利用DNA微阵列对微生物基因进行定量检测。
Quantitative detection of microbial genes by using DNA microarrays.
作者信息
Cho Jae-Chang, Tiedje James M
机构信息
Center for Microbial Ecology, Plant and Soil Sciences Bldg., Michigan State University, East Lansing, MI 48824, USA.
出版信息
Appl Environ Microbiol. 2002 Mar;68(3):1425-30. doi: 10.1128/AEM.68.3.1425-1430.2002.
Abstract
To quantify target genes in biological samples using DNA microarrays, we employed reference DNA to normalize variations in spot size and hybridization. This method was tested using nitrate reductase (nirS), naphthalene dioxygenase (nahA), and Escherichia coli O157 O-antigen biosynthesis genes as model genes and lambda DNA as the reference DNA. We observed a good linearity between the log signal ratio and log DNA concentration ratio at DNA concentrations above the method's detection limit, which was approximately 10 pg. This approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.
摘要
为了使用DNA微阵列定量生物样品中的靶基因，我们采用参考DNA来标准化斑点大小和杂交的变化。使用硝酸还原酶（nirS）、萘双加氧酶（nahA）和大肠杆菌O157 O抗原生物合成基因作为模型基因，并使用λDNA作为参考DNA对该方法进行了测试。我们观察到，在DNA浓度高于该方法的检测限（约10 pg）时，对数信号比与对数DNA浓度比之间具有良好的线性关系。这种设计定量微阵列的方法以及本研究推导的方程提供了一种简单便捷的方法，可根据杂交信号比估算靶基因浓度。
相似文献
1
Quantitative detection of microbial genes by using DNA microarrays.
Appl Environ Microbiol. 2002 Mar;68(3):1425-30. doi: 10.1128/AEM.68.3.1425-1430.2002.
2
A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2.
J Bacteriol. 1998 May;180(9):2522-30. doi: 10.1128/JB.180.9.2522-2530.1998.
3
Detection of genes for periplasmic nitrate reductase in nitrate respiring bacteria and in community DNA.
FEMS Microbiol Lett. 1999 Aug 15;177(2):263-70. doi: 10.1111/j.1574-6968.1999.tb13742.x.
4
Development and evaluation of functional gene arrays for detection of selected genes in the environment.
Appl Environ Microbiol. 2001 Dec;67(12):5780-90. doi: 10.1128/AEM.67.12.5780-5790.2001.
5
Escherichia coli O antigen typing using DNA microarrays.
Mol Cell Probes. 2006 Jun-Aug;20(3-4):239-44. doi: 10.1016/j.mcp.2006.01.001. Epub 2006 Mar 14.
6
Characterization of an oxygen-dependent inducible promoter, the Escherichia coli nar promoter, in gram-negative host strains.
Biotechnol Bioeng. 2003 May 5;82(3):271-7. doi: 10.1002/bit.10567.
7
Genes similar to naphthalene dioxygenase genes in trifluralin-degrading bacteria.
Pest Manag Sci. 2004 May;60(5):474-8. doi: 10.1002/ps.835.
8
Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo.
Science. 1983 Oct 14;222(4620):167-9. doi: 10.1126/science.6353574.
9
Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product.
Gene. 1985;36(3):301-9. doi: 10.1016/0378-1119(85)90185-4.
10
Dynamic changes in nahAc gene copy numbers during degradation of naphthalene in PAH-contaminated soils.
Appl Microbiol Biotechnol. 2006 Oct;72(6):1322-9. doi: 10.1007/s00253-006-0423-5. Epub 2006 Jun 28.
引用本文的文献
1
The Potential Correlation Between Bacterial Sporulation and the Characteristic Flavor of Chinese Maotai Liquor.
Front Microbiol. 2018 Jul 2;9:1435. doi: 10.3389/fmicb.2018.01435. eCollection 2018.
2
Microbial degradation of petrochemical waste-polycyclic aromatic hydrocarbons.
Bioresour Bioprocess. 2017;4(1):28. doi: 10.1186/s40643-017-0158-4. Epub 2017 Jun 30.
3
A Parametric Survival Model When a Covariate is Subject to Left-Censoring.
J Biom Biostat. 2012;Suppl 3(2). doi: 10.4172/2155-6180.S3-002.
4
Use of functional gene arrays for elucidating in situ biodegradation.
Front Microbiol. 2012 Sep 21;3:339. doi: 10.3389/fmicb.2012.00339. eCollection 2012.
5
SIZE DOESN'T MATTER: MICROBIAL SELECTION EXPERIMENTS ADDRESS ECOLOGICAL PHENOMENA.
Ecology. 2003 Jul;84(7):1679-1687. doi: 10.1890/0012-9658(2003)084[1679:SDMMSE]2.0.CO;2.
6
Adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37 degrees C and 55 degrees C.
Appl Environ Microbiol. 2010 Oct;76(19):6564-71. doi: 10.1128/AEM.00961-10. Epub 2010 Jul 30.
7
Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.
Appl Environ Microbiol. 2010 Feb;76(4):1088-94. doi: 10.1128/AEM.02749-09. Epub 2009 Dec 28.
8
Oligonucleotide microarray technology and its application to Mycobacterium avium subsp. paratuberculosis research: a review.
Mol Biotechnol. 2009 May;42(1):30-40. doi: 10.1007/s12033-008-9137-5. Epub 2009 Jan 6.
9
Large scale multiplex PCR improves pathogen detection by DNA microarrays.
BMC Microbiol. 2009 Jan 3;9:1. doi: 10.1186/1471-2180-9-1.
10
Transcriptome analysis of Lactococcus lactis in coculture with Saccharomyces cerevisiae.
Appl Environ Microbiol. 2008 Jan;74(2):485-94. doi: 10.1128/AEM.01531-07. Epub 2007 Nov 9.
本文引用的文献
1
Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters.
Appl Environ Microbiol. 1993 Dec;59(12):4101-14. doi: 10.1128/aem.59.12.4101-4114.1993.
2
DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes.
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9853-8. doi: 10.1073/pnas.171178898. Epub 2001 Aug 7.
3
Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.
Appl Environ Microbiol. 2001 Aug;67(8):3677-82. doi: 10.1128/AEM.67.8.3677-3682.2001.
4
Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR.
Appl Environ Microbiol. 2001 Feb;67(2):760-8. doi: 10.1128/AEM.67.2.760-768.2001.
5
High-density microarray-mediated gene expression profiling of Escherichia coli.
J Bacteriol. 2001 Jan;183(2):545-56. doi: 10.1128/JB.183.2.545-556.2001.
6
Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions.
J Bacteriol. 2000 Aug;182(16):4458-65. doi: 10.1128/JB.182.16.4458-4465.2000.
7
Monitoring gene expression using DNA microarrays.
Curr Opin Microbiol. 2000 Jun;3(3):285-91. doi: 10.1016/s1369-5274(00)00091-6.
8
Universal DNA microarray method for multiplex detection of low abundance point mutations.
J Mol Biol. 1999 Sep 17;292(2):251-62. doi: 10.1006/jmbi.1999.3063.
9
Development of primers to O-antigen biosynthesis genes for specific detection of Escherichia coli O157 by PCR.
Appl Environ Microbiol. 1999 Jul;65(7):2954-60. doi: 10.1128/AEM.65.7.2954-2960.1999.
10
Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays.
Nat Genet. 1999 Jun;22(2):164-7. doi: 10.1038/9674.
Zotero 插件