Estimation of Free Energy Systematic Errors in Molecular Simulations of Globular Proteins Surrounded by Finite Water Clusters. One Center Multipole Expansion of Reaction Field Differences

Free energy calculated in simulations on the atomic level (Monte Carlo or Molecular Dynamics) has a systematic error, if the water shell surrounding a globular protein is finite. The error (“cluster error”) is equal to a difference of free energies obtained in simulations with an infinite and finite water shell. In this work a continuum dielectric model was used to estimate the “cluster error”. A multipole expansion of the estimate was performed for a water shell with a spherical outer boundary. The expansion has very simple form. Each term is a product of two functions, one of them depending only on the charge's conformation, and the other one only on dielectric properties of the system. There are two practical uses of the expansion. First, it may be used to estimate the “cluster error” in a simulation already made; second, it may be used to plan a simulation in such a way that the “cluster error” is minimal. Numerical values of the largest terms in the multipole expansion corresponding to a typical system in simulations of globular proteins are given.     

The influence of earthworms (Lumbricidae) on the nitrogen dynamics in the soil litter system of a deciduous forest

Summary The influence of earthworms (Aporrectodea caliginosa (Savigny) and Lumbricus castaneus (Savigny)) on the rate of nitrogen net mineralization of the soil was studied in the laboratory and in the field. The additional mineralization of nitrogen cause by the burrowing activity of the substrat feeding earthworm A. caliginosa (N _L )was directly correlated to the biomass of the lumbricids independently of their number. A rise in temperature caused an exponential increase in N _L values. The Q ₁₀ value of this process (2.18) was found to be much higher than that of the nitrogen mineralization without earthworms (Q ₁₀=1.22). At 15°C the N _L value caused by A. caliginosa was calculated to be about 250 g N g^-1 fresh body wt d^-1. Using the experimentally determined exponential relationship between temperature and N _L values, the additional nitrogen mineralization caused by a population of A. caliginosa in a beechwood on limestone was calculated to be 4.23 kg ha^-1 a^-1.In contrast to A. caliginosa the litter dwelling species L. castaneus lost considerable amounts of biomass (56%) during the 4 week incubation period. Only 1/3 of the nitrogen equivalent to the weight loss of the animals was recovered in the mineral nitrogen pool.The addition of litter (old beech leaf litter, freshly fallen beech and ash leaf litter) had a pronounced effect on both nitrogen net mineralization and N _L values of the soil. Presence of old beech leaves caused an increase in both values, wheres the other litter types effected a decrease in nitrogen net mineralization. Fragmented ash litter was found to have the most distinct effect on N _L values (-69%) and nitrogen net mineralization (-74%).     

高压静电场(HVEF)对柑桔青、绿霉病菌的抑制效果

用高压静电场(HVEF)对柑桔青霉菌 (P.italicum )和绿霉菌 (P.digitatum)分别进行了不同时间和方法的处理 ,以比较这些处理对病菌孢子在不同温度下萌发力和致病力的抑制效果。结果表明 ,HVEF处理后病菌孢子的萌发率、芽管长度和产孢量都显著地低于对照。而且处理时间越长 ,效果越明显。处理的孢子接种在柑桔果实上的感病率也显著低于对照 ,并能有效地抑制感病果实病斑的扩展。     

Extracellular polysaccharides of cowpea rhizobia: compositional and functional studies

Polysaccharides excreted by cowpea Rhizobium strains JLn(c) and RA-1 were mixtures of complex acidic exopolysaccharides and low molecular weight neutral glucans. These polymers were fractionated using gel filtration chromatography. Purified fractions of the acidic heteropolymer reacted with peanut agglutinin to give precipitin bands when subjected to Ouchterlony gel diffusion. The acidic exopolysaccharide was found to contain mainly glucose, galactose, glucuronic acid, mannose and fucose. The non-carbohydrate substituents of the acidic heteropolymer were pyruvate, acetate and uronate which were identified by infrared and proton nuclear magnetic resonance spectroscopy as well as by chemical analysis.Abbreviations EPS Extracellular polysaccharide - YEM yeast extract mannitol - PNA peanut agglutination - ¹H-NMR proton nuclear magnetic resonance     

一类具饱和传染力和常数输入的SIRS脉冲接种模型研究

利用Floquet乘子理论,研究了一类具饱和传染力和常数输入的SIRS脉冲接种模型,得到了无病周期解全局渐近稳定和系统持久的充分条件.     

气相色谱法测定寨香祛痛凝胶的4 种有效成分的含量

目的:采用气相色谱法,程序升温方式同时测定麝香祛痛凝胶中主要成分麝香酮、樟脑、薄荷脑、冰片的含量。方法:采用玻璃柱3 m×3．2 mm,担体Chro2mosorb W 60-80目,涂布6％聚乙二醇(PEG)-20M,2％苯基(50％)甲基硅酮(OV-17)。从80℃到180℃程序升温;载气:高纯氮,流量:50ml·min-1;FID检测器;进样体积6μL。结果:试验表明,樟脑、薄荷脑、冰片、麝香酮分别在1-8μg,0．6-4．8μg,1-8μg,0．15-1．2μg范围内呈良好的线性关系,回归方程分别为Y=18 062 X-483(r=0．999 9),Y= 9 829 X 61(r=0．999 6),Y=21 006X 562(r=0．999 1),Y=286 986X 406(r=0．999 4)。平均回收率分别为99．78％,100．9％,98．81％,98．68(n=5)。结论:该法可靠简便,结果准确,可作为控制麝香祛痛凝胶质量的方法。     

乳杆菌对数生长期培养基滤液核酸组分分析

目的通过对乳杆菌对数生长期培养基滤液中核酸组分的分析,阐明乳杆菌DM9811对数生长期培养基滤液中核酸的性质。方法应用核酸的分离、纯化及电泳分析技术。结果乳杆菌对数生长期培养基滤液中核酸组分为RNA,其片段大小为100 bp左右。乳杆菌对数生长期培养基滤液中核酸组分为RNA,为对数期产生且呈时间依赖关系。结论核酸组分不仅仅是遗传信息的载体,还可能作为有效的信息分子。     

Oligomerization of the Cu(II) and Ni(II) tetraazaannulene complexes: A pulse radiolysis study of the associated reaction mechanism

The oligomerization of [Cu^II(H_x(tmdnTAA))]^x+ (x = 0, 1, 2 and (tmdnTAA))²⁻ is 2,4,9,11-tetramethyl-dinaphto[14]-2,4,6,9,11,13-hexaeneN₄) was initiated in homogeneous solution via the reaction of this Cu(II) complex with pulse radiolytically generated radicals. The reaction produces Cu(III) intermediates which are rapidly converted to Cu(II) ligand-radical species. In contrast to the mechanism proposed for the electrochemical oligomerization, where the local concentration of radicals is probably high, the reaction kinetics in homogeneous solution is propagated by a process where the Cu(II) ligand-radical precursors react with [Cu^II(H_x(tmdnTAA))]^x+.     

The use of Quantitative Agarose Gel Electrophoresis for rapid analysis of the integrity of protein-DNA complexes

Recent biochemical studies evaluated the affinity of histones to DNA in the context of nucleosome core particle (NCP). These have indicated a concentration-dependence for nucleosome stability. However, when studying chromatin the preferred templates are nucleosome arrays (NA) and not the NCP. Biochemical methods are poorly suited for structural analysis of chromatin. To overcome that technical hindrance, and investigate the effect of concentration on stability of the histone-DNA interactions, we have applied the multigel Quantitative Agarose Gel Electrophoresis (QAGE) method to in vitro-assembled nucleosomal arrays. The results demonstrated the method to be extremely valuable for the evaluation of the effect of low concentration on NA. However, QAGE is a fairly time-demanding and complex method. To maximize the efficiency of use of this technology, we devised a protocol that allowed for multiple sets of templates to be analyzed simultaneously. Briefly, samples can be loaded at regular intervals and analyzed individually for their molecular composition. The technique presented in this study describes the calibration steps and proof of concept necessary to validate the use of multiple loading of multigel to evaluate the composition of nucleosomal arrays as a function of concentration.     

A new pachyosteomorph arthrodire (Pisces: Placodermi) from the Upper Frasnian of the Central Devonian Field,Russia

A new genus and species of pachyosteomorph arthrodire, Omalosteus krutoensis gen. et sp. nov. from shallow-water marine deposits of the Evlanovo Regional Stage (Upper Frasnian, Upper Devonian) of the Central Devonian Field is described. It is tentatively referred to the family Trematosteidae Gross, 1932, which was earlier believed to be endemic to central Europe. The new genus is characterized by a rounded, dorsoventrally compressed cross section of the pectoral region and smooth head shield and postcranial membrane bones. The centrale is elongated, forming a narrow lateral lobe. The praeorbitale, postorbitale, and centrale come in contact in the center of the orbital region. The mediodorsale is wide, its carinal process projects considerably posteriorly. The anterior margin of the anterior ventrolaterale lacks articular facets for the interlaterale.