麦田土壤解无机磷细菌的分离、筛选及其解磷效果

通过选择性解磷细菌培养基从麦田土壤中分离、纯化解无机磷细菌,并用钼蓝比色法定量研究磷细菌的解磷效果。结果表明通过选择性平板分离,发现麦田土壤中有15个菌株有解无机磷的作用,根据菌株直径和其解磷圈的大小,确定解磷能力较强的菌株9个;经过进一步分离纯化,选出单一无杂菌的菌株7个。解磷菌株经摇瓶培养后,比色测定培养液中磷的含量,通过比较发现其中5个菌株的解磷效果要显著优于其它两个菌株（P=0.05）。     

Structural and functional alterations of myoglobin by glucose-protein interactions

Quorum sensing (QS) is a process of bacterial communication and cooperation mediated by the release of jointly exploited signals and “public goods” into the environment. There are conflicting reports on the behavior of mutants deficient in the release of these materials. Namely, mutants that appear perfectly viable and capable of outgrowing wild type cells in a closed model system such as a culture flask, may not be viable or invasive on open surfaces such as agar plates. Here we show via agent-based computational simulations that this apparent discrepancy is due to the difference between open and closed systems. We suggest that the experimental difference is due to the fact that wild type cells can easily saturate a well-mixed culture flask with signals and public goods so QS will be not necessary after a certain time point. As a consequence, QS-deficient mutants can continue to grow even after the wild type population has vanished. This phenomenon is not likely to occur in open environments including open surfaces and agar plate models. In other words, even if QS is required for survival, QS deficient mutants may grow faster initially in short term laboratory experiments or computer simulations, while only WT cells appear stable over longer time scales, especially when adaptation to changing environments is important.     

Comparison of two methods for rapid detection of cytomegalovirus viraemia in cell culture

Two methods for rapid CMV viraemia detection in cell culture with immunoperoxidase staining performed 40 h post-inoculation were compared, on 230 blood samples: (1) a 24-well plate centrifugation assay and (2) a 25-cm²-culture flask technique, without centrifugation. The flask technique was significantly more sensitive than the 24-well plate technique. Moreover, the flask assay was more cost-effective and offered other advantages such as easier sterile handling and less damage of the cell monolayer.     

DESIGN: computerized optimization of experimental design for estimating Kd and Bmax in ligand binding experiments. I. Homologous and heterologous binding to one or two classes of sites

We have developed a versatile computer program for optimization of ligand binding experiments (e.g., radioreceptor assay system for hormones, drugs, etc.). This optimization algorithm is based on an overall measure of precision of the parameter estimates (D-optimality). The program DESIGN uses an exact mathematical model of the equilibrium ligand binding system with up to two ligands binding to any number of classes of binding sites. The program produces a minimal list of the optimal ligand concentrations for use in the binding experiment. This potentially reduces the time and cost necessary to perform a binding experiment. The program allows comparison of any proposed experimental design with the D-optimal design or with assay protocols in current use. The level of nonspecific binding is regarded as an unknown parameter of the system, along with the affinity constant (Kd) and binding capacity (Bmax). Selected parameters can be fixed at constant values and thereby excluded from the optimization algorithm. Emphasis may be placed on improving the precision of a single parameter or on improving the precision of all the parameters simultaneously. We present optimal designs for several of the more commonly used assay protocols (saturation binding with a single labeled ligand, competition or displacement curve, one or two classes of binding sites), and evaluate the robustness of these designs to changes in parameter values of the underlying models. We also derive the theoretical D-optimal design for the saturation binding experiment with a homogeneous receptor class.     

Biosynthesis and metabolic engineering of 1-hydroxyphenazine in Pseudomonas chlororaphis H18

The split GFP assay is a well-known technology for activity-independent screening of target proteins. A superfolder GFP is split into two non-fluorescent parts, GFP11 which is fused to the target protein and GFP1-10. In the presence of both, GFP1-10 and the GFP11-tag are self-assembled and a functional chromophore is formed. However, it relies on the availability and quality of GFP1-10 detector protein to develop fluorescence by assembly with the GFP11-tag connected to the target protein. GFP1-10 detector protein is often produced in small scale shake flask cultivation and purified from inclusion bodies. The production of GFP1-10 in inclusion bodies and purification was comprehensively studied based on Escherichia coli as host. Cultivation in complex and defined medium as well as different feed strategies were tested in laboratory-scale bioreactor cultivation and a standardized process was developed providing high quantity of GFP1-10 detector protein with suitable quality. Split GFP assay was standardized to obtain robust and reliable assay results from cutinase secretion strains of Corynebacterium glutamicum with Bacillus subtilis Sec signal peptides NprE and Pel. Influencing factors from environmental conditions, such as pH and temperature were thoroughly investigated. GFP1-10 detector protein production could be successfully scaled from shake flask to laboratory scale bioreactor. A single run yielded sufficient material for up to 385 96-well plate screening runs. The application study with cutinase secretory strains showed very high correlation between measured cutinase activity to split GFP fluorescence signal proofing applicability for larger screening studies.     

Azoreductase activity of anaerobic bacteria isolated from human intestinal microflora

A plate assay was developed for the detection of anaerobic bacteria that produce azoreductases. With this plate assay, 10 strains of anaerobic bacteria capable of reducing azo dyes were isolated from human feces and identified as Eubacterium hadrum (2 strains), Eubacterium spp. (2 species), Clostridium clostridiiforme, a Butyrivibrio sp., a Bacteroides sp., Clostridium paraputrificum, Clostridium nexile, and a Clostridium sp. The average rate of reduction of Direct Blue 15 dye (a dimethoxybenzidine-based dye) in these strains ranged from 16 to 135 nmol of dye per min per mg of protein. The enzymes were inactivated by oxygen. In seven isolates, a flavin compound (riboflavin, flavin adenine dinucleotide, or flavin mononucleotide) was required for azoreductase activity. In the other three isolates and in Clostridium perfringens, no added flavin was required for activity. Nondenaturing polyacrylamide gel electrophoresis showed that each bacterium expressed only one azoreductase isozyme. At least three types of azoreductase enzyme were produced by the different isolates. All of the azoreductases were produced constitutively and released extracellularly.     

Azoreductase activity of anaerobic bacteria isolated from human intestinal microflora.

A plate assay was developed for the detection of anaerobic bacteria that produce azoreductases. With this plate assay, 10 strains of anaerobic bacteria capable of reducing azo dyes were isolated from human feces and identified as Eubacterium hadrum (2 strains), Eubacterium spp. (2 species), Clostridium clostridiiforme, a Butyrivibrio sp., a Bacteroides sp., Clostridium paraputrificum, Clostridium nexile, and a Clostridium sp. The average rate of reduction of Direct Blue 15 dye (a dimethoxybenzidine-based dye) in these strains ranged from 16 to 135 nmol of dye per min per mg of protein. The enzymes were inactivated by oxygen. In seven isolates, a flavin compound (riboflavin, flavin adenine dinucleotide, or flavin mononucleotide) was required for azoreductase activity. In the other three isolates and in Clostridium perfringens, no added flavin was required for activity. Nondenaturing polyacrylamide gel electrophoresis showed that each bacterium expressed only one azoreductase isozyme. At least three types of azoreductase enzyme were produced by the different isolates. All of the azoreductases were produced constitutively and released extracellularly.     

Large-Plate Method for the Assay of Neomycin in Serum

A large-plate method employing radial diffusion from small paper discs for assaying serum levels of neomycin is described. More than 120 discs placed on a loading plate and loaded with 20 muliters of sample could all be brought into contact with the agar plate at one time. The requirement for elaborate statistical design to compensate for time-dependent bias was thus eliminated. The dose-response curve was linear for a range of at least 0.5 to 2.5 mug/ml. The experimental limits for the actual zone width (distance from the edge of the paper disc to the outer edge of the inhibition zone) for 120 repetitions of the assay of neomycin in one and the same serum, carried out simultaneously on one large plate, were about +/- 6% (95% confidence interval). The 95% confidence interval for the distribution of difference between duplicate zones obtained for the assay of neomycin in 34 different sera, also carried out on one plate, was about +/- 10%. The dose-response lines for a standard and for three unknown sera, when carried out together on one plate, were parallel within the variability (+/- SD one) of the zone width. The large-plate method is considered to be more efficient than the use of the smaller petri dishes. The method is suitable for the assay of penicillin in serum and can most probably be used for the assay of a wide variety of substances for which radial diffusion from paper discs into agar is feasible.     

Two-Level factorial screening of new plasmid/strain combinations for prodution of recombinant-DNA products

This article treats the basic problem of selection of experimental conditions for microbiological experiments for evaluation of newly isolated bacterial strains, mutants, or plasmid/strain combinations. For this purpose shake flask experiments in a 2(10-4)confounded factorial design at resolution IV with four blocks of 16 flasks were used. The design was used for testing of two new strain/plasmid combinations (E. coli MT 102/403-SD2 and W 3110/403-SD2) i.e., both strains with the same plasmid 403-SD2. Both strains were integrated in the design, so both strains were tested with nine factors (temperature, aeration, glucose, initial pH, pH regulation, reduced aeration, chloramphenicol, acetate, and glycerol). With both strains the interaction between initial pH and reduced aeration had a significant influence on the yield of the recombinant-DNA product nuclease. There was more than a factor of 10 between lowest and highest yield of product. In this interactive system the strains reacted differently. MT 102/403-SD2 had highest yields at high initial pH (8.4) and no reduction in aeration, whereas W 3110/403-SD2 had highest yields of nuclease at low initial pH (7.4) and reduced aeration (rubber stopper inserted after cultivation for 12 h). These data (and previous work) clearly demonstrate that it is impossible to suggest a simple set of experimental conditions for testing of new plasmid/strain combinations. It is clear that the exclusive application of a standardized growth technique e.g., LB-medium at 37 degrees C at an unspecified and uncontrolled aeration level, may lead to wrong conclusions on properties and potentials of now plasmid/strain combinations and may lead to rejection of useful strains or plasmids.     

A practical approach to optimization and validation of a HPLC assay for analysis of polyribosyl-ribitol phosphate in complex combination vaccines

The use of multi-factor statistical experimental design methodology minimized the vaccine material and laboratory resources required for optimization and validation of an HPLC assay for quantitation of depolymerized and total PRP. Components of the assay selected for optimization were adjuvant dissolution, ultracentrifuge conditions including ultracentrifuge model, sample diluent, mobile phase and column oven temperature. Previous experience has shown these components of the assay to be most troublesome and therefore required optimization prior to validation. Specificity, linearity, precision, accuracy and ruggedness were confirmed through a validation of the optimized assay. The validation also established the assay to be stability indicating, by showing that changes to the integrity of the PRP-OMPC conjugate could be detected.     

Validation and characterization of uninhibited enzyme kinetics performed in multiwell plates

Several systematic errors may occur during the analysis of uninhibited enzyme kinetic data using commercially available multiwell plate reader software. A MATLAB program is developed to remove these systematic errors from the data analysis process for a single substrate-enzyme system conforming to Michaelis-Menten kinetics. Three experimental designs that may be used to validate a new enzyme preparation or assay methodology and to characterize an enzyme-substrate system, while capitalizing on the ability of multiwell plate readers to perform multiple reactions simultaneously, are also proposed. These experimental designs are used to (i) test for enzyme inactivation and the quality of data obtained from an enzyme assay using Selwyn's test, (ii) calculate the limit of detection of the enzyme assay, and (iii) calculate Km and Vm values. If replicates that reflect the overall error in performing a measurement are used, the latter two experiments may be performed with internal estimation of the error structure. The need to correct for the systematic errors discussed and the utility of the proposed experimental designs were confirmed by numerical simulation. The proposed experiments were conducted using recombinant inducible nitric oxide synthase preparations and the oxyhemoglobin assay.     

D-泛酸高产菌株C21的筛选及鉴定

从10个植物根际土样中分离出315株根际微生物,然后采用泛酸测定平板初筛和摇瓶复筛的方法,从中筛选到7株D-泛酸高产菌株,其中从菜豆根际土壤分离到的菌株C21的D-泛酸产量最高,达到24.1mg/L。最后通过形态和生理生化特性以及16SrDNA鉴定,确定菌株C21为恶臭假单胞菌(Pseudomonas putida)。     

Evaluation of the Accuracy and Precision of Enumerating Aerobic Heterotrophs in Water Samples by the Spread Plate Method

Factors associated with accuracy and precision in the enumeration of aquatic aerobic heterotrophs by the spread plate method were evaluated by using a nested analysis of variance experimental design. Variances associated with individual components of the spread plate procedure were isolated, and optimal replications of each step were allocated. A practical scheme for optimal allocation of resources is proposed, consisting of four subsamples and two plates per subsample and yielding a total variance decrease of 70% from a single-subsample, 10-plate series. Data transformation was, in general, unnecessary for intraexperiment or intrasample statistical analysis, whereas interexperiment or intersample comparisons may require transformation of data. Rapid changes in the numbers of organisms in stored water samples were observed that were not reproducible and did not follow detectable trends, with increases or decreases in counts occurring in samples regardless of whether they were stored at room temperature or refrigerated, or stored in plastic or glass containers. Rapid sample handling is strongly recommended to minimize variations in the microbial populations of samples for aquatic environments.     

Optimisation of the microbiological mutagenicity assay based on genetically modified Vibrio harveyi strains

Recently, we have developed a novel assay designed for detection of mutagenic pollution of the marine environment. This assay is based on the use of a series of genetically modified strains (named BB7, BB7M, BB7X and BB7XM) of a marine bacterium Vibrio harveyi. Sensitivity of the V. harveyi mutagenicity assay was found to be similar to, or even somewhat higher than, that of the commonly used Ames test. Subsequent studies indicated that this assay may be useful in assessment of mutagenic contamination of the marine environment. Nevertheless, we assumed that improvement of this assay is still possible, and thus we aimed to optimise its procedures. Here we present our research on the optimisation of the V. harveyi mutagenicity assay, which indicated that different tester strains used in this assay give the best results depending upon the experimental conditions employed. Incubation of bacteria in a buffer, rather than in a nutrient broth, containing a mutagen, increased the efficiency of the assay with BB7 and BB7M strains, but had a deleterious effect in the case of BB7X and BB7XM. The latter couple of strains revealed higher mutagenicity in the plate assay, as compared to the liquid medium assay. However, the opposite effect was observed for BB7 and BB7M. Low-dose (1 J m(-2)) UV irradiation, as well as 30 min incubation in 0.1 M CaCl2, had no significant effect on the efficiency of the assay when using BB7 and BB7M, whereas the number of mutagen-induced mutants of BB7X and BB7XM strains increased about two times under these conditions. Our previous experiments indicated that various tester strains revealed different sensitivity to particular mutagens. Thus, a series of strains should be used in the assay. Results presented in this report show that different conditions should be used for two pairs of the tester strains: BB7 and BB7M, and BB7X and BB7XM.     

The scope for improving the design of laboratory animal experiments.

The factors which need to be taken into account in designing a 'good' experiment are reviewed. Such an experiment should be unbiased, have high precision, a wide range of applicability, it should be simple, and there should be a means of quantifying uncertainty (Cox 1958). The relative precision due to the use of randomized block designs was found to range from 96% to 543% in 5 experiments involving 30 variables. However, a survey of 78 papers published in two toxicology journals showed that such designs were hardly used. Similarly, designs in which more than one factor was varied simultaneously ('factorial designs') were only used in 9% of studies, though interactions between variables such as dose and strain of animal may be common, so that single factor experiments could be misleading. The consequences of increased within-group variability due to infection and genetic segregation were quantified using data published by G?rtner (1990). Both substantially reduced precision, but toxicologists continue to use non-isogenic laboratory animals, leading to experiments with a lower level of precision than is necessary. It is concluded that there is scope for improving the design of animal experiments, which could lead to a reduction in animal use. People using animals should be required to take formal training courses which include sessions on experimental design in order to minimize animal use and to increase experimental efficiency.     

The influence of biosurfactants released by S. mitis BMS on the adhesion of pioneer strains and cariogenic bacteria

The influence of Streptococcus mitis BMS biosurfactants on the adhesion of eight pioneer and four cariogenic oral bacterial strains was, for a first screening, examined in a microtiter plate assay. The adhesion to pellicle-coated wells of three cariogenic strains was inhibited >70% by the biosurfactants, while only one pioneer strain showed >70% reduction. The reduction for the other strains did not exceed 50%. Subsequently, adhesion of Streptococcus mutans ATCC 25175 and Streptococcus sobrinus HG 1025, both cariogenic strains, and Actinomyces naeslundii T14V-J1 and Streptococcus oralis J22, two pioneer strains, to biosurfactants-coated enamel with and without a salivary pellicle was studied in a parallel plate flow chamber. A biosurfactants coating to enamel with or without a pellicle caused a reduction in the number of adhering cariogenic organisms, although no such reduction was observed for the pioneer strains. Consequently, it is concluded that S. mitis BMS biosurfactants may play a protective role against adhesion of cariogenic bacteria.     

Preparation of Mutants Resistant to Catabolite Repression of Trichoderma reesei

The development of agar plate screening techniques has allowed the isolation of mutants of Trichoderma reesei capable of synthesizing cellulase under the conditions of a high concentration of glucose. Mutants resistant to catabolite repression by glycerol or glucose were isolated on Walseth’s cellulose (WC) agar plates containing 5% glycerol or 5% glucose, respectively. Mutants resistant to catabolite repression by glycerol were not derepressed enough for the production of cellulase on WC agar plates containing 5% glucose or in flask cultures with a mixture of 1% Avicel and 3% glucose. On the contrary, two mutant strains resistant to catabolite repression by glucose (KDD-10 and DGD-16) produced large clearing zones on WC agar plates containing 5% glucose. Both strains could begin to produce CMCase even in the presence of residual glucose and finally produced 1.5 times the CMCase activity, in flask cultures on 1% Avicel and 3% glucose, than that with 1% Avicel alone. These results suggest that KDD-10 and DGD-16 are comparatively derepressed by glucose for cellulase production.     

The ATP dependence of the incision and resynthesis steps of excision repair.

Escherichia coli made permeable by treatment with toluene can perform a mode of DNA synthesis that is stimulated by ultraviolet radiation and closely resembles the resynthesis step of excision repair. If ultraviolet-irradiated toulene-treated cells are incubated in an assay mixture with ATP but without the four deoxyribonucleoside triphosphates (dNTPs) or NAD, accumulations of single-strand breaks in the DNA are detected by alkaline sucrose gradient analysis. A second incubation with the dNTP'S and NAD but without ATP produces nonconservative DNA synthesis in strains with normal levels of DNA polymerase I. However, in PolA strains, ATP must be present during the second incubation in order to produce measurable amounts of ultraviolet-stimulated DNA synthesis. These results suggest that in strains deficient in DNA polymerase I there may be two ATP-dependent steps in this repair pathway, one required for incision and one associated with resynthesis.     

Design and statistical methods in studies using animal models of development

Experiments involving neonates should follow the same basic principles as most other experiments. They should be unbiased, be powerful, have a good range of applicability, not be excessively complex, and be statistically analyzable to show the range of uncertainty in the conclusions. However, investigation of growth and development in neonatal multiparous animals poses special problems associated with the choice of "experimental unit" and differences between litters: the "litter effect." Two main types of experiments are described, with recommendations regarding their design and statistical analysis: First, the "between litter design" is used when females or whole litters are assigned to a treatment group. In this case the litter, rather than the individuals within a litter, is the experimental unit and should be the unit for the statistical analysis. Measurements made on individual neonatal animals need to be combined within each litter. Counting each neonate as a separate observation may lead to incorrect conclusions. The number of observations for each outcome ("n") is based on the number of treated females or whole litters. Where litter sizes vary, it may be necessary to use a weighted statistical analysis because means based on more observations are more reliable than those based on a few observations. Second, the more powerful "within-litter design" is used when neonates can be individually assigned to treatment groups so that individuals within a litter can have different treatments. In this case, the individual neonate is the experimental unit, and "n" is based on the number of individual pups, not on the number of whole litters. However, variation in litter size means that it may be difficult to perform balanced experiments with equal numbers of animals in each treatment group within each litter. This increases the complexity of the statistical analysis. A numerical example using a general linear model analysis of variance is provided in the Appendix. The use of isogenic strains should be considered in neonatal research. These strains are like immortal clones of genetically identical individuals (i.e., they are uniform, stable, and repeatable), and their use should result in more powerful experiments. Inbred females mated to males of a different inbred strain will produce F1 hybrid offspring that will be uniform, vigorous, and genetically identical. Different strains may develop at different rates and respond differently to experimental treatments.