. 21 crowns were successfully fabricated from one group according to the improved techniques. 18 crowns were fabricated by traditional method. A reference mark was scribed 90 degrees apart at four sites on the margin of each wax pattern and respective die. The distance between the margins of the wax pattern and the die was measured under a stereomicroscope. Similar method was also applied to measure the margin of castings. The castings were longitudinally split through midline. The distance between the 4 points(B',C',D',E') selected in the inner part of the crown and the die was respectively examined. RESULTS: Castings acquired by the improved method were more complete and had smoother surface. Marginal discrepancy value had significant difference between the two groups. Value in experimental group was smaller. Distance from B',E' to die between the two groups had no significant difference, but the distance from C',D' to the die was significantly different. The experimental group was smaller. CONCLUSION: Standardized crowns fabricated by the improved titanium casting technique were more accurate, but special investment for titanium crowns and bridges should be developed to compensate the casting shrinkage of metal.
Crowns↗
[Advances research of periodontal disease and preterm low birth weight deliveries].
Explore the source record for details and available documents.
Female↗
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.
Lipid rafts were prepared according to standard protocols from Jurkat T cells stimulated via T cell receptor/CD28 cross-linking and from control (unstimulated) cells. Co-isolating proteins from the control and stimulated cell preparations were labeled with isotopically normal (d0) and heavy (d8) versions of the same isotope-coded affinity tag (ICAT) reagent, respectively. Samples were combined, proteolyzed, and resultant peptides fractionated via cation exchange chromatography. Cysteine-containing (ICAT-labeled) peptides were recovered via the biotin tag component of the ICAT reagents by avidin-affinity chromatography. On-line micro-capillary liquid chromatography tandem mass spectrometry was performed on both avidin-affinity (ICAT-labeled) and flow-through (unlabeled) fractions. Initial peptide sequence identification was by searching recorded tandem mass spectrometry spectra against a human sequence data base using SEQUEST software. New statistical data modeling algorithms were then applied to the SEQUEST search results. These allowed for discrimination between likely "correct" and "incorrect" peptide assignments, and from these the inferred proteins that they collectively represented, by calculating estimated probabilities that each peptide assignment and subsequent protein identification was a member of the "correct" population. For convenience, the resultant lists of peptide sequences assigned and the proteins to which they corresponded were filtered at an arbitrarily set cut-off of 0.5 (i.e. 50% likely to be "correct") and above and compiled into two separate datasets. In total, these data sets contained 7667 individual peptide identifications, which represented 2669 unique peptide sequences, corresponding to 685 proteins and related protein groups.
Amino Acid Sequence↗
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation.
Proteomic approaches to biological research that will prove the most useful and productive require robust, sensitive, and reproducible technologies for both the qualitative and quantitative analysis of complex protein mixtures. Here we applied the isotope-coded affinity tag (ICAT) approach to quantitative protein profiling, in this case proteins that copurified with lipid raft plasma membrane domains isolated from control and stimulated Jurkat human T cells. With the ICAT approach, cysteine residues of the two related protein isolates were covalently labeled with isotopically normal and heavy versions of the same reagent, respectively. Following proteolytic cleavage of combined labeled proteins, peptides were fractionated by multidimensional chromatography and subsequently analyzed via automated tandem mass spectrometry. Individual tandem mass spectrometry spectra were searched against a human sequence database, and a variety of recently developed, publicly available software applications were used to sort, filter, analyze, and compare the results of two repetitions of the same experiment. In particular, robust statistical modeling algorithms were used to assign measures of confidence to both peptide sequences and the proteins from which they were likely derived, identified via the database searches. We show that by applying such statistical tools to the identification of T cell lipid raft-associated proteins, we were able to estimate the accuracy of peptide and protein identifications made. These tools also allow for determination of the false positive rate as a function of user-defined data filtering parameters, thus giving the user significant control over and information about the final output of large-scale proteomic experiments. With the ability to assign probabilities to all identifications, the need for manual verification of results is substantially reduced, thus making the rapid evaluation of large proteomic datasets possible. Finally, by repeating the experiment, information relating to the general reproducibility and validity of this approach to large-scale proteomic analyses was also obtained.
Amino Acid Sequence↗
Abundance ratio-dependent proteomic analysis by mass spectrometry.
The goal of quantitative proteomics is to determine the identity and relative quantity of each protein present in two or more complex protein samples. Here we describe a novel approach to quantitative proteomics. It is based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification. The method is capable of detecting and selectively identifying those proteins within a complex mixture that show a difference in relative abundance. We demonstrate the effectiveness and the versatility of this approach in the analysis of a standard protein mixture, protein expression profiling in a human prostate cancer cell line model, and identification of the specific components of the multiprotein transcriptional machinery in S. cerevisiae.
Humans↗