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Xia H, Zhang Z, Luo C, Wei K, Li X, Mu X, Duan M, Zhu C, Jin L, He X, Tang L, Hu L, Guan Y, Lam DCC, Yang J. MultiPrime: A reliable and efficient tool for targeted next-generation sequencing. IMETA 2023; 2:e143. [PMID: 38868227 PMCID: PMC10989836 DOI: 10.1002/imt2.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 06/14/2024]
Abstract
We present multiPrime, a novel tool that automatically designs minimal primer sets for targeted next-generation sequencing, tailored to specific microbiomes or genes. MultiPrime enhances primer coverage by designing primers with mismatch tolerance and ensures both high compatibility and specificity. We evaluated the performance of multiPrime using a data set of 43,016 sequences from eight viruses. Our results demonstrated that multiPrime outperformed conventional tools, and the primer set designed by multiPrime successfully amplified the target amplicons. Furthermore, we expanded the application of multiPrime to 30 types of viruses and validated the work efficacy of multiPrime-designed primers in 80 clinical specimens. The subsequent sequencing outcomes from these primers indicated a sensitivity of 94% and a specificity of 89%.
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Affiliation(s)
- Han Xia
- School of Automation Science and Engineering, Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'anChina
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'anChina
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Zhe Zhang
- Department of Mechanical and Aerospace EngineeringThe Hong Kong University of Science and TechnologyHong KongChina
| | - Chen Luo
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Kangfei Wei
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Xuming Li
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Xiyu Mu
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Meilin Duan
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Chuanlong Zhu
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Luyi Jin
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Xiaoqing He
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Lingjie Tang
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Long Hu
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - Yuanlin Guan
- Department of Research and DevelopmentHugobiotechBeijingChina
| | - David C. C. Lam
- Department of Mechanical and Aerospace EngineeringThe Hong Kong University of Science and TechnologyHong KongChina
| | - Junbo Yang
- Department of Research and DevelopmentHugobiotechBeijingChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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Kreer C, Döring M, Lehnen N, Ercanoglu MS, Gieselmann L, Luca D, Jain K, Schommers P, Pfeifer N, Klein F. openPrimeR for multiplex amplification of highly diverse templates. J Immunol Methods 2020; 480:112752. [PMID: 31991148 DOI: 10.1016/j.jim.2020.112752] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/19/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022]
Abstract
To study the diversity of immune receptors and pathogens, multiplex PCR has become a central approach in research and diagnostics. However, insufficient primer design against highly diverse templates often prevents amplification and therefore limits the correct understanding of biological processes. Here, we present openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers. openPrimeR provides a functional and intuitive interface and uses either a greedy algorithm or an integer linear program to compute the minimal set of primers that performs full target coverage. As proof of concept, we used openPrimeR to find optimal primer sets for the amplification of highly mutated immunoglobulins. Comprehensive analyses on specifically generated immunoglobulin variable gene segment libraries resulted in the composition of highly effective primer sets (oPR-IGHV, oPR-IGKV and oPR-IGLV) that demonstrated to be particularly suitable for the isolation of novel human antibodies.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Nathalie Lehnen
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Domnica Luca
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Kanika Jain
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany; Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany; Medical Faculty, University of Tübingen, 72076 Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.
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Döring M, Kreer C, Lehnen N, Klein F, Pfeifer N. Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features. Sci Rep 2019; 9:10748. [PMID: 31341211 PMCID: PMC6656877 DOI: 10.1038/s41598-019-47173-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/10/2019] [Indexed: 11/09/2022] Open
Abstract
Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efficiently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplification status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifies a template given their nucleotide sequences. The model suggests that the free energy of annealing, ΔG, is the key driver of amplification (p = 7.35e-12) and that 3' mismatches should be considered in dependence on ΔG and the mismatch closest to the 3' terminus (p = 1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR ( http://openPrimeR.mpi-inf.mpg.de ).
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Affiliation(s)
- Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Christoph Kreer
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
| | - Nathalie Lehnen
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
- German Center for Infection Research, Cologne-Bonn Partner Site, Cologne, Germany
| | - Florian Klein
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
- German Center for Infection Research, Cologne-Bonn Partner Site, Cologne, Germany
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany.
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Medical Faculty, Geissweg 5, University of Tübingen, 72076, Tübingen, Germany.
- German Center for Infection Research, Tübingen Partner Site, Tübingen, Germany.
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Jaing C, Thissen JB, Gardner S, McLoughlin K, Slezak T, Bossart GD, Fair PA. Pathogen surveillance in wild bottlenose dolphins Tursiops truncatus. DISEASES OF AQUATIC ORGANISMS 2015; 116:83-91. [PMID: 26480911 DOI: 10.3354/dao02917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The number and prevalence of diseases is rapidly increasing in the marine ecosystem. Although there is an increase in the number of marine diseases observed world-wide, current understanding of the pathogens associated with marine mammals is limited. An important need exists to develop and apply platforms for rapid detection and characterization of pathogenic agents to assess, prevent and respond to disease outbreaks. In this study, a broad-spectrum molecular detection technology capable of detecting all sequenced microbial organisms, the Lawrence Livermore Microbial Detection Array, was used to assess the microbial agents that could be associated with wild Atlantic dolphins. Blowhole, gastric, and fecal samples from 8 bottlenose dolphins were collected in Charleston, SC, as part of the dolphin assessment effort. The array detected various microbial agents from the dolphin samples. Clostridium perfringens was most prevalent in the samples surveyed using the microarray. This pathogen was also detected using microbiological culture techniques. Additionally, Campylobacter sp., Staphylococcus sp., Erwinia amylovora, Helicobacter pylori, and Frankia sp. were also detected in more than one dolphin using the microarray, but not in culture. This study provides the first survey of pathogens associated with 3 tissue types in dolphins using a broad-spectrum microbial detection microarray and expands insight on the microbial community profile in dolphins.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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Kim H, Kang N, Chon KW, Kim S, Lee N, Koo J, Kim MS. MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR. Nucleic Acids Res 2015; 43:e130. [PMID: 26109350 PMCID: PMC4787749 DOI: 10.1093/nar/gkv632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 06/05/2015] [Indexed: 11/24/2022] Open
Abstract
Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That approach is inconvenient for many target sequences of quantitative PCR (qPCR) due to considering the same stringent and allele-invariant constraints. To address this issue, we propose an entirely new method called MRPrimer that can design all feasible and valid primer pairs existing in a DNA database at once, while simultaneously checking a multitude of filtering constraints and validating primer specificity. Furthermore, MRPrimer suggests the best primer pair for each target sequence, based on a ranking method. Through qPCR analysis using 343 primer pairs and the corresponding sequencing and comparative analyses, we showed that the primer pairs designed by MRPrimer are very stable and effective for qPCR. In addition, MRPrimer is computationally efficient and scalable and therefore useful for quickly constructing an entire collection of feasible and valid primers for frequently updated databases like RefSeq. Furthermore, we suggest that MRPrimer can be utilized conveniently for experiments requiring primer design, especially real-time qPCR.
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Affiliation(s)
- Hyerin Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - NaNa Kang
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Kang-Wook Chon
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Seonho Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - NaHye Lee
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - JaeHyung Koo
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Min-Soo Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
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Salazar JK, Wang Y, Yu S, Wang H, Zhang W. Polymerase chain reaction-based serotyping of pathogenic bacteria in food. J Microbiol Methods 2015; 110:18-26. [DOI: 10.1016/j.mimet.2015.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
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Gardner SN, Jaing CJ. Bioinformatics for microbial genotyping of equine encephalitis viruses, orthopoxviruses, and hantaviruses. J Virol Methods 2013; 193:112-20. [PMID: 23714768 DOI: 10.1016/j.jviromet.2013.04.019] [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: 08/17/2012] [Revised: 04/18/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Microbial genotyping is essential for forensic discrimination of pathogen strains, tracing epidemics, and understanding evolutionary processes. Phylogenetic analyses were performed and genotyping assays designed for five viral species complexes or genera: Western, Eastern, and Venezuelan equine encephalitis viruses, hantavirus segments L, M, and S, and orthopoxviruses. For each group, sequence alignments and phylogenetic trees were built. PCR signatures composed of primer pairs or TaqMan™ triplets were designed and mapped to nodes of the trees for sub-type or strain specific PCR-based identification. In addition, single nucleotide polymorphisms (SNPs) were identified and mapped to trees, and SNP microarray probes were designed to enable highly multiplexed genotyping of an unsequenced sample by hybridization. SNP-based trees corresponded well with MSA trees. Near-perfect isolate resolution was possible for all viruses analyzed computationally using either SNPs or PCR signatures. More tree nodes were represented by SNP loci than by PCR signatures, as PCR signatures often represented subsets of strains not corresponding to a branch. However, while PCR genotyping is possible, the number of PCR signatures needed to characterize an unknown can be very large. SNP microarrays are a suitable alternative, as arrays enable highly multiplexed, high resolution genotyping of an unknown in a single hybridization assay.
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Affiliation(s)
- Shea N Gardner
- Global Security, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States.
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8
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Gemi: PCR primers prediction from multiple alignments. Comp Funct Genomics 2012; 2012:783138. [PMID: 23316117 PMCID: PMC3535827 DOI: 10.1155/2012/783138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/19/2012] [Indexed: 12/31/2022] Open
Abstract
Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size.
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Hysom DA, Naraghi-Arani P, Elsheikh M, Carrillo AC, Williams PL, Gardner SN. Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments. PLoS One 2012; 7:e34560. [PMID: 22485178 PMCID: PMC3317645 DOI: 10.1371/journal.pone.0034560] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 03/05/2012] [Indexed: 11/18/2022] Open
Abstract
PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-~100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux.
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Affiliation(s)
- David A. Hysom
- Computations, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Pejman Naraghi-Arani
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Maher Elsheikh
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - A. Celena Carrillo
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Peter L. Williams
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, United States of America
| | - Shea N. Gardner
- Computations, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail:
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Leung AKW, Nagai K, Li J. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Nature 2011; 473:536-9. [PMID: 21516107 PMCID: PMC3103711 DOI: 10.1038/nature09956] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 02/17/2011] [Indexed: 11/12/2022]
Abstract
The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B', SmD1, SmD2, SmD3, SmE, SmF and SmG) in common. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle. Core domain formation is a prerequisite for re-import into the nucleus, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 Å resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE-SmG-SmD3-SmB-SmD1-SmD2-SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 Å resolution reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.
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Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. J Virol 2010; 84:6033-40. [PMID: 20375174 DOI: 10.1128/jvi.02690-09] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Metagenomics and a panmicrobial microarray were used to examine eight live-attenuated viral vaccines. Viral nucleic acids in trivalent oral poliovirus (OPV), rubella, measles, yellow fever, varicella-zoster, multivalent measles/mumps/rubella, and two rotavirus live vaccines were partially purified, randomly amplified, and pyrosequenced. Over half a million sequence reads were generated covering from 20 to 99% of the attenuated viral genomes at depths reaching up to 8,000 reads per nucleotides. Mutations and minority variants, relative to vaccine strains, not known to affect attenuation were detected in OPV, mumps virus, and varicella-zoster virus. The anticipated detection of endogenous retroviral sequences from the producer avian and primate cells was confirmed. Avian leukosis virus (ALV), previously shown to be noninfectious for humans, was present as RNA in viral particles, while simian retrovirus (SRV) was present as genetically defective DNA. Rotarix, an orally administered rotavirus vaccine, contained porcine circovirus-1 (PCV1), a highly prevalent nonpathogenic pig virus, which has not been shown to be infectious in humans. Hybridization of vaccine nucleic acids to a panmicrobial microarray confirmed the presence of endogenous retroviral and PCV1 nucleic acids. Deep sequencing and microarrays can therefore detect attenuated virus sequence changes, minority variants, and adventitious viruses and help maintain the current safety record of live-attenuated viral vaccines.
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Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Hang X, Wang X, Zhao D, Zhang C. MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinformatics 2010; 11:143. [PMID: 20298595 PMCID: PMC2858037 DOI: 10.1186/1471-2105-11-143] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 03/18/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility. RESULTS A program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2x to 5x plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy), which has 79 exons, for 20x, 20x, 20x, 14x, and 5x plex PCR reactions in five tubes to detect underlying exon deletions. CONCLUSIONS MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.
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Affiliation(s)
- Zhiyong Shen
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, PR China
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