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Xing Zhang

Publications and source records attributed to Xing Zhang.

At least 37 records · Page 2Linked to original sources
PubMed2005

A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures.

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).

Algorithms↗
PubMed2005

Identification and characterization of the methyl arginines in the fragile X mental retardation protein Fmrp.

Fragile X syndrome is the most common form of inherited mental retardation and is caused by the absence of expression of the FMR1 gene. The protein encoded by this gene, Fmrp, is an RNA-binding protein that binds a subset of mRNAs and regulates their translation, leading to normal cognitive function. Although the association with RNAs is well established, it is still unknown how Fmrp finds and assembles with its RNA cargoes and how these activities are regulated. We show here that Fmrp is post-translationally methylated, primarily on its arginine-glycine-glycine box. We identify the four arginines that are methylated and show that cellular Fmrp is monomethylated and asymmetrically dimethylated. We also show that the autosomal paralog Fxr1 and the Drosophila ortholog dFmr1 are methylated post-translationally. Recombinant protein arginine methyl transferase 1 (PRMT1) methylates Fmrp on the same arginines in vitro as in cells. In vitro methylation of Fmrp results in reduced binding to the minimal RNA sequence sc1, which encodes a stem loop G-quartet structure. Our data identify an additional mechanism, arginine methylation, for modifying Fmrp function and suggest that methylation occurs to limit or modulate RNA binding by Fmrp.

Animals↗
PubMed2005

Expression of serine protease SNC19/matriptase and its inhibitor hepatocyte growth factor activator inhibitor type 1 in normal and malignant tissues of gastrointestinal tract.

AIM: To provide the expression profile of serine protease SNC19/matriptase and its inhibitor hepatocyte growth factor activator inhibitor type 1 (HAI-1) in normal and malignant tissues of gastrointestinal tract at mRNA level for further study on their correlations with tumor progression and metastasis. METHODS: Total RNAs were prepared from 37 samples of colorectal cancer tissues, 40 samples of gastric cancer tissues, and their adjacent normal tissues. The expression of SNC19/matriptase and HAI-1 in these samples was detected by real-time fluorescent quantitative PCR using glyceraldehyde-3-phosphate dehydrogenase as internal standard, and the clinical significance for the correlation with clinicopathological parameters was evaluated. RESULTS: In gastric cancer tissues the expression of HAI-1 and SNC19/matriptase was significantly lower than that in the corresponding adjacent normal tissues (Z = -3.280, P = 0.006; Z = -4.651, P = 0.000). HAI-1:SNC19/matriptase ratio showed no difference between normal and malignant tissues (P>0.05). Analysis of clinicopathological parameters showed decreased expression of HAI-1 and HAI-1:SNC19/matriptase ratio associated with stage III/IV gastric tumors as compared to stage I/II ones (Z = -2.140, P = 0.031; Z = -2.155, P = 0.031), and with lymph node-positive gastric cancer tissues as compared to lymph node-negative ones (Z = -2.081, P = 0.036; Z = -2.686, P = 0.006). The expression of SNC19/matriptase had no relationship with stages and lymph node metastasis (P>0.05). The expression of HAI-1 and HAI-1:SNC19/matriptase ratio increased in well-differentiated gastric cancer tissues, but there was no statistical significance (P>0.05). The difference of SNC19/matriptase expression was not significant in gastric cancer tissues of different histological differentiation status (P>0.05). In colorectal cancer tissues, the expression of HAI-1 and SNC19/matriptase was also markedly lower than that in their adjacent normal tissues (Z = -3.100, P = 0.002; Z = -2.731, P = 0.006), whereas HAI-1:SNC19/matriptase ratio showed no difference. Decreased expression of HAI-1 was associated with increased invasive depth and lymph node metastasis, but there was no statistical significance (P>0.05). The difference of SNC19/matriptase expression and HAI-1:SNC19/matriptase ratio was not significant in different stages and different lymph node metastasis status (P>0.05). The expression of SNC19/matriptase, HAI-1 or HAI-1:SNC19/martiptase ratio showed no difference in colorectal cancer tissues of different histological differentiation status (P>0.05). CONCLUSION: The expressions of SNC19/matriptase and its inhibitor HAI-1 are decreased in gastrointestinal cancer tissues compared to their normal counterparts, and the decreased expression of HAI-1 may correlate with invasion and lymph node metastasis. The possible mechanisms involved need to be further investigated.

Adult↗
PubMed2005

Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction.

Among members of the genus Orthoreovirus, family Reoviridae, a group of non-enveloped viruses with genomes comprising ten segments of double-stranded RNA, only the "non-fusogenic" mammalian orthoreoviruses (MRVs) have been studied to date by electron cryomicroscopy and three-dimensional image reconstruction. In addition to MRVs, this genus comprises other species that induce syncytium formation in cultured cells, a property shared with members of the related genus Aquareovirus. To augment studies of these "fusogenic" orthoreoviruses, we used electron cryomicroscopy and image reconstruction to analyze the virions of a fusogenic avian orthoreovirus (ARV). The structure of the ARV virion, determined from data at an effective resolution of 14.6 A, showed strong similarities to that of MRVs. Of particular note, the ARV virion has its pentameric lambda-class core turret protein in a closed conformation as in MRVs, not in a more open conformation as reported for aquareovirus. Similarly, the ARV virion contains 150 copies of its monomeric sigma-class core-nodule protein as in MRVs, not 120 copies as reported for aquareovirus. On the other hand, unlike that of MRVs, the ARV virion lacks "hub-and-spokes" complexes within the solvent channels at sites of local sixfold symmetry in the incomplete T=13l outer capsid. In MRVs, these complexes are formed by C-terminal sequences in the trimeric mu-class outer-capsid protein, sequences that are genetically missing from the homologous protein of ARVs. The channel structures and C-terminal sequences of the homologous outer-capsid protein are also genetically missing from aquareoviruses. Overall, the results place ARVs between MRVs and aquareoviruses with respect to the highlighted features.

Amino Acid Sequence↗
PubMed2005

Measuring the thermal conductivity of a single carbon nanotube.

Although the thermal properties of millimeter-sized carbon nanotube mats and packed carbon nanofibers have been readily measured, measurements for a single nanotube are extremely difficult. Here, we report a novel method that can reliably measure the thermal conductivity of a single carbon nanotube using a suspended sample-attached T-type nanosensor. Our experimental results show that the thermal conductivity of a carbon nanotube at room temperature increases as its diameter decreases, and exceeds 2000 W/mK for a diameter of 9.8 nm. The temperature dependence of the thermal conductivity for a carbon nanotube with a diameter of 16.1 nm appears to have an asymptote near 320 K. The present method is, in principle, applicable to any kind of a single nanofiber, nanowire, and even single-walled carbon nanotube.

Journal Article↗
PubMed2005

Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity.

UV-B radiation causes diverse morphological and physiological responses in plants, but the underlying mechanisms governing these integrated responses are unknown. In this study, we systematically surveyed responses of maize leaves to UV-B radiation using DIGE 2D gels and identified selected proteins by mass spectrometry and immunodetection analysis. To identify changes in protein accumulation in response to UV-B radiation, a line (b, pl W23) deficient in flavonoid sunscreen compounds and hence similar to commercial corn was used. In addition, its proteome in natural UV-B conditions was compared with that of two maize landraces from high altitudes (Cacahuacintle and Confite Puneño) that have improved UV-B tolerance. Protein patterns in adult maize leaves (Zea mays) were documented after growth for 21 days in sunlight depleted of UV-B radiation or growth in sunlight including an 8-h UV-B supplementation during 1 day in the field. We found that there is a very high correlation between previously documented mRNA accumulation assessed by microarray hybridization and quantitative real time reverse transcription-PCR and protein expression after UV-B irradiation in leaves of W23. Multiple isoforms were confirmed for some proteins; at least one protein, pyruvate, phosphate dikinase, is regulated post-translationally by phosphorylation by UV-B exposure. Proteins differentially regulated by UV-B radiation in W23 with higher levels under similar UV-B conditions in high altitude plants were also identified. These could be genetically fixed traits conferring UV-B tolerance and offer clues to specific adaptations to living in high ambient UV-B conditions.

Amino Acid Sequence↗
PubMed2005

Avidin plate assay system for enzymatic characterization of a histone lysine methyltransferase.

Modification of proteins by protein methyltransferases has several important biological functions. Here, we study the methylation of histone H3 tail at position Lys9 by the Dim-5 histone lysine methyltransferase, which is involved in epigenetic signaling and gene silencing and which triggers DNA methylation in Neurospora crassa. We have developed a new assay to detect protein methylation using a biotinylated synthetic peptide substrate and a radioactively labeled coenzyme. We show that the assay is linear with respect to time and enzyme concentration (under multiple turnover conditions) and that its background is very low. Data points were reproducible within 3%. At least 200 pmol of biotinylated peptide is bound completely to the microplate. We employed the assay system to determine the K(m) and k(cat) values of the Dim-5 enzyme for the methylation of a 20 mer peptide to be 7.4 microM and 2.3 min(-1), respectively. In addition, we determined the activity of four Dim-5 variants, ranging from full activity to less than 1% of residual activity. The microplate biotin/avidin peptide methylation assay developed here is convenient, very accurate, reproducible, and inexpensive. Because it yields quantitative results, it can be employed for a characterization of the enzymatic properties of histone lysine methyltransferases and other protein methyltransferases. The assay also is well suited for high-throughput applications.

Avidin↗
PubMed2005

Tumor metastasis and the reciprocal regulation of heparanase gene expression by nuclear factor kappa B in human gastric carcinoma tissue.

AIM: To investigate whether NF-kappaB is activated in human gastric carcinoma tissues and, if so, to study whether there is any correlation between NF-kappaB activity and heparanase expression in gastric carcinoma. METHODS: NF-kappaB activation was assayed by immunohistochemical staining in formalin-fixed, paraffin-embedded specimens from 45 gastric carcinoma patients. Electrophoretic mobility shift assay (EMSA) method was used for nuclear protein from these fresh tissue specimens. Heparanase gene expression was quantified using quantitative RT-PCR. RESULTS: The nuclear translocation of RelA (marker of NF-kappaB activation) was significantly higher in tumor cells compared to adjacent and normal epithelial cells ((41.3+/-3.52)% vs (0.38+/-0.22) %, t = 10.993, P = 0.000<0.05; (41.3+/-3.52)% vs (0+/-0.31)%, t = 11.484, P = 0.000<0.05). NF-kappaB activation was correlated with tumor invasion-related clinicopathological features such as lymphatic invasion, pathological stage, and depth of invasion (Z = 2.148, P = 0.032<0.05; chi(2) = 8.758, P = 0.033<0.05; chi(2) = 18.531, P = 0.006<0.05). NF-kappaB activation was significantly correlated with expression of heparanase gene (r = 0.194, P = 0.046<0.05). CONCLUSION: NF-kappaB RelA (p65) activation was related with increased heparanase gene expression and correlated with poor clinicopathological characteristics in gastric cancers. This suggests NF-kappaB as a major controller of the metastatic phenotype through its reciprocal regulation of some metastasis-related genes.

Electrophoretic Mobility Shift Assay↗
PubMed2005

Development of an enzyme-linked immunosorbent assay for podophyllotoxin.

A competitive indirect enzyme-linked immunosorbent assay (ciELISA) for podophyllotoxin was developed by using polyclonal antibody, and its suitability for the determination of this analyte in spiked water samples was studied. To avoid antibody production to the linker, the succinoyl-podophyllotoxin (hapten) mimicking the analyte was synthesized and conjugated with the carrier proteins bovine serum albumin (BSA) and ovalbumin (OVA) by mixed anhydride reaction (MAR) and active ester method (AEM). Polyclonal antibodies raised against Hapten-BSA(1) synthesized by MAR and Hapten-BSA(2) by AEM were screened and selected for the ciELISA. One set of antibodies from the rabbit M4440 immunized with Hapten--BSA(1) showed an I(50) value of 2.21 microg/mL with a detection limit of 0.12 microg/mL, and the other set from the rabbit M4469 immunized with Hapten-BSA(2) had an I(50) value of 0.7897 microg/mL with a detection limit of 0.0056 microg/mL. This assay showed the cross-reactivities with the structurally closely related compounds. Recoveries from the podophyllotoxin-fortified tap water in the assay were in the range of 72--115%. A good correlation between podophyllotoxin concentration measured by the ELISA and HPLC (R(2)=0.9924, Y=1.195X-0.257) was obtained from linear regression analysis. These results indicate that the ELISA could be a convenient and supplemental analytical tool for monitoring podophyllotoxin and its analogues in waters without previous extraction or cleanup.

Animals↗
PubMed2005

Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution.

Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry.

Algorithms↗
PubMed2005

Structural and sequence motifs of protein (histone) methylation enzymes.

With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.

Amino Acid Motifs↗
PubMed2005

[Epidermal growth factor receptor mutation in Chinese patients with non-small cell lung cancer].

BACKGROUND & OBJECTIVE: Recent studies showed that somatic mutations in epidermal growth factor receptor (EGFR) tyrosine kinase (TK) domain are associated with sensitivity of non-small cell lung cancer(NSCLC) to TK inhibitor gefitinib. The mutations, including in-frame deletions at exon 19 and substitutions at exon 18 or exon 21, cluster around ATP-binding pocket of TK domain. The frequency of mutations are higher in Japanese patients than in American patients. This study was to analyze EGFR mutations in Chinese patients with NSCLC. METHODS: From Jun. to Oct. 2004, fresh specimens of lung cancer and corresponding normal lung tissue were collected from 52 consecutive NSCLC patients (39 men and 13 women) treated in Cancer Center of Sun Yat-sen University. All patients had not received treatment of gefitinib. DNA was extracted from the 52 specimens. Exons 19 and 21 were amplified by polymerase chain reaction (PCR), and sequenced and analyzed from both sense and antisense directions. RESULTS: Somatic mutations in TK domain of EGFR in tumors were identified from 10 of the 52 (19.2%) patients, including 7 cases of in-frame deletion in exon 19 and 3 cases of amino acid substitution in exon 21. Mutation rate was significantly higher in adenocarcinoma, adeno-squamous carcinoma, and bronchioloalveolar cancer than in squamous cell carcinoma [26.1% (6/23), 40.0% (2/5), and 50.0% (2/4) vs. 0 (0/20), P=0.025], and significantly higher in non-smokers than in smokers [41.8% (7/17) vs. 8.6% (3/35), P=0.009]. Mutation rate in women was similar to that in men [23.1% (3/13) vs. 18.0% (7/39), P=0.697]. CONCLUSION: EGFR mutation rate in Chinese NSCLC patients is similar to that in Japanese patients, and is obviously higher than that in Caucasian population.

Adenocarcinoma↗
PubMed2005

Synthesis and identification of antigenic conjugates of podophyllotoxin.

AIM: To synthesize and identify artificial antigen of podophyllotoxin for the production of podophyllotoxin polyclonal antibody. METHODS: The hapten was synthesized by two different chemical approaches and characterized by TLC, IR, NMR, and MS. Mixed anhydride reaction (MAR) and active ester method (AEM) were used to couple the podophyllotoxin to carrier proteins (BSA and OVA). Characterization of artificial antigens was done by using spectroscopy and electrophoresis. The anti-podophyllotoxin polyclonal antibodies were obtained through immunizing rabbits. RESULTS: The results from IR, NMR and MS showed that 4-O-succinoyl podophyllotoxin (hapten) was successfully synthesized. The coupling molar ratios of the hapten and carrier proteins were 88.6 for Hapten-BSA1, 40.3 for Hapten-BSA2, 17.8 for Hapten-OVA1, and 54.2 for Hapten-OVA2. Hapten conjugates coupled with BSA yielded two sets of the specific and affinitive polyclonal antibodies. One set of antibodies showed an IC50 value of 2.21 microg.mL(-1) with a detection limit of 0.12 microg.mL(-1). CONCLUSION: Antigenic conjugates were artificially synthesized, and based on these artificial antigens, polyclonal antibodies against podophyllotoxin were raised from rabbits immunized with two different immunogens and characterized with an indirect ELISA format.

Animals↗
PubMed2005

[Correlation of GLC-82 lung carcinoma cell aggregation in suspension culture to the activation of protein kinases FAK, AKT, ERK, and SRC].

BACKGROUND & OBJECTIVE: Our previous study revealed that tyrosine kinase FAK can partly mediate the aggregation of tumor cells in suspension culture, therefore, suppress cell apoptosis and promote cell proliferation. However, the downstream pathway of FAK in the formation of cell aggregation is unclear. This study was to investigate the roles of FAK and its potential downstream molecules ERK, AKT, and SRC in mediating aggregation of lung adenocarcinoma GLC-82 cells in suspension culture. METHODS: Morphology of the aggregations of GLC-82 cells and normal lung HBE cells in polyHEMA suspension culture was observed. Cell apoptosis was studied by DNA electrophoresis on agarose gel. The ability of cell transformation was studied by colony formation assay. The phosphorylation of the protein kinases was investigated by Western blot. FAK was silenced by RNA interference. RESULTS: GLC-82 cells survived and aggregated in suspension culture; while apoptosis occurred in HBE cells which formed no aggregation in suspension culture. Phosphorylation levels of FAK, ERK, AKT, and SRC were related to GLC-82 cell aggregation. FAK silencing partly blocked the formation of GLC-82 cell aggregation, and decreased the phosphorylation levels of ERK and AKT; the colony formation rate in soft agar was significantly lower in GLC-82 cells with FAK silencing than in GLC-82 cells without FAK silencing [(12.2+/-1.1)% vs. (3.6+/-0.7)%, P=0.001]. CONCLUSION: The formation of GLC-82 cell aggregation is partly mediated by FAK signal pathway, and ERK and AKT are the downstream molecules of FAK.

Adenocarcinoma↗
PubMed2005

[Study on technique of thermal imaging and soft-sensing].

The differences of body surface temperature reflect the changes of the status of body tissues. In this regard, detecting and forecasting the changes of the surface temperature is the objective of the technique of medical thermal diagnosis, and how to diagnose the disease earlier with the use of thermal images is a common problem in the field of medical diagnostics and biological engineering. The authors put forward that utilizing the soft-sensing techniques in the field of engineering will be a good solution.

Body Temperature↗