肠球菌在海水中的消亡机制研究进展

肠球菌作为近岸海域粪便污染的指示细菌和条件致病菌,在海水中的生长与消亡对水质监测以及公众健康具有重要影响.本文简述肠球菌在海水中的生理及分布特征,综述肠球菌在关键环境因子和生物因子影响下的消亡规律,并着重介绍肠球菌在细胞和分子水平的消亡机制与消亡动力学模型,同时对肠球菌的研究方向进行展望.通过构建肠球菌浓度预测模型,以...     

Bioluminescence decay kinetics in the reaction of bacterial luciferase with different aldehydes

At 22°C the bioluminescence decay kinetics in the in vitro reaction catalysed by Vibrio harveyi luciferase in the presence of different aldehydes–-nonanal, decanal, tridecanal and tetradecanal did not follow the simple exponential pattern and could be fitted to a two-exponential process. One more principal distinction from the first-order kinetics is the dependence of the parameters on aldehyde concentration. The complex bioluminescence decay kinetics are interpreted in terms of a scheme, where bacterial luciferase is able to perform multiple turnovers using different flavin species to produce light. The initial phase of the bioluminescent reaction appears to proceed mainly with fully reduced flavin as the substrate while the final one results from the involvement of flavin semiquinone in the catalytic cycle.     

Chlorine decay and bacterial inactivation kinetics in drinking water in the tropics

The decay of free chlorine (Cl₂) and combined chlorine (mostly monochloramine: NH₂Cl) and the inactivation of bacteria was examined in Dar es Salaam, Tanzania. Batch experiments, pilot-scale pipe experiments and full-scale pipe experiments were carried out to establish the kinetics for both decay and inactivation, and to compare the two disinfectants for use under tropical conditions. The decay of both disinfectants closely followed first order kinetics, with respect to the concentration of both disinfectant and disinfectant-consuming substances. Bacterial densities exhibited a kinetic pattern consisting of first order inactivation with respect to the density of the bacteria and the concentration of the disinfectant, and first order growth with respect to the bacterial density. The disinfection kinetic model takes the decaying concentration of the disinfectant into account. The decay rate constant for free chlorine was 114 lg^-1h^-1, while the decay rate constant for combined chlorine was 1.84 lg^-1h^-1 (1.6% of the decay rate for free chlorine). The average concentration of disinfectant consuming substances in the water phase was 2.6 mg Cl₂/l for free chlorine and 5.6 mg NH₂Cl/l for combined chlorine. The decay rate constant and the concentration of disinfectant consuming substances when water was pumped through pipes, depended on whether or not chlorination was continuous. Combined chlorine especially could clean the pipes of disinfectant consuming substances. The inactivation rate constant , was estimated at 3.06×10⁴ lg^-1h^-1. Based on the inactivation rate constant, and a growth rate constant determined in a previous study, the critical concentration of free chlorine was found to be 0.08 mg Cl₂/l. The critical concentration is a value below which growth rates dominate over inactivation.The authors are with the Technical University of Denmark, IMT, CDC, Build. 208, DK-2800 Lyngby, Denmark     

Fluorescence decay kinetics in phycobilisomes isolated from the bluegreen alga Synechococcus 6301

The picosecond fluorescence and energy-transfer kinetics of isolated phycobilisomes from Synechococcus 6301 were studied under low intensity excitation. Different combinations of excitation and emission wavelengths were used in order to monitor selectively the fluorescence of the pigments phycocyanin and allophycocyanin. The relatively long overall energy-transfer time of 120 ps from the phycocyanin rods to the allophycocyanin-core is rationalized in terms of the special structure of the rods being built up of several phycocyanin hexamers in this alga species. The fluorescence lifetime of the terminal chromophores in the core was determined to be 1.8–1.9 ns depending on the excitation wavelength. A fast decay component of 20 ± 10 ps which is most prominent at short emission wavelengths is assigned to arise mainly from energy transfer within the C-phycocyanin-units from ‘sensitizing’ to ‘fluorescing’ chromophores.     

A second generation global analysis program for the recovery of complex inhomogeneous fluorescence decay kinetics

A flourescence spectroscopy global data analysis environment is described. Within this analysis environment multidimensional fluoroscence decay data (time and frequency domains) can be analyzed in terms of a wide variety of photophysical models. A generalized compartmental analysis structure is utilized, where one can specify the functions used to link the various compartments together. All fitting parameters may be characterized by either discrete or distributed values. Applications of these new analysis programs to the examination of phase transitions in lipid/membrane systems are described.     

DNA reassociation kinetics of closely related species

The kinetics of reassociation of the DNA of three groups of closely related organisms were examined. The laboratory mouse was compared to an Asiatic mouse, whose chromosome number is the same but whose chromosome organization is different. Chinese hamster (2N=22) was compared to Syrian hamster (2N=44), and Haplopappus gracilis (2N=4) was compared to H. ravenit (2N=8). It was found that the most highly repeated DNA fractions of the three comparative sets of organisms differ in their reaction rates. However, these fractions of the related hamsters, haplopappi, and probably the mice, do not differ in the amount of DNA composing the fractions. The intermediately fast reassociating DNA and the unique DNA do not differ between members of related pairs of organisms. The implication of these results is that a short sequence of DNA may be highly copied in one organism, while in a related organism a longer DNA sequence is repeated a fewer number of times, and the total amount of repeated DNA may be the same in both related organisms.     

The fluorescence decay kinetics of in vivo chlorophyll measured using low intensity excitation

We report fluorescence lifetimes for in vivo chlorophyll a using a time-correlated single-photon counting technique with tunable dye laser excitation. The fluorescence decay of dark-adapted chlorella is almost exponential with a lifetime of 490 ps, which is independent of excitation from 570 nm to 640 nm.Chloroplasts show a two-component decay of 410 ps and approximately 1.4 ns, the proportion of long component depending upon the fluorescence state of the chloroplasts. The fluorescence lifetime of Photosystem I was determined to be 110 ps from measurements on fragments enriched in Photosystem I prepared from chloroplasts with digitonin.     

ATP-dependent translocation of proteins along single-stranded DNA: models and methods of analysis of pre-steady state kinetics

Processive DNA helicases are able to translocate along single-stranded DNA (ssDNA) with biased directionality in a nucleoside triphosphate-dependent reaction, although translocation is not generally sufficient for helicase activity. An understanding of the mechanism of protein translocation along ssDNA requires pre-steady state transient kinetic experiments. Although ensemble experimental approaches have been developed recently for the study of translocation of proteins along DNA, quantitative analysis of the complete time-courses from these experiments, which is needed to obtain quantitative estimates of translocation kinetic parameters (rate constants, processivity, step sizes and ATP coupling) has been lacking. We discuss three ensemble transient kinetic experiments that can be used to study protein translocation along ssDNA, along with the advantages and limitations of each approach. We further describe methods to analyze the complete kinetic time-courses obtained from such experiments performed with a series of ssDNA lengths under "single-round" conditions (i.e. in the absence of re-binding of dissociated protein to DNA). These analysis methods utilize a sequential "n-step" model for protein translocation along ssDNA and enable quantitative determinations of the rate constant, processivity and step size for translocation through global non-linear least-squares fitting of the full time-courses.     

Natural Attenuation Rate Clarifications: The True Picture is in the Details

The term “Natural Attenuation” (NA) has been defined as naturally occurring processes in soil and groundwater environments that act without human intervention to reduce the mass, toxicity, mobility, volume, or concentration of contaminants in those media. Monitored natural attenuation (MNA) protocols generally involve the collection of biogeochemical data from groundwater monitoring wells at sites. The data are correlated in time and space with the various chemicals of concern (COC's) to establish predominant biodegradation mechanisms. Modelers using the first-order decay expression typically use the rate coefficient as a calibration parameter and adjust it until the transport model results match field data. With this approach, uncertainties with a number of parameters (e.g., dispersion, sorption, biodegradation, etc.) are lumped together in a single calibration parameter. The problems associated with the lumped parameter approach are illustrated using two commonly used models, BIOSCREEN and Buscheck/Alcantar Analytical Solution, in a variety of practical examples. The natural attenuation decay rate estimated using the lumped parameter approach is distinguished from a biodegradation rate established by isolating processes and examining biodegradation lines of evidence. The half-life determined from empirical data using the lumped parameter approach is often mistakenly interchanged with a biodegradation half-life when it is an all-encompassing half-life based on the interaction of numerous processes. Isolation of the processes, as they are represented in the governing transport equation, and a rationale approach at parameter estimation to avoid the potential pitfalls of the all-inclusive “attenuation rate,” are provided. In closing, it is imperative to implement the following steps to dissern lumped process degradation rates from biodegradation half-lives: (a) be sure the rate/half-life processes are clarified as to what they encompass, (b) establish exactly how the rate/half-life was determined, (c) make certain other processes, such as dispersion, were estimated correctly, and (d) if the half-life is presented as a first-order biodegradation rate, examine the available lines of evidence to substantiate it.     

DNA extraction from plants: The use of pectinase

Several earlier protocols for extracting plant DNA or RNA do not work well for a variety of plants because contaminating substances coprecipitate with the nucleic acids and, thus, are present even at the last DNA-hydration step. While DNA extraction protocols have been published in which pectinase is employed to break down these contaminating substances, here we present an alternative modified pectinase protocol that potentially uses fewer steps and avoids the use of ethylene glycol monoethyl ether and phenol. DNA analyses results are described for 6 plant species demonstrating that the method works across distantly related plant taxa.     

The functional half-life of an mRNA depends on the ribosome spacing in an early coding region

Bacterial mRNAs are translated by closely spaced ribosomes and degraded from the 5′-end, with half-lives of around 2 min at 37 °C in most cases. Ribosome-free or “naked” mRNA is known to be readily degraded, but the initial event that inactivates the mRNA functionally has not been fully described. Here, we characterize a determinant of the functional stability of an mRNA, which is located in the early coding region. Using literature values for the mRNA half-lives of variant lacZ mRNAs in Escherichia coli, we modeled how the ribosome spacing is affected by the translation rate of the individual codons. When comparing the ribosome spacing at various segments of the mRNA to its functional half-life, we found a clear correlation between the functional mRNA half-life and the ribosome spacing in the mRNA region approximately between codon 20 and codon 45. From this finding, we predicted that inserts of slowly translated codons before codon 20 or after codon 45 should shorten or prolong, respectively, the functional mRNA half-life by altering the ribosome density in the important region. These predictions were tested on eight new lacZ variants, and their experimentally determined mRNA half-lives all supported the model. We thus suggest that translation-rate-mediated differences in the spacing between ribosomes in this early coding region is a parameter that determines the mRNAs functional half-life. We present a model that is in accordance with many earlier observations and that allows a prediction of the functional half-life of a given mRNA sequence.     

Stereoselective degradation kinetics of tebuconazole in rabbits

Tebuconazole[(RS)-1-p-chlorophenyl-4,4-dimethyl-3-(1H-1,2,4-triazol-1-ylmethyl)pentan-3-ol] is a potent triazole fungicide and consists of a pair of enantiomers. The enantioselective degradation kinetics of tebuconazole was investigated in rabbits by intravenous (iv) injection. The concentrations of (-)-(R)-tebuconazole and (+)-(S)-tebuconazole in plasma and tissues were determined by HPLC with a cellulose tris(3,5-dimethylphenylcarbamate)-based chiral stationary phase. Enantioselective analysis methods for this fungicide in plasma and tissues were developed and validated. Good linearities were obtained over the concentration range of 0.25-25 mg/l for both enantiomers. The degradation followed pseudo-first-order kinetics and the degradation of the (+)-(S)-tebuconazole was much faster than that of the (-)-(R)-tebuconazole in plasma after administration of racemic tebuconazole. This study also indicated that environmental assessment of enantiomeric degradation may be needed to fully evaluate risks of tebuconazole use.     

The thermal history of human fossils and the likelihood of successful DNA amplification

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.     

中国东北第四纪晚期哺乳动物化石样品的古DNA损伤分析

二代测序技术的进步推动了古DNA研究的发展,古DNA研究在人类起源、动物演化等领域已经做出突出贡献。如何针对特定地点的古DNA样品特征,有效提取挖掘其中蕴含的古生物遗传信息,是发挥古代生物样品在诸多研究领域重要作用的前提。本研究将DNA损伤的两个主要指标(末端碱基替换率、平均片段长度)与样品的埋藏时间、所属地质时期、样品材料类型和建库方法相联系,分析不同因素对古DNA损伤的影响。结果表明:中国东北古脊椎动物样品中的古DNA分子的末端碱基替换率与埋藏点的含水量、样品埋藏时间呈正相关;不同地质时期的样品之间古DNA末端碱基替换率有显著差异;不同样品材料类型对于古DNA的末端碱基替换率未见明显影响;样品古DNA的平均片段长度与以上所研究的因素均无明显关系。研究结果为探明中国东北古脊椎动物样品的古DNA特征提供了分子依据,为有效选取不同地区的古脊椎动物样品及样品发掘后的合理保存提供了借鉴和参考。     

Fluorescence decay kinetics of mutants of corn deficient in photosystem I and photosystem II

The fast fluorescence decay kinetics of two photosynthetic mutants of corn (Zea mays) have been compared with those of normal corn. The fluorescence of normal corn can be resolved into three exponential decay components of lifetime 900–1500 ps (slow), 300–500 ps (middle) and 50–120 ps (fast), the yields of which are affected by light intensity and Mg²⁺ levels. The Photosystem II-(PS II)-defective mutant hcf-3 has similar decay lifetimes (approx. 1200, 450 and 100 ps) but is not affected by light intensity, reflecting the absence of PS II charge recombination. However, yields do respond to Mg²⁺ in a fashion typical of normal corn, which may be correlated with the presence of normal levels of light-harvesting chlorophyll a + b complex (LHCP). The PS I mutant hcf-50 also shows three-component decay kinetics. In conjunction with the results on the LHCP-deficient mutant of barley presented in a recent paper (Karukstis, K.K. and Sauer, K. (1984) Biochim. Biophys. Acta 766, 148–155), these data suggest that the slow component of normal chloroplasts is kinetically controlled by the decay processes of the LHCP and that the energy comes from one of two sources: (a) charge recombination in the reaction centre or (b) energy transferred within or between LHCP units only. The fast component appears to originate from both PS I and PS II. The complex response of the middle component to cations and light intensity, and its presence in all of the mutants, suggests that it also may have multiple origins.     

The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation

DNA polymerases maintain genomic integrity by copying DNA with high fidelity, part of which relies on the polymerase fingers opening-closing transition, a series of conformational changes during the DNA synthesis reaction cycle. Fingers opening and closing has been challenging to study, mainly due to the need to synchronise molecular ensembles. We previously studied fingers opening-closing on single polymerase-DNA complexes using single-molecule FRET; however, our work was limited to pre-chemistry reaction steps. Here, we advance our analysis to extensible substrates, and observe DNA polymerase (Pol) conformational changes across the entire DNA polymerisation reaction in real-time, gaining direct access to an elusive post-chemistry step rate-limiting for DNA synthesis. Our results showed that Pol adopts the fingers-closed conformation during polymerisation, and that the post-chemistry rate-limiting step occurs in the fingers-closed conformation. We found that fingers-opening in the Pol-DNA binary complex in the absence of polymerisation is slow (～5.3 s^?1), and comparable to the rate of fingers-opening after polymerisation (3.4 s^?1); this indicates that the fingers-opening step itself could be largely responsible for the slow post-chemistry step, with the residual rate potentially accounted for by pyrophosphase release. We also observed that DNA chain-termination of the 3′ end of the primer increases substantially the rate of fingers-opening in the Pol-DNA binary complex (5.3 → 29 s^?1), demonstrating that the 3′-OH residue is important for the kinetics of fingers conformational changes. Our observations offer mechanistic insight and tools to offer mechanistic insight for all nucleic acid polymerases.