Biomedical subjects

Dong Xu

Publications and source records attributed to Dong Xu.

101 records · Page 6Linked to original sources

PubMed2002

B lymphocyte stimulator protein-associated increase in circulating autoantibody levels may require CD4+ T cells: lessons from HIV-infected patients.

To assess the helper T cell dependence of B lymphocyte stimulator (BLyS) protein-driven autoantibody production in vivo, serum levels of BLyS protein, total IgG, and anti-IgG anti-phospholipid (aPhL) autoantibodies from HIV-infected patients (n = 105) with varying degrees of CD4+ cell depletion and healthy control donors at low risk for HIV (n = 64) were determined. Peripheral blood mononuclear cells from these subjects were stained for surface expression of BLyS protein. Monocyte surface expression and serum levels of BLyS protein were increased in HIV-infected patients as were serum total IgG and IgG aPhL autoantibody levels. No associations were detected between increased serum BLyS protein levels and patient age, sex, disease duration, history of opportunistic infection or malignancy, or serum total IgG levels. However, serum levels of IgG aPhL autoantibodies were greater in patients with high serum BLyS protein levels than in those with normal serum BLyS protein levels. Importantly, this association between serum levels of BLyS protein and IgG aPhL was appreciated only in patients who were not severely CD4+ cell-depleted and not in patients who were severely CD4+ cell-depleted (peripheral blood CD4+ cell counts <or= 200/mm(3)). Thus, BLyS protein may preferentially facilitate IgG autoantibody production in vivo in a helper T cell-dependent manner. This raises the possibility that the combination of a BLyS protein antagonist with an agent that targets (helper) T cells may have salutary synergistic effects on autoantibody production in diseases such as systemic lupus erythematosus.

Adult↗

PubMed2002

Oxidants painting the cysteine chapel: redox regulation of PTPs.

Growth factors and cytokines appear to stimulate the intracellular production of reactive oxygen species (ROS). Evidence suggests that this alteration in the cellular redox state is essential for downstream signaling, but the precise mechanism has remained elusive. A new study now demonstrates that ligand-stimulated intracellular hydrogen peroxide can specifically and reversibly regulate the activity of protein tyrosine phosphatases.

Cysteine↗

PubMed2002

Evaluation of strategies for the intracellular delivery of proteins.

PURPOSE: The intracellular delivery of functionally active protein represents an important emerging strategy for laboratory investigation and therapeutic applications. Although a number of promising approaches for protein delivery have been developed, thus far there has been no attempt to compare the merits of the various deliver technologies. This issue is addressed in the current study. METHODS: In this study we utilize a sensitive luciferase reporter gene assay to provide unambiguous and quantitative evaluation of several strategies for the intracellular delivery of a biologically active protein comprised of the Gal4 DNA binding domain and the VP16 transactivating domain. RESULTS: Both a cationic lipid supramolecular complex and a poly meric complex were able to effectively deliver the chimeric transcription factor to cultured cells. In addition, protein chimeras containing the Tat cell penetrating peptide, but not those containing the VP22 peptide, were somewhat effective in delivery. CONCLUSIONS: Both supramolecular protein-carrier complexes and protein chimeras with certain cell penetrating peptides can support intracellular delivery of proteins. In the cell culture setting the supramolecular complexes are more effective, but their large size may present problems for in vivo applications.

Cell Line↗

PubMed2002

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO(2) are important terms in the global environmental response to anthropogenic atmospheric inputs of CO(2) and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.

Algorithms↗

PubMed2002

PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.

MOTIVATION: DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs). RESULTS: PRIMEGENS first carries out a BLAST search for each target ORF against all other ORFs of the genome to quickly identify possible homologous sequences. Then it performs optimal sequence alignment between the target ORF and each of its homologous ORFs using dynamic programming. PRIMEGENS uses the sequence alignments to select gene- specific fragments, and then feeds the fragments to the Primer3 program to design primer pairs for PCR amplification. PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone package or it can be used from a Web interface. The program runs efficiently, and it takes a few seconds per sequence on a typical workstation. PCR primers specific to individual ORFs from Shewanella oneidensis MR-1 and Deinococcus radiodurans R1 have been designed. The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis.

Algorithms↗

PubMed2002

Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.

MOTIVATION: Gene expression data clustering provides a powerful tool for studying functional relationships of genes in a biological process. Identifying correlated expression patterns of genes represents the basic challenge in this clustering problem. RESULTS: This paper describes a new framework for representing a set of multi-dimensional gene expression data as a Minimum Spanning Tree (MST), a concept from the graph theory. A key property of this representation is that each cluster of the expression data corresponds to one subtree of the MST, which rigorously converts a multi-dimensional clustering problem to a tree partitioning problem. We have demonstrated that though the inter-data relationship is greatly simplified in the MST representation, no essential information is lost for the purpose of clustering. Two key advantages in representing a set of multi-dimensional data as an MST are: (1) the simple structure of a tree facilitates efficient implementations of rigorous clustering algorithms, which otherwise are highly computationally challenging; and (2) as an MST-based clustering does not depend on detailed geometric shape of a cluster, it can overcome many of the problems faced by classical clustering algorithms. Based on the MST representation, we have developed a number of rigorous and efficient clustering algorithms, including two with guaranteed global optimality. We have implemented these algorithms as a computer software EXpression data Clustering Analysis and VisualizATiOn Resource (EXCAVATOR). To demonstrate its effectiveness, we have tested it on three data sets, i.e. expression data from yeast Saccharomyces cerevisiae, expression data in response of human fibroblasts to serum, and Arabidopsis expression data in response to chitin elicitation. The test results are highly encouraging. AVAILABILITY: EXCAVATOR is available on request from the authors.

Algorithms↗

PubMed2002

Selective inhibition of P-glycoprotein expression in multidrug-resistant tumor cells by a designed transcriptional regulator.

Selective inhibition of the multidrug resistance 1 (MDR1) gene and its product, the P-glycoprotein, a membrane transporter responsible for multidrug resistance, could be an important approach for enhancing cancer therapeutics. An emerging strategy for selective gene regulation involves designed zinc finger proteins that can recognize specific sequences in the promoter regions of disease-related genes. Herein, we investigate the behavior of clones of multidrug-resistant NCI/ADR-RES breast carcinoma cells displaying ponasterone-inducible expression of a designed transcriptional repressor targeted to the MDR1 promoter. The controlled production of this novel repressor resulted in major reductions in P-glycoprotein levels in these otherwise highly drug-resistant tumor cells. The regulated reduction of MDR1 expression in NCI/ADR-RES cells was accompanied by a marked increase in the rate of uptake of the P-glycoprotein substrate rhodamine 123. In addition, the cytotoxicity profile of the antitumor drug doxorubicin was dramatically altered in the induced cells compared with controls. The expression levels of other genes were examined both by a DNA array analysis of approximately 2000 genes and by biochemical techniques. Although some changes were observed in mRNA levels of nontargeted genes, the most dramatic effect by far was on MDR1, indicating that the action of the designed transcriptional repressor was quite selective. This study suggests that designed transcriptional regulators can be used to strongly and selectively influence expression of cancer-related genes, even under circumstances of extensive amplification of the target gene.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2002

[Effects of anti-ABL tyrosine kinase intrabody on the growth of K562 cells in nude mice].

OBJECTIVE: To study the effects of anti-ABL tyrosine kinase intrabody on the growth of human chronic myelogenous leukemia (CML) cells in nude mice. METHODS: A recombinant retroviral vector MSCV-ibE-IRES-eGFP was constructed to express intracellular single-chain antibody (intrabody) against ABL tyrosine kinase domain in CML cells. K562 cells were transduced with the retrovirus, eGFP+ cells were then selected by fluorescence-activated cell sorting (FACS). The intrabody mRNA expression was determined by reverse transcription (RT)-polymerase chain reaction (PCR). BCR/ABL and c-ABL protein tyrosine kinase (PTK) activity in the cells was examined. Transduced cells and control group K562 cells were transplanted into nude mice respectively and the tumor sizes were dynamically observed. RESULTS: K562-ibE cell was obtained. Expression of the BCR/ABL and c-ABL protein tyrosine kinase activity of harvested K562-ibE cells were markedly inhibited. At 14, 21 and 28 days after cell injection, the tumor volumes of experimental mice were obviously smaller than that of control mice, about one half of the control groups (P < 0.05). CONCLUSION: The growth of K562-ibE cells was significantly inhibited in vivo. It is possible that inhibition of the BCR/ABL protein tyrosine kinase activity by the intrabody blocked BCR/ABL signal transduction pathway, promoted apoptosis and reduced tumorigenicity of K562 cells in vivo.

Animals↗

PubMed2002

[Study on making pneumoconiosis model and method of lung lavage in rabbit].

OBJECTIVE: To provide an intact rabbit pneumoconiosis model and a method of lung lavage for studying the pathogenesis and treatment of pneumoconiosis. METHODS: The dust particles(< or = 5 microns diameter) were poured into the trachea of rabbit by trachea spile. The lung lavage of rabbit was carried out by the improved trachea catheter method. RESULTS: The rabbit lungs exposed to coal dust showed many black dust spots and there were proliferation of fibroblasts. The rabbit lungs exposed to silica dust showed nodules and several fusing nodules. The X-ray film showed that there were small irregular shadows, or fusing together into flake-like or round shadows in both lungs. The recovery rate of the lung lavage was 89%-94%. CONCLUSION: The model made by trachea spile and the method of lung lavage by the improved trachea catheter were simple, safe and without being injured.

Animals↗

PubMed2002

An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on our recent work towards automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques and a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm.

Algorithms↗

PubMed2001

Poly[[[tri(urea-kappaO)manganese(II)]-mu-thiocyanato-kappa2N:S-mercury(II)]-tri-mu-tetrathiocyanato].

The title complex, [MnHg(SCN)4(CH4N2O)3]n, consists of slightly distorted octahedral MnN3O3 and tetrahedral HgS4 units. The Mn(II) atom is coordinated by the O atoms of three urea molecules and by the N atoms of three SCN- ions; Hg(II) is coordinated by four S atoms from SCN- ions. Each pair of Mn(II) and Hg(II) atoms is connected by an -SCN- bridge, forming infinite two-dimensional -Mn-NCS-Hg- networks.

Journal Article↗