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Search Results: 1 - 10 of 72897 matches for " Xiao-Dong Su "
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Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer
Xiang Liu, Heng Zhang, Xiao-Jun Wang, Lan-Fen Li, Xiao-Dong Su
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024227
Abstract: The crystal structures of two proteins, a putative pyrazinamidase/nicotinamidase from the dental pathogen Streptococcus mutans (SmPncA) and the human caspase-6 (Casp6), were solved by de novo arsenic single-wavelength anomalous diffraction (As-SAD) phasing method. Arsenic (As), an uncommonly used element in SAD phasing, was covalently introduced into proteins by cacodylic acid, the buffering agent in the crystallization reservoirs. In SmPncA, the only cysteine was bound to dimethylarsinoyl, which is a pentavalent arsenic group (As (V)). This arsenic atom and a protein-bound zinc atom both generated anomalous signals. The predominant contribution, however, was from the As anomalous signals, which were sufficient to phase the SmPncA structure alone. In Casp6, four cysteines were found to bind cacodyl, a trivalent arsenic group (As (III)), in the presence of the reducing agent, dithiothreitol (DTT), and arsenic atoms were the only anomalous scatterers for SAD phasing. Analyses and discussion of these two As-SAD phasing examples and comparison of As with other traditional heavy atoms that generate anomalous signals, together with a few arsenic-based de novo phasing cases reported previously strongly suggest that As is an ideal anomalous scatterer for SAD phasing in protein crystallography.
Bioinformatics and Structural Characterization of a Hypothetical Protein from Streptococcus mutans: Implication of Antibiotic Resistance
Jie Nan, Erik Brostromer, Xiang-Yu Liu, Ole Kristensen, Xiao-Dong Su
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0007245
Abstract: As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.
TIM-Finder: A new method for identifying TIM-barrel proteins
Jing-Na Si, Ren-Xiang Yan, Chuan Wang, Ziding Zhang, Xiao-Dong Su
BMC Structural Biology , 2009, DOI: 10.1186/1472-6807-9-73
Abstract: To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at webcite.Proteins have complex three-dimensional (3D) shapes, a fact well demonstrated by more than 60,000 experimentally determined structures deposited in the current PDB database http://www.rcsb.org/pdb/home/home.do webcite. The number of unique protein folds (or architectural types) should be much smaller than the number of protein families defined by sequence similarity [1]. As more structures are determined, it also becomes increasingly clear that the distribution of proteins between different folds is not even [2]. Although many folds have so far been observed for only a few proteins, some protein folds (known as superfolds) occur frequently. As reported by Salem et al. (1999), the top ten superfolds could account for approximately one third of all proteins in the PDB database.One of the top ten superfolds is the triosephosphate isomerase (TIM)-barrel fold (Figure 1A). It was first observed in triosephosphate isomerase and consists of eight α-helices on the outside and eight parallel β-strands on the inside that alternate along the peptide backbone [3]. In the past, many protein structures w
Simulation of microstructure of liquid-crystalline polymers in nonhomogenous shear flow by EFG method

Wang Xiao-Dong,Ouyang Jie,Su Jin,

物理学报 , 2010,
Abstract: Complex microstructures of liquid-crystalline polymers in nonhomogenous shear flow are studied by element free Galerkin (EFG) method based on the micro-macro dualscale model. The dualscale model combines the orientational diffusion equation in microscale with the flow governing equations in macroscale. The EFG method which has the merits of high accuracy and good stability can ensure the reliability of the simulation results. One simple and five composite structures of liquid-crystalline polymers in nonhomogenous shear flow are predicted by studying the influences of Deborah number on microstructures of liquid-crystalline polymers in plane Poiseuille flow. It shows that the instabilities in the transition region of the composite structures can cause some defects.
Micro-macro numerical simulation of rod-like polymeric solutions

Su Jin,Ouyang Jie,Wang Xiao-Dong,

物理学报 , 2010,
Abstract: In this paper the complex rheological behaviors of rod-like polymer solutions in plane Couette flow are studied using micro-macro simulation. The micro-macro model is described by Doi theory with local inhomogeneous fluid. The finite volume method is used to solve the conservation equation on the macroscopic level and the Smoluchowski equation on the microscopic level in the numerical simulation. The numerical results predict several plane flow modes including some typical plane modes and two new complicated modes. Furthermore, simulation results show that the rheological phase diagrams for solutions of rigid rod molecules are mainly dependent on the Deborah number, the concentration of solutions and molecular scale, and the varying Deborah number have great influence on some micro-properties of tumbling period and orientation angle of flow-aligning.
Lattice Boltzmann method for an advective transport equation coupled with incompressible flow field

Su Jin,Ouyang Jie,Wang Xiao-Dong,

物理学报 , 2012,
Abstract: In this paper, an improved numerical scheme based on the lattice BGK method (LBM) is proposed for solving the advective transport equation coupled with an incompressible flow. We utilize the LBM to solve the equations of flow field and build a second order discrete scheme for the advective transport equations using the probability density function of LBM. Meanwhile, the validity of the method is verified by an advective transport in a planar channel flow. Numerical results show that the method reduces the numerical dissipation efficiently and it involves consistently smaller memory requirements compared with previous studies.
Shuai-Jun Wang,Qiang Gu,Qing Su,Xiao-Dong Chen
Acta Crystallographica Section E , 2009, DOI: 10.1107/s1600536809049514
Abstract: In the crystal of the title compound, C15H10N2O3, the molecules are linked together by intermolecular N—H...N hydrogen bonds into chains along the c axis. The crystal structure also shows weak intermolecular C—H...π hydrogen bonds. The three furanyl rings bonded to the imidazole core are not coplanar with the latter; the dihedral angles between the furanyl and imidazole ring planes are 29.3 (2), 19.4 (2), and 4.8 (2)°.
Effect of Xiaotan Sanjie Recipe on growth of transplanted tumor and expressions of proliferating cell nuclear antigen and epidermal growth factor receptor in tissue of gastric carcinoma of nude mice
Xiao-dong GUO
Zhong Xi Yi Jie He Xue Bao , 2007,
Abstract: Objective: To observe the influence of Xiaotan Sanjie Recipe on growth of the transplanted tumor and expressions of proliferating cell nuclear antigen (PCNA) and epidermal growth factor receptor (EGFR) in tissue of the gastric carcinoma of nude mice, and to explore the mechanism of Xiaotan Sanjie Recipe in restraining the multiplication of the stomach cancer.Methods: MKN-45 gastric carcinoma model in nude mice was established. Forty-five nude mice were randomly divided into control group, Xiaotan Sanjie group and 5-fluorouracil (5-FU) group. Drugs were given on the next day of innoculation. Mice in the control group were given normal saline, and mice in the Xiaotan Sanjie group were given Xiaotan Sanjie Recipe. Intraperitoneal injection of 5-FU was administered in the 5-FU group. The expressions of PCNA and EGFR were examined by using streptavidin peroxidase (SP) conjugate technique, and the tumor weight and pathological characteristics were also observed.Results: Compared with the control group, Xiaotan Sanjie Recipe significantly restrained the growth of the transplanted tumor, and reduced the expressions of PCNA and EGFR in tissue of the gastric carcinoma of nude mice (P<0.05).Conclusion: Xiaotan Sanjie Recipe can disturb the synthesis of DNA and reduce the proliferous activity of cancer cells by decreasing the expressions of PCNA and EGFR.
Clinical observation on treatment of IgA nephropathy with Huobahuagen Tablets and irbesartan
GUAN Xiao-Dong
Zhong Xi Yi Jie He Xue Bao , 2005,
Abstract: Objective: To observe the effects of Huobahuagen Tablets combined with irbesartan on the risk factors of IgA nephropathy. Methods: Sixty-two patients diagnosed as IgA nephropathy were randomly divided into control group and treatment group. Thirty patients in the control group were treated with Huobahuagen Tablets (5 tablets po t.i.d.), and 32 patients in the treatment group were treated with irbesartan (150 to 300 mg po q.d.), besides the same treatment as the control group. After 3 months of treatment, the levels of blood pressure (BP), 24 h urine protein (Upr), urinary red blood cells (URBC), blood triglycerides (TG), total cholesterol (TC), albumin (Alb), alanine transaminase (ALT), white blood cells (WBC) and serum creatinine (Scr) were observed. Results: After treatment, the levels of Upr, URBC and Scr in both groups were decreased, as compared with those before treatment (P<0.05 or P<0.01), and the levels of BP, Upr, URBC and Scr in the treatment group were lower than those in the control group (P<0.01). The levels of Alb in both groups were increased, as compared with those before treatment (P<0.05 or P<0.01), and the level of Alb in the treatment group was higher than that in the control group (P<0.05). Conclusion: Huobahuagen Tablets, when used together with irbesartan, may improve the renal function of the patients with IgA nephropathy and slow the deterioration of the disease by reducing BP, Upr, URBC and Scr.
Effects of Chinese herbal medicine Shenlong Decoction on mRNA expressions of matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-1 in lung tissue of rats with pulmonary fibrosis induced by bleomycin
Xiao-dong Lu
Zhong Xi Yi Jie He Xue Bao , 2010,
Abstract: Objective: To observe the expressions of matrix metalloproteinase-2 (MMP-2) and tissue inhibitor of metalloproteinase-1 (TIMP-1) in rats with pulmonary fibrosis (PF) induced by bleomycin, and to explore the mechanisms of Shenlong Decoction in preventing and treating PF.Methods: A total of 230 Wistar rats were divided into normal control group, untreated group, prednisone group, and low-, medium- and high-dose Shenlong Decoction groups. Wistar rats were intratracheally injected with bleomycin to induce PF. From the 2nd day, rats in the normal control and untreated groups were lavaged with normal saline (NS), and rats in the other groups were lavaged with prepared Shenlong Decoction by the same amount. Hemotoxylin-eosin (HE) staining and Masson staining were used to observe pathological changes in lung tissue at different time points, and to evaluate whether the model was successfully induced. Expressions of MMP-2 and TIMP-1 mRNAs in rats’ lung tissue were measured by reverse transcription-polymerase chain reaction (RT-PCR).Results: Expressions of MMP-2 and TIMP-1 mRNAs in lung tissue of rats were observed from all groups at each time point. In comparison with the normal control group, on the 7th day, the transcription levels of MMP-2 and TIMP-1 mRNAs, especially the former, of the untreated group increased significantly (P<0.05 or P<0.01). On the 14th day, the transcription levels of MMP-2 and TIMP-1 mRNAs kept rising, especially the latter (P<0.05 or P<0.01). On the 28th day, the transcription level of MMP-2 decreased a little, while the transcription level of TIMP-1 mRNA did not stop increasing (P<0.05 or P<0.01). Compared with the untreated group, decrease of the transcription levels of MMP-2 and TIMP-1 mRNAs were observed in the treatment groups, especially the former, and this effect continued to the 28th day with the medium-dose Shenlong Decoction group decreasing most obviously (P<0.05 or P<0.01).Conclusion: Shenlong Decoction may inhibit the expression of MMP-2 mRNA by up-regulating the expression of TIMP-1 mRNA so as to slow the progression of PF.
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