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Search Results: 1 - 10 of 38434 matches for " TAN Ren-Xiang "
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Hopeahainol C monohydrate
Hoong-Kun Fun,Kanokorn Sudto,Hui-Ming Ge,Ren-Xiang Tan
Acta Crystallographica Section E , 2011, DOI: 10.1107/s1600536811017053
Abstract: In the structure of the title compound, C28H16O6·H2O [systematic name 3,11-bis(4-hydroxyphenyl)-4,12-dioxapentacyclo[,5.013,17.09,18]octadeca-1(16),2,5(18),6,8,10,13(17),14-octaene-7,15-diol monohydrate], the hopeahainol C molecule lies about an inversion center with the solvent water molecule located on a crystallographic twofold axis. Hopeahainol C is an oligostillbenoid compound and was isolated from the bark of Shorea roxburghii G. Don. The five central fused rings are essentially planar with an r.m.s. deviation of 0.0173 (3) . The 4-hydroxyphenyl ring is twisted with respect to this plane, with the dihedral angle between the phenyl ring and the fused-ring system being 41.70 (10)°. The crystal features intermolecular O—H...O hydrogen bonds. These interactions link the hopeahainol C molecules into chains along the b axis. Water molecules are located interstitially between the hopeahainol C molecules linked by O(water)—H...O(hydroxy) and O(hydroxy)—H...O(water) hydrogen bonds. π–π interactions are also observed with centroid–centroid distances of 3.6056 (17) and 3.5622 (17) . Short O...O contacts [2.703 (2)–2.720 (3) ] are also present in the crystal.
Anti-proliferative and pro-apoptotic effects of tectorigenin on hepatic stellate cells
Jun-Hua Wu, Yu-Rong Wang, Wu-Yang Huang, Ren-Xiang Tan
World Journal of Gastroenterology , 2010,
Abstract: AIM: To investigate the effect of tectorigenin on proliferation and apoptosis of hepatic stellate cells (HSC)-T6 cells.METHODS: HSC-T6 cells were incubated with tectorigenin at different concentrations, and their proliferation was assessed by bromodeoxyuridine incorporation assay. Apoptosis was detected by ow cytometry assay with Hoechst 33342 staining. Also, generation of reactive oxygen species (ROS), intracellular [Ca2+]i, potential of mitochondrial membrane, activities of cytochrome c and caspase-9 and -3 were investigated to explore a conceivable apoptotic pathway.RESULTS: Tectorigenin suppressed the proliferation of HSC-T6 cells and induced apoptosis of HSC-T6 cells in a time- and dose-dependent manner. Tectorigenin at the concentration of 100 μg/mL greatly inhibited the viability of HSC-T6 cells and induced the condensation of chromatin and fragmentation of nuclei. When treated for 48 h, the percentage of cell growth and apoptosis reached 46.3% ± 2.37% (P = 0.004) and 50.67% ± 3.24% (P = 0.003), respectively. Furthermore, tectorigenin-induced apoptosis of HSC-T6 cells was associated with the generation of ROS, increased intracellular [Ca2+]i, loss of mitochondrial membrane potential, translocation of cytochrome c, and activation of caspase-9 and -3.CONCLUSION: Tectorigenin inhibits proliferation of HSC-T6 cells and induces apoptosis of HSC-T6 cells.
Isochromophilones from an endophytic fungus Diaporthe sp.
Le-Yun Zang,Wei Wei,Ting Wang,Ye Guo,Ren-Xiang Tan,Hui-Ming Ge
Natural Products and Bioprospecting , 2012, DOI: 10.1007/s13659-012-0023-2
Abstract: Three new azaphilone compounds, isochromophilones X–XII (1–3), together with two known ones sclerotioramine (4) and isochromophilone VI (5) were isolated from the cultures of an endophytic fungus Diaporthe sp. The structures were elucidated by extensive HRESIMS and NMR spectroscopic analyses. All compounds were tested for their cytotoxicities against five human cancer cell lines by MTT method, among which compound 1 showed moderate inhibitory effects on these cell lines. This was the first report of azaphilones isolated from Diaporthe sp.
The Preparation of an Elicitor from a Fungal Endophyte to Enhance Artemisinin Production in Hairy Root Cultures of Artemisia annua L.

WANG Jian-Wen,ZHENG Li-Ping,TAN Ren-Xiang,

生物工程学报 , 2006,
Abstract: The different components of crude mycelium of the predominant endophytic Colletotrichum gloeosporioides of Artemisa annua have been extracted by the methods of acid hydrolysate. We compared the effect of the isolated components on artemisin biosynthesis in hairy root cultures. Therefore, the oligosaccharide elicitor from C. gloeosporioides has been partially purified by column chromatography of Sephadex G25. The isolated oligosaccharide B II (elicitor, MW < 2500) has been revealed to promote the production of artemisinin in Artemisia annua hairy root cultures. When hairy roots of 23-day old cultures (later growth phase) were exposed to the elicitor at 0.4 mg/mL for 4 days, the maximum production of artemisinin reached to 13.51 mg/L, a 51.63% increase over the control. This is the first report on the stimulation of artemisinin production in hairy roots by the oligosaccharide elicitor from an endophytic fungus of A. annua.
Outer membrane proteins can be simply identified using secondary structure element alignment
Ren-Xiang Yan, Zhen Chen, Ziding Zhang
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-76
Abstract: Based on the observation that almost all OMPs consist of antiparallel β-strands in a barrel shape and that their secondary structure arrangements differ from those of other types of proteins, we propose a simple method called SSEA-OMP to identify OMPs using secondary structure element alignment. Through intensive benchmark experiments, the proposed SSEA-OMP method is better than some well-established OMP detection methods.The major advantage of SSEA-OMP is its good prediction performance considering its simplicity. The web server implements the method is freely accessible at http://protein.cau.edu.cn/SSEA-OMP/index.html webcite.Outer membrane proteins (OMPs), an important class of proteins, are found in gram-negative bacteria, mitochondria and chloroplasts. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery. A variety of OMP identification methods have been elegantly developed [1-27] and some web servers have also been freely accessible to the research community [2,7,13,16,21,27]. However, OMPs are difficult to be discriminated from other types of proteins, and the existing methods are not entirely satisfactory, mainly because the membrane-spanning regions of OMPs are shorter and these regions usually have higher variations in properties when compared with α-helical membrane proteins [28]. Therefore, the development of new OMP identification methods with improved performance is needed. Meanwhile, it is also hoped that new OMP identification methods will be helpful to accelerate the exploration of the sequence-structure protein landscape in OMPs.The existing OMP predictors can be categorized through different ways. According to the adopted algorithms, the predictors can be divided into simple statistical theory- and machine learning-based methods. The highlight of simple statistical methods is that the biological meanings of the established statistical mode


物理学报 , 1981,
Abstract: A "rectangular" phenomenological model of interaction between ms pulses of laser beam and metals has been set up. When power density is greater than the damage threshold, the metal possesses a constant ablation rate. A differential equation has been obtained by combining propagation of a Gaussian beam. Through numerical calculation, relations of the dependence of depth and shape of hole on the target position, lens focal length, directionality and energy of laser beam have been discussed.
Natural orifice transluminal endoscopic surgery: New minimally invasive surgery come of age
Chen Huang,Ren-Xiang Huang,Zheng-Jun Qiu
World Journal of Gastroenterology , 2011, DOI: 10.3748/wjg.v17.i39.4382
Abstract: Although in the past two decades, laparoscopic surgery, considered as a great revolution in the minimally invasive surgery field, has undergone major development worldwide, another dramatic surgical revolution has quietly appeared in recent years. Ever since Kalloo’s first report on transgastric peritoneoscopy in a porcine model in 2004, interest in a new surgical procedure named natural orifice transluminal endoscopic surgery (NOTES) has blossomed worldwide. Considering that a NOTES procedure could theoretically avoid any abdominal incision, operation-related pain and scarring, many surgeons and endoscopists have been enthusiastic in their study of this new technique. In recent years, several NOTES studies have been carried out on porcine models and even on humans, including transvaginal cholecystectomy, transgastric appendectomy, transvaginal appendectomy, and transvesical peritoneoscopy. So what is the current situation of NOTES and how many challenges do we still face? This review discusses the current research progress in NOTES.
Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach
Xiao-Feng Wang, Zhen Chen, Chuan Wang, Ren-Xiang Yan, Ziding Zhang, Jiangning Song
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026767
Abstract: Integral membrane proteins constitute 25–30% of genomes and play crucial roles in many biological processes. However, less than 1% of membrane protein structures are in the Protein Data Bank. In this context, it is important to develop reliable computational methods for predicting the structures of membrane proteins. Here, we present the first application of random forest (RF) for residue-residue contact prediction in transmembrane proteins, which we term as TMhhcp. Rigorous cross-validation tests indicate that the built RF models provide a more favorable prediction performance compared with two state-of-the-art methods, i.e., TMHcon and MEMPACK. Using a strict leave-one-protein-out jackknifing procedure, they were capable of reaching the top L/5 prediction accuracies of 49.5% and 48.8% for two different residue contact definitions, respectively. The predicted residue contacts were further employed to predict interacting helical pairs and achieved the Matthew's correlation coefficients of 0.430 and 0.424, according to two different residue contact definitions, respectively. To facilitate the academic community, the TMhhcp server has been made freely accessible at http://protein.cau.edu.cn/tmhhcp.
DescFold: A web server for protein fold recognition
Ren-Xiang Yan, Jing-Na Si, Chuan Wang, Ziding Zhang
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-416
Abstract: In seeking more powerful descriptors, the profile-profile alignment score generated from the COMPASS algorithm was first considered as a new descriptor (i.e., PPA). When considering a profile-profile alignment between two proteins in the context of fold recognition, one protein is regarded as a template (i.e., its 3D structure is known). Instead of a sequence profile derived from a Psi-blast search, a structure-seeded profile for the template protein was generated by searching its structural neighbors with the assistance of the TM-align structural alignment algorithm. Moreover, the COMPASS algorithm was used again to derive a profile-structural-profile-alignment-based descriptor (i.e., PSPA). We trained and tested the new DescFold in a total of 1,835 highly diverse proteins extracted from the SCOP 1.73 version. When the PPA and PSPA descriptors were introduced, the new DescFold boosts the performance of fold recognition substantially. Using the SCOP_1.73_40% dataset as the fold library, the DescFold web server based on the trained SVM models was further constructed. To provide a large-scale test for the new DescFold, a stringent test set of 1,866 proteins were selected from the SCOP 1.75 version. At a less than 5% false positive rate control, the new DescFold is able to correctly recognize structural homologs at the fold level for nearly 46% test proteins. Additionally, we also benchmarked the DescFold method against several well-established fold recognition algorithms through the LiveBench targets and Lindahl dataset.The new DescFold method was intensively benchmarked to have very competitive performance compared with some well-established fold recognition methods, suggesting that it can serve as a useful tool to assist in template-based protein structure prediction. The DescFold server is freely accessible at webcite.Template-based protein structure prediction methods (often known as comparative modeling and fold recognit
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
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