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Novel single nucleotide polymorphisms in the heat shock protein 70.1 gene in South African Nguni crossbred cattle. Trop Anim Health Prod 2019; 52:893-901. [DOI: 10.1007/s11250-019-02088-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/11/2019] [Indexed: 01/27/2023]
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2
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Wu M, Cong F, Zhu Y, Lian Y, Chen M, Huang R, Guo P. Multiplex Detection of Five Canine Viral Pathogens for Dogs as Laboratory Animals by the Luminex xTAG Assay. Front Microbiol 2018; 9:1783. [PMID: 30174654 PMCID: PMC6107692 DOI: 10.3389/fmicb.2018.01783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/16/2018] [Indexed: 01/07/2023] Open
Abstract
More and more dogs have been used as a disease model for medical research and drug safety evaluation. Therefore, it is important to make sure that the dogs and their living houses are special pathogen free. In this study, the development and evaluation of a Luminex xTAG assay for simultaneous detection of five canine viruses was carried out, including canine distemper virus, canine parvovirus, canine parainfluenza virus, canine adenovirus, and rabies virus. Assay specificity was accomplished by targeting conserved genomic regions for each virus. Hybridization between multiplexed PCR products and the labeled fluorescence microspheres was detected in a high throughput format using a Luminex fluorescence reader. The Luminex xTAG assay showed high sensitivity with limits of detection for the five viruses was 100 copies/μL. Specificity of the xTAG assay showed no amplification of canine coronavirus, pseudorabies virus and canine influenza virus indicating that the xTAG assay was specific. Seventy-five clinical samples were tested to evaluate the xTAG assay. The results showed 100% coincidence with the conventional PCR method. This is the first report of a specific and sensitive multiplex Luminex xTAG assay for simultaneous detection of five major canine viral pathogens. This assay will be a useful tool for quality control and environmental monitoring for dogs used as laboratory animals, may even be applied in laboratory epidemiological investigations.
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Affiliation(s)
- Miaoli Wu
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China.,Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yujun Zhu
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yuexiao Lian
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Meili Chen
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Ren Huang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Pengju Guo
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
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3
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Wollhofen R, Axmann M, Freudenthaler P, Gabriel C, Röhrl C, Stangl H, Klar TA, Jacak J. Multiphoton-Polymerized 3D Protein Assay. ACS APPLIED MATERIALS & INTERFACES 2018; 10:1474-1479. [PMID: 29280613 PMCID: PMC5773935 DOI: 10.1021/acsami.7b13183] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/27/2017] [Indexed: 05/08/2023]
Abstract
Multiphoton polymerization (MPP) enables 3D fabrication of micro- and nanoscale devices with complex geometries. Using MPP, we create a 3D platform for protein assays. Elevating the protein-binding sites above the substrate surface allows an optically sectioned readout, minimizing the inevitable background signal from nonspecific protein adsorption at the substrate surface. Two fluorescence-linked immunosorbent assays are demonstrated, the first one relying on streptavidin-biotin recognition and the second one on antibody recognition of apolipoprotein A1, a major constituent of high-density lipoprotein particles. Signal-to-noise ratios exceeding 1000 were achieved. The platform has high potential for 3D multiplexed recognition assays with an increased binding surface for on-chip flow cells.
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Affiliation(s)
- Richard Wollhofen
- Institute of Applied
Physics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Markus Axmann
- Institute of Medical Chemistry, Center
for Pathobiochemistry and Genetics, Medical
University of Vienna, 1090 Vienna, Austria
| | - Peter Freudenthaler
- Upper Austrian University of Applied Sciences, Campus Linz, 4020 Linz, Austria
| | - Christian Gabriel
- Ludwig
Boltzmann Institute for Experimental and Clinical Traumatology, 1220 Vienna, Austria
| | - Clemens Röhrl
- Institute of Medical Chemistry, Center
for Pathobiochemistry and Genetics, Medical
University of Vienna, 1090 Vienna, Austria
| | - Herbert Stangl
- Institute of Medical Chemistry, Center
for Pathobiochemistry and Genetics, Medical
University of Vienna, 1090 Vienna, Austria
| | - Thomas A. Klar
- Institute of Applied
Physics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Jaroslaw Jacak
- Institute of Applied
Physics, Johannes Kepler University Linz, 4040 Linz, Austria
- Upper Austrian University of Applied Sciences, Campus Linz, 4020 Linz, Austria
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4
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Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
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Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
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5
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Lee SH, Choi HB, Yu SY, Chang UJ, Kim CK, Kim HJ. Detection of first-line anti-tuberculosis drug resistance mutations by allele-specific primer extension on a microsphere-based platform. Ann Lab Med 2016. [PMID: 26206684 PMCID: PMC4510500 DOI: 10.3343/alm.2015.35.5.487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Resistance of Mycobacterium tuberculosis to anti-tuberculosis (TB) drugs is almost exclusively due to spontaneous chromosomal mutations in target genes. Rapid detection of drug resistance to both first- and second-line anti-TB drugs has become a key component of TB control programs. Technologies that allow rapid, cost-effective, and high-throughput detection of specific nucleic acid sequences are needed. This study was to develop a high-throughput assay based on allele-specific primer extension (ASPE) and MagPlex-TAG microspheres to detect anti-TB drug resistance mutations. Methods DNA samples from 357 M. tuberculosis clinical isolates and H37Rv were amplified by multiplex PCR using four primer sets, followed by multiplex ASPE using 23 TAG-ASPE primers. The products were sorted on the TAG-ASPE array and detected by using the Luminex xMAP system. Genotypes were also determined by sequencing. Results Genetic drug susceptibility typing by the TAG-ASPE method was 100% concordant with those obtained by sequencing. Compared with phenotypic drug susceptibility testing (DST) as a reference method, the sensitivity and specificity of the TAG-ASPE method were 83% (95% confidence interval [CI], 79-88%) and 97% (95% CI, 90-100%) for isoniazid. For rifampin testing, the sensitivity and specificity were 90% (95% CI, 86-93%) and 100% (95% CI, 99-100%). Also, the sensitivity and specificity were 58% (95% CI, 51-65%) and 86% (95% CI, 79-93%) for ethambutol. Conclusions This study demonstrated the TAG-ASPE method is suitable for highly reproducible, cost-effective, and high-throughput clinical genotyping applications.
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Affiliation(s)
| | | | - Sung Yul Yu
- Department of Pathology, Semyung University, Jecheon, Korea
| | | | - Chang Ki Kim
- Korean Institute of Tuberculosis, Cheongju, Korea
| | - Hee Jin Kim
- Korean Institute of Tuberculosis, Cheongju, Korea
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Cao D, Li CY, Kang YF, Lin Y, Cui R, Pang DW, Tang HW. Dual-component gene detection for H7N9 virus – The combination of optical trapping and bead-based fluorescence assay. Biosens Bioelectron 2016; 86:1031-1037. [DOI: 10.1016/j.bios.2016.07.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/24/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
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7
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Multiplex Technologies. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Jang JP, Baek IC, Choi EJ, Kim TG. Multiplex genotyping of cytokine gene SNPs using fluorescence bead array. PLoS One 2015; 10:e0118008. [PMID: 25689696 PMCID: PMC4331502 DOI: 10.1371/journal.pone.0118008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 01/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.
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Affiliation(s)
- Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
- * E-mail:
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9
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Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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10
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Detection of food spoilage and pathogenic bacteria based on ligation detection reaction coupled to flow-through hybridization on membranes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:156323. [PMID: 24818128 PMCID: PMC4004135 DOI: 10.1155/2014/156323] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/14/2014] [Indexed: 11/17/2022]
Abstract
Traditional culturing methods are still commonly applied for bacterial identification in the food control sector, despite being time and labor intensive. Microarray technologies represent an interesting alternative. However, they require higher costs and technical expertise, making them still inappropriate for microbial routine analysis. The present study describes the development of an efficient method for bacterial identification based on flow-through reverse dot-blot (FT-RDB) hybridization on membranes, coupled to the high specific ligation detection reaction (LDR). First, the methodology was optimized by testing different types of ligase enzymes, labeling, and membranes. Furthermore, specific oligonucleotide probes were designed based on the 16S rRNA gene, using the bioinformatic tool Oligonucleotide Retrieving for Molecular Applications (ORMA). Four probes were selected and synthesized, being specific for Aeromonas spp., Pseudomonas spp., Shewanella spp., and Morganella morganii, respectively. For the validation of the probes, 16 reference strains from type culture collections were tested by LDR and FT-RDB hybridization using universal arrays spotted onto membranes. In conclusion, the described methodology could be applied for the rapid, accurate, and cost-effective identification of bacterial species, exhibiting special relevance in food safety and quality.
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12
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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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Hadd AG, Brown JT, Andruss BF, Ye F, WalkerPeach CR. Adoption of array technologies into the clinical laboratory. Expert Rev Mol Diagn 2014; 5:409-20. [PMID: 15934817 DOI: 10.1586/14737159.5.3.409] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Array-based methods are making substantial contributions to the discovery of disease biomarkers and are fueling the growth of multianalyte testing for disease diagnosis and treatment. The distillation of high-density array results into sets of signature markers promises to improve disease staging, risk stratification and treatment decisions. To accommodate the growing requirement for multiplex testing, clinical laboratories are converting several single-analyte tests into array-based formats. However, adoption of array technologies provides several challenges to the laboratory, which must evaluate these new formats, train laboratory personnel, market the new services and obtain reimbursement for new analytes. Liquid-bead arrays are an attractive format for routine clinical diagnostics due to a combination of appropriate analyte density, simultaneous array decoding and detection, and flexibility for rapid customization. In this review, the suitability of several array platforms to diagnostic testing and applications of liquid-bead arrays for cystic fibrosis testing, multidisease carrier status assays and leukemia subtyping are discussed. As our understanding of the clinical utility of new or established biomarkers and recommendations for testing change, flexibility and adaptability of array platforms will be imperative. Future development of novel assay formats and improved quantitation will expand the number of diseases tested and lead to further integration into the diagnostic laboratory.
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Affiliation(s)
- Andrew G Hadd
- Ambion Diagnostics, 2130 Woodward Street, Austin, TX 78744, USA.
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14
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Abstract
DNA is the only chemistry that allows for molecular recognition on demand. Unlike any other molecular recognition chemistry, DNA enables the simple design and rapid synthesis of molecule sets that will recognize each other and self-assemble into nanostructures. In molecular diagnostics, DNA is used to capture complementary sequences in order to decode complex mixes. Expanding DNA chemistry to include additional base pairs enables a more precise manipulation of nanostructures constructed with DNA. MultiCode technology is that type of expanded DNA chemistry. The technology exploits DNA hydrogen bonding patterns that differ from natural DNA, thereby enabling a simple means of transcending problems that are otherwise unsolvable. Made up of additional base pairs (not simply single bases), MultiCode technology is used today to decode sequences in an orthogonal manner to natural DNA. This review will discuss MultiCode technology and specifically focus on how the technology can be used to build molecular testing platforms.
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15
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Romkes M, Buch SC. Genotyping technologies: application to biotransformation enzyme genetic polymorphism screening. Methods Mol Biol 2014; 1105:99-115. [PMID: 24623222 DOI: 10.1007/978-1-62703-739-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Pharmacogenomics encompasses several major areas: the study of polymorphic variations to drug response and disease susceptibility, identification of the effects of drugs/xenobiotics at the genomic level, and genotype/phenotype associations. The most common type of human genetic variations is single-nucleotide polymorphisms (SNPs). Several novel approaches to detection of SNPs are currently available. The range of new methods includes modifications of several conventional techniques such as PCR, mass spectrometry, and sequencing as well as more innovative technologies such as fluorescence resonance energy transfer and microarrays. The application of each of these techniques is largely dependent on the number of SNPs to be screened and sample size. The current chapter presents an overview of the general concepts of a variety of genotyping technologies with an emphasis on the recently developed methodologies, including a comparison of the advantages, applicability, cost efficiency, and limitations of these methods.
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Affiliation(s)
- Marjorie Romkes
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, 5117 Centre Avenue, Suite 1.32e, Pittsburgh, PA, 15213, USA,
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16
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Longuet H, Sautenet B, Gatault P, Thibault G, Barbet C, Marliere JF, Halimi JM, Lebranchu Y, Baron C, Büchler M. Risk factors for impaired CD4+ T-cell reconstitution following rabbit antithymocyte globulin treatment in kidney transplantation. Transpl Int 2013; 27:271-9. [PMID: 24279588 PMCID: PMC4282399 DOI: 10.1111/tri.12249] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 07/28/2013] [Accepted: 11/23/2013] [Indexed: 12/29/2022]
Abstract
To describe long-term CD4+ T-cell reconstitution after rabbit antithymocyte globulin (rATG) treatment and identify predictive factors following kidney transplantation. A single-center retrospective study analyzed lymphocyte subsets in rATG-treated kidney transplant recipients (1986–2009). 589 patients were analyzed (maximum follow-up 21 years). A comparator group (n = 298) received an anti-IL-2 receptor monoclonal antibody. CD4+ T-cell lymphopenia (<200/mm3) was present in 48.5%, 9.2%, 6.7%,2.0%, and 0% of patients at one, three, five, 10, and 20 years post-transplant, respectively. CD4+ T-cell count increased during the first 10 years but remained below the pretransplant count even after 20 years. At 1, 3, and 6 months post-transplant, mean CD4+ T-cell count was significantly lower in patients with CD4+ T-cell lymphopenia at 12 months versus patients without lymphopenia. On multivariate analyses, significant independent predictors for long-term impaired CD4 T-cell reconstitution were recipient age, pretransplant CD4+ T-cell count, 12-month CD4+ T-cell count, and tacrolimus or MMF therapy. Recipient age >40 years was identified as a cutoff point. CD4+ T-cell reconstitution following rATG treatment remains impaired even after 21 years. Most risk factors for long-term impaired CD4+ T-cell reconstitution may be evaluated pretransplant or are modifiable post-transplant.
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Affiliation(s)
- Hélène Longuet
- Department of Nephrology and Clinical Immunology, CHRU Tours, Tours, France
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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Detection and characterization of pathogenic vibrios in shellfish by a Ligation Detection Reaction-Universal Array approach. Int J Food Microbiol 2012; 153:474-82. [DOI: 10.1016/j.ijfoodmicro.2011.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 09/23/2011] [Accepted: 11/11/2011] [Indexed: 11/23/2022]
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19
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YOSHINAGA H, NAKANO K, SOH N, IMATO T. AFM-Imaging Diagnosis Method for Single Nucleotide Polymorphism Using Molecular Beacon DNA as an Intramolecular Ligation Template of Target DNA and a Viewable Indicator. ANAL SCI 2012; 28:939-45. [DOI: 10.2116/analsci.28.939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hisao YOSHINAGA
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | - Koji NAKANO
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | | | - Toshihiko IMATO
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
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Thiollet S, Higson S, White N, Morgan SL. Investigation and Development of Quantum Dot-Encoded Microsphere Bioconjugates for DNA Detection by Flow Cytometry. J Fluoresc 2011; 22:685-97. [DOI: 10.1007/s10895-011-1004-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/18/2011] [Indexed: 12/01/2022]
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21
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Giestas L, Lima JC, Baptista PV. Coupling single base extension to a spectral codification tool for increased throughput screening. J Biotechnol 2011; 154:199-204. [DOI: 10.1016/j.jbiotec.2011.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/09/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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22
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Lee J, Jung J, Park S, Chen J, Choi J, Hyun J. Microarray of stimuli-responsive microbeads for duplexed immunoassay. BIOCHIP JOURNAL 2011. [DOI: 10.1007/s13206-011-5209-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Gassman NR, Nelli JP, Dutta S, Kuhn A, Bonin K, Pianowski Z, Winssinger N, Guthold M, Macosko JC. Selection of bead-displayed, PNA-encoded chemicals. J Mol Recognit 2010; 23:414-22. [PMID: 19957300 DOI: 10.1002/jmr.1007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lack of efficient identification and isolation methods for specific molecular binders has fundamentally limited drug discovery. Here, we have developed a method to select peptide nucleic acid (PNA) encoded molecules with specific functional properties from combinatorially generated libraries. This method consists of three essential stages: (1) creation of a Lab-on-Bead library, a one-bead, one-sequence library that, in turn, displays a library of candidate molecules, (2) fluorescence microscopy-aided identification of single target-bound beads and the extraction--wet or dry--of these beads and their attached candidate molecules by a micropipette manipulator, and (3) identification of the target-binding candidate molecules via amplification and sequencing. This novel integration of techniques harnesses the sensitivity of DNA detection methods and the multiplexed and miniaturized nature of molecule screening to efficiently select and identify target-binding molecules from large nucleic acid encoded chemical libraries. Beyond its potential to accelerate assays currently used for the discovery of new drug candidates, its simple bead-based design allows for easy screening over a variety of prepared surfaces that can extend this technique's application to the discovery of diagnostic reagents and disease markers.
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Affiliation(s)
- Natalie R Gassman
- Department of Physics, Wake Forest University, Winston Salem, NC, USA
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25
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Lauri A, Castiglioni B, Morabito S, Tozzoli R, Consolandi C, Mariani P. A tool based on Ligation Detection Reaction-Universal Array (LDR-UA) for the characterization of VTEC by identification of virulence-associated and serogroup-specific genes. Mol Cell Probes 2010; 25:35-43. [PMID: 20969949 DOI: 10.1016/j.mcp.2010.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/30/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
Abstract
Verocytoxigenic Escherichia coli (VTEC) are zoonotic pathogens whose natural reservoir is represented by ruminants, particularly cattle. Infections are mainly acquired by consumption of undercooked contaminated food of animal origin, contact with infected animals and contaminated environment. VTEC O157 is the most frequently isolated serogroup from cases of human disease, however, other VTEC serogroups, such as O26, O111, O145 and O103, are increasingly reported as causing Hemolytic Uremic Syndrome (HUS) worldwide. The identification of VTEC is troublesome, hindering the development of effective prevention strategies. In fact, VTEC are morphologically indistinguishable from harmless E. coli and their pathogenic potential is not strictly dependent on the serogroup, but relies on the presence of a collection of virulence genes. We developed a diagnostic tool for VTEC based on the Ligation Detection Reaction coupled to Universal Array (LDR-UA) for the simultaneous identification of virulence factors and serogroup-associated genes. The method includes the investigation of 40 sites located in 13 fragments from 12 genes (sodCF1/F2, adfO, terB, ehxA, eae, vtx1, vtx2, ihp1, wzx, wbdI, rfbE, dnaK) and was evaluated by performing a trial on a collection of 67 E. coli strains, both VTEC and VT-negative E. coli, as well as on 25 isolates belonging to other related species. Results of this study showed that the LDR-UA technique was specific in identifying the target microorganism. Moreover, due to its higher throughput, the LDR-UA can be a valid and cheaper alternative to real time PCR-based (rt-PCR) methods for VTEC identification.
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Lauri A, Castiglioni B, Severgnini M, Gorni C, Mariani P. A method based on the ligation detection reaction–universal array (LDR–UA) for the detection and characterization of Listeria and Campylobacter strains. Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1353-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Jenkins S, Gibson N. High-throughput SNP genotyping. Comp Funct Genomics 2010; 3:57-66. [PMID: 18628885 PMCID: PMC2447245 DOI: 10.1002/cfg.130] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2001] [Accepted: 11/19/2001] [Indexed: 12/24/2022] Open
Abstract
Whole genome approaches using single nucleotide polymorphism (SNP) markers have the
potential to transform complex disease genetics and expedite pharmacogenetics research.
This has led to a requirement for high-throughput SNP genotyping platforms.
Development of a successful high-throughput genotyping platform depends on coupling
reliable assay chemistry with an appropriate detection system to maximise efficiency with
respect to accuracy, speed and cost. Current technology platforms are able to deliver
throughputs in excess of 100 000 genotypes per day, with an accuracy of >99%, at a cost
of 20–30 cents per genotype. In order to meet the demands of the coming years, however,
genotyping platforms need to deliver throughputs in the order of one million genotypes per
day at a cost of only a few cents per genotype. In addition, DNA template requirements
must be minimised such that hundreds of thousands of SNPs can be interrogated using a
relatively small amount of genomic DNA. As such, it is predicted that the next generation
of high-throughput genotyping platforms will exploit large-scale multiplex reactions and
solid phase assay detection systems.
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Affiliation(s)
- Suzanne Jenkins
- R&D Genetics, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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29
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Wan Y, Lao R, Liu G, Song S, Wang L, Li D, Fan C. Multiplexed Electrochemical DNA Sensor for Single-Nucleotide Polymorphism Typing by Using Oligonucleotide-Incorporated Nonfouling Surfaces. J Phys Chem B 2010; 114:6703-6. [DOI: 10.1021/jp100871u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Wan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Ruojun Lao
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Gang Liu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Lihua Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Di Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
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30
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Ginya H, Matsushita R, Yohda M. Quantification and improvement of error rate during ligase detection reaction. J Biosci Bioeng 2010; 109:202-4. [DOI: 10.1016/j.jbiosc.2009.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 07/17/2009] [Accepted: 07/17/2009] [Indexed: 11/28/2022]
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31
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Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 2010; 22:611-33. [PMID: 19822891 DOI: 10.1128/cmr.00019-09] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.
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32
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Deng W, Drozdowicz-Tomsia K, Jin D, Goldys EM. Enhanced flow cytometry-based bead immunoassays using metal nanostructures. Anal Chem 2009; 81:7248-55. [PMID: 19715357 DOI: 10.1021/ac900947h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While the principle of fluorescence enhancement of metal nanostructures is well-known, the utility of this effect in practical methodologies used in analytical laboratories remains to be established. In this work, we explore the advantage of fluorescence enhancement for flow cytometry. We report the observation of metal-enhanced fluorescence emission of fluorophores located on the surface of silica beads coated with nanostructured silver, suitable for flow cytometry detection. The fluorescence enhancement was investigated using a model AlexaFluor 430 IgG immunoassay and AlexaFluor 430 labeling. Approximately 8.5-fold and 10.1-fold higher fluorescence intensities at 430 nm excitation were, respectively, observed from silvered approximately 400 nm and 5 microm silica beads deposited on glass as compared to the control sample. The 400 nm and 5 microm beads were compatible with the flow cytometry readout, although lower enhancement factors of 3.0 and 3.7 were obtained. We show that such values are consistent with less favorable overlap of the plasmon resonance in silver nanostructures with 488 nm excitation wavelength used in the flow cytometry experiment. We, thus, demonstrated that the silvered silica beads are able to provide intensified fluorescence signals in flow cytometry which can improve the sensitivity of flow cytometry-based bioassay systems.
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Affiliation(s)
- Wei Deng
- Department of Engineering and Physics, Macquarie University, North Ryde 2109 NSW, Australia
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33
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Purcell CM, Harrison JS, Edmands S. Isolation and characterization of 10 polymorphic microsatellite markers from striped marlin, Tetrapturus audax. Mol Ecol Resour 2009; 9:1556-9. [PMID: 21564958 DOI: 10.1111/j.1755-0998.2009.02709.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the isolation and characterization of 10 microsatellite loci for striped marlin, Tetrapturus audax. Thirty individuals from each of four locations revealed that all loci were polymorphic with two to 31 alleles per locus. Observed levels of heterozygosity ranged from 0.3000 to 0.9667. Significant deviations from Hardy-Weinberg equilibrium were detected in two loci, TA105 in Hawaii and New Zealand and TA155 in Hawaii, and null alleles may be present in loci TA105 and TA155 in those locations, and in locus TA193 in Mexico. No significant linkage disequilibrium was detected in any pairwise-locus comparison.
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Affiliation(s)
- C M Purcell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA Department of Biology, Georgia Southern University, Statesboro, GA 30460, USA
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34
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Cremonesi P, Pisoni G, Severgnini M, Consolandi C, Moroni P, Raschetti M, Castiglioni B. Pathogen detection in milk samples by ligation detection reaction-mediated universal array method. J Dairy Sci 2009; 92:3027-39. [DOI: 10.3168/jds.2008-1773] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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The single-nucleotide primer extension (SNuPE) method for the multiplex detection of various DNA sequences: from detection of point mutations to microbial ecology. Biochem Soc Trans 2009; 37:454-9. [PMID: 19290881 DOI: 10.1042/bst0370454] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Methods based on SNuPE (single-nucleotide primer extension) have become invaluable tools for the rapid and highly specific detection of point mutations and single-nucleotide polymorphisms in the field of human genetics. In the primer extension reaction, a DNA polymerase is used to label a specific primer hybridized to the target sequence by incorporating a single labelled ddNTP (dideoxynucleotide). This labelling provides not only information about the complementary nucleotide of interest in the opposite strand but also a semiquantitative analysis of the sequence targeted by the primer. Since several subdisciplines of microbiology increasingly require cultivation-independent molecular screening tools for elucidating differences between either strains or community structures based on sequence variations of marker genes, SNuPE offers a promising alternative to the existing tool box. The present review describes the method in detail and reports the state-of-the-art applications of this technique both in the field of nucleic acid detections in human genetics and in microbiology.
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36
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Wang WP, Zhang RH, Wu P, Wang S, Li R. Estimation of allele frequency in pooled DNA by using PCR–RFLP combined with microchip electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1603-6. [DOI: 10.1016/j.jchromb.2009.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 03/28/2009] [Accepted: 04/01/2009] [Indexed: 11/25/2022]
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37
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Lee J, Kim O, Jung J, Na K, Heo P, Hyun J. Simple fabrication of a smart microarray of polystyrene microbeads for immunoassay. Colloids Surf B Biointerfaces 2009; 72:173-80. [PMID: 19410434 DOI: 10.1016/j.colsurfb.2009.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/24/2009] [Accepted: 03/30/2009] [Indexed: 11/25/2022]
Abstract
We describe a simple method to fabricate an array of polystyrene microbeads (PS microbeads) conjugated with an elastin-like polypeptide (ELP) on a glass surface using a removable polymer template (RPT). A thin layer of adhesive was spun-cast on glass and cured by UV radiation. Micropatterns of an RPT were then transferred onto the surface by microcontact printing. The adhesion of PS microbeads on the surface depended on the adhesion performance of the adhesive layer, which could be adjusted by irradiation time. An array of PS microbeads conjugated with ELP was used for a smart immunoassay of prostate-specific antigen (PSA), a cancer marker. By controlling the phase transition of ELP molecules, PSA molecules were selectively adhered or released from the bead surface. The selective and reversible binding of PSA molecules on the bead surface was characterized with fluorescence microscopy.
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Affiliation(s)
- Jonghwan Lee
- Department of Biosystems and Biomaterials Science and Engineering, Seoul National University, Seoul 151-742, Republic of Korea
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38
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Glynne-Jones P, J Boltryk R, Hill M, Zhang F, Dong L, Wilkinson JS, Melvin T, R Harris N, Brown T. Flexible acoustic particle manipulation device with integrated optical waveguide for enhanced microbead assays. ANAL SCI 2009; 25:285-91. [PMID: 19212067 DOI: 10.2116/analsci.25.285] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Realisation of a device intended for the manipulation and detection of bead-tagged DNA and other bio-molecules is presented. Acoustic radiation forces are used to manipulate polystyrene micro-beads into an optical evanescent field generated by a laser pumped ion-exchanged waveguide. The evanescent field only excites fluorophores brought within approximately 100 nm of the waveguide, allowing the system to differentiate between targets bound to the beads and those unbound and still held in suspension. The radiation forces are generated in a standing-wave chamber that supports multiple acoustic modes, permitting particles to be both attracted to the waveguide surface and also repelled. To provide further control over particle position, a novel method of switching rapidly between different acoustic modes is demonstrated, through which particles are manipulated into an arbitrary position within the chamber. A novel type of assay is presented: a mixture of streptavidin coated and control beads are driven towards a biotin functionalised surface, then a repulsive force is applied, making it possible to determine which beads became bound to the surface. It is shown that the quarter-wave mode can enhance bead to surface interaction, overcoming potential barriers caused by surface charges. It is demonstrated that by measuring the time of flight of a microsphere across the device the bead size can be determined, providing a means of multiplexing the detection, potentially detecting a range of different target molecules, or varying bead mass.
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Affiliation(s)
- Peter Glynne-Jones
- School of Engineering Sciences, University of Southampton, SO17 1BJ, UK.
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39
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Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem. Electrophoresis 2009; 29:4130-40. [PMID: 18991264 DOI: 10.1002/elps.200800097] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PCR experiments using DNA primers forming mismatch pairing with template lambda DNA at the 3' end were carried out in order to develop allele-specific primers capable of detecting SNP in genomes without generating pseudopositive amplification products, and thus avoiding the so-called pseudopositive problem. Detectable amounts of PCR products were obtained when primers forming a single or two mismatch pairings at the 3' end were used. In particular, 3' terminal A/C or T/C (primer/template) mismatches tended to allow PCR amplification to proceed, resulting in pseudopositive results in many cases. While less PCR product was observed for primers forming three terminal mismatch pairings, target DNA sequences were efficiently amplified by primers forming two mismatch pairings next to the terminal G/C base pairing. These results indicate that selecting a primer having a 3' terminal nucleotide that recognizes the SNP nucleotide and the next two nucleotides that form mismatch pairings with the template sequence can be used as an allele-specific primer that eliminates the pseudopositive problem. Trials with the human ABO genes demonstrated that this primer design is also useful for detecting a single base pair difference in gene sequences with a signal-to-noise ratio of at least 45.
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40
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Appleby N, Edwards D, Batley J. New technologies for ultra-high throughput genotyping in plants. Methods Mol Biol 2009; 513:19-39. [PMID: 19347650 DOI: 10.1007/978-1-59745-427-8_2] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready marker technology (MRT); DArT genotyping; SNP genotyping using the Invader assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex system, and Illumina GoldenGate and Infinium methods.
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Affiliation(s)
- Nikki Appleby
- Australian Centre for Plant Functional Genomics, Institute for Molecular Biosciences and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, Australia
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41
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Deshpande A, Valdez Y, Nolan JP. Multiplexed SNP genotyping using primer single-base extension (SBE) and microsphere arrays. ACTA ACUST UNITED AC 2008; Chapter 13:Unit13.4. [PMID: 18770820 DOI: 10.1002/0471142956.cy1304s34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Single-nucleotide polymorphisms (SNPs), genome sites with single-base sequence differences between individual chromosomes, are the most common type of genetic variation. Single-base changes can result in disease phenotypes, confer susceptibility or resistance to toxins or pathogens, or serve as markers for distinct allelic segments of DNA, making SNPs an important emerging tool in both basic and clinical research. This unit presents detailed protocols for multiplexed SNP genotyping using primer single-base extension (SBE) adapted to microspheres and flow cytometry. The methods described are best suited for typing a modest number of SNPs in a large number of samples. The Basic Protocol describes extension of the genotyping primers by one nucleotide, a labeled dideoxyribonucleotide that reveals the nucleotide base at that position on the template strand. The extended primers are then captured onto microspheres bearing an oligonucleotide "address" that is the reverse complement of a sequence on the 5' end of the genotyping primers and subsequently measured using flow cytometry.
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Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, Briley LP, Maruyama Y, Waterworth DM, Waeber G, Vollenweider P, Oksenberg JR, Hauser SL, Stirnadel HA, Kooner JS, Chambers JC, Jones B, Mooser V, Bustamante CD, Roses AD, Burns DK, Ehm MG, Lai EH. The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 2008; 83:347-58. [PMID: 18760391 DOI: 10.1016/j.ajhg.2008.08.005] [Citation(s) in RCA: 244] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 08/08/2008] [Accepted: 08/08/2008] [Indexed: 02/05/2023] Open
Abstract
Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP).
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Rantala A, Rizzi E, Castiglioni B, de Bellis G, Sivonen K. Identification of hepatotoxin-producing cyanobacteria by DNA-chip. Environ Microbiol 2008; 10:653-64. [DOI: 10.1111/j.1462-2920.2007.01488.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Technical standards and guidelines for reproductive screening in the Ashkenazi Jewish population. Genet Med 2008; 10:57-72. [PMID: 18197058 DOI: 10.1097/gim.0b013e31815f6eac] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
DISCLAIMER These Technical Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular standard or guidelines was adopted, and to consider other relevant medical and scientific information that becomes available after that date.
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45
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Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ. Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping. BMC Genomics 2008; 9:80. [PMID: 18282271 PMCID: PMC2275739 DOI: 10.1186/1471-2164-9-80] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 02/18/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite (SSR) and single nucleotide polymorphism (SNP) markers are widely used in plant breeding and genomic research. Thus, methods to improve the speed and efficiency of SSR and SNP genotyping are highly desirable. Here we describe a new method for multiplex PCR that facilitates fluorescence-based SSR genotyping and the multiplexed preparation of DNA templates for SNP assays. RESULTS We show that multiplex-ready PCR can achieve a high (92%) success rate for the amplification of published sequences under standardised reaction conditions, with a PCR specificity comparable to that of conventional PCR methods. We also demonstrate that multiplex-ready PCR supports an improved level of multiplexing in plant genomes of varying size and ploidy, without the need to carefully optimize assay conditions. Several advantages of multiplex-ready PCR for SSR and SNP genotyping are demonstrated and discussed. These include the uniform amplification of target sequences within multiplexed reactions and between independent assays, and the ability to label amplicons during PCR with specialised moieties such fluorescent dyes and biotin. CONCLUSION Multiplex-ready PCR provides several technological advantages that can facilitate fluorescence-based SSR genotyping and the multiplexed preparation of DNA templates for SNP assays. These advantages can be captured at several points in the genotyping process, and offer considerable cost and labour savings. Multiplex-ready PCR is broadly applicable to plant genomics and marker assisted breeding, and should be transferable to any animal or plant species.
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Affiliation(s)
- Matthew J Hayden
- Molecular Plant Breeding CRC, PMB 1, Glen Osmond, SA, 5064, Australia.
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Li CX, Pan Q, Guo YG, Li Y, Gao HF, Zhang D, Hu H, Xing WL, Mitchelson K, Xia K, Dai P, Cheng J. Construction of a multiplex allele-specific PCR-based universal array (ASPUA) and its application to hearing loss screening. Hum Mutat 2008; 29:306-14. [PMID: 18161878 PMCID: PMC7165727 DOI: 10.1002/humu.20622] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We demonstrate a new method, using a universal array approach termed multiplex allele‐specific PCR‐based universal array (ASPUA), and applied it to the mutation detection of hereditary hearing loss. Mutations in many different genes may be the cause of hereditary hearing loss, a sensory defect disorder. Effective methods for genetic diagnosis are clearly needed to provide clinical management. Owing to the broad genetic basis of this condition, clinical assay of such a highly heterogeneous disorder is expensive and time consuming. In ASPUA, the allele discrimination reaction is carried out in solution by multiplex allele‐specific PCR and a universal solid phase array with different tag probes is used to display the PCR result. The purpose of developing the ASPUA platform was to utilize the rapidity and simplicity of the amplification refractory mutation system (ARMS) with the detection power of microarray hybridization. This is the first report of the combination of these two technologies, which allow for the completion of allele‐specific detection of 11 of the most frequent mutations causing hereditary hearing loss in under 5 hr. The ASPUA platform was validated by accurately analyzing 141 patient samples that had been previously genotyped for GJB2, GJB3, SLC26A4, and MTRNR1. In addition, we also developed a simplified assay by using streptavidin‐coated magnetic beads instead of fluorescence for signal display that can be assessed through a conventional light microscope. We demonstrate that the ASPUA platform is rapid, cost‐effective, and easily‐used, and is especially appropriate for mutation detection in clinical genetic diagnostics. Hum Mutat 29(2), 306–314, 2008. © 2007 Wiley‐Liss, Inc.
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Affiliation(s)
- Cai-Xia Li
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing, China
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Application of a microsphere-based array for rapid identification of Acinetobacter spp. with distinct antimicrobial susceptibilities. J Clin Microbiol 2007; 46:612-7. [PMID: 18039798 DOI: 10.1128/jcm.01798-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter spp. have emerged as important nosocomial and multidrug-resistant pathogens in the last decade. A. calcoaceticus, A. baumannii, Acinetobacter genospecies 3, and Acinetobacter genospecies 13TU are genetically closely related and are referred to as the A. calcoaceticus-A. baumannii complex (ACB complex). Distinct Acinetobacter spp. may be associated with differences in antimicrobial susceptibility, so it is important to identify Acinetobacter spp. at the species level. We developed a microsphere-based array that combines an allele-specific primer extension assay and microsphere hybridization for the identification of Acinetobacter spp. This assay can discriminate the 13 different Acinetobacter spp. in less than 8.5 h, and it has high specificity without causing cross-reactivity with 14 other common nosocomial bacterial species. The sensitivity of this assay was 100 A. baumannii cells per ml of blood, and it could discriminate multiple species in various mixture ratios. The developed assay could differentiate clinical Acinetobacter spp. isolates with a 90% identification rate. The antimicrobial susceptibility test showed that A. baumannii isolates were resistant to most antimicrobial agents other than imipenem, while the genospecies 3 and 13TU isolates were more susceptible to most antimicrobial agents, especially ciprofloxacin and ampicillin-sulbactam. These results supported the idea that this assay possibly could be applied to clinical samples and provide accurate species identification, which might be helpful for clinicians when they are treating infections caused by Acinetobacter spp.
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Wilson GD, Marples B. Flow cytometry in radiation research: past, present and future. Radiat Res 2007; 168:391-403. [PMID: 17903043 DOI: 10.1667/rr1042.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Accepted: 05/30/2007] [Indexed: 11/03/2022]
Abstract
Flow cytometry is an invaluable technique in research and clinical laboratories. The technique has been applied extensively to many areas of radiation research at both the experimental and clinical level. In the past few years, there has been a significant increase in the capabilities of modern flow cytometers to undertake multicolor analysis in a user-friendly manner. The developments in cytometric technology are being matched by the rapid development of new reagents, new fluorochromes and new platforms such as bead arrays. These developments are facilitating many new applications in both basic and clinical research that have relevance for many fields of biology, including radiation research. This review provides a historical overview of the application of flow cytometry to radiobiology and an update on how technology and reagents have changed and cites examples of new applications relevant to radiation researchers. In addition, some entirely new flow instrumentation is currently under development that has significant potential for applications in radiation research.
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Affiliation(s)
- George D Wilson
- Department of Radiation Oncology, William Beaumont Hospital, Royal Oak, Michigan 48073, USA.
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