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PubMed2004

Chip-based nanoelectrospray mass spectrometry for protein characterization.

In the last several years, significant progress has been made in the development of microfluidic-based analytical technologies for proteomic and drug discovery applications. Chip-based nanoelectrospray coupled to a mass spectrometer detector is one of the recently developed analytical microscale technologies. This technology offers unique advantages for automated nanoelectrospray including reduced sample consumption, improved detection sensitivity and enhanced data quality for proteomic studies. This review presents an overview and introduction of recent developments in chip devices coupled to electrospray mass spectrometers including the development of the automated nanoelectrospray ionization chip device for protein characterization. Applications using automated chip-based nanoelectrospray ionization technology in proteomic and bioanalytical studies are also extensively reviewed in the fields of high-throughput protein identification, protein post-translational modification studies, top-down proteomics, biomarker screening by pattern recognition, noncovalent protein-ligand binding for drug discovery and lipid analysis. Additionally, future trends in chip-based nanoelectrospray technology are discussed.

Ligands↗
PubMed2005

Simultaneous determination of single nucleotide polymorphisms of MDR1 genes by electrochemical DNA chip.

The on-chip genotyping system ("the electrochemical DNA chip") has been developed as a more cost-effective genotyping system and was applied to MDR1 genotyping in the present study, which is required for wide use in clinical application and for personalized medication based on genotype. The electrochemical DNA chip was optimized and applied to simultaneous genotyping of four MDR1 polymorphisms (T-129C, C1236T, G2677(A,T) and C3435T) using synthetic model oligonucleotide DNA and human genomic DNA. The electrochemical DNA chip successfully gave the T-129C, C1236T, G2677(A,T) and C3435T genotypes, which were completely consistent with those determined by direct sequencing. In conclusion, the electrochemical DNA chip is useful for simultaneous determination of some genotypes and haplotypes, and efficient genotyping using this system can support future genotype-phenotype studies at a large scale.

Base Sequence↗
PubMed2006

Transparent polymeric cell culture chip with integrated temperature control and uniform media perfusion.

Modern microfabrication and microfluidic technologies offer new opportunities in the design and fabrication of miniaturized cell culture systems for online monitoring of living cells. We used laser micromachining and thermal bonding to fabricate an optically transparent, low-cost polymeric chip for long-term online cell culture observation under controlled conditions. The chip incorporated a microfluidic flow equalization system, assuring uniform perfusion of the cell culture media throughout the cell culture chamber. The integrated indium-tin-oxide heater and miniature temperature probe linked to an electronic feedback system created steady and spatially uniform thermal conditions with minimal interference to the optical transparency of the chip. The fluidic and thermal performance of the chip was verified by finite element modeling and by operation tests under fluctuating ambient temperature conditions. HeLa cells were cultured for up to 2 weeks within the cell culture chip and monitored using a time-lapse video recording microscopy setup. Cell attachment and spreading was observed during the first 10-20 h (lag phase). After approximately 20 h, cell growth gained exponential character with an estimated doubling time of about 32 h, which is identical to the observed doubling time of cells grown in standard cell culture flasks in a CO2 incubator.

Cell Culture Techniques↗
PubMed2003

Possibility of using DNA chip technology for diagnosis of human papillomavirus.

To explore the application of DNA chip technology for the detection and typing of Human Papillomavirus (HPV), the HPV6, 11, 16 and 18 gene fragments were isolated and printed onto aminosilane-coated glass slides by a PixSys 5500 microarrayer as probes to prepare the HPV gene chips. HPV samples, after being labeled with fluorescent dye by restriction display PCR (RD-PCR) technology, were hybridized with the microarray, which was followed by scanning and analysis. The experimental condition for preparing the HPV gene chips was investigated, and the possibility of HPV genotyping using gene chips was discussed. The technique that was established in this study for preparing HPV gene chips is practical. The results of the present study demonstrated the versatility and inspiring prospect of using this technology to detect and genotype HPV.

DNA Probes↗
PubMed2000

Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples.

BACKGROUND: Testing for mutations of the TP53 gene in tumors is a valuable predictor for disease outcome in certain cancers, but the time and cost of conventional sequencing limit its use. The present study compares traditional sequencing with the much faster microarray sequencing on a commercially available chip and describes a method to increase the specificity of the chip. METHODS: DNA from 140 human bladder tumors was extracted and subjected to a multiplex-PCR before loading onto the p53 GeneChip from Affymetrix. The same samples were previously sequenced by manual dideoxy sequencing. In addition, two cell lines with two different homozygous mutations at the TP53 gene locus were analyzed. RESULTS: Of 1464 gene chip positions, each of which corresponded to an analyzed nucleotide in the sequence, 251 had background signals that were not attributable to mutations, causing the specificity of mutation calling without mathematical correction to be low. This problem was solved by regarding each chip position as a separate entity with its own noise and threshold characteristics. The use of background plus 2 SD as the cutoff improved the specificity from 0.34 to 0.86 at the cost of a reduced sensitivity, from 0.92 to 0.84, leading to a much better concordance (92%) with results obtained by traditional sequencing. The chip method detected as little as 1% mutated DNA. CONCLUSIONS: Microarray-based sequencing is a novel option to assess TP53 mutations, representing a fast and inexpensive method compared with conventional sequencing.

Humans↗
PubMed2001

[Rapid detection of Mycobacterium tuberculosis resistance to rifampin using DNA chip].

OBJECTIVE: To develop a new method, DNA chip, which can be used for rapid detection of Mycobacterium tuberculosis resistance to RFP. METHODS: Designing probe according to the sequence of Mycobacterium tuberculosis rpoB gene and fabricating DNA chip. The DNA fragment which contains hot mutation sites of rpoB gene was labelled with cy5 fluorescence and amplified by PCR technique. Then it was hybridized with DNA chip. DNA sequence was used as the control. RESULTS: 14 strains were detected out of 17 randomly selected Mycobacterium tuberculosis resistant to RFP using DNA chip. The efficiency was 83%. A little bit DNA in the sick sputa was sufficient for drug resistance detection without being incubated. CONCLUSION: It showed higher specialty and sensitivity using DNA chip to detect Mycobacterium tuberculosis resistance to RFP. This method was rapid and accurate and could be used for clinical detection of RFP-resistant strains.

Antibiotics, Antitubercular↗
PubMed2001

Biofilter media mixture ratio of wood chips and compost treating swine odors.

Biofilter media mixtures were compared in 18 pilot-scale biofilters treating pit gases from a swine facility. The compost and wood chips mixtures ranged from 100% wood chips to a 50-50 blend in 10% increments. The effect of three media moisture contents (low, medium, and high) on biofilter performance was also evaluated. Odor and hydrogen sulfide reduction did not change significantly for mixtures with greater than 20% compost. For efficient odor, hydrogen sulfide, and ammonia reduction media moisture must be greater than 40% wb. Media moisture content influenced odor, hydrogen sulfide, and ammonia reduction more than the ratio of compost and wood chips. The count of heterotrophic or sulfur-oxidizing bacteria did not change in a discernable pattern with respect to media mixture or moisture content. As the amount of compost increased in the media mixtures, the pressure drop also increased. Based on this experiment, the recommended mixing ratio of compost to wood chips for biofilters on swine facilities is minimum 30% compost and 70% wood chips by weight.

Agriculture↗
PubMed2002

[Location of the probe dots in gene chip image with the medialness function].

For acquisition of the gene chip information, how to correctly locate the probe dots in the chip's scanning image is the base of the chip information processing. Here we present a new approach for locating the probe dots in the gene chip image. First, a medialness function, which is good at detection of circle area with radius given in advance, is used for calculating the medialness map in which the center of circle sample area of the gene chip image is disclosed prominently. Then, a method to locate the probe dots center is given based on the medialness map and the 2D space configuration of the probe dots. The experiments show that the new approach correctly locates the probe dots while against noise affection robustly.

Algorithms↗
PubMed2002

[DNA chip technology and its application in toxicology [correction of toxiology]].

DNA chip is a new molecular biology technology rapidly developed in recent years. It fixes thousands of oligonucleotide on a silicon chip of 1 cm2, hybridizes the measuring materials marked with fluorescein or isotope with probe in DNA chip, and gets the fluorescent signal of hybridized probe through the scan of confocalmicroscope. This technology has been extensively used in HGP, DNA sequencing, transcript analysis, gene diagnosis etc. Toxicology is an important branch of life science. DNA chip can be extensively used in the toxicological [correction of toxiological] field. This paper reviewed the DNA chip technology in mechanism, manufacturing method, signal check, advantages and application prospect in toxicology.

Aerospace Medicine↗
PubMed2003

Clinical application of a DNA chip in the field of liver diseases.

DNA chips can be used for many different purposes, most prominently to measure levels of gene expression for tens of thousands of genes simultaneously. Some of the possible clinical applications of DNA chips for liver diseases are studied in our laboratory. Expression profiles of liver diseases were examined by SAGE (serial analysis of gene expression), and many new transcripts were found in the SAGE libraries. The SAGE information is important to make DNA chips for the analysis of liver diseases. Expression profiles of 26 patients with chronic hepatitis and 10 patients with hepatocellular carcinoma were analyzed by DNA chips. The analyses revealed new information about liver disease. These results imply a DNA chip may be a good tool in routine clinical settings in the near future.

Gene Expression Profiling↗
PubMed2003

[Advances in the applications of DNA chips and proteomics approaches for neurosciences].

DNA chips and proteomics are two of the recently developed high-throughput technologies that allow us to simultaneously analyze the expression levels of multiple genes and the interactions of their products in the brain. Their applications in neuroscience provide us with the unprecedented opportunities for understanding of the brain. A typical gene chip experiment contains a series of steps, including preparations (or purchase) of DNA chips, target DNA and probes, hybridization of chips with target DNA, chip scanning, and imaging analysis. The technologies in proteomics are more complicated, which comprise of three main aspects of technologies: protein isolation, identification and bioinformatic analysis of data. If protein isolation is based on 2-D, it includes the preparation of protein sample, 2-D, staining gels, spot excision, proteolysis, mass spectrometry of purified protein and finally undergoing bioinformatic analysis. Here we review the two technologies with emphasis on their applications in neurosciences. The challenges, advantages and disadvantages of the two techniques, and perspectives for their developments are discussed.

Animals↗
PubMedDate not supplied

A protein chip system for parallel analysis of multi-tumor markers and its application in cancer detection.

BACKGROUND: Tumor markers are routinely measured in clinical oncology. However, their value in cancer detection has been controversial largely because no single tumor marker is sensitive and specific enough to meet strict diagnostic criteria. One strategy to overcome the shortcomings of single tumor markers is to measure a combination of tumor markers to increase sensitivity and look for distinct patterns to increase specificity. This study aimed to develop a system for parallel detection of tumor markers as a tool for tumor detection in both cancer patients and asymptomatic populations at high risk. MATERIALS AND METHODS: A protein chip was fabricated with twelve monoclonal antibodies against the following tumor markers respectively: CA125, CA15-3, CA19-9, CA242, CEA, AFP, PSA, free-PSA, HGH, beta-HCG, NSE and ferritin. Tumor markers were captured after the protein chip was incubated with serum samples. A secondary antibody conjugated with HRP was used to detect the captured tumor markers using chemiluminescence technique. Quantification of the tumor markers was obtained after calibration with standard curves. RESULTS: The chip system showed an overall sensitivity of 68.18% after testing 1147 cancer patients, with high sensitivities for liver, pancreas and ovarian tumors and low sensitivities for gastrointestinal tumors, and a specificity of 97.1% after testing 793 healthy individuals. Application of the chip system in physical checkups of 15,867 individuals resulted in 16 cases that were subsequently confirmed as having cancers. Analysis of the detection results with a Support Vector Machine algorithm considerably increased the specificity of the system as reflected in healthy individuals and hepatitis/cirrhosis patients, but only modestly decreased the sensitivity for cancer patients. CONCLUSION: This protein chip system is a potential tool for assisting cancer diagnosis and for screening cancer in high-risk populations.

Antibodies, Monoclonal↗
PubMed2004

[The use of gene chip in detecting Mycobacterium tuberculosis resistant to rifampin and isoniazid].

OBJECTIVE: To study the application of gene chip in detecting Mycobacterium tuberculosis resistant to rifampin (RFP) and isoniazid (INH). METHODS: Probes were designed and the gene chip was fabricated according to the 30 single nucleotide polymorphisms of 11 mutations on 4 genes associated with RFP and INH resistance. The mutations in Mycobacterium tuberculosis were detected by gene chip to analyze the resistance to INH and RFP. RESULTS: 85 of 110 (77.3%) strains resistant to INH and 22 of 30 (73.3%) strains sensitive to INH were detected, while 77 of 94 (81.9%) strains resistant to RFP and 40 of 46 (87.0%) strains sensitive to RFP were detected. The results from the gene-chip detection were consistent with the sequence information. CONCLUSION: The gene-chip technology, a fast test with high accuracy, specificity and sensitivity, as shown in our study, is promising in the clinical detection of Mycobacterium tuberculosis resistant to INH and RFP.

Drug Resistance, Bacterial↗
PubMed2003

[Establishing DNA chip technique for detecting hepatitis C virus genotypes and primary application].

OBJECTIVE: To establish a new method based DNA chip technique for detecting HCV genotypes. METHODS: Genotyping probes were designed according to the sequence of HCV 5' NCR to generate DNA chip. The probes on DNA chip contains 5 major genotypes and 8 subtypes. The DNA fragment amplified by labeling Cy5 fluorescence was hybridized with DNA chip. RESULTS: Fifty-five out of 65 isolates detected by DNA chip belonged to 1b- DNA sequencing of form a part of the isolates was used as the control. The results of both were completely consistent. CONCLUSION: The method is simple and rapid with high specificity and sensitivity. It can be applied in detection of HCV RNA and genotypes.

5' Untranslated Regions↗
PubMed2005

Forensic applications of infrared chemical imaging: multi-layered paint chips.

This paper examines the potential of infrared chemical (hyperspectral) imaging as a technique for the forensic analysis of automotive paint chips in particular, and multicomponent (e.g., layered) samples in general. Improved sample preparation procedures for the infrared analysis of paint chips are detailed, with the recommendation that where mounting resins are chemically incompatible with the sample, it is better to mount and section the sample in a soft wax from which the sections can be removed and pressed into a KBr disk for transmission analysis. Infrared chemical images of multilayered paint chips have been successfully obtained, with the chief advantage over conventional infrared analysis being that thousands of infrared spectra are collected in a few minutes across the whole sample, at a spatial resolution of around 5 microm. As with conventional infrared spectroscopy, chemical species can be identified from their spectra, but the wealth of information available can be also extracted in a number of different ways that make multicomponent spectral (and hence chemical) comparisons between two samples easy to visualize and understand. In one approach, the infrared chemical images of two paint chips being compared side-by-side can be viewed as a "movie," in which each frame is an intensity map of the two samples at a given wavenumber (frequency) value. In another approach, the spectra (pixels) in the image files are classified into chemically similar groups, resulting in a "cluster" image that makes it possible to simultaneously compare all of the layers in two paint chips. These methods are applicable to other multicomponent samples, and also to other chemical imaging techniques.

Journal Article↗
PubMed2005

Dielectrophoresis-based 'Lab-on-a-chip' devices for programmable binding of microspheres to target cells.

There is a general agreement on the fact that the Laboratory on chip (Lab-on-a-chip) technology will enable laboratory testing to move from laboratories employing complex equipments into non-laboratory settings. In this respect, dielectrophoresis (DEP) is a very valuable approach to design and produce Lab-on-a-chip devices able to manipulate microparticles and cells. In this study, we report the application of DEP-based devices for facilitating programmable interactions between microspheres and target tumor cells. We used two Lab-on-a-chip devices, one (the SmartSlide) carrying 193 parallel electrodes and generating up to 50 cylinder-shaped DEP cages, the other (the DEP array) carrying 102,400 arrayed electrodes and generating more than 10,000 spherical DEP cages. We determined whether these devices can be used to levitate and move microspheres and cells in order to obtain a forced interaction between microspheres and target cells. The first major point of this manuscript is that the DEP-based SmartSlide can be used for transfection experiments in which microspheres and target cells are forced to share the same DEP cage, leading to efficient binding of the microspheres to target cells. The data obtained using the DEP array show that this system allows the sequential, software-controlled binding of individually and independently moved single microspheres to a single target tumor cell. To our knowledge, this is the first report on the possible use of a DEP-based Lab-on-a-chip device for guided multiple binding of singularly moved microspheres to a single tumor cell. This approach can be of interest in the field of drug discovery, delivery and diagnosis.

Algorithms↗
PubMed2005

[Thinking of application of gene chip technique in the study of channel-viscera correlativity].

OBJECTIVE: To probe into thinking and prospect of application of gene chip technique to research of the channel-viscera correlativity. METHODS: Adopt literature analytic method, review and analyze current state of application of gene chip in biology and medicine, and achievements in studies of channel-viscera correlativity. RESULTS: In biological and medical fields, gene chip can be applied to high flux expression parallel analysis, large-scale gene discovery and gene analysis, gene polymorphous analysis, genome study, etc, especially, it has important application values in gene expression map; channel-viscera correlativity need stereo-crossing studies by multiple subjects, multiple systems, multiple directions and multiple levels, being more systematic and sequential, and gene chip technique is applicable to this requirement. CONCLUSION: Wide application of gene chip technique will comprehensively promote deep study of channel-viscera correlativity.

Gene Expression↗
PubMed2006

[DNA typing of HLA-I and II antigens with medium resolution method by DNA chip technique].

OBJECTIVE: To establish a DNA typing method for the HLA-I and II antigens in the Chinese of Han Nationality in Northern China with medium resolution method by DNA chip technique. METHODS: Corresponding primers for the sense exon fragments of HLA-A, HLA-B, HLA-DR, HLA-DQB, and HLA-DQA were designed. A DNA typing chip was made with specific medium resolution typing probes designed according to the gene frequency of HLA-I and II alleles among the Chinese of Han nationality in Northern China. Unsymmetrical PCR was used to amplify the HLA-I and II exon2 and exon3 in 30 samples from the Chinese of Han nationality in Northern China, and then the PCR products were labeled and hybridized with the probes on the chip. The typing of HLA-I and II was certified by scanning the hybridized products and analyzing them with a set of computer software. RESULTS: HLA-I and II alleles were successfully typed in 30 clinical samples. The h probes with medium resolution were able to discern 42 HLA-I and II alleles accurately. By using this chip 30 HLA-I and II alleles were distinguished and 6 new specific alleles were found. CONCLUSION: DNA typing of HLA-I and II by chip has been proven to be a high-resolution and high-specificity method. It is able to check out new alleles that can not be distinguished by other methods with the same resolution, and it is more intuitive and more suitable for clinical application.

Adult↗