An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles

A new molecular dynamics method for calculating free energy profiles for rare events is presented. The new method is based on the creation of an adiabatic separation between the reaction coordinate subspace and the remaining degrees of freedom within a molecular dynamics run. This is achieved by associating with the reaction coordinate(s) a high temperature and large mass, thereby allowing the activated process to occur while permitting the remaining degrees of freedom to respond adiabatically. In this limit, by applying a formal multiple time scale Liouville operator factorization, it can be rigorously shown that the free energy profiles are obtained directly from the probability distribution of the reaction coordinate subspace and, therefore, require no postprocessing of the output data. The new method is applied to a variety of model problems and its performance tested against free energy calculations using the "bluemoon ensemble" approach. The comparison shows that free energy profiles can be calculated with greater ease and efficiency using the new method.     

Application of the ‘profiles of relationship’ method to distantly related proteins

Summary An analysis is made of the applicability of the recently published profiles of relationship method for establishing evolutionary relatedness among proteins by using the distantly related proinsulin and neurotoxin protein se-quences as a test object. The method is based on a simultaneous group analysis of both the frequency of acceptance of mutations and their genetic code inter-changeability. Regularities in the patterns of the profiles, which reflect decreased similarity with the passage of time, are established for typical cases of closely related, distantly related and unrelated proteins. This makes it possible to distinguish distantly related from unrelated proteins without extensive statistical randomization procedures. New evidence is stated in favour of a previously suggested definition of interchangeability which does not consider the third base in the codon. The applicability of the profiles of relationship method is examined on the distant relationship between proinsulin and the snake and scorpion neurotoxins which has been established previously by means of conventional approaches.     

Toxicological Study and Oxidative Stress Evaluation for Safety Assessment of Xylanase Preparations in Wistar Rats

Acute and 90‐day subchronic oral toxicity studies were conducted to establish the safety evaluation of xylanases preparations. A potential oxidative stress evaluation was also performed through testing the generation of oxidative radicals, depletion of antioxidants via oxidative modification of lipids, proteins and DNA of organ cells. During the subchronic oral toxicity study, no mortality was observed, obvious treatment‐related clinical signs and urinalysis parameters were in normal range. Differences in some hematological parameters, biochemistry, relative organ weight, and histopathology examinations between the treated group and the control group were not judged to be adverse. Our results indicated that the no‐observed‐adverse‐effect level for xylanases was 1,500 TXU/kg/day and the plasma antioxidant assays showed that these xylanases did not produce free‐radicals nor oxidative injuries. On the basis of the bacterial reverse mutation assay data, it is concluded that the expressed xylanase in Pichia pastoris do not present any mutagenic potential when tested in relevant genotoxicological assays.     

Effect of 3,4-di(OH)-cinnamate synthetic derivative on plasma and hepatic cholesterol level and antioxidant enzyme activities in high cholesterol-fed rats

The effect of 3,4-di(OH)-phenylpropionic acid (L-phenylalanine methyl ester) amide (SL-1063), a synthetic derivative of 3,4-di(OH)-cinnamate, on the cholesterol metabolism and antioxidant enzyme system was examined in rats. Diets that included either SL-1063 (0.046%, w/w) or lovastatin (0.02%, w/w) as a supplement, plus 1 g cholesterol/100 g diet were fed to rats ad libitum for 5 weeks. The total plasma cholesterol and triglyceride levels were significantly lowered by the SL-1063 supplement compared to the control group. Meanwhile, the levels of plasma HDL-cholesterol and ratio of HDL-cholesterol/total cholesterol (%) were significantly higher in the SL-1063 group than in the control group. However, the lovastatin supplement did not affect the plasma lipid level. The hepatic cholesterol level and 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase activity were significantly lowered in the lovastatin group compared to the SL-1063 group; however, the hepatic triglyceride level did not differ among the groups. The activity of hepatic acyl CoA: cholesterol acyltransferase (ACAT), the enzyme that catalyzes hepatic cholesterol esterification, was significantly lower in the lovastatin and SL-1063 groups than in the control group. Furthermore, the SL-1063 supplement elevated the excretion of fecal sterols. As regards the hepatic antioxidant enzyme system, the superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), and glutathione reductase (GR) activities were all significantly higher in the SL-1063 group compared to the control group, whereas only the GR activity was significantly increased by the lovastatin supplement. No marked difference in the GSH levels and glucose-6-phosphate dehydrogenase (G6PD) activities was observed among the groups. The levels of plasma and hepatic thiobarbituric acid reactive substances (TBARS) were lowered by the SL-1063 supplement compared to the control group. Accordingly, the current results suggest that SL-1063, a synthetic derivative of 3,4-di(OH)-cinnamate, is effective in lowering the plasma lipids and improving the antioxidant enzyme system.     

HPLC Profiles and Biomarker Contents of Australian‐Grown Salvia miltiorrhiza f. alba Roots

Salvia miltiorrhiza f. alba (Baihua Danshen) is a Chinese medicinal herb commonly used for treating cardiovascular disease. It has been grown in Australia, although the quality of its main medicinal part (dried root) has not been assessed. In this study, we investigated HPLC profiles and biomarker contents of Australian‐grown S. miltiorrhiza f. alba roots. Patterns of HPLC profiles were established in MeOH, and aqueous extracts in terms of number of common characteristic peaks and their relative retention times. The contents of three tanshinone biomarkers (cryptotanshinone ( 3 ), tanshinone I ( 1 ), and tanshinone IIA ( 2 )) were significantly higher (p<0.05) in the roots of one‐year‐old plants than those of two‐year‐old plants. In contrast, salvianolic acid B ( 4 ) content was significantly higher in the roots of two‐year‐old plants than in those of one‐year‐old plants. The findings suggest that the biomarker contents in Australian‐grown S. miltiorrhiza f. alba roots vary with the growth periods of the plants, which may be important in determining the optimal harvest time for the plant roots with targeted levels of tanshinones and salvianolic acid B ( 4 ).     

洞庭湖湿地土壤碳、氮、磷及其与土壤物理性状的关系

以洞庭湖3类典型湿地的8个土壤剖面为代表,研究了土壤碳、氮、磷,微生物量碳、氮、磷和土壤物理性状的分布特征.结果表明,土壤表层有机碳含量为19.63～50.20 g·kg^-1,微生物量碳为424.63～1 597.36 mg·kg^-1,微生物量碳占有机碳的比例为3.17%～4.82%;土壤表层全氮1.85～4.45 g·kg^-1,微生物量氮5.90～259.47 mg·kg^-1,微生物量氮占全氮的比例3.13%～6.42%;土壤表层微生物量磷含量顺序为:湖草洲滩地(200.99 mg·kg^-1)＞垦殖水田(163.27 mg·kg^-1)＞芦苇洲滩地(24.16 mg·kg^-1),微生物量磷占全磷的比例为1.09%～11.20%;土壤表层容重0.65～1.04 g·cm^-3;土壤表层粘粒(＜0.001mm)26.24%～39.48%.土壤表层有机碳、全氮、微生物量氮、微生物量磷的含量,湖草洲滩地＞垦殖水田＞芦苇洲滩地.土壤表层微生物量碳,垦殖水田和湖草洲滩地接近,而大于芦苇湿地;土壤表层容重,芦苇洲滩地＞垦殖水田＞湖草洲滩地;土壤表层＜0.01 mm、＜0.001 mm粘粒,湖草洲滩地、芦苇洲滩地＞垦殖水田.湿地土壤剖面中有机碳、微生物量碳、全氮、微生物量氮、微生物量磷、容重以及微生物量碳占有机碳的比例、微生物量氮占全氮的比例、微生物量磷占全磷的比例均随深度的增加而降低,至一定深度稳定,而土壤全磷在剖面上下的差异很小.湿地土壤微生物量碳、氮、磷之间呈极显著的正相关关系;土壤容重与有机碳、全氮、微生物量碳、氮、磷之间呈极显著指数负相关关系.湿地土壤＜0.001 mm粘粒与有机碳、全氮、微生物量碳、氮、磷含量呈极显著对数正相关关系.     

Laminated microbial ecosystems on sheltered beaches in Scapa Flow, Orkney Islands

Abstract Laminated microbial sediment ecosystems which develop in the upper tidal zone of Scapa Flow beaches, Orkney Islands were investigated with respect to depth profiles of chlorophyll a , bacteriochlorophyll a , pH, redox, oxygen and the following inorganic sulfur compounds: free sulfide, FeS, polysulfides, polythionates, elemental sulfur and thiosulfate. In addition, particle size distribution and light penetration were determined at all sampling locations.
Three main types of laminated sediment ecosystems were recognized, designated the 'classical' type (layer of cyanobacteria underlain by layer of purple sulfur bacteria), the 'single-layer' type (chlorophyll a containing organisms absent, purple sulfur bacteria at sediment surface), and the 'inverted' type (chlorophyll a containing organisms underlying purple sulfur bacteria). The dominant purple sulfur bacterium was Thiocapsa roseopersicina and Chromatium vinosum was observed less commonly. The principal cyanobacterium found in these sulfureta was Oscillatoria sp.
The depth horizon at which maximum populations of purple sulfur bacteria were recorded often did not coincide with the sulfide/oxygen interface but was located closer to the sediment surface where polysulfides, polythionates, elemental sulfur and occasionally thiosulfate were present. The structure of these sulfureta is discussed in relation to the chemolithotrophic growth capacities of Thiocapsa in the presence of oxygen.