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Sequence-Specific End Labeling of Oligonucleotides (SSELO)-Based Microbial Detection. Methods Mol Biol 2019; 1918:47-56. [PMID: 30580398 DOI: 10.1007/978-1-4939-9000-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The sequence-specific end labeling of oligonucleotides (SSELO) is an alternative labelling approach for the short-oligonucleotide diagnostic microarrays that was firstly described by Rudi and coworkers (ScientificWorldJournal 3:578-584, 2003). SSELO approach is unique in a way that it shifts the specificity determining step from hybridization to labeling, ensuring both high specificity (with careful probe design even single nucleotide polymorphisms (SNPs) can be detected) and sensitivity (detection sensitivity in the range of 0.1% relative abundance has been demonstrated) of the diagnostic system. These features make SSELO approach a perfect choice for the development of microbial diagnostic microarrays, in particular in the frame of foodborne bacterial pathogen detection.
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Elucidating Waterborne Pathogen Presence and Aiding Source Apportionment in an Impaired Stream. Appl Environ Microbiol 2018; 84:AEM.02510-17. [PMID: 29305503 DOI: 10.1128/aem.02510-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. The direct detection of pathogens in water and simultaneous identification of the source of fecal contamination are possible with microarrays, circumventing the drawbacks to FIB approaches. A multigene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired mixed-use watershed. The results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criterion standards. However, waterborne pathogens are still prevalent in the watershed, as viruses (bocavirus, hepatitis E and A viruses, norovirus, and enterovirus G), bacteria (Campylobacter spp., Clostridium spp., enterohemorrhagic and enterotoxigenic Escherichia coli, uropathogenic E. coli, Enterococcus faecalis, Helicobacter spp., Salmonella spp., and Vibrio spp.), and eukaryotes (Acanthamoeba spp., Entamoeba histolytica, and Naegleria fowleri) were detected. A comparison of the stream microbial ecology with that of sewage, cattle, and swine fecal samples revealed that human sources of fecal contamination dominate in the watershed. The methodology presented is applicable to a wide range of impaired streams for the identification of human health risk due to waterborne pathogens and for the identification of areas for remediation efforts.IMPORTANCE The direct detection of waterborne pathogens in water overcomes many of the limitations of the fecal indicator paradigm. Furthermore, the identification of the source of fecal impairment aids in identifying areas for remediation efforts. Multitarget gene microarrays are shown to simultaneously identify waterborne pathogens and aid in determining the sources of impairment, enabling further focused investigations. This study shows the use of this methodology in a historically impaired watershed in which total maximum daily load reductions have been successfully implemented to reduce risk. The results suggest that while the fecal indicators have been reduced more than 96% and are nearing recreational water criterion levels, pathogens are still detectable in the watershed. Microbial source tracking results show that additional remediation efforts are needed to reduce the impact of human sewage in the watershed.
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Su JQ, Cui L, Chen QL, An XL, Zhu YG. Application of genomic technologies to measure and monitor antibiotic resistance in animals. Ann N Y Acad Sci 2016; 1388:121-135. [DOI: 10.1111/nyas.13296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
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Degefu Y, Somervuo P, Aittamaa M, Virtanen E, Valkonen JPT. Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples. ACTA ACUST UNITED AC 2016. [DOI: 10.1111/epp.12263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y. Degefu
- Green Technology, Plant and Animal Genetics; Natural Resources Institute Finland; University of Oulu; PO Box 413¸ Paavo Havaksen tie 3 Oulu 90014 Finland
| | - P. Somervuo
- Institutes of Biotechnology; University of Helsinki; Viikinkaari 1, PO Box 65 Helsinki 00014 Finland
| | - M. Aittamaa
- Department of Agricultural Sciences; University of Helsinki; Latokartanonkaari 7, PO Box 27 Helsinki 00014 Finland
| | - E. Virtanen
- Green Technology, Plant and Animal Genetics; Natural Resources Institute Finland; University of Oulu; PO Box 413¸ Paavo Havaksen tie 3 Oulu 90014 Finland
| | - J. P. T. Valkonen
- Department of Agricultural Sciences; University of Helsinki; Latokartanonkaari 7, PO Box 27 Helsinki 00014 Finland
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Fluorescence-based bioassays for the detection and evaluation of food materials. SENSORS 2015; 15:25831-67. [PMID: 26473869 PMCID: PMC4634490 DOI: 10.3390/s151025831] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.
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Li X, Harwood VJ, Nayak B, Staley C, Sadowsky MJ, Weidhaas J. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7319-7329. [PMID: 25970344 DOI: 10.1021/acs.est.5b00980] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs.
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Affiliation(s)
- Xiang Li
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
| | - Valerie J Harwood
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Bina Nayak
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher Staley
- §BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Michael J Sadowsky
- ∥Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Jennifer Weidhaas
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
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McCoy GR, Kegel JU, Touzet N, Fleming GTA, Medlin LK, Raine R. An assessment of RNA content in Prymnesium parvum, Prymnesium polylepis, cf. Chattonella sp. and Karlodinium veneficum under varying environmental conditions for calibrating an RNA microarray for species detection. FEMS Microbiol Ecol 2014; 88:140-59. [PMID: 24392749 DOI: 10.1111/1574-6941.12277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/06/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022] Open
Abstract
Traditional methods of identification and enumeration can be somewhat ambiguous when identifying phytoplankton that requires electron microscopic examination to verify specific morphological features. Members of the genus Prymnesium (division Haptophyta), members of the Raphidophyceae and naked dinoflagellates are examples of such phytoplankton whose identification can be difficult. One alternative to traditional microscopy-based methods of identification is to use molecular protocols to detect target species. Methods that measure cellular DNA and RNA content can be used to estimate the number of cells present in a sample. This study investigated the variation of RNA yields in Prymnesium parvum, P. polylepis, cf. Chattonella sp. and Karlodinium veneficum cells grown under different light, temperature, salinity and inorganic nutrient conditions. This information was used to calibrate the signal intensity of a variety of oligonucleotide probes spotted onto the microarrays for the detection of toxic algae (MIDTAL), which is being developed to aid national monitoring agencies and to provide a faster means of identifying and quantifying harmful phytoplankton in water column samples.
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Affiliation(s)
- Gary R McCoy
- The Ryan Institute, National University of Ireland, Galway, Ireland
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Vázquez-Villegas P, Espitia-Saloma E, Rito-Palomares M, Aguilar O. Low-abundant protein extraction from complex protein sample using a novel continuous aqueous two-phase systems device. J Sep Sci 2013; 36:391-9. [PMID: 23255256 DOI: 10.1002/jssc.201200584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 12/16/2023]
Abstract
The present work describes the application of a novel continuous aqueous two-phase system prototype for the recovery of biomolecules. The prototype is an alternative platform for protein recovery and α-amylase from soybean extracts was used as a model system. The system was selected as an example of low-abundant protein present in complex mixtures. Compared with batch systems, continuous operation in this prototype seems to increase partition coefficient with higher recovery efficiencies. Processing time is reduced at least three times in the continuous system when compared to batch mode, while hold up (volumetric quantity of the opposing phase in a determined phase sample) decreases with decreasing phases flow. Furthermore, similar partition coefficient (Kp > 4) with a higher top phase enzyme recovery (81%) is also obtained in this system probably due to better contact surface between phases, compared with that obtained in batch (79%). A continuous aqueous two-phase system process with purification factor 40-fold higher than batch experiments was achieved. These preliminary results exhibit the potential of continuous systems for the recovery of low-abundant proteins from complex mixtures. The promising performance of this prototype can raise the attention of the industry for the adoption of aqueous two-phase system processes.
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Affiliation(s)
- Patricia Vázquez-Villegas
- Departamento de Biotecnología e Ingeniería de Alimentos, Centro de Biotecnología-FEMSA, Tecnológico de Monterrey, Monterrey, NL, México
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A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food. J Pathog 2012; 2012:627036. [PMID: 23125935 PMCID: PMC3483683 DOI: 10.1155/2012/627036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/02/2012] [Accepted: 08/05/2012] [Indexed: 11/17/2022] Open
Abstract
The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.
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Gubala V, Harris LF, Ricco AJ, Tan MX, Williams DE. Point of Care Diagnostics: Status and Future. Anal Chem 2011; 84:487-515. [DOI: 10.1021/ac2030199] [Citation(s) in RCA: 832] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladimir Gubala
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Leanne F. Harris
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Antonio J. Ricco
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Ming X. Tan
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - David E. Williams
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
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Kostić T, Sessitsch A. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. ACTA ACUST UNITED AC 2011; 1:3-24. [PMID: 27605332 PMCID: PMC5007712 DOI: 10.3390/microarrays1010003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 01/02/2023]
Abstract
Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.
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Affiliation(s)
- Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria.
- Christian Doppler Laboratory for Molecular Food Analytics, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria.
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria
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Kostić T, Stessl B, Wagner M, Sessitsch A. Microarray analysis reveals the actual specificity of enrichment media used for food safety assessment. J Food Prot 2011; 74:1030-4. [PMID: 21669087 DOI: 10.4315/0362-028x.jfp-10-388] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Microbial diagnostic microarrays are tools for simultaneous detection and identification of microorganisms in food, clinical, and environmental samples. In comparison to classic methods, microarray-based systems have the potential for high throughput, parallelism, and miniaturization. High specificity and high sensitivity of detection have been demonstrated. A microbial diagnostic microarray for the detection of the most relevant bacterial food- and waterborne pathogens and indicator organisms was developed and thoroughly validated. The microarray platform based on sequence-specific end labeling of oligonucleotides and the phylogenetically robust gyrB marker gene allowed a highly specific (resolution on genus and/or species level) and sensitive (0.1% relative and 10(4) CFU absolute sensitivity) detection of the target pathogens. In initial challenge studies of the applicability of microarray-based food analysis, we obtained results demonstrating the questionable specificity of standardized culture-dependent microbiological detection methods. Taking into consideration the importance of reliable food safety assessment methods, comprehensive performance assessment is essential. Results demonstrate the potential of this new pathogen diagnostic microarray to evaluate culture-based standard methods in microbiological food analysis.
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Affiliation(s)
- Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-2444 Seibersdorf, Austria.
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Daniels C, Krell T, Michán C, Ramos JL. Struggling to get a universal meningococcal vaccine and novel uses for bacterial toxins in cancer treatment. Microb Biotechnol 2011; 3:359-61. [PMID: 21255335 PMCID: PMC3815803 DOI: 10.1111/j.1751-7915.2010.00195.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, C.H. Best Institute, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
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Gehring AG, Tu SI. High-throughput biosensors for multiplexed food-borne pathogen detection. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:151-172. [PMID: 21689045 DOI: 10.1146/annurev-anchem-061010-114010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Incidental contamination of foods by pathogenic bacteria and/or their toxins is a serious threat to public health and the global economy. The presence of food-borne pathogens and toxins must be rapidly determined at various stages of food production, processing, and distribution. Producers, processors, regulators, retailers, and public health professionals need simple and cost-effective methods to detect different species or serotypes of bacteria and associated toxins in large numbers of food samples. This review addresses the desire to replace traditional microbiological plate culture with more timely and less cumbersome rapid, biosensor-based methods. Emphasis focuses on high-throughput, multiplexed techniques that allow for simultaneous testing of numerous samples, in rapid succession, for multiple food-borne analytes (primarily pathogenic bacteria and/or toxins).
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Affiliation(s)
- Andrew G Gehring
- Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania 19038, USA
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Michán C, Daniels C, Ramos J. New molecular techniques for pathogen analysis, in silico
determination of RND efflux pump substrate specificity, shotgun proteomic monitoring of bioremediation and yeast bio-applications. Microb Biotechnol 2010. [PMCID: PMC3815337 DOI: 10.1111/j.1751-7915.2010.00225.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Dept. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C‐6, 2 Planta, 14071, Córdoba, Spain
| | - Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, C.H. Best Institute 112 College Street, M5G 1L6, Toronto, Ontario, Canada
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, E‐18008 Granada, Spain
- *E‐mail ; Tel. (+34) 958 181608; Fax (+34) 958 135740
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