Characterization of mucoid Pseudomonas aeruginosa strains isolated from technical water systems

The occurrence of mucoid Pseudomonas aeruginosa strains was investigated in water samples and surface material from non-clinical aquatic environments. Ten of 81 environmental isolates displayed a mucoid colony type after incubation at 36°C for 24 h on Pseudomonas Isolation Agar. The mucoid strains obtained exclusively from surfaces of technical water systems were characterized in terms of medium-dependent expression of mucoid colonial phenotype, exoenzyme profile, pigment production and O-antigen type. The mucoid strains secreted substantially higher quantities of carbohydrate and uronic acid-containing material compared to non-mucoid environmental isolates. Major slime components of the mucoid strains were identified as O-acetylated alginates that contained higher proportions of mannuronate than guluronate monomer residues and were composed of blocks of poly-mannuronate and poly-mannuronate/guluronate, whereas blocks of poly-guluronate were absent. The results suggest that surfaces in aquatic environments may represent a natural habitat for mucoid (i.e. alginate-overproducing) strains of Ps. aeruginosa with properties similar to clinical mucoid strains.     

Construction of a recombinant Trichoderma reesei strain expressing Aspergillus aculeatus β-glucosidase 1 for efficient biomass conversion

To develop a Trichoderma reesei strain appropriate for the saccharification of pretreated cellulosic biomass, a recombinant T. reesei strain, X3AB1, was constructed that expressed an Aspergillus aculeatus β-glucosidase 1 with high specific activity under the control of the xyn3 promoter. The culture supernatant from T. reesei X3AB1 grown on 1% Avicel as a carbon source had 63- and 25-fold higher β-glucosidase activity against cellobiose compared to that of the parent strain PC-3-7 and that of the T. reesei recombinant strain expressing an endogenous β-glucosidase I, respectively. Further, the xylanase activity was 30% lower than that of PC-3-7 due to the absence of xyn3. X3AB1 grown on 1% Avicel-0.5% xylan medium produced 2.3- and 3.3-fold more xylanase and β-xylosidase, respectively, than X3AB1 grown on 1% Avicel. The supernatant from X3AB1 grown on Avicel and xylan saccharified NaOH-pretreated rice straw efficiently at a low enzyme dose, indicating that the strain has good potential for use in cellulosic biomass conversion processes.     

An effective method for isolating alginate lyase-producing Bacillus sp. ATB-1015 strain and purification and characterization of the lyase

A new alginate lyase-producing micro-organism, designated as Bacillus sp. strain ATB-1015, was effectively isolated from soil samples pretreated for 3 months with a substrate of the enzyme, sodium alginate. Alginate lyase activity was assayed by the degrading activity of biofilm on Teflon sheet discs, which was formed by a mucoid strain of Pseudomonas aeruginosa PAM3 selected from clinical isolates. The extracellular alginate lyase was precipitated with ammonium sulphate from the culture broth, and purified by gel filtration and anion exchange chromatography. The molecular weight of the lyase was estimated to be 41 kDa by SDS polyacrylamide gel electrophoresis and Sephacryl S-200 HR column chromatography. The optimum pH and temperature for the enzyme activity were around 7·5 and 37 °C, respectively, and the Km value was 0·17% with the substrate, sodium alginate. The lyase activity was completely inhibited by treatment with 1 mmol l⁻¹ of EDTA and the decreased activity was almost completely recovered by the addition of 2 mmol l⁻¹ of CaCl₂. The activity was not affected by treatment with the protein denaturants, 0·01 mol l⁻¹ of SDS or 1 mmol l⁻¹ of urea. The lyase had substrate specificity for both the poly-guluronate and poly-mannuronate units in the alginate molecule.     

Purification and characterization of a Na/K dependent alginate lyase from turban shell gut Vibrio sp. YKW-34

An alginate lyase with high specific enzyme activity was purified from Vibrio sp. YKW-34, which was newly isolated from turban shell gut. The alginate lyase was purified by in order of ion exchange, hydrophobic and gel filtration chromatographies to homogeneity with a recovery of 7% and a fold of 25. This alginate lyase was composed of a single polypeptide chain with molecular mass of 60 kDa and isoelectric point of 5.5–5.7. The optimal pH and temperature for alginate lyase activity were pH 7.0 and 40 °C, respectively. The alginate lyase was stable over pH 7.0–10.0 and at temperature below 50 °C. The alginate lyase had substrate specificity for both poly-guluronate and poly-mannuronate units. The k_cat/K_m value for alginate (heterotype) was 1.7 × 10⁶ s⁻¹ M⁻¹. The enzyme activity was completely lost by dialysis and restored by addition of Na⁺ or K⁺. The optimal activity exhibited in 0.1 M of Na⁺ or K⁺. This enzyme was resistant to denaturing reagents (SDS and urea), reducing reagents (β-mercaptoethanol and DTT) and chelating reagents (EGTA and EDTA).     

Purification and characterization of a Na+/K+ dependent alginate lyase from turban shell gut Vibrio sp. YKW-34

An alginate lyase with high specific enzyme activity was purified from Vibrio sp. YKW-34, which was newly isolated from turban shell gut. The alginate lyase was purified by in order of ion exchange, hydrophobic and gel filtration chromatographies to homogeneity with a recovery of 7% and a fold of 25. This alginate lyase was composed of a single polypeptide chain with molecular mass of 60 kDa and isoelectric point of 5.5–5.7. The optimal pH and temperature for alginate lyase activity were pH 7.0 and 40 °C, respectively. The alginate lyase was stable over pH 7.0–10.0 and at temperature below 50 °C. The alginate lyase had substrate specificity for both poly-guluronate and poly-mannuronate units. The k_cat/K_m value for alginate (heterotype) was 1.7 × 10⁶ s⁻¹ M⁻¹. The enzyme activity was completely lost by dialysis and restored by addition of Na⁺ or K⁺. The optimal activity exhibited in 0.1 M of Na⁺ or K⁺. This enzyme was resistant to denaturing reagents (SDS and urea), reducing reagents (β-mercaptoethanol and DTT) and chelating reagents (EGTA and EDTA).     

An optimization approach to predicting protein structural class from amino acid composition.

Proteins are generally classified into four structural classes: all-alpha proteins, all-beta proteins, alpha + beta proteins, and alpha/beta proteins. In this article, a protein is expressed as a vector of 20-dimensional space, in which its 20 components are defined by the composition of its 20 amino acids. Based on this, a new method, the so-called maximum component coefficient method, is proposed for predicting the structural class of a protein according to its amino acid composition. In comparison with the existing methods, the new method yields a higher general accuracy of prediction. Especially for the all-alpha proteins, the rate of correct prediction obtained by the new method is much higher than that by any of the existing methods. For instance, for the 19 all-alpha proteins investigated previously by P.Y. Chou, the rate of correct prediction by means of his method was 84.2%, but the correct rate when predicted with the new method would be 100%! Furthermore, the new method is characterized by an explicable physical picture. This is reflected by the process in which the vector representing a protein to be predicted is decomposed into four component vectors, each of which corresponds to one of the norms of the four protein structural classes.     

A practical and reliable method for determination of urinary 3-methylhistidine

A practical and reliable semiautomated method for analysis of urinary 3-methylhistidine (3-MH) was designed combining the isolation of 3-MH by ion-exchange chromatography with the color reaction given by ninhydrin-orthopthalaldehyde (ninhydrin-OPT) reagent after alkalinization. 2 ml of urine were passed through disposable columns packed with an ion-exchange resin (Dowex 50-X8, 200–400 mesh) and the acidic and neutral amino acids were eluted with 10 ml of 0.2 M pyridine solution. Then, the 3-MH was quantitatively eluted and separated from histidine with a volume of 9 ml of a 1.5 M pyridine solution. Standard Autoanalyzer equipment was used for the automation of spectrophotometry. The method permits the analysis of 40 samples in duplicate per day. The 3-MH color reaction was linear for concentrations from 0.015 to 0.24 μ mol/ml. The mean recoveries of 3-MH from standards and urine were 98.6 ± 1.3 and 99.0 ± 1.3%, respectively. Duplicate determinations of urine samples showed a variation coefficient of 1.88%. An excellent agreement was obtained between urine samples analyzed by the present method and by an amino acid analyzer. The need for the elimanation of the interfering amino acids was clearly demonstrated.     

Rapid analysis of low levels of indolyl-3-acryloylglycine in human urine by high-performance liquid chromatography

There have been several reports of increased levels of excretion of indolyl-3-acryloylglycine (IAcrGly) in human urine in a number of disease states. However, the metabolic source of this compound is still not clear and there is the possibility of more than one mechanism for IAcrGly production. There was therefore a need for a rapid, low limit of quantitation assay for IAcrGly to enable further study in this area. In the assay described here, these analytical requirements were addressed by utilising a solid-phase extraction method for sample clean-up, reversed-phase LC with an on-column focusing method of sample introduction and UV absorbance detection at 326 nm. The limit of quantitation of this method was 26.2 ng ml⁻¹. It was also noted that IAcrGly undergoes isomerisation when exposed to light and that this process is reversible.     

Quantification of 3-hydroxyglutaric acid in urine,plasma, cerebrospinal fluid and amniotic fluid by stable-isotope dilution negative chemical ionization gas chromatography-mass spectrometry

This paper describes a stable isotope dilution method for quantification of 3-hydroxyglutaric acid (3-HGA) in body fluids. The method comprises a solid-phase extraction procedure, followed by gas chromatographic separation and negative chemical ionization mass spectrometric detection. This method is selective and sensitive, and enables measurement of 3-HGA concentrations in urine-, plasma-, and CSF- samples of controls. The control ranges for 3-HGA were: urine 0.88-4.5 mmol/mol creatinine (n=12); plasma 0.018-0.10 micro mol/l (n=10), CSF 0.022-0.067 micro mol/l (n=10). We applied this method to measure 3-HGA in body fluids of three patients with glutaric aciduria type I. We also quantified 3-HGA in amniotic fluid of controls (range 0.056-0.11 micro mol/l; n=12) and in two samples from fetuses affected with glutaric aciduria type I.     

Analytical method for the determination of urinary 3-phenoxybenzoic acid in subjects occupationally exposed to pyrethroid insecticides

The determination of urinary 3-phenoxybenzoic acid enables exposure to pyrethroid insecticides to be evaluated. A method for the quantitative determination of this metabolite in urine is described. The compound and the internal standard (2-phenoxybenzoic acid) are derivatized with pentafluorobenzylbromide and transformed into pentafluorobenzyl esters, which are determined by gas chromatography with an intermediate polarity capillary column and an electron-capture detector. Before GC analysis, the urinary extracts are purified on LC-Si SPE columns. The proposed method has a detection limit of 0.5 μg/l and a mean recovery of 91.3%. The coefficient of variation of the analytical procedure, evaluated at a concentration of 24.96 μg/l, was 9.58%. Storage of the urine samples for 3 months at −18°C did not lead to significant changes in the concentration of analyte. The method was tested analysing the urine of a farm worker with symptoms of pyrethroid poisoning, occupationally exposed to esfenvalerate.     

Three-dimensional bioprinting human cardiac tissue chips of using a painting needle method

Three-dimensional (3D) printers are attracting attention as a method for arranging and building cells in three dimensions. Bioprinting technology has potential in tissue engineering for the fabrication of scaffolds, cells, and tissues. However, these various printing technologies have limitations with respect to print resolution and due to the characteristics of bioink such as viscosity. We report a method for constructing of 3D tissues with a “microscopic painting device using a painting needle method” that, when used with the layer-by-layer (LbL) cell coating technique, replaces conventional methods. This method is a technique of attaching the high viscosity bioink to the painting needle tip and arranging it on a substrate, and can construct 3D tissues without damage to cells. Cell viability is the same before and after painting. We used this biofabrication device to construct 3D cardiac tissue (LbL-3D Heart) using human-induced pluripotent stem cell–derived cardiomyocytes. The constructed LbL-3D Heart chips had multiple layers with a thickness of 60 µm, a diameter of 1.1 mm, and showed synchronous beating (50–60 beats per min). The aforementioned device and method of 3D tissue construction can be applied to various kinds of tissue models and would be a useful tool for pharmaceutical applications.     

快速城市化区域生态安全的空间模糊综合评价——以广州市为例

随着经济的快速发展,城市生态安全状况令人担忧。进行城市生态安全评价,了解城市生态安全状况成为城市生态建设、改善和提高城市生态安全状况的前提。基于TM遥感数据以及GIS平台,构建评价指标体系,采用空间模糊评价方法进行生态安全的空间综合评价,进而分析其时间与空间变化。生态安全空间分布图及其属性的统计结果表明,整体上讲,广州市生态安全等级为一般,并且随时间推移,生态安全状态比较稳定,但是在1995年受到较大的破坏;不同区域之间生态安全的对比分析显示,广州市生态安全的城乡差异明显,中心城区生态安全状态堪忧;将研究结果与作者早已经完成的同区域基于统计数据的生态安全评价分析结果进行趋势对比,二者显示出一致性,表明基于格网的空间模糊综合评价方法用于生态安全评价是可行的,研究的设计也是合理的,但是这种空间综合评价方法却具有传统方法不具备的优点：不仅具有可视化的表达效果,还有利于不同范围大小区域之间的对比研究。     

不同荧光定量PCR分析方法检测大鼠脑缺血再灌注损伤中Caspase-3基因的表达研究

目的:应用实时荧光PCR检测大鼠脑缺血/再灌注损伤组织中的Caspase-3基因表达变化,并比较了相对定量与绝对定量分析方法的技术优劣.方法:相对定量实验中,以β-actin基因作为内参,采用Delta-delta Ct法计算目的基因表达变化.而在绝对定量实验中,构建了含Caspase-3基因的重组质粒,以该重组质粒作...     

Novel method to differentiate 3T3 L1 cells in vitro to produce highly sensitive adipocytes for a GLUT4 mediated glucose uptake using fluorescent glucose analog

Adipocytes play a vital role in glucose metabolism. 3T3 L1 pre adipocytes after differentiation to adipocytes serve as excellent in vitro models and are useful tools in understanding the glucose metabolism. The traditional approaches adopted in pre adipocyte differentiation are lengthy exercises involving the usage of IBMX and Dexamethasone. Any effort to shorten the time of differentiation and quality expression of functional differentiation in 3T3 L1 cells in terms of enhanced Insulin sensitivity has an advantage in the drug discovery process. Thus, there is a need to develop a new effective method of differentiating the pre adipocytes to adipocytes and to use such methods for developing efficacious therapeutic molecules. We observed that a combination of Dexamethasone and Troglitazone generated differentiated adipocytes over fewer days as compared to the combination of IBMX and Dexamethasone which constitutes the standard protocol followed in our laboratory. The experiments conducted to compare the quality of differentiation yielded by various differentiating agents indicated that the lipid droplet accumulation increased by 112 % and the GLUT4 mediated glucose uptake by 137 % in cells differentiated with Troglitazone and Dexamethasone than in cells differentiated traditionally. The comparative studies conducted for evaluating efficient measurable glucose uptake by GOPOD assay, radioactive ³H-2-deoxy-D-glucose assay and by non-radioactive 6-NBDG (fluorescent analog of glucose) indicated that the non-radioactive method using 6-NBDG showed a higher signal to noise ratio than the conventional indirect glucose uptake method (GOPOD assay) and the radioactive ³H-2-deoxy-D-glucose uptake method. Differentiated 3T3 L1 cells when triggered with 2.5 ng/mL of Insulin showed 3.3 fold more glucose uptake in non-radioactive method over the radioactive ³H-2-deoxy-D-glucose uptake method. The results of this study have suggested that a combination of Dexamethasone and Troglitazone for 3T3 L1 cell differentiation helps in better quality differentiation over a short period of time with increased sensitivity to Insulin. The application of these findings for developing new methods of screening novel Insulin mimetics and for evaluating the immunological responses has been discussed.     

小鼠前脂肪细胞中AP-2α相互作用蛋白质的分离和鉴定

转录因子AP-2是一个功能重要的基因家族,AP-2α,在协同调控脂肪细胞分化成熟,以及脂肪因子分泌的过程中发挥重要作用.为了阐明其协同调控的机制,本文采用anti-AP-2α抗体免疫共沉淀技术,从小鼠前脂肪细胞313-L1中分离AP-2α相互作用蛋白,然后用基质辅助激光解吸/电离飞行时间质谱结合数据库查询鉴定AP-2a...     

Liquid chromatographic assay in plasma of one of the members of a new series of anticonvulsants: -3-hydroxy-3-ethyl-3-phenylpropionamide

A method for the simultaneous determination of HEPP ( -3-hydroxy-3-ethyl-3-phenylpropionamide), a member of a new homologous series of phenylamide-derivative anticonvulsants, with six other antiepileptic drugs (ethosuximide, primidone, phenobarbital, phenytoin, carbamazepine and clonazepam) in plasma by high-performance liquid chromatography is described. These drugs are extracted from plasma by adding an equal volume of acetonitrile. An aliquot of the extract is then injected on a reversed-phase column with a acetonitrile-methanol-phosphate buffer mobile phase. The total time required for the whole analytical process, including the plasma pretreatment and chromatography, is approximately 30 min. The assay method is simple, rapid and reproducible, and therefore considered suitable for routine use in clinical investigations monitoring HEPP simultaneously with common antiepileptic drugs.     

Virtual taphonomy: A new method integrating excavation and postprocessing in an archaeological context

The objective of this paper was to integrate excavation and post‐processing of archaeological and osteological contexts and material to enhance the interpretation of these with specific focus on the taphonomical aspects. A method was designed, Virtual Taphonomy, based on the use and integration of image‐based 3D modeling techniques into a 3D GIS platform, and tested on a case study. Merging the 3D models and a database directly in the same virtual environment allowed the authors to fully integrate excavation and post‐processing in a complex spatial analysis reconnecting contexts excavated on different occasions in the field process. The case study further demonstrated that the method enabled a deeper understanding of the taphonomic agents at work and allowed the construction of a more detailed interpretation of the skeletal remains than possible with more traditional methods. The method also proved to add transparency to the entire research process from field to post‐processing and interpretation. Other benefits were the timesaving aspects in documentation, not only in the excavation process but also in post‐processing without creating additional costs in material, as the equipment used is available in most archaeological excavations. The authors conclude that this methodology could be employed on a variety of investigations from archaeological to forensic contexts and add significant value in many different respects (for example, detail, objectivity, complexity, time‐efficiency) compared to methods currently used. Am J Phys Anthropol 157:305–321, 2015. © 2015 Wiley Periodicals, Inc.     

A new evaluation method for quantifying PI3K activity by HTRF assay

PIK3CA, coding a catalytic subunit of PI3K p110α, is frequently mutated in cancer. In previous studies, p110α with hotspot mutations such as E545K and H1047R were shown to be gain-of-function mutations. However, quantitative evaluation of these mutants was not well established. Recently, a new method for measuring PI3K activity using homogeneous time-resolved fluorescence (HTRF) has been developed. Using this method, we constructed a quantitative evaluation system for PI3K activity. Serial dilutions of standard PIP3 were subjected to the PI3K-HTRF assay in order to establish a regression line for calibration. The recombinant FLAG-tagged p110α proteins were engineered together with a regulatory subunit p85α in human embryonic kidney 293T cells. Anti-FLAG-Ig immunoprecipitates were then subjected to the assay, which enabled us to quantitatively evaluate the activities of hotspot mutants of p110α. We believe this method will also be applicable to the evaluation of p110α having uncharacterized mutations found in cancer.