T细胞亚群CD4测定方法的研究

为比较外周血T淋巴细胞亚群CD4不同测定方法的差别,以流式细胞术为定量手段,测定了猴外周血中三种不同方法处理后CD4的表达.结果表明：先标后溶法——先用异硫氰荧光素标记的单克隆抗体（FITC-CD4 McAb）标记后,再加入红细胞溶解液溶掉红细胞的处理方法,结果基本等同于传统的淋巴细胞分离法,但样本用量仅为传统方法的1/5,且操作简单.激光共焦显微术的形态学研究也证实：先标后溶法与淋巴细胞分离法相似,其细胞膜表面荧光标记清晰,优于先溶后标法.     

Analysis of qPCR data by converting exponentially related Ct values into linearly related X0 values

A common method for calculating results from qPCR experiments is the comparative Ct method, also called the 2(-ΔΔCt) method. However, several assumptions are included in the 2(-ΔΔCt) method and standard statistical analyses are not directly applicable. Here, we describe a different method, the X(0) method, for result calculations and statistical analysis from qPCR experiments. The X(0) method differs from the 2(-ΔΔCt) method by introducing a conversion of the exponentially related Ct values into linearly related X(0) values, which represent the amount of starting material in a qPCR experiment. Results calculated by the X(0) method are illustrated for qPCR experiments with technical and biological replicates, including procedures to calculate standard deviations. Incorporation of primer efficiencies in calculations by the X(0) method is also described. Altogether, the X(0) method constitutes a very simple and accurate alternative to the 2(-ΔΔCt) method for result calculations from qPCR data.     

Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (R(d)) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate R(d) indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating R(d) in five C(3) and one C(4) crop species. Values estimated by this new method agreed with those by the Laisk method for the C(3) species. The Laisk method, however, is only valid for C(3) species and requires measurements at very low CO(2) levels. In contrast, the new method can be applied to both C(3) and C(4) plants and at any CO(2) level. The R(d) estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that R(d) varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements.     

Comparison of three methods detection of slime production by Staphylococcus aureus and Staphylococcus epidermidis

In this article, slime production of Staphylococcus aureus and Staphylococcus epidermidis strains from infective skin lesions was evaluated by three different methods: Congo red agar method (CRA), Christensen tube method (CT) and spectrophotometric method (SC). All strains by CT method interpreted as negative (dark-claret or red colonies of the surface). 12 (37.5%) strains of S. aureus, 16 (50.0%) strains of S. epidermidis produced slime as shown by CT method, 6 (18.7%) strains of S. aureus, 8 (25,0%) strains of S. epidermidis by SC method. They also found a correlation of slime production by CT and SC method (p > 0.05).     

Method for rapid screening of pesticide mineralization in soil

A method has been developed for the analysis of (14)CO(2) evolution from the mineralization of (14)C-labelled organic compounds in soil samples. The new method is less space demanding and substantially cuts down laborious manual work compared to the traditional incubation bottle method used. Furthermore, the use of scintillation cocktail is largely reduced with the new method. In the new method, (14)CO(2) is trapped in filter paper held in the lid of a 20 ml glass vial by surface tension. The trapping solution used is Ca(OH)(2), which fixates CO(2) in the filter paper and the analysis of trapped (14)CO(2) is done using the Cyclone trade mark Storage Phosphor system. The lids are placed in a 32 well holder and exposed to a phosphor screen prior to scanning in a Cyclone trade mark scanner. The new filter method has been tested and compared to results obtained using the traditional method. The results show good agreement but due to a smaller capacity for CO(2) with the filter method compared to the traditional method, the interval between sampling has to be shorter using the filter method when the CO(2) development is high. The detection limits for the filter method is higher compared to the traditional method. With the filter method, the level of radioactivity has to exceed 300 dpm before detection is possible, while the same limit for the traditional method is around 30 dpm. On the other hand, the gas trapping faster and the efficiency is higher with the filter method.     

Freezing of bovine embryos: Effects of a one-step addition of 1.4 M glycerol

The effects of a one-step addition of 1.4 M glycerol (method A) upon morphological appearance and developmental capacity of frozen/thawed day 7 bovine embryos were investigated and compared to a standard stepwise addition of 1.0 M glycerol (method B). With method A, the percentage of intact embryos (classified as excellent, good and poor) was 95.3% (61 out of 64) without differences between morulae (96.5%) and blastocysts (94.4%). With method B, the percentage of intact embryos was 83.0% (44 out of 53). The percentage was similar for blastocysts (89.2%) and significantly (p < 0.05) lower for morulae (68.8%) when compared to method A. The percentage of embryos with a damaged zona pellucida was considerably increased with method A (26.6%) when compared to method B (13.2%). The proportion of embryos with excluded blastomeres was similar in both methods (21.9% method A, 17.0% method B). With method A, pregnancy rates after nonsurgical transfer were 51.0% (25 out of 49) and were better than with method B (40.5%; 15 out of 37). Embryos with a damaged zona pellucida resulted in a high pregnancy rate of 66.7% (8 out of 12). A pregnancy rate of 52.9% (10 out of 17) was obtained with embryos showing some excluded blastomeres. Thus, a one-step addition of 1.4 M glycerol facilitates and accelerates the process of embryo cryopreservation and is compatible with high pregnancy rates. Damage of the zona pellucida does not impair further development of frozen/thawed bovine embryos provided blastomeres are intact.     

Interaction amongst calcineurin subunits. Stimulatory and inhibitory effects of subunit B on calmodulin stimulation of subunit A phosphatase activity depend on Mn2+ exposure of the holoenzyme prior to its dissociation by urea

Calcineurin was dissociated into subunits A and B by 6 M urea in the presence (method A) and absence (method B) of MnCl2 and dissociated subunits were isolated by gel filtration in urea in the absence (method B) or presence (method A) of MnCl2. Phosphatase activity was associated with the A subunit isolated by either method. The phosphatase activity (nmol/mg) of subunit A isolated by method A was greater (2-5-fold) than by method B. Mn2+ increased subunit A phosphatase and calmodulin further increased the enzyme activity. Subunit B isolated by method A or B increased Mn2+ + calmodulin stimulated subunit A phosphatase prepared by method B but interestingly and unexpectedly inhibited such stimulated activity of the subunit A prepared by method A. These results imply the tightly bound cation (in our case, most likely Mn2+) with subunit A dramatically and differentially influences the effects of two Ca2+-binding proteins, calmodulin and subunit B, on the subunit A phosphatase.     

Kinetic analysis of the interaction between amphotericin B and human serum albumin using surface plasmon resonance and fluorescence spectroscopy.

The binding interaction between amphotericin B and human serum albumin (HSA) has been studied using surface plasmon resonance (SPR) spectroscopy combined with a fluorescence quenching method to confirm the binding kinetic results. In this paper, the SPR method used to study the drug-protein interaction has been described in detail. The association rate constant, dissociation rate constant and the equilibrium association constant of amphotericin B binding to HSA were obtained using this method. To confirm the feasibility of the SPR method, a fluorescence quenching method was performed to obtain the equilibrium constant. In order to obtain more accurate results, experiment design was used to optimize the fluorescence quenching process. The two equilibrium association constants obtained using the two methods were 4.017 x 10(4) M(-1) (SPR) and 3.656 x 10(4) M(-1) (fluorescence quenching method) respectively.     

Effective DNA extraction method for fragment analysis using capillary sequencer of the kelp, Saccharina

Deoxyribonucleic acid (DNA) fragment analysis can become an effective tool to study genetic differences between species and individuals on saccharinan kelp from which the little genetic diversity has been reported. Here, extraction methods of DNA suitable for use in analysis with a capillary sequencer is examined on Saccharina japonica var. diabolica which contains abundant polysaccharide. When amplified fragment length polymorphism was performed using genomic DNA extracted by seven different methods: (1) commercial kit, (2) original cetyl trimethylammonium bromide (CTAB) method, (3)–(5) three types of modified CTAB method, (6) modified sodium dodecyl sulfate (SDS) method, (7) combination of CTAB method and SDS method, a high reproducible peak that was suitable for analysis was noticeable in the electropherogram in the experiment with the last combination method (7). It is considered that the pretreatment washing of polysaccharide and the subsequent purification for protein and ribonucleic acid in SDS method and for polysaccharide in CTAB method are effective to obtain the high-purity DNA.     

Assessment of HER2 Status Using Immunohistochemistry (IHC) and Fluorescence In Situ Hybridization (FISH) Techniques in Mucinous Epithelial Ovarian Cancer: A Comprehensive Comparison between ToGA Biopsy Method and ToGA Surgical Specimen Method

We aimed to compare the assay performance characteristics of HER2 status in mucinous epithelial ovarian cancer (EOC) by ToGA (Trastuzumab for Gastric Cancer) biopsy versus ToGA surgical specimen methods. Forty-nine tissue microarray (TMA) samples of mucinous EOC from Asian women were analyzed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) tests using ToGA trial HER2 scoring methods. The overall concordance between IHC and FISH by the ToGA surgical specimen method is 97.56% and by the ToGA biopsy specimen method is 97.14%. The agreements of HER2 IHC results under both biopsy and surgical specimen methods were nearly perfect (weighted kappa = 0.845). Additionally, the percentage of Her2 FISH amplification showed increasing trend with increasing HER2 IHC ordinals (negative, equivocal, positive) by both TOGA biopsy (P<0.001) and surgical specimen method (P<0.001). After excluding equivocal cases, the sensitivity (100%), PPV (88.89%) and NPV (100%) of HER2 IHC were unchanged under either surgical specimen method or biopsy method. However, the specificity (96.97%) and accuracy (97.56%) of HER2 IHC was slightly higher under the surgical specimen method than those (specificity 96.30%, accuracy 97.14%) under the biopsy method. Of the total 49 cases, the number (n = 14) of HER2 IHC equivocal results under the ToGA biopsy method was 1.75-fold higher than those (n = 8) under the ToGA surgical specimen method (28.57% vs. 16.32%). Therefore, compared to ToGA surgery specimen method, the ToGA biopsy method caused more equivocal IHC cases to be referred to FISH testing and did not increase the detection rates of Her2 FISH amplification.     

An effective method to increase solvability in biochemical systems using S-system

In this paper we propose an effective method to estimate the intrinsic values in an immobilized enzyme system, i.e., Michaelis constant K(m) and the maximum reaction rate V(m). We combine three techniques: (1) the non-linear least square method for estimating the kinetic values, (2) orthogonal collocation with the Gauss integration method, and (3) Newton-Raphson method (NRM) or S-system method (SSM) as Newton-like method. We build a procedure to combine the first two methods to estimate the unknown kinetic values in a system. We apply this procedure to solve the intrinsic kinetic parameters determination problem in an immobilized enzyme systems following Michaelis-Menten reaction. To demonstrate the effectiveness of the current method, we test their convergence performance in detail. The results show that the basin of attraction in the current method is extremely enlarged compared with that of the S-system alone. We suggest that the current method is one of the most effective ways to solve fairly complicated biochemical reaction systems in general.     

一种联合MALDI-TOF MS直接鉴定阳性血培养瓶方法改进及与Sepsityper Kit试剂盒法、SELTERS法和血清分离胶法的比较

目的评价直接使用基质辅助激光解析电离飞行时间质谱(MALDI-TOF MS)联合Sepsityper Kit试剂盒法(简称试剂盒法)、SELTERS法和血清分离胶法(简称分离胶法)鉴定阳性血培养瓶血中细菌的符合率,并对SELTERS方法进行改进,以缩短样本处理时间。方法对656例临床血培养阳性标本,应用试剂盒法、SELTERS方法或分离胶法处理后,直接使用质谱仪快速鉴定菌株,同时进行传统培养,比较分析二者之间的差异。结果656例血培养阳性标本共分离出626株单种菌感染和30株多种菌感染标本。MALDI-TOF MS联合试剂盒法、SELTERS法或分离胶法可在1 h内快速鉴定血培养阳性标本。在单种细菌感染中,MALDI-TOF MS联合试剂盒法直接鉴定革兰阳性菌的种、属符合率分别是66.8%(141/211)、21.3%(45/211),革兰阴性菌的种、属符合率分别是97.1%(367/378)、0.8%(3/378),真菌的种、属符合率分别是32.4%(12/37)、0.0%(0/37);MALDI-TOF MS联合SELTERS法直接鉴定革兰阳性菌的种、属符合率分别是66.8%(141/211)、21.3%(45/211),革兰阴性菌的种、属符合率分别是96.3%(364/378)、2.4%(9/378),真菌的种、属符合率分别是32.4%(12/37)、2.7%(1/37);MALDI-TOF MS联合分离胶法直接鉴定革兰阳性菌的种、属符合率分别是51.2%(108/211)、20.9%(44/211),革兰阴性菌的种、属符合率分别是93.4%(353/378)、1.6%(6/378),真菌的种、属符合率分别是13.5%(5/37)、2.7%(1/37);MALDI-TOF MS联合改良SELTERS法直接鉴定革兰阳性菌的种、属符合率分别是59.1%(13/22)、18.2%(4/22),革兰阴性菌的种、属符合率分别是88.5%(23/26)、3.8%(1/26),真菌的种、属符合率分别是0.0%(0/2)、50.0%(1/2)。而对于多种菌感染的血培养瓶,3种方法鉴定率均较低。结论MALDI-TOF MS联合试剂盒法、SELTERS法或分离胶直接鉴定阳性血标本中的病原菌,其结果可在1 h内获得,并与传统培养结果相比具有较高的符合率。但是这些方法检测更快速、操作更简便,同时改良SELTERS法样本处理时间缩短,成本降低,且符合率与前3种方法没有区别。这4种方法均能满足临床快速诊断和及时有效抗菌治疗的需求,临床可根据自身情况选择。     

A method for measuring the oxygen consumption of intact cell monolayers

This report describes an open-air method for measuring the O(2) consumption (QO(2)) of intact monolayers of cultured cells. This method is based on Fick's second law of diffusion. It requires only a micromanipulator and a miniature O(2) electrode to measure the PO(2) gradient in the culture medium in the well. It was compared with the conventional oxygraph chamber method. Both methods gave the same value for QO(2) in freshly isolated rat type II cells: 166 +/- 15.3 nmol. h(-1). 10(6) cells(-1) for the open-air method and 151 +/- 11.6 nmol. h(-1). 10(6) cells(-1) for the oxygraph chamber method (n = 11 experiments). But the open-air method gave significantly larger values for QO(2) in cells cultured for 2 days (236 +/- 8.8 nmol. h(-1). 10(6) cells(-1)) than the oxygraph method (71 +/- 15.2 nmol. h(-1). 10(6) cells(-1); P < 0.001; n = 12 experiments). This suggests that the way cells are detached from their substratum to be placed in the oxygraph chamber affects their QO(2). The open-air method may be useful for studies on the metabolic properties of monolayers because the cells do not risk being damaged.     

Sub-Parts-Per-Billion Nitrate Method: Use of an N(2)O-Producing Denitrifier to Convert NO(3) or NO(3) to N(2)O

A more sensitive analytical method for NO(3) was developed based on the conversion of NO(3) to N(2)O by a denitrifier that could not reduce N(2)O further. The improved detectability resulted from the high sensitivity of the Ni electron capture gas chromatographic detector for N(2)O and the purification of the nitrogen afforded by the transformation of the N to a gaseous product with a low atmospheric background. The selected denitrifier quantitatively converted NO(3) to N(2)O within 10 min. The optimum measurement range was from 0.5 to 50 ppb (50 mug/liter) of NO(3) N, and the detection limit was 0.2 ppb of N. The values measured by the denitrifier method compared well with those measured by the high-pressure liquid chromatographic UV method above 2 ppb of N, which is the detection limit of the latter method. It should be possible to analyze all types of samples for nitrate, except those with inhibiting substances, by this method. To illustrate the use of the denitrifier method, NO(3) concentrations of <2 ppb of NO(3) N were measured in distilled and deionized purified water samples and in anaerobic lake water samples, but were not detected at the surface of the sediment. The denitrifier method was also used to measure the atom% of N in NO(3). This method avoids the incomplete reduction and contamination of the NO(3) -N by the NH(4) and N(2) pools which can occur by the conventional method of NO(3) analysis. N(2)O-producing denitrifier strains were also used to measure the apparent K(m) values for NO(3) use by these organisms. Analysis of N(2)O production by use of a progress curve yielded K(m) values of 1.7 and 1.8 muM NO(3) for the two denitrifier strains studied.     

山羊体外受精胚性别鉴定不同取样方法的研究

为了不断完善山羊早期胚胎性别鉴定技术,实现奶山羊雌性胚胎的体外生产与商业化,本研究对胚胎性别鉴定的两种采样方法进行比较。结果表明,两种取样方法性别鉴定结果的准确性没有差异,桑椹胚经打孔法采样后胚胎妊娠率(36．84％)明显高于切割法(31．25％),囊胚经切割法采样后胚胎妊娠率(31．58％)明显高于打孔法(23．53％),综合比较,胚胎性别鉴定应以打孔法采集早期桑椹胚为宜。     

A method for determining the apoplastic water volume of conifer needles

A method for direct estimation of percentage apoplastic water volume (% APO) in conifer needles is described. The method presented here, and designated the pressure-needle (P-N) method, measures the relative water content of the needles to develop a curve similar to the pressure-volume (P-V) curve. P-V and P-N curves were developed for Picea pungens Engelm. cv. Hoopsi, Pinus sylvestris L., Abies gradis (Dougl.) L., and Pseudotsuga menziesii (Mirb) Franco. The % APO estimated by the two procedures varied as much as 2-fold, while other parameters were similar. The P-V method generated consistently higher and more variable % APO than the P-N method, due to the inclusion of the apoplastic water of the stem in the P-V method. For conifers, the P-N method offers a more accurate and precise method for determining % APO.     

Correlation of egg counts of Clonorchis sinensis by three methods of fecal examination

The Kato-Katz (KK) method is a well-known method of fecal examination for helminthiases. Its diagnostic sensitivity was found very high for clonorchiasis. The present study evaluated the correlation of Clonorchis sinensis egg counts by the KK method with those by direct smear and formalin-ether (FE) technique. The egg counts obtained by the KK method (Y) were correlated with the counts by direct smear (X) with the equation of Y = 659.4 + 0.266X (r2 = 0.738), but not with those by the FE method. The present study demonstrated that the KK method and direct smear were useful for both qualitative and quantitative diagnosis of clonorchiasis, especially in the field.     

Analysis of five sampling methods for the preparation of cervical smears

The quality of the cervical smear, a decisive factor in the efficacy of population screening, can depend on the sampling method utilized. An analysis was made of the performance of five sample takers in a screening program, each of whom had made approximately 5,000 smears, and of the five sampling methods each had used: spatula alone (method A), Cytobrush plus spatula (method B), Cytopick (method C), cotton swab plus spatula (method D) and Cervex brush (method E). The differences between the sample takers and the sampling methods were significant in both the detection of grade III cervical intraepithelial neoplasia (CIN III) (P less than .01) and in the production of smears containing endocervical cells (EC+) (P less than .018). The data obtained firmly establish the importance of the presence of endocervical cells for smear adequacy. The results of this study indicate that (1) method B (Cytobrush plus spatula) and method C (Cytopick) give superior results in the preparation of EC+ smears and in the detection of CIN III and thus should be used in population screening programs, and (2) methods A and D should not be used for cervical cytologic sampling in such programs.     

Simple and rapid determination of metabolite content in plant cell culture medium using an FT-IR/ATR method

A simple, rapid and accurate mid-infrared (MIR) spectroscopic method for simultaneously determining the product (ethanol) content and the nutrient (sugar) content in plant-cell culture media was developed using a Fourier transform infrared (FT-IR) spectrometer equipped with an attenuated total reflectance (ATR) accessory. We assessed the potential of this method by comparing it to a high-performance liquid chromatography (HPLC) method, and using the developed method to measure the ethanol and sugar contents simultaneously in liquid culture media with rice and tabacum cell suspensions, respectively. The experimental results suggest that the sugar consumption and ethanol production behaviors of the plant cell suspensions can be non-destructively and simultaneously monitored using the developed method. Furthermore, the spectroscopic method provided in this study could be developed into a technique that could be used to analyze the overall kinetics of the metabolism of the plant cell suspensions.     

Estimating species trees from unrooted gene trees

In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.