Detection of dopamine using a silicon nanowire patterned by nanoimprint lithography

Dopamine is one of the most important catecholamine neurotransmitter in the nucleus accumbens of wide variety of animals, including humans. In this study, silicon nanowire FET device was fabricated by UV-assisted NIL method and dopamine was successfully measured by conductance versus time characteristics within 10 pM to 100 nM.     

Detection of echoes using time-frequency analysis techniques

The following is a presentation of echo detection techniques based on time-frequency signal analysis for the measuring of thickness in thin multilayer structures. These techniques are shown to provide high-resolution signal characterization in a time-frequency space, and good noise rejection performance. In particular, the short-time Fourier transform, the Gabor expansion, the cross-ambiguity function and the Wigner-Ville distribution are analyzed and compared with techniques such as the logarithmic power spectrum, cepstrum and the segmented chirp Z-Transform. A suitable operating procedure was set up, based on an initial emulation phase in which simulated signals were considered, followed by a second phase in which real signals were processed. The results show the optimum performances of these new techniques compared with the traditional ones and, in particular, that the accurate measurement of thickness can be obtained also when waveform transients partially overlap     

Detection of Salmonella spp. using microsphere-based, fiber-optic DNA microarrays

Salmonella spp. are one of the most problematic food pathogens in public health, as they are responsible for food poisoning associated with contamination of meat, poultry, and eggs. Thus, rapid and sensitive detection of Salmonella spp. is required to ensure food safety. In this study, a fiber-optic DNA microarray using microsphere-immobilized oligonucleotide probes specific for the Salmonella invA and spvB genes was developed for detection of Salmonella spp. Microarrays were prepared by randomly distributing DNA probe-functionalized microspheres (3.1-microm diameter) into microwells created by etching optical fiber bundles. Hybridization of the probe-functionalized microspheres to target DNA from Salmonella was performed and visualized using Cy3-labeled secondary probes in a sandwich-type assay format. In this study, 10(3)-10(4) cfu/mL of the target organism could be detected after 1-h hybridization without any additional amplification. The DNA microarray showed no cross-reactivity with other common food pathogens, including E. coli and Y. enterocolitica, and could even detect Salmonella spp. from cocktails of bacterial strains with only moderate loss of sensitivity due to nonspecific binding. This work suggests that fiber-optic DNA microarrays can be used for rapid and sensitive detection of Salmonella spp. Since fiber-optic microarrays can be prepared with different probes, this approach could also enable the simultaneous detection of multiple food pathogens.     

Detection of DNA sequences using an alternating electric field in a nanopore capacitor

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.     

Detection of cytochrome C in a single cell using an optical nanobiosensor

In this work, the intracellular measurement of cytochrome c using an optical nanobiosensor is demonstrated. The nanobiosensor is a unique fiberoptics-based tool which allows the minimally invasive analysis of intracellular components. Cytochrome c is a very important protein to the process which produces cellular energy. In addition, cytochrome c is well-known as the protein involved in apoptosis, or programmed cell death. delta-Aminolevulinic acid (5-ALA) was used to induce apoptosis in MCF-7 human breast carcinoma cells. 5-ALA, a photodynamic therapy (PDT) drug in cells was activated by a HeNe laser beam. After the PDT photoactivation, the release of cytochrome c from the mitochondria to the cytoplasm in a MCF-7 cell was monitored by the optical nanobiosensor inserted inside the single cell and followed by an enzyme-linked immunosorbent assay (ELISA) outside the cell. The combination of the nanobiosensor with the ELISA immunoassay improved the detection sensitivity of the nanobiosensor due to enzymatic amplification. Our results lead to the investigation of an apoptotic pathway at the single cell level.     

Detection of G-quartet structure in a DNA aptamer stationary phase using a fluorescent dye

The fluorescent porphyrin dye N-methylmesoporphyrin IX (NMM) was used to provide direct evidence of intramolecular G-quartet formation by an oligonucleotide immobilized at the inner surface of a fused silica capillary. The oligonucleotide is the thrombin-binding DNA aptamer, which has been used in several analytical applications, including a stationary phase for open tubular capillary electrochromatography. Spectroscopic studies of the dye in batch solutions of the aptamer and of an oligonucleotide with the same base composition, but in a different, "scrambled" sequence that does not form an intramolecular G-quartet, provided evidence of selective fluorescence enhancement of NMM by the aptamer in the intramolecular G-quartet structure. On-column experiments compared results for injections of NMM onto an aptamer-coated capillary, a capillary coated with the scrambled sequence oligonucleotide, and a bare fused silica capillary. Results show that while NMM adsorbs to both coated capillaries, the selective fluorescence enhancement provides evidence of the intramolecular G-quartet structure on the aptamer-coated capillary.     

Detection of abasic sites on individual DNA molecules using atomic force microscopy

We have developed an atomic force microscopy-based method for detecting abasic sites (AP sites) on individual DNA molecules. By using uracil and uracil DNA glycosylase, we first prepared a 250-bp DNA template consisting of two AP sites at specific locations. We then detected the AP sites by marking them with biotinylated aldehyde-reactive probes and monomeric avidin. We demonstrate here that (i) the location of monomeric avidin bound on a single DNA molecule was detectable by atomic force microscopy; (ii) the observed location of avidin was in good agreement to the predicted AP sites at a few nanometer resolution; and (iii) by end-labeling the 5'-terminus of one DNA strand, the AP sites were determined without directional ambiguity. The technique described here will provide a sensitive way of locating AP sites and contribute to screen DNA damages from individual molecules.     

Detection of human immunodeficiency virus type 1 DNA sequence using plasmonics nanoprobes

This paper describes the use of plasmonics-based nanoprobes that act as molecular sentinels for DNA diagnostics. The plasmonics nanoprobe comprises a metal nanoparticle and a stem-loop DNA molecule tagged with a Raman label. The nanoprobe utilizes the specificity and selectivity of the DNA hairpin probe sequence to detect a specific target DNA sequence of interest. In the absence of target DNA, the stem-loop configuration maintains the Raman label in proximity to the metal nanoparticle, inducing an intense surface-enhanced Raman scattering (SERS) effect that produces a strong Raman signal upon laser excitation. Upon hybridization of a complementary target DNA sequence to the nanoprobe, the stem-loop configuration is disrupted, causing the Raman label to physically separate from the metal nanoparticle, thus quenching the SERS signal. The usefulness and potential application of the plasmonics nanoprobe for diagnosis is demonstrated using the gag gene sequence of the human immunodeficiency virus type 1 (HIV-1). We successfully demonstrated the specificity and selectivity of the plasmonics nanoprobes to detect PCR amplicons of the HIV gene. The potential for combining the spectral selectivity and high sensitivity of the SERS process with inherent molecular specificity of DNA hairpins to diagnose molecular target sequences in homogeneous solutions is discussed.     

Single cell DNA damage/repair assay using HaloChip

The molecular level damage to DNA is important due to DNA's susceptibility to free radical attacks and crucial roles in maintaining cell functions. Although a panel of techniques can be used to detect DNA damages, most of them are limited due to low sensitivity, low throughput, incompatibility for automated data analysis, and labor-intensive operations. We have developed a cell array based DNA damage assay in which mammalian cells are attached on an array of microfabricated patterns through electrostatic interactions. After trapping patterned cells inside gels, damaged DNA fragment can diffuse out of the nucleus and form a halo around each cell inside gels. The halo array can be observed fluorescently after labeling DNA with ethidium bromide. DNA damages can be determined sensitively at the single cell level, accurately due to the symmetric shape of the halo, and automatically due to the spatial registry of each cell and the nonoverlapping halos surrounding cells. The HaloChip can be used to detect DNA damages caused by chemicals and ultraviolet and X-ray irradiations with high efficiency. A major advantage of HaloChip is the ability to increase throughout by spatially encoding multiple dosing conditions on the same chip. Most importantly, the method can be used to measure variations in response to DNA damaging agents within the same cell population. Compared with halo assay or comet assay alone, this method allows automated analysis of a million cells without an overlapping issue. Compared with the microwell array based comet assay, this method can selectively capture and analyze cells, and the results can be easily analyzed to provide precise information on DNA damage. This method can be used in a broad range of clinical, epidemiological, and experimental settings.     

Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes

We demonstrate the optical detection of DNA hybridization on the surface of solution suspended single-walled carbon nanotubes (SWNTs) through a SWNT band gap fluorescence modulation. Hybridization of a 24-mer oligonucleotide sequence with its complement produces a hypsochromic shift of 2 meV, with a detection sensitivity of 6 nM. The energy shift is modeled by correlating the surface coverage of DNA on SWNT to the exciton binding energy, yielding an estimated initial fractional coverage of 0.25 and a final coverage of 0.5. Hybridization on the nanotube surface is confirmed using Forster resonance energy transfer of fluorophore-labeled DNA oligonucleotides. This detection is enabled through a new technique to suspend SWNTs using adsorption of single-stranded DNA and subsequent removal of free DNA from solution. While the kinetics of free DNA hybridization are relatively fast (<10 min), the kinetics of the process on SWNTs are slower under comparable conditions, reaching steady state after 13 h at 25 degrees C. A second-order kinetic model yields a rate constant of k = 4.33 x 10(5) (M h)(-1). This optical, selective detection of specific DNA sequences may have applications in the life sciences and medicine as in vitro or in vivo detectors of oligonucleotides.     

DNA microsatellite analysis using ion-pair reversed-phase high-performance liquid chromatography

Genotyping based on short tandem repeat (STR) regions is used in human identification and parentage testing, gene mapping studies, cancer diagnostics, and diagnosis of hereditary diseases. Analysis of STR systems using slab gel electrophoresis requires lengthy and labor-intensive procedures. Therefore, alternative methods such as capillary electrophoresis or ion-pair reversed-phase high-performance liquid chromatography (IPRP HPLC) have been used to analyze DNA. IPRP HPLC offers an attractive substitute to gel electrophoresis for STR analysis because of the reduced analysis time, and there is no need for the waste disposal associated with radioisotopic, enzyme-linked, or fluorescence detection systems. We evaluated the use of IPRP HPLC for the sizing and typing of STR alleles from the HUMTHO1 locus. The IPRP HPLC conditions (column temperature, flow rate, percent organic modifier per minute) were optimized for the separation of PCR products. Using the optimized separation conditions, the alleles of the HUMTHO1 system were sized in their native state (double standard) with the use of internal markers. The typing results correlated 100% to accepted methods of DNA typing. The analysis time for the HUMTHO1 locus was less than 14 min, and the alleles could be peak captured for further examination following such as sequencing.     

Detection of outliers in gas emissions from urban areas using functional data analysis

In this work a solution for the problem of the detection of outliers in gas emissions in urban areas that uses functional data analysis is described. Different methodologies for outlier identification have been applied in air pollution studies, with gas emissions considered as vectors whose components are gas concentration values for each observation made. In our methodology we consider gas emissions over time as curves, with outliers obtained by a comparison of curves instead of vectors. The methodology, which is based on the concept of functional depth, was applied to the detection of outliers in gas omissions in the city of Oviedo and results were compared with those obtained using a conventional method based on a comparison of vectors. Finally, the advantages of the functional method are reported.     

Quantitative analysis of hydrogen in thin films using Time-of-Flight Elastic Recoil Detection Analysis

Determination of atomic concentrations in thin films is one of the key problems in materials science. Time-of-Flight Elastic Recoil Detection Analysis is a powerful method for depth profiling of light and medium mass elements in near surface layers of material. However, due to poor detection efficiency those spectrometers are not commonly used for hydrogen analysis. We have performed some improvements in order to increase detection efficiency and to make spectrometer more suitable for hydrogen analysis. The spectrometer performance was tested on amorphous Si samples implanted with H⁻ and D⁻ and hydrogenised Si standard reference sample. Sensitivity for hydrogen in silicon matrix was found to be several tens of ppm with a surface depth resolution of ~ 15 nm.     

Detection of DNA targets hybridized to solid surfaces using optical images of liquid crystals

In this paper, we report a method of detecting DNA targets hybridized to a solid surface by using liquid crystals (LC). The detection principle is based on different interference colors of LC supported on surfaces decorated with single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). However, the contrast between the ssDNA and dsDNA is not obvious, unless DNA-streptavidin complexes are introduced to the dsDNA to increase the surface mass density. Two different approaches of introducing streptavidin to the system are studied and compared. We find that by premixing the biotin-labeled DNA targets with streptavidin prior to the DNA hybridization, branched-streptavidin complexes are formed and clear LC signal can be observed. This LC-based DNA detection principle represents an important step toward the development of a simple, instrument- and fluorophore-free DNA detection method.     

Detection of low dose radiation induced DNA damage using temperature differential fluorescence assay.

A rapid and sensitive fluorescence assay for radiation-induced DNA damage is reported. Changes in temperature-induced strand separation in both calf thymus DNA and plasmid DNA (puc 19 plasmid from Escherichia coli) were measured after exposure to low doses of radiation. Exposures of between 0.004 and 1 Gy were measured with doses as low as 0.008 Gy yielding significant responses. The double-strand, sensitive dye PicoGreen was used as an indicator of DNA denaturation. Calibration plots indicate that fluorescence changes corresponding to amounts as low as 1 ng of double stranded DNA (10(6) copies for plasmid puc 19) are detected by this method.     

High-throughput single copy DNA amplification and cell analysis in engineered nanoliter droplets

A high-throughput single copy genetic amplification (SCGA) process is developed that utilizes a microfabricated droplet generator (microDG) to rapidly encapsulate individual DNA molecules or cells together with primer functionalized microbeads in uniform PCR mix droplets. The nanoliter volume droplets uniquely enable quantitative high-yield amplification of DNA targets suitable for long-range sequencing and genetic analysis. A hybrid glass-polydimethylsiloxane (PDMS) microdevice assembly is used to integrate a micropump into the microDG that provides uniform droplet size, controlled generation frequency, and effective bead incorporation. After bulk PCR amplification, the droplets are lysed and the beads are recovered and rapidly analyzed via flow cytometry. DNA targets ranging in size from 380 to 1139 bp at single molecule concentrations are quantitatively amplified using SCGA. Long-range sequencing results from beads each carrying approximately 100 amol of a 624 bp product demonstrate that these amplicons are competent for achieving attomole-scale Sanger sequencing from a single bead and for advancing pyrosequencing read-lengths. Successful single cell analysis of the glyceraldehyde 3 phosphate dehydrogenase (GAPDH) gene in human lymphocyte cells and of the gyr B gene in bacterial Escherichia coli K12 cells establishes that SCGA will also be valuable for performing high-throughput genetic analysis on single cells.     

Cell chip based monitoring of toxic effects on dopaminergic cell

Oxidative stress has been implicated in pesticide-induced neurotoxicity, base on its role in cascade of biochemical changes that lead to dopaminergic neuronal cell death. The present study examined the role of oxidative stress and the electrochemical detection by polychlorinated biphenyls (PCBs)-induced toxicant in SH-SY5Y cell. The cells were seed in the RED (Arg-Gly-Asp) nanopatterned coating gold substrate and treated with different concentration of PCBs for 24 h in culture, which induced the change of the cyclic voltammetry (CV) current peak. The CV results showed that PCB significantly decreased the current peaks in dose and time-dependent manner. After antioxidant treatment, the CV of the PCB-treated cell chip increased the current peak. Especially, gluthaione and catalase prevent PCB-induced decrease of CV current peak in the cell. The results demonstrated that the current peak decreased by the PCB and recovered by the antioxidant enzyme. In conclusion, results suggest that the electrochemical-based chip provide crucial information to improvement toward a cell chip system for drug screening application.     

Detection of outer raceway bearing defects in small induction motors using stator current analysis

We investigate the application of induction motor stator current spectral analysis (MCSA) for detection of rolling element bearing damage from the outer raceway. In this work, MCSA and vibration analysis are applied to induction motor to detect outer raceway defects in faulty bearings. Data acquisition, recording, and fast fourier transform (FFT) algorithms are done by using the Lab VIEW programming language. Experimental results verify the relationship between vibration analysis and MCSA, and identify the presence of outer raceway bearing defects in induction machines. This work also indicates that detecting fault frequencies by motor currents is more difficult than detecting them by vibration analysis. The use of intensive resolution FFT is recommended in MCSA for detecting faults easily. Reinstalling a faulty bearing can alter the characteristic frequencies and it is difficult to compare results from different bearings or even from the same bearing in different installations.     

Detection of copy number changes in DNA from formalin fixed paraffin embedded tissues using paralogue ratio tests

The purpose of this study was to evaluate whether paralogue ratio tests (PRT) using real-time PCR can accurately determine the DNA copy number (CN) using formalin fixed paraffin embedded (FFPE) tissue. Histopathology diagnostic archives are an enormous resource of FFPE tissue, but extracted DNA is of poor quality and may be unsuitable for CN assessment, thus representing a missed opportunity for studies of genetic association and somatic change in cancer in large cohorts of easily accessible samples. Assays with paralogues on chromosomes 18 and 20 (18|20 PRT) and chromosomes 13 and X (13|X PRT) were tested using archived FFPE pathology samples with known CN, including tonsil, placentae, and FFPE melanoma cell lines. The assay proved accurate over the dynamic range from 1:1 to 1:3 and gave precise results when repeated four times over several weeks. The precision of the assay was marginally reduced once the CT value for 10 ng of FFPE DNA increased above 30 cycles, reflecting importance of DNA quality. The assays distinguished changes in CN ratio with high sensitivity and specificity. The 13|X PRT could detect cells with distinct genotypes microdissected from within the same FFPE sample. Therefore, PRTs are suitable for analyzing CN in FFPE tissues.     

成像检测在DNA毛细管电泳中的应用

本文研究了成像检测方式以及阵列检测器在DNA毛细管电泳的荧光检测中的应用,目的在于减小检测过程引起的样品区带增宽,提高DNA毛细管电泳的分辨率和分离速度。依据分离度理论以及模拟计算结果,归纳了检测宽度的影响规律,指出减小检测宽度对于高效分离,特别是高速微流控系统电泳分离的重要性。实验测量并比较了成像检测与传统光强检测的结果。提出阵列检测器的信号增强方法,并进行了模拟验证。研究表明,成像检测可显著减小毛细管电泳的检测宽度,提高分离效率和分离速度。