高效液相色谱法测芽孢杆菌的DNA G+Cmol%

以往细菌分类鉴定都是以表形特征为基础,近年来开始对细菌的遗传物质进行研究,把细菌分类从人为的分类体系向自然的分类体系推进了一步.最先采用的方法是DNA G+Cmol%的测定.每种细菌都有其特定的G+Cmol%,而且其数值比较稳定,不受菌龄影响,也不因外界条件的改变而改变.据经验,一个种内各菌株间的G+Cmol% 不应相差5%以上,同一属不同种G+Cmol%不应相差15%以上. G+Cmol%用于芽孢杆菌分类,揭示了芽孢杆菌遗传上的异源性,结合其他方法,芽孢杆菌分类已由原来的一个属,发展到现在的七个属.本实验利用从神农架分离的芽孢杆菌,用高效液相色谱法测定了一些种的G+Cmol%,结果如下.     

A novel method to calculate the G+C content of genomic DNA sequences.

The base composition of a DNA fragment or genome is usually measured by the proportion of A+T or G+C in the sequence. The G+C content along genomic sequences is usually calculated using an overlapping or non-overlapping sliding window method. The result and accuracy of such an approach depends on the size of the window and the moving distance adopted. In this paper, a novel windowless technique to calculate the G+C content of genomic sequences is proposed. By this method, the G+C content can be calculated at different "resolution". In an extreme case, the G+C content may be computed at a specific point, rather than in a window of finite size. This is particularly useful to analyze the fine variation of base composition along genomic sequences. As the first example, the variation of G+C content along each of 16 yeast chromosomes is analyzed. The G+C-rich regions with length larger than 5 kb sequences are detected and listed in details. It is found that each chromosome consists of several G+C-rich and G+C-poor regions alternatively, i.e., a mosaic structure. Another example is to analyze the G+C content for each of the two chromosomes of the Vibrio cholerae genome. Based on the variations of the G+C content in each chromosome, it is shown that some fragments in the Vibrio cholerae genome may have been transferred from other species. Especially, the position and size of the large integron island on the smaller chromosome was precisely predicted. This method would be a useful tool for analyzing genomic sequences.     

Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content

The relationship between the overall G+C content of the genome (GC) and the GC content at the third codon positions (GC3) of genes, which we refer to as a GC3-plot, was examined using 15 currently available complete genome sequences. A remarkably linear relationship was found between these two quantities, confirming previous observations of a strong positive correlation in the GC3-plot. In order to conduct a more detailed analysis of the GC3-plot, we examined the GC3 content by separating orthologous codons into three categories: synonymously different codons (namely identical amino acids, IA), different amino acids (DA), and identical codons (IC), for a pairwise comparison of two closely related species. When we took pairwise species comparisons between Mycoplasma genitalium (Mg) and Mycoplasma pneumoniae (Mp) and between Mycobacterium tuberculosis (Mt) and Mycobacterium leprae (Ml) as examples, we found that for Mp and Ml, the GC3 for IA deviated the most from the linear expectation in the GC3-plot, whereas for Mg and Mt the deviation was minimal. These findings suggest that the major changes of GC content took place in Mp and Ml, but not in Mg and Mt. This analysis also enables us to predict the future direction of the evolutionary changes of the genomic GC content.     

A fluorimetric method for the estimation of the critical micelle concentration of surfactants

The present work investigates the possibility of a rapid estimation of critical micelle concentration (cmc) of surfactants by means of soluble fluorescent probes. The effect of nonionic or differently charged surfactants on the fluorescent properties of the anionic 8-anilino-1-naphtalenesulfonic acid magnesium salt (ANS) or cationic rhodamine 6G has been investigated. The possibility of cmc evaluation depends on the appropriate selection of the dye-detergent couple. ANS has to be used with anionic surfactants; on the other hand, rhodamine 6G has to be used with cationic detergents. Both ANS and rhodamine 6G have been proved to be effective with either zwitterionic or nonionic surfactants. Plots of ANS fluorescence increase or rhodamine 6G decrease vs surfactant concentration give two straight lines whose intersection indicates the cmc of the detergent. Under all these conditions the fluorescent probe does not interfere with the micellization process. Excitation of the fluorescent probes at the isosbestic point does not affect the evaluation of the cmc of the detergent. The method applies for linear or steroid surfactants and is independent of the cmc value within a wide range of concentrations.     

反相高效液相色谱法测定Bacillus claussi的DNA G+Cmol%

目的:为了建立细菌DNA G Cmol%的快速准确的测定方法,选用反相高效液相色谱法测定Bacillus claussiDNA的G C mol%。方法:以已完成全基因测序的Bacillus haloduransC-125作为标准菌株,作者实验室新分离鉴定的2株Bacillus claussi作为待测菌株。采用80 mmol/L磷酸二氢钾溶液(pH5.6)20%甲醇为移动相,检测波长260nm,流速1ml.min-1,在Kromasil C18柱上对4种碱基进行分离。结果:DNA碱基分离效果好,无杂峰干扰,以峰面积计算得到标准菌株Bacillus haloduransC-125的G C mol%为44.23%,待测菌株的G C mol%分别为45.75%、43.35%,经过统计学分析,与已经报道的G C mol%差异不显著。结论:实验结果充分显示高效反相液相色谱法测定细菌DNAG C mol%快速、准确、结果稳定,是细菌精确分类鉴定的一种可靠方法。     

On the possibility of true phase transition in heterogeneous DNA during thermal denaturation under conditions close to equal stability of A+T and G+C pairs

The DNA helix–coil transition has been studied in the presence of high concentrations of manganese ions (about 10^?3M), which corresponds to the conditions close to equal stability of the A+T and G+C pairs, at the ionic strengths of 10^?1, 10^?2, and 1.6 × 10^?3M Na⁺. With the Mn²⁺ ion effect, the transition range is significantly reduced to not more than 0.2°C at 1.2 × 10^?3M Mn²⁺ and 1.6 × 10^?3M Na⁺. The melting curves display a sharp kink at the end of the helix–coil transition, which is interpreted as an indication of the second-order phase transition. It is shown that the melting curves obtained can be approximated by a simple analytical expression 1 – θ = exp[–a(t_c - t)], where θ is the DNA helix fraction, t_c is the phase transition temperature, and a is an empirical parameter characterizing the breadth of the melting range and responsible for the magnitude of a jump of the helicity derivative with respect to the temperature at the phase transition point.     

Determination of the G + C content of twoSyntrophus buswellii strains by ultracentrifugation techniques

An anaerobic syntrophic bacterial culture degrading benzoate was isolated from a river sediment. The syntrophic organism was grown in coculture in the presence of a hydrogenotrophic strain,Desulfovibrio fructosovorans orMethanospirillum hungatei. The G+C content of the syntrophic benzoate degrader determined by density gradient ultracentrifugation was similar to that ofSyntrophus buswellii (54.3%). A method ensuring the G+C% determination of syntrophic bacteria is presented.     

Hydroxyproline content determines the denaturation temperature of chick tendon collagen

A series of nine procollagen samples in which the hydroxyproline content varied from <1% to 44% of the total imino acids was prepared by incubating embryonic chick tendon cells with varying concentrations of α,α′-dipyridyl, an inhibitor of proline hydroxylase. The thermal stability of these procollagen preparations was then investigated by using pepsin digestion at different temperatures as an enzymatic probe of conformation. Using this technique, the denaturation temperature of the procollagen was found to be directly proportional to the hydroxyproline content. A denaturation temperature of 23.5 °C was found for the unhydroxylated procollagen and 37.9 °C for fully hydroxylated procollagen. These results suggest that hydroxyproline is crucial to the thermal stability of the collagen triple helix. They also imply that unhydroxylated molecules are not triple helical within the cell at 37 °C and that triple helix formation may be necessary for normal secretion.     

Nucleotide distribution in bacterial DNA's differing in G + C content

Summary The DNA's ofMicrococcus lysodeikticus andClostridium perfringens were fragmented to about 7 000 nucleotide pairs long by shear and fractionated with respect to buoyant density of mercury complexes in Cs₂SO₄. The distribution of G + C content in both DNA's was characteristically asymmetric. InM. lysodeikticus DNA, low G + C fragments were more numerous than high G + C fragments, whereas inC. perfringens DNA, high G + C fragments were more numerous than low G + C fragments. The G + C content of fragments ofM. lysodeikticus DNA varied from 70 to 77%, with a mean and standard deviation of 73.7 ± 1.92% G + C and that ofC. perfringens DNA varied from 27 to 34%, with a mean and standard deviation of 29.8 ± 1.34% G + C. The standard deviation was smaller than that ofEscherichia coli DNA fragments of similar size. Biological meanings of relatively low heterogeneity in nucleotide composition inM. lysodeikticus andC. perfringens are discussed.     

Semi-automated fluorimetric method for the estimation of urinary catecholamines using high-performance liquid chromatography

A high-performance liquid chromatographic method for the quantitation of adrenaline and noradranaline in urine is described, using fluorescence detection. The effluent from the liquid chromatograph is led directly into an analyser to produce the fluorescent trihydroxyindoles from the catecholamines. The method is more reliable and specific than conventional fluorescence techniques. Both catecholamines can be detected at levels of 0.5 ng on the column.     

A fluorimetric method for the determination of pepsin activity

An intramolecularly quenched fluorogenic peptide containing o-aminobenzoyl (Abz) and ethylenediamine 2,4-dinitrophenyl (Eddnp) groups at amino- and carboxyl-terminal amino acid residues, Abz-Lys-Pro-Ile-Glu-Phe-Phe-Arg-Leu-Eddnp, was hydrolyzed by purified human pepsin, gastricsin, and gastric juice uniquely at the Phe-Phe bond. Kinetic parameters determined for purified pepsin were K(m)=0.68+/-0.11 microM; k(cat)=6.3+/-0.16s(-1); k(cat)/K(m)=9.26s(-1) microM(-1); Gastricsin showed K(m)=2.69+/-0.18 microM; k(cat)=0.03+/-0.005s(-1); k(cat)/K(m)=0.011s(-1) microM(-1). Gastric juice (21 samples) from subjects without gastric disorders at endoscopy examination showed activities varying from 0.0008 to 9.72 micromolml(-1)min(-1). Pepstatin A inhibition of gastric juice enzymatic activity was complete at 3.4x10(-5)M (final concentration) inhibitor. In the proposed method the presence of a unique scissile bond in the synthetic substrate provides a direct ratio between enzymatic activity and amount of substrate hydrolyzed, and a unique step reaction facilitates the use of this assay for the determination of the activity of aspartic proteinases in biological fluids and during enzyme purification procedures.     

On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors

The correlation between genomic G+C content and optimal growth temperature in prokaryotes has gained renewed interest after Musto et al. [H. Musto, H. Naya, A. Zavala, H. Romero, F. Alvarex-Valin, G. Bernardi, Correlations between genomic GC levels and optimal growth temperatures in prokaryotes, FEBS Lett. 573 (2004) 73-77], reported that positive correlations exist in 15 families studied. We have reanalyzed their data and found that when genome size and data quality were adjusted for, there was no significant evidence of relationship between optimal temperature and GC content for two of the families that had previously shown strongly significant correlations. Using updated temperature optima for Halobacteriaceae species we found the correlation is insignificant in this family. For the family Enterobacteriaceae when genome size and optimal temperature are included in a multiple linear regression, only genome size is significant as a predictor of GC content. We showed that more profound statistical methods than simple two factor correlation analysis should be used for analyzing complex intrinsic and extrinsic factors that affect genomic GC content. We further found that a positive correlation between temperature and genomic GC is only evident in free-living species of low optimal growth temperatures.     

The thermal denaturation of human oxyhaemoglobins A, A2, C and S

1. The time-courses of thermal denaturation of human oxyhaemoglobins A, A(2), C and S at 45 degrees C were studied by following the increase in protein fluorescence. Haemoglobins S and C were less stable than haemoglobin A, whereas haemoglobin A(2) was considerably more stable. 2. The time-courses of denaturation did not follow first-order kinetics and could be fitted most simply to a co-operative scheme in which the partial denaturation of the alpha chain preceded that of the beta chain. 3. The denaturation of these haemoglobins was studied as a function of temperature by using optical rotatory dispersion. Haemoglobin A(2) was again more stable than the others. The addition of small quantities of haemoglobin A(2) had a disproportionate effect on the stability of haemoglobin C. 4. The thermodynamic parameters of the denaturation process were calculated.     

A fluorimetric method for the determination of tryptophan in animal tissues

Tryptophan, tryptamine and peptides containing N-terminal tryptophan give two highly fluorescent products on treatment with dithiothreitol and acid ninhydrin reagent 1 or 2. The first fluorescent product (product A) gives an emission at 500nm on activation at 390–400nm and is stable for 20min. The second product (product B), which gives an emission at 530nm on activation at 470nm, is detectable within 1h after the reaction. It gives almost maximum intensity in 4h and is stable for at least 48h. Except lysine, which in equimolar amounts gives less than 1% of a product similar to product B, no other naturally occurring amino compounds give fluorescent products. A procedure is given for the determination of 0.05–34nmol of tryptophan in tissue extracts. By using this procedure rat brain was found to contain 17.56±0.76 (s.e.m.) nmol/g wet wt.