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Dong Xu

Publications and source records attributed to Dong Xu.

At least 37 records · Page 2Linked to original sources
PubMed2006

Bioinformatics and its applications in plant biology.

Bioinformatics plays an essential role in today's plant science. As the amount of data grows exponentially, there is a parallel growth in the demand for tools and methods in data management, visualization, integration, analysis, modeling, and prediction. At the same time, many researchers in biology are unfamiliar with available bioinformatics methods, tools, and databases, which could lead to missed opportunities or misinterpretation of the information. In this review, we describe some of the key concepts, methods, software packages, and databases used in bioinformatics, with an emphasis on those relevant to plant science. We also cover some fundamental issues related to biological sequence analyses, transcriptome analyses, computational proteomics, computational metabolomics, bio-ontologies, and biological databases. Finally, we explore a few emerging research topics in bioinformatics.

Computational Biology↗
PubMed2006

Quantitative real-time RT-PCR detection for CEA, CK20 and CK19 mRNA in peripheral blood of colorectal cancer patients.

This study is aimed at establishing a sensitive approach to detect disseminated tumor cells in peripheral blood and evaluate its clinical significance. A total of 198 blood samples including 168 from colorectal carcinoma (CRC) patients and 30 from healthy volunteers were examined by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) to evaluate the expression of carcinoembryonic antigen (CEA), cytokeratin 20 (CK20) and cytokeratin 19 (CK19) mRNA. CEA mRNA was detected in 35.8% of patients and 3.3% of controls, CK20 mRNA in 28.3% of patients and 6.7% of controls, and CK19 mRNA in 41.9% of patients and 3.3% of controls. CEA and CK20 mRNA positive ratio increased with the advancing Dukes stages, but there was no significant difference in positive ratio between any two stages (P>0.05). Also, relatively high positive ratio of CEA, CK20 and CK19 mRNA expression was observed in some CRC patients with earlier Dukes stages. A higher positive ratio was obtained when two or three detection markers were combined compared to a single marker. Our study indicates that quantitative real-time RT-PCR detection for CEA, CK20 and CK19 mRNA in peripheral blood is a valuable tool for monitoring early stage dissemination of CRC cells in blood circulation.

Adult↗
PubMed2006

[Detection of bcr/abl fusion gene from K562 cell line and mononuclear cells of CML patients by DNA-PCR].

OBJECTIVE: To detect bcr/abl fusion gene at DNA level in K562 cell line and mononuclear cells from patients with chronic myelogenous leukemia (CML). METHODS: Based on previous research, a set of DNA-PCR primers was redesigned. DNA from K562 cells and mononuclear cells of CML patients was extracted respectively. After DNA-PCR for bcr/abl fusion gene the amplified fragments were then sequenced. RESULT: At DNA level the bcr/abl fusion gene in K562 cells and mononuclear cells of 2 CML patients was amplified. Furthermore, the DNA breakpoint of fusion gene in the above samples through sequencing of amplified fragments was localized. CONCLUSION: DNA-PCR offers a new detection technology for bcr/abl fusion without the expression of fusion gene.

Fusion Proteins, bcr-abl↗
PubMed2006

[Determination of urinary catecholamines with neuroblastoma in children by HPLC].

OBJECTIVE: To develop the method of high performance liquid chromatography (HPLC) to determine the level of catecholamines (CAs) in 24h urinary, such as norepinephrine (NE), epinephrine (E), dopamine (DA), and to apply in the diagnosis of neuroblastoma (NB). METHODS: The determination was performed in a Zorbax SB-Aq-C18 (4.6 x 150 mm, 5 microm) column with a mobile phase of 0.02 mol/L KH2PO4 solution, and with fluorescence detector. In the condition, the levels of 24 h urinary NE, E, DA were detected by HPLC in healthy children, and in children with NB. RESULTS: The recovery rates of NE, E and DA were 92.20%-94.38%, 94.60%-95.85% and 88.43%-91.68%, respectively, the corresponding with-day precisions (n=6) were 5.46%, 3.96% and 4.49%, respectively, and the between-day precisions (n=6) were 6.48%, 4.67% and 5.43%, respectively. The linear scopes of NE and E were 25-800 microg/L, respectively, the linear scope of DA was 50-1600 microg/L. The least detections were 2.5, 1.5, 0.5 microg/L, respectively. CONCLUSION: This method is simple, accurate and high specificity, and can be used for the clinical diagnosis of NB.

Catecholamines↗
PubMed2006

[Spectra analysis of [MnHg(SCN)4 (H2O)2 x 2C4H9NO (MMTWD) crystals].

The factor group symmetry analysis method was used to predict lattice vibrational modes of MMTWD single crystal, and it was found that there are no more than 297 and 148 theoretically observable Raman peaks and infrared reflection bands, respectively. The Raman and IR spectra were measured at room temperature. All the Raman and IR spectra peaks were assigned on the basis of the group theory and lattice dynamics theory. According to the Raman and IR spectra, the molecular structure of MMTWD crystal was discussed. From the results of the present theoretical and experimental works, the three-dimensional network structure of MMTWD crystal was identified. This structure provides the crystal with a large interaction force between molecules, which in turn induces high stability and macroscopic nonlinear optical properties.

English Abstract↗
PubMed2006

[Comparative study of endoluminal ultrasonography and spiral computed tomography in preoperative staging of rectal carcinoma].

OBJECTIVE: To compare the efficacy of endoluminal ultrasonography (EUS) and spiral computed tomography (SCT) in preoperative staging of rectal carcinoma. METHODS: Both EUS and SCT were performed prior to surgery in 68 patients with rectal carcinoma. After radical surgery, the preoperative findings were compared with histologic findings of the operative specimens, and the efficacy of EUS and SCT in staging the rectal carcinoma were evaluated. RESULTS: For T stage, EUS accuracy was 86.8%, while SCT was 70.6%. The difference was significant (P<0.05). For N stage, EUS accuracy was 67.6% and SCT was 63.2%. The difference was not significant (P>0.05). CONCLUSION: EUS is superior to SCT for the judgement of tumor infiltration depth, but neither is able to provide satisfactory assessment of lymph node metastases.

Adult↗
PubMed2005

Iron substitution for sodium in a carboxylate-bridged, heterodinuclear sodium-iron complex.

The synthesis and structural characterization of the carboxylate-bridged, heterodinuclear iron-sodium complex [NaFe(PIC2DET)(mu-O2CTrp)3] (2), where PIC2DET (1) is a 2,3-diethynyltriptycene-linked dipicolinic methyl ester ligand and Trp is 9-triptycenyl, are described. The metal ions in 2 are bridged by three triptycene carboxylates with an Fe...Na distance of 3.181(2) A, and each is coordinated to a pyridine nitrogen and carbonyl oxygen atom of 1, forming two five-membered chelate rings. A linkage isomer in which Fe1 is bound by the other ester oxygen atom of 1 was identified by X-ray crystallographic analysis. Treatment of 2 with Fe(OTf)2.2MeCN resulted in substitution of sodium by iron(II) to give the cationic diiron(II) complex [Fe2(PIC2DET)(mu-O2CTrp)3][OTf] (3). This reaction was investigated by UV-vis, IR, MS, and stopped-flow spectroscopy. The substitution is first order with respect to 2 and zero order with respect to Fe(OTf)2.2MeCN (kobs = 21 +/- 2 s-1), consistent with a dissociative mechanism. A positive enthalpy of activation (DeltaH = 59 +/- 6 kJ mol-1) and negative entropy of activation (DeltaS = -20 +/- 6 J mol-1 K-1) were calculated from the temperature dependence of the rate-determining dissociation step.

Carboxylic Acids↗
PubMed2005

Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma.

In response to DNA damage, the p53 tumor suppressor can elicit either apoptosis or cell-cycle arrest and repair, but how this critical decision is made in specific cell types remains largely undefined. We investigated the mechanism by which the transcriptional repressor Slug specifically rescues hematopoietic progenitor cells from lethal doses of gamma radiation. We show that Slug is transcriptionally induced by p53 upon irradiation and then protects the damaged cell from apoptosis by directly repressing p53-mediated transcription of puma, a key BH3-only antagonist of the antiapoptotic Bcl-2 proteins. We established the physiologic significance of Slug-mediated repression of puma by demonstrating that mice deficient in both genes survive doses of total-body irradiation that lethally deplete hematopoietic progenitor populations in mice lacking only slug. Thus, Slug functions downstream of p53 in developing blood cells as a critical switch that prevents their apoptosis by antagonizing the trans-activation of puma by p53.

Animals↗
PubMed2005

4,5-Bis(furoylsulfanyl)-1,3-dithiole-2-thione.

The title compound, C13H6O4S5, possesses crystallographically imposed mirror symmetry, with the atoms of the C=S group lying on the mirror plane. It is an example of the general formula [RCO]2(dmit), where R is a furan ring and dmit is 2-thioxo-1,3-dithiole-4,5-dithiolate. The components exhibit some polarization of their molecular-electronic structure. The dmit and furan moieties exhibit a high degree of conjugation, as the introduction of C=O connecting the conjugated furan (donor) and dmit (acceptor) rings forms a good conjugated system with high delocalization. A polar three-dimensional framework is built from a combination of intermolecular contacts, namely SS interactions and C-HO hydrogen bonding. The structural characteristics lead to good second-order non-linear optical properties.

Journal Article↗
PubMed2005

Regulation of p21-activated kinase-independent Rac1 signal transduction by nischarin.

Nischarin regulates Rac1-dependent cell motility by interaction with and inhibition of the p21-activated kinase (PAK1). In addition to regulating the activation of PAK1, Rac1 controls multiple downstream pathways to regulate cell growth and differentiation, as well as cell motility. Signaling by a constitutively activated Rac1 mutant deficient in PAK binding (Rac1Q61L-40C) was examined to determine whether Nischarin impinges on these other Rac1 effector pathways. Nischarin formed immunoprecipitatable complexes with Rac1Q61L and Rac1Q61L-40C when the proteins were co-expressed. In NIH3T3 cells, Rac1Q61L and Rac1Q61L-40C stimulation of a minimal NF-kappaB response element or the cyclin D1 promoter, a downstream target of NF-kappaB, was inhibited by co-expression of Nischarin. Additionally, suppression of endogenous Nischarin protein with small interfering RNA in PC12 cells enhanced Rac1Q61L and Rac1Q61L-40C activation of NF-kappaB. In further support of Nischarin suppressing PAK independent Rac signaling, foci formation in monolayers of NIH3T3 cells by Rac1Q61L-40C in cooperation with c-Raf/CAAX was inhibited by the presence of Nischarin. Nischarin alters the cellular localization of Rac1Q61L and Rac1Q61L-40C to vesicles and this positively correlates with the repression of the Rac1 signal. Thus, Nischarin, in addition to regulating the PAK strand of Rac1 signaling, can also regulate other links in the web of Rac1 signaling pathways.

Animals↗
PubMed2005

Epigenetic manipulation of gene expression: a toolkit for cell biologists.

Cell biologists have been afforded extraordinary new opportunities for experimentation by the emergence of powerful technologies that allow the selective manipulation of gene expression. Currently, RNA interference is very much in the limelight; however, significant progress has also been made with two other approaches. Thus, antisense oligonucleotide technology is undergoing a resurgence as a result of improvements in the chemistry of these molecules, whereas designed transcription factors offer a powerful and increasingly convenient strategy for either up- or down-regulation of targeted genes. This mini-review will highlight some of the key features of these three approaches to gene regulation, as well as provide pragmatic guidance concerning their use in cell biological experimentation based on our direct experience with each of these technologies. The approaches discussed here are being intensely pursued in terms of possible therapeutic applications. However, we will restrict our comments primarily to the cell culture situation, only briefly alluding to fundamental differences between utilization in animals versus cells.

Animals↗
PubMed2005

Poly[bis(N-methylformamide)tetra-mu-thiocyanato-manganese(II)mercury(II)].

The title complex, [MnHg(NCS)4(C2H5NO)2]n, consists of slightly distorted MnN4O2 octahedra and HgS4 tetrahedra. Each Mn(II) cation is bound to four N atoms of the NCS groups and two O atoms of the N-methylformamide (NMF) ligands in a cis configuration. Each Hg(II) cation is coordinated to four S atoms of NCS groups. Each pair of Mn(II) and Hg(II) cations is connected by an -NCS- bridge, forming an infinite three-dimensional -Mn-NCS-Hg- network.

Manganese Compounds↗
PubMed2005

BAFF overexpression and accelerated glomerular disease in mice with an incomplete genetic predisposition to systemic lupus erythematosus.

OBJECTIVE: To determine whether overexpression of BAFF can accelerate the development of systemic lupus erythematosus-associated end-organ disease in hosts with an underlying autoimmune diathesis. METHODS: We introduced a BAFF transgene (Tg) into autoimmune-prone B6.Sle1 and B6.Nba2 mice and evaluated these mice for serologic autoimmunity and renal pathology. RESULTS: B6.Sle1.BAFF and B6.Nba2.BAFF mice, but not non-Tg littermates, frequently developed severe glomerular pathology by 3 months of age. Age-matched B6.BAFF mice, despite renal Ig deposits and increases in B cells and Ig production similar to those in B6.Sle1.BAFF and B6.Nba2.BAFF mice, did not develop glomerular pathology. In B6.Sle1.BAFF and B6.Nba2.BAFF mice, severity of glomerular disease did not obligately correlate with circulating levels of IgG anti-chromatin and/or anti-double-stranded DNA antibodies or with amounts of these autoantibodies deposited in the kidneys. Even in mice with severe glomerular disease, renal tubulointerstitial infiltrates were very limited, and increased proteinuria was not detected. CONCLUSION: BAFF-driven effects on glomerular pathology may be mediated, at least in part, by autoantibodies with specificities other than chromatin and/or by autoantibody-independent means. There is an uncoupling of BAFF-driven precocious glomerular pathology from concomitant development of clinically apparent renal disease, strongly suggesting that BAFF overexpression works in concert with other factors to promote overt renal disease.

Animals↗
PubMed2005

Psychogenic tremor disorders identified using tree-based statistical algorithms and quantitative tremor analysis.

Detecting psychogenic tremors (PsychT) is often challenging. As there are no laboratory investigations or imaging techniques that can confirm the diagnosis, PsychT is identified on a clinical basis. We present a tree-based statistical algorithm derived from quantitative computerized tremor recordings as a novel method to help in the recognition of PsychT. The goal of this study was to show that objective data from computerized tremor recordings, when processed through a tree-based statistical algorithm, can be used to determine whether a patient can be classified as having PsychT.

Adult↗
PubMed2005

Humoral autoimmunity in mice overexpressing B cell surface CD19: vital role for MHC class II.

B6 mice bearing a transgene (Tg) for human CD19 (hCD19) harbor increased numbers of splenic Ig-secreting cells (IgSC), increased serum levels of total Ig and autoantibodies, but decreased numbers of splenic B cells. To assess the influence of MHC class II (MHCII) to this phenotype, MHCII-deficient CD19-Tg mice were generated. Compared to MHCII-sufficient CD19-Tg mice, splenic IgSC numbers and serum Ig and autoantibody levels were markedly diminished, and the decrease in splenic B cell numbers was aggravated. Remarkably, genetic reconstitution of these MHCII-deficient mice with a human DQ8 Tg resulted in a hierarchical restorative pattern. Restoration of splenic B cell numbers was complete; restoration of numbers of splenic IgSC and of serum Ig levels was partial; and restoration of circulating autoantibody levels was virtually non-existent. Thus, MHCII expression has a profound effect on B cells which can be uncoupled from global Ig and autoantibody production in the hCD19-Tg model. This raises the possibility that MHCII affects B cells in a manner that, at least in part, is independent of helper T cell function.

Animals↗
PubMed2005

Spectroscopic characterization of effective components anthraquinones in Chinese medicinal herbs binding with serum albumins.

The interactions of serum albumins such as human serum albumin (HSA) and bovine serum albumin (BSA) with emodin, rhein, aloe-emodin and aloin were assessed employing fluorescence quenching and absorption spectroscopic techniques. The results obtained revealed that there are relatively strong binding affinity for the four anthraquinones with HSA and BSA and the binding constants for the interactions of anthraquinones with HSA or BSA at 20 degrees C were obtained. Anthraquinone-albumin interactions were studied at different temperatures and in the presence of some metal ions. And the competition binding of anthraquinones with serum albumins was also discussed. The Stern-Volmer curves suggested that the quenching occurring in the reactions was the static quenching process. The binding distances and transfer efficiencies for each binding reactions were calculated according to the Föster theory of non-radiation energy transfer. Using thermodynamic equations, the main action forces of these reactions were also obtained. The reasons of the different binding affinities for different anthraquinone-albumin reactions were probed from the point of view of molecular structures.

Anthraquinones↗
PubMed2005

Delivery of MDR1 small interfering RNA by self-complementary recombinant adeno-associated virus vector.

Small interfering RNAs (siRNAs) are potentially powerful tools for therapeutic gene regulation. DNA cassettes encoding RNA polymerase III promoter-driven hairpin siRNAs allow long-term expression of siRNA in targeted cells. A variety of viral vectors have been used to deliver such cassettes to cells. Here we report on the development and use of a self-complementary recombinant adeno-associated virus (scAAV) vector for siRNA delivery into mammalian cells. We demonstrate that this modified vector efficiently delivers siRNA into multidrug-resistant human breast and oral cancer cells and suppresses MDR1 gene expression. This results in rapid, profound, and durable reduction in the expression of the P-glycoprotein multidrug transporter and a substantial reversion of the drug-resistant phenotype. This research suggests that scAAV-based vectors can be very effective agents for efficient delivery of therapeutic siRNA.

ATP Binding Cassette Transporter, Subfamily B, Mem↗