Evolution of nucleic acid replication: The possible role of simple repeating sequence polypeptides therein

Summary Our concept of nucleic acid replication does not explain the movement in that process—i.e., the existence of a socalled growing point. This omission may manifest itself in a failure to understand primitive nucleic acid replication. The latter may not be merely a templating process. Primitive nucleic acid replication is postulated to involve a particular type of peptide that establishes a growing point—a polypeptide in whichalternate amino acid residues are basic. Possible interactions of such a peptide with single and double stranded nucleic acid and its possible mode(s) of synthesis in a primitive environment are discussed.     

Restriction site insertion-PCR (RSI-PCR) for rapid discrimination and typing of closely related microbial strains

Taking advantage of point mutations between DNA sequences of closely related microbial strains, PCR primers modified with respect to the target sequence at positions 2-5 near the 3' end were designed to obtain a fragment harbouring an artificial restriction site specific for a given strain. The modified forward primer coupled with a specific reverse primer allows for the amplification of DNA fragments which can be digested with the specific endonuclease only in those strains where the restriction site is inserted by the DNA polymerase. The effectiveness of the method, named restriction site insertion-PCR (RSI-PCR), was tested on isolates of the 'Bacillus cereus group' for the rapid typing and discrimination of these closely related strains.     

一例乙型肝炎患者体内不同HBV克隆的序列差异

采用ＰＣＲ扩增、噬菌体克隆和核苷酸序列分析的方法对一例乙型肝炎患者体内ＨＢＶ的ＨＢｓＡｇ编码区和部分前Ｓ２区进行序列分析。结果发现同一患者体内获得的不同ＨＢＶＤＮＡ克隆间存在个别碱基的差异,而这种差异并非方法学本身产生的。由此得出的结论是,这种碱基“突变”反映了乙型肝炎患者体内ＨＢＶ基因组实际存在的多态性。     

Conditional Point Estimation in Adaptive Group Sequential Test Designs

It is well known that point estimates in group sequential designs are biased. This also applies to adaptive designs that enable, e.g., data driven reassessments of group sample sizes. For triangular designs, Whitehead (1986) (Biometrika 73 , 573–581) proposed a bias adjusted estimate. But this estimate is not feasible in adaptive designs although it is in group sequential designs. Furthermore, there is a waste of information because it does not use the information at which stage the trial was stopped. We present a modification which does use this information and which is applicable to adaptive designs. The modified estimate achieves an improvement in group sequential designs and shows similar results in adaptive designs.     

太白山牛皮桦-巴山冷杉混交林空间格局及关联性研究

采用改进的点格局分析法——邻域密度函数（Neighborhood Density Function,NDF）对太白山地区桦林-冷杉林交错区内主要树种的空间分布格局、种间空间关联性及其更新空间关联性进行了分析。结果表明：各树种所有个体整体上都呈随机分布,划分不同层级后,则各林层个体分布格局各异,各树种在较低的林层呈明显聚集分布,随林层增高,中、高层内个体聚集分布的空间尺度降低。两个主要竞争种牛皮桦（Betula albo-sinensis var．septentrionalis）和巴山冷杉（Abies fargesii）整体表现出显著空间负相关,巴山冷杉与玉皇柳（Salix yuhuangshanensis）未表现出明显相关性,而牛皮桦与玉皇柳间则有空间负相关的趋势。牛皮桦的更新格局仅依靠自身倒木扰动产生的机会,且被限定在较小尺度上。巴山冷杉在小尺度上会限制自身更新,此外与牛皮桦在小尺度上竞争激烈,可占据利用其空间位置进行更新。从空间格局分析角度认识牛皮桦和巴山冷杉的生态学特性,为进一步研究其共存机制,认识太白山桦林在秦岭植被垂直带中的作用和地位提供参考依据。     

Higher order multipole moments for molecular dynamics simulations

In conventional force fields, the electrostatic potential is represented by atom-centred point charges. This choice is in principle arbitrary, but technically convenient. Point charges can be understood as the first term of multipole expansions, which converge with an increasing number of terms towards the accurate representation of the molecular potential given by the electron density distribution. The use of multipole expansions can therefore improve the force field accuracy. Technically, the implementation of atomic multipoles is more involved than the use of point charges. Important points to consider are the orientation of the multipole moments during the trajectory, conformational dependence of the atomic moments and stability of the simulations which are discussed here.

Point pattern analysis under conditions of replicated sampling北大核心CSCD

Aims: The analysis of point patterns, which deals with data sets consisting of mapped locations of organisms in a study region, is especially important to plant ecological studies because the locations of plants can often be approximated as points. However, few studies used point pattern analysis with data collected by replicated sampling. a principle procedure of acquiring data in ecological research. Therefore, we explore the applicability of point pattern analysis under conditions of replicated sampling in this study. Methods: Three replicated 5 m × 5 m plots of homogenous communities were established on a site with eight years of restoration in Nei Mongol steppe. In each plot, the locations of individuals in Leymus chinensis and Stipa grandis populations were mapped. O-Ring function was used to describe the population patterns and species association between L. chinensis and S. grandis for each plot as well as the integrative data of the three replicates. Important findings: Population patterns and species associations differed among the three replicated plots. This illustrates that if point pattern analysis was applied to describe the population patterns and species associations only by using data from a single plot sampling, the results could be misleading. Whereas it would be more reliable to integrate the data of replicated plots in the point pattern analysis because in this way the resulting O-Ring function is a weighted average, where the weight is the number of points in the replicate i divided by the total number of points in all replicated plots.     

SOE-LRed: A simple and time-efficient method to localize genes with point mutations onto the Escherichia coli chromosome

We use a powerful method to replace wild-type genes on the chromosome of Escherichia coli. Using a unique form of PCR, we generate easily constructible gene fusions bearing single point mutations. Used in conjunction with homologous recombination, this method eliminates cloning procedures previously used for this purpose.     

Discovery of a novel site regulating glucokinase activity following characterization of a new mutation causing hyperinsulinemic hypoglycemia in humans

Type 2 diabetes is a global problem, and current ineffective therapeutic strategies pave the way for novel treatments like small molecular activators targeting glucokinase (GCK). GCK activity is fundamental to beta cell and hepatocyte glucose metabolism, and heterozygous activating and inactivating GCK mutations cause hyperinsulinemic hypoglycemia (HH) and maturity onset diabetes of the young (MODY) respectively. Over 600 naturally occurring inactivating mutations have been reported, whereas only 13 activating mutations are documented to date. We report two novel GCK HH mutations (V389L and T103S) at residues where MODY mutations also occur (V389D and T103I). Using recombinant proteins with in vitro assays, we demonstrated that both HH mutants had a greater relative activity index than wild type (6.0 for V389L, 8.4 for T103S, and 1.0 for wild type). This was driven by an increased affinity for glucose (S(0.5), 3.3 ± 0.1 and 3.5 ± 0.1 mm, respectively) versus wild type (7.5 ± 0.1 mm). Correspondingly, the V389D and T103I MODY mutants had markedly reduced relative activity indexes (<0.1). T103I had an altered affinity for glucose (S(0.5), 24.9 ± 0.6 mm), whereas V389D also exhibited a reduced affinity for ATP and decreased catalysis rate (S(0.5), 78.6 ± 4.5 mm; ATP(K(m)), 1.5 ± 0.1 mm; K(cat), 10.3 ± 1.1s(-1)) compared with wild type (ATP(K(m)), 0.4 ± <0.1; K(cat), 62.9 ± 1.2). Both Thr-103 mutants showed reduced inhibition by the endogenous hepatic inhibitor glucokinase regulatory protein. Molecular modeling demonstrated that Thr-103 maps to the allosteric activator site, whereas Val-389 is located remotely to this position and all other previously reported activating mutations, highlighting α-helix 11 as a novel region regulating GCK activity. Our data suggest that pharmacological manipulation of GCK activity at locations distal from the allosteric activator site is possible.     

Regulatory networks,genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention

Understanding network topology through embracing the global dynamical regulation of genes in an active state space rather than traditional one-gene–one trait approach facilitates the rational drug development process. Schistosomiasis, a neglected tropical disease, has glycerophospholipids as abundant molecules present on its surface. Lack of effective clinical solutions to treat pathogens encourages us to carry out systems-level studies that could contribute to the development of an effective therapy. Development of a strategy for identifying drug targets by combined genome-scale metabolic network and essentiality analyses through in silico approaches provides tantalizing opportunity to investigate the role of protein/substrate metabolism. A genome-scale metabolic network model reconstruction represents choline–phosphate cytidyltransferase as the rate limiting enzyme and regulates the rate of phosphatidylcholine (PC) biosynthesis. The uptake of choline was regulated by choline concentration, promoting the regulation of phosphocholine synthesis. In Schistosoma, the change in developmental stage could result from the availability of choline, hampering its developmental cycle. There are no structural reports for this protein. In order to inhibit the activity of choline–phosphate cytidyltransferase (CCT), it was modeled by homology modeling using 1COZ as the template from Bacillus subtilis. The transition-state stabilization and catalytic residues were mapped as ‘HXGH’ and ‘RTEGISTT’ motif. CCT catalyzes the formation of CDP-choline from phosphocholine in which nucleotidyltransferase adds CTP to phosphocholine. The presence of phosphocholine permits the parasite to survive in an immunologically hostile environment. This feature endeavors development of an inhibitor specific for cytidyltransferase in Schistosoma. Flavonolignans were used to inhibit this activity in which hydnowightin showed the highest affinity as compared to miltefosine.