Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

Case study on a deep excavation in soft ground by centrifuge model tests

This paper provides a case study on the deepest excavation carried out so far in the construction of the metro network in Shanghai, which typically features soft ground. The excavation is 38 m deep with retaining walls 65 m deep braced by 9 levels of concrete props. To obtain a quick and rough prediction, two centrifuge model tests were conducted, in which one is for the 'standard' section with green field surrounding and the other with an adjacent piled building. The tests were carried out in a run-stop-excavation-run style, in which excavation was conducted manually. By analyzing the lateral wall displacement, ground deformation, bending moment and earth pressure, the test results are shown to be reasonably convincing and the design and construction were validated. Such industry orientated centrifuge modeling was shown to be useful in understanding the performance of geotechnical processes, especially when engineers lack relevant field experience. © 2010 Taylor & Francis Group, London.

Enhancement of Construction Equipment Detection in Video Frames by Combining with Tracking

Vision-based object detection has been introduced in construction for recognizing and locating construction entities in on-site camera views. It can provide spatial locations of a large number of entities, which is beneficial in large-scale, congested construction sites. However, even a few false detections prevent its practical applications. In resolving this issue, this paper presents a novel hybrid method for locating construction equipment that fuses the function of detection and tracking algorithms. This method detects construction equipment in the video view by taking advantage of entities' motion, shape, and color distribution. Background subtraction, Haar-like features, and eigen-images are used for motion, shape, and color information, respectively. A tracking algorithm steps in the process to make up for the false detections. False detections are identified by catching drastic changes in object size and appearance. The identified false detections are replaced with tracking results. Preliminary experiments show that the combination with tracking has the potential to enhance the detection performance.

Changes in the Mg profile and in dislocations induced by high temperature annealing of blue LEDs

The efficiency of the injection and recombination processes in InGaN/GaN LEDs is governed by the properties of the active region of the devices, which strongly depend on the conditions used for the growth of the epitaxial material. To improve device quality, it is very important to understand how the high temperatures used during the growth process can modify the quality of the epitaxial material. With this paper we present a study of the modifications in the properties of InGaN/GaN LED structures induced by high temperature annealing: thermal stress tests were carried out at 900 °C, in nitrogen atmosphere, on selected samples. The efficiency and the recombination dynamics were evaluated by photoluminescence measurements (both integrated and time-resolved), while the properties of the epitaxial material were studied by Secondary Ion Mass Spectroscopy (SIMS) and Rutherford Backscattering (RBS) channeling measurements. Results indicate that exposure to high temperatures may lead to: (i) a significant increase in the photoluminescence efficiency of the devices; (ii) a decrease in the parasitic emission bands located between 380 nm and 400 nm; (iii) an increase in carrier lifetime, as detected by time-resolved photoluminescence measurements. The increase in device efficiency is tentatively ascribed to an improvement in the crystallographic quality of the samples. © 2013 SPIE.

Rapid quantification of total microcystins in cyanobacterial samples by periodate-permanganate oxidation and reversed-phase liquid chromatography

Microcystins (MCs) comprise a family of more than 80 related cyclic hepatotoxic heptapeptides. Oxidation of MCs causes cleavage of the chemically unique C-20 beta-amino acid (2S, 3S, 8S, 9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (Adda) amino to form 2-methyl-3-methoxy-4-phenylbutanoic acid (MMPB), which has been exploited to enable analysis of the entire family. In the present study, the reaction conditions (e.g. concentration of the reactants. temperature and pH) used in the production of MMPB by oxidation of cyanobacterial samples with permanganate-periodate were optimized through a series of well-controlled batch experiments. The oxidation product (MMPB) was then directly analyzed by high-performance liquid chromatography with diode array detection. The results of this study provided insight into the influence of reaction conditions on the yield of MMPB. Specifically, the optimal conditions, including a high dose of permanganate (>= 50 mM) in saturated periodate solution at ambient temperature under alkaline conditions (pH similar to 9) over 1-4 h were proposed, as indicated by a MMPB yield of greater than 85%. The technique developed here was applied to determine the total concentration of MCs in cyanobacterial bloom samples, and indicated that the MMPB technique was a highly sensitive and accurate method of quantifying total MCs. Additionally, these results will aid in development of a highly effective analytical method for detection of MMPB as an oxidation product for evaluation of total MCs in a wide range of environmental sample matrices, including natural waters, soils (sediments) and animal tissues. (C) 2009 Elsevier B.V. All rights reserved.

Quantitative Determination of Microcystins in Rat Plasma by LC-ESI Tandem MS

A rapid and sensitive method was developed and validated for the determination of MCYST (microcystin)-RR, -LR, and [Dha(7)] MCYST-LR in rat plasma by liquid chromatography-tandem mass spectrometry. The analytes were extracted from rat plasma by protein precipitation, followed by solid-phase extraction. Liquid chromatography with electrospray ionization mass spectrometry, operating in selected reaction monitoring (SRM) mode, was used to quantify MCYST-RR, -LR, and [Dha(7)] MCYST-LR in rat plasma. The recoveries for each analyte in rat plasma ranged from 70.8 to 88.7%. The calibration curve was linear within the range from 0.005 to 1.25 mu g mL(-1). The limit of detection were 1.4, 1.0, 0.6 ng mL(-1) for MCYST-RR, -LR, and [Dha(7)] MCYST-LR. The overall precision was determined on three different days. The values for within- and between-day precision in rat plasma were within 15%. This method was applied to the identification and quantification of microcystins in rat plasma with acute exposure of microcystins via intravenous injection.

Simultaneous determination of microcystin-LR and its glutathione conjugate in fish tissues by liquid chromatography-tandem mass spectrometry

A sensitive and selective liquid chromatography-tandem mass spectrometry method was developed and validated for the simultaneous quantitative determination of microcystin-LR (MC-LR) and its glutathione conjugate (MC-LR-GSH) in fish tissues. The analytes were extracted from fish liver and kidney using 0.01 M EDTA-Na-2-5% acetic acid, followed by a solid-phase extraction (SPE) on Oasis HLB and silica cartridges. High-performance liquid chromatography (HPLC) with electrospray ionization mass spectrometry, operating in selected reaction monitoring (SRM) mode, was used to quantify MC-LR and its glutathione conjugate in fish liver and kidney. Recoveries of analytes were assessed at three concentrations (0.2, 1.0, and 5 mu g g(-1) dry weight [DW]) and ranged from 91 to 103% for MC-LR, and from 65.0 to 75.7% for MC-LR-GSH. The assay was linear within the range from 0.02 to 5.0 mu g g(-1) DW, with a limit of quantification (LOQ) of 0.02 mu g g(-1) DW. The limit of detection (LOD) of the method was 0.007 mu g g(-1) DW in both fish liver and kidney. The overall precision was determined on three different days. The values for within- and between-day precision in liver and kidney were within 15%. This method was applied to the identification and quantification of MC-LR and its glutathione conjugate in liver and kidney of fish with acute exposure of MC-LR. (c) 2007 Elsevier B.V. All rights reserved.

Knock down of gfp and no tail expression in zebrafish embryo by in vivo-transcribed short hairpin RNA with T7 plasmid system

A short-hairpin RNA (shRNA) expression system, based on T7 RNA polymerase (T7RP) directed transcription machinery, has been developed and used to generate a knock down effect in zebrafish embryos by targeting green fluorescent protein (gfp) and no tail (ntl) mRNA. The vector pCMVT7R harboring T7RP driven by CMV promoter was introduced into zebrafish embryos and the germline transmitted transgenic individuals were screened out for subsequent RNAi application. The shRNA transcription vectors pT7shRNA were constructed and validated by in vivo transcription assay. When pT7shGFP vector was injected into the transgenic embryos stably expressing T7RP, gfp relative expression level showed a decrease of 68% by analysis of fluorescence real time RT-PCR. As a control, injection of chemical synthesized siRNA resulted in expression level of 40% lower than the control when the injection dose was as high as 2 mu g/mu l. More importantly, injection of pT7shNTL vector in zebrafish embryos expressing T7RP led to partial absence of endogenous ntl transcripts in 30% of the injected embryos when detected by whole mount in situ hybridization. Herein, the T7 transcription system could be used to drive the expression of shRNA in zebrafish embryos and result in gene knock down effect, suggesting a potential role for its application in RNAi studies in zebrafish embryos.

Development of novel EST-SSR markers in common carp by data mining from public EST sequences

Expressed sequence tags (ESTs) are a source for microsatellite development. In the present study, EST-derived microsatelltes (EST-SSRs) were generated and characterized in the common carp (Cyprinus carpio) by data mining from updated public EST databases and by subsequent testing for polymorphism. About 5.5% (555) of 10,088 ESTs contain repeat motifs of various types and lengths with CA being the most abundant dinucleotide one. Out of the 60 EST-SSRs for which PCR primers were designed, 25 loci showed polymorphism in a common carp population with the alleles per locus ranging from 3 to 17 (mean 7). The observed (H-O) and expected (HE) heterozygosities of these EST-SSRs were 0.13-1.00 and 0.12-0.91, respectively. Six EST-SSR loci significantly deviated from the Hardy-Weinberg equilibrium (HWE) expectation, and the remaining 19 loci were in HWE. Of the 60 primer sets, the rates of polymorphic EST-SSRs were 42% in common carp, 17% in crucian carp (Carassius auratus), and 5% in silver carp (Hypophthalmichthys molitrix), respectively. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of the common carp and its closely related fishes. (c) 2007 Published by Elsevier B.V.

Determination of sexual hormones in liquid cosmetics by polymer monolith microextraction coupled with high performance liquid chromatography

A method was presented for the determination of testosterone, methyltestosterone and progesterone in liquid cosmetics by coupling polymer monolith microextraction (PMME) to high performance liquid chromatography with UV detection. A poly (methacrylic acid-ethylene glycol dimethacrylate) monolithic capillary column was selected as the extraction medium, which showed high extraction capacity towards these compounds. To achieve optimum extraction performance, several parameters relating to PMME were investigated, including extraction flow rate and pH value, inorganic salt and organic phase concentration of the sample matrix. By simple dilution with phosphate solution and filtering, the sample solution then could be directly injected into the device for extraction. The limits of detection of testosterone, methyltestosterone and progesterone were calculated to be 2, 3, 2, 8 and 4.6 mu g/L. Good linearity was achieved in the range of 10 to 1000 mu g/L with a linear coefficient. r value above 0. 996. Excellent method reproducibility was found by intra- and inter-day precisions, yielding the relative standard deviations of < 7. 7 % and < 7. 5 %, respectively. Recovery for them in the real samples was between 83% and 119%.

Simultaneous determination of chromium(VI) and chromium(III) of bioavailable fraction in bottom mud by flow injection-atomic absorption spectroscopy

A rapid and sensitive method for separation and determination of Cr(VI) and Cr(III) in bottom mud of lake by flow injection on-line preconcentrtion system and GFAAS was developed. The available Cr(VI) and Cr(III) were extracted by HOAc or EDTA + NH4 NO3 and adsorbed simultaneously by an anion and a cation resin microclummn and then eluted simultaneously by 2 mol/L NH4 NO3 + 0.05 mol/L ascorbate and 2 mol/L H2SO4, respectively. The elution was performed for 50 s after adsorption for 2 min, and the efficiencies of elution were 85.4% - 94.8% and 96.7% - 106% for Cr(VI) and Cr(M) respectively. The detection limits of the method were 0.9 mu g/L and 2.7 mu g/L with relative standard deviations of 3.5% and 6.4% for the determination of Cr(VI) and Cr(III) in sample, respectively.

Determinations of residual furazolidone and its metabolite, 3-amino-2-oxazolidinone (AOZ), in fish feeds by HPLC-UV and LC-MS/MS, respectively

The antibacterial drug furazolidone belonging to the group of nitrofuran antibacterial agents has been widely used as an antibacterial and antiprotozoal feed additive for poultry, cattle, and farmed fish in China. During application a large proportion of the administered drug may reach the environment directly or via feces. Although the use of furazolidone is prohibited in numerous countries, there are indications of its illegal use. It is known that furazolidone can be rapidly metabolized to 3-amino-2-oxazolidinone (AOZ) in the body of the target organism. In this study, a total of 21 fish feed samples, including 17 commercial fish feeds from local markets in China (representing 15 different formulations) and 4 fish feeds obtained from Germany and Turkey, respectively, are analyzed to determine whether the drug is still illegally used or commercially available feeds are contaminated by this drug. High-performance liquid chromatography (HPLC) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) methods have been implemented to determine furazolidone and its metabolite AOZ in fish feeds containing animal protein, respectively. An efficient and convenient cleanup method for the determination of furazolidone in fish feeds is developed, and a simple cleanup method for the determination of AOZ is used. Method recoveries for samples used were determined as 87.7-98.3% for furazolidone at two spike levels of 2.0 and 5.0 ng g(-1) and as 95.6-102.8% for AOZ at spike levels of 0.4 and 0.8 ng g(-1). Limits of detections were 0.4 ng g(-1) for furazolidone and 0.05 ng g(-1) for AOZ. The established methods are therefore suitable for the determination of furazolidone and its metabolite AOZ in fish feeds at trace contamination levels. Using the established methods, all fish feed samples have been proved to be furazolidone negative; however, AOZ is tested in 16 of 17 fish feeds obtained from local markets in the Hubei province of China, with a positive rate as high as 94.1%.

Degradation of 17 alpha-ethinylestradiol in aqueous solution by ozonation

This study investigates the ozonation of 17 alpha-ethinylestradiol (EE2) in aqueous solution. The affecting factors on the degradation of EE2 were studied and described in details, such as initial EE2 concentration, initial pH value and ozone concentration. In addition, some parameters such as pH. electrical conductivity, mineralization efficiency and degradation products were monitored during the process. The mineralization efficiency of EE2 could reach 53.9%. During the ozonation process the rapid decrease of pH and the sharp increase of electrical conductivity indicated the fort-nation of acidic by-products, small fragments and ions which were confirmed by high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GUMS) analysis. Results showed that there were intermediate products of smaller molecule with higher polarity produced during the course of EE2 degradation. Then a possible reaction pathway for EE2 degradation involving all intermediates detected is proposed. During the ozonation process EE2 was first oxidized into hydroxyl-semiquinone isomers which were subsequently degraded into low molecular weight compounds such as oxalic acid, malonate, glutarate, and so on. Furthermore. these organic acids are easily oxidized by ozone into carbon dioxide (CO2). This work shows that ozonation process is promising for the removal of EE2. The results can provide some useful information for the potential treatment of EE2 by ozonation in aqueous solution. (c) 2005 Elsevier B.V. All rights reserved.