Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation

The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant.     

Endcaps for stabilizing short DNA duplexes

The syntheses of endcaps for covalently linking the 3' and 5' hydroxyl groups of blunt end double-stranded DNA are described. Endcap diols were converted into DMTr protected phosphoramidites and incorporated between nucleotides 4 and 5 of a self-complementary octamer. The stabilizing effect of the endcaps on duplex DNA was determined by Tm experiments on the self-complementary octamer.     

A new computational approach for real protein folding prediction

An effective and fast minimization approach is proposed for the prediction of protein folding, in which the 'relative entropy' is used as a minimization function and the off-lattice model is used. In this approach, we only use the information of distances between the consecutive Calpha atoms along the peptide chain and a generalized form of the contact potential for 20 types of amino acids. Tests of the algorithm are performed on the real proteins. The root mean square deviations of the structures of eight folded target proteins versus the native structures are in a reasonable range. In principle, this method is an improvement on the energy minimization approach.     

小麦丛矮病毒NS蛋白基因的克隆及序列分析

利用与Ｎ蛋白ｍＲＮＡ３＇末端顺序相同的２０寡聚核苷酸引物,通过点杂交、限制性内切酶分析从小麦丛矮病毒（ＷＲＳＶ）ｃＤＮＡ文库中筛选到编码Ｎ蛋白基因下游顺序的ｃＤＮＡ克隆。序列分析表明,该ｃＤＮＡ片段含有一编码的４０ｋＤ蛋白的开放读框。将该读框的全长ｃＤＮＡ经ＰＣＲ扩增后,克隆到ｐＧＥＸ－３Ｘ上,在大肠杆菌ＤＥ３中用ＩＰＴＧ诱导表达,经蛋白质印迹鉴定,该基因为小麦丛矮病毒ＮＳ蛋白基因。     

小麦丛矮病毒M蛋白基因的序列测定,表达和鉴定

从小麦丛矮病毒（ＷＲＳＶ）基因文库含磷蛋白ＮＳ基因的质粒中,经亚克隆、测序,得到ＮＳ蛋白基因的下游序列,其中含有一读框４５３ｎｔ、编码一分子量约１７ｋＤ蛋白。用ＰＣＲ方法获得该读框全长片段并克隆到表达载体ｐＧＥＸ－３Ｘ,在大肠杆菌ＢＬ２１（ＤＥ３）菌株中以ＩＰＴＧ诱导表达,产物由谷胱甘肽Ｓ－转移酶（ＧＳＴ）亲和层析柱纯化后,用蛋白质印迹分析鉴定,结果表明,该读框为编码病毒基质蛋白Ｍ的基因。     

高山红景天（Rhodiola sachalinensis）遗传变异及其濒危机制的探讨

采用淀粉凝胶电泳手段,等位酶分析技术对分布于黑龙江大海林林业局高山红景天天然分布区内３个亚种群及吉林长白山１个亚种群的９种酶系统１８个位点进行了遗传分析,结果表明种群内存在一定的遗传变异（从态位点百分比为３０．５５％,等位基因平均数为１．３３３）但不是很丰富,主要是该种类狭窄的分布区致使生境单一及人为破坏其本身的生物学特性长期的进化过程中相互适应相互选择的结果。在黑龙江的分布区内各亚种群之间一致度     

A rapid enzymatic assay for high-throughput screening of adenosine-producing strains

Adenosine is a major local regulator of tissue function and industrially useful as precursor for the production of medicinal nucleoside substances. High-throughput screening of adenosine overproducers is important for industrial microorganism breeding. An enzymatic assay of adenosine was developed by combined adenosine deaminase (ADA) with indophenol method. The ADA catalyzes the cleavage of adenosine to inosine and NH₃, the latter can be accurately determined by indophenol method. The assay system was optimized to deliver a good performance and could tolerate the addition of inorganic salts and many nutrition components to the assay mixtures. Adenosine could be accurately determined by this assay using 96-well microplates. Spike and recovery tests showed that this assay can accurately and reproducibly determine increases in adenosine in fermentation broth without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. This assay was also applied to high-throughput screening for high adenosine-producing strains. The high selectivity and accuracy of the ADA assay provides rapid and high-throughput analysis of adenosine in large numbers of samples.     

Adaptive Evolution of Defense Ability Leads to Diversification of Prey Species

In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey–two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex–concave–convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale.     

Significance of consensus CYC‐binding sites found in the promoters of both ChCYC and ChRAD genes in Chirita heterotricha (Gesneriaceae)

Abstract CYC‐like genes are widely conserved in controlling floral dorsoventral asymmetry (zygomorphy) through persistent expression in corresponding domains in core eudicots. To understand how CYC‐like gene expression is maintained during flower development, we selected Chirita heterotricha as a material and isolated the promoter sequences of the ChCYC1C and ChCYC1D genes, homologs of CYC, by inverse polymerase chain reaction. Further promoter analyses led to the identification of a putative cis‐regulatory element in each promoter matching the consensus DNA binding site for Antirrhinum CYC protein: GGCCCCTC at ?165 for ChCYC1C, and GGCCCCCC at ?163 for ChCYC1D. This indicates that both the ChCYC1C and ChCYC1D genes have probably evolved autoregulatory loops to sustain their expression in developing flowers. We also isolated the coding and promoter sequences of the ChRAD gene, a homolog of Antirrhinum RAD. Promoter analysis showed that the ChRAD gene promoter also contained a putative CYC‐binding site (GGCCCAC at ?134). Therefore, ChRAD is likely a direct target of the ChCYC1 genes, which is similar to Antirrhinum RAD. These results imply that the establishment of floral zygomorphy in Chirita may have been achieved by the evolution of an autoregulatory loop for CYC‐like genes, which was probably accompanied by simultaneous co‐option of the RAD‐like gene into their regulatory network.