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dna microarray for microbial biotechnology:: Gene expression profiles in Escherichia coli during protein overexpression

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JOURNAL OF THE CHINESE INSTITUTE OF CHEMICAL ENGINEERS 2002年第1期33卷 103-112页

作者： Rohlin, L Oh, MK Liao, JC Univ Calif Los Angeles Dept Chem Engn Los Angeles CA 90024 USA

dna microarray has emerged as a powerful technique for parallel detecting of all the mRNA levels in the cell. With this technology, transcription profiles at the genomic scale can be readily obtained. This technology has typically been applied to eukaryotic systems and medical problems. Here we demonstrated an application to microbial biotechnology, protein production in Escherichia coli. The gene expression pattern of the E. coli was determined during high level expression of a model protein, the a-subunit of luciferase (the luxA gene product). The whole set of E. coli genes was amplified and printed on a glass slide as a probe to determine the mRNA level of E. coli during overexpression of LuxA. With a proper statistical treatment, we found that at least 10% of E. coli genes were perturbed during protein overexpression. Almost all the known heat shock genes were up-regulated. Most of glucose transport and glycolytic genes were down-regulated. In addition, there are numerous genes up-or down-regulated that cannot be readily explained by existing mechanisms. These results offer an opportunity for further improvement of the host strain, growth medium, and bioprocessing conditions.

关键词： dna microarray E. coli gene expression

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dna microarray applications in environmental microbiology

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ANALYTICAL LETTERS 2003年第15期36卷 3165-3184页

作者： Letowski, J Brousseau, R Masson, L Natl Res Council Canada Biotechnol Res Inst Montreal PQ H4P 2R2 Canada

Although the majority of microarray reports are concerned with gene expression profiling in health-related studies, the use of dna microarray technology is expanding into new fields and new applications. In environmental microbiology, developments are also focusing on the detection of specific sequences in complex environmental samples and on genomic comparisons. Despite the fact that some limitations still exist, microarrays offer several advantages over the more traditional approaches. In this review, we will present examples of specific applications of this exciting new technology relating to the better understanding of the microbial world, with particular emphasis on strain detection, as well as the assessment of microbial diversity, adaptation, and evolution.

关键词： dna microarray strain detection phylogeny microbial diversity microbial adaptation microbial evolution

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dna microarray-based solid-phase PCR on copoly (DMA-NAS-MAPS) silicon coated slides: An example of relevant clinical application

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BIOSENSORS & BIOELECTRONICS 2016年 78卷 367-373页

作者： Damin, Francesco Galbiati, Silvia Ferrari, Maurizio Chiari, Marcella CNR Ist Chim Riconoscimento Mol Via Mario Bianco 9 I-20131 Milan Italy IRCCS San Raffaele Sci Inst Div Genet & Cell Biol Unit Genom Diag Human Pathol Milan Italy IRCCS Osped San Raffaele Lab Clin Mol Biol Milan Italy Univ Vita Salute San Raffaele Milan Italy

In a previous study we developed a highly sensitive dna microarray for the detection of common KRAS oncogenic mutations, which has been proven to be highly specific in assigning the correct genotype without any enrichment strategy even in the presence of minority mutated alleles. However, in this approach, the need of a spotter for the deposition of the purified PCR products on the substrates and the purification step of the conventional PCR are serious drawbacks. To overcome these limitations we have introduced the solid-phase polymerase chain reaction (SP-PCR) to form the array of PCR products starting from the oligonucleotide primers. This work was possible thanks to the great thermal stability of the copoly (DMA-NAS-MAPS) coating which withstands PCR thermal cycling temperatures. As an example of the application of this platform we performed the analysis of six common mutations in the codon 12 of KRAS gene (G12A, G12C, G12D, G12R, G12S, and G12V). In conclusion solid -phase PCR, combined with dual-color hybridization, allows mutation analysis in a shorter time span and is more suitable for automation. (C) 2015 Elsevier B.V. All rights reserved.

关键词： dna microarray Solid-phase PCR Polymer coated silicon slide Genotyping

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Optimization of dna microarray biosensors enables rapid and sensitive detection

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BIOTECHNOLOGY AND BIOPROCESS ENGINEERING 2017年第4期22卷 469-473页

作者： Hwang, Byeong Hee Shin, Hwa Hui Cha, Hyung Joon Pohang Univ Sci & Technol Dept Chem Engn Pohang 790784 South Korea Incheon Natl Univ Div Bioengn Incheon 406772 South Korea

dna microarray biosensors are essential tools for analyzing transcriptome expression levels and single nucleotide polymorphisms in disease pathology and diagnostics. Since rapid and quantitative detection is necessary for these applications, optimization of the experimental conditions is essential. Here, experimental conditions for dna microarray biosensors were optimized using an artificial target strategy without reaction or purification bias. Most importantly, hybridization time was reduced to one hour for rapid and homogeneous detection of target dna. High and low concentrations of capture probe are appropriate for optimizing the limit of detection and dynamic range, respectively. Bleaching effects can be minimized by measuring fluorescence intensity at night. These conditions enable quantitative and precise detection of target dna and offer experimental guidelines for genobiosensors in general.

关键词： dna microarray biosensor detection pathogen optimization quantification

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dna microarray analysis suggests that zinc pyrithione causes iron starvation to the yeast Saccharomyces cerevisiae

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JOURNAL OF BIOSCIENCE AND BIOENGINEERING 2010年第5期109卷 479-486页

作者： Yasokawa, Daisuke Murata, Satomi Iwahashi, Yumiko Kitagawa, Emiko Kishi, Katsuyuki Okumura, Yukihiro Iwahashi, Hitoshi Hokkaido Food Proc Res Ctr Dept Food Biotechnol Ebetsu Hokkaido 0690836 Japan Natl Inst Adv Ind Sci & Technol HTRC Tsukuba Ibaraki 3058569 Japan Natl Agr & Food Res Org NARO Natl Food Res Inst NFRI Tsukuba Ibaraki 3058642 Japan Japan Pulp & Paper Res Inst Inc Tsukuba Ibaraki 3002635 Japan

Zinc pyrithione has been used in anti-dandruff shampoos and in anti-fouling paint on ships. However, little is known of its mode of action. We characterized the effects of sub-lethal concentrations of zinc pyrithione (Zpt) on Saccharomyces cerevisiae using dna microarrays. The majority of the strongly upregulated genes are related to iron transport, and many of the strongly downregulated genes are related to the biosynthesis of cytochrome (heme). These data suggest that Zpt induces severe iron starvation. To confirm the dna microarray data, we supplemented cultures containing Zpt with iron, and the growth of the yeast was restored significantly. From these results, we propose that the principal toxicity of zinc pyrithione arises from iron starvation. (C) 2009, The Society for Biotechnology, Japan. All rights reserved.

关键词： Zinc pyrithione dna microarray Saccharornyces cerevisiae Iron Toxicity Cytochrome

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dna microarray chips: Fabrication and cutting-edge applications

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CHEMICAL ENGINEERING JOURNAL 2024年 499卷

作者： Xu, Jiaxin Chun, Honggu Wang, Lingwei Mei, Hui Chen, Shanze Huang, Xiaoluo Southern Univ Sci & Technol Jinan Univ Shenzhen Peoples HospClin Med Coll 2 Affiliated Hosp 1Dept Pulm & Crit Care MedInst R Shenzhen 518020 Guangdong Peoples R China Jinan Univ Postdoctoral Sci Res Stn Basic Med Guangzhou 510632 Guangdong Peoples R China Korea Univ Dept Biomed Engn Hana Sci Hall145 Anamro Seoul 02841 South Korea Chinese Acad Sci Shenzhen Inst Synthet Biol Shenzhen Inst Adv TechnolKey Lab Quantitat Synthe Shenzhen Key Lab Synthet GenomGuangdong Prov Key Shenzhen 518055 Guangdong Peoples R China

For decades, dna chips, also known as dna microarrays, have been extensively utilized for high-throughput gene expression analysis and single nucleotide polymorphism (SNP) genotyping. However, its utility extends far beyond these applications. Its use as a chip for Next Generation Sequencing (NGS) has brought about a revolutionary impact on many aspects of life science research. Additionally, dna microarray chip plays a cutting-edge role in spatial transcriptomics and dna data storage. Starting from fundamentals for dna microarray fabrication, this review aims to provide an overview and highlight the major applications that make use of this technology. Furthermore, we delve into the current issues that dna microarray holds and discuss its potential for future research. We anticipate that this review will offer a fresh perspective on dna microarray chip and foster its continued advancement.

关键词： dna microarray Next generation sequencing Spatial transcriptomics Digital data storage

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dna microarray for rapid detection of mitochondrial dna haplotypes of chum salmon

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MARINE BIOTECHNOLOGY 2004年第5期6卷 430-434页

作者： Moriya, S Urawa, S Suzuki, O Urano, A Abe, S Nisshinbo Ind Inc Ctr Res & Dev Midori Ku Chiba 2670056 Japan Natl Salmon Resources Ctr Genet Sect Toyohira Ku Sapporo Hokkaido 0620922 Japan Hokkaido Univ Div Biol Sci Grad Sch Sci Sapporo Hokkaido 0600810 Japan Hokkaido Univ Lab Anim Cytogenet Ctr Adv Sci & Technol Kita Ku Sapporo Hokkaido 0600810 Japan Hokkaido Univ Lab Breeding Sci Div Marine Biosci Grad Sch Fisheries Sci Hakodate Hokkaido 0418611 Japan

For use in genetic stock identification, we developed an oligonucleotide (dna) microarray hybridization method for rapid and accurate detection of nucleotide sequence variations in 20 previously identified variable nucleotide sites in about 500 bp within the 5' half of the control region of mitochondrial dna of chum salmon (Oncorhynchus keta). The method includes immobilization of synthesized oligonucleotides containing respective polymorphic sites on a glass slide precoated with polycarbodiimide resin, a 2-hour hybridization with dna microarray of biotinylated polymerase chain reaction fragments spanning the 5' variable portion followed by short washing, and visualization of hybridization signals by conventional ABC method and scanner-assisted computation of signal intensity on a computer. The entire process of hybridization and detection was completed within 4 hours. The resulting dna microarray could detect all of the single nucleotide mutations and therefore could be used to identity the sequence variations defining 30 mtdna haplotypes of chum salmon as revealed previously by nucleotide sequence analysis.

关键词： dna microarray chum salmon mtdna haplotype stock identification

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dna microarray analysis of genes differentially expressed in adipocyte differentiation

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JOURNAL OF BIOSCIENCES 2014年第3期39卷 415-423页

作者： Yin, Chunyan Xiao, Yanfeng Zhang, Wei Xu, Erdi Liu, Weihua Yi, Xiaoqing Chang, Ming Xi An Jiao Tong Univ Affiliated Hosp 2 Xian 710049 Shangxi Peoples R China Fourth Mil Med Univ Dept Microbiol Xian 710032 Shangxi Peoples R China

In the present study, the human liposarcoma cell line SW872 was used to identify global changes in gene expression profiles occurring during adipogenesis. We further explored some of the genes expressed during the late phase of adipocyte differentiation. These genes may play a major role in promoting excessive proliferation and accumulation of lipid droplets, which contribute to the development of obesity. By using microarray-based technology, we examined differential gene expression in early differentiated adipocytes and late differentiated adipocytes. Validated genes exhibited a >= 10-fold increase in the late phase of adipocyte differentiation by polymerase chain reaction (RT-PCR). Compared with undifferentiated preadipocytes, we found that 763 genes were increased in early differentiated adipocytes, and 667 genes were increased in later differentiated adipocytes. Furthermore, 21 genes were found being expressed 10-fold higher in the late phase of adipocyte differentiation. The results were in accordance with the RTPCR test, which validated 11 genes, namely, CIDEC, PID1, LYRM1, ADD1, PPAR gamma 2, ANGPTL4, ADIPOQ, ACOX1, FLP1L1, MAP3K2 and PEX14. Most of these genes were found being expressed in the later phase of adipocyte differentiation involved in obesity-related diseases. The findings may help to better understand the mechanism of obesity and related diseases.

关键词： Adipocyte differentiation dna microarray gene expression PCR SW872 cells

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dna microarray analysis of hematopoietic stem cell-like fractions from individuals with the M2 subtype of acute myeloid leukemia

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LEUKEMIA 2003年第10期17卷 1990-1997页

作者： Oshima, Y Ueda, M Yamashita, Y Choi, YL Ota, J Ueno, S Ohki, R Koinuma, K Wada, T Ozawa, K Fujimura, A Mano, H Jichi Med Sch Div Clin Pharmacol Kawachigun Tochigi Japan Jichi Med Sch Div Hematol Kawachigun Tochigi Japan Jichi Med Sch Div Funct Genom Kawachigun Tochigi 3290498 Japan Jichi Med Sch Div Cardiol Kawachigun Tochigi 3290498 Japan Jichi Med Sch Dept Surg Kawachigun Tochigi 3290498 Japan Jichi Med Sch Dept Gynecol Kawachigun Tochigi 3290498 Japan CREST JST Saitama Japan

Acute myeloid leukemia (AML) may develop de novo or secondarily to myelodysplastic syndrome (MDS). Although the clinical outcome of MDS-related AML is worse than that of de novo AML, it is not easy to differentiate between these two clinical courses without a record of prior MDS. Large-scale profiling of gene expression by dna microarray analysis is a promising approach with which to identify molecular markers specific to de novo or MDS-related AML. This approach has now been adopted with AC133-positive hematopoietic stem cell-like fractions purified from 10 individuals, each with either de novo or MDS-related AML of the M2 subtype. Sets of genes whose activity was associated with either disease course were identified. Furthermore, on the basis of the expression profiles of these genes, it was possible to predict correctly the clinical diagnosis for 17 (85%) of the 20 cases in a cross-validation trial. Similarly, different sets of genes were identified whose expression level was associated with clinical outcome after induction chemotherapy. These data suggest that, at least in terms of gene expression profiles, de novo AML and MDS-related AML are distinct clinical entities.

关键词： dna microarray acute myeloid leukemia myelodysplastic syndrome DLK M2 subtype

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dna microarray-based detection and identification of bacterial and viral pathogens of maize

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JOURNAL OF PLANT DISEASES AND PROTECTION 2017年第6期124卷 577-583页

作者： Krawczyk, Krzysztof Uszczynska-Ratajczak, Barbara Majewska, Alicja Borodynko-Filas, Natasza Natl Res Inst Inst Plant Protect Virol & Bacteriol Dept Wladyslawa Wegorka 20 PL-60318 Poznan Poland Ctr Genom Regulat Dr Aiguader 88 Barcelona 08003 Catalonia Spain UPF Barcelona Spain Warsaw Univ Life Sci Dept Physiol Sci Fac Vet Med Nowoursynowska 159C PL-02776 Warsaw Poland

We describe the construction and evaluation of dna microarray for simultaneous detection and identification of five microbial pathogens of maize: Pantoea ananatis, P. agglomerans, Enterobacter cloaceae subsp. dissolvens, Maize dwarf mosaic virus (MDMV) and Sugarcane mosaic virus (SCMV). Unlike other dna microarrays described, our microarray comprises probes targeting the whole genomes of the tested pathogens. Control probes are complementary to genomes of closely related microorganisms that are nonpathogenic to maize and against maize and human genome sequences in order to avoid the potential false-positive results. Obtained results indicate that the fluorescence signals from pathogen and control probes are well distinguished in all performed experiments. The microarray's performance was compared with classical PCR-based pathogen detection method, and the versatility of the assay was tested in silico.

关键词： dna microarray Maize pathogen detection Pantoea ananatis P. agglomerans Enterobacter cloaceae subsp dissolvens Maize dwarf mosaic virus (MDMV) Sugarcane mosaic virus (SCMV)

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