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Patientenantikörper als Informationsquelle. BIOSPEKTRUM 2020; 26:556-558. [PMID: 32921927 PMCID: PMC7474495 DOI: 10.1007/s12268-020-1440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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3
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Rajagopalan RM, Fujimura JH. Variations on a Chip: Technologies of Difference in Human Genetics Research. JOURNAL OF THE HISTORY OF BIOLOGY 2018; 51:841-873. [PMID: 30338423 DOI: 10.1007/s10739-018-9543-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this article we examine the history of the production of microarray technologies and their role in constructing and operationalizing views of human genetic difference in contemporary genomics. Rather than the "turn to difference" emerging as a post-Human Genome Project (HGP) phenomenon, interest in individual and group differences was a central, motivating concept in human genetics throughout the twentieth century. This interest was entwined with efforts to develop polymorphic "genetic markers" for studying human traits and diseases. We trace the technological, methodological and conceptual strategies in the late twentieth century that established single nucleotide polymorphisms (SNPs) as key focal points for locating difference in the genome. By embedding SNPs in microarrays, researchers created a technology that they used to catalog and assess human genetic variation. In the process of making genetic markers and array-based technologies to track variation, scientists also made commitments to ways of describing, cataloging and "knowing" human genetic differences that refracted difference through a continental geographic lens. We show how difference came to matter in both senses of the term: difference was made salient to, and inscribed on, genetic matter(s), as a result of the decisions, assessments and choices of collaborative and hybrid research collectives in medical genomics research.
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Affiliation(s)
- Ramya M Rajagopalan
- Institute for Practical Ethics, University of California, San Diego, 9500 Gilman Drive, MC 0406, San Diego, CA, 92093, USA.
| | - Joan H Fujimura
- Department of Sociology and Holtz Center for Science and Technology Studies, University of Wisconsin-Madison, 8128 Sewell Social Sciences Building 1180 Observatory Drive, Madison, WI, 53706, USA
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4
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High-Throughput Sequencing of the Major Histocompatibility Complex following Targeted Sequence Capture. Methods Mol Biol 2017. [PMID: 28138842 DOI: 10.1007/978-1-4939-6750-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The Human Major Histocompatibility Complex (MHC) is a highly polymorphic region full of immunoregulatory genes. The MHC codes for the human leukocyte antigens (HLA), proteins that present on the cellular surface and that are involved in self-non-self recognition. For matching donors and recipients for organ and stem-cell transplants it is important to know an individual's HLA haplotype determinable in this region. Now, as next-generation sequencing (NGS) platforms mature and become more and more accepted as a standard method, NGS applications have spread from research laboratories to the clinic, where they provide valid genetic insights. Here, we describe a cost-effective microarray-based sequence capture, enrichment, and NGS sequencing approach to characterize MHC haplotypes. Using this approach, ~4 MB of MHC sequence for four DNA samples (donor, recipient and the parents of the recipient) were sequenced in parallel in one NGS instrument run. We complemented this approach using microarray-based genome-wide SNP analysis. Taken together, the use of recently developed tools and protocols for sequence capture and massively parallel sequencing allows for detailed MHC analysis and donor-recipient matching.
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Kwarciak K, Radom M, Formanowicz P. A multilevel ant colony optimization algorithm for classical and isothermic DNA sequencing by hybridization with multiplicity information available. Comput Biol Chem 2016; 61:109-20. [PMID: 26878124 DOI: 10.1016/j.compbiolchem.2016.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 12/02/2015] [Accepted: 01/24/2016] [Indexed: 11/28/2022]
Abstract
The classical sequencing by hybridization takes into account a binary information about sequence composition. A given element from an oligonucleotide library is or is not a part of the target sequence. However, the DNA chip technology has been developed and it enables to receive a partial information about multiplicity of each oligonucleotide the analyzed sequence consist of. Currently, it is not possible to assess the exact data of such type but even partial information should be very useful. Two realistic multiplicity information models are taken into consideration in this paper. The first one, called "one and many" assumes that it is possible to obtain information if a given oligonucleotide occurs in a reconstructed sequence once or more than once. According to the second model, called "one, two and many", one is able to receive from biochemical experiment information if a given oligonucleotide is present in an analyzed sequence once, twice or at least three times. An ant colony optimization algorithm has been implemented to verify the above models and to compare with existing algorithms for sequencing by hybridization which utilize the additional information. The proposed algorithm solves the problem with any kind of hybridization errors. Computational experiment results confirm that using even the partial information about multiplicity leads to increased quality of reconstructed sequences. Moreover, they also show that the more precise model enables to obtain better solutions and the ant colony optimization algorithm outperforms the existing ones. Test data sets and the proposed ant colony optimization algorithm are available on: http://bioserver.cs.put.poznan.pl/download/ACO4mSBH.zip.
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Affiliation(s)
- Kamil Kwarciak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Marcin Radom
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Piotr Formanowicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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6
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Kierzek R, Turner DH, Kierzek E. Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Res 2014; 43:1-12. [PMID: 25505162 PMCID: PMC4288193 DOI: 10.1093/nar/gku1303] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure-function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.
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Affiliation(s)
- Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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7
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Pirrung MC, Southern EM. The genesis of microarrays. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 42:106-113. [PMID: 24344052 DOI: 10.1002/bmb.20756] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/23/2013] [Accepted: 10/23/2013] [Indexed: 06/03/2023]
Abstract
This review provides a perspective on the initial development of microarray technologies by two independent groups in the late 1980s.
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Affiliation(s)
- Michael C Pirrung
- Department of Chemistry, University of California, Riverside, California, 92521
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8
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Abstract
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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Affiliation(s)
- Max Käller
- AlbaNova University Center, School of Biotechnology, Department of Gene Technology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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Brovarets’ OO, Hovorun DM. Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis. J Biomol Struct Dyn 2013; 31:913-36. [PMID: 22962845 DOI: 10.1080/07391102.2012.715041] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Lemetre C, Zhang ZD. A brief introduction to tiling microarrays: principles, concepts, and applications. Methods Mol Biol 2013; 1067:3-19. [PMID: 23975782 DOI: 10.1007/978-1-62703-607-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Technological achievements have always contributed to the advancement of biomedical research. It has never been more so than in recent times, when the development and application of innovative cutting-edge technologies have transformed biology into a data-rich quantitative science. This stunning revolution in biology primarily ensued from the emergence of microarrays over two decades ago. The completion of whole-genome sequencing projects and the advance in microarray manufacturing technologies enabled the development of tiling microarrays, which gave unprecedented genomic coverage. Since their first description, several types of application of tiling arrays have emerged, each aiming to tackle a different biological problem. Although numerous algorithms have already been developed to analyze microarray data, new method development is still needed not only for better performance but also for integration of available microarray data sets, which without doubt constitute one of the largest collections of biological data ever generated. In this chapter we first introduce the principles behind the emergence and the development of tiling microarrays, and then discuss with some examples how they are used to investigate different biological problems.
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Affiliation(s)
- Christophe Lemetre
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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11
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Wong VY, Duval MX. Inter-Laboratory Variability in Array-Based RNA Quantification Methods. GENOMICS INSIGHTS 2013. [PMID: 26217107 PMCID: PMC4510603 DOI: 10.4137/gei.s11909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. The short half-life property, inherent to RNA, benefits cells that do not need to express their entire repertoire of proteins. The cellular machinery turns off the production of a given protein by shutting down the transcription of its cognate coding gene and by either actively degrading the remaining mRNA or allowing it to decay on its own. The steady-state level of each mRNA in a given cell varies continuously and is specified by changing kinetics of synthesis and degradation. Because it is technically possible to simultaneously measure thousands of nucleic acid molecules, these quantities have been studied by the life sciences community to investigate a range of biological problems. Since the RNA abundance can change according to a wide range of perturbations, this makes it the molecule of choice for exploring biological systems; its instability, on the other hand, could be an underestimated source of technical variability. We found that a large fraction of the RNA abundance originally present in the biological system prior to extraction was masked by the RNA labeling and measurement procedure. The method used to extract RNA molecules from cells and to label them prior to hybridization operations on DNA arrays affects the original distribution of RNA. Only if RNA measurements are performed according to the same procedure can biological information be inferred from the assay read out.
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Affiliation(s)
- Victoria Y Wong
- Pfizer Global Research and Development, External Research solutions Groton CT 06333, USA
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Jakubek YA, Cutler DJ. A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays. BMC Genomics 2012; 13:737. [PMID: 23270536 PMCID: PMC3548757 DOI: 10.1186/1471-2164-13-737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 12/16/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. RESULTS For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. CONCLUSIONS To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These two factors are sequence dependent and have a large impact on probe intensity. The results presented here provide novel insight into the effect of probe synthesis errors on Affymetrix microarrays; furthermore, the algorithms developed in this work provide useful tools for the analysis of cross-hybridization, probe synthesis efficiency, fragmentation, wash stringency, temperature, and salt concentration on microarray intensities.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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13
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Expression profiles of genes regulating dairy cow fertility: recent findings, ongoing activities and future possibilities. Animal 2012; 2:1158-67. [PMID: 22443728 DOI: 10.1017/s1751731108002371] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Subfertility has negative effects for dairy farm profitability, animal welfare and sustainability of animal production. Increasing herd sizes and economic pressures restrict the amount of time that farmers can spend on counteractive management. Genetic improvement will become increasingly important to restore reproductive performance. Complementary to traditional breeding value estimation procedures, genomic selection based on genome-wide information will become more widely applied. Functional genomics, including transcriptomics (gene expression profiling), produces the information to understand the consequences of selection as it helps to unravel physiological mechanisms underlying female fertility traits. Insight into the latter is needed to develop new effective management strategies to combat subfertility. Here, the importance of functional genomics for dairy cow reproduction so far and in the near future is evaluated. Recent gene profiling studies in the field of dairy cow fertility are reviewed and new data are presented on genes that are expressed in the brains of dairy cows and that are involved in dairy cow oestrus (behaviour). Fast-developing new research areas in the field of functional genomics, such as epigenetics, RNA interference, variable copy numbers and nutrigenomics, are discussed including their promising future value for dairy cow fertility.
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Rubtsova MY, Ulyashova MM, Bachmann TT, Schmid RD, Egorov AM. Multiparametric determination of genes and their point mutations for identification of beta-lactamases. BIOCHEMISTRY (MOSCOW) 2011; 75:1628-49. [PMID: 21417998 DOI: 10.1134/s0006297910130080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
More than half of all currently used antibiotics belong to the beta-lactam group, but their clinical effectiveness is severely limited by antibiotic resistance of microorganisms that are the causative agents of infectious diseases. Several mechanisms for the resistance of Enterobacteriaceae have been established, but the main one is the enzymatic hydrolysis of the antibiotic by specific enzymes called beta-lactamases. Beta-lactamases represent a large group of genetically and functionally different enzymes of which extended-spectrum beta-lactamases (ESBLs) pose the greatest threat. Due to the plasmid localization of the encoded genes, the distribution of these enzymes among the pathogens increases every year. Among ESBLs the most widespread and clinically relevant are class A ESBLs of TEM, SHV, and CTX-M types. TEM and SHV type ESBLs are derived from penicillinases TEM-1, TEM-2, and SHV-1 and are characterized by several single amino acid substitutions. The extended spectrum of substrate specificity for CTX-M beta-lactamases is also associated with the emergence of single mutations in the coding genes. The present review describes various molecular-biological methods used to identify determinants of antibiotic resistance. Particular attention is given to the method of hybridization analysis on microarrays, which allows simultaneous multiparametric determination of many genes and point mutations in them. A separate chapter deals with the use of hybridization analysis on microarrays for genotyping of the major clinically significant ESBLs. Specificity of mutation detection by means of hybridization analysis with different detection techniques is compared.
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Affiliation(s)
- M Yu Rubtsova
- Chemical Faculty, Lomonosov Moscow State University, Russia.
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15
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Ozsolak F, Milos PM. Single-molecule direct RNA sequencing without cDNA synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:565-70. [PMID: 21957044 DOI: 10.1002/wrna.84] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and human disease biology and have begun to be utilized in various clinical diagnostic applications. Current methods, however, typically require RNA to be converted to complementary DNA prior to measurements. This step has been shown to introduce many biases and artifacts. In order to best characterize the 'true' transcriptome, the single-molecule direct RNA sequencing (DRS) technology was developed. This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, MA, USA.
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16
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Abstract
Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic applications. Today, current methods utilized by the scientific community typically require RNA to be converted to cDNA prior to comprehensive measurements. However, this cDNA conversion process has been shown to introduce many biases and artifacts that interfere with the proper characterization and quantitation of transcripts. We have developed a direct RNA sequencing (DRS) approach, in which, unlike other technologies, RNA is sequenced directly without prior conversion to cDNA. The benefits of DRS include the ability to use minute quantities (e.g. on the order of several femtomoles) of RNA with minimal sample preparation, the ability to analyze short RNAs which pose unique challenges for analysis using cDNA-based approaches, and the ability to perform these analyses in a low-cost and high-throughput manner. Here, we describe the strategies and procedures we employ to prepare various RNA species for analysis with DRS.
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17
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LeProust EM, Peck BJ, Spirin K, McCuen HB, Moore B, Namsaraev E, Caruthers MH. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 2010; 38:2522-40. [PMID: 20308161 PMCID: PMC2860131 DOI: 10.1093/nar/gkq163] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology).
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Affiliation(s)
- Emily M LeProust
- Agilent Technologies Inc., LSSU - Genomics, 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA.
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18
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Lowe AM, Ozer BH, Bai Y, Bertics PJ, Abbott NL. Design of surfaces for liquid crystal-based bioanalytical assays. ACS APPLIED MATERIALS & INTERFACES 2010; 2:722-31. [PMID: 20356273 PMCID: PMC2862361 DOI: 10.1021/am900753v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Surface-induced ordering of liquid crystals (LCs) offers the basis of a label-free analytical technique for the detection of surface-bound biomolecules. The orientation-dependent energy of interaction of a LC with a surface (anchoring energy of LC), in particular, is both sensitive to the presence of surface-bound molecules and easily quantified. Herein, we report a study that analyzes a simple model of twisted nematic LC systems and thereby identifies surfaces with LC anchoring energies in the range of 0.5 microJ/m(2) to 2.0 microJ/m(2) to be optimal for use with LC-based analytical methods. Guided by these predictions, we demonstrate that analytic surfaces possessing anchoring energies within this range can be fabricated with a high level of precision (< 0.1 microJ/m(2)) through formation of monolayers of organothiols (with omega-functional groups corresponding to oligoethyleneglycols and amines) on gold films deposited by physical vapor deposition at oblique angles of incidence. Finally, by using the human epidermal growth factor receptor (EGFR) as a model protein analyte, we have characterized the influence of the anchoring energies of the surfaces on the response of the LC to the presence of surface-bound EGFR. These results, when combined with (32)P-radiolabeling of the EGFR to independently quantify the surface concentration of EGFR, permit identification of surfaces that allow use of LCs to report surface densities of EGFR of 30-40 pg/mm(2). Overall, the results reported in this paper guide the design of surfaces for use in LC-based analytical systems.
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Affiliation(s)
- Aaron M. Lowe
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Byram H. Ozer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Yiqun Bai
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Paul J. Bertics
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
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Kothiyal P, Cox S, Ebert J, Husami A, Kenna MA, Greinwald JH, Aronow BJ, Rehm HL. High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays. BMC Biotechnol 2010; 10:10. [PMID: 20146813 PMCID: PMC2841091 DOI: 10.1186/1472-6750-10-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/10/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting. RESULTS We leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison. CONCLUSIONS Together, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity.
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Affiliation(s)
- Prachi Kothiyal
- 1Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Fassbender A, Lewin J, König T, Rujan T, Pelet C, Lesche R, Distler J, Schuster M. Quantitative DNA methylation profiling on a high-density oligonucleotide microarray. Methods Mol Biol 2010; 576:155-170. [PMID: 19882262 DOI: 10.1007/978-1-59745-545-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recently, the analysis and functional elucidation of CpG island methylation has become a focus area of genomic research. Deviations from the normal parental imprinting pattern have been shown to cause developmental defects associated with serious symptoms. Aberrant DNA methylation of tumor suppressor and other functional genes, especially when found in 5' untranslated regions and early exons, has been associated with tumorigenesis. In the context of applying DNA methylation analysis for the molecular characterization of cancer and other diseases, standardized protocols enabling parallel genome-wide methylation profiling of numerous samples are required. DNA methylation profiling is described using a CpG island microarray representing more than 50,000 CpG-rich DNA fragments. Fragments were selected to represent the vast majority of known 5'-untranslated regions as well as the first exons of thousands of genes. Measurement probes were designed to represent these fragments were displayed on an Affymetrix custom array. A modified procedure for differential methylation hybridization (DMH) is described for methylation enrichment. Application of a novel signal normalization concept enables accurate and reproducible measurements using a single fluorescence channel. The use of defined calibrator material allows quantification of DNA methylation patterns by DMH in a massively parallel fashion.
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21
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Tian J, Ma K, Saaem I. Advancing high-throughput gene synthesis technology. MOLECULAR BIOSYSTEMS 2009; 5:714-22. [DOI: 10.1039/b822268c] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Bugert P. The 'Whole Genome Age'. Transfus Med Hemother 2009; 36:244-245. [PMID: 21049074 DOI: 10.1159/000228919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Peter Bugert
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty of Mannheim, Germany
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23
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A multidisciplinary approach for molecular diagnostics based on biosensors and microarrays. Ing Rech Biomed 2008. [DOI: 10.1016/j.rbmret.2007.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ericsson O, Jarvius J, Schallmeiner E, Howell M, Nong RY, Reuter H, Hahn M, Stenberg J, Nilsson M, Landegren U. A dual-tag microarray platform for high-performance nucleic acid and protein analyses. Nucleic Acids Res 2008; 36:e45. [PMID: 18346972 PMCID: PMC2377440 DOI: 10.1093/nar/gkn106] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve specificity of detection and dynamic range. To further extend the utility of DNA microarray-based approaches we present a high-performance tag microarray procedure that enables probe-based analysis of as little as 100 target cDNA molecules, and with a linear dynamic range close to 10(5). Furthermore, the protocol radically decreases the risk of cross-hybridization on microarrays compared to current approaches, and it also allows for quantification by single-molecule analysis and real-time on-chip monitoring of rolling-circle amplification. We provide proof of concept for microarray-based measurement of both mRNA molecules and of proteins, converted to tag DNA sequences by padlock and proximity probe ligation, respectively.
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Affiliation(s)
- Olle Ericsson
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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26
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Rehbock C, Beutel S, Brückerhoff T, Hitzmann B, Riechers D, Rudolph G, Stahl F, Scheper T, Friehs K. Bioprozessanalytik. CHEM-ING-TECH 2008. [DOI: 10.1002/cite.200700164] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Abstract
Improvements of microarray techniques for genotyping purposes have focused on increasing the reliability of this method. Here we report the development of a genotyping method where a microarray was spotted with stemloop probes, especially designed to optimize the hybridization specificity of complementary DNA sequences. This accurate method was used to screen for four common disease-causing mutations involved in a neurological disorder called Charcot-Marie-Tooth disease (CMT). Healthy individuals' and patients' DNA were amplified and labeled by PCR and hybridized on microarray. The spot signal intensities were 81 to 408 times greater for perfect compared with mismatched target sequences, differing by only one nucleotide (discrimination ratio) for healthy individual "homozygous" DNA. On the other hand, "heterozygous" mutant DNA samples gave rise to signal intensity ratios close to 1, as expected. The genotypes obtained by this method were perfectly consistent with those determined by direct PCR sequencing. Cross-hybridization rates were very low, resulting in further multiplexing improvements. In this study, we also demonstrated the feasibility of real-time hybridization detection of labeled synthetic oligonucleotides with concentrations as low as 2.5 nM.
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Abstract
This chapter describes methodology for the labeling, hybridization, and detection of amplicon target DNA to arrays of oligonucleotide probes attached to plastic substrates. A systematic approach to target discrimination based on both hybridization and wash stringency is provided.
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Construction of oligonucleotide microarrays (biochip) using heterobifunctional reagents. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2007. [PMID: 17984518 DOI: 10.1007/978-1-59745-303-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
A number of hetero- and homobifunctional reagents have been reported to immobilize biomolecules on a variety of supports. However, efforts are on to search for a method, which is relatively simple, involving minimum of steps, cost effective, easy to reproduce, and that produces stable oligonucleotide arrays. Two new reagents, viz., [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], and [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide] have been designed considering the above points. These reagents contain different functional groups at their two ends. In [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], one end (triethoxysilyl) is capable of binding to the virgin glass surface and the other one consists of trifluoroethanesulfonate (tresyl) function specific toward aminoalkyl and mercaptoalkyl functionalities, which are easy to introduce at the 3'- or 5'-end of oligonucleotides. Likewise, in [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide], one end consists of photoactivatable moiety (anthraquinone) capable of reacting to a C-H containing surface and the tresyl function at the other end reacts specifically with aminoalkyl and mercaptoalkyl functionalities in modified oligonucleotides. These reagents have successfully been utilized to construct a number of oligonucleotide arrays and subsequently used for the detection of mismatches.
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30
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Construction of in situ oligonucleotide arrays on plastic. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2007. [PMID: 17984522 DOI: 10.1007/978-1-59745-303-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The concept of DNA arrays was first introduced in the early 1980s, by Sir Edwin Southern. Since then, many research institutions and biotechnology companies have investigated the potential use of arrays in fields ranging from genetic diagnostics to forensics investigations. A 64-channel automated chemical delivery system, known as the Southern Array Maker, which synthesizes oligonucleotides directly onto an aminated polypropylene substrate has been constructed. Many different arrays have been synthesized for the purpose of detecting single point mutations, which might be either indicators of, or directly responsible for, many different types of genetic diseases and cancers. These include cystic fibrosis, H-ras, K-ras, and other mutations. In addition to the synthesized arrays, we are also looking into various alternative methods of producing both high-and low-density DNA arrays. This chapter is intended to demonstrate the synthesis of oligoarrays by in situ method using standard phosphoramidite chemistry. Phosphoramidate linkage to the aminated polypropylene is quite stable under oligo cleavage and deprotection conditions. Oligonucleotide density is approx 3 pmole or 10(1)2 molecules/mm(2).
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31
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Microarray-based DNA resequencing using 3' blocked primers. Anal Biochem 2007; 374:41-7. [PMID: 18023400 DOI: 10.1016/j.ab.2007.10.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 11/22/2022]
Abstract
To exceed the throughput and accuracy of conventional sequencing technologies, we tested a method (pyrophosphorolysis-activated polymerization [PAP]) of nucleic acid amplification that uses 3' blocked primers (P*s). As proof-of-principle, we resequenced a 20-bp region of the factor IX gene with a microarray of P*s. P*s discriminate 3' end mismatches with ultra-high specificity as well as mismatches along their lengths with high specificity. We correctly identified two wild-type samples as well as all mismatches, including three single-base substitutions, one microdeletion, one microinsertion, and one heterozygous mutation. Despite limitations in the primer purity, the signal/noise ratio between the matched and mismatched P*s sometimes exceeded 1000. Thus, PAP resequencing shows great potential for accurate and high-throughput microarray-based resequencing.
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Abstract
Although DNA microarrays are now widely used in research settings, they have been slow to penetrate clinical practice in spite of their apparent advantages. This is due to the very different requirements for a clinical test in contrast to a research tool, and to a strict necessity for demonstrated clinical utility. There is a clear differentiation between two types of DNA array tests: "genomic" diagnostics, developed to ascertain the presence or absence of mutations, deletions or duplications, and for which clinical evidence is already established, and tests using expression profiling for prognosis or predictive purposes, in which case the clinical correlate must be proven. Most array diagnostics currently used belong, understandably, to the "genomic" variety. It is to be expected that future improvements in tailored technology, as well as a logical trend towards measuring an ever-increasing number of parameters, will ensure an important diagnostic role for DNA arrays in the coming decade.
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Affiliation(s)
- Bertrand R Jordan
- Marseille-Nice Genopole, Luminy Science Parc, 13278 Marseille Cedex 9, France.
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34
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Becker T, Hitzmann B, Muffler K, Pörtner R, Reardon KF, Stahl F, Ulber R. Future aspects of bioprocess monitoring. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 105:249-93. [PMID: 17408086 DOI: 10.1007/10_2006_036] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Nature has the impressive ability to efficiently and precisely control biological processes by applying highly evolved principles and using minimal space and relatively simple building blocks. The challenge is to transfer these principles into technically applicable and precise analytical systems that can be used for many applications. This article summarizes some of the new approaches in sensor technology and control strategies for different bioprocesses such as fermentations, biotransformations, and downstream processes. It focuses on bio- and chemosensors, optical sensors, DNA and protein chip technology, software sensors, and modern aspects of data evaluation for improved process monitoring and control.
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Affiliation(s)
- Thomas Becker
- Universität Hohenheim, Process Analysis, Garbenstrasse 25, 70599 Stuttgart, Germany
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35
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Segmented Solid Supports: My Personal Addiction to Merrifield’s Solid Phase Synthesis. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-006-9067-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Abstract
Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.
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Affiliation(s)
- Hartmut Seliger
- Arbeitsgruppe Chemische Funktionen in Biosystemen, Universitat Ulm, Ulm, Germany
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37
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Matson RS, Milton RC, Rampal JB, Chan TS, Cress MC. Overprint immunoassay using protein A microarrays. Methods Mol Biol 2007; 382:273-286. [PMID: 18220238 DOI: 10.1007/978-1-59745-304-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The ability to perform microarray-based immunoassays without the need for wells or other fluid barriers were demonstrated. Both contact and noncontact microarray printing technology is used to prepare spotted arrays of analyte binding sites, as well as, to deliver samples, secondary antibodies and other signal development reagents directly to these sites in a parallel fashion are called as overprint immunoassays. A micro-ELISA is demonstrated based upon the use of Protein A as a universal microarray. All components of the assay (capture antibody, antigen, and signal development reagents) were site-specifically dispensed in parallel fashion to the surface in nanoliter volumes. This represents a 1000-fold reduction in reagent consumption from that used in a conventional 96-well microtiter plate assay. Overprinting nanoliter volumes directly onto 200-300 microm spots yields similar levels of sensitivity achieved with the bulk dispensing of microliter volumes into wells.
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38
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Beier M, Hoheisel JD. New Developments in Light-Controlled Synthesis of DNA-Arrays. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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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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40
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Giegrich H, Eisele-Bühler S, Hermann C, Kvasyuk E, Charubala R, Pfleiderer W. New Photolabile Protecting Groups in Nucleoside and Nucleotide Chemistry—Synthesis, Cleavage Mechanisms and Applications. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004738] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- H. Giegrich
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
| | - S. Eisele-Bühler
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
| | - Chr Hermann
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
| | - E. Kvasyuk
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
| | - R. Charubala
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
| | - W. Pfleiderer
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434 , Konstanz , Germany
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41
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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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42
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Bader R, Brugger H, Hinz M, Rembe C, Hofer EP, Seliger H. A Rapid Method for the Preparation of a One Dimensional Sequence-Overlapping Oligonucleotide Library. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- R. Bader
- a University of Ulm, Sektion Polymere , D-89069, Ulm
| | - H. Brugger
- b University of Ulm , Abteilung Meß-, Regel- und Mikrotechnik, D-89069, Ulm
| | - M. Hinz
- a University of Ulm, Sektion Polymere , D-89069, Ulm
| | - C. Rembe
- b University of Ulm , Abteilung Meß-, Regel- und Mikrotechnik, D-89069, Ulm
| | - E. P. Hofer
- b University of Ulm , Abteilung Meß-, Regel- und Mikrotechnik, D-89069, Ulm
| | - H. Seliger
- a University of Ulm, Sektion Polymere , D-89069, Ulm
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Buchholz S, Stahl F, Scheper T. Automatisierte RNA-Aufreinigung ausEscherichia coli zur Standardisierung von Microarray-Experimenten. CHEM-ING-TECH 2006. [DOI: 10.1002/cite.200500169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Liu RH, Nguyen T, Schwarzkopf K, Fuji HS, Petrova A, Siuda T, Peyvan K, Bizak M, Danley D, McShea A. Fully Integrated Miniature Device for Automated Gene Expression DNA Microarray Processing. Anal Chem 2006; 78:1980-6. [PMID: 16536436 DOI: 10.1021/ac0518553] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A DNA microarray with 12,000 features was integrated with a microfluidic cartridge to automate the fluidic handling steps required to carry out a gene expression study of the human leukemia cell line (K562). The fully integrated microfluidic device consists of microfluidic pumps/mixers, fluid channels, reagent chambers, and a DNA microarray silicon chip. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated into the cartridge to provide pumping of liquid solutions. The device was completely self-contained: no external pressure sources, fluid storage, mechanical pumps, mixers, or valves were necessary for fluid manipulation, thus eliminating possible sample contamination and simplifying device operation. Fluidic experiments were performed to study the on-chip washing efficiency and uniformity. A single-color transcriptional analysis of K562 cells with a series of calibration controls (spiked-in controls) to characterize this new platform with regard to sensitivity, specificity, and dynamic range was performed. The device detected sample RNAs with a concentration as low as 0.375 pM. Experiment also showed that the performance of the integrated microfluidic device is comparable with the conventional hybridization chambers with manual operations, indicating that the on-chip fluidic handling (washing and reaction) is highly efficient and can be automated with no loss of performance. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps in genomic analysis.
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Affiliation(s)
- Robin Hui Liu
- CombiMatrix Corporation, 6500 Harbor Heights Parkway, Mukilteo, Washington 98275, USA.
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OHTAKE T. Development of High Sensitive DNA Sensor by Using Probe PNA with IS-FET Electrode. ELECTROCHEMISTRY 2006. [DOI: 10.5796/electrochemistry.74.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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46
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Affiliation(s)
- Edwin Southern
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Abstract
Microarrays have become standard tools for gene expression profiling as the mRNA levels of a large number of genes can be measured in a single assay. Many technical aspects concerning microarray production and laboratory usage have been addressed in great detail, but it remains still crucial to establish this technology in new research fields such as human nutrition and food-related areas. The correlation between diet and inter-individual variation in gene expression is an important and relatively unexplored issue in human nutrition. Therefore, nutritionists changed their research field dramatically from epidemiology and physiology towards the "omics" sciences. Nutrigenomics as a field of research is based on the complete knowledge of the human genome and refers to the entire spectrum of human genes that determine the interactions of nutrition with the organism. Nutrigenetics is based on the inter-individual, genetically determined differences in metabolism. Nutrigenomics and nutrigenetics carry the hope that individualized diet can improve human health and prevent nutrition-related diseases. In this article we give an overview of current DNA and protein microarray techniques (including fabrication, experimental procedure and data analysis), we describe their applications to nutrition and food research and point out the limitations, problems and pitfalls of microarray experiments.
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Affiliation(s)
- Bettina Spielbauer
- Neuro and Sensory Physiology, University of Göttingen, Göttingen, Germany
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Riva A, Carpentier AS, Torrésani B, Hénaut A. Comments on selected fundamental aspects of microarray analysis. Comput Biol Chem 2005; 29:319-36. [PMID: 16219488 DOI: 10.1016/j.compbiolchem.2005.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 11/17/2022]
Abstract
Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.
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Affiliation(s)
- Alessandra Riva
- Laboratoire Génome et Informatique UMR 8116 Tour Evry2, 523 Place des Terrasses, 91034 Evry Cedex, France.
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49
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del Campo A, Bruce IJ. Substrate Patterning and Activation Strategies for DNA Chip Fabrication. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b137073] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Qin S, Zhao X, Pan Y, Liu J, Feng G, Fu J, Bao J, Zhang Z, He L. An association study of the N-methyl-D-aspartate receptor NR1 subunit gene (GRIN1) and NR2B subunit gene (GRIN2B) in schizophrenia with universal DNA microarray. Eur J Hum Genet 2005; 13:807-14. [PMID: 15841096 DOI: 10.1038/sj.ejhg.5201418] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Dysfunction of the N-methyl-D-aspartate (NMDA) receptors has been implicated in the etiology of schizophrenia based on psychotomimetic properties of several antagonists and on observation of genetic animal models. To conduct association analysis of the NMDA receptors in the Chinese population, we examined 16 reported SNPs across the NMDA receptor NR1 subunit gene (GRIN1) and NR2B subunit gene (GRIN2B), five of which were identified in the Chinese population. In this study, we combined universal DNA microarray and ligase detection reaction (LDR) for the purposes of association analysis, an approach we considered to be highly specific as well as offering a potentially high throughput of SNP genotyping. The association study was performed using 253 Chinese patients with schizophrenia and 140 Chinese control subjects. No significant frequency differences were found in the analysis of the alleles but some were found in the haplotypes of the GRIN2B gene. The interactions between the GRIN1 and GRIN2B genes were evaluated using the multifactor-dimensionality reduction (MDR) method, which showed a significant genetic interaction between the G1001C in the GRIN1 gene and the T4197C and T5988C polymorphisms in the GRIN2B gene. These findings suggest that the combined effects of the polymorphisms in the GRIN1 and GRIN2B genes might be involved in the etiology of schizophrenia.European Journal of Human Genetics (2005) 13, 807-814. doi:10.1038/sj.ejhg.5201418 Published online 20 April 2005.
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Affiliation(s)
- Shengying Qin
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, Shanghai 230030, PR China
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