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A method for automatically extracting infectious disease-related primers and probes from the literature

Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez, Víctor Maojo
2010 BMC Bioinformatics  
In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature.  ...  Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases.  ...  AC participated in the creation of the method and in the design of the experiment, wrote the software tool implementing the presented method, and helped to draft the manuscript.  ... 
doi:10.1186/1471-2105-11-410 pmid:20682041 pmcid:PMC2923139 fatcat:g6pmf7asujamtjsjet5xtcqsla

Polymerase chain reaction (PCR) amplification of a nucleoprotein gene sequence of infectious hematopoietic necrosis virus

CK Arakawa, RE Deering, KH Higman, KH Oshima, PJ O'Hara, JR Winton
1990 Diseases of Aquatic Organisms  
We thank Pete Lockhart for technical assistance with the synthesis of the primers and probes used in this study.  ...  Portions of this work were conducted with funds from the Western Regional Aquaculture Consortiun~ under U S. Department of Agriculture Grant No 87-CRSR-2-3219. LITERATURE CITED Amos, K. H. (1985).  ...  Because of these substantial advantages, the combination of PCR and nucleic acid probe methods will find increasing use in fish disease diagnostics.  ... 
doi:10.3354/dao008165 fatcat:icpu7yrysjailpdqgyx2pajkbm

Nucleic Acid Amplification Based Diagnostic of Lyme (Neuro-)borreliosis – Lost in the Jungle of Methods, Targets, and Assays?

Oliver Nolte
2012 Open Neurology Journal  
Laboratory based diagnosis of infectious diseases usually relies on culture of the disease causing microorganism, followed by identification and susceptibility testing.  ...  NAT uses nucleic acids of the disease causing micro-organism as template for amplification, isolated from various sources of clinical specimens.  ...  Depending on the extraction kit used and the automat available, volumes between 200 µL and 1 mL are being processed.  ... 
doi:10.2174/1874205x01206010129 pmid:23230454 pmcid:PMC3514706 fatcat:r6zvte5hjnd3fi4v6q7q4bkofe

Occurrence of Human Adenoviruses at Two Recreational Beaches of the Great Lakes

I. Xagoraraki, D. H.-W. Kuo, K. Wong, M. Wong, J. B. Rose
2007 Applied and Environmental Microbiology  
Human adenoviruses (HAdVs) have been related to several waterborne diseases such as acute gastroenteritis, conjunctivitis, and respiratory illness, and it has been shown that an important human exposure  ...  The concentrations of HAdVs ranged from (1.7 ؎ 0.7) ؋ 10 1 to (3.4 ؎ 0.8) ؋ 10 2 and from (7 ؎ 2) ؋ 10 0 to (3.8 ؎ 0.3) ؋ 10 3 virus particles/liter for Silver Beach and Washington Park Beach, respectively  ...  ACKNOWLEDGMENTS This study was funded by a research grant from the Center for Water Sciences at Michigan State University and by NOAA Center of Excellence for Great Lakes and Human Health, Great Lakes  ... 
doi:10.1128/aem.01239-07 pmid:17933924 pmcid:PMC2168141 fatcat:asgdwyjfcfbl3cic5y6jlztbkq

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Susana Barreda-García, Rebeca Miranda-Castro, Noemí de-los-Santos-Álvarez, Arturo J. Miranda-Ordieres, María Jesús Lobo-Castañón
2017 Analytical and Bioanalytical Chemistry  
Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide.  ...  Consequently, there is a strong interest in developing costeffective, robust, and portable platforms for early detection of these harmful microorganisms.  ...  CTQ2015-63567-R), the Principado de Asturias government (Project FC15-GRUPIN14-025), and cofinanced by FEDER funds.  ... 
doi:10.1007/s00216-017-0620-3 pmid:28932883 fatcat:i45iimfux5coxgmavkhlo6eypy

Principles and applications of polymerase chain reaction in medical diagnostic fields: a review

Marcela Agne Alves Valones, Rafael Lima Guimarães, Lucas André Cavalcanti Brandão, Paulo Roberto Eleutério de Souza, Alessandra de Albuquerque Tavares Carvalho, Sergio Crovela
2009 Brazilian Journal of Microbiology  
The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances  ...  Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology  ...  MGB is released from a probe that binds to the minor groove of the dsDNA (consisting of part of the MGB probe and complementary target sequence by which it is hybridized) related to the nucleotide sequence  ... 
doi:10.1590/s1517-83822009000100001 pmid:24031310 pmcid:PMC3768498 fatcat:ouug5hnr5bfadl62knt7vhdtyi

Integrated Amplification Microarrays for Infectious Disease Diagnostics

Darrell Chandler, Lexi Bryant, Sara Griesemer, Rui Gu, Christopher Knickerbocker, Alexander Kukhtin, Jennifer Parker, Cynthia Zimmerman, Kirsten George, Christopher Cooney
2012 Microarrays  
enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.  ...  Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system.  ...  This results presented here would not be possible without the contributions of Amy Dean and Daryl Lamson from the Laboratory of Viral Diseases at the Wadsworth Center, New York State Department of Health  ... 
doi:10.3390/microarrays1030107 pmid:27605339 pmcid:PMC5003434 fatcat:byfg4xukenhknhl4d4rlssqvui

Multiplex Molecular Point-of-Care Test for Syndromic Infectious Diseases

Hanbi Kim, Hee Jae Huh, Eunkyoung Park, Doo-Ryeon Chung, Minhee Kang
2021 BioChip Journal  
This review focuses on state-of-the-art multiplexed molecular point-of-care tests (POCT) for infectious diseases and efforts to overcome their limitations, especially related to inadequate throughput for  ...  Point-of-care (POC) molecular diagnostics for clinical microbiology and virology has primarily focused on the detection of a single pathogen.  ...  For instance, molecular diagnostics (MDx) involves numerous steps and reagents for sample preparation, including extractions and the purification of nucleic acids from specimens, amplification of a specific  ... 
doi:10.1007/s13206-021-00004-5 pmid:33613852 pmcid:PMC7883532 fatcat:z4mtcdl565d27b6ey3vaq2rm6e

Emergence of New Delhi Metallo-Beta-Lactamase (NDM) and Klebsiella pneumoniae Carbapenemase (KPC) Production by Escherichia coli and Klebsiella pneumoniae in Southern Vietnam and Appropriate Methods of Detection: A Cross-Sectional Study

Cuong Q. Hoang, Hai D. Nguyen, Huy Q. Vu, Anh T. Nguyen, Binh T. Pham, Trung L. Tran, Hanh T. H. Nguyen, Y. M. Dao, Tuyet S. M. Nguyen, Dung A. Nguyen, Hang T. T. Tran, Lan T. Phan
2019 BioMed Research International  
Most of isolates were collected from patients in ICU, Infectious Disease Department, and Department of Urologic Surgery. Urine and sputum were two common specimens.  ...  We suggest that CDT can be used as a low-priced and accurate method of detection.  ...  Minh City for the comments and suggestions.  ... 
doi:10.1155/2019/9757625 fatcat:5cefsj4atjcftjkskefqsdo2zu

Quantification of Enteric Viruses, Pathogen Indicators, and Salmonella Bacteria in Class B Anaerobically Digested Biosolids by Culture and Molecular Methods

K. Wong, B. M. Onan, I. Xagoraraki
2010 Applied and Environmental Microbiology  
The observed high quantitative and infectivity levels of adenoviruses in MAD biosolids indicate that adenovirus is a good indicator for the evaluation of sludge treatment efficiency.  ...  Infectious HAdV was detected more frequently than infectious EV, and all infectious HAdV were detected when samples were propagated in A549 cells.  ...  A special thanks to all the wastewater treatment operators for assisting with sample collection and to Fred Simmons, Arun Kumar, and Matthew Fields for assisting with laboratory analysis.  ... 
doi:10.1128/aem.02685-09 pmid:20693452 pmcid:PMC2950467 fatcat:tbyligagvfgptcdh7tx767qpni

NEW MICROBIOLOGY TOOLS FOR PUBLIC HEALTH AND THEIR IMPLICATIONS

Betty H. Robertson, Janet K.A. Nicholson
2005 Annual Review of Public Health  
investigate and evaluate epidemics and assess endemic diseases.  ...  diagnostic assays for detection of acute infections is rapidly changing from antibody detection to pathogen detection, from clinical laboratory based to point-of-care based, from single analyte detection  ...  The ability to evaluate host and microbial markers in situations such as these infectious diseases may lead to methods for treatment or prevention.  ... 
doi:10.1146/annurev.publhealth.26.021304.144522 pmid:15760290 fatcat:ilkw2mb55bh45gbsxtmgo2q3zi

Invasive anisakiasis by the parasite Anisakis pegreffii (Nematoda: Anisakidae): diagnosis by real-time PCR hydrolysis probe system and immunoblotting assay

Simonetta Mattiucci, Michela Paoletti, Alessandra Colantoni, Antonella Carbone, Raffaele Gaeta, Agnese Proietti, Stefano Frattaroli, Paolo Fazii, Fabrizio Bruschi, Giuseppe Nascetti
2017 BMC Infectious Diseases  
The Real-time PCR primers/probe system, showed a fluorescent signal at 510 nm for A. pegreffii, in all the three cases.  ...  Methods: Parasite DNA was extracted from parasites removed in the three patients.  ...  Acknowledgments Parasitology, "Sapienza University of Rome" and "Umberto I" Teaching Hospital, P.le Aldo Moro, 5, 00185 Rome, Italy. 2 Department of Ecological and Biological Sciences, "Tuscia University  ... 
doi:10.1186/s12879-017-2633-0 pmid:28764637 pmcid:PMC5539894 fatcat:fxyuqtwthrhe5lvkxjd25mb4ey

Detecting virus contamination in seafood [chapter]

A. Bosch, R.M. Pintó, D.H. Lees, C.-H. von Bonsdorff, L. Croci, D. De Medici, F.S. Le Guyader
2008 Improving Seafood Products for the Consumer  
with the same combination of primers and probes as those used for the actual virus.  ...  The methods used for nucleic acid extraction are dependent on those used for virus elution and concentration.  ... 
doi:10.1533/9781845694586.3.194 fatcat:fzxesk23ova2tniyaq6c7tvsse

Signal to cut-off (S/CO) ratio and detection of HCV genotype 1 by real-time PCR one-step method: is there any direct relationship?

Guilherme Albertoni, CP Arnoni, PRB Araújo, FO Carvalho, JA Barreto
2010 Brazilian Journal of Infectious Diseases  
Study Design and Methods: Sera from blood donors were analyzed by Enzyme-Linked Immunosorbent Assay (ELISA) and RT-PCR assay to detect HCV infection.  ...  Polymerase chain reaction (PCR) methods play an essential role in providing data related to diagnosis, monitoring and treatment of hepatitis C virus (HCV) infection.  ...  Use of the PCR technique The development of DNA segments amplifi cation using PCR opened vast prospects for analysis of genes, diagnosis of genetic diseases, and detection of infectious agents, such as  ... 
doi:10.1590/s1413-86702010000200006 pmid:20563440 fatcat:mps6dlz3pjbw3dxzduunkpstdy

Signal to cut-off (S/CO) ratio and detection of HCV genotype 1 by real-time PCR one-step method: is there any direct relationship?

Guilherme Albertoni, C.P. Arnoni, P.R.B. Araújo, F.O. Carvalho, J.A. Barreto
2010 Brazilian Journal of Infectious Diseases  
Study Design and Methods: Sera from blood donors were analyzed by Enzyme-Linked Immunosorbent Assay (ELISA) and RT-PCR assay to detect HCV infection.  ...  Polymerase chain reaction (PCR) methods play an essential role in providing data related to diagnosis, monitoring and treatment of hepatitis C virus (HCV) infection.  ...  Use of the PCR technique The development of DNA segments amplifi cation using PCR opened vast prospects for analysis of genes, diagnosis of genetic diseases, and detection of infectious agents, such as  ... 
doi:10.1016/s1413-8670(10)70028-3 fatcat:c7i3ntgc4bcqhlx6da6iwoigaa
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