201
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Huang X, Li Y, Niu Q, Zhang K. Suppression Subtractive Hybridization (SSH) and its modifications in microbiological research. Appl Microbiol Biotechnol 2007; 76:753-60. [PMID: 17634936 DOI: 10.1007/s00253-007-1076-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2007] [Revised: 06/04/2007] [Accepted: 06/05/2007] [Indexed: 11/27/2022]
Abstract
Suppression subtractive hybridization (SSH) is an effective approach to identify the genes that vary in expression levels during different biological processes. It is often used in higher eukaryotes to study the molecular regulation in complex pathogenic progress, such as tumorigenesis and other chronic multigene-associated diseases. Because microbes have relatively smaller genomes compared with eukaryotes, aside from the analysis at the mRNA level, SSH as well as its modifications have been further employed to isolate specific chromosomal locus, study genomic diversity related with exceptional bacterial secondary metabolisms or genes with special microbial function. This review introduces the SSH and its associated methods and focus on their applications to detect specific functional genes or DNA markers in microorganisms.
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Affiliation(s)
- Xiaowei Huang
- Lab for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
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202
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Greenhall JA, Zapala MA, Cáceres M, Libiger O, Barlow C, Schork NJ, Lockhart DJ. Detecting genetic variation in microarray expression data. Genome Res 2007; 17:1228-35. [PMID: 17609390 PMCID: PMC1933513 DOI: 10.1101/gr.6307307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data for evidence of genetic variation. To demonstrate the performance of the algorithm, the hybridization patterns in data obtained previously from SAMP8/Ta, SAMP10/Ta, and SAMR1/Ta inbred mice and from humans and chimpanzees were analyzed. Genes with consistent strain-specific and species-specific hybridization pattern differences were identified, and approximately 90% of the candidate genes were independently confirmed to harbor sequence differences. Importantly, the quality of gene expression data was also improved by masking the probes of regions with putative sequence differences between species and strains. To illustrate the application to human disease groups, data from an inflammatory bowel disease study were analyzed. GeSNP identified sequence differences in candidate genes previously discovered in independent association and linkage studies and uncovered many promising new candidates. This approach enables the opportunistic extraction of genetic variation information from new or pre-existing gene expression data obtained with high-density oligonucleotide arrays.
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Affiliation(s)
- Jennifer A. Greenhall
- The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Neurosciences Graduate Program, School of Medicine, University of California, San Diego, California 92093, USA
| | - Matthew A. Zapala
- Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, California 92093, USA
- Polymorphism Research Laboratory, Department of Psychiatry, University of California, San Diego, California 92093, USA
| | - Mario Cáceres
- The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), Barcelona 08003, Spain
| | - Ondrej Libiger
- Polymorphism Research Laboratory, Department of Psychiatry, University of California, San Diego, California 92093, USA
| | - Carrolee Barlow
- The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Brain Cells, Inc., San Diego, California 92121, USA
| | - Nicholas J. Schork
- Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, California 92093, USA
- Polymorphism Research Laboratory, Department of Psychiatry, University of California, San Diego, California 92093, USA
| | - David J. Lockhart
- The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Amicus Therapeutics, Cranbury, New Jersey 08512, USA
- Corresponding author.E-mail ; fax (609) 662-2001
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203
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Rajendar B, Sato Y, Nishizawa S, Teramae N. Improvement of base selectivity and binding affinity by controlling hydrogen bonding motifs between nucleobases and isoxanthopterin: Application to the detection of T/C mutation. Bioorg Med Chem Lett 2007; 17:3682-5. [PMID: 17470392 DOI: 10.1016/j.bmcl.2007.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Revised: 04/03/2007] [Accepted: 04/13/2007] [Indexed: 11/20/2022]
Abstract
At an abasic site in an oligo-DNA duplex, isoxanthopterin (IX)(dagger) can bind to thymine (T) and cytosine (C) with strong affinity compared to adenine and guanine, but the base selectivity for T against C is moderate. In order to improve both binding affinity and base selectivity for T against C, a methyl group is introduced to IX, which is known as 3-methyl isoxanthopterin (3-MIX),(dagger) by which binding affinity for C is expected to decrease. Indeed, 3-MIX specifically binds to T more strongly than IX and loses its binding affinity for C. The improved binding ability of 3-MIX for T would be suitable for the practical use in SNP typing related to T.
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Affiliation(s)
- Burki Rajendar
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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204
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Rivera-Gandía J, Cabrera CR. Self-assembled monolayers of 6-mercapto-1-hexanol and mercapto-n-hexyl-poly(dT)18-fluorescein on polycrystalline gold surfaces: An electrochemical impedance spectroscopy study. J Electroanal Chem (Lausanne) 2007. [DOI: 10.1016/j.jelechem.2007.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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205
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Liu Y, Elsholz B, Enfors SO, Gabig-Ciminska M. Confirmative electric DNA array-based test for food poisoning Bacillus cereus. J Microbiol Methods 2007; 70:55-64. [PMID: 17466398 DOI: 10.1016/j.mimet.2007.03.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 02/20/2007] [Accepted: 03/20/2007] [Indexed: 11/18/2022]
Abstract
Detection of the full set of toxin encoding genes involved in gastrointestinal diseases caused by B. cereus was performed. Eight genes determining the B. cereus pathogenicity, which results in diarrhea or emesis, were simultaneously evaluated on a 16-position electrical chip microarray. The DNA analyte preparation procedure comprising first 5 min of ultrasonic treatment, DNA extraction, and afterwards an additional 10 min sonication, was established as the most effective way of sample processing. No DNA amplification step prior to the analysis was included. The programmed assay was carried out within 30 min, once the DNA analyte from 10(8) bacterial cells, corresponding to one agar colony, was subjected to the assay. In general, this work represents a mature analytical way for DNA review. It can be used under conditions that require almost immediate results.
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Affiliation(s)
- Yanling Liu
- School of Biotechnology, Royal Institute of Technology (KTH), S-10691, Stockholm, Sweden
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206
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Liang P, Meade JD, Pardee AB. A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling. Nat Protoc 2007; 2:457-70. [PMID: 17406608 DOI: 10.1038/nprot.2007.46] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since its invention in the early 1990s, differential display (DD) has become one of the most commonly used techniques for identifying differentially expressed genes at the mRNA level. Unlike other genomic approaches, such as DNA microarrays, DD systematically detects changes in mRNA profiles among multiple samples being compared without the need of any prior knowledge of genomic information of the living organism being studied. Here, we present an optimized DD protocol with a fluorescent digital readout as well as traditional radioactive labeling. The resulting streamlined fluorescent DD process offers an unprecedented accuracy, sensitivity and throughput in comprehensive and quantitative analysis of eukaryotic gene expression. Results usually can be obtained within days using a limited number of primer combinations, but a comprehensive DD screen may take weeks or months to accomplish, depending on gene coverage required and the number of differentially expressed genes present within a biological system being compared.
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Affiliation(s)
- Peng Liang
- GenHunter Corporation, 624 Grassmere Park Dr, Suite 17, Nashville, Tennessee 37211, USA.
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207
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Miyatake T, Ueda Y, Nakashima R, Yoshino K, Kimura T, Murata T, Nomura T, Fujita M, Buzard GS, Enomoto T. Down-regulation of insulin-like growth factor binding protein-5 (IGFBP-5): novel marker for cervical carcinogenesis. Int J Cancer 2007; 120:2068-77. [PMID: 17290407 DOI: 10.1002/ijc.22264] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To better understand the underlying pathways of cervical carcinogenesis, cDNA microarray analysis was performed on 2 sets of squamous cell carcinomas (SCCs) and their adjacent normal squamous epithelia. Consistently altered expression was detected for 32 genes. Real-time RT-PCR analysis was conducted on a selected subset of these genes (S100A2, GPC4, p72, IGFBP-5, TRIM2 and NAB2) for 14 additional SCCs and 10 normal epithelia. This found that, of the 6 candidate genes, only the insulin-like growth factor binding protein-5 (IGFBP-5) mRNA was generally and significantly under-expressed in SCCs (p < 0.001). All normal cervical epithelia (30 of 30) stained positively for IGFBP-5 protein, with 70% showing strong staining, whereas 65% (17/26) of SCC had complete loss of IGFBP-5, and only 8% (2/26) SCC retained strong expression (p < 0.001). Immunohistochemistry of premalignant cervical intraepithelial neoplasia (CIN) lesions shows a significantly weaker or negative staining in advanced CIN3 lesions compared with normal squamous epithelia (p = 0.001). This is the first study to show that down-regulation of IGFBP-5 protein correlates with cervical carcinogenesis and does so at a preneoplastic stage.
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MESH Headings
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/virology
- DNA, Viral/analysis
- Down-Regulation
- Female
- Gene Expression Regulation, Neoplastic
- Human papillomavirus 16/classification
- Human papillomavirus 16/genetics
- Humans
- Immunohistochemistry
- Insulin-Like Growth Factor Binding Protein 5/biosynthesis
- Insulin-Like Growth Factor Binding Protein 5/deficiency
- Insulin-Like Growth Factor Binding Protein 5/genetics
- Neoplasm Staging
- Oligonucleotide Array Sequence Analysis/methods
- Papillomavirus Infections/genetics
- Papillomavirus Infections/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/pathology
- Uterine Cervical Neoplasms/virology
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Affiliation(s)
- Takashi Miyatake
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 1-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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208
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von Nussbaum F, Brands M, Hinzen B, Weigand S, Häbich D. Antibacterial natural products in medicinal chemistry--exodus or revival? Angew Chem Int Ed Engl 2007; 45:5072-129. [PMID: 16881035 DOI: 10.1002/anie.200600350] [Citation(s) in RCA: 467] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.
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Affiliation(s)
- Franz von Nussbaum
- Bayer HealthCare AG, Medicinal Chemistry Europe, 42096 Wuppertal, Germany.
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209
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Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, Bicknell D, Bodmer WF, Davis RW, Ji H. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci U S A 2007; 104:9387-92. [PMID: 17517648 PMCID: PMC1871563 DOI: 10.1073/pnas.0702165104] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing.
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Affiliation(s)
- Fredrik Dahl
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
- To whom correspondence may be addressed. E-mail: , , or
| | - Johan Stenberg
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Clark Center W300, 318 Campus Drive, Stanford, CA 94305-5440
| | - Simon Fredriksson
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Katrina Welch
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Michael Zhang
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Mats Nilsson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden; and
| | - David Bicknell
- Cancer Research UK Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Walter F. Bodmer
- Cancer Research UK Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Ronald W. Davis
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
- To whom correspondence may be addressed. E-mail: , , or
| | - Hanlee Ji
- *Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Clark Center W300, 318 Campus Drive, Stanford, CA 94305-5440
- To whom correspondence may be addressed. E-mail: , , or
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210
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Tsai KY, Tsao H. Primer on the human genome. J Am Acad Dermatol 2007; 56:719-35. [PMID: 17437886 DOI: 10.1016/j.jaad.2006.10.985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 08/21/2006] [Accepted: 10/31/2006] [Indexed: 11/20/2022]
Abstract
UNLABELLED The study of the expression patterns of many genes, or even the entire genome, is now routinely possible. Such powerful tools have enabled hypothesis-generating research at a scale never before possible. Moreover, spatially or temporally linked gene and protein expression, implying co-regulation and functional relatedness, has led to the identification of particular clusters of genes important for fundamental biologic processes, such as development and cancer. Not only is this expected to yield further mechanistic insights into disease processes, but perhaps most exciting, it will likely establish the foundation of predictive medicine, in which understanding of individual genomic signatures leads to the use of appropriately targeted therapy. LEARNING OBJECTIVE At the conclusion of this learning activity, participants should be able to understand the fundamental tenets of molecular biology as they relate to the field of genomics.
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211
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Eszlinger M, Krohn K, Kukulska A, Jarzab B, Paschke R. Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors. Endocr Rev 2007; 28:322-38. [PMID: 17353294 DOI: 10.1210/er.2006-0047] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microarray technology has become a powerful tool to analyze the gene expression of tens of thousands of genes simultaneously. Microarray-based gene expression profiles are available for malignant thyroid tumors (i.e., follicular thyroid carcinoma, and papillary thyroid carcinoma), and for benign thyroid tumors (such as autonomously functioning thyroid nodules and cold thyroid nodules). In general, the two main foci of microarray investigations are improved understanding of the pathophysiology/molecular etiology of thyroid neoplasia and the detection of genetic markers that could improve the differential diagnosis of thyroid tumors. Their results revealed new features, not known from one-gene studies. Simultaneously, the increasing number of microarray analyses of different thyroid pathologies raises the demand to efficiently compare the data. However, the use of different microarray platforms complicates cross-analysis. In addition, there are other important differences between these studies: 1) some studies use intraindividual comparisons, whereas other studies perform interindividual comparisons; 2) the reference tissue is defined as strictly nonnodular healthy tissue or also contains benign lesions such as goiter, follicular adenoma, and hyperplastic nodules in some studies; and 3) the widely used Affymetrix GeneChip platform comprises several GeneChip generations that are only partially compatible. Moreover, the different studies are characterized by strong differences in data analysis methods, which vary from simple empiric filters to sophisticated statistic algorithms. Therefore, this review summarizes and compares the different published reports in the context of their study design. It also illustrates perspectives and solutions for data set integration and meta-analysis, as well as the possibilities to combine array analysis with other genetic approaches.
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Affiliation(s)
- Markus Eszlinger
- III. Medical Department, University of Leipzig, Ph.-Rosenthal-Str. 27, D-04103 Leipzig, Germany
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212
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Jackson SA, Mammel MK, Patel IR, Mays T, Albert TJ, LeClerc JE, Cebula TA. Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays. Forensic Sci Int 2007; 168:183-99. [PMID: 16934953 DOI: 10.1016/j.forsciint.2006.06.079] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 10/24/2022]
Abstract
Here, we describe a novel microarray-based approach for investigating the genomic diversity of Escherichia coli O157:H7 in a semi-high throughput manner using a high density, oligonucleotide-based microarray. This microarray, designed to detect polymorphisms at each of 60,000 base-pair (bp) positions within an E. coli genome, is composed of overlapping 29-mer oligonucleotides specific for 60 equally spaced, 1000-bp loci of the E. coli O157:H7 strain EDL933 chromosome. By use of a novel 12-well microarray that permitted the simultaneous investigation of 12 strains, the genomes of 44 individual isolates of E. coli O157:H7 were interrogated. These analyses revealed more than 150 single nucleotide polymorphisms (SNPs) and several deletions and amplifications in the test strains. Pyrosequencing was used to confirm the usefulness of the novel SNPs by determining their allelic frequency among a collection of diverse isolates of E. coli O157:H7. The tiling DNA microarray system would be useful for the tracking and identification of individual strains of E. coli O157:H7 needed for forensic investigations.
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Affiliation(s)
- Scott A Jackson
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
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213
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Abstract
The establishment of an aptamer-based biochip for protein detection is described. Using a model system comprising human IgE as the analyte and single-stranded DNA aptamers specific for IgE or anti-IgE antibodies as immobilized ligands on chips, we could demonstrate that aptamers were equivalent or superior to antibodies in terms of specificity and sensitivity, respectively. Aptamer-based analyte detection on glass slides could clearly be demonstrated at minimum concentrations of 10 ng/mL IgE. In addition, we successfully showed specific analyte recognition in complex protein samples by the aptamer-based biochip system. Using DNA aptamers specific for human thrombin as an additional model receptor/ligand system, dual protein detection on a single slide could be proven. In conclusion, we could show the suitability of nucleic acid aptamers as low molecular weight receptors on biochips for sensitive and specific protein detection, representing an innovative tool for future proteomics.
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Affiliation(s)
- Karin Stadtherr
- Institut für Medizinische Mikrobiologie und Hygiene, Universität Regensburg, Regensburg, Germany
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214
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DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. MICROBIAL ECOLOGY 2007; 53:371-83. [PMID: 17334858 DOI: 10.1007/s00248-006-9134-9] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 06/20/2006] [Indexed: 05/14/2023]
Abstract
Molecular approaches aimed at detection of a broad-range of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 high-quality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it reveals greater diversity in environmental samples than sequencing a typically sized clone library. Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology.
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Affiliation(s)
- Todd Z DeSantis
- Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA
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215
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Del Giallo ML, Lucarelli F, Cosulich E, Pistarino E, Santamaria B, Marrazza G, Mascini M. Steric factors controlling the surface hybridization of PCR amplified sequences. Anal Chem 2007; 77:6324-30. [PMID: 16194095 DOI: 10.1021/ac0506175] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study elucidated the hybridization behavior of surface-bound oligonucleotides to their longer PCR-amplified targets. The screen-printed gold surface of disposable electrodes was the platform onto which thiol-tethered oligonucleotides (21-mer) were immobilized by chemisorption. As a model case, approximately 600-bp amplicons were studied. Surface hybridization was monitored by means of an enzyme-linked assay with electrochemical detection. Use of different surface-tethered probe sequences over a wide range of surface densities was explored to achieve the highest duplex yield. Both the surface coverage by the probe and its relative position on the target strand were found to control the efficiency of capture of the target sequence. Interfacial hybridization occurred with the highest efficiency for a probe coverage of approximately 2.9 x 10(12) molecules/cm2 and when the 3' end of the amplicon was involved. An unusual (bell-shaped) response/amplicon concentration profile was additionally found. It was hypothesised that when the amount of solution-phase target is relatively high, random collisions make reannealing of the approximately 600-bp strands favored over formation of the surface-tethered probe-amplicon complex. This paper also describes a strategy to enhance the sensitivity of enzyme-linked hybridization assays. Such a strategy relies on formation, around the long target sequence, of dendritic-like structures, which could offer multiple anchoring points for the enzyme conjugate. The results shown in this work might have great significance for the practical application of hybridization to oligonucleotide chips.
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Affiliation(s)
- Maria Lisa Del Giallo
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto F.no, Florence, Italy
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216
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Royce TE, Rozowsky JS, Gerstein MB. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 2007; 23:988-97. [PMID: 17387113 DOI: 10.1093/bioinformatics/btm052] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
MOTIVATION Increases in microarray feature density allow the construction of so-called tiling microarrays. These arrays, or sets of arrays, contain probes targeting regions of sequenced genomes at regular genomic intervals. The unbiased nature of this approach allows for the identification of novel transcribed sequences, the localization of transcription factor binding sites (ChIP-chip), and high resolution comparative genomic hybridization, among other uses. These applications are quickly growing in popularity as tiling microarrays become more affordable. To reach maximum utility, the tiling microarray platform needs be developed to the point that 1 nt resolutions are achieved and that we have confidence in individual measurements taken at this fine of resolution. Any biases in tiling array signals must be systematically removed to achieve this goal. RESULTS Towards this end, we investigated the importance of probe sequence composition on the efficacy of tiling microarrays for identifying novel transcription and transcription factor binding sites. We found that intensities are highly sequence dependent and can greatly influence results. We developed three metrics for assessing this sequence dependence and use them in evaluating existing sequence-based normalizations from the tiling microarray literature. In addition, we applied three new techniques for addressing this problem; one method, adapted from similar work on GeneChip brand microarrays, is based on modeling array signal as a linear function of probe sequence, the second method extends this approach by iterative weighting and re-fitting of the model, and the third technique extrapolates the popular quantile normalization algorithm for between-array normalization to probe sequence space. These three methods perform favorably to existing strategies, based on the metrics defined here. AVAILABILITY http://tiling.gersteinlab.org/sequence_effects/
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Affiliation(s)
- Thomas E Royce
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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217
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Athanassiadou P, Grapsa D. Recent advances in the detection of bone marrow micrometastases: A promising area for research or just another false hope? A review of the literature. Cancer Metastasis Rev 2007; 25:507-19. [PMID: 17160555 DOI: 10.1007/s10555-006-9030-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The presence of early disseminated tumor cells (DTC), otherwise termed micrometastases or minimal residual disease, in the bone marrow (BM), or other secondary compartments, such as the blood and the lymph nodes, is the main reason for recurrence of patients with early stage epithelial cancers after "curative" resection of the primary tumor. There is increasing evidence, that the detection of DTC in BM aspirates may provide additional and independent prognostic information and aid in the stratification of these patients for adjuvant clinical treatment. However, the clinical relevance of micrometastases has not yet been firmly established. In addition, the molecular events and interactions that prevail in early metastatic disease and determine the formation or not of overt metastases remain poorly understood. The methods currently used for the detection of micrometastatic cells include extremely sensitive immunocytochemical and molecular assays, often in conjunction with enrichment techniques for the purification of tumor cells and additional increase of their sensitivity. Nevertheless, the specificity of these methods is mostly inadequate. After the impressive advances of molecular cytogenetics, a highly accurate and global assessment of the genetic status of tumors is now possible. Therefore, the greatest challenge of our time is the application of these novel technologies for the clarification of the key molecular events that initiate metastatic spread. This will further enable us to identify the highly specific and sensitive diagnostic and prognostic markers as well as the therapeutic targets which are so urgently needed.
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Affiliation(s)
- Pauline Athanassiadou
- Pathology Laboratory-Cytology Department, Medical School, Athens University, 75 Mikras Asias Str., 11527, Athens, Greece
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218
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Fredriksson S, Banér J, Dahl F, Chu A, Ji H, Welch K, Davis RW. Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res 2007; 35:e47. [PMID: 17317684 PMCID: PMC1874629 DOI: 10.1093/nar/gkm078] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one assay with uniform abundance of the final products. Amplification is initiated by a multiplex PCR in this case with 170 primer pairs. Each PCR product is then specifically circularized by ligation on a Collector probe capable of juxtapositioning only the perfectly matched cognate primer pairs. Any amplification artifacts typically associated with multiplex PCR derived from the use of many primer pairs such as false amplicons, primer-dimers etc. are not circularized and degraded by exonuclease treatment. Circular DNA molecules are then further enriched by randomly primed rolling circle replication. Amplification was successful for 90% of the targeted amplicons as seen by hybridization to a custom resequencing DNA micro-array. Real-time quantitative PCR revealed that 96% of the amplification products were all within 4-fold of the average abundance. Gene-Collector has utility for numerous applications such as high throughput resequencing, SNP analyses, and pathogen detection.
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Affiliation(s)
- Simon Fredriksson
- Stanford Genome Technology Center, Bio-X, Stanford, California 94305, USA.
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219
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Grubbs EG, Abdel-Wahab Z, Tyler DS, Pruitt SK. Utilizing quantitative polymerase chain reaction to evaluate prostate stem cell antigen as a tumor marker in pancreatic cancer. Ann Surg Oncol 2007; 13:1645-54. [PMID: 16957968 DOI: 10.1245/s10434-006-9029-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Real-time quantitative polymerase chain reaction (qPCR) may prove to be a sensitive technique by which to evaluate potential tumor markers in pancreatic cancer. METHODS The prostate stem cell antigen (PSCA) gene was identified as a marker highly expressed in pancreatic adenocarcinoma and not normal pancreas. RNA from pancreatic and nonpancreatic cancer cell lines as well as tissue and blood from pancreatic cancer and control patients was reverse-transcribed and PSCA quantified by qPCR. RESULTS Individual operator experience affects the results of qPCR, with significantly different copy numbers at experiment numbers 5, 15, and 40. Five of six pancreatic cell lines had PSCA/actin ratios 10-fold greater than nonpancreatic cancer lines. Mean PSCA expression in pancreatic tumor tissue was significantly higher (P < 0.05, Student's t-test) than in the tissue of benign pancreatic processes. The close correlation of PSCA/actin copy number with number of tumor cells in the blood was demonstrated by regression analysis (r = 0.768, P = 0.0001). PSCA copy number was significantly higher in the blood of patients with metastatic pancreatic cancer than in that of normal patients (P < 0.05, Student's t-test). CONCLUSIONS Such trends suggest that PSCA may prove to be a valuable pancreatic cancer tumor marker. More generally, the technique of qPCR is shown to provide a sensitive method of evaluating markers in cancer patients.
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Affiliation(s)
- Elizabeth G Grubbs
- Department of General Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
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220
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Abstract
This article is a tribute to Dr. Arthur Pardee, one of the most innovative and brilliant scientists of our time, on the occasion of his 85th birthday. In this partially perspective and partially review piece, I look back how fate, by twist and turn, has led me eventually to his lab at Harvard where we worked out the Differential Display technology from scratch, how the method has revolutionized the field of gene expression analysis and where DD is taking us in the "era" of DNA microarrays.
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Affiliation(s)
- Peng Liang
- Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.
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221
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Mao Y, Liu D, Wang S, Luo S, Wang W, Yang Y, Ouyang Q, Jiang L. Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH. Nucleic Acids Res 2007; 35:e33. [PMID: 17264114 PMCID: PMC1865044 DOI: 10.1093/nar/gkl1161] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2006] [Revised: 12/17/2006] [Accepted: 12/19/2006] [Indexed: 11/18/2022] Open
Abstract
Macroscopically realizable applications of DNA-based molecular devices require individual molecules to cooperate with each other. However, molecular crowding usually introduces disorder to the system, thus jeopardizing the molecular cooperation and slowing down their functional performance dramatically. A challenge remaining in this field is to obtain both smarter response and better cooperation simultaneously. Here, we report a swift-switching DNA nanodevice that is enhanced by an alternating electric field. The device, self-assembled from folded four-stranded DNA motifs, can robustly switch between closed and open states in smart response to pH stimulus, of which the closed state forms a nanometer-height container that is impermeable to small molecules. This character was used to directly and non-specifically catch and release small molecules emulating mechanical hand in a controllable way. The alternating electric field was used to accelerate molecular cooperative motion during the device switching, which in turn shortened the closing time remarkably to thirty seconds.
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Affiliation(s)
- Youdong Mao
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Dongsheng Liu
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Shutao Wang
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Songnian Luo
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Wenxing Wang
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Yanlian Yang
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Qi Ouyang
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
| | - Lei Jiang
- National Centre for NanoScience and Technology, Beijing 100080, China, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and Department of Physics, Peking University, Beijing 100871, China
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222
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Bracco L, Throo E, Cochet O, Einstein R, Maurier F. Methods and platforms for the quantification of splice variants' expression. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2007; 44:1-25. [PMID: 17076262 DOI: 10.1007/978-3-540-34449-0_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The relatively limited number of human protein encoding genes highlights the importance of the diversity generated at the level of the mRNA transcripts. As alternative RNA splicing plays a key role in mediating this diversity, it becomes critical to develop the tools and platforms that will deliver quantitative information on the specific expression levels associated with splice isoforms. This chapter describes the constraints generated by this global transcriptome analysis and the state-of-the-art techniques and products available to the scientific community.
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Affiliation(s)
- Laurent Bracco
- ExonHit Therapeutics, 65 Boulevard Masséna, F-75013 Paris
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223
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Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques 2007; 41:673, 675, 677 passim. [PMID: 17191608 DOI: 10.2144/000112322] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
With the number of organisms whose genomes have been sequenced, a vast amount of information concerning the genetic structure of an organism's genome has been collected. However, effective experiment means to study how this information is accessed have only recently been developed. In this review, three basic methods for identifying regions of protein-DNA interaction will be introduced. The first two, chromatin immunoprecipitation (ChIP)-chip and ChIP-PET (for paired-end ditag), rely on the enrichment provided by chromosomal immunoprecipitation to interrogate the genomic sequence for the interaction sites of a protein of interest. In contrast, protein microarrays allow the identification of DNA binding protein that interacts with a DNA sequence of interest. These complementary methods of exploring protein-DNA interactions will increase our fundamental knowledge of how the information contained within the genome sequence is accessed and processed.
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224
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Coyle DE. Spinal cord transcriptional profile analysis reveals protein trafficking and RNA processing as prominent processes regulated by tactile allodynia. Neuroscience 2007; 144:144-56. [PMID: 17069981 DOI: 10.1016/j.neuroscience.2006.08.081] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/14/2006] [Accepted: 08/30/2006] [Indexed: 11/29/2022]
Abstract
Since partial peripheral injury does not necessarily lead to the development of neuropathic pain it is possible that a set of genes is directly regulated by the development of neuropathic pain independent of the genes regulated by nerve injury. This study identifies the genes expressed within the spinal cord that are uniquely regulated by tactile allodynia in rats. Using subtractive methods, genes regulated by allodynia were differentiated from those of nerve injury. Gene ontology analysis identified that allodynic genes are involved in a variety of processes including myelination, actin cytoskeleton reorganization, dephosphorylation, phosphorylation, response to stress, as well as protein trafficking and RNA processing. The processes of protein trafficking and RNA processing were found to be as statistically significant as other processes that have been associated with neuropathic pain development such as response to stress, phosphorylation, and cell migration. Trafficking and transcription are linked and undergo activity dependent regulation which results in both rapid and gradual synaptic changes (plasticity). The data presented here greatly expand the list of genes regulated by the development of tactile allodynia and reveal protein trafficking and RNA processing as prominent biological processes that may be involved in synaptic plasticity changes within the spinal cord in response to allodynia.
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Affiliation(s)
- D E Coyle
- Department of Anesthesiology, University of Cincinnati, 231 Albert Sabin Way, PO Box 670531, Cincinnati, OH 45267-0531, USA.
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225
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Claus H, Vogel U, Swiderek H, Frosch M, Schoen C. Microarray analyses of meningococcal genome composition and gene regulation: a review of the recent literature: Table 1. FEMS Microbiol Rev 2007; 31:43-51. [PMID: 17096662 DOI: 10.1111/j.1574-6976.2006.00047.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The development of microarrays for genome comparison and transcriptional profiling along with the public availability of several meningococcal genome sequences has promoted studies elucidating (i) intraspecific and interspecific genomic differences of members of the genus Neisseria, and (ii) the transcriptional response of meningococci to a variety of environmental stresses such as heat shock, iron starvation, serum treatment, and contact with eukaryotic cells. Furthermore, microarray-based finetyping of meningococci is in development. It will remain a difficult, but important, goal to identify sets of genes determining the virulence potential of hypervirulent meningococcal lineages in comparison with apathogenic ones. The recent identification of the meningococcal disease-associated island through the application of microarray analyses has been a step towards this aim. Transcriptional profiling of meningococci has brought about the compilation of large datasets, which also provide information about several regulons. Meningococcal microarray analysis has established a basis for studies clarifying the function of previously unknown genes, and has supported the identification of interesting vaccine candidates. However, harmonization of protocols and tools, as well as central databases are needed to foster the comparability of studies and the integration of knowledge.
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Affiliation(s)
- Heike Claus
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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226
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Abstract
Microarrays and related technologies have allowed investigators to ask biological questions in far greater detail than has previously been possible. Microarrays had a troubled beginning, but most of these problems resulted from the growing pains of this technology, which, like many new things, was initially more promise than delivery. Nevertheless, over the past few years, investigators have learned how to achieve optimal performance of technology, and now exciting discoveries are made using microarray-based research. Many of the advances have come from the realization that microarrays are not a magic tool but rather are like any other measurement device. Unless microarray experimentation is coupled with good experimental practices, it will not yield valid results or, worse yet, may lead to misleading results. In this chapter, we highlight some of the important steps that should be taken to successfully conduct a microarray study. These steps include a clearly stated biological question, experimental design, careful experimental conduct, complete statistical analysis, validation/verification of results, and dissemination of the data.
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Affiliation(s)
- Grier P Page
- Department of Biostatistics, University of Alabama at Birmingham, Hoover, AL, USA
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227
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228
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Zhang H, Zhang H, Li Z, Zheng G. Statistical methods for haplotype-based matched case-control association studies. Genet Epidemiol 2007; 31:316-26. [PMID: 17285622 DOI: 10.1002/gepi.20212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Kraft et al. [2005] proposed a method for matched haplotype-based association studies and compared the performances of six analytic strategies for estimating the odds ratio parameters using a conditional likelihood function. Zhang et al. [2006] modified the conditional likelihood and proposed a new method for matched haplotype-based association studies. The main assumptions of Zhang et al. were that the disease was rare, the population was in Hardy-Weinberg equilibrium (HWE), and the haplotypes were independent of the covariates and matching variable(s). In this article, we modify the estimation procedure proposed by Zhang et al. and introduce a fixation index so that the assumption of HWE is relaxed. Using the Wald test, we compare the current modified method with the procedure developed by Kraft et al. through simulations. The results show that the modified method is uniformly more powerful than that described in Kraft et al. Furthermore, the results indicate that the modified method is quite robust to the rare disease assumption.
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Affiliation(s)
- Han Zhang
- Department of Statistics and Finance, University of Science and Technology of China, PR China
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229
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Affiliation(s)
- Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.
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230
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Sulaiman IM, Tang K, Osborne J, Sammons S, Wohlhueter RM. GeneChip resequencing of the smallpox virus genome can identify novel strains: a biodefense application. J Clin Microbiol 2006; 45:358-63. [PMID: 17182757 PMCID: PMC1829075 DOI: 10.1128/jcm.01848-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We developed a set of seven resequencing GeneChips, based on the complete genome sequences of 24 strains of smallpox virus (variola virus), for rapid characterization of this human-pathogenic virus. Each GeneChip was designed to analyze a divergent segment of approximately 30,000 bases of the smallpox virus genome. This study includes the hybridization results of 14 smallpox virus strains. Of the 14 smallpox virus strains hybridized, only 7 had sequence information included in the design of the smallpox virus resequencing GeneChips; similar information for the remaining strains was not tiled as a reference in these GeneChips. By use of variola virus-specific primers and long-range PCR, 22 overlapping amplicons were amplified to cover nearly the complete genome and hybridized with the smallpox virus resequencing GeneChip set. These GeneChips were successful in generating nucleotide sequences for all 14 of the smallpox virus strains hybridized. Analysis of the data indicated that the GeneChip resequencing by hybridization was fast and reproducible and that the smallpox virus resequencing GeneChips could differentiate the 14 smallpox virus strains characterized. This study also suggests that high-density resequencing GeneChips have potential biodefense applications and may be used as an alternate tool for rapid identification of smallpox virus in the future.
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Affiliation(s)
- Irshad M Sulaiman
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Atlanta, GA 30333, USA.
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231
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Abstract
Over 120 inherited primary immunodeficiency diseases (PIDs) are known to exist. The genes responsible for many of these diseases have also been identified. Recent advances in diagnostic procedures have enabled these to be identified earlier and appropriately treated. While a number of approaches are available to identify mutations, direct sequencing remains the gold standard. This approach identifies the exact genetic change with substantial precision. We suggest that a sensitive and economical approach to mutation detection could be the direct sequencing of cDNA followed by the confirmatory sequencing of the corresponding exon. While screening techniques such as single-stranded conformation polymorphism (SSCP), heteroduplex analysis (HA), denaturing gradient gel electrophoresis (DGGE), and denaturing high-performance liquid chromatography (dHPLC) have proven useful, each has inherent advantages and disadvantages. We discuss these advantages and disadvantages and also discuss the potential of future sequencing technologies such as pyrosequencing, combinatorial sequencing-by-hybridization, multiplex polymerase colony (polony), and resequencing arrays as tools for future mutation detection. In addition we briefly discuss several high-throughput SNP detection technologies.
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Affiliation(s)
- Maurizio Costabile
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.
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232
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Garaizar J, Brena S, Bikandi J, Rementeria A, Pontón J. Use of DNA microarray technology and gene expression profiles to investigate the pathogenesis, cell biology, antifungal susceptibility and diagnosis of Candida albicans. FEMS Yeast Res 2006; 6:987-98. [PMID: 17042748 DOI: 10.1111/j.1567-1364.2006.00108.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The use of DNA microarrays is becoming the method of choice for assaying gene expression, particularly as costs and complexity are being reduced as the technology becomes more widespread and better standardized. A DNA array is nothing but a collection of probes fixed on a solid support. The probes can be PCR products of ORFs or short intragenic oligonucleotides deposited or synthesized in situ by photolithographic methods. To date, sequencing projects for fungal genomes have yielded 10 complete genomes and 21 whole shotgun sequences, including Candida albicans strain SC5314. Sequencing of the C. albicans genome has led to the construction of whole-genome DNA microarrays for in vitro transcription profiling by several universities and companies. The use of microarray or DNA chip techniques for Candida research has started recently but the number of studies using this technology is increasing rapidly, in order to address important remaining questions about pathogenesis, cell biology, antifungal susceptibility, and diagnosis.
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Affiliation(s)
- Javier Garaizar
- Department of Immunology, Microbiology, and Parasitology, Faculty of Pharmacy, Vitoria-Gasteiz, Spain.
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233
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Shiu SH, Borevitz JO. The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity (Edinb) 2006; 100:141-9. [PMID: 17091126 DOI: 10.1038/sj.hdy.6800916] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microarray technology is one of the key developments in recent years that has propelled biological research into the post-genomic era. With the ability to assay thousands to millions of features at the same time, microarray technology has fundamentally changed how biological questions are addressed, from examining one or a few genes to a collection of genes or the whole genome. This technology has much to offer in the study of genome evolution. After a brief introduction on the technology itself, we then focus on the use of microarrays to examine genome dynamics, to uncover novel functional elements in genomes, to unravel the evolution of regulatory networks, to identify genes important for behavioral and phenotypic plasticity, and to determine microbial community diversity in environmental samples. Although there are still practical issues in using microarrays, they will be alleviated by rapid advances in array technology and analysis methods, the availability of many genome sequences of closely related species and flexibility in array design. It is anticipated that the application of microarray technology will continue to better our understanding of evolution and ecology through the examination of individuals, populations, closely related species or whole microbial communities.
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Affiliation(s)
- S-H Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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234
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Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 2006; 72:6288-98. [PMID: 16957256 PMCID: PMC1563607 DOI: 10.1128/aem.00246-06] [Citation(s) in RCA: 374] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.
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Affiliation(s)
- Eoin L Brodie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
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235
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Shackel NA, Seth D, Haber PS, Gorrell MD, McCaughan GW. The hepatic transcriptome in human liver disease. COMPARATIVE HEPATOLOGY 2006; 5:6. [PMID: 17090326 PMCID: PMC1665460 DOI: 10.1186/1476-5926-5-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 11/07/2006] [Indexed: 02/07/2023]
Abstract
The transcriptome is the mRNA transcript pool in a cell, organ or tissue with the liver transcriptome being amongst the most complex of any organ. Functional genomics methodologies are now being widely utilized to study transcriptomes including the hepatic transcriptome. This review outlines commonly used methods of transcriptome analysis, especially gene array analysis, focusing on publications utilizing these methods to understand human liver disease. Additionally, we have outlined the relationship between transcript and protein expressions as well as summarizing what is known about the variability of the transcriptome in non-diseased liver tissue. The approaches covered include gene array analysis, serial analysis of gene expression, subtractive hybridization and differential display. The discussion focuses on primate whole organ studies and in-vitro cell culture systems utilized. It is now clear that there are a vast number research opportunities for transcriptome analysis of human liver disease as we attempt to better understand both non-diseased and disease hepatic mRNA expression. We conclude that hepatic transcriptome analysis has already made significant contributions to the understanding of human liver pathobiology.
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Affiliation(s)
- Nicholas A Shackel
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Devanshi Seth
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Paul S Haber
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Mark D Gorrell
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Geoffrey W McCaughan
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
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236
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Kopitar-Jerala N. The role of cystatins in cells of the immune system. FEBS Lett 2006; 580:6295-301. [PMID: 17098233 DOI: 10.1016/j.febslet.2006.10.055] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/22/2006] [Accepted: 10/24/2006] [Indexed: 11/25/2022]
Abstract
The cystatins constitute a large group of evolutionary related proteins with diverse biological activities. Initially, they were characterized as inhibitors of lysosomal cysteine proteases - cathepsins. Cathepsins are involved in processing and presentation of antigens, as well as several pathological conditions such as inflammation and cancer. Recently, alternative functions of cystatins have been proposed: they also induce tumour necrosis factor and interleukin 10 synthesis and stimulate nitric oxide production. The aim of the present review was the analysis of data on cystatins from NCBI GEO database and the literature, and obtained in microarray and serial analysis of gene expression (SAGE) experiments. The expression of cystatins A, B, C, and F in macrophages, dendritic cells and natural killer cells of the immune system, during differentiation and activation is discussed.
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Affiliation(s)
- Natasa Kopitar-Jerala
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
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237
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Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1409-20. [PMID: 17033786 DOI: 10.1007/s00122-006-0365-4] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 07/06/2006] [Indexed: 05/02/2023]
Abstract
Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.
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Affiliation(s)
- Mona Akbari
- Triticarte P/L, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT, 2600, Australia
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238
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Kumar Khanna V. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering. Biotechnol Adv 2006; 25:85-98. [PMID: 17157471 DOI: 10.1016/j.biotechadv.2006.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 07/31/2006] [Accepted: 10/21/2006] [Indexed: 11/24/2022]
Abstract
The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.
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Affiliation(s)
- Vinod Kumar Khanna
- MEMS and Microsensors, Solid-State Devices Division, Central Electronics Engineering Research Institute, Pilani-333031 (Rajasthan), India.
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239
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Abstract
DNA sequencing can be used to gain important information on genes, genetic variation and gene function for biological and medical studies. The growing collection of publicly available reference genome sequences will underpin a new era of whole genome re-sequencing, but sequencing costs need to fall and throughput needs to rise by several orders of magnitude. Novel technologies are being developed to meet this need by generating massive amounts of sequence that can be aligned to the reference sequence. The challenge is to maintain the high standards of accuracy and completeness that are hallmarks of the previous genome projects. One or more new sequencing technologies are expected to become the mainstay of future research, and to make DNA sequencing centre stage as a routine tool in genetic research in the coming years.
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240
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Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006. [PMID: 17033786 DOI: 10.1007/s00122‐006‐0365‐4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.
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241
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Coppola G, Geschwind DH. Technology Insight: querying the genome with microarrays--progress and hope for neurological disease. ACTA ACUST UNITED AC 2006; 2:147-58. [PMID: 16932541 DOI: 10.1038/ncpneuro0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 01/09/2006] [Indexed: 01/23/2023]
Abstract
The ability to perform large-scale analysis of the genome at the level of gene sequence, gene copy number and messenger RNA transcript expression characterizes the post-genomic era. In the past decade, the microarray-based approach has emerged as one of the major tools in this area of genome biology, contributing to advances in the understanding of Mendelian and complex neurological disorders. Despite technical issues regarding design, data analysis and validation that have to be addressed in the planning and interpretation of a microarray study, microarray-based approaches for studying transcript expression, single-nucleotide-polymorphism genotyping and gene resequencing are becoming more widely adopted. Genomic microarrays are providing an unprecedented opportunity to dissect the genetic risk for complex neurological disorders. Numerous clinical and preclinical applications are likely to dominate the ambitious microarray agenda within the next decade.
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Affiliation(s)
- Giovanni Coppola
- Neurogenetics Program, Center for Autism Research, University of California Los Angeles, CA 90095, USA
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242
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Horne MT, Fish DJ, Benight AS. Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions. Biophys J 2006; 91:4133-53. [PMID: 16963510 PMCID: PMC1635677 DOI: 10.1529/biophysj.106.090662] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization reactions are considered to occur in isolation; and multiplex hybridization, where desired and competitive cross-hybrid reactions between all possible pairs of strands are considered. In addition, sensitivities of the hybridization process of the perfect match duplex, to temperature, target concentration, and existence of sequence homology with other strands, are examined. This general approach also considers explicit sequence-dependent interactions between targets and probes involved in the reactions. Sequence-dependent stabilities of all perfect match and mismatch duplex complexes are explicitly considered and effects of relative stability of cross-hybrid complexes are also explored. Results reveal several interdependent factors that strongly influence DNA multiplex hybridization behavior. These include: relative concentrations of all probes and targets; relative thermodynamic stability of all perfect match and mismatch complexes; sensitivity to temperature, particularly for mismatches; and amount of sequence homology shared by the probe and target strands in the multiplex mix.
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Affiliation(s)
- M T Horne
- Department of Chemistry, Portland State University, Portland, OR, USA
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243
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Abstract
Recent developments in highly parallel genome-wide assays are transforming the study of human health and disease. High-resolution whole-genome association studies of complex diseases are finally being undertaken after much hypothesizing about their merit for finding disease loci. The availability of inexpensive high-density SNP-genotyping arrays has made this feasible. Cancer biology will also be transformed by high-resolution genomic and epigenomic analysis. In the future, most cancers might be staged by high-resolution molecular profiling rather than by gross cytological analysis. Here, we describe the key developments that enable highly parallel genomic assays.
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Affiliation(s)
- Jian-Bing Fan
- Illumina Inc., 9885 Towne Centre Drive, San Diego, California 92121, USA
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244
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Chin D, Boyle GM, Theile DR, Parsons PG, Coman WB. The human genome and gene expression profiling. J Plast Reconstr Aesthet Surg 2006; 59:902-11. [PMID: 16920579 DOI: 10.1016/j.bjps.2006.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 09/09/2005] [Accepted: 01/13/2006] [Indexed: 11/16/2022]
Abstract
The mapping and sequencing of the human genome has generated a large resource for answering questions about human disease. This achievement is akin in scientific importance to developing the periodic table of elements. Plastic surgery has always been at the frontier medical research. This resource will help us to improve our understanding on the many unknown physiological and pathogical conditions we deal with daily, such as wound healing keloid scar formation, Dupuytren's disease, rheumatoid arthritis, vascular malformation and carcinogenesis. We are primed in obtaining both disease and normal tissues to use this resource and applying it to clinical use. This review is about the human genome, the basis of gene expression profiling and how it will affect our clinical and research practices in the future and for those embarking on the use of this new technology as a research tool, we provide a brief insight on its limitations and pitfalls.
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Affiliation(s)
- David Chin
- Melanoma Genomics Group, The Queensland Institute of Medical Research, Herston, Brisbane 4029, Queensland, Australia.
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245
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Feng CL, Embrechts A, Vancso GJ, Schönherr H. Reactive μCP on ultrathin block copolymer films: Localized chemistry for micro- and nano-scale biomolecular patterning. Eur Polym J 2006. [DOI: 10.1016/j.eurpolymj.2006.06.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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246
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Mahajan S, Kumar P, Gupta KC. An efficient and versatile approach for the construction of oligonucleotide microarrays. Bioorg Med Chem Lett 2006; 16:5654-8. [PMID: 16934460 DOI: 10.1016/j.bmcl.2006.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 07/18/2006] [Accepted: 08/02/2006] [Indexed: 11/17/2022]
Abstract
A new immobilization chemistry for covalent attachment of phosphorylated oligonucleotides on epoxy-activated glass surface via opening of oxirane ring is described. The proposed strategy results in excellent immobilization efficiency, spot homogeneity, and morphology. The constructed microarray was successfully demonstrated for discrimination of nucleotide mismatches.
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Affiliation(s)
- S Mahajan
- Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi-110,007, India
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247
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Geiger A, Lester A, Kleiber J, Ørum H. Pna Array Technology in Molecular Diagnostics. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Albert Geiger
- a PNA Diagnostics A/S , Ronnegade 2, DK-21OO , Copenhagen Ø , Denmark
| | - Ane Lester
- a PNA Diagnostics A/S , Ronnegade 2, DK-21OO , Copenhagen Ø , Denmark
| | - Jörg Kleiber
- b Boehringer Mannheim GmbH, Molecular Diagnostics , D-82377 , Penzberg , Germany
| | - Henrik Ørum
- a PNA Diagnostics A/S , Ronnegade 2, DK-21OO , Copenhagen Ø , Denmark
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248
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Cantor CR, Tang K, Graber JH, Maloney M, Fu DJ, Broude NE, Siddiqi F, Koester H, Smith CL. Dna Sequencing After the Human Genome Project. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Charles R. Cantor
- a Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Boston University , Boston , MA , 02215 , USA
| | - Kai Tang
- b Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Sequenom, Inc , San Diego
| | - Joel H. Graber
- a Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Boston University , Boston , MA , 02215 , USA
| | - Maryanne Maloney
- b Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Sequenom, Inc , San Diego
| | - Dong Jing Fu
- b Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Sequenom, Inc , San Diego
| | - Natalia E. Broude
- a Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Boston University , Boston , MA , 02215 , USA
| | - Fouad Siddiqi
- a Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Boston University , Boston , MA , 02215 , USA
| | | | - Cassandra L. Smith
- a Center for Advanced Biotechnology and Departments of Biomedical Engineering, Biology, and Pharmacology and Experimental Therapeutics , Boston University , Boston , MA , 02215 , USA
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249
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von Nussbaum F, Brands M, Hinzen B, Weigand S, Häbich D. Antibakterielle Naturstoffe in der medizinischen Chemie – Exodus oder Renaissance? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600350] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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250
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Tengs T, Lee JC, Paez JG, Zhao X, LaFramboise T, Giannoukos G, Thomas RK. A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing. Cancer Lett 2006; 239:227-33. [PMID: 16171945 DOI: 10.1016/j.canlet.2005.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2005] [Revised: 07/26/2005] [Accepted: 08/03/2005] [Indexed: 10/25/2022]
Abstract
We have designed resequencing microarrays to test the performance of this platform when interrogating a large number of exons (164 total) from genes associated with cancer. To evaluate false positive and negative rates, dideoxy sequencing was done for 335,420 bases interrogated by the arrays. From the array data, calls could be made for approximately 97.5% of the bases, and false positive rates were very low with only a single mutation reported from the array dataset for which the corresponding dideoxy trace had a clean wildtype sequence. For the nucleotide positions where array calls were made, false negative rates were 1.41% for heterozygous mutations. All the homozygous mutations were detected, but 8.11% were erroneously reported as heterozygous changes from the reference sequence by the array analysis software. In addition, 20 non-small cell lung cancer (NSCLC) samples were analyzed using the arrays, and both somatic and germline mutations were found. The most interesting findings were two MET mutations that have recently been implemented in NSCLC. Large scale MALDI-TOF genotyping indicated that one of these mutations (T1010I) might represent a true cancer-causing genotype, whereas the other (N375S) appears to be a common germline polymorphism.
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Affiliation(s)
- Torstein Tengs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
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