Microarray gene expression analysis free of reverse transcription and dye labeling

A new microarray system has been developed for gene expression analysis using cationic gold nanoparticles with diameters of 250 nm as a target detection reagent. The approach utilizes nonlabeled target molecules hybridizing with complementary probes on the array, followed by incubation in a colloidal gold solution. The hybridization signal results from the precipitation of nanogold particles on the hybridized spots due to the electrostatic attraction of the cationic gold particles and the anionic phosphate groups in the target DNA backbone. In contrast to conventional fluorescent detection, this nanoparticle-based detection system eliminates the target labeling procedure. The visualization of hybridization signals can be accomplished with a flatbed scanner instead of a confocal laser scanner, which greatly simplifies the process and reduces the cost. The sensitivity is estimated to be less than 2 pg of DNA molecules captured on the array surface. The signal from hybridized spots quantitatively represents the amount of captured target DNA and therefore permits quantitative gene expression analysis. Cross-array reproducibility is adequate for detecting twofold or less signal changes across two microarray experiments.     

Real-time detection of DNA hybridization on microarray using a CCD-based imaging system equipped with a rotated microlens array disk

This work describes a novel charge-coupled device (CCD)-based imaging system (MB Biochip Reader?) for real-time detection of DNA hybridization to DNA microarrays. The MB Biochip Reader? consisted of a laser light source (532 nm), a microlens array for generation of a multi-beam laser, and a CCD for 2-D signal imaging. The MB Biochip Reader? with a rotated microlens array, allowed large-field imaging (6.2 mm × 7.6 mm with 6.45 μm resolution) with fast time-resolution at 0.2 s without speckle noise. Furthermore, real-time detection of DNA hybridization, which is sufficient to obtain accurate data from tens of thousands of array element per field, was successfully performed without the need for laser scanning. The performance of the MB Biochip Reader? for DNA microarray imaging was similar to the commercially available photomultiplier tube (PMT)-based microarray scanner, ScanArray Lite. The system potentially could be applied toward real-time analysis in many other fluorescent techniques in addition to real-time DNA microarray analysis.     

Accurate determination of cobalt traces in several biological reference materials

A newly devised, very accurate (“definitive”) method for the determination of trace amounts of cobalt in biological materials was validated by the analysis of several certified reference materials. The method is based on a combination of neutron activation and selective and quantitative postirradiation isolation of radiocobalt from practically all other radionuclides by ion-exchange and extraction chromatography followed by γ-ray spectrometric measurement. The significance of criteria that should be fulfilled in order to accept a given result as obtained by the “definitive method” is emphasized. In view of the demonstrated very good accuracy of the method, it is suggested that our values for cobalt content in those reference materials in which it was originally not certified (SRM 1570 spinach, SRM 1571 orchard leaves, SRM 1577 bovine liver, and Czechoslovak bovine liver 12-02-01) might be used as provisional certified values.     

In vivo monitoring of pancreatic beta-cells in a transgenic mouse model

We generated a transgenic mouse model (RIP-luc) for the in vivo monitoring of pancreatic islet mass and function in response to metabolic disease. Using the rat insulin promoter fused to firefly luciferase, and noninvasive technology to detect luciferase activity, we tracked changes in reporter signal during metabolic disease states and correlated the changes in luciferase signal with metabolic status of the mouse. Transgene expression was found to be specific to the pancreatic islets in this transgenic model. Basal transgene expression was tracked in male and female mice fed either a chow or a high-fat diet and in response to treatment with streptozotocin. Pancreatic bioluminescent signal increased in mice fed a high-fat diet compared with chow-fed animals. In a model of chemically induced diabetes, the bioluminescent signal decreased in accordance with the onset of diabetes and reduction of islet beta-cell number. Preliminary studies using islets transplanted from this transgenic model suggest that in vivo image analysis can also be used to monitor transplanted islet viability and survival in the host. This transgenic model is a useful tool for in vivo studies of pancreatic beta-cells and as a donor for islet transplantation studies.     

基于夹心免疫分析的抗体微阵列的构建

目的：建立一种基于夹心免疫分析的抗体微阵列构建的优化方法。方法：将MCP-1的捕获抗体点样于修饰后的玻片,标准抗原加样覆盖所点阵列,生物素标记抗体和链酶亲和素-cy3依次加样孵育, 激光共聚焦扫描仪获取图象并进行数据分析。对捕获抗体浓度、封闭液种类、系统可重复性和定量检测能力、两种因子平行性检测对信号分析的影响及点样后玻片稳定性进行分析和评价。结果：随着捕获抗体浓度的升高,信号强度逐渐增加;2℅ BSA/PBS和5℅ 酪蛋白可作为本系统的封闭液;所构建系统具有较好的可重复性（组内变异 1.3%,组间变异8.7%）和定量分析能力（所建立的抗原浓度-相对信号强度标准曲线相关系数达0.9995）;并实现了两因子的平行性分析和点样后玻片的稳定性。结论：确立了基于夹心免疫分析的抗体微阵列构建的优化方法,为进一步构建多因子定量检测抗体微阵列奠定了基础。     

Direct observation of the structural change of Tyr174 in the primary reaction of sensory rhodopsin II

Sensory rhodopsin II (SRII) is a negative phototaxis receptor containing retinal as its chromophore, which mediates the avoidance of blue light. The signal transduction is initiated by the photoisomerization of the retinal chromophore, resulting in conformational changes of the protein which are transmitted to a transducer protein. To gain insight into the SRII sensing mechanism, we employed time-resolved ultraviolet resonance Raman spectroscopy monitoring changes in the protein structure in the picosecond time range following photoisomerization. We used a 450 nm pump pulse to initiate the SRII photocycle and two kinds of probe pulses with wavelengths of 225 and 238 nm to detect spectral changes in the tryptophan and tyrosine bands, respectively. The observed spectral changes of the Raman bands are most likely due to tryptophan and tyrosine residues located in the vicinity of the retinal chromophore, i.e., Trp76, Trp171, Tyr51, or Tyr174. The 225 nm UVRR spectra exhibited bleaching of the intensity for all the tryptophan bands within the instrumental response time, followed by a partial recovery with a time constant of 30 ps and no further changes up to 1 ns. In the 238 nm UVRR spectra, a fast recovering component was observed in addition to the 30 ps time constant component. A comparison between the spectra of the WT and Y174F mutant of SRII indicates that Tyr174 changes its structure and/or environment upon chromophore photoisomerization. These data represent the first real-time observation of the structural change of Tyr174, of which functional importance was pointed out previously.     

An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression

The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12–14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.     

Aminoquinolines as fluorescent labels for hydrophilic interaction liquid chromatography of oligosaccharides

Abstract In this study, we investigated the potential of four different aminoquinoline (AQ) compounds as fluorescent labels for glycan analysis using hydrophilic interaction liquid chromatography (HILIC) and fluorescence detection (FLD). We confirmed the optimal excitation and emission wavelengths of 3-AQ and 6-AQ conjugated to glycan standards using three-dimensional fluorescent spectral scanning. The optimal excitation and emission wavelengths for 6-AQ were confirmed at λex=355 nm and λem=440 nm. We concluded that the optimal wavelengths for 3-AQ were λex=355 nm and λem=420 nm, which differed considerably from the wavelengths applied in previous reports. HILIC-FLD chromatograms using experimentally determined wavelengths were similar to 2-aminobenzamide controls, but the peak capacity and resolution differed significantly when published 3-AQ λex/em values were applied. Furthermore, we found that 5-AQ and 8-AQ labeled maltohexaose did not display any fluorescent pro\xadperties when used as a carbohydrate tag for HPLC analysis. Finally, we applied experimentally determined wavelengths to 3-AQ labeled N-glycans released from human IgG to illustrate changes in retention time as well as to demonstrate that AQ labeling is applicable to complex sample analysis via exoglycosidase sequencing.     

Action spectra of the female's response in the firefly Photinus pyralis (Coleoptera: Lampyridae): evidence for an achromatic detection of the bioluminescent optical signal

Behavioural action spectra of the threshold of the Photinus pyralis female response to light stimuli simulating the bioluminescent optical signal of the conspecific male firefly were determined in the laboratory. The action spectra (Fig. 1) were narrow and peaked in the yellow region of the spectrum. The females responded only to stimuli of wavelengths longer than 480 nm and not to stimuli in the blue (420-460 nm) part of the spectrum. The shape of the function corresponds with (a) the electroretinographic spectral sensitivity function in the long wavelength (520-660 nm) region of the spectrum, (b) the action spectrum of the female response (Fig. 1), (c) the species yellow bioluminescence emission spectrum and (d) the action spectrum of the intracellular response from single retinular cells (Fig. 2) of the compound eyes in the firefly. Such a correspondence suggests that the narrow yellow receptors of the female mediate the detection and processing of the optical signal of the conspecific male. Since the bioluminescent optical signal is processed exclusively by a single receptor class, signal detection is achromatic.     

Microchamber array based DNA quantification and specific sequence detection from a single copy via PCR in nanoliter volumes

A novel method for DNA quantification and specific sequence detection in a highly integrated silicon microchamber array is described. Polymerase chain reaction (PCR) mixture of only 40 nL volume could be introduced precisely into each chamber of the mineral oil layer coated microarray by using a nanoliter dispensing system. The elimination of carry-over and cross-contamination between microchambers, and multiple DNA amplification and detection by TaqMan chemistry were demonstrated, for the first time, by using our system. Five different gene targets, related to Escherichia coli were amplified and detected simultaneously on the same chip by using DNA from three different serotypes as the templates. The conventional method of DNA quantification, which depends on the real-time monitoring of variations in fluorescence intensity, was not applied to our system, instead a simple method was established. Counting the number of the microchambers with a high fluorescence signal as a consequence of TaqMan PCR provided the precise quantification of trace amounts of DNA. The initial DNA concentration for Rhesus D (RhD) gene in each microchamber was ranged from 0.4 to 12 copies, and quantification was achieved by observing the changes in the released fluorescence signals of the microchambers on the chip. DNA target could be detected as small as 0.4 copies. The amplified DNA was detected with a CCD camera built-in to a fluorescence microscope, and also evaluated by a DNA microarray scanner with associated software. This simple method of counting the high fluorescence signal released in microchambers as a consequence of TaqMan PCR was further integrated with a portable miniaturized thermal cycler unit. Such a small device is surely a strong candidate for low-cost DNA amplification, and detected as little as 0.4 copies of target DNA.     

Bilirubin dehydrogenase,an enzyme in Aspergillus ochraceus IB-3 useful for diagnostic measurement of bilirubin

Bilirubin dehydrogenase, a membrane-bound enzyme that catalyzes the one-step oxidation of ditaurobilirubin and bilirubin to ditaurobiliverdin and biliverdin, respectively, in the presence of an electron acceptor, was found in Aspergillus ochraceus IB-3, and purified from the membrane fraction through solubilization by Triton X-100. Phenazine and quinone derivatives acted as electron acceptors. Accumulation of ditaurobiliverdin and biliverdin by enzyme catalysis increased the absorbance at 660 nm, which is far from the range of wavelengths affected by serum ingredients. The enzyme selectively oxidized ditaurobilirubin at low pH, so changes in the reaction pH enable the enzyme to discriminate between the bilirubin fractions ditaurobilirubin (an example of conjugated bilirubin) and bilirubin (an example of unconjugated bilirubin). Using the enzyme, 2 to 80 microM of ditaurobilirubin were measured accurately by monitoring the changes in absorbance at 660 nm.     

Monitoring recombinant inclusion body recovery in an industrial disc stack centrifuge

A simple and rapid spectrophotometric method for measuring recombinant inclusion body concentrations in the presence of Escherichia coli cell debris has been applied to monitoring the performance of an industrial disc stack centrifuge. Turbidimetric measurements were made at two wavelengths, i.e., 600 nm and 420 nm, and the ratios of OD(600nm)/OD(420nm) related to the particle composition in suspension. The principle behind the technique is that inclusion body particles scatter light at 600 nm more effectively than do smaller cell debris particles when compared with the degree of light scatter at 420 nm. This technique may have broad potential application in developing an automatic monitoring and control system for industrial-scale inclusion body recovery. (c) 1994 John Wiley & Sons, Inc.     

Signal stability of Cy3 and Cy5 on antibody microarrays

Background  

The antibody microarray technique is a newly emerging proteomics tool for differential protein expression analyses that uses fluorescent dyes Cy 3 and Cy 5. Environmental factors, such as light exposure, can affect the signal intensity of fluorescent dyes on microarray slides thus, it is logical to scan microarray slides immediately after the final wash and drying processes. However, no research data are available concerning time-dependent changes of fluorescent signals on antibody microarray slides to this date. In the present study, microarray slides were preserved at -20°C after regular microarray experiments and were rescanned at day 10, 20 and 30 to evaluate change in signal intensity.     

Innovative instrumentation for microarray scanning and analysis: application for characterization of oligonucleotide duplexes behavior.

Accuracy in microarray technology requires new approaches to microarray reader development. A microarray reader system (optical scanning array or OSA reader) based on automated microscopy with large field of view, high speed 3 axis scanning at multiple narrow-band spectra of excitation light has been developed. It allows fast capture of high-resolution, multi-fluorescence images and is characterized by a linear dynamic range and sensitivity comparable to commonly used photo-multiplier tube (PMT)-based laser scanner. Controlled by high performance software, the instrument can be used for scanning and quantitative analysis of any type of dry microarray. Studies implying temperature-controlled hybridization chamber containing a microarray can also be performed. This enables the registration of kinetics and melting curves. This feature is required in a wide range of on-chip chemical and enzymatic reactions including on-chip PCR amplification. We used the OSA reader for the characterization of hybridization and melting behaviour of oligonucleotide:oligonucleotide duplexes on three-dimensional Code Link slides.     

Light-Induced Pigment Aggregation in Xanthophores of the Medaka,Oryzias latipes

The response mechanism of medaka xanthophores to light was examined at the cellular level. Innervated and denervated xanthophores of adult medakas responded to light (9,000 lux) within 30 sec by pigment aggregation, and this aggregation was not mediated through α-adrenoceptors on the cell membrane. Maximum sensitivity to light was at wavelengths of 410–420 nm, and the direct effect of light was reversible. Xanthophore responsiveness to light in summer was higher than that in winter. Ca²⁺ and calmodulin were not involved in the response, but rather, an important role for cAMP and phos-phodiesterase (PDE) was suggested. It seems likely that photoreception by visual pigment which is sensitive to light at wavelengths of 410–420 nm increases PDE activity, probably via a G-protein, such as occurs with visual cells in the retina, which causes a decrease in levels of cytosolic cAMP, in turn leading to pigment aggregation within medaka xanthophores.     

Optical signals from surface and T system membranes in skeletal muscle fibers. Experiments with the potentiometric dye NK2367

Absorbance signals were recorded from cut single skeletal muscle fibers stained with the nonpenetrating potentiometric dye NK2367 and mounted in a three-vaseline-gap voltage clamp. The characteristics of the optical signals recorded under current and voltage-clamp conditions were studied at various wavelengths between 500 and 800 nm using unpolarized light. Our results indicate that the absorbance signals recorded with this dye reflect potential changes across both the surface and T system membranes and that the relative contribution of each of these membrane compartments to the total optical change is strongly wavelength dependent. A peak intensity change was detected at 720 nm for the surface membrane signal and at 670 nm for the T system. Evidence for this wavelength-dependent separation derives from an analysis of the kinetics and voltage dependence of the optical signals at different wavelengths, and results obtained in detubulated fibers. The 670-nm optical signal was used to demonstrate the lack of potential control in the T system by the voltage clamp and the effect of a tetrodotoxin (TTX)-sensitive sodium conductance on tubular depolarization.     

落叶松林土壤溶液吸光度与土壤碳、氮含量的相关性

通过4个土壤深度100个样品14个波长(250、254、260、265、272、280、285、300、340、350、365、400、436和465 nm)土壤溶液吸光度值和土壤碳(可溶性碳DOC、全碳SOC)、土壤氮(可溶性氮DON、全氮SON)的测定,旨在探讨土壤溶液吸光度指示土壤碳氮指标的可行性及土壤深度对其可能影响。结论如下:(1)表层土壤和深层土壤吸光度值均随波长增加而指数下降,但表层土壤吸光度值较高,下降速度较快,较低波长更有利于区分表层和深层土壤溶液吸光度差异;和深层土壤相比,表层0～20 cm土壤SOC、DON和SON与不同波长吸光度有更好的相关性,但DOC与不同波长吸光度的相关性表层和深层差异较小;(2)250～300 nm的8个吸光度值具有高度相关性,它们在分析土壤溶液吸光度变化时具有等效性;基于所有数据的拟合分析发现,低波长(如254 nm)吸光度与土壤SOC、DON和SON相关性最高(R2=0.53～0.59),而更高波长(340 nm及以上)相关性明显降低。但DOC与254、340、365和400 nm吸光度相关性相差不大(R2=0.25～0.33)。这些发现说明,土壤溶液吸光度值,特别是低波长(250～300 nm)可以表征落叶松林土壤碳、氮相关指标的变化,但是需要考虑不同碳氮指标以及不同土层之间的差异。     

Evaluating quantum yield and ultraviolet–visible reflectance in baby pumpkins: Implications for oviposition behavior of pumpkin fruit flies

Frugivorous insects utilize both olfactory and visual cues to locate their host plants. Although volatiles have been extensively studied for detecting infested fruits, the role of visual cues in oviposition site selection remains mostly unknown among frugivorous insects. To investigate physiological changes in a host plant, we measured the quantum yield and reflectance of three wavelengths of light (350, 450 and 520 nm) after puncturing the surfaces of commercially grown pumpkins using insect pins during two different seasons outdoors. Quantum yields did not show significant differences between undamaged and simulated oviposition sites. Two wavelengths within the visual spectrum were similar between the two treatments. However, photon counts at 350 nm, in the ultraviolet range, were 1.76 fold higher in simulated oviposition sites than in undamaged sites, which was consistently observed across three field seasons. Considering that frugivorous insects and other phytophagous insects recognize the 350 nm wavelength for host identification and oviposition, we conclude that the disparities in ultraviolet reflectance can serve as a baseline for assessing the actual oviposition response of fruit flies. This finding contributes to the role of visual cues in the oviposition behavior of frugivorous insects and the development of a nondestructive detection method for pumpkin fruit flies.     

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology

Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small-molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis-driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot-gun-based tandem MS (LC-MS/MS) methods. Unlike LC-MS/MS, which requires computationally intensive informatic postanalysis, SRM requires preacquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web-based and stand-alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC-MS data acquired by SRM.