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oligonucleotide array analysis of cyclic tension-responsive genes in human periodontal ligament fibroblasts

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY 2007年第5期39卷 910-921页

作者： Yamashiro, Keisuke Myokai, Fumio Hiratsuka, Koichi Yamamoto, Tadashi Senoo, Kyoko Arai, Hideo Nishimura, Fusanori Abiko, Yoshimitsu Takashiba, Shogo Okayama Univ Grad Sch Med Dent & Pharmaceut Sci Dept Pathophysiol Periodontal Sci Okayama 7008525 Japan Nihon Univ Sch Dent Matsudo Dept Biochem & Mol Biol Matsudo Chiba 2718587 Japan

Mechanical stress results in differential gene expression that is critical to convert the stimulus into biochemical signals. Under physiological stress such as occlusal force, human periodontal ligament fibroblasts (HPLF) are associated with homeostasis of periodontal tissues however the changes in response to mechanotransduction remain uncharacterized. We hypothesized that cyclic tension-responsive (CT) genes may be used to identify a set of fundamental pathways of mechanotransduction. Our goal was to catalogue CT genes in cultured HPLE HPLF were subjected to cyclic tension up to 16 h, and total RNA was isolated from both tension-loaded and static HPLE The oligonucleotide arrays analysis revealed significant changes of mRNA accumulation for 122 CT genes, and their kinetics were assigned by the K-means clustering methods. Ingenuity Pathway Analysis was completed for HPLF mechanotransduction using 50 CT genes. This analysis revealed that cyclic tension immediately down-regulated all nuclear transcription factors except v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS) reacting as an early responsive gene. In turn, transcription factors such as tumor protein p53 binding protein 2 (TP53BP2), and extra-nuclear molecules such as adrenergic receptor beta 2 (ADRB2) were up-regulated after 1-2 h, which may result in fundamental HPLF functions to adapt to cyclic tension. Subsequent inhibition assays using Y27632, a pharmacologic inhibitor of Rho-associated kinase (ROCK), suggested that HPLF has both ROCK-dependent and ROCK-independent CT genes. Mechanical stress was found to effect the expression of numerous genes, in particular, expression of an early responsive gene;FOS initiates alteration of HPLF behaviors to control homeostasis of the periodontal ligament. (C) 2007 Elsevier Ltd. All rights reserved.

关键词： cyclic tension-responsive genes oligonucleotide array human periodontal ligament fibroblasts pathway analysis Rho-associated kinase

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A low-density oligonucleotide array study for parallel detection of harmful algal. species using hybridization of consensus PCR products of LSU rDNA D2 domain

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BIOSENSORS & BIOELECTRONICS 2006年第9期21卷 1812-1821页

作者： Ki, JS Han, MS Hanyang Univ Dept Life Sci Coll Nat Sci Seoul 133791 South Korea

A low-density oligonucleotide array approach based on the hybridization of consensus PCR products of LSU rDNA was developed in order to simultaneously detect various harmful algae. A set of oligonucleotide probes for the hybridization of specific LSU rDNA D2 regions was developed for the identification of 10 representative harmful microalgae. Each probe was spotted onto a streptoavidin-coated glass slide by pipetting. Universal primers were designed within the conserved regions adjacent to the D2 regions of all harmful algae and used to PCR amplify the complete D2 regions. The PCR products were hybridized to the oligonucleotides arrayed on the slide. The array produced unique hybridization patterns for each species of harmful algae and allowed us to differentiate the closely related species. Furthermore, we were able to simultaneously detect several predominant HAB species from a mixture of Culture strains and from a natural sample. These results show that DNA microarray call be a new technical platform for parallel discrimination of harmful algae and has great potential to alter the manner in which researchers monitor these microorganisms. (c) 2005 Elsevier B.V. All rights reserved.

关键词： harmful algae LSU rDNA D2 region oligonucleotide array simultaneous identification parallel detection

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Probe selection algorithm for oligonucleotide array-based medium-resolution genotyping

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MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING 2004年第6期42卷 812-816页

作者： Zhou, Y Peng, S Gao, H Cheng, J Tsinghua Univ Dept Biol Sci & Biotechnol Beijing Peoples R China Peking Univ Sch Math Sci Beijing 100871 Peoples R China Natl Engn Res Ctr Beijing Biochip Technol Beijing Peoples R China Tsinghua Univ State Key Lab Biomembrane & Membrane Biotechnol Beijing Peoples R China

Medium-resolution genotyping has the goal of distinguishing different subgroups instead of each element in a group. An oligonucleotide array provides an inexpensive, high-throughput method to identify differences in DNA sequence among individuals, which is fundamental for genotyping. As the cost and difficulty of designing and fabricating the oligonucleotide array dramatically increase with the number of probes used, it is therefore important to have a design with a minimum number of probes meeting the requirement of medium-resolution genotyping. The first algorithm for designing and selecting probes for oligonucleotide array-based medium-resolution typing is reported. The goal in deriving the algorithm was to select a minimum number of probes from a large probe set on the premise of minimum loss of resolution. The algorithm, which was based on entropy, conditional entropy and mutual information theory, was used to select the minimum number of probes from a large probe set. The algorithm was tested on a human leukocyte antigen (HLA) sequence data set. Thirty probes were selected from 390 probes for HLA-A, and 60 probes were selected from 767 probes for HLA-B. Although the number of probes was reduced by almost ten times, the distinguishability was reduced only a little, by 0.45% (from 99.90% to 99.45%) for HLA-A and 0.27% (from 99.84% to 99.57%) for HLA-B, respectively. This is a satisfactory and practical result.

关键词： probe selection mutual information oligonucleotide array genotyping

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Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections

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JOURNAL OF MICROBIOLOGICAL METHODS 2004年第3期58卷 403-411页

作者： Hong, BX Jiang, LF Hu, YS Fang, DY Guo, HY Sun Yatsen Univ Sch Med Dept Microbiol Guangzhou 510089 Peoples R China

A rapid and accurate method for detection for common pathogenic bacteria in foodborne infections was established by using oligonucleotide array technology. Nylon membrane was used as the array support. A mutation region of the 23S rRNA gene was selected as the discrimination target from 14 species (genera) of bacteria causing foodborne infections and two unrelated bacterial species. A pair of universal primers was designed for PCR amplification of the 23S rRNA gene. Twenty-one species (genera)-specific oligonucleotide detection probes were synthesized and spotted onto the nylon membranes. The 23S rRNA gene amplification products of 14 species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that nine species of pathogenic bacteria (Escherichia coli. Campylobacter jejuni, Shigella dysenteriae, Vibrio cholerae, Vibrio parahaemolyticus, Proteus vulgaris, Bacillus cereus, Listeria monocytogenes and Clostridium botulinum) showed high sensitivity and specificity for the oligonucleotide array. Two other species (Salmonella enterica and Yersinia enterocolitica) gave weak cross-reaction with E. coli, but the reaction did not affect their detection. After redesigning the probes, positive hybridization results were obtained with Staphylococcus aureus, but not with Clostridium perfringens and Streptococcus pyogenes. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections. (C) 2004 Elsevier B.V. All rights reserved.

关键词： oligonucleotide array foodborne infections PCR

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Feasibility of diagnosing renal allograft dysfunction by oligonucleotide array: Gene expression profile correlates with histopathology

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TRANSPLANT IMMUNOLOGY 2011年第3期24卷 172-180页

作者： Mao, You-ying Yang, Hao Wang, Minmin Peng, Wenhan He, Qiang Shou, Zhang-fei Jiang, Hua Wu, Jianyong Fang, Yong-qi Dong, Hai-tao Chen, Jiang-hua Zhejiang Univ Coll Med Affiliated Hosp 1 Kidney Dis Ctr Hangzhou 310003 Zhejiang Peoples R China Zhejiang Univ Sch Agr & Biotechnol Bioinformat & Gene Network Res Grp Hangzhou Peoples R China Minist Publ Hlth Key Lab Combined Multi Organ Transplantat Hangzhou Peoples R China State Adm tradit Chinese Med Grade Lab 3 Kidney Dis Immunol Lab Hangzhou Zhejiang Peoples R China

Background: Effective non-invasive monitoring method to tell histopathology is a big challenge in renal transplantation. Methods: We used 70-mer long oligonucleotide array with 449 immune related genes to determine gene expression profiles of peripheral blood mononuclear cells (PBMCs) under different immune status including stable renal function (TX), acute tubular necrosis (ATN), biopsy conformed acute rejection (AR), clinical rejection with pathology of borderline changes (BL), clinical rejection without biopsy proven/presumed rejection (PR) and renal dysfunction without rejection (NR). Results: Distinct molecular expression signatures in each group were found to correlate with histopathology. And we concluded that B cell chemokine CXCL13 and mast cell may play a role in renal allograft rejection through significant difference analysis and functional pathway analysis. Conclusions: It provides a potential non-invasive method for monitoring renal allograft function and immune status of renal transplant recipients. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Renal transplant Acute allograft rejection oligonucleotide array Gene expression Immune status

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Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

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INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY 2006年第2期107卷 131-137页

作者： Chiang, YC Yang, CY Li, C Ho, YC Lin, CK Tsen, HY Hung Kuang Univ Dept Food Sci & Nutr Shalu Taichung Taiwan Vanung Univ Dept Biotechnol Taoyuan Taiwan Natl Chung Hsing Univ Dept Food Sci Taichung 40227 Taiwan Chung Shan Univ Dept Microbiol & Immunol Taichung Taiwan

Rapid identification of the genus and species of bacteria in foods and clinical specimens is important. In this report, DNA sequences of bacterial 16S rDNA were used to develop the oligonucleotide array for the identification of bacterial strains of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. Most of these bacterial strains may cause food-borne outbreaks or sporadic cases. A rapid ( < 4 h) detection method that used universal PCR primers to amplify the variable regions of bacterial 16S rDNA, followed by reverse hybridization of the PCR products, which were biotin labeled, to the oligonucleotides arrayed on the chip was developed. Fifteen oligonucleotide probes were selected and spotted on the nylon strip to determine the array hybridization patterns. It was successful in discriminating Bacillus spp., F. coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with identification, in general, to the genus level, not species level. As 182 randomly selected strains were assayed, the detection rate was found higher than 98%. Except for 3 strains, the remaining 179 strains were correctly identified and no cross reactions were observed. These 179 strains generated five hybridization patterns. Adding more oligonucleotide probes to the array may allow the detection of more bacterial genera and species without significantly increasing the complexity or cost. (c) 2005 Elsevier B.V. All rights reserved.

关键词： 16S ribosomal DNA oligonucleotide array food pathogen

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Application of an oligonucleotide array assay for rapid detecting and genotyping of Chlamydia trachomatis from urogenital specimens

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DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE 2007年第1期57卷 1-6页

作者： Zheng, He-ping Jiang, Li-fang Fang, Dan-yun Xue, Yao-hua Wu, Ya-an Huang, Jin-mei Ou, Zhi-ying Sun Yat Sen Univ Sch Med Dept Microbiol Guangzhou 510089 Peoples R China Guangdong Ctr Skin Dis & STIs Control & Prevent Guangzhou 510500 Peoples R China

An oligonucleotide array technology was established for rapidly detecting and genotyping Chlamydia trachomatis in urogenital infections. The VS1-VS2 region of the omp1 gene was used to design oligonucleotide probes. Eleven serovar-specific probes to serovars A, B, C, D, E, F, G, H, I, J, and K, and 3 group-specific probes to group B (B, Ba, D, E, L1, and L2), group C (A, C, H, I, J, K, and L3), and an intermediate group (F and G) were synthesized and spotted onto the nylon membrane. Two pairs of universal primers were designed for the nested polymerase chain reaction (PCR) amplification of the VS1-VS2 gene. Digoxigenin-labeled amplicons of the VS1-VS2 gene of C trachomatis were hybridized to the membrane array. Hybridization signals were read by the nitroblue tetrazolium/5-bromo-4-chloro-3-indolylphosphate color development. The assay developed was tested with reference strains of C. trachomatis serovars and clinical samples. The sensitivity was evaluated for 57 samples previously found to be positive for C trachomatis by using plasmid PCR, and 98.2% (56/57) concordance was obtained. Fourteen oligonucleotide probes were optimized by trying different reaction conditions, showing specific hybridization with the corresponding reference strains, but no cross-reactions with other urogenital microorganisms. Using this procedure, a total of 59 strains were detected from 56 chlamydial samples. Eight genotypes were found, and type D, E, F, and H were the most frequently observed types (77.9%). Three cases (5.4%) had multiple infections with serovars: 1.D/E, 2.D/F, and 3.F/K. To validate the reference strains and confirm the genotype identity as determined by the oligonucleoticle array technology, we sequenced all reference strains and 10 selected specimens across variable sequence VS1 and VS2. No discrepancies were found between the array typing and the genotype identity confirmed by nucleotide sequencing of the PCR product. The findings from this study indicated that the ol

关键词： oligonucleotide array Chlamydia trachomatis urogenital

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PCR and oligonucleotide array for detection of Enterobacter sakazakii in infant formula

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MOLECULAR AND CELLULAR PROBES 2006年第1期20卷 11-17页

作者： Liu, Y Gao, QL Zhang, X Hou, YM Yang, JL Huang, XT Nankai Univ Coll Life Sci Dept Biochem & Mol Biol Tianjin 300071 Peoples R China Tianjin Entry Exit Inspect & Quarantine Bur Tianjin 300457 Peoples R China

Enterobacter sakazakii has been implicated in a several form of neonatal meningitis with a high mortality rate. In the present study, the species-specific PCR and oligonucleotide array assays were developed to detect the 16S-23S rDNA internal transcribed spacer (ITS) of E. sakazakii. Two pairs of specific PCR primers and 10 oligonucleotide probes were designed by sequencing the ITS of six strains of E. sakazakii and BLAST of GenBank. The specificity and efficiency of the PCR and oligonucleotide array methods were tested against a panel of numerous strains from 88 different bacterial strains. All of the E. sakazakii strains generated positive signal, and no cross-reaction was observed with non-E. sakazakii strains in the PCR and oligonLiCleotide array detections based on ITS sequences. Sensitivity of the detections is 1.3 CFU/100 g infant formula with the selective enrichment. Both of the PCR and oligonucleotide array procedures take only 48 h including the enrichment culture, whereas the conventional methods required at least 5 days. This study demonstrated that both of the pathogenic detections are time-saved and reliable. (c) 2005 Elsevier Ltd. All rights reserved.

关键词： detection E. sakazalii ITS PCR oligonucleotide array

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An oligonucleotide array to detect genetically modified events in potato

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PLANT MOLECULAR BIOLOGY REPORTER 2003年第3期21卷 259-270页

作者： Nagarajan, MM De Boer, SH Canadian Food Inspect Agcy Saskatoon SK Canada

For rapid and simultaneous detection of transgenic elements in genetically modified (GM) food crops, we explored DNA array technology. Forty-four oligonucleotide 23- to 31-mers were selected to use in an array on the basis of melting temperature and sequence specificity. Selected oligonucleotides consisted of DNA fragments corresponding to structural and regulatory elements and selectable markers used in developing transgenic crops, such as potato. Other oligonucleotides represented endogenous genes from potato to serve as positive controls and from heterologous crops, such as soybean and canola, to serve as negative controls. Amino-terminated oligonucleotides were hand-spotted on activated nylon membrane with a commercial spotting device. Target DNA was isolated from foliage of transgenic and nontransgenic crops, including potato, and labeled with digoxigenin-dUTP by random priming following restriction digestion to reduce DNA fragment size. Hybridization signals were visualized by an alkaline phosphatase anti-DIG-Fab conjugate and the chemiluminescent substrate, CDP-star. We detected the presence or absence of transgenic elements in transgenic and nontransgenic potato samples. Preliminary studies demonstrated that more specific and sensitive hybridization signals were generated from an oligonucleotide probe array than from a PCR product array. We anticipate that oligonucleotide probe arrays will be useful for regulatory monitoring of transgenic events.

关键词： GMO detection oligonucleotide array potato transgenic crops

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Parallel profiling of active transcription factors using an oligonucleotide array-based transcription factor assay (OATFA)

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JOURNAL OF PROTEOME RESEARCH 2005年第4期4卷 1451-1456页

作者： Shao, W Wei, HJ Qiao, JY Zhao, YC Sun, YM Zhou, YX Cheng, J Tsinghua Univ Dept Biol Sci & Biotechnol Beijing 100084 Peoples R China Tsinghua Univ Sch Med Med Syst Biol Res Ctr Beijing 100084 Peoples R China Natl Engn Res Ctr Beijing Biochip Technol Beijing 102206 Peoples R China CapitalBio Corp Beijing 102206 Peoples R China Tsinghua Univ State Key Lab Biomembrane & Membrane Biotechnol Beijing 100084 Peoples R China

Cell/tissue-specific gene expression are tightly regulated by various combinations of multiple transcription factors (TFs). Here, we present an oligonucleotide array-based transcription factor assay (OATFA), which allows the simultaneous assay of multiple active TFs. In this proof-of-principle work, both purified TFs and cell extracts were analyzed using OATFA and further antibody-based validation confirmed the chip data. This method could simplify the assay of multiple TFs and may facilitate high-throughput profiling of large numbers of TFs.

关键词： transcription factor EMSA DNA-binding activity oligonucleotide array oligonucleotide array-based transcription factor assay (OATFA)

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