Improvement of the 15N dilution method for estimation of absorption of NOx by plants supplied with 15N-labelled fertilizer

To develop further the methods for estimation of NOx absorption by plants supplied with ¹⁵N-labelled fertilizer, we proposed a new calculation method, total N fixed method (TNF), and compared with the ¹⁵N dilution method and the classical mass balance method (MB).
Hydroponically grown soybean plants were supplied with ¹⁵N-labelled nitrate and exposed to 200–250 nl l⁻¹ NO₂ for 7 d. The proportions of the N derived from NO₂ to total N in exposed plants were estimated by the three methods.
The reported rates of NO₂ absorption by several plant species, estimated by the ¹⁵N dilution method, were recalculated using the TNF method. The results of the two methods were compared and showed that: (1) The ¹⁵N dilution method overestimated the content of NO₂-N in exposed plants compared with the MB method whilst the TNF method produced estimations of NO₂-N closer to those by the MB method when the plants were supplied with 5 m M nitrate. (2) The differences in estimations between the MB method and either the ¹⁵N dilution method or the TNF method increased with decreasing supply of ¹⁵N-labelled nitrate to roots.     

洗发、护发化妆品微生物检查方法学研究

为提高化妆品潜在微生物的阳性检出率,建立洗发、护发类化妆品微生物限度和控制菌检查方法。采用常规法、培养基稀释法、薄膜过滤法对4种洗发、护发类化妆品进行微生物限度与控制菌方法学研究。结果显示,飘柔长效柔顺滋养洗发露、海飞丝去屑洗发露、飘柔人参滋养润发精华素、力士密集滋养修复-发膜级精华素菌落总数检测方法分别为0.2 m L/皿法、800 m L/膜法、0.5 m L/皿法和300 m L/膜法;霉菌及酵母菌检测方法分别为300 m L/膜法、300 m L/膜法、1 m L/皿法和1 m L/皿法;除海飞丝去屑洗发露采用培养基稀释法,其他均采用常规法进行控制菌检查。建议在化妆品微生物检验前应进行微生物方法研究,从而提高化妆品"潜在"病原菌的检出率。     

TEMPO/TVC法与国标方法测定食品中菌落总数的比较研究

【目的】确证TEMPO/TVC计数食品中菌落总数的检测性能。【方法】使用TEMPO/TVC法和国标方法GB4789.2对熟肉制品、方便食品、速冻食品、膨化食品、糖果、糕点、调味品7类食品进行菌落总数测定。【结果】TEMPO/TVC法和国标方法检测食品中菌落总数的检测结果一致性较好(符合率95.4%);且两种方法检测7类食品样品的检测结果P值均大于0.05,无显著性差异。【结论】TEMPO/TVC法具有操作简便、快速、高效和人为误差小的特点,在日常检测中值得推广应用。     

烟草种质资源AFLP分析中DNA模板的制备

采用CTAB法和SDS法提取烟草基因组DNA,经检测表明,CTAB法提取的基因组DNA纯度高于SDS法;CTAB法提取的DNA,其OD₂₆₀/OD₂₈₀值均高于1.8,相对分子量23kb左右,且能完全被EcoRⅠ和MseⅠ酶切消化,并能获得清晰的AFLP指纹图谱。     

Sensitive high-performance liquid chromatographic method for the determination of methyl N-[5-[[4-(2-pyridinyl)-1-piperazinyl]carbonyl]-1H-benzimidazol-2-yl] carbamate in rat blood

A sensitive high-performance liquid chromatographic assay has been developed and validated for the determination of methyl N-[5-[[4-(2-pyridinyl)-1-piperazinyl]carbonyl]-1H-benzimidazol-2-yl] carbamate (CDRI compound 81/470) in normal rat blood. The method described herein is simple, with improved selectivity and sensitivity over a previously reported HPLC method. The limit of quantitation is 10 ng/ml (method 1) and 2.5 ng/ml (method 2) in blood, as compared with 40 ng/ml for the previous method. The standard curve in blood is linear over the concentration range 10–1000 ng/ml in method 1 and 2.5–1000 ng/ml in method 2 and the extraction recovery is higher than 80% for both methods.     

Dimethylsulfoxide-quenched hydrogen/deuterium exchange method to study amyloid fibril structure

A general method to analyze the structure of a supramolecular complex of amyloid fibrils at amino acid residue resolution has been developed. This method combines the NMR-detected hydrogen/deuterium (H/D) exchange technique to detect hydrogen-bonded amide groups and the ability of the aprotic organic solvent dimethylsulfoxide (DMSO) to dissolve amyloid fibrils into NMR-observable, monomeric components while suppressing the undesired H/D exchange reaction. Moreover, this method can be generally applied to amyloid fibrils to elucidate the distribution of hydrogen-bonded amino acid residues in the three-dimensional molecular organization in the amyloid fibrils. In this study, we describe theoretical considerations in the H/D exchange method to obtain the structural information of proteins, and the DMSO-quenched H/D exchange method to study a supramolecular complex of amyloid fibrils. A possible application of this method to study the interaction of a protein/peptide with phospholipid membrane is also discussed.     

Dimethylsulfoxide-quenched hydrogen/deuterium exchange method to study amyloid fibril structure

A general method to analyze the structure of a supramolecular complex of amyloid fibrils at amino acid residue resolution has been developed. This method combines the NMR-detected hydrogen/deuterium (H/D) exchange technique to detect hydrogen-bonded amide groups and the ability of the aprotic organic solvent dimethylsulfoxide (DMSO) to dissolve amyloid fibrils into NMR-observable, monomeric components while suppressing the undesired H/D exchange reaction. Moreover, this method can be generally applied to amyloid fibrils to elucidate the distribution of hydrogen-bonded amino acid residues in the three-dimensional molecular organization in the amyloid fibrils. In this study, we describe theoretical considerations in the H/D exchange method to obtain the structural information of proteins, and the DMSO-quenched H/D exchange method to study a supramolecular complex of amyloid fibrils. A possible application of this method to study the interaction of a protein/peptide with phospholipid membrane is also discussed.     

Using LUMA: a Luminometric-Based Assay for Global DNA-Methylation

Changes in genomic DNA methylation are important events in normal and pathological cellular processes, contributing both to normal development and differentiation as well as to cancer and other diseases. We describe here a method to analyze global genomic DNA methylation, using a luminometric technology to quantitate methylation sensitive restriction digestions. The method is called LUminometric Methylation Assay (LUMA), and is based on a polymerase extension assay using the the Pyrosequencing? platform. The method is quantitative, highly reproducible and uses an internal control for DNA input. No modification of genomic DNA is needed and the total running time is only six hours. The method is suitable for analyzing clinical material, as well as determining dynamic changes in global methylation/demethylation events. This report describes the method in detail and gives an example of its application in epigenetic research.      

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。     

MINIATURIZED TWO-FOLD DILUTION METHOD FOR ENUMERATING TOTAL MICROBIAL LOAD AND COLIFORMS IN RAW MILK

A rapid and simple method for enumerating total aerobic plate counts (APC) and coliforms in raw milk was developed and compared with conventional plating method. Following two-fold serial dilution of samples in a 96 well microtiter plate, double strength of two different modified media for APC or coliforms was added to each well. The final positive well (purple to yellow color) was determined and converted to dilution factors. The dilution factor of each sample was converted to Log₁₀ DF (Dilution factors) and compared to actual microbial numbers Log₁₀ CFU/mL. The results of 2-fold dilution method (Log₁₀ DF) were strongly correlated to conventional plating method (Log₁₀ CFU/mL) (P < 0.05). The correlation of the scatterplot of spread plating and 2-fold dilution method indicated a high level of agreement between two methods (R²= 0.921 for total counts and R²= 0.916 for forms from raw milk). This 2-fold dilution method is an easy, rapid, and economical method for enumeration of total microbial loads and coliforms in raw milk.     

Determination of serum uric acid using high-performance liquid chromatography (HPLC)/isotope dilution mass spectrometry (ID-MS) as a candidate reference method

Uric acid is an important diagnostic marker of catabolism of the purine nucleosides, and accurate measurements of serum uric acid are necessary for proper diagnosis of gout or renal disease appearance. A candidate reference method involving isotope dilution coupled with liquid chromatography/mass spectrometry (LC/MS) has been described. An isotopically labeled internal standard, [1,3-(15)N(2)] uric acid, was added to serum, followed by equilibration and protein removal clean up to prepare samples for liquid chromatography/mass spectrometry electrospray ionization (LC/MS-ESI) analyses. (M-H)(-) ions at m/z 167 and 169 for uric acid and its labeled internal standard were monitored for LC/MS. The accuracy of the measurement was evaluated by a comparison of results of this candidate reference method on lyophilized human serum reference materials for uric acid (Standard Reference Materials SRM909b) with the certified values determined by gas chromatography/mass spectrometry reference methods and by a recovery study for the added uric acid. The method performed well against the established reference method of ion-exchange followed by derivatization isotope dilution (ID) gas chromatography mass spectrometry (ID-GC/MS). The results of this method for uric acid agreed well with the certified values and were within 0.10%. The amounts of uric acid recovered and added were in good agreement for the three concentrations. This method was applied to determine uric acid in samples of frozen serum pools. Excellent precision was obtained with within-set CVs of 0.08-0.18% and between-set CVs of 0.02-0.07% for LC/MS analyses. Liquid chromatography/tandem mass spectrometry electrospray ionization (LC/MS/MS-ESI) analysis was also performed. The LC/MS and LC/MS/MS results were in very good agreement (within 0.14%). This LC/MS method, which demonstrates good accuracy and precision, and is in the speed of analysis without the need for a derivatization stage, qualifies as a candidate reference method. This method can be used as an alternative reference method to provide an accuracy base to which the routine methods can be compared.     

重组人粒细胞集落刺激因子缓释微球的研究

目的：研究固体／油／水法制备重组人粒细胞集落刺激因子缓释微球,为开发其缓释剂型进行初步研究。方法：以聚乳酸．聚羟乙酸共聚物（PLGA）为载体材料：用固体／油／水法和水／油／水法制备载rhG-CSF缓释微球;考察粒径大小、外观、包封率等理化性质;用MieroBCA法考察微球的体外释药特性及影响因素;用SEC-HPLC和MTT比色法初步评价了微球制备工艺过程对rhG-CSF稳定性的影响。结果：两种方法制得的微球形态圆整、分散性良好,包封率均超过80％。固／油／水法制得的微球体外释放在2周内可超过90％,而水／油／水法制得的微球在相同的时间内仅释放30％。对于固／油／水法制备过程,SEC-HPLC法测定蛋白无明显聚集体出现,MTT法测定蛋白活性无明显损失。结论：实验证明了固／油／水法制备的PLGA微球可以实现2周以上的体外缓释。     

Molecular hydrogen upregulates heat shock response and collagen biosynthesis,and downregulates cell cycles: meta-analyses of gene expression profiles

Molecular hydrogen exerts its effect on multiple pathologies, including oxidative stress, inflammation, and apoptosis. However, its molecular mechanisms have not been fully elucidated. In order to explore the effects of molecular hydrogen, we meta-analysed gene expression profiles modulated by molecular hydrogen. We performed microarray analysis of the mouse liver with or without drinking hydrogen water. We also integrated two previously reported microarray datasets of the rat liver into meta-analyses. We used two categories of meta-analysis methods: the cross-platform method and the conventional meta-analysis method (Fisher’s method). For each method, hydrogen-modulated pathways were analysed by (i) the hypergeometric test (HGT) in the class of over-representation analysis (ORA), (ii) the gene set enrichment analysis (GSEA) in the class of functional class scoring (FCS), and (iii) the signalling pathway impact analysis (SPIA), pathway regulation score (PRS), and others in the class of pathway topology-based approach (PTA).

Pathways in the collagen biosynthesis and the heat-shock response were up-regulated according to (a) HGT with the cross-platform method, (b) GSEA with the cross-platform method, and (c) PRS with the cross-platform method. Pathways in cell cycles were down-regulated according to (a) HGT with the cross-platform method, (b) GSEA with the cross-platform method, and (d) GSEA with the conventional meta-analysis method.

Because the heat-shock response leads to up-regulation of collagen biosynthesis and a transient arrest of cell cycles, induction of the heat-shock response is likely to be a primary event induced by molecular hydrogen in the liver of wild-type rodents.     

Selecting near-native protein structures from ab initio models using ensemble clustering

Background: Ab initio protein structure prediction is to predict the tertiary structure of a protein from its amino acid sequence alone. As an important topic in bioinformatics, considerable efforts have been made on designing the ab initio methods. Unfortunately, lacking of a perfect energy function, it is a difficult task to select a good near-native structure from the predicted decoy structures in the last step. Methods: Here we propose an ensemble clustering method based on k-medoids to deal with this problem. The k-medoids method is run many times to generate clustering ensembles, and then a voting method is used to combine the clustering results. A confidence score is defined to select the final near-native model, considering both the cluster size and the cluster similarity. Results: We have applied the method to 54 single-domain targets in CASP-11. For about 70.4% of these targets, the proposed method can select better near-native structures compared to the SPICKER method used by the I-TASSER server. Conclusions: The experiments show that, the proposed method is effective in selecting the near-native structure from decoy sets for different targets in terms of the similarity between the selected structure and the native structure.     

QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.     

A new method for estimating effective population sizes from a single sample of multilocus genotypes

Equations for the effective size ( N_e ) of a population were derived in terms of the frequencies of a pair of offspring taken at random from the population being sibs sharing the same one or two parents. Based on these equations, a novel method (called sibship assignment method) was proposed to infer N_e from the sibship frequencies estimated from a sibship assignment analysis, using the multilocus genotypes of a sample of offspring taken at random from a single cohort in a population. Comparative analyses of extensive simulated data and some empirical data clearly demonstrated that the sibship assignment method is much more accurate [measured by the root mean squared error, RMSE, of 1/(2 N_e )] than other methods such as the heterozygote excess method, the linkage disequilibrium method, and the temporal method. The RMSE of 1/(2 N_e ) from the sibship assignment method is typically a small fraction of that from other methods. The new method is also more general and flexible than other methods. It can be applied to populations with nonoverlapping generations of both diploid and haplodiploid species under random or nonrandom mating, using either codominant or dominant markers. It can also be applied to the estimation of N_e for a subpopulation with immigration. With some modification, it could be applied to monoecious diploid populations with self-fertilization, and to populations with overlapping generations.     

两种精原干细胞高效能纯化方法的比较研究*

目的: 比较贴壁分离法和免疫磁珠法纯化小鼠精原干细胞(mSSCs) 的优缺点。方法: 分别选取10只12-15日龄的雄性C57BL/6小鼠,颈椎脱臼法处死,摘取睾丸用酶消化法获得曲细精管单细胞悬液,分别用贴壁分离法和免疫磁珠法从单细胞悬液中分离纯化mSSCs,并针对两种方法在细胞数量、分离效率以及对细胞增殖生长的影响等方面进行比较。结果: 两种纯化方法均可从小鼠曲细精管单细胞悬液中分离纯化得到干细胞,并可在体外培养后呈现出典型的精原干细胞特有的葡萄串状克隆,体外连续培养增殖超3个月。10只小鼠的睾丸经差异贴壁法纯化后可以得到3×10⁵±0.4×10⁵个mSSCs(n=5),细胞回收率(纯化后细胞数/曲细精管单细胞悬液细胞数)为1.5%±0.1%(n=5);经免疫磁珠法可以得到6×10⁵±0.4×10⁵个mSSCs(n=5),细胞回收率为3.0%±0.1%(n=5),免疫磁珠法得到的干细胞数量更高。差异贴壁法得到的干细胞更纯,因为体外培养5 d左右即得到干细胞集落,而免疫磁珠法得到的干细胞则约10 d才可以看到明显的细胞集落,但是两种纯化方法对细胞体外长期增殖生长没有明显的影响。结论: 两种方法均可以纯化得到高质量的mSSCs,,但两种方法各有优缺点。差异贴壁法较免疫磁珠法经济、实用,无需购买专门的设备和抗体磁珠,但获得的细胞数量相对较低,用时也较长。     

水产品和水体中灿烂弧菌现场可视化环介导等温扩增快检方法的建立及应用

基于环介导等温扩增(LAMP)技术建立水产品和养殖水域中灿烂弧菌现场可视化的快速、简便检测方法.以灿烂弧菌等作为研究对象,以灿烂弧菌的toxR基因作为靶基因,确定煮沸法为适合于弧菌基因组DNA提取的快捷方法,优化筛选的引物可以特异地检测灿烂弧菌,检测核酸浓度的灵敏度可以达到10-9g/L,并且结果稳定、可靠.采用该方法...     

Bacterial aerosol emission rates from municipal wastewater aeration tanks.

In this report we describe the results of a study conducted to determine the rates of bacterial aerosol emission from the surfaces of the aeration tanks of the Metropolitan Water Reclamation District of Greater Chicago John E. Egan Water Reclamation Plant. This study was accomplished by conducting test runs in which Andersen six-stage viable samplers were used to collect bacterial aerosol samples inside a walled tower positioned above an aeration tank liquid surface at the John E. Egan Water Reclamation Plant. The samples were analyzed for standard plate counts (SPC), total coliforms (TC), fecal coliforms, and fecal streptococci. Two methods of calculation were used to estimate the bacterial emission rate. The first method was a conventional stack emission rate calculation method in which the measured air concentration of bacteria was multiplied by the air flow rate emanating from the aeration tanks. The second method was a more empirical method in which an attempt was made to measure all of the bacteria emanating from an isolated area (0.37 m2) of the aeration tank surface over time. The data from six test runs were used to determine bacterial emission rates by both calculation methods. As determined by the conventional calculation method, the average SPC emission rate was 1.61 SPC/m2/s (range, 0.66 to 2.65 SPC/m2/s). As determined by the empirical calculation method, the average SPC emission rate was 2.18 SPC/m2/s (range, 1.25 to 2.66 SPC/m2/s). For TC, the average emission rate was 0.20 TC/m2/s (range, 0.02 to 0.40 TC/m2/s) when the conventional calculation method was used and 0.27 TC/m2/s (range, 0.04 to 0.53 TC/m2/s) when the empirical calculation method was used.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparison Between Different Assays for Superoxide Dismutase-Like Activity

The direct and indirect methods for assaying the superoxide dismutase activity of a compound are compared. With the use of a direct method. the mechanism of the catalysis of O₂-dismutation by the tested compound can be determined. while with the indirect method it cannot. and this may lead to misinterpretation of the results. Assuming that the catalysis occurs via the 'ping-pong' mechanism, both the direct and indirect methods are limited to the determination of values of k_cat ≥ 10⁵M^-1s^-1 and k_cat ≥ 3 × 10⁶M^-1s^-1. respectively. Moreover, many side reactions may occur with the indirect method which may interfere with the measurements. Nevertheless. the indirect method approximates better the in vivo conditions than the direct method, and a tested compound that has high SOD activity using a direct method and low SOD activity using an indirect method. will most probably be a poor SOD mimic in vivo.