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At least 739 records · Page 41Linked to original sources
PubMed2002

Application of restriction display PCR in preparing the probes of the gene chip for investigating gene expression profile of K562 cells.

OBJECTIVE: To collect the gene fragments of the gene chips for investigating the expression profile of K562 cells. METHODS: The mRNA was extracted from cultured K562 cells to obtain cDNA by reverse transcription-PCR. The gene fragment products of different groups were acquired and isolated by reverse display PCR (RD-PCR). RESULT: The probes for the gene chip were successfully prepared. CONCLUSION: RD-PCR adapted in this study suits the needs for collecting the probes for the gene chips.

DNA Probes↗
PubMed2002

CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery.

The potential for gene discovery, fueled by DNA microchip technology and the sequencing of hundreds of genomes, is unprecedented. In this context, trying to discover genes that are actually of significance rather than merely appearing so due to noise is of utmost importance. We present a web application, CHIP TUNER, which assists in this gene discovery process. Our system uses evidence-based noise reduction to help delineate candidate target genes of biological importance. Specifically, CHIP TUNER learns from redundant experiments an "identity mask" that defines a region of noise inherent to biological sampling and DNA microarray processing; it then takes this into account during actual sample comparisons. The goal of CHIP TUNER is to improve the chances that newly discovered "important" genes are actually of importance before large amounts of time and resources are invested.

Computational Biology↗
PubMed2002

[Contribution of DNA chips in lung cancer: an update].

Progress in techniques and computer processing over the last few years have led to the development of new methods of molecular biology. These new methods allow rapid data processing, often allowing data to be shared via networks. An example of this new technology is the transcriptome analysis via a microarray chip. This chip allows analysis of a very large number of RNA messenger transcripts that can be used for diagnostic or prognostic purposes. The first applications in lung cancer have been aimed to distinguish pulmonary adenocarcinoma from other adenocarcinomas. Another approach is to use these chips as a diagnostic tool to identify genes with expressions specific for non-small-cell lung cancer. The early results have been promising and encouraging for future developments, particularly in the domain of applied therapeutics.

Adenocarcinoma↗
PubMed2002

Single framework recombinant antibody fragments designed for protein chip applications.

High-throughput proteomics, based on the microarray platform, requires stable, highly functional components that will yield a highly sensitive read-out of low abundance proteins. Although antibodies are the best characterized binding molecules for this purpose, only a fraction of them appear to behave satisfactorily in the chip format. Therefore, high demands need to be placed on their molecular design. In the present study, we have focused on recombinant antibody design based on a single framework for protein chip applications, aiming at defining crucial molecular probe parameters. Our results show that engineered human recombinant scFv antibody fragments that displayed appropriate biophysical properties (molecular [functional] stability in particular) can be generated, making them prime candidates for high-density antibody arrays. In fact, a superior framework that displays both multifaceted adsorption properties and very high functional stability over several months on chips (stored in a dried-out state) was identified. Taken together, designed scFv fragments based on a single molecular scaffold, readily accessible in large phage display libraries, can undoubtedly meet the requirements of probe content in antibody microarrays, particularly for global proteome analysis.

Antibodies, Monoclonal↗
PubMed2000

[Development of integrated capillary electrophoresis chips].

Capillary electrophoresis in its different operation modes has been demonstrated that it is suitable to be integrated into a planar microdevice which is called integrated capillary electrophoresis chip (ICE chip) or microchip. The use of microfabrication and micromachining allows the integration of complex channel nets and functional units such as pre- and post-column reaction chambers on a single chip, providing good sensitivity and high separation efficiency with low reagent consumption and short analysis time. In the last 10 years an important number of publications have been reported in this area. In the present paper, the development and applications are systematically reviewed with 39 references.

Amino Acids↗
PubMed2001

[Capillary electrophoresis and chip capillary electrophoresis of carbohydrate].

Carbohydrate has many important functions in various biologic processes. Capillary electrophoresis (CE) is one of the key tools of carbohydrate analysis. Chip CE is a new but efficient technique in the study of life science. Carbohydrate analysis with CE and Chip CE are reviewed. Separation strategies and detection of CE for various carbohydrates, including monosaccharides, polysaccharides and glycoconjugates are described. The application and potential ability of Chip CE in carbohydrate research are reviewed as well.

Carbohydrates↗
PubMed2003

[Preparation of gene chip probes for Bacillus anthracis protective antigen].

OBJECTIVE: To study the method for rapid preparation of the gene chip probes for Bacillus anthracis protective antigen (pag). METHODS: According to the sequences of pag published on PubMed, a pair of primers was designed to amplify the PA gene of Bacillus anthracis. Restriction enzyme digestion and AT clone were employed to rapidly screen out the recons of PA segments for the preparation of the gene chip probes. The DNA sequences of these segments were determined with 377 DNA Sequencer, and the resultant sequences analyzed with Bioinformatic software. RESULTS: With the designed primers, the pag 2,205 bp in length was amplified. After enzyme digestion and AT clone, 7 fragments of varied lengths were screened, which underwent analysis with the basic local alignment sequence tool (BLAST) and 377 DNA Sequencer. BLAST analysis showed that all the fragments cloned belonged to Bacillus anthracis. CONCLUSION: PCR in conjunction with restriction enzyme digestion and AT clone is rapid and simple to prepare the desired gene chip probes.

Antigens, Bacterial↗
PubMed2003

Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases.

The increasing popularity of DNA chip technology for the study of gene expression is producing, for each experiment, a sizable quantity of numerical data to analyse and an accompanying large number of gene identifiers that should be associated with the relevant biological annotation. We describe here a website at IFOM (FIRC Institute of Molecular Oncology) where we release regularly updated annotation tables for the most used Affymetrix oligonucleotide DNA chips and for the whole Research Genetics 46K clone collection for cDNA arrays. These tables are synchronised with every new release of the mouse and human UniGene databases (NCBI; National Center for Biotechnology Information), allowing fast and easy preliminary annotation of DNA array experiments. We also report some comparative evidence about the importance of biological database synchronisation and cross-references in the process of generating annotation tables for DNA chips.

Abstracting and Indexing↗
PubMed2004

Implementation of DNA chips obtained by microprojection for diagnostic and personalized medicine.

It is expected that rapidly emergent new fields of application for DNA chips will be Diagnostic and Personalized Medicine. These new applications will require a limited number of probes, generally from 100 to 1000. So, after a brief review of the existing techniques to manufacture DNA chips, which are efficient for R&D applications and which often require a higher number of probes, we shall first report some advances in the silanization of the substrates and the grafting of probes to improve the robustness and the reliability of the devices. Then we shall discuss two manufacturing processes working at the scale of a nanoliter of reactant: ex situ and in situ fabrication by microprojection. We shall see how these processes are complementary and may be used to design and produce chips, at a large scale, for these new applications.

Equipment Design↗
PubMedDate not supplied

[Manufacture of DNA chips in a laboratory for internal use: legislation and quality assurance].

Manufacturing and using DNA chips in a laboratory, while respecting legality and good practices, require a review of the regulatory framework and relevant documentation for implementing a quality assurance system. Using DNA chips, either as a research tool, or as an in vitro diagnostic medical device, does not come within the same regulations: none in the first case, and european directive 98/79/CE in the second one. It is the same for research practice, for which the law to be enforced has been primarily conditioned to ethics, while carrying out medical analyses has been framed in France by the GBEA. The regulatory approach laid down in the GBEA is a first step for implementing a quality assurance system, but this must be extended to the manufacturing process of DNA chips. International standards (ISO 9001: 2000, ISO/IEC 15189...) provide documentation to meet this last requirement, but also enable one to carry on the quality approach up to the certification of the laboratory or its accreditation.

Clinical Medicine↗
PubMed2004

[Study on the expression of hematopoietic growth factor gene in human umbilical vein endothelial cells using gene chip].

In order to detect the hematopoietic growth factor gene expressed in human umbilical vein endothelial cells using gene chip, human umbilical vein endothelial cells (ECV304) were cultured in vitro and divided into VEGF group and control group in same medium. 50 ng/ml hVEGF165 was added in the VEGF group. After culture for 24 hours all cells were collected for total RNA extraction. Then, cDNAs were marked with Cy3 and Cy5 for control group and VEGF group, respectively, and hybridized with gene chip. Hybridization signals were collected and analyzed following scanning by laser co-focal microscopy. The results showed that a large number of hematopoietic growth factor and receptor genes (Epo/R, GM-CSF/R, G-CSF/R, LIF, IL-3, TPO, Flt-3, SCF) were expressed in both groups, while many other growth factors (VEGF, IGF2, PDGFA, PDGFB, TGFbeta1) and receptors (neuropilin-1, neuropilin-2, TGFbeta-R1)were expressed. The differentially expressed genes amounted to 24. It is concluded that many hematopoietic growth factors and receptors expressed by hUVECs could be analyzed in a short period by using gene chip, which provides a powerful method for further studies on characteristics of vascular endothelial cells.

Cells, Cultured↗
PubMed2004

DNA chip technology in cardiovascular research.

Global and/or dynamic analysis of the cardiac transcriptome may improve our understanding of the adaptation of cardiac tissue or cells to different physiological or pathological conditions. The achievement of sequencing projects on mammalian genomes and the development of DNA chip technology have dramatically extended the scale of gene expression studies from a candidate gene approach to a system approach. In current DNA chip experiments, expression levels of thousands of genes can be determined simultaneously. Obviously, the huge quantities of objects and information generated by these experiments require a computational management of the expression data with adequate mathematical (mostly statistical) algorithms. Here, we will discuss the principle and experimental key points of DNA chips. Four examples will be cited to illustrate applications in the cardiovascular system.

Animals↗
PubMed2004

[Theoretical study of contactless conductivity detector for electrophoresis chip].

Currently most electrophoresis chips use optical detection methods, which brings some difficulties in micromation and integration of electrophoresis chips. In order to solve this problem, a new high-frequency contactless conductivity detector for electrophoresis chip is designed. At the same time, theoretical study and analysis of this new detector are carried out, based on the construction of an equivalent circuit mode of high-frequency conductivity detector and the design of the structure. With the consideration of many factors including band broadening, the dimensions of the structure were designed and optimized. In summary, the detector has many advantages such as wide application range, simple structure and easy integration.

Conductometry↗
PubMed2005

[The joint applications of DNA chips and single nucleotide polymorphisms in forensic science].

DNA chip technology, being a new high-technology, shows its vigorous life and rapid growth. Single Nucleotide Polymorphisms (SNPs) is the most common diversity in the human genome. It provides suitable genetic markers which play a key role in disease linkage study, pharmacogenomics, forensic medicine, population evolution and immigration study. Their advantage such as being analyzed with DNA chips technology, is predicted to play an important role in the field of forensic medicine, especially in paternity test and individual identification. This report mainly reviews the characteristics of DNA chip and SNPs, and their joint applications in the practice of forensic medicine.

Forensic Medicine↗
PubMed2005

[Study on expression of genes in Tamarix androssowii under NaHCO3 stress using gene chip technology].

Gene chip technology was employed to study gene expression in Tamarix androssowii under NaHCO3 stress. cDNAs from T. androssowii treated with NaHCO3 solution and that from control group were labeled with fluorescent dye CyS and Cy3 respectively. The two fluorescent cDNA probes were mixed and hybridized to gene chips containing T. androssowii genes, and the chips were scanned using biochip scanning system. Differential expression of genes was analyzed through calculation of the ratio of Cy5 to Cy3 signal intensities. Total of 89 genes differentially expressed were identified, among them, 27 showed down regulated expression and 62 showed up regulated expression. Blastx analysis showed that the function of the differentially expressed genes could be grouped into some categorizations such as photosynthesis, reactive oxygen species eliminated, regulation of osmotic potential, regulation of gene expression and signal transduction, metabolism, development, ribosomal protein, protein breakdown and recycling, transporter, water channel proteins and so on. Based on this research, some function-unknown or novel unreported genes that respond to salt stress were also identified, and these genes may have important functions in salt resistance of T. androssowii. Some important pathways of salt resistance in T. androssowii are revealed, and the gene expression profiling of T. androssowii under salt stress and without stress is obtained in this study.

DNA, Complementary↗
PubMed2005

[A gene-chip image grid localization method based on profiles of image].

Automatic gene-chip image grid localization is an essential task for gene-chip image analysis. Now an method based on profiles of gene-chip image is proposed. Using the differences between two profiles after filtration by arithmetic mean method, we can easily find the local grayscale minimum between two probe spots, then the probe spots are automatically located. The experiments show that the new approach correctly locates the probes while giving protection against noise affection robustly. Grid location

Algorithms↗
PubMed2005

Characterization of protein glycosylation using chip-based nanoelectrospray with precursor ion scanning quadrupole linear ion trap mass spectrometry.

Glycosylation is one of the most important posttranslational modifications affecting the functions of proteins and cell activities. Mass spectrometry (MS) has proven to be an effective tool for structural glycobiology and has helped gain an understanding of glycoprotein-mediated diseases. Although electro-spray ionization-tandem MS remains widely recognized as an effective means for oligosaccharide characterization, the hydrophilic nature of glycans has often caused the poor ionization efficiency requiring either derivatization or nanoelectrospray to improve detection sensitivity. In this report we describe the use of a chip-based infusion nanoelectrospray platform coupled with the hybrid triple quadrupole/linear ion trap for identification and characterization of glycosylation in complex mixtures. The high-mannose-type N-glycosylation in ribonuclease B was used to map the glycosylation site and obtain glycan structures. Using the chip-based nanoelectro-spray with precursor ion scanning linear ion trap MS, we were able to map the glycosylation site and obtain the glycan structures in ribonuclease B at 100 fmol/microL in a single analysis. In addition, a new, low-abundant glycoform with an additional hexose (Hex10GlcNAc2) attached to ribonuclease B was discovered. The results reported here demonstrate that the chip-based infusion nanoelectrospray ionization coupled to a quadrupole/linear ion trap platform is a valuable system, as it provides high sensitivity and stability for nanoelectrospray analysis, and allows extended acquisition time for completing precursor ion scanning and subsequent MS2 and MS3 information in a single analysis.

Alkylation↗
PubMed2006

[The research and development of new diagnostic gene chips for SARS coronavirus].

The loci of cDNA sequences for valid diagnosis have been identified through the selection of the genome of SARS coronaries. The gene chips for diagnosing such virus have been developed, based on our own-developed technology for manufacturing and application of gene chips. The diagnoses given by such gene chips were consistent well with the reports of clinical laboratories (94.29%) and the sensitivity reached 10(-2)/ml virus molecules. This method is well suited for the clinical use in SARS coronaries diagnosis.

Humans↗