A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.     

Comparison of two methods for the measurement of rat liver methylmalonyl-coenzyme A mutase activity: HPLC and radioisotopic assays

Methylmalonyl-coenzyme A mutase (MCM) is a 5'-deoxyadenosylcobalamin-linked mitochondrial enzyme that catalyzes the isomerization of L-methylmalonyl-coenzyme A to succinyl-coenzyme A. In vitro assays of total and holo-MCM activities are important tools for investigating the cobalamin pathway. Several methods have been described for measuring MCM activity. The most commonly-used method is a radioassay based on the permanganate oxidation of DL[CH(3)-(14)C]methylmalonyl-coenzyme A, but radiometric methods are insensitive, laborious, and time-consuming. Therefore, we have compared this method with a nonradiometric assay, potentially most sensitive, based on the separation of methylmalonyl-coenzyme A and succinyl-coenzyme A by high performance liquid chromatography (HPLC). We determined the optimal assay conditions and the reproducibility and sensitivity of each technique. The results obtained by the two techniques were very different: the specific activities obtained by the permanganate oxidation method (0.039 +/- 0.013 nmol/min/mg protein for the holo-MCM activity and 1.90 +/- 0.69 nmol/min/mg protein for the total-MCM activity) were threefold lower than those obtained with the HPLC method (0.124 +/- 0.011 nmol/min/mg protein for the holo-MCM activity and 6.15 +/- 0.76 nmol/min/mg protein for the total-MCM activity). The coefficients of variation for the radiometric method (18.4-40.6%) were three to five times greater than those for the HPLC assay (3.5-12.2%). This demonstrates the lack of sensibility and reproducibility of the permanganate radioassay. Thus, the radiometric method is not suitable for measuring low mutase activities such as the holo activities in tissues. The intrinsic inconvenience of the radiometric assay indicates that the HPLC method is a method of choice for measuring MCM activity.     

Structure-genotoxic activity relationships of pesticides: comparison of the results from several short-term assays

The Computer-Automated Structure Evaluation (CASE) program has been applied to the analysis of the genotoxic activity of 54 pesticides (31 insecticides, 15 herbicides and 8 fungicides) in 5 different short-term test systems measuring gene mutation and DNA damage. The database contains compounds presenting diverse structures including carbamates, thiocarbamates, organophosphates, halo-aromatics and other functionalities. Some significant relationships between common structural features and the genotoxic activity displayed by these chemicals have been found. Among the most relevant fragments, automatically selected by the program, a methoxyphosphinyl and a chlorovinyl group appear as the common structural subunits responsible for the activities detected in the battery composed of the Salmonella typhimurium histidine reversion assay, the mouse lymphoma gene mutation assay and recombination in the yeast Saccharomyces cerevisiae.     

两种微生物法测定食品中叶酸含量的比较

比较酪乳酸杆菌(Lactobacillus casei,L.casei ATCC 7469)、粪链球菌(Streptococcus faecalis,S.aecalisATCC 8043)测定强化食品中叶酸的含量,结果表明,S.faecalis比L.casei检测时限短1d,实验操作容易把握,分别对两种菌检测结果重现性进行比较,P＞0.05,差异无统计学意义,两种方法实验结果比较,P＞0.05,差异无统计学意义.     

Treatment of hyperthyroidism with radioiodine targeted activity: A comparison between two dosimetric methods

Radioiodine therapy is an effective and safe treatment of hyperthyroidism due to Graves’ disease, toxic adenoma, toxic multinodular goiter. We compared the outcomes of a traditional calculation method based on an analytical fit of the uptake curve and subsequent dose calculation with the MIRD approach, and an alternative computation approach based on a formulation implemented in a public-access website, searching for the best timing of radioiodine uptake measurements in pre-therapeutic dosimetry. We report about sixty-nine hyperthyroid patients that were treated after performing a pre-therapeutic dosimetry calculated by fitting a six-point uptake curve (3–168 h). In order to evaluate the results of the radioiodine treatment, patients were followed up to sixty-four months after treatment (mean 47.4 ± 16.9). Patient dosimetry was then retrospectively recalculated with the two above-mentioned methods. Several time schedules for uptake measurements were considered, with different timings and total number of points. Early time schedules, sampling uptake up to 48 h, do not allow to set-up an accurate treatment plan, while schedules including the measurement at one week give significantly better results. The analytical fit procedure applied to the three-point time schedule 3(6)–24–168 h gave results significantly more accurate than the website approach exploiting either the same schedule, or the single measurement at 168 h. Consequently, the best strategy among the ones considered is to sample the uptake at 3(6)–24–168 h, and carry out an analytical fit of the curve, while extra measurements at 48 and 72 h lead only marginal improvements in the accuracy of therapeutic activity determination.     

A comparison of four assays detecting oxidizing species

Quin2, a fluorescent calcium probe, has a low affinity for calcium in comparison to its affinities for transition metal ions. Chelation of ferric ion with quin2 strongly enhanced the formation of oxidizing species in the presence of bolus H₂O₂ as detected with four assays, electron spin resonance with the spin-trap DMPO, the deoxyribose assay, the DMSO assay, and plasmid DNA strand breakage. In comparison, Fe(III)-EDTA reacted with bolus H₂O₂ only as detected with electron spin resonance and the deoxyribose assay, but not as detected with the two latter assays. The addition of reductants, like ascorbate or superoxide generated by hypoxanthine/xanthine oxidase, to Fe(III)-EDTA in the presence of H₂O₂ produced plasmid DNA strand breakage and strong reactivity in both the DMSO and the deoxyribose assays. Our findings suggest that the main oxidizing species produced in Fenton-type reactions is hydroxyl radical. However, the reaction between Fe(III)-EDTA and bolus H₂O₂ appears to be exceptional and dominated by a nonhydroxyl radical species.     

A comparison of two microbial detection methods used in aseptic processing of musculoskeletal allograft tissues

Tissues from 78 musculoskeletal donors were concurrently tested for microorganisms using both a swab and liquid culture method. An aggregate total of 20 organisms were detected by both methods. The swab detected 4/20 organisms while the liquid culture detected 18/20 organisms. The swab method yielded sensitivity and negative predictive values of 20 and 92.3%, respectively. Comparatively, the liquid culture displayed a sensitivity of 90% and a negative predictive value of 99%. These results clearly demonstrate that the liquid culture method is superior to swab cultures in microbial detection. Additional studies are necessary to determine the optimal culture conditions for different types of tissues when utilizing the liquid culture method.     

A comparison between two brine shrimp assays to detect in vitro cytotoxicity in marine natural products

Background  

The brine shrimp lethality assay is considered a useful tool for preliminary assessment of toxicity. It has also been suggested for screening pharmacological activities in plant extracts. However, we think that it is necessary to evaluate the suitability of the brine shrimp methods before they are used as a general bio-assay to test natural marine products for pharmacological activity.     

A microbial carbon-phosphorus bond cleavage enzyme requires two protein components for activity.

Enterobacter aerogenes IFO 12010 contains a carbon-phosphorus (C-P) bond cleavage enzyme catalyzing the liberation of inorganic phosphate from various alkyl- and phenylphosphonic acids. The enzyme in the bacterium was found to be composed of two physically different protein components, E2 and E3. The molecular weights of E2 and E3 were 560,000 and 110,000, respectively, and E3 was resolved into two apparently homogeneous subunits. Neither component alone could catalyze the C-P bond cleavage reaction, but the reaction was efficiently catalyzed when the components were mixed.     

Measuring plasminogen activator inhibitor activity in plasma by two enzymatic assays

We compared two methods that measure plasminogen activator inhibitor (PAI) activity in plasma based on the ability of PAI to inhibit tissue plasminogen activator (tPA) or urokinase (uPA) in order to determine which method most accurately measures plasma PAI activity after stressors, like hemorrhage. Plasma PAI activity was significantly elevated after hemorrhage in both assays. Using standard curves derived from rhPAI-1, we found that the tPA-PAI assay was more sensitive than the uPA-PAI assay. However, we measured a 10-fold difference in PAI activity as measured between assays, suggesting that some endogenous plasma constituents (tPA, uPA, plasminogen or plasmin) may interfere with the accurate determination of PAI activity. Increasing the amount of plasma in each assay led to a progressive increase in PAI activity. However, removing either tPA or plasminogen from the tPA-PAI assay unmasked the presence of some endogenous tPA and plasminogen. Furthermore, increasing plasma volume in either assay increases measured plasma tPA, but not uPA. Finally, plasma tPA is elevated after hemorrhage, whereas plasma uPA is not. These results suggest that endogenous tPA and plasminogen may interfere with the measurement of plasma PAI activity in the tPA-PAI assay after hemorrhage or other stresses. The uPA-PAI assay does not have this confounding problem because endogenous uPA does not interfere with the assay, nor does it rise during hemorrhage.     

Bioassay of growth-stimulating activity of serum: comparison of lymphocyte and cartilage assays in normal and growth hormone-deficient children

The somatomedin and/or growth-stimulating activity of serum from hypopituitary children and short children with normal growth hormone (GH) response to stimulation tests were studied using different bioassays: thymidine incorporation into human activated lymphocytes; sulfate incorporation into chick embryo cartilage; and simultaneous thymidine uptake into the same cartilages. The results showed that lymphocyte assay is highly sensitive to small amounts of serum and is GH-dependent in children with low GH secretion. On the contrary, the cartilage assays need higher serum concentration and their GH-dependence appears only in subjects with normal or low-normal GH secretion. The lack of correlation between the results of the three bioassays suggests that they measure both somatomedins and different serum factors involved in the regulation of growth.     

Evaluating statistical analyses and reproducibility of microbial mutagenicity assays

The NCI/NTP has completed the first phase of a 4-laboratory study on the reproducibility of testing chemicals for mutagenicity in the Salmonella/microsome assay. This paper is report of the statistical analysis of some of that data. This analysis involved (1) identifying and removing spurious data; (2) determining the adequacy of the remaining data in making a decision on the mutagenicity of the test chemical; (3) performing the statistical tests; and (4) interpreting the results. Using this procedure, 7 approaches were used to determine the mutagenicity of a test. These approaches were the (1) 2-fold rule, (2) modified 2-fold rule, (3) one-way analysis of variance (homogeneity test), (4) test for linear trend, (5) combination of 3 and 4, (6) 97.5th percentile threshold rule and (7) confidence interval threshold rule. The conclusions drawn by each rule were compared to the microbiologists' interpretation, and the results of these comparisons were presented. In addition, the strengths and weaknesses of each rule were discussed. The reproducibility of the assay in this study was examined, and a discussion of the significance of these results was presented.     

Effect of glyphosate on the microbial activity of two Romanian soils

Glyphosate applied to soils potentially affect microbial activity. A series of field and laboratory experiments assessed the effect of this herbicide on soil microorganisms. The aim of experiments was to evaluate the effect of glyphosate application on the soil microbial community structure, function and their activity. We studied "in vitro", changes in the microbial activity of typical Chernozem and Gleysol soils, with and without applied glyphosate. The herbicide was applied at a rate of 2, respectively 4 mg kg(-1) of soil and microbial activity were measured by fluorescein diacetate (FDA) hydrolysis. We found an increase of 9 to 13% in FDA hydrolyses in the presence of glyphosate in rate of 2 mg kg (-1) compared with the same type of soil which had never received herbicide. The double quantity of glyphosate decrease soil microbial activity; the amount of hydrolyzed fluorescein is lower than the addition of 2 ppm. The greater decrease was observed in the Gleysol type where the fluorescein hydrolyzed is with 4, 85% lower than version control without glyphosate. Chemical characters of soil, influence soil biological activity when herbicide is added. In Chemozem case, rich in humus, whose predominant micro flora is represented by actinomycetes through glyphosate treatment these organisms growths of as major producers of antibiotics actinomycetes determine an inhibitory effect on eubacteria and micromycetes growth, which is highlighted by estimating a relatively small number of them. After 10 days, once with decreasing of glyphosate content in soil, decreases the number of active actinomycetes, therefore we are witnessing to a numerical growth of bacterial population. In Gleysol type the indigenous micro flora is represented by eubacteria, so when the glyphosate is added it was registered a high growth of these organisms fraction.