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Koo DH, Ju Y, Putta K, Sathishraj R, Roma-Burgos N, Jugulam M, Friebe B, Gill BS. Extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. PEST MANAGEMENT SCIENCE 2023; 79:4290-4294. [PMID: 37345512 DOI: 10.1002/ps.7626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND An Italian ryegrass population from Arkansas, USA developed glyphosate resistance due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. The plants in this population with approximately 70 EPSPS copies were used in the present study for the physical mapping of amplified copies of EPSPS gene to determine the possible mechanism of EPSPS gene amplification conferring glyphosate resistance in Italian ryegrass. RESULT Fluorescence in situ hybridization (FISH) analysis of glyphosate resistant (GR) Italian ryegrass plants with approximately 70 EPSPS copies displayed EPSPS hybridization signals randomly on most of the metaphase chromosomes. Glyphosate susceptible (GS) Italian ryegrass plants with one EPSPS copy displayed single prominent EPSPS hybridization signal, which was co-localized with 5S rDNA locus along with few additional signals on the outside of chromosomes. Pulsed-field gel electrophoresis (PFGE) followed by DNA blot using EPSPS gene as a probe identified a prominent EPSPS hybridization around the 400 kb region in GR DNA samples, but not in GS DNA samples. CONCLUSION We report the extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. Physical mapping of amplified copies of EPSPS gene in Italian ryegrass by FISH gives us a clue that the amplified copies of EPSPS gene may be present in the extrachromosomal DNA elements. Further analysis by PFGE followed by DNA blotting revealed that the extrachromosomal DNA containing EPSPS is approximately 400 kb similar in size with that of eccDNA replicon in Amaranthus palmeri. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yoonha Ju
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Rajendran Sathishraj
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Nilda Roma-Burgos
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
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Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong ITL, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, González RC, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law JA, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nat Genet 2022; 54:1746-1754. [PMID: 36253572 PMCID: PMC9649439 DOI: 10.1038/s41588-022-01190-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/22/2022] [Indexed: 12/15/2022]
Abstract
Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance. Targeted enrichment of ecDNA versus chromosomal DNA enabled phasing of genetic variants, identified the presence of an EGFRvIII mutation exclusively on ecDNAs and supported an excision model of ecDNA genesis in a glioblastoma model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNAs. We distinguished heterogeneous ecDNA species within the same sample by size and sequence with base-pair resolution and discovered functionally specialized ecDNAs that amplify select enhancers or oncogene-coding sequences.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Caterina I Colón
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shirley H Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kathleen E Houlahan
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenting Yang
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Zafar Khan MU, Khalid S, Humza M, Yang S, Alvi MA, Munir T, Ahmad W, Iqbal MZ, Tahir MF, Liu Y, Zhang J. Infection Dynamics of Clostridium perfringens Fingerprinting in Buffalo and Cattle of Punjab Province, Pakistan. Front Vet Sci 2022; 9:762449. [PMID: 35937290 PMCID: PMC9353052 DOI: 10.3389/fvets.2022.762449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/12/2022] [Indexed: 12/04/2022] Open
Abstract
Clostridium perfringens produces core virulence factors that are responsible for causing hemorrhagic abomasitis and enterotoxemia making food, animals, and humans susceptible to its infection. In this study, C. perfringens was isolated from necropsied intestinal content of buffalo and cattle belonging to four major bovine-producing regions in the Punjab Province of Pakistan for the purpose offind out the genetic variation. Out of total 160 bovine samples (n: 160), thirty-three (n: 33) isolates of C. perfringens were obtained from buffalo (Bubales bubalis) and cattle (Bos indicus) that were further subjected to biochemical tests; 16S rRNA based identification and toxinotyping was done using PCR (Polymerase Chain Reaction) and PFGE (Pulse Field Gel Electrophoresis) pulsotypesfor genetic diversity. Occurrence of C. perfringens was found to be maximum in zone-IV (Bhakkar and Dera Ghazi Khan) according to the heatmap. Correlation was found to be significant and positive among the toxinotypes (α-toxin, and ε-toxin). Response surface methodology (RSM) via central composite design (CCD) and Box-Behnken design (BBD) demonstrated substantial frequency of C. perfringens based toxinotypes in all sampling zones. PFGE distinguished all isolates into 26 different pulsotypes using SmaI subtyping. Co-clustering analysis based on PFGE further decoded a diversegenetic relationship among the collected isolates. This study could help us to advance toward disease array of C. perfringens and its probable transmission and control. This study demonstrates PFGE patterns from Pakistan, and typing of C. perfringens by PFGE helps illustrate and mitigate the incidence of running pulsotypes.
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Affiliation(s)
- Muhammad Umar Zafar Khan
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Shumaila Khalid
- Livestock and Dairy Development Department, Lahore, Pakistan
| | - Muhammad Humza
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Shunli Yang
- State Key Laboratory of Veterinary Etiological Biology of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Mughees Aizaz Alvi
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Tahir Munir
- Livestock and Dairy Development Department, Lahore, Pakistan
| | - Waqar Ahmad
- The Equine Clinic, Al-Hashar Stables, Muscat, Oman
| | - Muhammad Zahid Iqbal
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Yongsheng Liu
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- *Correspondence: Yongsheng Liu
| | - Jie Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Jie Zhang
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Abdeldayem OM, Dabbish AM, Habashy MM, Mostafa MK, Elhefnawy M, Amin L, Al-Sakkari EG, Ragab A, Rene ER. Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149834. [PMID: 34525746 PMCID: PMC8379898 DOI: 10.1016/j.scitotenv.2021.149834] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/18/2021] [Indexed: 05/06/2023]
Abstract
A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.
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Affiliation(s)
- Omar M Abdeldayem
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands.
| | - Areeg M Dabbish
- Biotechnology Graduate Program, Biology Department, School of Science and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Mahmoud M Habashy
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Mohamed K Mostafa
- Faculty of Engineering and Technology, Badr University in Cairo (BUC), Cairo 11829, Egypt
| | - Mohamed Elhefnawy
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Lobna Amin
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; Department of Built Environment, Aalto University, PO Box 15200, FI-00076, Aalto, Finland
| | - Eslam G Al-Sakkari
- Chemical Engineering Department, Cairo University, Cairo University Road, 12613 Giza, Egypt
| | - Ahmed Ragab
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; Faculty of Electronic Engineering, Menoufia University, 32952, Menouf, Egypt
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
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5
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Wang Y, Zhou Y, Zhang D, Wang X, Liu S. Extension of hydrodynamic chromatography to DNA fragment sizing and quantitation. Heliyon 2021; 7:e07904. [PMID: 34522803 PMCID: PMC8427238 DOI: 10.1016/j.heliyon.2021.e07904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/12/2021] [Accepted: 08/27/2021] [Indexed: 01/10/2023] Open
Abstract
Hydrodynamic chromatography (HDC) is a technique originally developed for separating particles. We have recently extended it to DNA fragment sizing and quantitation. In this review, we focus on this extension. After we briefly introduce the history of HDC, we present the evolution of open tubular HDC for DNA fragment sizing. We cover both the theoretical aspect and the experimental implementation of this technique. We describe various approaches to execute the separation, discuss its representative applications and provide a future perspective of this technique in the conclusion section of this review.
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Affiliation(s)
- Yanan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Yingyan Zhou
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Dongtang Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
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6
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Pilevar M, Kim KT, Lee WH. Recent advances in biosensors for detecting viruses in water and wastewater. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124656. [PMID: 33308919 DOI: 10.1016/j.jhazmat.2020.124656] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 05/09/2023]
Abstract
As there is a considerable number of virus particles in wastewater which cause numerous infectious diseases, it is necessary to eliminate viruses from domestic wastewater before it is released in the environment. In addition, on-site detection of viruses in wastewater can provide information on possible virus exposures in the community of a given wastewater catchment. For this purpose, the pre-detection of different strains of viruses in wastewaters is an essential environmental step. Epidemiological studies illustrate that viruses are the most challenging pathogens to be detected in water samples because of their nano sizes, discrete distribution, and low infective doses. Over the past decades, several methods have been applied for the detection of waterborne viruses which include polymerase chain reaction-based methods (PCR), enzyme-linked immunosorbent assay (ELISA), and nucleic acid sequence-based amplification (NASBA). Although they have shown acceptable performance in virus measurements, their drawbacks such as complicated and time-consuming procedures, low sensitivity, and high analytical cost call for alternatives. Although biosensors are still in an early stage for practical applications, they have shown great potential to become an alternative means for virus detection in water and wastewater. This comprehensive review addresses the different types of viruses found in water and the recent development of biosensors for detecting waterborne viruses.
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Affiliation(s)
- Mohsen Pilevar
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Keug Tae Kim
- Department of Environmental & Energy Engineering, The University of Suwon, 17 Wauan-gil, Bongdam-eup, Hwaseong-si, Gyeonggi-do 18323, South Korea
| | - Woo Hyoung Lee
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL 32816, USA.
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Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
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Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
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Lagos-Susaeta D, Salazar O, Asenjo JA. openPFGE: An open source and low cost pulsed-field gel electrophoresis equipment. HARDWAREX 2020; 8:e00128. [PMID: 35498240 PMCID: PMC9041189 DOI: 10.1016/j.ohx.2020.e00128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 06/14/2023]
Abstract
DNA electrophoresis is a fundamental technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp. Pulsed-field gel electrophoresis [PFGE] is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp. PFGE equipment is very expensive and it becomes an access barrier to many laboratories. Also, just a few privative designs of the equipment are available and it becomes difficult for the community to improve or customize their functioning. Here, we provide an open source PFGE equipment capable of the separation of DNA molecules up to, at least, ~2 Mbp and at low cost: USD$850, about 3% of the price of typical commercial equipment.
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Affiliation(s)
- Diego Lagos-Susaeta
- Corresponding author at: Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile.
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Phenotypic and Molecular Characterization of Plasmid-Mediated Virulence and Antimicrobial Resistance Traits among Multidrug Resistant Enterococcus spp. in Egypt. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.3.03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Enterococcus spp. are remarkable multidrug resistant (MDR) bacteria that are causing serious healthcare-associated infections. The current study investigated the frequency of Enterococcus spp., antimicrobial susceptibility, biofilm formation and the presence of some plasmid-mediated virulence characters and antimicrobial resistance determinants in enterococcal isolates from Egyptian hospitals in Cairo. Enterococcus bacterial isolates were recovered from different clinical specimens and identified using biochemical testing and KB005A HiStrep™ identification kit. Kirby-Bauer disc diffusion method and/or broth microdilution method were used to determine the antimicrobial susceptibility patterns. Phenotypic assays were performed to study biofilm formation and cytolysin and gelatinase production. PCR assays targeting the plasmid-carried genes aac(6’)-aph(2’), aph(3)-IIIa, vanA, agg and cylA were performed. In this study, 50 isolates of diverse Enterococcus spp. were identified with E. faecium was the most frequently isolated one. High resistance profiles were determined against tested antimicrobials and all isolates were MDR. Moderate biofilm formation was detected in 20% of isolates, 18% showed complete blood hemolysis and 12% produced gelatinase. All isolates carried the tested aminoglycosides resistance genes, while vanA was found only in 4 isolates (8%). The virulence genes agg and cylA were detected in 4% and 32% of isolates, respectively. In conclusion, E. faecium was the most prevalent species. The entire isolates set were MDR and the plasmid-carried aminoglycoside resistance genes were extensively disseminated among MDR isolates. Thus, regular surveillance studies, from the area of study or other geographical regions in Egypt, and strict infection control measures are required to monitor the emerging MDR enterococci.
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Takiguchi Y, Kariyazono R, Ohta K. Detection of DNA Damage-Induced DSBs by the Contour-Clamped Homogeneous Electric Field (CHEF) System in Mammalian Cells. Methods Mol Biol 2020; 2119:101-109. [PMID: 31989518 DOI: 10.1007/978-1-0716-0323-9_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Double-strand breaks (DSBs) and their repair mechanisms are essential for normal cell life. However, quantitative analysis of DSBs on mammalian whole chromosomes remains difficult. The method described here enables the quantitative detection of mammalian chromosomal DSBs by pulsed-field gel electrophoresis (PFGE) using a contour-clamped homogeneous electric field (CHEF). We illustrate this method by measuring DNA damage-induced DSBs in mammalian cells. The electrophoresis conditions presented here enabled the visualization of fragmented DNA (several mega-base pairs down to 500 kbp) as a single band. Using this protocol, about 10-45 samples can be analyzed on a single gel, depending on the direction of electrophoresis.
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Affiliation(s)
- Yuri Takiguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Ryo Kariyazono
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
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Abstract
Gel electrophoresis of DNA is one of the most frequently used techniques in molecular biology. Typically, it is used in the following: the analysis of in vitro reactions and purification of DNA fragments, analysis of PCR reactions, characterization of enzymes involved in DNA reactions, and sequencing. With some ingenuity gel electrophoresis of DNA is also used for the analysis of cellular biochemical reactions. For example, DNA breaks that accumulate in cells are analyzed by the comet assay and pulsed-field gel electrophoresis (PFGE). Furthermore, DNA replication intermediates are analyzed with two-dimensional (2D) gel electrophoresis. Moreover, several new methods for analyzing various chromosomal functions in cells have been developed. In this chapter, a brief introduction to these is given.
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Affiliation(s)
- Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, Yufu, Oita, Japan.
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Echeverri D, Romo J, Giraldo N, Atehortúa L. Microalgae protoplasts isolation and fusion for biotechnology research. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2019. [DOI: 10.15446/rev.colomb.biote.v21n1.80248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protoplasts are microbial or vegetable cells lacking a cell wall. These can be obtained from microalgae by an enzymatic hydrolysis process in the presence of an osmotic stabilizer. In general, protoplasts are experimentally useful in physiological, geneticand bio-chemical studies, so their acquisition and fusion will continue to be an active research area in modern biotechnology. The fusion of protoplasts in microalgae constitutes a tool for strain improvement because it allows both intra and interspecific genetic recombina-tion, resulting in organisms with new or improved characteristics of industrial interest. In this review we briefly describe themethod-ology for obtaining protoplasts, as well as fusion methods and the main applications of microalgal platforms.
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Yadav JP, Das SC, Dhaka P, Mukhopadhyay AK, Chowdhury G, Naskar S, Malik SS. Pulsed-field gel electrophoresis of enterotoxic Clostridium perfringens type A isolates recovered from humans and animals in Kolkata, India. Int J Vet Sci Med 2018; 6:123-126. [PMID: 30255089 PMCID: PMC6147381 DOI: 10.1016/j.ijvsm.2017.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 01/11/2023] Open
Abstract
Clostridium perfringens is one of the most important globally recognised gastroenteric pathogen in humans as well as animals. The present study was aimed to know the similarities/divergence among C. perfringens type A isolates of human and animal origin using the pulsed-field gel electrophoresis (PFGE) as a molecular tool. The enterotoxic isolates obtained by screening of human diarrhoeal cases (n = 130), diarrhoeal cases of pig (n = 52) and goat (n = 50), meat samples viz., pork (n = 59) and chevon (n = 57) were characterized by standard cultural and biochemical methods followed by PCR Assays. Accordingly, a total of 11 C. perfringens type A characterized isolates (16S rRNA+, cpa+, cpb2+ and cpe+) recovered from human diarrhoeal cases (n = 3); diarrhoeal cases of pig (n = 2) and goat (n = 2); meat samples viz. pork (n = 2) and chevon (n = 2) were examined employing PFGE. The observed clustering pattern in PFGE analysis showed the relatedness between isolates from diarrhoeal goat and chevon (90-100%); diarrhoeal pig and pork (65-68%); moreover, isolates from human diarrhoeal cases were exhibiting lineage to cases from goat and pig diarrhoea as well pork and chevon by 62-68% relatedness. The outcome of the present study indicates the probable contamination of this pathogen to the human food chain through faeces from suspected food animals viz. goat and pig and their improperly cooked meat.
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Affiliation(s)
- Jay P. Yadav
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
| | - Suresh C. Das
- Indian Veterinary Research Institute, Eastern Regional Station, 37, Belgachia Road, Kolkata 700 037, India
| | - Pankaj Dhaka
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata 700 010, India
| | - Goutam Chowdhury
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata 700 010, India
| | - Syamal Naskar
- Indian Veterinary Research Institute, Eastern Regional Station, 37, Belgachia Road, Kolkata 700 037, India
| | - Satyaveer S. Malik
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
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Marcone C. Pulsed-field gel electrophoresis for isolation of full-length phytoplasma chromosomes from plants. Methods Mol Biol 2013; 938:395-403. [PMID: 22987433 DOI: 10.1007/978-1-62703-089-2_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Pulsed-field gel electrophoresis (PFGE) is a powerful technique for genomic studies of unculturable plant-pathogenic phytoplasmas, which enables separation of full-length phytoplasma chromosomes from contaminating host plant nucleic acids. The PFGE method described here involves isolation of phytoplasmal DNA from high-titer phytoplasma-infected herbaceous plants using a phytoplasma enrichment procedure, embedding of phytoplasma chromosomes in agarose blocks, and separation of entire phytoplasma chromosomes from contaminating host plant nucleic acids by electrophoresis. Full-length phytoplasma chromosomes are resolved as single, discrete bands in the gel. The identity of these bands can be confirmed by Southern blot hybridization using a ribosomal DNA fragment as a probe. The method does not utilize gamma-irradiation to linearize phytoplasma chromosomes prior to electrophoresis.
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Affiliation(s)
- Carmine Marcone
- Department of Pharmaceutical and Biomedical Sciences, University of Salerno, Salerno, Italy.
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