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Yu Zheng

Publications and source records attributed to Yu Zheng.

At least 55 records · Page 3Linked to original sources
PubMed2004

Side-chain assignments of methyl-containing residues in a uniformly 13C-labeled hemoglobin in the carbonmonoxy form.

Sequence-specific assignment of the methyl groups in large proteins can be obtained from an MQ-(H)CC(m)H(m)-TOCSY experiment on uniformly (13)C-labeled proteins without deuteration (Yang et al., 2004). Here the procedure is further demonstrated on a uniformly (13)C-labeled alpha-chain or beta-chain of human normal adult hemoglobin (65 kDa) in the carbonmonoxy form. In addition, a strategy is presented for assigning protons of methyl-containing residues of uniformly (13)C-labeled large proteins, on the basis of prior methyl assignments based on MQ-(H)CCH-TOCSY and H(C)C(m)H(m)-TOCSY experiments. Assignment of about 80% of the side-chain resonances of methyl-containing residues of carbonmonoxyhemoglobin has been obtained.

Carbon Isotopes↗
PubMed2004

Measurement of dipolar cross-correlation in methylene groups in uniformly 13C-, 15N-labeled proteins.

A CC(CO)NH TOCSY-based 3D pulse scheme is presented for measuring (1)H-(13)C dipole-dipole cross-correlated relaxation at CH(2) positions in uniformly (13)C-, (15)N-labeled proteins. Simulations based on magnetization evolution under relaxation and scalar coupling interactions show that cross-correlation rates between (1)H-(13)C dipoles in CH(2) groups can be simply obtained from the intensities of (13)C triplets. The normalized cross-correlation relaxation rates are related to cross-correlation order parameters for macromolecules undergoing isotropic motion, which reflect the degrees of spatial restriction of CH(2) groups. The study on human intestinal fatty acid binding protein (131 residues) in the presence of oleic acid demonstrates that side chain dynamics at most CH(2) positions can be characterized for proteins less than 15 kDa in size, with the proposed TOCSY-based approach.

Carbon Isotopes↗
PubMed2004

Reorganization of cytoskeletal proteins of mouse oocytes mediated by integrins.

To study whether integrins on cell membrane ligate with intracellular cytoskeletal proteins and mediate their reorganization in egg activation, female mice were used for superovulation. The zona-free oocytes were incubated separately with specific ligand of integrins, an active RGD peptide, in vitro for certain period of time. RGE peptide and mouse capacitated sperm were used as controls. Freshly ovulated oocytes and those treated with different factors were immunostained with FITC-labeled anti-actin antibody, then detected with confocal microscope. The results demonstrated that freshly ovulated mouse oocytes, oocytes incubated for 2 h in vitro and those treated with control RGE peptide for 15 min showed hardly visible fluorescene or only thin fluorescence in plasma membrane region. Oocytes coincubated with sperms for 15 min and those treated with active RGD peptide for 10 min, 30 min and 2 hours respectively had strong and thick fluorescence in the plasma membrane and cortical region of oocytes, and some of them showed asymmetrically fluorescent distribution. It is proved that integrins on membrane are ligated directly with cytoskeletal protein. Integrins binding with their ligands regulate reorganization of cytoskelal protein, which may be involved in transmembrane signaling in egg activation.

Animals↗
PubMed2004

[The expression and activity detection of a variant N protein of SARS-CoV].

AIM: To construct an expression vector pGEX-2T/N, and to express the fusion protein consisting of N protein of SARS-CoV and GST in E.coli. METHODS: The N region gene of SARS-CoV was cloned by RT-PCR. The expression vector was constructed by DNA recombination. The recombinant plasmid was transformed into E.coli BL21(DE3). The expression of the fusion protein was detected by Western blot. RESULTS: (1) As compared with the sequences in GenBank, 20 bp were deleted in DNA sequence of the cloned N protein. (2) The fusion protein GST-N was soluble. Western blot analysis showed that the reaction of GST-N to anti-SARS-CoV sera was positive. CONCLUSION: The pGEX-2T/N has been constructed and expressed in the form of fusion protein GST-N successfully, which lays the foundation for further study of SARS-CoV N protein.

Base Sequence↗
PubMed2004

[Phacoemulsification with intraocular lens implantation through a 2.6 mm incision in high myopia].

PURPOSE: To evaluate the clinical effects of the low power and negative power acrylic foldable intraocular lens (AcrySof IOL) implatation through 2.6 mm incision. METHODS: Fifty-two cases (68 eyes) cataract with high myopia were performed phacoemulsification, applied Monarch II injection delivery system for IOL insertion to implant the low power and negative power AcrySof IOL through 2.6 mm incision. Intraoperative and postoperative complications, visual acuity were observed. The mean follow-up was 6 months (range, 3-12 months). RESULTS: All the IOL implantation were uneventful and no IOL damage occurred. No intraoperative complications happened. During 3 months of follow-up, the corrected visual acuity was 0.12-0.25 in 8 eyes (11.8%), 0.3-0.5 in 21 eyes (30.9%), 0.6-1.0 in 36 eyes (52.9%), more than 1.0 in 3 eyes (4.4%). Cystoid macular edema was found in 2 eyes. No retinal detachment and posterior capsular opacification were seen. CONCLUSION: It is safe and effective to applied Monarch II injection delivery system for IOL insertion to implant the low power and negative power AcrySof IOL through 2.6 mm incision.

Adult↗
PubMed2004

[Study on the spectroscopy of paramagnetic compounds [{Cu(bipy) [C6H4(COO)2]}2.H2O]n and [Cu(phen) [C6H4(COO)2]]n].

The cluster compounds with d9-d9 magnetic system were investigated because of their magnetic character. Some of the copper(II) compounds with terephthalato as bridged unit, [{Cu(bipy) [C6H4(COO)2]}2.H2O]n and [Cu(phen) [C6H4(COO)2]]n, have been synthesized through a solvothermal reaction, and their crystal structures have been determined by X-ray diffraction. Their shape looks like zigzag-chain. In this paper, the molecular vibration spectra of the title complexes have been studied in detail. The middle and far-infrared spectra, and Raman spectra of the compounds have been reported and their assignments have been made experientially. The characteristic carbonyl absorption of terephthalato group at 1688 cm(-1) disappeared while the complexes formed. The characteristic peaks of COO- group were splited into two peaks respectively that appeared at 1603, 1574 cm(-1) (vasCOO) and 1369, 1356 cm(-1) (vsCOO) in [{Cu(bipy)[C6H4(COO)2]}2.H2O]n, and at 1614, 1605 cm(-1) (vasCOO) and 1373, 1344 cm(-1) (vsCOO) in [Cu(phen) [C6H4(COO)2]]n. The relationship between the structures of the compounds and the spectra has been discussed as well. The coincidence between experiential assignments and the theoretic calculation will be confirmed.

English Abstract↗
PubMed2003

NMR solution structure and dynamics of an exchangeable apolipoprotein, Locusta migratoria apolipophorin III.

We report here the NMR structure and backbone dynamics of an exchangeable apolipoprotein, apoLp-III, from the insect Locusta migratoria. The NMR structure adopts an up-and-down elongated five-helix bundle, which is similar to the x-ray crystal structure of this protein. A short helix, helix 4', is observed that is perpendicular to the bundle and fully solvent-exposed. NMR experimental parameters confirm the existence of this short helix, which is proposed to serve as a recognition helix for apoLp-III binding to lipoprotein surfaces. The L. migratoria apoLp-III helix bundle displays several characteristic structural features that regulate the reversible lipoprotein binding activity of apoLp-III. The buried hydrophilic residues and exposed hydrophobic residues readily adjust the marginal stability of apoLp-III, facilitating the helix bundle opening. Specifically, upon lipoprotein binding the locations and orientations of the buried hydrophilic residues modulate the apoLp-III helix bundle to adopt a possible opening at the hinge that is opposite the recognition short helix, helix 4'. The backbone dynamics provide additional support to the recognition role of helix 4' and this preferred conformational adaptation of apoLp-III upon lipid binding. In this case, the lipid-bound open conformation contains two lobes linked by hinge loops. One lobe contains helices 2 and 3, and the other lobe contains helices 1, 4, and 5. This preferred bundle opening is different from the original proposal on the basis of the x-ray crystal structure of this protein (Breiter, D. R., Kanost, M. R., Benning, M. M., Wesenberg, G., Law, J. H., Wells, M. A., Rayment, I., and Holden, H. M. (1991) Biochemistry 30, 603-608), but it efficiently uses helix 4' as the recognition short helix. The buried interhelical H-bonds are found to be mainly located between the two lobes, potentially providing a specific driving force for the helix bundle recovery of apoLp-III from the lipid-bound open conformation. Finally, we compare the NMR structures of Manduca sexta apoLp-III and L. migratoria apoLp-III and present a united scheme for the structural basis of the reversible lipoprotein binding activity of apoLp-III.

Animals↗
PubMed2003

Measurement of methyl 13C-1H cross-correlation in uniformly 13C-, 15N-, labeled proteins.

An understanding of side chain motions in protein is of great interest since side chains often play an important role in protein folding and intermolecular interactions. A novel method for measuring the dynamics of methyl groups in uniformly 13C-, 15N-labeled proteins has been developed by our group. The method relies on the difference in peak intensities of 13C quartet components of methyl groups, in a spectrum recording the free evolution of 13C under proton coupling in a constant-time period. Cross-correlated relaxation rates between 13C-1H dipoles can be easily measured from the intensities of the multiplet components. The degree of the methyl restrictions (S(' 2)) can be estimated from the cross-correlated relaxation rate. The method is demonstrated on a sample of human fatty acid binding protein in the absence of fatty acid. We obtained relaxation data for 33 out of 46 residues having methyl groups in apo-IFABP. It has been found that the magnitude of the CSA tensor of spin 13C in a methyl group could be estimated from the intensities of the 13C multiplet components.

Carbon Isotopes↗
PubMed2003

Preconditioning with isoflurane produces dose-dependent neuroprotection via activation of adenosine triphosphate-regulated potassium channels after focal cerebral ischemia in rats.

UNLABELLED: In this study, we determined whether repeated brief isoflurane (Iso) anesthesia induces ischemic tolerance to focal cerebral ischemia in a dose-response manner and whether the effect is dependent on adenosine triphosphate-regulated potassium channels. In Experiment 1, 40 rats were randomly assigned to 4 groups: control animals received 100% oxygen 1 h/d for 5 days, whereas the isoflurane (Iso)1, Iso2, and Iso3 groups received 0.75%, 1.5%, or 2.25% Iso in oxygen 1 h/d for 5 days. In Experiment 2, 36 rats were randomly assigned to 4 groups: controls received 100% oxygen 1 h/d for 5 days; animals in the Iso and I+G (Iso+glibenclamide) groups received 2% Iso in oxygen 1 h/d for 5 days, and the I+G group received glibenclamide (GLB) (5 mg/kg intraperitoneally) before each Iso pretreatment. Animals in the GLB group received GLB (5 mg/kg intraperitoneally) once a day for 5 days. Twenty-four hours after the last pretreatment, the right middle cerebral artery was occluded for 120 min. Neurologic deficit scores (NDS) and brain infarct volumes were evaluated at 24 h. The NDS and infarct volumes of Iso2 and Iso3 were less than those of the controls (P < 0.05). The infarct volume in Iso3 was smaller than in Iso2 (P < 0.05). The NDS and infarct volume in the Iso group were less than in the control and I+G groups (P < 0.05). There was no statistical difference among the control, I+G, and GLB groups. The study demonstrated that repeated Iso anesthesia induces ischemic tolerance in rats in a dose-response manner. GLB, an adenosine triphosphate-regulated potassium channel blocker, abolished the tolerance induced by Iso. IMPLICATIONS: Brief isoflurane anesthesia induces ischemic tolerance in the brain. The effect was found to be dose dependent in a rat focal cerebral ischemia model. Ischemic tolerance induced by isoflurane preconditioning is dependent on activation of adenosine triphosphate-regulated potassium channels.

ATP-Binding Cassette Transporters↗
PubMed2003

Light-scattering instrument to detect thromboemboli in blood.

The characteristics and capabilities of a light-scattering microemboli detector (LSMD) are delineated by detailing its state-of-the-art configuration, by discussing the theoretical and empirical aspects of instrument calibration, and by summarizing various experimental studies that have benefited from this instrument. In the past, thromboembolism, which often results when blood contacts medical devices, has eluded scientific scrutiny due to the absence of instruments that could detect and quantify thromboemboli in circulating blood. More recently, the ability of the LSMD to provide continuous, noninvasive detection of thromboemboli in whole blood (meaning that the LSMD probe does not contact the blood) was exploited in various in vitro and ex vivo models to explore thromboembolic phenomena. Through this work, the LSMD evolved as a sensitive and an economical research tool for the study of thromboembolic phenomena.

Aneurysm↗
PubMed2003

[Study on the effect of integrin on human sperm activation].

OBJECTIVE: This study was aimed to disclose whether the VLA-5 integrin on human sperm membrane takes part in the activation of human spermatozoa. METHODS: Fluo-3/AM was coincubated with human spermatozoa. The change of intracellular calcium([Ca2+]i) was determined by flow cytometry when human sperms were exposed to Fibronectin(Fn) as the specific ligand of integrin VLA-5. Human sperm acrosome reaction(AR) rate was evaluated by triple-stain technique. RESULTS: Fn significantly raised the AR rate (P < 0.05) and the level of [Ca2+]i (P < 0.01) in the spermatozoa of fertile men. But there was no significant rise in the level of [Ca2+]i in the spermatozoa of infertile men. CONCLUSION: The VLA-5 integrin on human sperm membrane plays a role in the activation of sperm.

Acrosome Reaction↗
PubMed2003

[Expression of heme oxygenase-1 in rat prostate and effects of androgen and estrogen on it].

OBJECTIVE: To investigate the influences of androgen and estrogen on expression of HO-1 gene in rat ventral prostate. METHODS: To create the model of castrated male rats, the testes were removed via scrotal incision. HO-1 mRNA level was tested by RT-PCR. The use of immunohistochemical staining procedures with image analytic technical system allowed us to assess the effects of exogenous androgen and estrogen on expression and location of HO-1 protein in rat ventral prostate. RESULTS: The levels of HO-1 mRNA transcription and HO-1 protein expression in the castrated group were markedly decreased, compared with those in normal control group (P < 0.01); But both these levels in the groups of castration plus exogenous androgen and castration plus exogenous estrogen were much higher than those in the control group (P < 0.01). Furthermore, estrogen could increase the level of HO-1 protein expression in prostatic stroma. CONCLUSION: Carbon monoxide-heme oxygenase system might be involved in the pathologic processes of prostatic abnormal proliferation.

Androgens↗
PubMed2003

[Expression and biological activities of TRAIL fusion protein gene].

AIM: To obtain and express the full-length of TRAIL gene in prokaryocytes. METHODS: The full-length of TRAIL gene was amplified from peripheral blood cells(PBCs)by RT-PCR and then cloned into the expression vector pGEX-2T. The TRAIL-GST was expressed in E.coli. RESULTS: Sequence analysis indicated that the sequence of TRAIL gene was identical with that in the GenBank. The TRAIL-GST was expressed in E.coli. Expressed product could inhibit the proliferation of KB and Hela cells and finally lead to their apoptosis. CONCLUSION: The TRAIL-GST with biological activity has been expressed in the prokaryotic system.

Apoptosis↗
PubMed2002

Genomic functional annotation using co-evolution profiles of gene clusters.

BACKGROUND: The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS: As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS: The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles.

Alleles↗
PubMed2002

Computational identification of operons in microbial genomes.

By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genomes to identify putative operon structures. The predicted operons from Escherichia coli were compared with a selected metabolism-related operon dataset from the RegulonDB database, yielding a prediction sensitivity (89%) and specificity (87%) relative to this dataset. Several examples of detected operons are given and analyzed. Modular gene cluster transfer and operon fusion are observed. A further use of predicted operon data to assign function to putative genes was suggested and, as an example, a previous putative gene (MJ1604) from Methanococcus jannaschii is now annotated as a phosphofructokinase, which was regarded previously as a missing enzyme in this organism. GC content changes in the operon region and nonoperon region were examined. The results reveal a clear GC content transition at the boundaries of putative operons. We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution.

Algorithms↗
PubMed2002

[Sero-and molecular epidemiology of the gene of different ORF of transfusion transmitted virus (TTV) in different population of China].

BACKGROUND: To investigate the distribution of anti-TTV antibody and the different ORF gene in different populations of China. METHODS: The antibody to TTV in sera collected from different population were detected by using ELISA and the different ORF genes were amplified with PCR. RESULTS: The positive rates of TTV ORF1 DNA, ORF2 DNA and the antibody in various populations were as follows: 16.0% (12/75), 10.7% (8/75) and 25.3% (19/75) in paid blood donors; 10.0 (3/30), 16.7% (5/30) and 16.7% (5/30) in patients with hepatitis A, 47.5% (19/40), 42.5% (17/40) and 22.5% (9/40) in patients with hepatitis B; 42.9% (15/35), 37.1% (13/35) and 28.6% (10/35) in patients with hepatitis C; 20.0% (3/15), 26.7% (4/15) and 13.3% (2/15)in patients with hepatitis D; 16.7% (2/12),16.7% (2/12) and 33.3% (4/12)in patients with hepatitis E; 23.8% (5/21), 38.1% (8/21) and 23.8% (5/21) in patients with hepatitis G; 61.1% (11/18), 50.0% (9/18) and 44.4% (8/18) in patients with non A-G hepatitis, respectively. The positive rate of different ORF DNA had no significant difference. Significant differences were found in the positive rates of TTV DNA in various populations. There was no relationship between the TTV DNA and the antibody to TTV. CONCLUSIONS: The antibody to TTV and TTV DNA were found in every population of China. There was no significant difference in the positive rates of TTV DNA between ORF1 and ORF2. The positive rate in patients with non A-G hepatitis was higher than those in the other populations.

Adolescent↗
PubMed2002

[Preliminary study on the gene expression profiles of oligodendrogliom as with cDNA array].

OBJECTIVE: To study the gene expression profiles of oligodendrogliomas with gene cDNA array. METHODS: (32)P tagged cDNA probes converted from the total RNA, which had been extracted from 2 fresh samples of oligodendroglioma and 1 of normal brain tissue, were hybridized with the Atlas array. After washing the membranes, the autoradiography was performed and the autoradiograms were analyzed through the special software. RESULTS: As compared to the normal brain tissue, there were 63 co-upregulated genes and 4 co-downregulated genes in these 2 tumor samples. However, a significant quantitative difference existed between them. The expression trend of some genes differed from the known information. CONCLUSION: cDNA array is effective for studying the gene expression profiles of oligodendrogliomas and provides new information for the further research on their molecular mechanisms.

Brain Neoplasms↗