Value of Computerized 3D Shape Analysis in Differentiating Encapsulated from Invasive Thymomas

ObjectivesTo retrospectively investigate the added value of quantitative 3D shape analysis in differentiating encapsulated from invasive thymomas.ResultsSignificant differences were observed between encapsulated and invasive thymomas, in terms of cystic changes (p=0.004), sphericity (p=0.016), and discrete compactness (p=0.001). Subsequent binary logistic regression analysis revealed that absence of cystic change (adjusted odds ratio (OR) = 6.636; p=0.015) and higher discrete compactness (OR = 77.775; p=0.012) were significant differentiators of encapsulated from invasive thymomas. ROC analyses revealed that the addition of 3D shape analysis to clinical and CT features (AUC, 0.955; 95% CI, 0.935–0.975) provided significantly higher performance in differentiating encapsulated from invasive thymomas than clinical and CT features (AUC, 0.666; 95% CI, 0.626–0.707) (p<0.001).ConclusionAddition of 3D shape analysis, particularly discrete compactness, can improve differentiation of encapsulated thymomas from invasive thymomas.     

A computational study of binding between 3-(4-fluorophenyl)-N-((4-fluorophenyl)sulphonyl)acrylamide and tubulin

3-(4-Fluorophenyl)-N-((4-fluorophenyl)sulphonyl)acrylamide (FFSA) is a potential tubulin polymerisation inhibitor. In this article, a theoretical study of the binding between FFSA and tubulin in colchicine site was carried out by molecular docking, molecular dynamics (MD) simulation and binding free energy calculations. The docking calculations preliminarily indicate that there are three possible binding modes 1, 2 and 3; MD simulations and binding free energy calculations identify that binding mode 2 is the most favourable, with the lowest binding free energy of ? 29.54 kcal/mol. Moreover, our valuable results for the binding are as follows: the inhibitor FFSA is suitably located at the colchicine site of tubulin, where it not only interacts with residues Leu248β, Lys254β, Leu255β, Lys352β, Met259β and Val181a by hydrophilic interaction, but also interacts with Val181α and Thr179α by hydrogen bond interaction. These two factors are both essential for FFSA strongly binding to tubulin. These theoretical results help understanding the action mechanism and designing new compounds with higher affinity to tubulin.     

Enantioselective Inhibition of Carprofen Towards UDP‐glucuronosyltransferase (UGT) 2B7

UDP‐glucuronosyltransferases (UGTs)‐catalyzed glucuronidation conjugation reaction plays an important role in the elimination of many important clinical drugs and endogenous substances. The present study aims to investigate the enantioselective inhibition of carprofen towards UGT isoforms. In vitro a recombinant UGT isoforms‐catalyzed 4‐methylumbelliferone (4‐MU) glucuronidation incubation mixture was used to screen the inhibition potential of (R)‐carprofen and (S)‐carprofen towards multiple UGT isoforms. The results showed that (S)‐carprofen exhibited stronger inhibition potential than (R)‐carprofen towards UGT2B7. However, no significant difference was observed for the inhibition of (R)‐carprofen and (S)‐carprofen towards other UGT isoforms. Furthermore, the inhibition kinetic behavior was compared for the inhibition of (S)‐carprofen and (R)‐carprofen towards UGT2B7. A Lineweaver–Burk plot showed that both (S)‐carprofen and (R)‐carprofen exhibited competitive inhibition towards UGT2B7‐catalyzed 4‐MU glucuronidation. The inhibition kinetic parameter (K_i) was calculated to be 7.0 μM and 31.1 μM for (S)‐carprofen and (R)‐carprofen, respectively. Based on the standard for drug–drug interaction, the threshold for (S)‐carprofen and (R)‐carprofen to induce a drug–drug interaction is 0.7 μM and 3.1 μM, respectively. In conclusion, enantioselective inhibition of carprofen towards UDP‐glucuronosyltransferase (UGT) 2B7 was demonstrated in the present study. Using the in vitro inhibition kinetic parameter, the concentration threshold of (S)‐carprofen and (R)‐carprofen to possibly induce the drug–drug interaction was obtained. Therefore, clinical monitoring of the plasma concentration of (S)‐carprofen is more important than (R)‐carprofen to avoid a possible drug–drug interaction between carprofen and the drugs mainly undergoing UGT2B7‐catalyzed metabolism. Chirality 27:189–193, 2015. © 2014 Wiley Periodicals, Inc.     

具有抑菌作用的放线菌GNF1的分离鉴定和生物学活性的研究

从几种复合微生物有机肥中分离出一系列不同的菌株,与实验室保存的菌株GNW(自生固氮菌)和HP2(解磷菌)混合接种培养,检测是否因基因杂交、突变等原因而产生具有抑菌作用的菌株.结果分离出一株具有抑菌作用的放线菌菌株GNF1,根据其形态学特征、生理生化特征和基于16S rRNA基因序列的系统发育分析结果,鉴定其属于链霉菌属(Streptomyces)的一个菌株,GNF1菌株的代谢产物中存在具有抑菌作用的活性成分,与植物根际促生菌GNW、HP2以及某些原核病原微生物共培养培养时能明显抑制它们的生长.     

Biomass and Carbon Storage in an Age-Sequence of Korean Pine (<Emphasis Type="Italic">Pinus koraiensis</Emphasis>) Plantation Forests in Central Korea

This study examined the biomass and carbon pools of the main ecosystem components in an age sequence of five Korean pine plantation forest stands in central Korea. The C contents in the tree and ground vegetation biomass, coarse woody debris, forest floor, and mineral soil were estimated by analyzing the C concentration of each component. The aboveground and total tree biomass increased with increasing stand age. The highest C concentration across this chronosequence was found in the tree branch while the lowest C concentration was found in the ground vegetation. The observed C contents for tree components, ground vegetation, and coarse woody debris were generally lower than the predicted C contents estimated from a biomass C factor of 0.5. Forest floor C content was age-independent. Total mineral soil C content appeared to decline initially after establishing Korean pine plantations and recover by the stand age of 35 years. Although aboveground tree biomass C content showed considerable accumulation with increasing age, the relative contribution of below ground C to total ecosystem C content varied substantially. These results suggest that successional development as temporal factor has a key role in estimating the C storage in Korean pine plantation forests.     

八角叶总黄酮的提取及其捕获自由基作用研究

目的:为八角叶资源的合理开发和利用提供科学依据。方法:分别以乙醇、石油醚、水等作提取溶剂,用超声波与非超声波对比提取八角叶总黄酮,考察在不同温度、溶剂浓度、超声波功率、提取时间等不同条件下用超声波/乙醇浸提法提取八角叶总黄酮,对所提取的黄酮类物质进行验证,并用分光光度法测定含量,用八角叶总黄酮对羟自由基清除作用进行试验。结果:超声波乙醇浸提法提取八角叶总黄酮的最佳工艺条件为:溶剂90%乙醇,温度80℃,超声波功率60 W,提取时间3.0 h。百色、南宁、贺州、河池、钦州所产八角叶总黄酮的含量分别为0.1649mg/mL、0.1022 mg/mL、0.1122 mg/mL、0.1850 mg/mL、0.1693 mg/mL,八角叶总黄酮提取液对Fenton体系产生的.OH自由基有很好的清除作用。结论:超声波乙醇浸提法提取八角叶总黄酮的效果最佳,产总黄酮含量最高,提示八角叶具有较高的开发利用价值。     

Analysis of the <Emphasis Type="Italic">xynB5</Emphasis> gene encoding a multifunctional GH3-BglX β-glucosidase-β-xylosidase-α-arabinosidase member in <Emphasis Type="Italic">Caulobacter crescentus</Emphasis>

The Caulobacter crescentus (NA1000) xynB5 gene (CCNA_03149) encodes a predicted β-glucosidase-β-xylosidase enzyme that was amplified by polymerase chain reaction; the product was cloned into the blunt ends of the pJet1.2 plasmid. Analysis of the protein sequence indicated the presence of conserved glycosyl hydrolase 3 (GH3), β-glucosidase-related glycosidase (BglX) and fibronectin type III-like domains. After verifying its identity by DNA sequencing, the xynB5 gene was linked to an amino-terminal His-tag using the pTrcHisA vector. A recombinant protein (95 kDa) was successfully overexpressed from the xynB5 gene in E. coli Top 10 and purified using pre-packed nickel-Sepharose columns. The purified protein (BglX-V-Ara) demonstrated multifunctional activities in the presence of different substrates for β-glucosidase (pNPG: p-nitrophenyl-β-D-glucoside) β-xylosidase (pNPX: p-nitrophenyl-β-D-xyloside) and α-arabinosidase (pNPA: p-nitrophenyl-α-L-arabinosidase). BglX-V-Ara presented an optimal pH of 6 for all substrates and optimal temperature of 50 °C for β-glucosidase and α-l-arabinosidase and 60 °C for β-xylosidase. BglX-V-Ara predominantly presented β-glucosidase activity, with the highest affinity for its substrate and catalytic efficiency (K_m 0.24 ± 0.0005 mM, V_max 0.041 ± 0.002 µmol min^?1 mg^?1 and K_cat/K_m 0.27 mM^?1 s^?1), followed by β-xylosidase (K_m 0.64 ± 0.032 mM, V_max 0.055 ± 0.002 µmol min^?1 mg^?1 and K_cat/K_m 0.14 mM^?1s^?1) and finally α-l-arabinosidase (K_m 1.45 ± 0.05 mM, V_max 0.091 ± 0.0004 µmol min^?1 mg^?1 and K_cat/K_m 0.1 mM^?1 s^?1). To date, this is the first report to demonstrate the characterization of a GH3-BglX family member in C. crescentus that may have applications in biotechnological processes (i.e., the simultaneous saccharification process) because the multifunctional enzyme could play an important role in bacterial hemicellulose degradation.     

Template‐tethered collagen mimetic peptides for studying heterotrimeric triple‐helical interactions

Collagen mimetic peptides (CMPs) have been used to elucidate the structure and stability of the triple helical conformation of collagen molecules. Although CMP homotrimers have been widely studied, very little work has been reported regarding CMP heterotrimers because of synthetic difficulties. Here, we present the synthesis and characterization of homotrimers and ABB type heterotrimers comprising natural and synthetic CMP sequences that are covalently tethered to a template, a tris(2‐aminoethyl) amine (TREN) succinic acid derivative. Various tethered heterotrimers comprising synthetic CMPs [(ProHypGly)₆, (ProProGly)₆] and CMPs representing specific domains of type I collagen were synthesized and characterized in terms of triple helical structure, thermal melting behavior, and refolding kinetics. The results indicated that CMPs derived from natural type I collagen sequence can form stable heterotrimeric helical complexes with artificial CMPs and that the thermal stability and the folding rate increase with the increasing number of helical stabilizing amino acids (e.g. Hyp) in the peptide chains. Covalent tethering enhanced the thermal stability and refolding kinetics of all CMPs; however, their relative values were not affected suggesting that the tethered system can be used for comparative study of heterotrimeric CMP's folding behavior in regards to chain composition and for characterization of thermally unstable CMPs. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 94–104, 2011.