Mutagenicity testing of some commonly used dyes.

Seventeen commonly used dyes and 16 of their metabolites or derivatives were tested in the Salmonella-mammalian microsome mutagenicity test. Mutagens active with and without added Aroclor-induced rat liver microsome preparations (S9) were 3-aminopyrene, lithol red, methylene blue (USP), methyl yellow, neutral red, and phenol red. Those mutagenic only with S9 activation were 4-aminopyrazolone, 2,4-dimethylaniline, N,N-dimethyl-p-phenylenediamine, methyl red, and 4-phenyl-azo-1-naphthylamine. Orange II was mutagenic only without added S9. Nonmutagenic azo dyes were allura red, amaranth, ponceau R, ponceau SX, sunset yellow, and tartrazine. Miscellaneous dyes not mutagenic were methyl green, methyl violet 2B, and nigrosin. Metabolites of the azo dyes that were not mutagenic were 1-amino-2-naphthol hydrochloride, aniline, anthranilic acid, cresidine salt, pyrazolone T,R-amino salt (1-amino-2-naphthol-3,6-disulfonic disodium salt), R-salt, Schaeffer's salt (2-naphthol-6-sulfonic acid, sodium salt), sodium naphthionate, sulfanilamide, and sulfanilic acid. 4-Amino-1-naphthalenesulfonic acid sodium salt was also not mutagenic. Fusobacterium sp. 2 could reductively cleave methyl yellow to N,N-dimethyl-p-phenylenediamine which was then activated to a mutagen.     

On the efficacy of commonly used ribonuclease inhibitors.

The ability of a number of commonly used inhibitors to inhibit pancreatic ribonuclease has been studied. At ribonuclease concentrations of 10 or 100 g/ml, heparin, polyvinylsulfate and proteinase K, at concentrations reported for their use in the literature, were ineffective in inhibiting RNase digestion of ³H-uridine labelled RNA from $\text{Streptomyces antibioticus}$. In contrast, macaloid, diethylpyrocarbonate and sodium dodecyl sulfate were all effective inhibitors, with the degree of effectiveness decreasing in the order stated. Further, at inhibitor concentrations which allowed RNase conversion of only 50% of the labelled RNA to acid soluble products, a larger percentage of the acid insoluble digestion products sedimented in the “high molecular weight” range (4–16s) when macaloid was the inhibitor used than when diethylpyrocarbonate was the inhibitor.     

A functional analysis of N-glycosylation-related genes on sialylation of recombinant erythropoietin in six commonly used mammalian cell lines

Significant efforts have been made to improve the sialylation of recombinant glycoproteins with the aim of extending their in vivo circulation time. Here, we report a systematic functional analysis of 31 N-glycosylation-related genes on sialylation of recombinant EPO in six cell lines. BHK and CHO cells were found to sialylate recombinant EPO most effectively. None of the 31 genes, individually or in combination, was able to improve EPO sialylation in these cells. HEK293, Cos-7 and 3T3 cells showed intermediate sialylation capabilities, whereas NS0 cells sialylated recombinant EPO poorly. Overexpression of ST6GalI, ST3GalIII or ST3GalIV, but not ST3GalVI, was able to improve EPO sialylation in these four cell lines. qRT-PCR experiments revealed that ST3GalIII and ST3GalIV are indeed under expressed in HEK293, 3T3 and NS0 cells. Co-expression of upstream glycogenes failed to synergize with these sialyltransferases to further enhance sialylation, suggesting that the upstream glycogenes are all expressed at sufficient levels.     

Mu receptor binding of some commonly used opioids and their metabolites.

The binding affinity to the mu receptor of some opioids chemically related to morphine and some of their metabolites was examined in rat brain homogenates with 3H-DAMGO. The chemical group at position 6 of the molecule had little effect on binding (e.g. morphine-6-glucuronide Ki = 0.6 nM; morphine = 1.2 nM). Decreasing the length of the alkyl group at position 3 decreased the Ki values (morphine less than codeine less than ethylmorphine less than pholcodine). Analgesics with high clinical potency containing a methoxyl group at position 3 (e.g. hydrocodone, Ki = 19.8 nM) had relatively weak receptor binding, whilst their O-demethylated metabolites (e.g. hydromorphone, Ki = 0.6 nM) had much stronger binding. Many opioids may exert their pharmacological actions predominantly through metabolites.     

常见生物生长模型的时差性分析及其应用

生长曲线是估计生物年龄的重要方法之一.在实际工作中,有时会出现对生物年龄的计算起点时间存在着一定差异的情形.例如在一些有关哺乳动物生长的研究中,年龄有出生年龄和受精年龄的区分.这种年龄计算时间上的差异可能导致一些生物生长模型出现不同的拟合结果.本文分析了4种常见的三参数生长模型（Spillman、Logistic、Gompertz和Bertalanffy）的时差性特征.结果表明,这4个方程均具有时差不变性,即无论时间(年龄)起点如何,它们对生物生长数据的拟合结果都一致.文中还引用了小毛足鼠体质量生长数据,采用两种年龄进行了实例比较.     

Cytogenetic harvesting of commonly used tumor cell lines

Tumor cell lines are widely used both as disease models and, increasingly, as genomic resources for the ascertainment of new cancer genes. Cytogenetic analysis remains a major route to uncovering the cancer genome. However, cancer cell lines vary inexplicably in their harvesting preferences, which must, therefore, be determined by trial and error. This article describes harvesting protocols optimized empirically for 550 commonly used, mainly human, cancer cell lines together with evidence-based procedures to assist in determining conditions for unlisted cell lines and subsidiary protocols for cytogenetic analysis using G-banding and fluorescence in situ hybridization.     

Structural specificities of five commonly used DNA nucleases

Five commonly used nucleases were surveyed for their ability to distinguish among several different DNA backbone configurations. The digestion data suggest that: (1) DNAase I binds across the minor groove; whereas (2) nuclease S1 and (3) micrococcal nuclease bind to an exposed single strand; (4) copper/phenanthroline seeks a base-pair step; and (5) DNAase II requires just a stacked single strand of limited exposure. Only micrococcal nuclease is demonstrably base-specific, with a strong preference for T, A over C, G in any structural context.     

Cytotoxicity of commonly used nitroxide radical spin probes

Since nitroxide radical spin probes are used frequently to test biophysical properties of cells, their use should be restricted to conditions that do not perturb normal cell growth and viability. Eight commonly used nitroxide radical spin probes have been tested for their effects on the survival of CHO cells. These include water-soluble spin probes Tempol, Tempamine, CTPO, CTPC and 4-maleimido-Tempo, and lipid soluble spin probes 5-Doxyl-, 12-Doxyl-, and 16-Doxylstearates. With the exception of 4-maleimido-Tempo, none of the water soluble spin labels inhibited cell survival at concentrations as high as 1 mM. At concentrations of 75 microM and higher, 4-maleimido-Tempo inhibited cell survival in a dose dependent manner. At concentrations commonly used for spin labeling of cells (30-50 microM) none of the lipid soluble spin probes tested was cytotoxic. At 100 microM only 5-Doxylstearate inhibited cell survival, whereas 12-Doxylstearate and 16-Doxylstearate had no effect.     

Cytotoxicity of commonly used solvents at elevated temperatures

At 43 degrees C (but not at 41 degrees C), organic solvents used to dissolve water-insoluble chemotherapeutic agents become themselves lethal to cells. This finding is not unique to Chinese hamster cells (HA-1); mouse mammary sarcoma cells (EMT-6) behave similarly. The solvent concentrations involved are in the range of those needed to make drug solutions. Hence experiments measuring drug-cell interactions at elevated temperatures must include controls which independently measure solvent effects.     

Comparison of statistical methods commonly used in predictive modelling

Logistic Multiple Regression, Principal Component Regression and Classification and Regression Tree Analysis (CART), commonly used in ecological modelling using GIS, are compared with a relatively new statistical technique, Multivariate Adaptive Regression Splines (MARS), to test their accuracy, reliability, implementation within GIS and ease of use. All were applied to the same two data sets, covering a wide range of conditions common in predictive modelling, namely geographical range, scale, nature of the predictors and sampling method. We ran two series of analyses to verify if model validation by an independent data set was required or cross‐validation on a learning data set sufficed. Results show that validation by independent data sets is needed. Model accuracy was evaluated using the area under Receiver Operating Characteristics curve (AUC). This measure was used because it summarizes performance across all possible thresholds, and is independent of balance between classes. MARS and Regression Tree Analysis achieved the best prediction success, although the CART model was difficult to use for cartographic purposes due to the high model complexity.     

常见SPF级小鼠和大鼠肠道菌群多样性研究

目的研究常见SPF级小鼠和大鼠的肠道菌群多样性。方法分别采集广东地区三家实验动物生产单位的C57BL/6、ICR、BALB/c小鼠和Wistar、SD大鼠的盲肠内容物样品,用细菌16S rDNA通用引物扩增V4-V5区域,采用Illumina Miseq 2×300 bp测序平台进行测序,使用生物信息学方法进行微生物群落分析、Alpha多样性分析与Beta多样性分析。结果对序列去杂优化后OTU聚类分析,稀释性曲线说明本次测序的数据量合理;实验小鼠和大鼠肠道菌群共分成八个门,其中拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)占据主要地位,属水平上主要是拟杆菌属(Bacteroides)、Hungatella、副杆状菌属(Parabacteroides)、乳酸杆菌属(Lactobacillus)等;样品间差异性分析显示相同设施来源动物的菌群组成相似性较高;Alpha分析结果显示来源于同种设施的动物物种丰富度相近;Beta分析显示相同设施动物的肠道菌群差异较小,但品系对肠道菌群差异性有所影响。结论不同来源设施的饲养环境是动物肠道菌群多样性的主要影响因素,不同品系对肠道菌群多样性有一定影响。     

Examination of six commonly used laboratory fixatives in HAB monitoring programs for their use in quantitative PCR based on Taqman probe technology

Due to the need for more rapid and reliable detection, quantification and enumeration of harmful algal species the use of molecular methods are increasingly being used in monitoring and field studies. However, many studies often require sample fixation to allow for transportation before analyses are conducted. Here, we describe the effects of six fixatives (acidified Lugol's iodine with or without sodium thiosulphate, glutaraldehyde, paraformaldehyde (PFA), formalin and ethanol) on quantitative real-time polymerase chain reaction (qPCR) amplification with Taqman probes. We applied extracted total genomic DNA from four harmful algal species from Danish waters, representing three dinoflagellates (Alexandrium tamarense, Karenia mikimotoi, Karlodinium veneficum and a haptophyte (Prymnesium parvum). The C_q values generated on the qPCR amplification plot were compared to those of an unfixed sample that acted as a control. For all species positive amplifications were achieved from DNA templates from all preserved samples. However, amplification efficiencies between fixatives and species varied. Yet it was found that Lugol's iodine was the most ideal short-term fixative for enumeration of cells by qPCR as well as being the safest to handle. The effect of age on Lugol's iodine fixed samples was also addressed. Samples were fixed and stored at 5 °C in the dark and total genomic DNA extracted after 24 h, 72 h, 1 week, 2 weeks, 1 month and 2 months. Samples remained stable for 1 month for A. tamarense and K. veneficum and 2 months for K. mikimotoi and P. parvum.