Simplification of Stochastic Chemical Reaction Models with Fast and Slow Dynamics

Biological systems often involve chemical reactions occurring in low-molecule-number regimes, where fluctuations are not negligible and thus stochastic models are required to capture the system behaviour. The resulting models are generally quite large and complex, involving many reactions and species. For clarity and computational tractability, it is important to be able to simplify these systems to equivalent ones involving fewer elements. While many model simplification approaches have been developed for deterministic systems, there has been limited work on applying these approaches to stochastic modelling. Here, we describe a method that reduces the complexity of stochastic biochemical network models, and apply this method to the reduction of a mammalian signalling cascade and a detailed model of the process of bacterial gene expression. Our results indicate that the simplified model gives an accurate representation for not only the average numbers of all species, but also for the associated fluctuations and statistical parameters.     

甘油生物歧化非线性动力系统的平衡点及其稳定性分析

针对甘油生物歧化为1,3-丙二醇过程的酶催化动力系统,利用符号化实根隔离法求解系统的平衡点,验证了系统的多稳态现象,利用微分方程稳定性理论,分析了平衡点的稳定性,并结合数值结果讨论了系统的多态现象．本文的结果可为微生物发酵甘油生产1,3-丙二醇的实验优化参数设计提供参考．     

Micro-droplet Digital Polymerase Chain Reaction and Real-Time Quantitative Polymerase Chain Reaction Technologies Provide Highly Sensitive and Accurate Detection of Zika Virus

The establishment of highly sensitive diagnostic methods is critical in the early diagnosis and control of Zika virus(ZIKV)and in preventing serious neurological complications of ZIKV infection. In this study, we established micro-droplet digital polymerase chain reaction(ddPCR) and real-time quantitative PCR(RT-qPCR) protocols for the detection of ZIKV based on the amplification of the NS5 gene. For the ZIKV standard plasmid, the RT-qPCR results showed that the cycle threshold(Ct) value was linear from 10~1 to 10~8 copy/l L, with a standard curve R~2 of 0.999 and amplification efficiency of 92.203%;however, a concentration as low as 1 copy/l L could not be detected. In comparison with RT-qPCR, the dd PCR method resulted in a linear range of 10~1–10~4 copy/l L and was able to detect concentrations as low as 1 copy/l L. Thus, for detecting ZIKV from clinical samples, RT-qPCR is a better choice for high-concentration samples(above 10~1 copy/l L),while ddPCR has excellent accuracy and sensitivity for low-concentration samples. These results indicate that the ddPCR method should be of considerable use in the early diagnosis, laboratory study, and monitoring of ZIKV.     

Modulation of the shape and speed of a chemical wave in an unstirred Belousov–Zhabotinsky reaction by a rotating magnet

The objective of this study was to observe whether a rotating magnetic field (RMF) could change the anomalous chemical wave propagation induced by a moderate‐intensity gradient static magnetic field (SMF) in an unstirred Belousov–Zhabotinsky (BZ) reaction. The application of the SMF (maximum magnetic flux density = 0.22 T, maximum magnetic flux density gradient = 25.5 T/m, and peak magnetic force product (flux density × gradient) = 4 T²/m) accelerated the propagation velocity in a two‐dimensional pattern. Characteristic anomalous patterns of the wavefront shape were generated and the patterns were dependent on the SMF distribution. The deformation and increase in the propagation velocity were diminished by the application of an RMF at a rotation rate of 1 rpm for a few minutes. Numerical simulation by means of the time‐averaged value of the magnetic flux density gradient or the MF gradient force over one rotation partially supported the experimental observations. These considerations suggest that RMF exposure modulates the chemical wave propagation and that the degree of modulation could be, at least in part, dependent on the time‐averaged MF distribution over one rotation. Bioelectromagnetics 34:220–230, 2013. © 2012 Wiley Periodicals, Inc.     

球形红假单胞菌反应中心中蛋白的量子化学研究

采用重叠二体近似方法和建立在从算水平上的扩展负本征值因数计算方法（extended negative factor counter method）研究了球形红假单胞菌（Rhodobacter sphaeroides(Van Niel)Imhoff,Truper et Pfennin）中兴合反应中心中蛋白链L及M的电子结构。结果表明：（1）对组成蛋白链L（M）的前线轨道有重要贡献的氨基酸残基分布在L链的自由螺旋区（M链的α螺旋区）。由于自由螺旋是有柔曲性的,它易于在电子转移的过程中改变其构象并降低体系的能量,而α螺旋结构却相对稳定,这种差别有可能是光合反庆中心中电子转移只沿L支进行的原因之一。（2）与特殊对分子及辅助叶绿素分子形成轴向配位的组氨酸残基对于特殊对P和辅助叶绿素分子的ELUMO有重要影响,但此组氨酸的相应分子轨道的贡献并没有出现在蛋白链的前线轨道组成中。这意味着色素分子与蛋白链之间的相互作用对蛋白链前线轨道的贡献没有影响,但却能影响相应色素分子的ELUMO能级。     

Degradation of a Polymerase Chain Reaction (PCR) Product by Heat-Stable Deoxyribonuclease (DNase) Produced from Yersinia enterocolitica

When crude deoxyribonucleic acid (DNA) preparations by boiling were used for the polymerase chain reaction (PCR) from pathogenic and non-pathogenic Yersinia enterocolitica strains, the amplified products were degraded after their storage at 4 C. The degradation of products was prevented by the addition of ethylenediaminetetraacetate (EDTA) or treatment with proteinase K. These findings indicate that Y. enterocolitica produced heat-stable deoxyribonuclease (DNase). Proteinase K treatment would be recommended to prevent heat-stable DNase contamination in the DNA preparations for PCR from Y. enterocolitica strains.     

Sperm Mediated Transfer of Genes into Goldfish and Detection by Polymerase Chain Reaction

Goldfish sperms were mixed with eggs for fertilization after incubation with antifreeze protein gene(AFP)from ocean pout for 30 min.A number of embryos and 145 adult goldfish were obtained.DNA from adult goldfish and embryos was extracted separately.Results of the amplification by PCRand Southern blot molecular hybridization indicate the integration of exogenous antifreeze gene intothe genome of a part of the recipient goldfish.Of the 45 samples detected by PCR,twelve showedpositive reaction with distinct hybridization band.The positive rate was 26%.     

芒果DNA提取方法比较及ISSR反应体系的优化

为从芒果幼叶中提取高质量的核总DNA,比较了5种DNA提取方法提取芒果叶片核DNA的效果,结果表明:改良CTAB法1提取的DNA A260/A280值最好,ISSR-PCR扩增效果最佳,是有效提取芒果基因组DNA的方法。为得到最佳的芒果ISSR-PCR反应体系,以(ATG)6为引物,采用单因素实验法,优化了ISSR-PCR反应体系:在总体积25μl的反应体系中,含1×反应缓冲液,0.20mmol.L-1dNTPs,0.20μmol.L-1引物,0.60 UTaqDNA聚合酶,30-50 ng DNA模板,不足体积用无菌超纯水补足。     

The use of noise equivalent count rate and the NEMA phantom for PET image quality evaluation

PET image quality is directly associated with two important parameters among others: count-rate performance and image signal-to-noise ratio (SNR). The framework of noise equivalent count rate (NECR) was developed back in the 1990s and has been widely used since then to evaluate count-rate performance for PET systems. The concept of NECR is not entirely straightforward, however, and among the issues requiring clarification are its original definition, its relationship to image quality, and its consistency among different derivation methods. In particular, we try to answer whether a higher NECR measurement using a standard NEMA phantom actually corresponds to better imaging performance. The paper includes the following topics: 1) revisiting the original analytical model for NECR derivation; 2) validating three methods for NECR calculation based on the NEMA phantom/standard; and 3) studying the spatial dependence of NECR and quantitative relationship between NECR and image SNR.     

Chemical Synthesis of Human β-Defensin (hBD)-1, -2, -3 and -4: Optimization of the Oxidative Folding Reaction

Reduced human β-defensin (hBD)-1, -2, -3 and -4 synthesized by Boc chemistry were subjected to oxidative folding reaction under optimal conditions. Among the factors affecting the oxidative folding in the presence of reduced and oxidized glutathione (GSH/GSSG), the buffer concentration and reaction temperature were essential for the predominant formation of the native disulfide structure. The homogeneity of the four synthetic hBDs was confirmed by analytical procedures using RP-HPLC, IEX-HPLC, capillary zone electrophoresis (CZE) and MALDI-TOF MS as well as sequencing, although high temperature (70 °C) was used for the RP-HPLC analysis of hBD-3 and hBD-4 to exclude the influence of equilibrium with the respective conformers having native disulfide pairing. All synthetic hBDs were shown to possess the native disulfide structure by sequential analyses and mass measurements with cystine segments obtained by enzymatic digestion. Upon digestion of hBD-1 and hBD-4 with proline specific endopeptidase, the Cys-X bond was found to be reproducibly cleaved together with the Pro-X bond although the cleavage of Cys-X afforded the appropriate cystine segments for determining the disulfide structure of hBD-1 and hBD-4. With respect to antimicrobial activity against E. coli, the four synthetic hBDs of high homogeneity possessed the same potencies as those reported previously.Australian Peptide Conference Issue     

Chemical interactions in diatoms: role of polyunsaturated aldehydes and precursors

Chemicals produced by aquatic organisms, and especially micro-organisms, have received increasing attention in the last decade for their role in shaping interactions and communities. Several cases emphasize the fact that chemical signals or defence may modulate interspecific interactions. Notably, it has been shown that diatoms, unicellular algae and key primary producers in aquatic ecosystems produce a wide range of bioactive metabolites. Among these compounds, polyunsaturated short-chain aldehydes in vitro strongly impair the reproduction of various potential grazers. In the field, the relationship between aldehyde production and reproductive failure in copepods remains unclear. Recent studies have suggested that these putative defence compounds may also be involved in intercellular communication and in interactions with competitors. Potential effects of the aldehyde precursors on various organisms have also been described. This review presents an overview of various results obtained in the last decade that could help us to understand the role of polyunsaturated aldehydes and their precursors in the ecology of diatoms. It is focused on the dichotomy between freshwater and marine environments. Indeed, most of the results on anti-proliferative aldehydes concern marine planktonic diatoms, whereas they are also known to be produced by benthic and freshwater species.     

激光极化技术制备核磁共振探针的方法和应用原理

通过激光增强核自旋极化技术,可以得到很高的非热平衡极化度和长驰豫时间的惰性气体（129Xe和3He),其作为核磁共振探针,具有广泛的生物医学应用价值,该文探讨了激光增强129Xe和3He核自旋极化的磁共振成像和波谱学原理,介绍了激光极化惰性气体的设备和方法,以及极化气体的收集贮存和输入过程,最后对氢核及极化核的磁共振成像,极化气体129Xe和3He的应用进行了比较性总结。     

Taurine Stimulation of Isolated Hamster Brain Na+, K+-ATPase: Activation Kinetics and Chemical Specificity

Epileptic foci are associated with locally reduced taurine (2-aminoethanesulfonic acid) concentration and Na⁺, K⁺-ATPase (EC 3.6.1.3) specific activity. Topically applied and intraperitoneally administered taurine can prevent the development and/or spread of foci in many animal models. Taurine has been implicated as a possible cytosolic modulator of monovalent ion distribution, cytosolic “free” calcium activity, and neuronal excitability. Taurine may act in part by modulating Na⁺, K⁺-ATPase activity of neuronal and glial cells. We characterized the requirements for in vitro modulation of Na⁺, K⁺-ATPase by taurine. Normal whole brain homogenate Na⁺, K⁺-ATPase activity is 5.1 ± 0.4 (4) μmol P_i± h^?1± mg^?1 Lowry protein. Partial purification of the plasma membrane fraction to remove cytosolic proteins and extrinsic proteins and to uncouple cholinergic receptors yields a membrane-bound Na⁺, K⁺-ATPase activity of 204.6 ± 5.8 (4) mol P_i± h^?1± mg^?1 Lowry protein. Taurine activates the Na⁺, K⁺-ATPase at all levels of purification. The concentration dependence of activation follows normal saturation kinetics (K_1/2= 39 mM taurine, activation maximum =+87%). The activation exhibits chemical specificity among the taurine analogues and metabolites: taurine = isethionic acid > hypotaurine > no activation =β-alanine = methionine = choline = leucine. Taurine can act as an endogenous activator/modulator of Na⁺, K⁺-ATPase. Its action is mediated by a membrane-bound protein.     

Detection of Mycobacterium avium ssp. paratuberculosis in cheese, milk powder and milk using IS900 and f57-based qPCR assays

Aims: To develop a quantitative PCR assay for sensitive and specific detection of Mycobacterium avium ssp. paratuberculosis (Map) in a range of dairy products. Methods and Results: TaqMan^® assays were designed to target the IS900 and f57 genetic elements of Map. Both real‐time PCR assays were integrated with the Adiapure^® Map DNA extraction kit and assessed separately for the detection/quantification of Map in spiked milk, Cheddar cheese and milk powder. Assays were validated against Cheddar cheese samples containing known concentrations of Map. The IS900 qPCR assay was significantly more sensitive than the assay based on the f57 primer/probe. At a threshold cycle value of 38, limits of detection (LOD) for the IS900 qPCR assay were 0·6 CFU ml^?1, 2·8 CFU g^?1 and 30 CFU g^?1 for artificially contaminated pasteurized milk, whole milk powder and Cheddar cheese, respectively. The respective LOD’s for the f57 assay were 6·2 CFU ml^?1, 26·7 CFU g^?1 and 316 CFU g^?1. Conclusion: The integrated Adiapure^® extraction – IS900 real time assay described is a sensitive, quantitative method for the detection of Map in dairy products. This is the first study to consider qPCR as a quantitative estimation of Map‐DNA in cheese and whole milk powder. Significance and Impact of the Study: The assay developed allows sensitive detection and quantification of Map DNA in a range of dairy products which is valuable for the screening and surveillance of this potential zoonotic organism.     

A Pseudo-Atomic Model for the Capsid Shell of Bacteriophage Lambda Using Chemical Cross-Linking/Mass Spectrometry and Molecular Modeling

Bacteriophage lambda is one of the most exhaustively studied of the double-stranded DNA viruses. Its assembly pathway is highly conserved among the herpesviruses and many of the bacteriophages, making it an excellent model system. Despite extensive genetic and biophysical characterization of many of the lambda proteins and the assembly pathways in which they are implicated, there is a relative dearth of structural information on many of the most critical proteins involved in lambda assembly and maturation, including that of the lambda major capsid protein. Toward this end, we have utilized a combination of chemical cross-linking/mass spectrometry and computational modeling to construct a pseudo-atomic model of the lambda major capsid protein as a monomer, as well as in the context of the assembled procapsid shell. The approach described here is generalizable and can be used to provide structural models for any biological complex of interest. The procapsid structural model is in good agreement with published biochemical data indicating that procapsid expansion exposes hydrophobic surface area and that this serves to nucleate assembly of capsid decoration protein, gpD. The model further implicates additional molecular interactions that may be critical to the assembly of the capsid shell and for the stabilization of the structure by the gpD decoration protein.     

利用正交设计优化兴安落叶松RAPD-PCR反应体系

以兴安落叶松针叶DNA为模板,对影响落叶松RAPD-PCR 扩增的重要参数进行了优化试验,以期建立兴安落叶松RAPD PCR反应的最佳体系。通过采用正交设计L₁₆(4⁵)对兴安落叶松RAPD-PCR反应的5因素(Taq酶、Mg²⁺、dNTP、模板DNA、引物)在4个水平上进行优化试验,结果表明兴安落叶松最佳的RAPD-PCR的反应体系(20 μL)中含有模板90 ng,0.5 μmol·L^-1的引物,1×反应缓冲液,DNTP各为0.25 mmol·L^-1,1 U的Taq DNA聚合酶,Mg²⁺ 2.5 mmol·L^-1。在此基础上筛选出20个扩增稳定、多态性丰富的RAPD引物,并通过梯度 PCR试验,确定了引物最佳退火温度。     

Chemical diversity and variation of pyrrolizidine alkaloids of the senecionine type: biological need or coincidence?

Laboratory and field tracer experiments with ¹⁴C-labelled senecionine N–oxide (SO) and distant biosynthetic precursors such as [¹⁴C]putrescine revealed that pyrrolizidine alkaloid N-oxides (PAs) in Senecio vernalis Waldstr. & Kit. (Asteraceae) show no significant turnover over periods of up to 29 d. However, PAs are spatially mobile, they are continuously allocated, and labelled PAs are even detectable in leaves and capitula developed weeks after tracer application. Chemical diversification of SO, the common product of PA biosynthesis in roots, was studied in five Senecio species (i.e. S. vernalis Waldstr. & Kit., S. vulgaris L, S. inaequidens DC, two chemotypes of S. jacobaea L. and S. erucifolius L.). Tracer experiments revealed that shoots are capable of transforming [¹⁴ C]SO into the unique species–specific PA patterns. Within a plant, the transformation efficiency of SO can vary quantitatively and qualitatively between shoot organs (i.e. leaves, stems and inflorescences). All transformations proceed position-specifically and stereoselectively. They comprise simple one-step or two-step reactions such as hydroxylations, epoxidations, dehydrogenations, and O-acetylations, as well as the more complex conversion of the retronecine into the otonecine base moiety (e.g. SO into senkirkine). Taking all the evidence together, the qualitative and quantitative composition of the Senecio PA pattern is a dynamic and sensitive equilibrium between a number of interacting processes: (i) constant rate of de-novo synthesis of SO in roots, (ii) continuous long-distance translocation of SO into shoots, (iii) efficiency of SO transformations which may vary between plant organs, (iv) continuous allocation of PAs in the plant, and (v) efficiency and tissue selectivity of vacuolar storage. We suggest that in constitutive plant defence, without significant turnover of its components, such a highly plastic system provides a powerful strategy to successfully defend and possibly escape herbivory. Received: 27 March 1998 / Accepted: 19 May 1998     

Synthesis of Novel Chiral Tridentate Schiff‐Base Ligands and Their Applications in Catalytic Asymmetric Henry Reaction

A series of chiral tridentate Schiff‐bases were prepared and used as ligands in the catalytic asymmetric Henry reaction. Under the optimal conditions, a variety of arylaldehydes were smoothly converted into corresponding adducts with high yields (up to 98%) and excellent enantioselectivities (up to 97% ee). Chirality 26: 780–783, 2014. © 2014 Wiley Periodicals, Inc.