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Biomedical subjects

Dong Xu

Publications and source records attributed to Dong Xu.

At least 73 records · Page 4Linked to original sources
PubMed2004

Dichotomous effects of complete versus partial class II major histocompatibility complex deficiency on circulating autoantibody levels in autoimmune-prone mice.

OBJECTIVE: To assess the effects of altered class II major histocompatibility complex (MHCII) expression on circulating autoantibody levels in C57BL/6 (B6) mice congenic for the Sle1 (B6.Sle1 mice) or Nba2 (B6.Nba2 mice) regions. METHODS: H-2Ab(+/+) (MHCII-intact), H-2Ab(+/-) (MHCII-intermediate), and H-2Ab(-/-) (MHCII-deficient) littermate B6.Sle1 and B6.Nba2 mice were evaluated for spleen cell phenotype, numbers of splenic Ig-secreting cells, and serum levels of total IgM, total IgG, IgG antichromatin, IgG antihistone, and IgG anti-double-stranded DNA (anti-dsDNA). RESULTS: Compared with their MHCII-intact littermates, MHCII-deficient B6.Sle1 and B6.Nba2 mice developed markedly decreased circulating levels of IgG autoantibodies, along with decreased circulating levels of total IgG. In sharp contrast, MHCII-intermediate mice developed increased circulating levels of IgG autoantibodies. This was associated with increased numbers of splenic Ig-secreting cells and serum levels of total IgG in B6.Sle1 mice, but it occurred without concomitant increases in the numbers of splenic Ig-secreting cells or serum total IgG levels in B6.Nba2 mice. CONCLUSION: In 2 clinically healthy strains of mice with a genetic proclivity for developing autoantibodies, the effects of class II MHC expression on levels of circulating IgG autoantibodies were found to be complex. In the absence of MHCII expression, circulating IgG autoantibody levels were minimal. With full MHCII expression, circulating IgG autoantibody levels were considerable. With intermediate MHCII expression, circulating IgG autoantibody levels were even greater. These last findings may help explain why heterozygosity at the H-2 locus is associated with increased autoantibody titers and aggravated disease in certain lupus-prone mice.

Animals↗
PubMed2004

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST.

High-throughput protein identification in mass spectrometry is predominantly achieved by first identifying tryptic peptides by a database search and then by combining the peptide hits for protein identification. One of the popular tools used for the database search is SEQUEST. Peptide identification is carried out by selecting SEQUEST hits above a specified threshold, the value of which is typically chosen empirically in an attempt to separate true identifications from false ones. These SEQUEST scores are not normalized with respect to the composition, length and other parameters of the peptides. Furthermore, there is no rigorous reliability estimate assigned to the protein identifications derived from these scores. Hence, the interpretation of SEQUEST hits generally requires human involvement, making it difficult to scale up the identification process for genome-scale applications. To overcome these limitations, we have developed a method, which combines a neural network and a statistical model, for normalizing SEQUEST scores, and also for providing a reliability estimate for each SEQUEST hit. This method improves the sensitivity and specificity of peptide identification compared to the standard filtering procedure used in the SEQUEST package, and provides a basis for estimating the reliability of protein identifications.

Algorithms↗
PubMed2004

Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae.

Characterizing gene function is one of the major challenging tasks in the post-genomic era. To address this challenge, we have developed GeneFAS (Gene Function Annotation System), a new integrated probabilistic method for cellular function prediction by combining information from protein-protein interactions, protein complexes, microarray gene expression profiles, and annotations of known proteins through an integrative statistical model. Our approach is based on a novel assessment for the relationship between (1) the interaction/correlation of two proteins' high-throughput data and (2) their functional relationship in terms of their Gene Ontology (GO) hierarchy. We have developed a Web server for the predictions. We have applied our method to yeast Saccharomyces cerevisiae and predicted functions for 1548 out of 2472 unannotated proteins.

Automation↗
PubMed2004

Strategies for inhibition of MDR1 gene expression.

Several distinct strategies have been used to modulate the expression of cancer-associated genes, including antisense oligonucleotides, small interfering RNAs (siRNAs), and artificial transcriptional factors. One major cause for chemotherapeutic treatment failure in cancer is the overexpression of P-glycoprotein, the product of the multidrug resistance gene MDR1. In this study, we tested the ability of siRNAs to inhibit MDR1 gene expression. We evaluated the efficiency of chemically synthesized dsRNAs as well as vector-based hairpin siRNAs and investigated the behavior of clones of multidrug-resistant NCI/ADR-RES breast carcinoma cells stably transfected with hairpin siRNA vectors. The effects of siRNA on the MDR phenotype were compared with those elicited by antisense oligonucleotides or by designed transcription factors targeting the MDR1 promoter. These studies suggest that there are several comparably effective strategies for inhibiting MDR1 expression.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2004

Preliminary study on the photoproduction of hydroxyl radicals in aqueous solution with Aldrich humic acid, algae and Fe(III) under high-pressure mercury lamp irradiation.

Under a high-pressure mercury lamp (HPML) and using an exposure time of 4 h, the photoproduction of hydroxyl radicals (*OH) could be induced in an aqueous solution containing humic acid (HA). Hydroxyl radicals were determined by high-performance liquid chromatography using benzene as a probe. The results showed that *OH photoproduction increased from 1.80 to 2.74 microM by increasing the HA concentration from 10 to 40 mg L(-1) at an exposure time of 4 h (pH 6.5). Hydroxyl radical photoproduction in aqueous solutions of HA containing algae was greater than that in the aqueous solutions of HA without algae. The photoproduction of *OH in the HA solution with Fe(III) was greater than that of the solution without Fe(III) at pH ranging from 4.0 to 8.0. The photoproduction of *OH in HA solution with algae with or without Fe(III) under a 250 W HPML was greater than that under a 125 W HPML. The photoproduction of *OH in irradiated samples was influenced by the pH. The results showed that HPML exposure for 4 h in the 4-8 pH range led to the highest *OH photoproduction at pH 4.0.

Benzene↗
PubMed2004

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.

Microarrays fabricated with oligonucleotides longer than 40 bp have been introduced for monitoring whole genome expression but have not been evaluated with environmental samples. To determine the potential of this type of microarray for environmental studies, a 50-mer oligonucleotide microarray was constructed using 763 genes involved in nitrogen cycling: nitrite reductase (nirS and nirK), ammonia monooxygenase (amoA), nitrogenase (nifH), methane monooxygenase (pmoA), and sulfite reductase (dsrAB) from public databases and our own sequence collections. The comparison of the sequences from pure cultures indicated that the developed microarrays could provide species-level resolution for analyzing microorganisms involved in nitrification, denitrification, nitrogen fixation, methane oxidation, and sulfite reduction. Sensitivity tests suggested that the 50-mer oligonucleotide arrays could detect dominant populations in the environments, although sensitivity still needs to be improved. A significant quantitative relationship was also obtained with a mixture of DNAs from eight different bacteria. These results suggest that the 50-mer oligonucleotide array can be used as a specific and quantitative parallel tool for the detection of microbial populations in environmental samples.

Base Sequence↗
PubMed2004

Computational and experimental studies on human misshapen/NIK-related kinase MINK-1.

We have studied the structure and function of Human Misshapen/NIK-related kinase (MINK-1) through a combination of computational methods and experimental approaches, including (1) fold recognition and sequence-structure alignment for each structural domain using the threading program PROSPECT, (2) gene expression and protein-protein interaction analysis of yeast homologs of human MINK-1 domains, and (3) yeast two-hybrid screening for proteins that interact with human MINK-1. Our structure prediction dissects MINK-1 into four domains: a conserved N-terminal kinase domain, followed by a coiled-coil region and a proline-rich region, and a C-terminal GCK domain. Gene expression and yeast two-hybrid analysis of yeast homologs of the MINK-1 domains suggest that MINK-1 may be involved in cell-cycle progression and cytoskeletal control. Consistent with these predicted functions, our in-house yeast two-hybrid screen for proteins that interact with human MINK-1 provides strong evidence that the coiled-coil and proline-rich domains of MINK-1 participate in the regulation of cytoskeletal organization, cell-cycle control and apoptosis. A homology model of the MINK-1 kinase domain was used to screen the NCI open compound database in DOCK, and chemical compounds with pharmaceutically acceptable properties were identified. Further medicinal chemistry compound structure optimization and kinase assays are underway.

Amino Acid Sequence↗
PubMed2004

[Significance of CK20 mRNA expression in peripheral blood of colorectal cancer patients by real-time fluorescent quantitative RT-PCR].

OBJECTIVE: To detect the expression of cytokeratin 20 (CK20) mRNA in peripheral blood of colorectal carcinoma and to discuss its clinical value. METHODS: Real-time fluorescent quantitative RT-PCR was used to detect the CK20 mRNA expression in the peripheral blood of 51 patients with colorectal carcinoma and 30 healthy volunteers. RESULTS: 27.45% of the patients showed CK20 mRNA expression, while it was 6.67% for the control group (P<0.025). With the progress of Dukes' stages, the expression level of CK20 mRNA increased, but there was no statistic significance (P<0.05). More samples in Dukes'C and D than in Dukes'A and B stages showed >10 copies/ml. CONCLUSION: The detection of CK20 mRNA expression in peripheral blood of patients with colorectal carcinoma may be helpful to identify early shedding tumor cells. It is also useful to monitor the progression of the disease and observe the effect of clinical treatment.

Adult↗
PubMed2004

[Cyclin D2 expression in chronic myelogenous leukemia].

OBJECTIVE: To investigate the relationship between cyclin D2 and P210(BCR/ABL) tyrosine kinase in chronic myelogenous leukemia (CML). METHODS: RT-PCR, Western blot and flow cytometry were performed to detect the expression of cyclin D2 in K562 cells and in K562-ib-eGFP cells which express intracellular single-chain antibody (sFv, intrabody) against ABL tyrosine kinase domain. RESULTS: Cyclin D2 expression in K562-ib-eGFP cells was 18.90% which was lower than that of control K562 cells (48.10%), and the number of S-phase cells in K562-ib-eGFP was 40.40% which was much lower than that in K562 cells (64.34%). CONCLUSION: Cyclin D2 is a potential down-stream signal molecule of the p210(BCR/ABL) tyrosine kinase in CML. The altered expression of cyclin D2 may contribute to the over proliferation of CML cells.

Blotting, Western↗
PubMed2004

[Emergence and clinical significance of YMDD and HBeAg-related mutations during lamivudine treatment].

OBJECTIVE: To explore YMDD and HBeAg related mutations of hepatitis B virus and its clinical significance during lamivudine therapy. METHODS: From sera of chronic hepatitis B patients with 9 - 30 months lamivudine therapy, signal-base mutations of YMDD motif, G1896A, A1814C, A1762T and G1764A were analyzed by gene chips technique. RESULTS: In the 102 patients with 18 months in average of lamivudine treatment, 22 were found to have YMDD mutations, including 8 with YMDD and HBeAg related mutants. 3 of the 8 patients had G1896A mutant, 2 had A1814C and the remaining had G1896A + A1814C, A1762T and G1764A, A1762T and G1764A + G1896A. The former 5 patients and signal YMDD mutant patients were HBeAg positive, while the latter 3 with YMDD and HBeAg related multiple mutants were HBeAg negative. One of the three patients with multiple mutants who continued lamivudine treatment 3 months more reversed to YMDD wide-type HBV with accompanying positive HBeAg. CONCLUSIONS: Mutant of YMDD associated with HBeAg related multiple mutations during lamivudine treatment may arise in patients with HBV DNA breakthrough and negative HBeAg. HBV DNA should be detected in the patients with HBeAg seroconversion to exclude the HBeAg related multiple mutations.

Adolescent↗
PubMed2003

[Coronary artery bypass grafting in patients following percutaneous coronary interventions].

OBJECTIVE: To investigate and analyze the clinical outcomes of coronary artery bypass grafting (CABG) in patients with history of previous percutaneous coronary interventions (PCI). METHODS: We studied 76 patients with a history of PCI who underwent CABG surgery in our institute from August of 1999 to April of 2002, which was 14.0 percent of concurrent CABG. There were 39 cases with PTCA alone and 37 combined with stent implantation, of whom 5 had undergone re-do PCI therapy. Then 46 patients encountered re-stenosis and 6 developed new lesion in native coronary arteries. There were 4 cases with unsuccessful PCI, 11 cases with residual lesion in important vessels and 9 cases with acute complications during PCI. There was a higher incidence of myocardial infarction in group PCI than that in group Non-PCI, and a lower incidence of triple vessel disease (P<0.01). RESULTS: Group PCI had more emergent surgeries (27.6% vs 13.3%) and fewer OPCAB procedures (91.3% vs 97.2%) than group Non-PCI (P<0.01). The mean number of distal anastomosis in group PCI was smaller than that in group Non-PCI (P<0.01). There were 6 people who died in group PCI, of whom 3 died of heart pump failure,1 of ventricular fibrillation, 1 of neurological complication, and 1 of renal failure. The mortality of group PCI was higher than group Non-PCI (7.9% vs 1.9%, P<0.01). In group PCI, there were 4 with peri-operative myocardial infarction, 1 with late death and 1 with recurrent angina pectoris. CONCLUSION: CABG is usually the most effective and necessary way to treat PCI failure, unsatisfactory revascularization and its acute complications. It is most important to promptly and appropriately deal with acute complications of PCI in reducing the mortality.

Aged↗
PubMed2003

A computational pipeline for protein structure prediction and analysis at genome scale.

MOTIVATION: Experimental techniques alone cannot keep up with the production rate of protein sequences, while computational techniques for protein structure predictions have matured to such a level to provide reliable structural characterization of proteins at large scale. Integration of multiple computational tools for protein structure prediction can complement experimental techniques. RESULTS: We present an automated pipeline for protein structure prediction. The centerpiece of the pipeline is our threading-based protein structure prediction system PROSPECT. The pipeline consists of a dozen tools for identification of protein domains and signal peptide, protein triage to determine the protein type (membrane or globular), protein fold recognition, generation of atomic structural models, prediction result validation, etc. Different processing and prediction branches are determined automatically by a prediction pipeline manager based on identified characteristics of the protein. The pipeline has been implemented to run in a heterogeneous computational environment as a client/server system with a web interface. Genome-scale applications on Caenorhabditis elegans, Pyrococcus furiosus and three cyanobacterial genomes are presented. AVAILABILITY: The pipeline is available at http://compbio.ornl.gov/proteinpipeline/

Algorithms↗
PubMed2003

EXCAVATOR: a computer program for efficiently mining gene expression data.

Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.

Algorithms↗
PubMed2003

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.

Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering approximately 94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.

Amino Acid Sequence↗
PubMed2003

Improving the performance of DomainParser for structural domain partition using neural network.

Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years of investigation, remains a challenging and unsolved problem. Manual inspection still plays a key role in domain decomposition of a protein structure. We have previously developed a computer program, DomainParser, using network flow algorithms. The algorithm partitions a protein structure into domains accurately when the number of domains to be partitioned is known. However the performance drops when this number is unclear (the overall performance is 74.5% over a set of 1317 protein chains). Through utilization of various types of structural information including hydrophobic moment profile, we have developed an effective method for assessing the most probable number of domains a structure may have. The core of this method is a neural network, which is trained to discriminate correctly partitioned domains from incorrectly partitioned domains. When compared with the manual decomposition results given in the SCOP database, our new algorithm achieves higher decomposition accuracy (81.9%) on the same data set.

Algorithms↗
PubMed2003

Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis.

OBJECTIVE: To determine whether synovial fluid (SF) levels and cell-surface expression of B lymphocyte stimulator (BLyS) protein and SF levels of APRIL are elevated in patients with inflammatory arthritis (IA). METHODS: Same-day blood and SF samples from 89 patients with 103 knee effusions (81 knees with IA and 22 with noninflammatory arthritis [NIA]) were evaluated for BLyS protein and APRIL levels by enzyme-linked immunosorbent assay. Blood and SF mononuclear cells were double-stained for surface BLyS protein and surface CD14 (monocyte marker) and were analyzed by flow cytometry. Complete blood cell counts and SF nucleated cell counts were performed by the clinical hematology laboratory. RESULTS: BLyS protein levels were higher in SF than in corresponding serum samples from both IA and NIA patients. SF BLyS protein levels, but not surface expression of BLyS protein, were disproportionately elevated in IA patients. APRIL levels were higher in SF than in corresponding serum samples from most IA patients but not NIA patients. SF BLyS protein and APRIL levels correlated with each other, and each correlated with SF monocyte, lymphocyte, neutrophil, and total nucleated cell counts. Although SF and serum BLyS protein levels correlated with each other, SF and serum APRIL levels did not, suggesting that SF BLyS protein levels are more dependent upon systemic factors than are SF APRIL levels. Moreover, in 8 patients who underwent sequential arthrocenteses, changes in SF BLyS protein levels did not immutably parallel changes in SF APRIL levels, indicating their differential regulation. CONCLUSION: BLyS protein and APRIL are locally produced in inflamed joints. Their respective SF levels are differentially regulated, suggesting that they serve different functions. Together, their local production may foster survival and/or expansion of B cells that produce pathogenic autoantibodies and/or promote local T cell activation and consequent joint destruction.

Adult↗
PubMed2003

B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations.

OBJECTIVE: To assess the overexpression of B lymphocyte stimulator (BLyS) over time in patients with systemic lupus erythematosus (SLE). METHODS: Sixty-eight SLE patients were followed up longitudinally for a median 369 days. At each physician encounter, disease activity was assessed by the Systemic Lupus Erythematosus Disease Activity Index, and blood was collected for determination of the serum BLyS level, blood BLyS messenger RNA (mRNA) level, and cell surface BLyS expression. Twenty normal control subjects underwent similar laboratory evaluations. RESULTS: In contrast to the uniformly normal serum BLyS and blood BLyS mRNA phenotypes in control subjects, SLE patients displayed marked heterogeneity, with 50% and 61% of patients manifesting persistently or intermittently elevated serum BLyS and blood BLyS mRNA phenotypes, respectively. Surface BLyS expression by SLE peripheral blood mononuclear cells was also often increased. Treatment of patients who had elevated serum BLyS levels with intensive courses of high-dose corticosteroids resulted in marked reductions in serum BLyS levels, and tapering of the corticosteroid dosage often resulted in increases in serum BLyS levels. Serum BLyS levels generally correlated with anti-double-stranded DNA (anti-dsDNA) titers (in those with detectable anti-dsDNA titers), but changes in serum BLyS levels did not correlate with changes in disease activity in individual patients. Serum BLyS phenotype did not associate with specific organ system involvement. CONCLUSION: Dysregulation of BLyS over extended periods of time is common in patients with SLE. Neutralization of BLyS activity with an appropriate BLyS antagonist may be therapeutically beneficial.

Adrenal Cortex Hormones↗