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Abstract
Affinity proteomics, represented by antibody arrays, is a multiplex technology for high-throughput protein expression profiling of crude proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are individually deposited in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified using mainly fluorescence as the mode of detection. The binding pattern is then converted into a relative protein expression map, or protein atlas, delineating the composition of the sample at the molecular level. The technology provides unique opportunities for various applications, such as protein expression profiling, biomarker discovery, disease diagnostics, prognostics, evidence-based therapy selection, and disease monitoring. Here, we describe the generation and use of planar antibody arrays for serum protein profiling.
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Borrebaeck CAK, Sturfelt G, Wingren C. Recombinant antibody microarray for profiling the serum proteome of SLE. Methods Mol Biol 2014; 1134:67-78. [PMID: 24497355 DOI: 10.1007/978-1-4939-0326-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe autoimmune connective tissue disease. Our current knowledge about the serum proteome, or serum biomarker panels, reflecting disease and disease status is still very limited. Affinity proteomics, represented by recombinant antibody arrays, is a novel, multiplex technology for high-throughput protein expression profiling of crude serum proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are deposited one by one in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified. The binding pattern is then converted into a relative protein expression map, or protein map, deciphering the composition of the sample at the molecular level. The methodology provides unique opportunities for delineating serum biomarkers reflecting SLE, thus paving the way for improved diagnosis, classification, and prognosis.
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Affiliation(s)
- Carl A K Borrebaeck
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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53
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Jiang W, Mao YQ, Huang R, Duan C, Xi Y, Yang K, Huang RP. Protein expression profiling by antibody array analysis with use of dried blood spot samples on filter paper. J Immunol Methods 2014; 403:79-86. [DOI: 10.1016/j.jim.2013.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/19/2013] [Accepted: 11/19/2013] [Indexed: 10/26/2022]
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54
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Cretich M, Damin F, Chiari M. Protein microarray technology: how far off is routine diagnostics? Analyst 2014; 139:528-42. [DOI: 10.1039/c3an01619f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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55
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Rostgaard KR, Frederiksen RS, Liu YCC, Berthing T, Madsen MH, Holm J, Nygård J, Martinez KL. Vertical nanowire arrays as a versatile platform for protein detection and analysis. NANOSCALE 2013; 5:10226-35. [PMID: 24062006 DOI: 10.1039/c3nr03113f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein microarrays are valuable tools for protein assays. Reducing spot sizes from micro- to nano-scale facilitates miniaturization of platforms and consequently decreased material consumption, but faces inherent challenges in the reduction of fluorescent signals and compatibility with complex solutions. Here we show that vertical arrays of nanowires (NWs) can overcome several bottlenecks of using nanoarrays for extraction and analysis of proteins. The high aspect ratio of the NWs results in a large surface area available for protein immobilization and renders passivation of the surface between the NWs unnecessary. Fluorescence detection of proteins allows quantitative measurements and spatial resolution, enabling us to track individual NWs through several analytical steps, thereby allowing multiplexed detection of different proteins immobilized on different regions of the NW array. We use NW arrays for on-chip extraction, detection and functional analysis of proteins on a nano-scale platform that holds great promise for performing protein analysis on minute amounts of material. The demonstration made here on highly ordered arrays of indium arsenide (InAs) NWs is generic and can be extended to many high aspect ratio nanostructures.
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Affiliation(s)
- Katrine R Rostgaard
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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Pauly F, Dexlin-Mellby L, Ek S, Ohlin M, Olsson N, Jirström K, Dictor M, Schoenmakers S, Borrebaeck CAK, Wingren C. Protein Expression Profiling of Formalin-Fixed Paraffin-Embedded Tissue Using Recombinant Antibody Microarrays. J Proteome Res 2013; 12:5943-53. [DOI: 10.1021/pr4003245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Frida Pauly
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Linda Dexlin-Mellby
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Sara Ek
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Niclas Olsson
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michael Dictor
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - Carl A. K. Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
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Wingren C. Novel type of protein chip for multiplex detection of autoantibodies. Expert Rev Proteomics 2013; 10:417-20. [PMID: 24088012 DOI: 10.1586/14789450.2013.842900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evaluation of: Akada J, Kamei S, Ito A et al. A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients. Proteome Sci. 11(1), 33 (2013). Unlocking the proteome and delivering biomarkers to the clinic will be critical for early and improved diagnosis and prognosis. Conventional protein microarrays have evolved as a promising proteomic technology with great potential for protein expression profiling in health and disease. In this study, Akada et al. explore a new type of protein chip, interfaced with a dual-color fluorescence-based read-out, for screening of autoantibodies in serum. Uniquely, the recombinant antigens were microarray adapted by molecular design to contain a five-cysteine tag for immobilization and green fluorescent protein for detection (color 1). The engineered antigens were immobilized on in-house-designed maleimide-incorporated diamond-like carbon substrates and subsequently heat treated in a solution of denaturing and reducing agents before any specifically bound serum autoantibodies were detected (color 2). The authors used a 4-plex array targeting hepatocellular carcinoma-related autoantibodies in the sera of hepatitis C virus-positive patients as model system to demonstrate proof-of-concept.
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Affiliation(s)
- Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, SE-22381 Lund, Sweden
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58
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Ierardi V, Ferrera F, Millo E, Damonte G, Filaci G, Valbusa U. Bioactive surfaces for antibody-antigen complex detection by Atomic Force Microscopy. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/439/1/012001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Laing S, Irvine EJ, Hernandez-Santana A, Smith WE, Faulds K, Graham D. Immunoassay Arrays Fabricated by Dip-Pen Nanolithography with Resonance Raman Detection. Anal Chem 2013; 85:5617-21. [DOI: 10.1021/ac4009012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Stacey Laing
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
| | - Eleanore J. Irvine
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
| | - Aaron Hernandez-Santana
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
| | - W. Ewen Smith
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
| | - Karen Faulds
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
| | - Duncan Graham
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow,
G1 1XL, U.K
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60
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Elramady MG, Aly SS, Rossitto PV, Crook JA, Cullor JS. Synergistic effects of lactic acid and sodium dodecyl sulfate to decontaminate Escherichia coli O157:H7 on cattle hide sections. Foodborne Pathog Dis 2013; 10:661-3. [PMID: 23594235 DOI: 10.1089/fpd.2012.1420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The objective of this study was to investigate the antibacterial properties of chitosan acetate (CA), sodium dodecyl sulfate (SDS), lactic acid (LA) and their synergism when combined against a nontoxigenic strain of Escherichia coli O157:H7. Treatments that significantly reduced the concentration of E. coli O157:H7 in vitro by more than two logs were further investigated using a cattle hide decontamination model. In vitro treatments included CA (1% chitosan in 1% acetic acid vol/vol), SDS (1% vol/vol), SDS (2% vol/vol), LA (1% vol/vol), CA-SDS combination (1% chitosan in 1% acetic acid vol/vol mixed with 1% SDS vol/vol), and LA-SDS combination in two different concentrations (1% LA mixed with 1% SDS vol/vol, and 1% LA mixed with 2% SDS vol/vol). Butterfield's Phosphate Buffer water was used as a control. The antibacterial effect of 1% CA solution alone and in combination with 1% SDS in vitro resulted in a 1.8 and 1.7 log colony-forming units (CFU)/mL reduction, respectively (p<0.05). Only 1% LA, 1% SDS, 2% SDS and their combinations resulted in a >2 log reduction in E. coli O157:H7. On hide sections, both 1% LA-1% SDS and 1% LA-2% SDS combinations significantly (p<0.05) reduced E. coli O157:H7 concentration by 4.6 and 4.7 log CFU/ cm(2) greater than the control, respectively. There was no significant difference in the antibacterial effect of 1% LA compared to the control, 2% SDS compared to the control, or 1% LA compared to 2% SDS. Hence, the antibacterial efficacy of 1% LA against E. coli O157:H7 on hide sections was significantly enhanced when combined with 1% SDS. Results of this study support the use of low concentration LA-SDS combination as a hide wash to reduce the risk of E. coli O157:H7 contamination.
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Affiliation(s)
- Mohamed G Elramady
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, California 93274, USA
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61
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Sandström A, Andersson R, Segersvärd R, Löhr M, Borrebaeck CAK, Wingren C. Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures. Proteomics Clin Appl 2013; 6:486-96. [PMID: 22930578 DOI: 10.1002/prca.201200051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Pancreatitis is an inflammatory state of the pancreas, for which high-performing serological biomarkers are lacking. The aim of the present study was to evaluate the use of affinity proteomics for identifying potential markers of disease and stratifying pancreatitis subtypes. EXPERIMENTAL DESIGN High-content, recombinant antibody microarrays were applied for serum protein expression profiling of 113 serum samples from patients with chronic, acute, and autoimmune pancreatitis, as well as healthy controls. The sample groups were compared using supervised classification based on support vector machine analysis. RESULTS This discovery study showed that pancreatitis subtypes could be discriminated with high accuracy. Using unfiltered data, the individual subtypes, as well as the combined pancreatitis cohort, were distinguished from healthy controls with high AUC values (0.96-1.00). Moreover, characteristic protein patterns and AUC values in the range of 0.69-0.95 were observed for the individual pancreatitis entities when compared to each other, and to all other samples combined. CONCLUSIONS AND CLINICAL RELEVANCE This study demonstrated the potential of the antibody microarray approach for stratification of pancreatitis. Distinct candidate multiplex serum biomarker signatures for chronic, acute, and autoimmune pancreatitis were defined, which could enhance our fundamental knowledge of the underlying molecular mechanisms, and potentially lead to improved diagnosis.
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Affiliation(s)
- Anna Sandström
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
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62
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SHA S, YIN Y, GAO XL, HUANG ZR, YU T, ZHENG XD. A New Method of Immobilizing Antibody Probes on Immunochips Based on DNA Hybridization. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60627-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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63
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Manzano-Román R, Díaz-Martín V, González-González M, Matarraz S, Álvarez-Prado AF, LaBaer J, Orfao A, Pérez-Sánchez R, Fuentes M. Self-assembled Protein Arrays from an Ornithodoros moubata Salivary Gland Expression Library. J Proteome Res 2012; 11:5972-82. [DOI: 10.1021/pr300696h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Raul Manzano-Román
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Veronica Díaz-Martín
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Maria González-González
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Angel Francisco Álvarez-Prado
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized
Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-6401, United States
| | - Alberto Orfao
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Ricardo Pérez-Sánchez
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Manuel Fuentes
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
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64
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Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012; 6:548-62. [PMID: 23027439 PMCID: PMC3600421 DOI: 10.1002/prca.201200041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
Abstract
Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology.
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Affiliation(s)
- Heng Zhu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, MD, USA.
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65
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Beuchat LR, Mann DA, Alali WQ. Evaluation of sanitizers for inactivating Salmonella on in-shell pecans and pecan nutmeats. J Food Prot 2012; 75:1930-8. [PMID: 23127701 DOI: 10.4315/0362-028x.jfp-12-133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Chlorine, organic acids, and water extracts of inedible pecan components were tested for effectiveness in killing Salmonella on pecans. In-shell pecans and nutmeats (U.S. Department of Agriculture medium pieces) were immersion inoculated with a mixture of five Salmonella serotypes, dried to 3.7% moisture, and stored at 4°C for 3 to 6 weeks. In-shell nuts were immersed in chlorinated water (200, 400, and 1,000 μg/ml), lactic acid (0.5, 1, and 2%), and levulinic acid (0.5, 1, and 2%) with and without 0.05% sodium dodecyl sulfate (SDS), and a mixed peroxyacid sanitizer (Tsunami 200, 40 μg/ml) for up to 20 min at 21°C. The rate of reduction of free chlorine in conditioning water decreased as the ratio of in-shell nuts/water was increased. The rate of reduction was more rapid when nuts were not precleaned before treatment. The initial population of Salmonella on in-shell nuts (5.9 to 6.3 log CFU/g) was reduced by 2.8 log CFU/g after treating with chlorinated water (1,000 μg/ml). Treatment with 2% lactic acid plus SDS or 2% levulinic acid plus SDS reduced the pathogen by 3.7 and 3.4 log CFU/g, respectively. Lactic and levulinic acids (2%) without SDS were less effective (3.3- and 2.1-log CFU/g reductions, respectively) than acids with SDS. Treatment with Tsunami 200 resulted in a 2.4-log CFU/g reduction. In-shell nuts and nutmeats were immersed in water extracts of ground pecan shucks (hulls), shells, a mixture of shells and pith, and pith. The general order of lethality of extracts to Salmonella was shuck < shell-pith ≤ shell ≤ pith < chlorine (400 μg/ml) and shuck < shell ≤ pith = shell-pith < chlorine (400 μg/ml). Results emphasize the importance of removing soil and dust on in-shell pecans before conditioning in chlorinated water and the need for sanitizers with increased effectiveness in killing Salmonella on pecans.
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Affiliation(s)
- Larry R Beuchat
- Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USA.
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66
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Liu H, Sun L, Wang Y, Lei X, Xu D. Modeling antimicrobial activity of lipopeptides from Bacillus amyloliquefaciens ES-2 against Shewanella putrefaciens in shrimp meat using a response surface method. J Food Prot 2012; 75:1855-8. [PMID: 23043837 DOI: 10.4315/0362-028x.jfp-12-073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacillus amyloliquefaciens ES-2 can produce antimicrobial lipopeptides, including surfactin and fengycin. In this study, the model of antimicrobial activity against Shewanella putrefaciens in shrimp meat by antimicrobial lipopeptides from B. amyloliquefaciens ES-2 was researched by response surface methodology. The results showed that S. putrefaciens had high sensitivity to antimicrobial lipopeptides, which had a MIC of 0.6 mg/ml. A quadratic mathematical model representative of the action of antimicrobial lipopeptides on S. putrefaciens in shrimp meat was developed as a function of concentration, time, and temperature. A reduction of S. putrefaciens cells of over 2 log cycles could be realized when the temperature was below 5.4°C, the time was over 6 h, and the concentration of the lipopeptides was over 0.3 mg/g.
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Affiliation(s)
- Huanming Liu
- School of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
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67
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Leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins. J Bacteriol 2012; 194:6074-87. [PMID: 22961849 DOI: 10.1128/jb.01119-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus Leptospira. The leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. Infection requires adherence to cell surfaces and extracellular matrix components of host tissues. These host-pathogen interactions involve outer membrane proteins (OMPs) expressed on the bacterial surface. In this study, we developed an Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 OMP microarray containing all predicted lipoproteins and transmembrane OMPs. A total of 401 leptospiral genes or their fragments were transcribed and translated in vitro and printed on nitrocellulose-coated glass slides. We investigated the potential of this protein microarray to screen for interactions between leptospiral OMPs and fibronectin (Fn). This approach resulted in the identification of the recently described fibronectin-binding protein, LIC10258 (MFn8, Lsa66), and 14 novel Fn-binding proteins, denoted Microarray Fn-binding proteins (MFns). We confirmed Fn binding of purified recombinant LIC11612 (MFn1), LIC10714 (MFn2), LIC11051 (MFn6), LIC11436 (MFn7), LIC10258 (MFn8, Lsa66), and LIC10537 (MFn9) by far-Western blot assays. Moreover, we obtained specific antibodies to MFn1, MFn7, MFn8 (Lsa66), and MFn9 and demonstrated that MFn1, MFn7, and MFn9 are expressed and surface exposed under in vitro growth conditions. Further, we demonstrated that MFn1, MFn4 (LIC12631, Sph2), and MFn7 enable leptospires to bind fibronectin when expressed in the saprophyte, Leptospira biflexa. Protein microarrays are valuable tools for high-throughput identification of novel host ligand-binding proteins that have the potential to play key roles in the virulence mechanisms of pathogens.
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68
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Borrebaeck CAK. Viewpoints in clinical proteomics: When will proteomics deliver clinically useful information? Proteomics Clin Appl 2012; 6:343-5. [DOI: 10.1002/prca.201200020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Díez P, Dasilva N, González-González M, Matarraz S, Casado-Vela J, Orfao A, Fuentes M. Data Analysis Strategies for Protein Microarrays. MICROARRAYS 2012; 1:64-83. [PMID: 27605336 PMCID: PMC5003438 DOI: 10.3390/microarrays1020064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/31/2012] [Indexed: 01/22/2023]
Abstract
Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.
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Affiliation(s)
- Paula Díez
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Translational Oncology Unit, Instituto de Investigaciones Biomédicas 'Alberto Sols', Spanish National Research Council (CSIC-UAM), 28029 Madrid, Spain.
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
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Cannon JL, Aydin A, Mann AN, Bolton SL, Zhao T, Doyle MP. Efficacy of a levulinic acid plus sodium dodecyl sulfate-based sanitizer on inactivation of human norovirus surrogates. J Food Prot 2012; 75:1532-5. [PMID: 22856583 DOI: 10.4315/0362-028x.11-572] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human noroviruses are the most common etiologic agent of foodborne illness in the United States. The inability to culture human noroviruses in the laboratory necessitates the use of surrogate viruses such as murine norovirus (MNV-1) and feline calicivirus (FCV) for inactivation studies. In this study, a novel sanitizer of organic acid (levulinic acid) plus the anionic detergent sodium dodecyl sulfate (SDS) was evaluated. Viruses were treated with levulinic acid (0.5 to 5%), SDS (0.05 to 2%), or combinations of levulinic acid plus SDS (1:10 solution of virus to sanitizer). MNV-1 inoculated onto stainless steel also was treated with a 5% levulinic acid plus 2% SDS liquid or foaming solution. Log reductions of viruses were determined with a plaque assay. Neither levulinic acid nor SDS alone were capable of inactivating MNV-1 or FCV, resulting in a ≤0.51-log reduction of the infectious virus titer. However, the combination of 0.5% levulinic acid plus 0.5% SDS inactivated both surrogates by 3 to 4.21 log PFU/ml after 1 min of exposure. Similarly, MNV-1 inoculated onto stainless steel was reduced by >1.50 log PFU/ml after 1 min and by >3.3 log PFU/ml after 5 min of exposure to a liquid or foaming solution of 5% levulinic acid plus 2% SDS. The presence of organic matter (up to 10%) in the virus inoculum did not significantly affect sanitizer efficacy. The fact that both of the active sanitizer ingredients are generally recognized as safe to use as food additives by the U.S. Food and Drug Administration further extends its potential in mitigating foodborne disease.
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Affiliation(s)
- Jennifer L Cannon
- Center for Food Safety, University of Georgia, Griffin, GA 30223, USA.
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71
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Wingren C, Sandström A, Segersvärd R, Carlsson A, Andersson R, Löhr M, Borrebaeck CAK. Identification of serum biomarker signatures associated with pancreatic cancer. Cancer Res 2012; 72:2481-90. [PMID: 22589272 DOI: 10.1158/0008-5472.can-11-2883] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pancreatic cancer is an aggressive disease with poor prognosis, due, in part, to the lack of disease-specific biomarkers that could afford early and accurate diagnosis. With a recombinant antibody microarray platform, targeting mainly immunoregulatory proteins, we screened sera from 148 patients with pancreatic cancer, chronic pancreatitis, autoimmune pancreatitis (AIP), and healthy controls (N). Serum biomarker signatures were derived from training cohorts and the predictive power was evaluated using independent test cohorts. The results identified serum portraits distinguishing pancreatic cancer from N [receiver operating characteristics area under the curve (AUC) of 0.95], chronic pancreatitis (0.86), and AIP (0.99). Importantly, a 25-serum biomarker signature discriminating pancreatic cancer from the combined group of N, chronic pancreatitis, and AIP was determined. This signature exhibited a high diagnostic potential (AUC of 0.88). In summary, we present the first prevalidated, multiplexed serum biomarker signature for diagnosis of pancreatic cancer that may improve diagnosis and prevention in premalignant diseases and in screening of high-risk individuals.
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72
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Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries. Proc Natl Acad Sci U S A 2012; 109:E2248-57. [PMID: 22843676 DOI: 10.1073/pnas.1205399109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have selected designed ankyrin repeat proteins (DARPins) from a synthetic library by using ribosome display that selectively bind to the mitogen-activated protein kinase ERK2 (extracellular signal-regulated kinase 2) in either its nonphosphorylated (inactive) or doubly phosphorylated (active) form. They do not bind to other kinases tested. Crystal structures of complexes with two DARPins, each specific for one of the kinase forms, were obtained. The two DARPins bind to essentially the same region of the kinase, but recognize the conformational change within the activation loop and an adjacent area, which is the key structural difference that occurs upon activation. Whereas the rigid phosphorylated activation loop remains in the same form when bound by the DARPin, the more mobile unphosphorylated loop is pushed to a new position. The DARPins can be used to selectively precipitate the cognate form of the kinases from cell lysates. They can also specifically recognize the modification status of the kinase inside the cell. By fusing the kinase with Renilla luciferase and the DARPin to GFP, an energy transfer from luciferase to GFP can be observed in COS-7 cells upon intracellular complex formation. Phosphorylated ERK2 is seen to increase by incubation of the COS-7 cells with FBS and to decrease upon adding the ERK pathway inhibitor PD98509. Furthermore, the anti-ERK2 DARPin is seen to inhibit ERK phosphorylation as it blocks the target inside the cell. This strategy of creating activation-state-specific sensors and kinase-specific inhibitors may add to the repertoire to investigate intracellular signaling in real time.
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73
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Bhagwat AA, Leow YN, Liu L, Dharne M, Kannan P. Role of Anionic Charges of Periplasmic Glucans ofShigella flexneriin Overcoming Detergent Stress. Foodborne Pathog Dis 2012; 9:632-7. [PMID: 22730962 DOI: 10.1089/fpd.2011.1090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Arvind A. Bhagwat
- Environmental Microbial and Food Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland
| | - Yi Ning Leow
- Environmental Microbial and Food Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland
| | - Liu Liu
- Environmental Microbial and Food Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland
| | - Mahesh Dharne
- Environmental Microbial and Food Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland
| | - Porteen Kannan
- Environmental Microbial and Food Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland
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74
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Kristensson M, Olsson K, Carlson J, Wullt B, Sturfelt G, Borrebaeck CA, Wingren C. Design of recombinant antibody microarrays for urinary proteomics. Proteomics Clin Appl 2012; 6:291-6. [DOI: 10.1002/prca.201100055] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Malin Kristensson
- Department of Immunotechnology; Lund University; Lund Sweden
- CREATE Health; Lund University; Lund Sweden
| | - Karolina Olsson
- Department of Immunotechnology; Lund University; Lund Sweden
| | - Joyce Carlson
- Department of Laboratory Medicine, Section of Clinical Chemistry; Lund University; Lund Sweden
| | - Björn Wullt
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology; Skånes University Hospital; Lund Sweden
| | - Gunnar Sturfelt
- Department of Clinical Sciences, Section of Rheumatology; Skånes University Hospital; Lund Sweden
| | - Carl A.K. Borrebaeck
- Department of Immunotechnology; Lund University; Lund Sweden
- CREATE Health; Lund University; Lund Sweden
| | - Christer Wingren
- Department of Immunotechnology; Lund University; Lund Sweden
- CREATE Health; Lund University; Lund Sweden
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75
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Olsson N, James P, Borrebaeck CAK, Wingren C. Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. Mol Cell Proteomics 2012; 11:342-54. [PMID: 22543061 PMCID: PMC3412966 DOI: 10.1074/mcp.m111.016238] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides.
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Affiliation(s)
- Niclas Olsson
- Department of Immunotechnology, Lund University, Lund, Sweden
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76
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Size matters: problems and advantages associated with highly miniaturized sensors. SENSORS 2012; 12:3018-36. [PMID: 22736990 PMCID: PMC3376590 DOI: 10.3390/s120303018] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/23/2012] [Accepted: 02/23/2012] [Indexed: 01/15/2023]
Abstract
There is no doubt that the recent advances in nanotechnology have made it possible to realize a great variety of new sensors with signal transduction mechanisms utilizing physical phenomena at the nanoscale. Some examples are conductivity measurements in nanowires, deflection of cantilevers and spectroscopy of plasmonic nanoparticles. The fact that these techniques are based on the special properties of nanostructural entities provides for extreme sensor miniaturization since a single structural unit often can be used as transducer. This review discusses the advantages and problems with such small sensors, with focus on biosensing applications and label-free real-time analysis of liquid samples. Many aspects of sensor design are considered, such as thermodynamic and diffusion aspects on binding kinetics as well as multiplexing and noise issues. Still, all issues discussed are generic in the sense that the conclusions apply to practically all types of surface sensitive techniques. As a counterweight to the current research trend, it is argued that in many real world applications, better performance is achieved if the active sensor is larger than that in typical nanosensors. Although there are certain specific sensing applications where nanoscale transducers are necessary, it is argued herein that this represents a relatively rare situation. Instead, it is suggested that sensing on the microscale often offers a good compromise between utilizing some possible advantages of miniaturization while avoiding the complications. This means that ensemble measurements on multiple nanoscale sensors are preferable instead of utilizing a single transducer entity.
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77
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Faith NG, Waldron T, Czuprynski CJ. Reduction in resident microflora, and experimentally inoculated Salmonella enterica, on spinach leaves treated with vinegar and canola oil. J Food Prot 2012; 75:567-72. [PMID: 22828283 DOI: 10.4315/0362-028x.jfp-11-337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, we explored the use of vinegar, or vinegar and canola oil as a salad dressing, to reduce bacterial levels on spinach leaves. We found that incubation of spinach leaves with various types of vinegar substantially reduced the predominantly gram-negative microflora. A similar response was observed when spinach leaves were incubated with white vinegar mixed in various proportions with canola oil, as used in salad dressing. We assessed the effects of vinegar, or vinegar and oil, on spinach leaves that had been experimentally inoculated with a cocktail of Salmonella enterica strains. Allowing the mixture to sit at room temperature for at least 20 min resulted in a substantial reduction (up to 2.0 log CFU) in numbers of S. enterica. Vinegar and oil caused a limited reduction in CFU (0.5 log) for spinach leaves experimentally inoculated with a cocktail of Listeria monocytogenes strains. These findings suggest that mixing spinach leaves with vinegar and oil as a salad dressing can reduce the bacterial load associated with the spinach leaves, including Salmonella if it is present.
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78
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Asanov A, Zepeda A, Vaca L. A platform for combined DNA and protein microarrays based on total internal reflection fluorescence. SENSORS 2012; 12:1800-15. [PMID: 22438738 PMCID: PMC3304140 DOI: 10.3390/s120201800] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/13/2012] [Accepted: 02/02/2012] [Indexed: 11/20/2022]
Abstract
We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax.
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Affiliation(s)
- Alexander Asanov
- TIRF Technologies, 951 Aviation Parkway, Suite 700, Morrisville, NC 27560, USA
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.Z.); Tel.: +525-5622-9215 (A.Z.); Fax: +525-5622-9182 (A.Z.)
| | - Angélica Zepeda
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, DF 04510, México
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.Z.); Tel.: +525-5622-9215 (A.Z.); Fax: +525-5622-9182 (A.Z.)
| | - Luis Vaca
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, DF 04510, México; E-Mail:
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79
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Song HY, Zhou X, Hobley J, Su X. Comparative study of random and oriented antibody immobilization as measured by dual polarization interferometry and surface plasmon resonance spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:997-1004. [PMID: 22126088 DOI: 10.1021/la202734f] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Dual polarization interferometry (DPI) is used for a detailed study of antibody immobilization with and without orientation control, using prostate specific antigen (PSA) and its antibody as model. Thiol modified DPI chips were activated by a heterobifunctional cross-linker (sulfo-GMBS). PSA antibody was either directly immobilized via covalent binding or coupled via the Fc-fragment to protein G covalently attached to the activated chip. The direct covalent binding leads to a random antibody orientation and the coupling through protein G leads to an end-on orientation. Ethanolamine (ETH) was used to block remaining active sites following the direct antibody immobilization and protein G immobilization. A homobifunctional cross-linker (BS3) was used to stabilize the antibody layer coupled on protein G. DPI provides a real-time measurement of the stepwise molecular binding processes and gives detailed geometrical and structural values of each layer, i.e., thickness, mass, and density. These values evidence the end-on orientation of closely packed antibody on protein G layer and reveal structural effects of ETH blocking/deactivation and BS3 stabilization. With the end-on immobilized antibody, PSA at 10 pg/mL can be detected by DPI through a sandwich complex that satisfies the clinical requirement (assuming <30 pg/mL as clinically safe). However, the randomly immobilized antibody failed to detect PSA at 1 ng/mL. In a parallel study using surface plasmon resonance (SPR) spectroscopy, random and end-on antibody immobilization on streptavidin-modified gold surface was evaluated to further validate the importance of antibody orientation control. With the closely packed antibody layer on protein G surface, SPR can also detect PSA at 10 pg/mL.
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Affiliation(s)
- Hong Yan Song
- Institute of Materials Research and Engineering, A*STAR, 3 Research Link, Singapore 117602
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80
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Zhao T, Zhao P, Cannon JL, Doyle MP. Inactivation of salmonella in biofilms and on chicken cages and preharvest poultry by levulinic Acid and sodium dodecyl sulfate. J Food Prot 2011; 74:2024-30. [PMID: 22186041 DOI: 10.4315/0362-028x.jfp-11-197] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Surface contamination (skin and feathers) of broilers with Salmonella occurs primarily during growth and transportation. Immediately after transporting chickens, chicken cage doors were sprayed with a foam containing 3% levulinic acid plus 2% sodium dodecyl sulfate (SDS). Samples were collected for Salmonella assay after 45 min. Salmonella on cage doors was reduced from 19% (19 of 100 doors) before treatment to 1% (1 of 100 doors) after treatment, coliform counts were reduced from 6 to 8 to 2 to 4 log CFU/9 cm(2), and aerobic plate counts were reduced from 7 to 9 to 4 to 6 log CFU/9 cm(2). Whole chicken carcasses with feathers were inoculated with 10(8) CFU of Salmonella Enteritidis, soaked for 5 min at 21°C in 72 liters of a treatment or control solution, and assayed for Salmonella. Salmonella counts on chickens treated with water were 6.8 to 8.5 log CFU/9 cm(2), those treated with 50 ppm of calcium hypochlorite were 7.6 to 8.9 log CFU/9 cm(2), and those treated with 3% levulinic acid plus 2% SDS were <1.7 to 2.8 CFU/9 cm(2) (>4-log reduction). Results of biofilm studies on surfaces of various materials revealed that a 3% levulinic acid plus 2% SDS treatment used as either a foam or liquid for 10 min effectively reduced Salmonella populations by 5 and >6 log CFU/cm(2), respectively.
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Affiliation(s)
- Tong Zhao
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia 30223, USA
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81
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Grace Ho KL, Luzuriaga DA, Rodde KM, Tang S, Phan C. Efficacy of a novel sanitizer composed of lactic acid and peroxyacetic acid against single strains of nonpathogenic Escherichia coli K-12, Listeria innocua, and Lactobacillus plantarum in aqueous solution and on surfaces of romaine lettuce and spinach. J Food Prot 2011; 74:1468-74. [PMID: 21902915 DOI: 10.4315/0362-028x.jfp-11-110] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A novel sanitizer composed of lactic acid and peroxyacetic acid (LA-PAA) was developed as an alternative to chlorinated water (CW) for fresh produce processing. Single strains of Lactobacillus plantarum, nonpathogenic Escherichia coli K-12, and Listeria innocua were used to demonstrate the microbial efficacy of LA-PAA. LA-PAA achieved a >7.8-log reduction of L. innocua and L. plantarum suspended in water at 4°C for 20 s, and LA, PAA, and CW achieved reductions of 0.4, 4.8, and 2.7 log, respectively. LA-PAA, when compared with LA, PAA, and CW, enhanced the reduction of L. innocua attached to romaine leaves by >2.2 log, and improved the removal of E. coli attached to spinach leaves by >2.4 log. The exponential improvement in the microbial efficacy of LA-PAA showed synergism between LA and PAA. LA-PAA microbial efficacy was inversely proportional to pH value and directly correlated with residence time and concentration. Despite an improvement in microbial reduction through the addition of surfactant to LA-PAA, the usage of surfactant in washing fresh produce was impeded by excessive foaming during actual processing. Effects of organic matter on the performance of LA-PAA were minimal. External sensory evaluations showed that LA-PAA had no negative effects on the quality of lettuce and tender leaves. Temperature-abuse studies demonstrated that LA-PAA reduced decay by ∼50% when compared with CW. Overall, these results support the premise that LA-PAA has significant potential to be an alternative to CW for fresh produce processing.
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Affiliation(s)
- Kai-Lai Grace Ho
- Research and Development Department, Chiquita Brands International, J. R. Lugg Research Center, 607 Brunken Avenue, Salinas, California 93901, USA.
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82
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Molecular serum portraits in patients with primary breast cancer predict the development of distant metastases. Proc Natl Acad Sci U S A 2011; 108:14252-7. [PMID: 21844363 DOI: 10.1073/pnas.1103125108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The risk of distant recurrence in breast cancer patients is difficult to assess with current clinical and histopathological parameters, and no validated serum biomarkers currently exist. Using a recently developed recombinant antibody microarray platform containing 135 antibodies against 65 mainly immunoregulatory proteins, we screened 240 sera from 64 patients with primary breast cancer. This unique longitudinal sample material was collected from each patient between 0 and 36 mo after the primary operation. The velocity for each serum protein was determined by comparing the samples collected at the primary operation and then 3-6 mo later. A 21-protein signature was identified, using leave-one-out cross-validation together with a backward elimination strategy in a training cohort. This signature was tested and evaluated subsequently in an independent test cohort (prevalidation). The risk of developing distant recurrence after primary operation could be assessed for each patient, using her molecular portraits. The results from this prevalidation study showed that patients could be classified into high- versus low-risk groups for developing metastatic breast cancer with a receiver operating characteristic area under the curve of 0.85. This risk assessment was not dependent on the type of adjuvant therapy received by the patients. Even more importantly, we demonstrated that this protein signature provided an added value compared with conventional clinical parameters. Consequently, we present here a candidate serum biomarker signature able to classify patients with primary breast cancer according to their risk of developing distant recurrence, with an accuracy outperforming current procedures.
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83
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De Marni ML, Monegal A, Venturini S, Vinati S, Carbone R, de Marco A. Antibody purification-independent microarrays (PIM) by direct bacteria spotting on TiO2-treated slides. Methods 2011; 56:317-25. [PMID: 21736943 DOI: 10.1016/j.ymeth.2011.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 11/30/2022] Open
Abstract
The preparation of effective conventional antibody microarrays depends on the availability of high quality material and on the correct accessibility of the antibody active moieties following their immobilization on the support slide. We show that spotting bacteria that expose recombinant antibodies on their external surface directly on nanostructured-TiO(2) or epoxy slides (purification-independent microarray - PIM) is a simple and reliable alternative for preparing sensitive and specific microarrays for antigen detection. Variable domains of single heavy-chain antibodies (VHHs) against fibroblast growth factor receptor 1 (FGFR1) were used to capture the antigen diluted in serum or BSA solution. The FGFR1 detection was performed by either direct antigen labeling or using a sandwich system in which FGFR1 was first bound to its antibody and successively identified using a labeled FGF. In both cases the signal distribution within each spot was uniform and spot morphology regular. The signal-to-noise ratio of the signal was extremely elevated and the specificity of the system was proved statistically. The LOD of the system for the antigen was calculated being 0.4ng/mL and the dynamic range between 0.4ng/mL and 10μg/mL. The microarrays prepared with bacteria exposing antibodies remain fully functional for at least 31 days after spotting. We finally demonstrated that the method is suitable for other antigen-antibody pairs and expect that it could be easily adapted to further applications such as the display of scFv and IgG antibodies or the autoantibody detection using protein PIMs.
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84
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Irvine EJ, Hernandez-Santana A, Faulds K, Graham D. Fabricating protein immunoassay arrays on nitrocellulose using dip-pen lithography techniques. Analyst 2011; 136:2925-30. [PMID: 21647488 DOI: 10.1039/c1an15178a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advancements in lithography methods for printing biomolecules on surfaces are proving to be potentially beneficial for disease screening and biological research. Dip-pen nanolithography (DPN) is a versatile micro and nanofabrication technique that has the ability to produce functional biomolecule arrays. The greatest advantage, with respect to the printing mechanism, is that DPN adheres to the sensitive mild conditions required for biomolecules such as proteins. We have developed an optimised, high-throughput printing technique for fabricating protein arrays using DPN. This study highlights the fabrication of a prostate specific antigen (PSA) immunoassay detectable by fluorescence. Spot sizes are typically no larger than 8 μm in diameter and limits of detection for PSA are comparable with a commercially available ELISA kit. Furthermore, atomic force microscopy (AFM) analysis of the array surface gives great insight into how the nitrocellulose substrate functions to retain protein integrity. This is the first report of protein arrays being printed on nitrocellulose using the DPN technique and the smallest feature size yet to be achieved on this type of surface. This method offers a significant advance in the ability to produce dense protein arrays on nitrocellulose which are suitable for disease screening using standard fluorescence detection.
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Affiliation(s)
- Eleanore Jane Irvine
- Centre for Nanometrology, Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, UK
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85
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Brody EN, Gold L, Lawn RM, Walker JJ, Zichi D. High-content affinity-based proteomics: unlocking protein biomarker discovery. Expert Rev Mol Diagn 2011; 10:1013-22. [PMID: 21080818 DOI: 10.1586/erm.10.89] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single protein biomarkers measured with antibody-based affinity assays are the basis of molecular diagnostics in clinical practice today. There is great hope in discovering new protein biomarkers and combinations of protein biomarkers for advancing medicine through monitoring health, diagnosing disease, guiding treatment, and developing new therapeutics. The goal of high-content proteomics is to unlock protein biomarker discovery by measuring many (thousands) or all (∼23,000) proteins in the human proteome in an unbiased, data-driven approach. High-content proteomics has proven technically difficult due to the diversity of proteins, the complexity of relevant biological samples, such as blood and tissue, and large concentration ranges (in the order of 10(12) in blood). Mass spectrometry and affinity methods based on antibodies have dominated approaches to high-content proteomics. For technical reasons, neither has achieved adequate simultaneous performance and high-content. Here we review antibody-based protein measurement, multiplexed antibody-based protein measurement, and limitations of antibodies for high-content proteomics due to their inherent cross-reactivity. Finally, we review a new affinity-based proteomic technology developed from the ground up to solve the problem of high content with high sensitivity and specificity. Based on a new generation of slow off-rate modified aptamers (SOMAmers), this technology is unlocking biomarker discovery.
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Affiliation(s)
- Edward N Brody
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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86
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Moreno M, González VM, Rincón E, Domingo A, Domínguez E. Aptasensor based on the selective electrodeposition of protein-linked gold nanoparticles on screen-printed electrodes. Analyst 2011; 136:1810-5. [PMID: 21394378 DOI: 10.1039/c1an15070g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The electrodeposition of DNA-gold nanoparticles previously developed in our group has been used as starting point for the electrodeposition of proteins attached to gold nanoparticles. We have performed a proof of principle by developing a methodology based on the electrodeposition of proteins bound to gold nanoparticles on screen-printed gold microelectrodes using, in a first approach, horseradish peroxide-conjugated gold nanoparticles (gold-HRP). The electrodeposition was achieved at a current positive potential of 800 mV vs. Ag/AgCl and the functionality of the electrodeposited HRP-particles was tested by electrochemical reduction of H(2)O(2). Furthermore, we used this proof of concept in an aptasensor application to detect Leishmania infantum KMP-11. Hence, we have demonstrated not only the functionality of the electrodeposition of proteins bound to gold nanoparticles, but also the utility of the method with the aim of developing a real biosensor containing multiple enzymes or proteins in a multimodular device.
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Affiliation(s)
- M Moreno
- Departamento Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Alcalá, 28871, Alcalá de Henares, Madrid, Spain.
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87
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Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011; 11:2139-61. [PMID: 21548090 DOI: 10.1002/pmic.201000460] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 02/28/2011] [Accepted: 03/07/2011] [Indexed: 01/22/2023]
Abstract
Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high-abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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88
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Dexlin-Mellby L, Sandström A, Antberg L, Gunnarsson J, Hansson SR, Borrebaeck CA, Wingren C. Design of recombinant antibody microarrays for membrane protein profiling of cell lysates and tissue extracts. Proteomics 2011; 11:1550-4. [DOI: 10.1002/pmic.200900808] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/14/2011] [Accepted: 01/24/2011] [Indexed: 11/06/2022]
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89
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Rivas LA, Aguirre J, Blanco Y, González-Toril E, Parro V. Graph-based deconvolution analysis of multiplex sandwich microarray immunoassays: applications for environmental monitoring. Environ Microbiol 2011; 13:1421-32. [PMID: 21401847 DOI: 10.1111/j.1462-2920.2011.02442.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sandwich microarray immunoassay (SMI) is a powerful technique for the analysis and characterization of environmental samples, from the identification of microorganisms to specific bioanalytes. As the number of antibodies increases, however, unspecific binding and cross-reactivity can become a problem. To cope with such difficulties, we present here the concept of antibody graph associated to a sandwich antibody microarray. Antibody graphs give valuable information about the antibody cross-reactivity network and all the players involved in the sandwich format: capturing and tracer antibodies, the antigenic sample and the degree of cross-reactivity between antibodies. Making use of the information contained in the antibody graph, we have developed a deconvolution method that disentangles the antibody cross-reactivity events and gives qualitative information about the composition of the experimental sample under study. We have validated the method by using a 66 antibody-containing microarray to describe known antigenic mixtures as well as natural environmental samples characterized by 16S-RNA gene phylogenetic analysis. The application of our antibody graph and deconvolution method allowed us to discriminate between true specific antigen-antibody reactions and spurious signals on a microarray designed for environmental monitoring.
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Affiliation(s)
- Luis A Rivas
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain.
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90
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Differential gene expression analysis of placentas with increased vascular resistance and pre-eclampsia using whole-genome microarrays. J Pregnancy 2011; 2011:472354. [PMID: 21490790 PMCID: PMC3066560 DOI: 10.1155/2011/472354] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/30/2010] [Accepted: 12/30/2010] [Indexed: 01/11/2023] Open
Abstract
Pre-eclampsia is a pregnancy complication characterized by hypertension and proteinuria. There are several factors associated with an increased risk of developing pre-eclampsia, one of which is increased uterine artery resistance, referred to as “notching”. However, some women do not progress into pre-eclampsia whereas others may have a higher risk of doing so. The placenta, central in pre-eclampsia pathology, may express genes associated with either protection or progression into pre-eclampsia. In order to search for genes associated with protection or progression, whole-genome profiling was performed. Placental tissue from 15 controls, 10 pre-eclamptic, 5 pre-eclampsia with notching, and 5 with notching only were analyzed using microarray and antibody microarrays to study some of the same gene product and functionally related ones. The microarray showed 148 genes to be significantly altered between the four groups. In the preeclamptic group compared to notch only, there was increased expression of genes related to chemotaxis and the NF-kappa B pathway and decreased expression of genes related to antigen processing and presentation, such as human leukocyte antigen B. Our results indicate that progression of pre-eclampsia from notching may involve the development of inflammation. Increased expression of antigen-presenting genes, as seen in the notch-only placenta, may prevent this inflammatory response and, thereby, protect the patient from developing pre-eclampsia.
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91
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Kim KM, Kang M, Yi EC. Applications of cell-based phage display panning to proteomic analysis. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0150-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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92
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Carlsson A, Wuttge DM, Ingvarsson J, Bengtsson AA, Sturfelt G, Borrebaeck CAK, Wingren C. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol Cell Proteomics 2011; 10:M110.005033. [PMID: 21350050 PMCID: PMC3098590 DOI: 10.1074/mcp.m110.005033] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are two severe autoimmune connective tissue diseases. The fundamental knowledge about their etiology is limited and the conditions display complex pathogenesis, multifaceted presentations, and unpredictable courses. Despite significant efforts, the lack of fully validated biomarkers enabling diagnosis, classification, and monitoring of disease activity represents significant unmet clinical needs. In this discovery study, we have for the first time used recombinant antibody microarrays for miniaturized, multiplexed serum protein profiling of SLE and SSc, targeting mainly immunoregulatory proteins. The data showed that several candidate SLE-associated multiplexed serum biomarker signatures were delineated, reflecting disease (diagnosis), disease severity (phenotypic subsets), and disease activity. Selected differentially expressed markers were validated using orthogonal assays and a second, independent patient cohort. Further, biomarker signatures differentiating SLE versus SSc were demonstrated, and the observed differences increased with severity of SLE. In contrast, the data showed that the serum profiles of SSc versus healthy controls were more similar. Hence, we have shown that affinity proteomics could be used to de-convolute crude, nonfractionated serum proteomes, extracting molecular portraits of SLE and SSc, further enhancing our fundamental understanding of these complex autoimmune conditions.
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Affiliation(s)
- Anders Carlsson
- Department of Immunotechnology, BMC D13, Lund University, SE-221 84 Lund, Sweden
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93
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Affiliation(s)
- Raoul K. Boughton
- Avian Ecology, Archbold Biological Station, 123 Main Drive, Venus, Florida, USA
| | - Gerrit Joop
- Institute of Integrative Biology,
Experimental Ecology, ETH Zürich, CH‐8092 Zürich, Switzerland
| | - Sophie A.O. Armitage
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D‐48149 Münster, Germany
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94
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Ortega YR, Torres MP, Tatum JM. Efficacy of levulinic acid-sodium dodecyl sulfate against Encephalitozoon intestinalis, Escherichia coli O157:H7, and Cryptosporidium parvum. J Food Prot 2011; 74:140-4. [PMID: 21219777 DOI: 10.4315/0362-028x.jfp-10-104] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Foodborne parasites are characterized as being highly resistant to sanitizers used by the food industry. In 2009, a study reported the effectiveness of levulinic acid in combination with sodium dodecyl sulfate (SDS) in killing foodborne bacteria. Because of their innocuous properties, we studied the effects of levulinic acid and SDS at various concentrations appropriate for use in foods, on the viability of Cryptosporidium parvum and Encephalitozoon intestinalis. The viability of Cryptosporidium and E. intestinalis was determined by in vitro cultivation using the HCT-8 and RK-13 cell lines, respectively. Two Escherichia coli O157:H7 isolates were also used in the present study: strain 932 (a human isolate from a 1992 Oregon meat outbreak) and strain E 0018 (isolated from calf feces). Different concentrations and combinations of levulinic acid and SDS were tested for their ability to reduce infectivity of C. parvum oocysts (10(5)), E. intestinalis spores (10(6)), and E. coli O157:H7 (10(7)/ml) when in suspension. Microsporidian spores were treated for 30 and 60 min at 20 ± 2°C. None of the combinations of levulinic acid and SDS were effective at inactivating the spores or oocysts. When Cryptosporidium oocysts were treated with higher concentrations (3% levulinic acid-2% SDS and 2% levulinic acid-1% SDS) for 30, 60, and 120 min, viability was unaffected. E. coli O157:H7, used as a control, was highly sensitive to the various concentrations and exposure times tested. SDS and levulinic acid alone had very limited effect on E. coli O157:H7 viability, but in combination they were highly effective at 30 and 60 min of incubation. In conclusion, Cryptosporidium and microsporidia are not inactivated when treated for various periods of time with 2% levulinic acid-1% SDS or 3% levulinic acid-2% SDS at 20°C, suggesting that this novel sanitizer cannot be used to eliminate parasitic contaminants in foods.
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Affiliation(s)
- Ynes R Ortega
- Center for Food Safety, University of Georgia, Griffin, Georgia 30223, USA.
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95
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Abstract
Affinity proteomics, mainly represented by antibody microarrays, has in recent years been established as a powerful tool for high-throughput (disease) proteomics. The technology can be used to generate detailed protein expression profiles, or protein maps, of focused set of proteins in crude proteomes and potentially even high-resolution portraits of entire proteomes. The technology provides unique opportunities, for example biomarker discovery, disease diagnostics, patient stratification and monitoring of disease, and taking the next steps toward personalized medicine. However, the process of designing high-performing, high-density antibody micro- and nanoarrays has proven to be challenging, requiring truly cross-disciplinary efforts to be adopted. In this mini-review, we address one of these key technological issues, namely, the choice of probe format, and focus on the use of recombinant antibodies vs. polyclonal and monoclonal antibodies for the generation of antibody arrays.
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96
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Whitcombe MJ, Chianella I, Larcombe L, Piletsky SA, Noble J, Porter R, Horgan A. The rational development of molecularly imprinted polymer-based sensors for protein detection. Chem Soc Rev 2011; 40:1547-71. [DOI: 10.1039/c0cs00049c] [Citation(s) in RCA: 569] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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97
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Protein microarrays and biomarkers of infectious disease. Int J Mol Sci 2010; 11:5165-83. [PMID: 21614200 PMCID: PMC3100839 DOI: 10.3390/ijms11125165] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/11/2010] [Accepted: 12/15/2010] [Indexed: 01/11/2023] Open
Abstract
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers.
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98
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99
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Zhao T, Zhao P, Doyle MP. Inactivation of Escherichia coli O157:H7 and Salmonella typhimurium DT 104 on alfalfa seeds by levulinic acid and sodium dodecyl sulfate. J Food Prot 2010; 73:2010-7. [PMID: 21219712 DOI: 10.4315/0362-028x-73.11.2010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Studies were conducted to determine the best concentration and exposure time for treatment of alfalfa seeds with levulinic acid plus sodium dodecyl sulfate (SDS) to inactivate Escherichia coli O157:H7 and Salmonella without adversely affecting seed germination. Alfalfa seeds inoculated with a five-strain mixture of E. coli O157:H7 or Salmonella Typhimurium were dried in a laminar flow hood at 21°C for up to 72 h. Inoculated alfalfa seeds dried for 4 h then treated for 5 min at 21°C with 0.5% levulinic acid and 0.05% SDS reduced the population of E. coli O157:H7 and Salmonella Typhimurium by 5.6 and 6.4 log CFU/g, respectively. On seeds dried for 72 h, treatment with 0.5% levulinic acid and 0.05% SDS for 20 min at 21°C reduced E. coli O157:H7 and Salmonella Typhimurium populations by 4 log CFU/g. Germination rates of alfalfa seeds treated with 0.5% levulinic acid plus 0.05% SDS for up to 1 h at 21°C were compared with a treatment of 20,000 ppm of calcium hypochlorite or tap water only. Treatment of alfalfa seeds with 0.5% levulinic acid plus 0.05% SDS for 5 min at 21°C resulted in a >3.0-log inactivation of E. coli O157:H7 and Salmonella.
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Affiliation(s)
- Tong Zhao
- Center for Food Safety, University of Georgia, 1109 Experiment Street, Griffin, Georgia 30223, USA
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100
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Jung HJ, Hwang I, Kim BJ, Min H, Yu H, Lee TG, Chung TD. Selective and direct immobilization of cysteinyl biomolecules by electrochemical cleavage of azo linkage. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15087-15091. [PMID: 20809594 DOI: 10.1021/la102489k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Controlled orientation and reserved activity of biomolecules, when site-selectively immobilized in a highly integrated manner on a minimal time scale, are crucial in designing biosensors for the multiplex detection. Here, we describe a novel method for the orientation-controlled immobilization of biomolecules based on site-selective electrochemical activation of p-hydroxyazobenzene self-assembled monolayer (SAM) followed by one-step coupling of cysteinyl biomolecules. The p-aminophenol, a product of reductive cleavage of p-hydroxyazobenzene, was subsequently oxidized to yield p-quinoneimine which then conjugated with cysteinyl biomolecules through 1,4-Michael addition, thus obviating additional linker agents and the related time consumption. Using this method, we selectively activated the electrode surface and immobilized laminin peptide IKVAV, a neurite promoting motif. When we cultured hippocampal neurons on the electrode, the extended neurites were found only within the electrochemically activated area. Hence, the proposed method represents a new promising platform for the patterning of functional peptides, active proteins, and live cells.
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Affiliation(s)
- Hyun Joo Jung
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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