A novel approach for dimension reduction of microarray

This paper proposes a new hybrid search technique for feature (gene) selection (FS) using Independent component analysis (ICA) and Artificial Bee Colony (ABC) called ICA + ABC, to select informative genes based on a Naïve Bayes (NB) algorithm. An important trait of this technique is the optimization of ICA feature vector using ABC. ICA + ABC is a hybrid search algorithm that combines the benefits of extraction approach, to reduce the size of data and wrapper approach, to optimize the reduced feature vectors. This hybrid search technique is facilitated by evaluating the performance of ICA + ABC on six standard gene expression datasets of classification. Extensive experiments were conducted to compare the performance of ICA + ABC with the results obtained from recently published Minimum Redundancy Maximum Relevance (mRMR) +ABC algorithm for NB classifier. Also to check the performance that how ICA + ABC works as feature selection with NB classifier, compared the combination of ICA with popular filter techniques and with other similar bio inspired algorithm such as Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). The result shows that ICA + ABC has a significant ability to generate small subsets of genes from the ICA feature vector, that significantly improve the classification accuracy of NB classifier compared to other previously suggested methods.     

Systematic ratio normalization of gas chromatography signals for biological sample discrimination and biomarker discovery

The present paper introduces a new gas chromatography data processing procedure dubbed systematic ratio normalization (SRN) enabling to improve both sample set discrimination and biomarker identification. SRN consists in (1) calculating, for each sample, all the log-ratios between abundances of chromatography-analyzed compounds, then (2) selecting the log-ratio(s) that best maximize the discrimination between sample-sets. The relevance of SRN was evaluated on two data sets acquired through gas chromatography–mass spectrometry as part of separate studies designed (i) to discriminate source-origins between vegetable oils analyzed via an analytical system exposed to instrument drift (data set 1) and (ii) to discriminate animal feed between meat samples aged for different durations (data set 2). Applying SRN to raw data made it possible to obtain robust discrimination models for the two data sets by enhancing the contribution to the data variance of the factor-of-interest while stabilizing the contribution of the disturbance factor. The most discriminant log-ratios were shown to employ the most relevant biomarkers presenting relative independence of the factor-of-interest as well as co-behavior of the disturbance effects potentially biasing the discrimination, such as instrument drift or sample biochemical changes. SRN can be run a posteriori on any data set, and might be generalizable to most of separating methods.     

Effect of local background intensities in the normalization of cDNA microarray data with a skewed expression profiles

Normalization of the data of cDNA microarray is an obligatory step during microarray experiments due to the relatively frequent non-specific errors. Generally, normalization of microarray data is based on the null hypothesis and variance model. In the Yang's model (Yang et al., 2001), at least two types of noises are included. The one is additive noise and the other is multiplicative noise. Usually, background is considered as one of additive noise to the signal and the variation between the signal pixels is the representative multiplicative noise. In this study, the relation between the signal (spot intensity minus background intensity) and background was observed and the influence of background on normalization as a representative additive factor was investigated. Although the relation has not been considered as a factor affecting the normalization, it could improve the accuracy of microarray data when the normalization was carried out considering signal/background ratio. The background dependent normalization decreased the number of genes whose expression levels were changed significantly and it could make their distribution more consistent through the whole range of signal intensities. In this study, printing pin dependent normalization was also carried out regarding the printing pin as a representative multiplicative noise. It improved the distribution of spots in the Cy3-Cy5 scatter plot, but its effect was slight. These studies suggest that there are some influences of the signals on the local backgrounds and they must be considered for the normalization of cDNA microarray data.     

Strategies for immobilization of biomolecules in a microarray

Recent advances in the generation of peptide and protein microarrays are reviewed, with special focuses on different strategies available for site-specific immobilization of proteins and peptides.     

CuO NPs@Starch as a novel chemotherapeutic drug for the treatment of several types of gastrointestinal system cancers including gastric,pancreatic, and colon cancers

Copper oxide nanoparticles were successfully synthesized through a simple and ‘green’ route using starch as a capping and stabilizing agent under ultrasonic irradiation in alkaline medium. Unique reaction condition was prepared by ultrasonic irradiation, releasing the stored energy in the collapsed bubbles and heats the bubble contents that leads to Cu(II) reduction in the presence of starch. The obtained nanoparticle (CuO NPs@Starch) was characterized by advanced physical and chemical techniques like Transmission Electron Microscope (TEM), Fourier-transform infrared spectroscopy (FTIR), Uv–Vis spectroscopy, scanning electron microscopy (SEM), X-ray Diffraction (XRD) and energy-dispersive X-ray analysis (EDX). The properties of CuO NPs@Starch against gastric cancer (AGS and KATO III), pancreatic cancer (AsPC-1 and MIA PaCa-2), and colon cancer (HCT 116 and HCT-8) were evaluated. The viability of malignant cancer cell lines reduced dose-dependently in the presence of CuO NPs@Starch. After clinical study, CuO NPs@Starch can be utilized as an efficient drug in the treatment of gastric, pancreatic, and colon cancers in humans.     

Mass-tag technology responding to intracellular signals as a novel assay system for the diagnosis of tumor

A novel mass spectrometry-based assay system for determining protein kinase activity employing mass-tagged substrate peptide probes was used for the diagnosis of tumors. Two peptide probes (H-type and D-type) were synthesized containing the same substrate peptide sequence for protein kinase C (PKC). The molecular weights of the two probes differ because of the incorporation of deuterium into the acetyl groups of the D-type probe. The lysates of the normal and tumor tissue were prepared and reacted with the H- and D-type peptide probes, respectively. The PKC activities of the normal and tumor tissues can be compared simply and directly by calculating the phosphorylated ratio to each peptide probe, obtained from the peak intensity of the mass spectrum after mixing of the two reaction solutions. The phosphorylation ratio for the reaction of the H-type peptide probe with the tumor tissue lysate (B16 melanoma) was more than three times higher than that of the D type peptide probe with the normal skin tissue lysate. These results show that the novel assay system for detecting protein kinase activity using mass-tag technology can be a simple and useful means to profile protein kinase activity for cell or tissue lysate samples, and can be applied to the diagnosis of tumors.     

Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications

The performance of protein and antibody microarrays is dependent on various factors, one of which is the use of an appropriate microarray surface for the immobilisation of either protein or antibody samples. We have investigated the properties of seven new surfaces in the context of both protein and antibody microarray technology. We have demonstrated the functionality of all new slide coatings and investigated the mean signal to spotted concentration ratio, determined detection limits and calculated coefficients of variation. Moreover, new concepts for slide coatings such as dendrimer and poly(ethylene glycol)-epoxy slides were evaluated and improved qualities of novel slide surfaces were observed. Optimal slide coatings for antibody and protein chips were proposed and the requirements for both technologies were discussed.     

A novel derivatization method for peptides to increase sensitivity and backbone fragmentation in liquid secondary-ion mass spectra.

Derivatization is used to increase both negative-ion sensitivity and positive-ion sequence information in the liquid secondary-ion mass spectra (LSIMS) of a series of peptides. The derivatization method involves acylation with pentafluorobenzoyl fluoride in a single-step reaction, and the reaction mixture is applied directly to the probe tip for analysis. Acylation takes place at the unprotected N-terminus, tyrosine, and lysine. The derivatives exhibit increased signal-to-noise ratio for [M-H]- ions, especially where there is not already an acidic amino acid residue in the peptide. In positive-ion LSIMS, the N-terminal group acts to retain the charge at the N-terminus, simplifying the fragmentation by producing N-terminal fragment ions. It also increases positive-ion fragmentation, sometimes very dramatically, making sequence determination more straightforward. The simplicity of the process, together with the enhancements it provides, make this a generally useful method for obtaining peptide structural information.     

Preclinical studies in normal canine prostate of a novel palladium-bacteriopheophorbide (WST09) photosensitizer for photodynamic therapy of prostate cancers

Photodynamic therapy (PDT) uses light to activate a photosensitizer to achieve localized tumor control. In this study, PDT mediated by a second-generation photosensitizer, palladium-bacteriopheophorbide WST09 (Tookad) was investigated as an alternative therapy for prostate cancer. Normal canine prostate was used as the animal model. PDT was performed by irradiating the surgically exposed prostate superficially or interstitially at 763 nm to different total fluences (100 or 200 J/cm2; 50, 100 or 200 J/cm) at 5 or 15 min after intravenous administration of the drug (2 mg/kg). Areas on the bladder and colon were also irradiated. The local light fluence rate and temperature were monitored by interstitial probes in the prostate. All animals recovered well, without urethral complications. During the 1 week to 3 month post-treatment period, the prostates were harvested for histopathological examination. The PDT-induced lesions showed uniform hemorrhagic necrosis and atrophy, were well delineated from the adjacent normal tissue and increased linearly in diameter with the logarithm of the delivered light fluence. A maximum PDT-induced lesion size of over 3 cm diameter could be achieved with a single interstitial treatment. There was no damage to the bladder or rectum caused by scattered light from the prostate. The bladder and rectum were also directly irradiated with PDT. At 80 J/cm2, a full-depth necrosis was observed but resulted in no perforation. At 40 J/cm2, PDT produced minimal damage to the bladder or rectum. On the basis of optical dosimetry, we have estimated that 20 J/cm2 is the fluence required to produce prostatic necrosis. Thus, the normal structure adjacent to the prostate can be safely preserved with careful dosimetry. At therapeutic PDT levels, there was no structural or functional urethral damage even when the urethra was within the treated region. Hence, Tookad-PDT appears to be a promising candidate for prostate ablation in patients with recurrent, or possibly even primary, prostate cancer.     

Development of polyaniline microarray electrodes for cadmium analysis

Disposable screen-printed electrodes (SPCE) were modified using a cosmetic product to partially block the electrode surface in order to obtain a microelectrode array. The microarrays formed were electropolymerized with aniline. Scanning electron microscopy was used to evaluate the modified and polymerized electrode surface. Electrochemical characteristics of the constructed sensor for cadmium analysis were evaluated by cyclic and square-wave voltammetry. Optimized stripping procedure in which the preconcentration of cadmium was achieved by depositing at ?1.20 V (vs. Ag/AgCl) resulted in a well defined anodic peak at approximately ?0.7 V at pH 4.6. The achieved limit of detection was 4 × 10^?9 mol dm^?3. Spray modified and polymerized microarray electrodes were successfully applied to quantify cadmium in fish sample digests.     

A new normalization method for determination of colloidal fouling potential in membrane processes

Normalization of permeate flux data is widely used to characterize membrane fouling under different experimental conditions. The main intention of normalization is to allow a fair comparison of feed water fouling potentials by eliminating the effects of different operational parameters used in the experiments, such as net driving pressure and clean-membrane resistance. However, it was demonstrated that the commonly used intuitive normalization methods usually could not serve their intended purpose. In this study, a new normalization method was proposed for characterizing water-fouling potential based on fundamental principles of membrane fouling. The intention of this normalization method was to define a fouling potential for feed water that was independent of, or at least, not strongly affected by operational conditions. Laboratory-scale ultrafiltration fouling tests were conducted under different colloid sizes, concentrations, and driving pressures. The experiments showed that the fouling potentials defined by the newly proposed normalization method were linearly related to the colloid concentration of the feed water and that the effect of operational conditions used in the fouling experiments on the fouling potential was minimal.     

A microarray chip for label-free detection of narcotics

A protein array chip for label-free optical detection of low molecular weight compounds has been developed. As a proof of principle, the chip is proven capable of rapidly (approximately 1 min) determining hits from aqueous cocktails composed of four common narcotics, cocaine, ecstasy, heroin, and amphetamine, using imaging surface plasmon resonance (SPR) as the detection principle. The chip is produced by injecting a mixture of antibodies and letting them self-sort and bind to narcotic analog coupled proteins already present in a predefined pattern on the supporting substrate. An indirect detection method, where antibodies are displaced from the surface upon recognition of their corresponding narcotics, is used to obtain the optical contrast and thus a detectable SPR and/or ellipsometric signal. Two types of readouts are possible from the present setup: intensity SPR images and SPR/ellipsometric sensorgrams. Positive hits were routinely obtained for analyte concentrations of 50 pg/μL and the limit of detection, without any parameter optimizations, seems to fall in the range 0.5 pg/μL (1.4 nM) for heroin, 2.5 pg/μL (8.2 nM) for cocaine, and 5 pg/μL for the other two narcotics (26 nM for ecstasy and 37 nM for amphetamine). With improved readout possibilities (sampling frequency), signal evaluation algorithms, and antibody–antigen design strategies, we believe this limit can be further improved. The chip is shown to work for many measurement cycles with excellent reproducibility. Moreover, with a more advanced fluidic system, excess injected antibodies could be collected and reused for many cycles, which could make the running costs of the system very low. The chip is in no way limited to detection of narcotics. Other low molecular weight compounds could easily be detected on the same chip. For example, trinitrotoluene detection has already been demonstrated using our chip. Possible areas of application for the system are therefore envisaged in airport and underground transport security, customs, drug interdiction, forensics, and as warning alerts on military equipment and personnel. Figure Narcotics chip (left) composed of spots of piezodispensed analog-coupled proteins that are loaded with antibodies to form a patterned regions represented by the capital letter of the four different narcotics in focus. (Right) The same chip showing hits for ectasy and herion in the cocktail. Both images are obtained in imaging surface plasmon resonance mode     

Donnan dialysis matrix normalization for the voltammetric determination of metal ions

The efficacy of Donnan dialysis for removal of interferences by surfactants, complexing agents, and electroactive organic compounds on anodic stripping voltammetry and differential pulse polarography is demonstrated. Up to at least 0.05% gelatin and 0.005% Triton X-100 do not alter the rate of dialysis of Cd(II), Pb(II), Zn(II), and Cu(II). As the ion-exchange membrane is not permeable to the surfactants, subsequent voltammetric determinations can be performed by a working curve method. Recoveries of metals from a variety of real samples were generally above 90%. The presence of humic acid (50 mg l^-1) does not alter the transport of Cu(II), Pb(II), or Cd(II) from pH 3 solution but does at pH 8. The transport is related to the free and labile-complexed ion concentration which suggests that Donnan dialysis can be used for speciation as well as for enrichment and matrix normalization.     

On the normalization of a mass spectrum for comparison of two spectra

It is indicated that for comparison of two mass-spectra the normalization of each ion current should be done such that each spectrum will form a unit vector, i.e., SigmaXi2 = 1, where Xi are the various components of the mass spectrum.     

Optimization of aptamer microarray technology for multiple protein targets

Aptamer-based microarrays for the quantitation of multiple protein analytes have been developed. A multiplex aptamer microarray was generated by printing two RNA aptamers (anti-lysozyme and anti-ricin) and two DNA aptamers (anti-IgE and anti-thrombin) on to either streptavidin (SA) or neutravidin (NA)-coated glass slides. However, substantial optimization was required in order to ensure the simultaneous function of the aptamer:analyte pairs. The effects of protein labeling, assay buffer, surface coating, and immobilization chemistry and orientation were investigated. A single buffer (PBS buffer containing 5 mM MgCl₂ and 0.1% Tween 20) was found to work well with all the aptamers, even though this was not the buffer originally used in their selection, while neutravidin-coated slides yielded a lower detection limit, wider detection range, and more uniform background than streptavidin-coated slides. Incubation with Cy3-labeled proteins yielded sensitive, target-specific, and dose-dependent responses to each protein. Target protein concentrations as low as 72 pg/mL (5 pM, lysozyme), 15 ng/mL (0.5 nM, ricin), 1.9 ng/mL (0.01 nM, IgE), and 170 ng/mL (5 nM, thrombin) could be detected. These results show that aptamer arrays can potentially be used with numerous proteins in parallel, furthering the notion that aptamer arrays may be useful in proteomics.     

Polymer microfluidic chip for online monitoring of microarray hybridizations

A disposable single use polymer microfluidics chip has been developed and manufactured by micro injection molding. The chip has the same outer dimensions as a standard microscope slide (25 x 76 x 1.1 mm) and is designed to be compatible with existing microscope slide handling equipment like microarray scanners. The chip contains an inlet, a 10 microL hybridization chamber capable of holding a 1000 spot array, a waste chamber and a vent to allow air to escape when sample is injected. The hybridization chamber ensures highly homogeneous hybridization conditions across the microarray. We describe the use of this chip in a flexible setup with fluorescence based detection, temperature control and liquid handling by computer controlled syringe pumps. The chip and the setup presented in this article provide a powerful tool for highly parallel studies of kinetics and thermodynamics of duplex formation in DNA microarrays. The experimental setup presented in this article enables the on-chip microarray to be hybridized and monitored at several different stringency conditions during a single assay. The performance of the chip and the setup is demonstrated by on-line measurements of a hybridization of a DNA target solution to a microarray. A presented numerical model indicates that the hybridization process in microfluidic hybridization assays is diffusion limited, due to the low values of the diffusion coefficients D of the DNA and RNA molecules involved.     

Dielectrophoresis-based cellular microarray chip for anticancer drug screening in perfusion microenvironments

We present a dielectrophoresis (DEP)-based cellular microarray chip for cell-based anticancer drug screening in perfusion microenvironments. Human breast cancer cells, MCF7, were seeded into the chip and patterned via DEP forces onto the planar interdigitated ring electrode (PIRE) arrays. Roughly, only one third of the cell amount was required for the chip compared to that for a 96-well plate control. Drug concentrations (cisplatin or docetaxel) were stably generated by functional integration of a concentration gradient generator (CGG) and an anti-crosstalk valve (ACV) to treat cells for 24 hours. Cell viability was quantified using a dual staining method. Results of cell patterning show substantial uniformity of patterned cells (92 ± 5 cells per PIRE). Furthermore, after 24 hour drug perfusion, no statistical significance in dose-responses between the chip and the 96-well plate controls was found. The IC(50) value from the chip also concurred with the values from the literature. Moreover, the perfusion culture exhibited reproducibility of drug responses of cells on different PIREs in the same chamber. The chip would enable applications where cells are of limited supply, and supplement microfluidic perfusion cultures for clinical practices.     

On the precision of quasi steady state assumptions in stochastic dynamics

Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)]. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.     

Equipment for digital recording of transient signals

The instrumentation for digital recording of transient signals was built and incorporated into a system for pulse radiolysis experiments. A single analog signal which is displayed on the screen of the oscilloscope is captured by a TV-camera in the measuring set up. The camera is connected to a Camac crate which is directly linked to a microcomputer. The analog signal can be digitized and memorized in 128×256 matrix points.