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Soliman MA, Azab MS, Hussein HA, Roushdy MM, Abu El-Naga MN. FBPP: software to design PCR primers and probes for nucleic acid base detection of foodborne pathogens. Sci Rep 2024; 14:1229. [PMID: 38216615 PMCID: PMC10786913 DOI: 10.1038/s41598-024-51372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024] Open
Abstract
Foodborne pathogens can be found in various foods, and it is important to detect foodborne pathogens to provide a safe food supply and to prevent foodborne diseases. The nucleic acid base detection method is one of the most rapid and widely used methods in the detection of foodborne pathogens; it depends on hybridizing the target nucleic acid sequence to a synthetic oligonucleotide (probes or primers) that is complementary to the target sequence. Designing primers and probes for this method is a preliminary and critical step. However, new bioinformatics tools are needed to automate, specific and improve the design sets to be used in the nucleic acid‒base method. Thus, we developed foodborne pathogen primer probe design (FBPP), an open-source, user-friendly graphical interface Python-based application supported by the SQL database for foodborne pathogen virulence factors, for (i) designing primers/probes for detection purposes, (ii) PCR and gel electrophoresis photo simulation, and (iii) checking the specificity of primers/probes.
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Affiliation(s)
- Mohamed A Soliman
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Mohamed S Azab
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hala A Hussein
- Department of Radiation Microbiology, National Centre for Radiation Research and Technology, Atomic Energy Authority, Nasr City, Cairo, Egypt
| | - Mohamed M Roushdy
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed N Abu El-Naga
- Department of Radiation Microbiology, National Centre for Radiation Research and Technology, Atomic Energy Authority, Nasr City, Cairo, Egypt
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Park HC, Ahn ER, Jung JY, Park JH, Lee JW, Lim SK, Kim W. Enhanced sensitivity of CpG island search and primer design based on predicted CpG island position. Forensic Sci Int Genet 2018; 34:134-140. [PMID: 29477876 DOI: 10.1016/j.fsigen.2018.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
Abstract
DNA methylation has important biological roles, such as gene expression regulation, as well as practical applications in forensics, such as in body fluid identification and age estimation. DNA methylation often occurs in the CpG site, and methylation within the CpG islands affects various cellular functions and is related to tissue-specific identification. Several programs have been developed to identify CpG islands; however, the size, location, and number of predicted CpG islands are not identical due to different search algorithms. In addition, they only provide structural information for predicted CpG islands without experimental information, such as primer design. We developed an analysis pipeline package, CpGPNP, to integrate CpG island prediction and primer design. CpGPNP predicts CpG islands more accurately and sensitively than other programs, and designs primers easily based on the predicted CpG island locations. The primer design function included standard, bisulfite, and methylation-specific PCR to identify the methylation of particular CpG sites. In this study, we performed CpG island prediction on all chromosomes and compared CpG island search performance of CpGPNP with other CpG island prediction programs. In addition, we compared the position of primers designed for a specific region within the predicted CpG island using other bisulfite PCR primer programs. The primers designed by CpGPNP were used to experimentally verify the amplification of the target region of markers for body fluid identification and age estimation. CpGPNP is freely available at http://forensicdna.kr/cpgpnp/.
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Affiliation(s)
- Hyun-Chul Park
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Eu-Ree Ahn
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
| | - Ju Yeon Jung
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
| | - Ji-Hye Park
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
| | - Jee Won Lee
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
| | - Si-Keun Lim
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Pandey RV, Pulverer W, Walter P, Kallmeyer R, Beikircher G, Pabinger S, Kriegner A, Weinhäusel A. MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research. Clin Epigenetics 2016; 8:26. [PMID: 26949424 PMCID: PMC4779238 DOI: 10.1186/s13148-016-0190-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 02/23/2016] [Indexed: 12/28/2022] Open
Abstract
Background Methylation-sensitive restriction enzymes—polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discovery studies provide many candidate regions for which the MSREqPCR approach can be very effective to confirm the findings. MSREqPCR provides high multiplexing capabilities also when starting with limited amount of DNA-like cfDNA to validate many targets in a time- and cost-effective manner. Multiplex design is challenging and cumbersome to define specific primers in an effective manner, and no suitable software tools are freely available for high-throughput primer design in a time-effective manner and to automatically annotate the resulting primers with known SNPs, CpG, repeats, and RefSeq genes. Therefore a robust, powerful, high-throughput, optimized, and methylation-specific primer design tool with great accuracy will be very useful. Results We have developed a novel pipeline, called MSRE-HTPrimer, to design MSRE-PCR and genomic PCR primers pairs in a very efficient manner and with high success rate. First, our pipeline designs all possible PCR primer pairs and oligos, followed by filtering for SNPs loci and repeat regions. Next, each primer pair is annotated with the number of cut sites in primers and amplicons, upstream and downstream genes, and CpG islands loci. Finally, MSRE-HTPrimer selects resulting primer pairs for all target sequences based on a custom quality matrix defined by the user. MSRE-HTPrimer produces a table for all resulting primer pairs as well as a custom track in GTF file format for each target sequence to visualize it in UCSC genome browser. Conclusions MSRE-HTPrimer, based on Primer3, is a high-throughput pipeline and has no limitation on the number and size of target sequences for primer design and provides full flexibility to customize it for specific requirements. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 190 primer pairs, 71 % could be successfully validated. The MSRE-HTPrimer software is freely available from http://sourceforge.net/p/msrehtprimer/wiki/Virtual_Machine/ as a virtual machine. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0190-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ram Vinay Pandey
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria ; Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Walter Pulverer
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Rainer Kallmeyer
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Gabriel Beikircher
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
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PRIMEGENSw3: a web-based tool for high-throughput primer and probe design. Methods Mol Biol 2015; 1275:181-99. [PMID: 25697661 DOI: 10.1007/978-1-4939-2365-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an interactive, user-friendly, and automatic fashion. The system runs the PRIMEGENS algorithm in the back-end on the high-performance server with the stored genomic database or user-provided custom database for cross-hybridization check. Cross-hybridization is checked not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online and also can be downloaded. The average success rate of primer design using PRIMEGENSw3 is ~90 %. The web server also supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.
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Nwaobi SE, Olsen ML. Correlating Gene-specific DNA Methylation Changes with Expression and Transcriptional Activity of Astrocytic KCNJ10 (Kir4.1). J Vis Exp 2015. [PMID: 26436772 DOI: 10.3791/52406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation serves to regulate gene expression through the covalent attachment of a methyl group onto the C5 position of a cytosine in a cytosine-guanine dinucleotide. While DNA methylation provides long-lasting and stable changes in gene expression, patterns and levels of DNA methylation are also subject to change based on a variety of signals and stimuli. As such, DNA methylation functions as a powerful and dynamic regulator of gene expression. The study of neuroepigenetics has revealed a variety of physiological and pathological states that are associated with both global and gene-specific changes in DNA methylation. Specifically, striking correlations between changes in gene expression and DNA methylation exist in neuropsychiatric and neurodegenerative disorders, during synaptic plasticity, and following CNS injury. However, as the field of neuroepigenetics continues to expand its understanding of the role of DNA methylation in CNS physiology, delineating causal relationships in regards to changes in gene expression and DNA methylation are essential. Moreover, in regards to the larger field of neuroscience, the presence of vast region and cell-specific differences requires techniques that address these variances when studying the transcriptome, proteome, and epigenome. Here we describe FACS sorting of cortical astrocytes that allows for subsequent examination of a both RNA transcription and DNA methylation. Furthermore, we detail a technique to examine DNA methylation, methylation sensitive high resolution melt analysis (MS-HRMA) as well as a luciferase promoter assay. Through the use of these combined techniques one is able to not only explore correlative changes between DNA methylation and gene expression, but also directly assess if changes in the DNA methylation status of a given gene region are sufficient to affect transcriptional activity.
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Affiliation(s)
- Sinifunanya E Nwaobi
- Department of Cell Developmental and Integrative Biology, University of Alabama at Birmingham
| | - Michelle L Olsen
- Department of Cell Developmental and Integrative Biology, University of Alabama at Birmingham;
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PRISE2: software for designing sequence-selective PCR primers and probes. BMC Bioinformatics 2014; 15:317. [PMID: 25252611 PMCID: PMC4261892 DOI: 10.1186/1471-2105-15-317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/20/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. RESULTS PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. CONCLUSIONS PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.
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7
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Tulpan D, Ghiggi A, Montemanni R. Computational Sequence Design Techniques for DNA Microarray Technologies. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.
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Affiliation(s)
- Dan Tulpan
- National Research Council of Canada, Canada
| | | | - Roberto Montemanni
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale, Switzerland
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8
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Abstract
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range of biological processes and diseases. The technology is now available for studying DNA methylation genome-wide, at a high resolution and in a large number of samples. This Review discusses relevant concepts, computational methods and software tools for analysing and interpreting DNA methylation data. It focuses not only on the bioinformatic challenges of large epigenome-mapping projects and epigenome-wide association studies but also highlights software tools that make genome-wide DNA methylation mapping more accessible for laboratories with limited bioinformatics experience.
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Affiliation(s)
- Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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Abstract
Bisulfite conversion of genomic DNA combined with next-generation sequencing (NGS) has become a very effective approach for mapping the whole-genome and sub-genome wide DNA methylation landscapes. However, whole methylome shotgun bisulfite sequencing is still expensive and not suitable for analyzing large numbers of human cancer specimens. Recent advances in the development of targeted bisulfite sequencing approaches offer several attractive alternatives. The characteristics and applications of these methods are discussed in this review article. In addition, the bioinformatic tools that can be used for sequence capture probe design as well as downstream sequence analyses are also addressed.
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10
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Baldwin S, Revanna R, Thomson S, Pither-Joyce M, Wright K, Crowhurst R, Fiers M, Chen L, Macknight R, McCallum JA. A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.). BMC Genomics 2012; 13:637. [PMID: 23157543 PMCID: PMC3534495 DOI: 10.1186/1471-2164-13-637] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Background Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. Results We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2 progeny from a very large F2 family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. Conclusions The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.
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Affiliation(s)
- Samantha Baldwin
- The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealand
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11
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Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces. Nucleic Acids Res 2012; 40:e115. [PMID: 22730293 PMCID: PMC3424584 DOI: 10.1093/nar/gks596] [Citation(s) in RCA: 5730] [Impact Index Per Article: 477.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
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Affiliation(s)
- Andreas Untergasser
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
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12
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Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
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Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
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Tulpan D, Ghiggi A, Montemanni R. Computational Sequence Design Techniques for DNA Microarray Technologies. SYSTEMIC APPROACHES IN BIOINFORMATICS AND COMPUTATIONAL SYSTEMS BIOLOGY 2011. [DOI: 10.4018/978-1-61350-435-2.ch003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.
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Affiliation(s)
- Dan Tulpan
- National Research Council of Canada, Canada
| | | | - Roberto Montemanni
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Switzerland
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Paprotka T, Deuschle K, Metzler V, Jeske H. Conformation-selective methylation of geminivirus DNA. J Virol 2011; 85:12001-12. [PMID: 21835804 PMCID: PMC3209285 DOI: 10.1128/jvi.05567-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/29/2011] [Indexed: 12/16/2022] Open
Abstract
Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially.
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Affiliation(s)
| | - K. Deuschle
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - V. Metzler
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - H. Jeske
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
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Mallona I, Egea-Cortines M, Weiss J. Conserved and divergent rhythms of crassulacean acid metabolism-related and core clock gene expression in the cactus Opuntia ficus-indica. PLANT PHYSIOLOGY 2011; 156:1978-89. [PMID: 21677095 PMCID: PMC3149932 DOI: 10.1104/pp.111.179275] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The cactus Opuntia ficus-indica is a constitutive Crassulacean acid metabolism (CAM) species. Current knowledge of CAM metabolism suggests that the enzyme phosphoenolpyruvate carboxylase kinase (PPCK) is circadian regulated at the transcriptional level, whereas phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), and pyruvate phosphate dikinase (PPDK) are posttranslationally controlled. As little transcriptomic data are available from obligate CAM plants, we created an expressed sequence tag database derived from different organs and developmental stages. Sequences were assembled, compared with sequences in the National Center for Biotechnology Information nonredundant database for identification of putative orthologs, and mapped using Kyoto Encyclopedia of Genes and Genomes Orthology and Gene Ontology. We identified genes involved in circadian regulation and CAM metabolism for transcriptomic analysis in plants grown in long days. We identified stable reference genes for quantitative polymerase chain reaction and found that OfiSAND, like its counterpart in Arabidopsis (Arabidopsis thaliana), and OfiTUB are generally appropriate standards for use in the quantification of gene expression in O. ficus-indica. Three kinds of expression profiles were found: transcripts of OfiPPCK oscillated with a 24-h periodicity; transcripts of the light-active OfiNADP-ME and OfiPPDK genes adapted to 12-h cycles, while transcript accumulation patterns of OfiPEPC and OfiMDH were arrhythmic. Expression of the circadian clock gene OfiTOC1, similar to Arabidopsis, oscillated with a 24-h periodicity, peaking at night. Expression of OfiCCA1 and OfiPRR9, unlike in Arabidopsis, adapted best to a 12-h rhythm, suggesting that circadian clock gene interactions differ from those of Arabidopsis. Our results indicate that the evolution of CAM metabolism could be the result of modified circadian regulation at both the transcriptional and posttranscriptional levels.
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Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res 2011; 39:e127. [PMID: 21785137 PMCID: PMC3201883 DOI: 10.1093/nar/gkr598] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21 408 CGIs and more than 15 946 transcriptional regulatory regions. Of the CpGs analyzed, 77–84% fell on or near capture probe sequences; 69–75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5′-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.
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Affiliation(s)
- Eun-Joon Lee
- GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA
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Srivastava GP, Hanumappa M, Kushwaha G, Nguyen HT, Xu D. Homolog-specific PCR primer design for profiling splice variants. Nucleic Acids Res 2011; 39:e69. [PMID: 21415011 PMCID: PMC3105385 DOI: 10.1093/nar/gkr127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 11/13/2022] Open
Abstract
To study functional diversity of proteins encoded from a single gene, it is important to distinguish the expression levels among the alternatively spliced variants. A variant-specific primer pair is required to amplify each alternatively spliced variant individually. For this purpose, we developed a new feature, homolog-specific primer design (HSPD), in our high-throughput primer and probe design software tool, PRIMEGENS-v2. The algorithm uses a de novo approach to design primers without any prior information of splice variants or close homologs for an input query sequence. It not only designs primer pairs but also finds potential isoforms and homologs of the input sequence. Efficiency of this algorithm was tested for several gene families in soybean. A total of 187 primer pairs were tested under five different abiotic stress conditions with three replications at three time points. Results indicate a high success rate of primer design. Some primer pairs designed were able to amplify all splice variants of a gene. Furthermore, by utilizing combinations within the same multiplex pool, we were able to uniquely amplify a specific variant or duplicate gene. Our method can also be used to design PCR primers to specifically amplify homologs in the same gene family. PRIMEGENS-v2 is available at: http://primegens.org.
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Affiliation(s)
- Gyan Prakash Srivastava
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Mamatha Hanumappa
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Garima Kushwaha
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Henry T. Nguyen
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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