1
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Tan J, Dong X, Liu H. Mitochondrial DNA is a sensitive surrogate and oxidative stress target in oral cancer cells. PLoS One 2024; 19:e0304939. [PMID: 39226291 PMCID: PMC11371132 DOI: 10.1371/journal.pone.0304939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/13/2024] [Indexed: 09/05/2024] Open
Abstract
Cellular oxidative stress mediated by intrinsic and/or extrinsic reactive oxygen species (ROS) is associated with disease pathogenesis. Oxidative DNA damage can naturally be substituted by mitochondrial DNA (mtDNA), leading to base lesion/strand break formation, copy number changes, and mutations. In this study, we devised a single test for the sensitive quantification of acute mtDNA damage, repair, and copy number changes using supercoiling-sensitive quantitative PCR (ss-qPCR) and examined how oxidative stress-related mtDNA damage responses occur in oral cancer cells. We observed that exogenous hydrogen peroxide (H2O2) induced dynamic mtDNA damage responses, as reflected by early structural DNA damage, followed by DNA repair if damage did not exceed a particular threshold. However, high oxidative stress levels induced persistent mtDNA damage and caused a 5-30-fold depletion in mtDNA copy numbers over late responses. This dramatic depletion was associated with significant growth arrest and apoptosis, suggesting persistent functional consequences. Moreover, oral cancer cells responded differentially to oxidative injury when compared with normal cells, and different ROS species triggered different biological consequences under stress conditions. In conclusion, we developed a new method for the sensitive detection of mtDNA damage and copy number changes, with exogenous H2O2 inducing dynamic mtDNA damage responses associated with functional changes in stressed cancer cells. Finally, our method can help characterize oxidative DNA damage in cancer and other human diseases.
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Affiliation(s)
- Jingyu Tan
- The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Xinlin Dong
- The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Haiwen Liu
- The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
- Liaoning Provincial Key Laboratory of Clinical Oncology Metabonomic, Jinzhou, China
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2
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Yu C, Asadian S, Tigano M. Molecular and cellular consequences of mitochondrial DNA double-stranded breaks. Hum Mol Genet 2024; 33:R12-R18. [PMID: 38779775 PMCID: PMC11112379 DOI: 10.1093/hmg/ddae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are subcellular organelles essential for life. Beyond their role in producing energy, mitochondria govern various physiological mechanisms, encompassing energy generation, metabolic processes, apoptotic events, and immune responses. Mitochondria also contain genetic material that is susceptible to various forms of damage. Mitochondrial double-stranded breaks (DSB) are toxic lesions that the nucleus repairs promptly. Nevertheless, the significance of DSB repair in mammalian mitochondria is controversial. This review presents an updated view of the available research on the consequences of mitochondrial DNA DSB from the molecular to the cellular level. We discuss the crucial function of mitochondrial DNA damage in regulating processes such as senescence, integrated stress response, and innate immunity. Lastly, we discuss the potential role of mitochondrial DNA DSB in mediating the cellular consequences of ionizing radiations, the standard of care in treating solid tumors.
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Affiliation(s)
- Chenxiao Yu
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Samieh Asadian
- Tehran University of Medical Sciences, Pour Sina St, Tehran 1416634793, Iran
| | - Marco Tigano
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
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3
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Wilkin T, Hamilton NA, Cawley AT, Bhat S, Baoutina A. PCR-Based Equine Gene Doping Test for the Australian Horseracing Industry. Int J Mol Sci 2024; 25:2570. [PMID: 38473816 DOI: 10.3390/ijms25052570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
The term 'gene doping' is used to describe the use of any unauthorized gene therapy techniques. We developed a test for five likely candidate genes for equine gene doping: EPO, FST, GH1, IGF1, and ILRN1. The test is based on real-time polymerase chain reaction (PCR) and includes separate screening and confirmation assays that detect different unique targets in each transgene. For doping material, we used nonviral (plasmid) and viral (recombinant adeno-associated virus) vectors carrying complementary DNA for the targeted genes; the vectors were accurately quantified by digital PCR. To reduce non-specific amplification from genomic DNA observed in some assays, a restriction digest step was introduced in the PCR protocol prior to cycling to cut the amplifiable targets within the endogenous genes. We made the screening stage of the test simpler and faster by multiplexing PCR assays for four transgenes (EPO, FST, IGF1, and ILRN1), while the GH1 assay is performed in simplex. Both stages of the test reliably detect at least 20 copies of each transgene in a background of genomic DNA equivalent to what is extracted from two milliliters of equine blood. The test protocol was documented and tested with equine blood samples provided by an official doping control authority. The developed tests will form the basis for screening official horseracing samples in Australia.
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Affiliation(s)
- Tessa Wilkin
- National Measurement Institute, Lindfield, NSW 2070, Australia
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW 2006, Australia
| | - Natasha A Hamilton
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW 2006, Australia
- Equine Genetics Research Centre, Racing Australia, Sydney, NSW 2000, Australia
| | - Adam T Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW 2000, Australia
- Racing Analytical Services Limited, Flemington, VIC 3031, Australia
| | - Somanath Bhat
- National Measurement Institute, Lindfield, NSW 2070, Australia
| | - Anna Baoutina
- National Measurement Institute, Lindfield, NSW 2070, Australia
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4
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Lautrup S, Myrup Holst C, Yde A, Asmussen S, Thinggaard V, Larsen K, Laursen LS, Richner M, Vægter CB, Prieto GA, Berchtold N, Cotman CW, Stevnsner T. The role of aging and brain-derived neurotrophic factor signaling in expression of base excision repair genes in the human brain. Aging Cell 2023; 22:e13905. [PMID: 37334527 PMCID: PMC10497833 DOI: 10.1111/acel.13905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/20/2023] Open
Abstract
DNA damage is a central contributor to the aging process. In the brain, a major threat to the DNA is the considerable amount of reactive oxygen species produced, which can inflict oxidative DNA damage. This type of damage is removed by the base excision repair (BER) pathway, an essential DNA repair mechanism, which contributes to genome stability in the brain. Despite the crucial role of the BER pathway, insights into how this pathway is affected by aging in the human brain and the underlying regulatory mechanisms are very limited. By microarray analysis of four cortical brain regions from humans aged 20-99 years (n = 57), we show that the expression of core BER genes is largely downregulated during aging across brain regions. Moreover, we find that expression of many BER genes correlates positively with the expression of the neurotrophin brain-derived neurotrophic factor (BDNF) in the human brain. In line with this, we identify binding sites for the BDNF-activated transcription factor, cyclic-AMP response element-binding protein (CREB), in the promoter of most BER genes and confirm the ability of BDNF to regulate several BER genes by BDNF treatment of mouse primary hippocampal neurons. Together, these findings uncover the transcriptional landscape of BER genes during aging of the brain and suggest BDNF as an important regulator of BER in the human brain.
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Affiliation(s)
- Sofie Lautrup
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
| | | | - Anne Yde
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Stine Asmussen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Vibeke Thinggaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Knud Larsen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Mette Richner
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience – DANDRITE, Nordic EMBL Partnership for Molecular MedicineAarhus UniversityAarhusDenmark
| | - Christian B. Vægter
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience – DANDRITE, Nordic EMBL Partnership for Molecular MedicineAarhus UniversityAarhusDenmark
| | - G. Aleph Prieto
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
- Instituto de NeurobiologíaUNAM‐JuriquillaJuriquillaMexico
| | - Nicole Berchtold
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Carl W. Cotman
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Tinna Stevnsner
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
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5
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Reyes-Calderón A, Mindreau-Ganoza E, Pardo-Figueroa B, Garcia-Luquillas KR, Yufra SP, Romero PE, Antonini C, Renom JM, Mota CR, Santa-Maria MC. Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption. Heliyon 2023; 9:e16130. [PMID: 37228686 PMCID: PMC10188194 DOI: 10.1016/j.heliyon.2023.e16130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/09/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl2 (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption.
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Affiliation(s)
- Alonso Reyes-Calderón
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Elías Mindreau-Ganoza
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, Peru
| | - Braulio Pardo-Figueroa
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Katherine R Garcia-Luquillas
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Sonia P Yufra
- Departamento de Ingeniería Metalúrgica e Ingeniería Ambiental, Universidad Nacional de San Agustín, Av. Independencia s/n, Arequipa, 04001, Peru
| | - Pedro E Romero
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, Peru
| | - Claudia Antonini
- Departamento de Ingeniería Industrial, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Jose-Miguel Renom
- Departamento de Ciencias, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Cesar R Mota
- Departamento de Engenharia Sanitária e Ambiental, Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, Belo Horizonte, 6.627, 31270-901, Brazil
| | - Monica C Santa-Maria
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
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6
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Damage to Nuclear and Mitochondrial DNA in Different Organs in Streptozotocin-Induced Diabetes Models in BALB/c Mice. Bull Exp Biol Med 2023; 174:349-353. [PMID: 36723752 DOI: 10.1007/s10517-023-05717-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 02/02/2023]
Abstract
Male BALB/c mice with streptozotocin-induced diabetes mellitus were used to study nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) damage using comet DNA assay and real-time PCR, respectively. In animals receiving single injection of streptozotocin in a dose of 200 mg/kg, severe hyperglycemia was observed on days 10 and 21 of the experiment, while after 5-fold administration of streptozotocin in a dose of 40 mg/kg, it developed on days 14 and 28. DNA damage and the level of atypical DNA comets in the liver increased both on days 10 and 21 after single administration of streptozotocin, and on days 14 and 28 after repeated administrations. The level of atypical DNA comets on day 21 after a single administration of streptozotocin increased in the kidneys, but not in the brain, testes, and pancreas. Real-time PCR revealed mtDNA damage in the liver, kidney, and pancreatic cells of mice with streptozotocin-induced diabetes. Thus, these animal models were found to reproduce pathognomic signs of diabetes, hyperglycemia, and nDNA damage; mtDNA damage was also detected.
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7
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Genome concentration, characterization, and integrity analysis of recombinant adeno-associated viral vectors using droplet digital PCR. PLoS One 2023; 18:e0280242. [PMID: 36696399 PMCID: PMC9876284 DOI: 10.1371/journal.pone.0280242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/24/2022] [Indexed: 01/26/2023] Open
Abstract
Precise, reproducible characterization of AAV is critical for comparing preclinical results between laboratories and determining a safe and effective clinical dose for gene therapy applications. In this study, we systematically evaluated numerous parameters to produce a simple and robust ddPCR protocol for AAV characterization. The protocol uses a low ionic strength buffer containing Pluronic-F68 and polyadenylic acid to dilute the AAV into the ddPCR concentration range and a 10-minute thermal capsid lysis prior to assembling ddPCR reactions containing MspI. A critical finding is that the buffer composition affected the ITR concentration of AAV but not the ITR concentration of a double stranded plasmid, which has implications when using a theoretical, stoichiometric conversion factor to obtain the titer based on the ITR concentration. Using this protocol, a more comprehensive analysis of an AAV vector formulation was demonstrated with multiple ddPCR assays distributed throughout the AAV vector genome. These assays amplify the ITR, regulatory elements, and eGFP transgene to provide a more confident estimate of the vector genome concentration and a high-resolution characterization of the vector genome identity. Additionally, we compared two methods of genome integrity analysis for three control sample types at eight different concentrations for each sample. The genome integrity was independent of sample concentration and the expected values were obtained when integrity was determined based on the excess number of positive droplets relative to the number of double positive droplets expected by chance co-encapsulation of two DNA targets. The genome integrity was highly variable and produced unexpected values when the double positive droplet percentage was used to calculate the genome integrity. A protocol using a one-minute thermal capsid lysis prior to assembling ddPCR reactions lacking a restriction enzyme used the non-ITR assays in a duplex ddPCR milepost experiment to determine the genome integrity using linkage analysis.
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Marra M, D’Errico C, Montemurro C, Ratti C, Baldoni E, Matic S, Accotto GP. Fast and Sensitive Detection of Soil-Borne Cereal Mosaic Virus in Leaf Crude Extract of Durum Wheat. Viruses 2022; 15:140. [PMID: 36680180 PMCID: PMC9866084 DOI: 10.3390/v15010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Soil-borne cereal mosaic virus (SBCMV) is a furovirus with rigid rod-shaped particles containing an ssRNA genome, transmitted by Polymyxa graminis Led., a plasmodiophorid that can persist in soil for up to 20 years. SBCMV was reported on common and durum wheat and it can cause yield losses of up to 70%. Detection protocols currently available are costly and time-consuming (real-time PCR) or have limited sensitivity (ELISA). To facilitate an efficient investigation of the real dispersal of SBCMV, it is necessary to develop a new detection tool with the following characteristics: no extraction steps, very fast results, and high sensitivity to allow pooling of a large number of samples. In the present work, we have developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) protocol with such characteristics, and we have compared it with real-time PCR. Our results show that the sensitivity of LAMP and real-time PCR on cDNA and RT-LAMP on crude extracts are comparable, with the obvious advantage that RT-LAMP produces results in minutes rather than hours. This paves the way for extensive field surveys, leading to a better knowledge of the impact of this virus on wheat health and yield.
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Affiliation(s)
- Monica Marra
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Chiara D’Errico
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
- European Laboratory for Non-Linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy
- Institute for Sustainable Plant Protection, National Research Council, 70126 Bari, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elena Baldoni
- Institute of Agricultural Biology and Biotechnology, National Research Council, 20133 Milan, Italy
| | - Slavica Matic
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
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Berden P, Wiederkehr RS, Lagae L, Michiels J, Stakenborg T, Fauvart M, Van Roy W. Amplification Efficiency and Template Accessibility as Distinct Causes of Rain in Digital PCR: Monte Carlo Modeling and Experimental Validation. Anal Chem 2022; 94:15781-15789. [DOI: 10.1021/acs.analchem.2c03534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pieter Berden
- Imec, Leuven 3001, Belgium
- Department of Physics and Astronomy, KU Leuven, Leuven 3001, Belgium
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
| | | | - Liesbet Lagae
- Imec, Leuven 3001, Belgium
- Department of Physics and Astronomy, KU Leuven, Leuven 3001, Belgium
| | - Jan Michiels
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
| | | | - Maarten Fauvart
- Imec, Leuven 3001, Belgium
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
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Najjari M, Sadjjadi SM, Khodadadi H, Farzaneh MR, Mattiucci S. Anisakis spp, DNA detection in paraffin-embedded tissue biopsies recovered from patients with gastritis using real-time PCR in Bushehr, Persian Gulf, Iran. Mol Biochem Parasitol 2022; 251:111494. [PMID: 35817309 DOI: 10.1016/j.molbiopara.2022.111494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Anisakiasis is a zoonotic fish-born parasitic disease caused by anisakid nematodes. Paraffin-embedded blocks containing biopsy samples taken from patients suffering gastritis with unknown causes were investigated by real-time PCR, in the Bushehr region, Iran; where human anisakiasis has not been reported, so far. A total of 50 paraffin-embedded blocks were randomly selected from 250 archived blocks of the patients with gastritis. A SYBER green-based real-time PCR targeting the ITS1 region was developed for the identification of Anisakis genus. An 86 bp partial fragment of the Anisakis spp. ITS1 gene was amplified successfully. A total of 3 out of 50 samples (6 %) had positive amplification in the samples and their pathology reports showed a significant finding of moderate chronic gastritis with or without ulcers. In conclusion, the developed qPCR could be used for detecting Anisakis spp. larval DNA in human biopsy blocks. This study showed the hidden human cases of anisakiasis in the Bushehr for the first time.
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Affiliation(s)
- Mohsen Najjari
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mahmoud Sadjjadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hossein Khodadadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Reza Farzaneh
- Department of Pathology, Faculty Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University, Rome, Italy.
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11
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PCR-Based Analytical Methods for Quantification and Quality Control of Recombinant Adeno-Associated Viral Vector Preparations. Pharmaceuticals (Basel) 2021; 15:ph15010023. [PMID: 35056080 PMCID: PMC8779925 DOI: 10.3390/ph15010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
Recombinant adeno-associated viral vectors (rAAV) represent a gene therapy tool of ever-increasing importance. Their utilization as a delivery vehicle for gene replacement, silencing and editing, among other purposes, demonstrate considerable versatility. Emerging vector utilization in various experimental, preclinical and clinical applications establishes the necessity of producing and characterizing a wide variety of rAAV preparations. Critically important characteristics concerning quality control are rAAV titer quantification and the detection of impurities. Differences in rAAV constructs necessitate the development of highly standardized quantification assays to make direct comparisons of different preparations in terms of assembly or purification efficiency, as well as experimental or therapeutic dosages. The development of universal methods for impurities quantification is rather complicated, since variable production platforms are utilized for rAAV assembly. However, general agreements also should be achieved to address this issue. The majority of methods for rAAV quantification and quality control are based on PCR techniques. Despite the progress made, increasing evidence concerning high variability in titration assays indicates poor standardization of the methods undertaken to date. This review summarizes successes in the field of rAAV quality control and emphasizes ongoing challenges in PCR applications for rAAV characterization. General considerations regarding possible solutions are also provided.
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12
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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13
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Cantera JL, White HN, Forrest MS, Stringer OW, Belizario VY, Storey HL, de Hostos EL, de los Santos T. Sensitive and semiquantitative detection of soil-transmitted helminth infection in stool using a recombinase polymerase amplification-based assay. PLoS Negl Trop Dis 2021; 15:e0009782. [PMID: 34516554 PMCID: PMC8459997 DOI: 10.1371/journal.pntd.0009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 09/23/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Soil-transmitted helminths (STHs) are parasitic nematodes that inhabit the human intestine. They affect more than 1.5 billion people worldwide, causing physical and cognitive impairment in children. The global strategy to control STH infection includes periodic mass drug administration (MDA) based on the results of diagnostic testing among populations at risk, but the current microscopy method for detecting infection has diminished sensitivity as the intensity of infection decreases. Thus, improved diagnostic tools are needed to support decision-making for STH control programs. Methodology We developed a nucleic acid amplification test based on recombinase polymerase amplification (RPA) technology to detect STH in stool. We designed primers and probes for each of the four STH species, optimized the assay, and then verified its performance using clinical stool samples. Principal findings Each RPA assay was as sensitive as a real-time polymerase chain reaction (PCR) assay in detecting copies of cloned target DNA sequences. The RPA assay amplified the target in DNA extracted from human stool samples that were positive for STH based on the Kato-Katz method, with no cross-reactivity of the non-target genomic DNA. When tested with clinical stool samples from patients with infections of light, moderate, and heavy intensity, the RPA assays demonstrated performance comparable to that of real-time PCR, with better results than Kato-Katz. This new rapid, sensitive and field-deployable method for detecting STH infections can help STH control programs achieve their goals. Conclusions Semi-quantitation of target by RPA assay is possible and is comparable to real-time PCR. With proper instrumentation, RPA assays can provide robust, semi-quantification of STH DNA targets as an alternative field-deployable indicator to counts of helminth eggs for assessing infection intensity. More than 1.5 billion people are infected with parasitic intestinal worms called soil-transmitted helminths. Infection is transmitted by helminth eggs in human feces, which contaminate soil in areas with poor sanitation. Adverse health effects include physical and cognitive impairment in children. A key strategy to control infection is periodic mass drug administration for populations with a high prevalence of disease based on the results of diagnostic testing. The current microscopy method for detecting infection, however, has limited ability to detect disease as the intensity of infection decreases with repeated mass drug administration. To address limitations of current diagnostic methods, we developed a novel technique to diagnose infections, including those at very low levels of intensity, by detecting helminth DNA in stool samples. Our initial studies suggest that the new diagnostic technique reliably detects the presence of intestinal worms, even at low intensities of infection, and may be more useful than currently available diagnostic tools for guiding the use of periodic mass drug administration to eliminate disease in low-resource settings.
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Affiliation(s)
| | | | | | | | - Vicente Y. Belizario
- Department of Parasitology, College of Public Health, University of the Philippines, Ermita, Manila, Philippines
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14
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Chik AHS, Glier MB, Servos M, Mangat CS, Pang XL, Qiu Y, D'Aoust PM, Burnet JB, Delatolla R, Dorner S, Geng Q, Giesy JP, McKay RM, Mulvey MR, Prystajecky N, Srikanthan N, Xie Y, Conant B, Hrudey SE. Comparison of approaches to quantify SARS-CoV-2 in wastewater using RT-qPCR: Results and implications from a collaborative inter-laboratory study in Canada. J Environ Sci (China) 2021; 107:218-229. [PMID: 34412784 PMCID: PMC7929783 DOI: 10.1016/j.jes.2021.01.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 05/20/2023]
Abstract
Detection of SARS-CoV-2 RNA in wastewater is a promising tool for informing public health decisions during the COVID-19 pandemic. However, approaches for its analysis by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) are still far from standardized globally. To characterize inter- and intra-laboratory variability among results when using various methods deployed across Canada, aliquots from a real wastewater sample were spiked with surrogates of SARS-CoV-2 (gamma-radiation inactivated SARS-CoV-2 and human coronavirus strain 229E [HCoV-229E]) at low and high levels then provided "blind" to eight laboratories. Concentration estimates reported by individual laboratories were consistently within a 1.0-log10 range for aliquots of the same spiked condition. All laboratories distinguished between low- and high-spikes for both surrogates. As expected, greater variability was observed in the results amongst laboratories than within individual laboratories, but SARS-CoV-2 RNA concentration estimates for each spiked condition remained mostly within 1.0-log10 ranges. The no-spike wastewater aliquots provided yielded non-detects or trace levels (<20 gene copies/mL) of SARS-CoV-2 RNA. Detections appear linked to methods that included or focused on the solids fraction of the wastewater matrix and might represent in-situ SARS-CoV-2 to the wastewater sample. HCoV-229E RNA was not detected in the no-spike aliquots. Overall, all methods yielded comparable results at the conditions tested. Partitioning behavior of SARS-CoV-2 and spiked surrogates in wastewater should be considered to evaluate method effectiveness. A consistent method and laboratory to explore wastewater SARS-CoV-2 temporal trends for a given system, with appropriate quality control protocols and documented in adequate detail should succeed.
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Affiliation(s)
- Alex H S Chik
- Consultant to Canadian Water Network Inc., Kitchener, Canada; Presently at Ontario Clean Water Agency, Mississauga, Canada
| | - Melissa B Glier
- Environmental Microbiology, BC Centre for Disease Control, Vancouver, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Chand S Mangat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Xiao-Li Pang
- Public Health Laboratory, Alberta Precision Laboratory, Edmonton, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada
| | | | - Jean-Baptiste Burnet
- Département des génies civil, géologique et des mines, Polytechnique Montréal, Montréal, Canada
| | | | - Sarah Dorner
- Département des génies civil, géologique et des mines, Polytechnique Montréal, Montréal, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - John P Giesy
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, Canada
| | - Robert Mike McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Natalie Prystajecky
- Environmental Microbiology, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, Canada
| | | | - Steve E Hrudey
- Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada.
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15
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Development of a Tetraplex qPCR for the Molecular Identification and Quantification of Human Enteric Viruses, NoV and HAV, in Fish Samples. Microorganisms 2021; 9:microorganisms9061149. [PMID: 34071891 PMCID: PMC8227966 DOI: 10.3390/microorganisms9061149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Human enteric viruses such as norovirus (NoV) and hepatitis A virus (HAV) are some of the most important causes of foodborne infections worldwide. Usually, infection via fish consumption is not a concern regarding these viruses, since fish are mainly consumed cooked. However, in the last years, raw fish consumption has become increasingly common, especially involving the use of seabass and gilthead seabream in dishes like sushi, sashimi, poke, and carpaccio. Therefore, the risk for viral infection via the consumption of raw fish has also increased. In this study, a virologic screening was performed in 323 fish specimens captured along the Portuguese coast using a tetraplex qPCR optimised for two templates (plasmid and in vitro transcribed RNA) to detect and quantify NoV GI, NoV GII and HAV genomes. A difference of approximately 1-log was found between the use of plasmid or in vitro transcribed RNA for molecular-based quantifications, showing an underestimation of genome copy-number equivalents using plasmid standard-based curves. Additionally, the presence of NoV genomic RNA in a pool of seabass brains was identified, which was shown to cluster with a major group of human norovirus sequences from genogroup I (GI.1) by phylogenetic analysis. None of the analysed fish revealed the presence of NoV GII or HAV. This result corroborates the hypothesis that enteric viruses circulate in seawater or that fish were contaminated during their transportation/handling, representing a potential risk to humans through raw or undercooked fish consumption.
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16
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Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Wang DY, Loh KS, Lu TK, Yu H. Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 2021; 274:120876. [PMID: 34034027 DOI: 10.1016/j.biomaterials.2021.120876] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Rapid diagnostics of adventitious agents in biopharmaceutical/cell manufacturing release testing and the fight against viral infection have become critical. Quantitative real-time PCR and CRISPR-based methods rapidly detect DNA/RNA in 1 h but suffer from inter-site variability. Absolute quantification of DNA/RNA by methods such as digital PCR reduce this variability but are currently too slow for wider application. Here, we report a RApid DIgital Crispr Approach (RADICA) for absolute quantification of nucleic acids in 40-60 min. Using SARS-CoV-2 as a proof-of-concept target, RADICA allows for absolute quantification with a linear dynamic range of 0.6-2027 copies/μL (R2 value > 0.99), high accuracy and low variability, no cross-reactivity to similar targets, and high tolerance to human background DNA. RADICA's versatility is validated against other targets such as Epstein-Barr virus (EBV) from human B cells and patients' serum. RADICA can accurately detect and absolutely quantify EBV DNA with similar dynamic range of 0.5-2100 copies/μL (R2 value > 0.98) in 1 h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based detection. RADICA therefore enables rapid and sensitive absolute quantification of nucleic acids which can be widely applied across clinical, research, and biomanufacturing areas.
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Affiliation(s)
- Xiaolin Wu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Cheryl Chan
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Yie Hou Lee
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Stacy L Springs
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - De Yun Wang
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Timothy K Lu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA.
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Institute of Bioengineering and Bioimaging, A*STAR, The Nanos, #04-01, 31, Biopolis Way, 138669, Singapore; Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, 117411, Singapore; Department of Physiology & the Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, 117593, Singapore.
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17
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Suoranta T, Laham-Karam N, Ylä-Herttuala S. Optimized Protocol for Accurate Titration of Adeno-Associated Virus Vectors. Hum Gene Ther 2021; 32:1270-1279. [PMID: 33560161 DOI: 10.1089/hum.2020.318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adeno-associated virus (AAV) is currently the most popular gene delivery vector for in vivo gene therapy. However, variability in titration methods between different laboratories affects the reproducibility of experiments and evaluation of safety and efficacy in clinical trials. We describe an optimized protocol for AAV titration, including quantitative PCR (qPCR) standard preparation and quantitation and treatment of AAV samples before qPCR and droplet digital PCR (ddPCR) titration. During the protocol development, we observed that quantitation of the qPCR standard was dependent on its conformation and that A260-based quantitation overestimated the plasmid copy numbers, introducing significant error. Linearized, free inverted terminal repeat (free-ITR), and supercoiled standards were compared with enhanced green fluorescent protein (EGFP), SV40p(A), and AAV2-ITR qPCR assays and we found that using the AAV2-ITR assay together with either linearized or supercoiled standard led to overestimation of the titers, while EGFP and SV40p(A) assays were more accurate with the linearized standard. Finally, we compared extraction of AAV1, AAV2, AAV5, AAV6, AAV8, and AAV9 genomes by heat denaturation, proteinase K treatment, and kit extraction. Kit extraction, which contained proteinase K treatment in denaturing buffer before spin-column purification, significantly increased the titers acquired for all the serotypes in both qPCR and ddPCR. These improvements resulted in an accurate quantitation of the ATCC reference standard and in a robust and reliable protocol for AAV titration.
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Affiliation(s)
- Tuisku Suoranta
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,Heart Center, Kuopio University Hospital, Kuopio, Finland.,Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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18
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Barkallah M, Elleuch J, Smith KF, Chaari S, Ben Neila I, Fendri I, Michaud P, Abdelkafi S. Development and application of a real-time PCR assay for the sensitive detection of diarrheic toxin producer Prorocentrum lima. J Microbiol Methods 2020; 178:106081. [PMID: 33035573 DOI: 10.1016/j.mimet.2020.106081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022]
Abstract
Prorocentrum lima (P. lima) is a widely spread dinoflagellate in the Mediterranean Sea and it has become increasingly involved in harmful algal blooms. The purpose of this study is to develop a probe-based real-time polymerase chain reaction (PCR) targeting the ITS1-5.8S-ITS2 region for the detection and absolute quantification of P. lima based on linear and circular DNA standards. The results have shown that the quantitative PCR (q-PCR), using circular plasmid as a template, gave a threshold cycle number 1.79-5.6 greater than equimolar linear standards. When microalgae, commonly found in aquatic samples were tested, no cross-amplification was observed. The q-PCR brought about a good intra and inter-run reproducibility and a detection limit of 5 copies of linear plasmid per reaction. A quantitative relationship between the cell numbers and their corresponding plasmid copy numbers was attained. Afterwards, the effectiveness of the developed protocol was tested with 130 aquatic samples taken from 19 Tunisian sampling sites. The developed q-PCR had a detection sensitivity of up to 1 cell. All the positive samples were taken from three sampling sites of Medenine Governorate with cell abundances that ranged from 22 to 156,000 cells L-1 of seawater. The q-PCR assay revealed a high sensitivity in monitoring the aquatic samples in which the low concentrations of P. lima were not accurately detected by light microscopy. Indeed, this approach is at the same time rapid, specific and sensitive than the traditional microscopy techniques and it represents a great potential for the monitoring of P. lima blooms.
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Affiliation(s)
- Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, 3038 Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, 3038 Sfax, Tunisia
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson 7042, New Zealand
| | - Siwar Chaari
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, 3038 Sfax, Tunisia
| | | | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the improvement of Cultures, Faculty of Sciences of Sfax, B.P. 1171, 3000, University of Sfax, 3029 Sfax, Tunisia
| | - Philippe Michaud
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, F-63000 Clermont-Ferrand, France
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, 3038 Sfax, Tunisia.
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19
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Patsali P, Papasavva P, Christou S, Sitarou M, Antoniou MN, Lederer CW, Kleanthous M. Relative and Absolute Quantification of Aberrant and Normal Splice Variants in HBBIVSI-110 (G > A) β-Thalassemia. Int J Mol Sci 2020; 21:E6671. [PMID: 32933098 PMCID: PMC7555009 DOI: 10.3390/ijms21186671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The β-thalassemias are an increasing challenge to health systems worldwide, caused by absent or reduced β-globin (HBB) production. Of particular frequency in many Western countries is HBBIVSI-110(G > A) β-thalassemia (HGVS name: HBB:c.93-21G > A). Its underlying mutation creates an abnormal splice acceptor site in the HBB gene, and while partially retaining normal splicing of HBB, it severely reduces HBB protein expression from the mutant locus and HBB loci in trans. For the assessment of the underlying mechanisms and of therapies targeting β-thalassemia, accurate quantification of aberrant and normal HBB mRNA is essential, but to date, has only been performed by approximate methods. To address this shortcoming, we have developed an accurate, duplex reverse-transcription quantitative PCR assay for the assessment of the ratio and absolute quantities of normal and aberrant mRNA species as a tool for basic and translational research of HBBIVSI-110(G > A) β-thalassemia. The method was employed here to determine mRNA ratios and quantities in blood and primary cell culture samples and correlate them with HBB protein levels. Moreover, with its immediate utility for β-thalassemia and the mutation in hand, the approach can readily be adopted for analysis of alternative splicing or for quantitative assays of any disease-causing mutation that interferes with normal splicing.
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Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; (P.P.); (P.P.); (M.K.)
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; (P.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 1683, Cyprus
| | | | - Maria Sitarou
- Thalassaemia Clinic Larnaca, Ministry of Health, Larnaca 6301, Cyprus;
| | - Michael N. Antoniou
- Department of Medical and Molecular Genetics, King’s College London, London SE1 9RT, UK;
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; (P.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 1683, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; (P.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 1683, Cyprus
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20
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Beinhauerova M, Babak V, Bertasi B, Boniotti MB, Kralik P. Utilization of Digital PCR in Quantity Verification of Plasmid Standards Used in Quantitative PCR. Front Mol Biosci 2020; 7:155. [PMID: 32850953 PMCID: PMC7403525 DOI: 10.3389/fmolb.2020.00155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/19/2020] [Indexed: 01/07/2023] Open
Abstract
Quantitative PCR (qPCR) is a widely used method for nucleic acid quantification of various pathogenic microorganisms. For absolute quantification of microbial load by qPCR, it is essential to create a calibration curve from accurately quantified quantification standards, from which the number of pathogens in a sample is derived. Spectrophotometric measurement of absorbance is a routine method for estimating nucleic acid concentration, however, it may be affected by presence of other potentially contaminating nucleic acids or proteins and salts. Therefore, absorbance measurement is not reliable for estimating the concentration of stock solutions of quantification standards, based on which they are subsequently diluted. In this study, we utilized digital PCR (dPCR) for absolute quantification of qPCR plasmid standards and thus detecting possible discrepancies in the determination of the plasmid DNA number of standards derived from UV spectrophotometry. The concept of dPCR utilization for quantification of standards was applied on 45 qPCR assays using droplet-based and chip-based dPCR platforms. Using dPCR, we found that spectrophotometry overestimated the concentrations of standard stock solutions in the majority of cases. Furthermore, batch-to-batch variation in standard quantity was revealed, as well as quantitative changes in standards over time. Finally, it was demonstrated that droplet-based dPCR is a suitable tool for achieving defined quantity of quantification plasmid standards and ensuring the quantity over time, which is crucial for acquiring homogenous, reproducible and comparable quantitative data by qPCR.
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Affiliation(s)
- Martina Beinhauerova
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vladimir Babak
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia
| | - Barbara Bertasi
- Controllo Alimenti, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Maria Beatrice Boniotti
- Tecnologie Biologiche Applicate, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia.,Department of Hygiene and Technology of Food of Animal Origin and of Gastronomy, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia
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21
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O'Hara R, Tedone E, Ludlow A, Huang E, Arosio B, Mari D, Shay JW. Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution. Genome Res 2019; 29:1878-1888. [PMID: 31548359 PMCID: PMC6836731 DOI: 10.1101/gr.250480.119] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation, and motility, as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here, we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method, droplet digital mitochondrial DNA measurement (ddMDM), to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 h, is optimized for 96-well plates, and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. We show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.
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Affiliation(s)
- Ryan O'Hara
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Enzo Tedone
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Ludlow
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ejun Huang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Beatrice Arosio
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, 20122 Milan, Italy.,Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Daniela Mari
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, 20122 Milan, Italy.,Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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22
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Guo Y, He Y, Wu S, Zhang S, Song D, Zhu Z, Guo Z, Wang X. Enhancing Cytotoxicity of a Monofunctional Platinum Complex via a Dual-DNA-Damage Approach. Inorg Chem 2019; 58:13150-13160. [PMID: 31539237 DOI: 10.1021/acs.inorgchem.9b02033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) is an attractive cellular target for anticancer agents in addition to nuclear DNA (nDNA). The cationic platinum(II) complex cis-[Pt(NP)(NH3)2Cl]NO3 (PtNP, NP = N-(2-ethylpyridine)-1,8-naphthalimide) bearing the DNA-intercalating moiety NP was designed. The structure of PtNP was fully characterized by single-crystal X-ray crystallography, NMR, and HRMS. PtNP is superior to cisplatin in both in vitro and in vivo anticancer activities with low systemic toxicity. The interaction of PtNP with CT-DNA demonstrated that PtNP could effectively bind to DNA through both covalent and noncovalent double binding modes. In addition to causing significant damage to nDNA and remarkable inhibition to DNA damage repair, PtNP also distributed in mitochondria, inducing mtDNA damage and affecting the downstream transcriptional level of mitochondrion-encoded genes. In addition, PtNP disturbed the physiological processes of mitochondria by reducing the mitochondrial membrane potential and promoting the generation of reactive oxygen species. Mechanistic studies demonstrate that PtNP induced apoptosis via mitochondrial pathways by upregulating Bax and Puma and downregulating Bcl-2 proteins, leading to the release of cytochrome c and activation of caspase-3 and caspase-9. As a dual-DNA-damage agent, PtNP is able to improve the anticancer activity by damaging both nuclear and mitochondrial DNA, thus providing a new anticancer mechanism of action for the naphthalimide monofunctional platinum(II) complexes.
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Affiliation(s)
- Yan Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Yafeng He
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Shengde Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Shuren Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Zhenzhu Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Xiaoyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , People's Republic of China
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23
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Zhao W, Wang Q, Xu Z, Liu R, Cui F. Distinct replication and gene expression strategies of the Rice Stripe virus in vector insects and host plants. J Gen Virol 2019; 100:877-888. [PMID: 30990404 DOI: 10.1099/jgv.0.001255] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Persistent propagative plant viruses are usually transmitted between a vector insect and a host plant. To adapt to the two different organisms, viruses may show distinct genomic replication or gene expression patterns. To verify this hypothesis, we applied an aboslute real-time quantitative PCR method to measure and compare the replication levels of four genomic RNA segments and the expression levels of seven genes of rice stripe virus (RSV) according to the infection time in the small brown planthopper and rice plant, respectively. In the vector insect, RNA3 began replicating later than the other segments, and RNA2 remained nearly constant during the infection process. RNA1 was the dominant segment, and a difference of over 300-fold appeared among the four segments. In rice plants, the size of the four segments increased with infection time, but decreased to a low level in the late infection period. The ratios of the four segments varied by no more than 15-fold. In planthoppers, three expression patterns were observed for the seven viral genes during viral infection, while in rice plants, the expression patterns of the seven viral genes were similar. These results reflect distinct genomic replication and gene expression patterns in a persistent propagative plant virus in adapting to vector insects and host plants.
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Affiliation(s)
- Wan Zhao
- 1State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qianshuo Wang
- 1State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
- 2Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, PR China
| | - Zhongtian Xu
- 3Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, PR China
- 4University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Renyi Liu
- 5College of Horticulture and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Feng Cui
- 1State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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24
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Döring J, Hurek T. Dual coding potential of a 2',5'-branched ribonucleotide in DNA. RNA (NEW YORK, N.Y.) 2019; 25:105-120. [PMID: 30361268 PMCID: PMC6298571 DOI: 10.1261/rna.068486.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
Branchpoints in RNA templates are highly mutagenic, but it is not known yet whether this also applies to branchpoints in DNA templates. Here, we report how nucleic acid polymerases replicate a 2',5'-branched DNA (bDNA) molecule. We constructed long-chained bDNA templates containing a branch guanosine and T7 promoters at both arms by splinted ligation. Quantitative real-time PCR analysis was used to investigate whether a branchpoint blocks DNA synthesis from the two arms in the same manner. We find that the blocking effect of a branchpoint is arm-specific. DNA synthesis from the 2'-arm is more than 20,000-fold decreased, whereas from the 3'-arm only 15-fold. Our sequence analysis of full-length nucleic acid generated by Taq DNA polymerase, Moloney murine leukemia virus reverse transcriptase, and T7 RNA polymerase from the 2'-arm of bDNA shows that the branched guanine has a dual coding potential and can base-pair with cytosine and guanine. We find that branchpoint templating is influenced by the type of the surrounding nucleic acid and is probably modulated by polymerase and RNase H active sites. We show that the branchpoint bypass by the polymerases from the 3'-arm of bDNA is predominantly error-free, indicating that bDNA is not as highly mutagenic as 2',5'-branched RNA.
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Affiliation(s)
- Jessica Döring
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
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25
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Chen Z, Tian Y, Zhu C, Liu B, Zhang Y, Lu Z, Zhou Q, Wu Z. Sensitive detection of oxidative DNA damage in cyanobacterial cells using supercoiling-sensitive quantitative PCR. CHEMOSPHERE 2018; 211:164-172. [PMID: 30071428 DOI: 10.1016/j.chemosphere.2018.06.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/25/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
Supercoiling-sensitive quantitative PCR (ss-qPCR) is a sensitive technique to detect DNA damage in cultured animal cells and cultured/clinical human cells in vitro. In this study, we investigated whether the ss-qPCR method can be applied as a sensitive means to detect oxidative DNA damage in unicellular organisms. We used the model cyanobacterium Synechococcus elongatus PCC 7942 as a test organism and H2O2 as an exogenetic oxidative toxicant. Results showed that a significant increase in the plasmid DNA damage of S. elongatus PCC 7942 was induced by H2O2 in a dose- and time-dependent manner. The sensitivity of ss-qPCR in detecting DNA damage of the cyanobacterium was higher than the cell inhibition method (up to 255 times) as calculated from the slopes of fitted curves in the tested sub-toxic concentration range of 1-5 mM H2O2. Ss-qPCR also detected repairable low-intensity DNA damage in the cyanobacterium when DNA repair inhibitors were used. The detection limit of modified ss-qPCR was one tenth of that of previous methods. We also observed that ss-qPCR can be used to detect genomic DNA conformation change of cyanobacterium exposed to H2O2. Thus, this method will provide a powerful technical support for investigating the mechanisms of cyanobacterial DNA damage by environmental factors, especially intracellular reactive oxygen species enhancement-related factors.
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Affiliation(s)
- Zhilan Chen
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Hunan University of Science and Technology, Taoyuan Road, Yuhu District, Xiangtan 411201, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing, China; Hunan Province Key Laboratory of Coal Resources Clean-utilization and Mine Environment Protection, Hunan University of Science and Technology, Taoyuan Road, Yuhu District, Xiangtan 411201, China
| | - Yun Tian
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
| | - Chenhong Zhu
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Hunan University of Science and Technology, Taoyuan Road, Yuhu District, Xiangtan 411201, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing, China
| | - Biyun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
| | - Yongyuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
| | - Zhiying Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China.
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
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26
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Shirima RR, Maeda DG, Kanju E, Ceasar G, Tibazarwa FI, Legg JP. Absolute quantification of cassava brown streak virus mRNA by real-time qPCR. J Virol Methods 2017; 245:5-13. [PMID: 28315718 PMCID: PMC5429390 DOI: 10.1016/j.jviromet.2017.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 11/18/2022]
Abstract
Cassava brown streak disease (CBSD) is the most important virus disease of cassava and a major food security threat in Africa. Yearly economic losses of up to $100 million USD have been attributed to CBSD. The lack of information on plant-virus interactions has restricted progress in breeding for CBSD resistance. Virus quantification is becoming a major tool for the quick and reliable assessment of plant host resistance. Therefore, a protocol for specific absolute quantification of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) was developed. CBSV and UCBSV coat protein (CP) specific standard templates: CBSV (pFer2, 826bp) and UCBSV (pUF1-R1-1, 732) respectively were generated and maintained in a TA cloning vector. These were used to construct standard curves using a TaqMan qPCR assay. Standard curves with acceptable amplification efficiencies (90-105%) and coefficients of determination (R2) greater than 0.99 were obtained. Infected cassava plants were sampled from a screenhouse and the field and used to validate this assay. Results obtained by testing several screenhouse and field samples revealed consistent absolute quantification assays for different CBSV and UCBSV isolates. This study presents the first protocol for absolute quantification of CBSVs and is expected to accelerate screening for CBSD resistance and hence breeding for CBSD resistance. The use of the method presented here should improve the clarity of virus quantification data as the results obtained are not influenced by varietal, host, seasonal or environmental conditions. Screening efficiency will also be greatly improved as there is no need for the use of reference genes consequently allowing for a larger number of samples to be analyzed. This will increase experimental precision in a timely and cost effective manner.
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Affiliation(s)
- Rudolph R Shirima
- International Institute of Tropical Agriculture, P. O. Box 34441, Dar es Salaam, Tanzania; University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania.
| | - Daniel G Maeda
- University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Edward Kanju
- International Institute of Tropical Agriculture, P. O. Box 34441, Dar es Salaam, Tanzania
| | - Gloria Ceasar
- International Institute of Tropical Agriculture, P. O. Box 34441, Dar es Salaam, Tanzania
| | - Flora I Tibazarwa
- Tanzania Commission for Science and Technology, P.O. Box 4302, Dar es Salaam, Tanzania
| | - James P Legg
- International Institute of Tropical Agriculture, P. O. Box 34441, Dar es Salaam, Tanzania
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27
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Gureev AP, Shaforostova EA, Starkov AA, Popov VN. Simplified qPCR method for detecting excessive mtDNA damage induced by exogenous factors. Toxicology 2017; 382:67-74. [PMID: 28286206 DOI: 10.1016/j.tox.2017.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 02/08/2023]
Abstract
Damage to mitochondrial DNA (mtDNA) is a meaningful biomarker for evaluating genotoxicity of drugs and environmental toxins. Existing PCR methods utilize long mtDNA fragments (∼8-10kb), which complicates detecting exact sites of mtDNA damage. To identify the mtDNA regions most susceptible to damage, we have developed and validated a set of primers to amplify ∼2kb long fragments, while covering over 95% of mouse mtDNA. We have modified the detection method by greatly increasing the enrichment of mtDNA, which allows us solving the problem of non-specific primer annealing to nuclear DNA. To validate our approach, we have determined the most damage-susceptible mtDNA regions in mice treated in vivo and in vitro with rotenone and H2O2. The GTGR-sequence-enriched mtDNA segments located in the D-loop region were found to be especially susceptible to damage. Further, we demonstrate that H2O2-induced mtDNA damage facilitates the relaxation of mtDNA supercoiled conformation, making the sequences with minimal damage more accessible to DNA polymerase, which, in turn, results in a decrease in threshold cycle value. Overall, our modified PCR method is simpler and more selective to the specific sites of damage in mtDNA.
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Affiliation(s)
- Artem P Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Ekaterina A Shaforostova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Anatoly A Starkov
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY, USA.
| | - Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
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28
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Pastukh VM, Gorodnya OM, Gillespie MN, Ruchko MV. Regulation of mitochondrial genome replication by hypoxia: The role of DNA oxidation in D-loop region. Free Radic Biol Med 2016; 96:78-88. [PMID: 27091693 PMCID: PMC4912408 DOI: 10.1016/j.freeradbiomed.2016.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 03/18/2016] [Accepted: 04/14/2016] [Indexed: 02/04/2023]
Abstract
Mitochondria of mammalian cells contain multiple copies of mitochondrial (mt) DNA. Although mtDNA copy number can fluctuate dramatically depending on physiological and pathophysiologic conditions, the mechanisms regulating mitochondrial genome replication remain obscure. Hypoxia, like many other physiologic stimuli that promote growth, cell proliferation and mitochondrial biogenesis, uses reactive oxygen species as signaling molecules. Emerging evidence suggests that hypoxia-induced transcription of nuclear genes requires controlled DNA damage and repair in specific sequences in the promoter regions. Whether similar mechanisms are operative in mitochondria is unknown. Here we test the hypothesis that controlled oxidative DNA damage and repair in the D-loop region of the mitochondrial genome are required for mitochondrial DNA replication and transcription in hypoxia. We found that hypoxia had little impact on expression of mitochondrial proteins in pulmonary artery endothelial cells, but elevated mtDNA content. The increase in mtDNA copy number was accompanied by oxidative modifications in the D-loop region of the mitochondrial genome. To investigate the role of this sequence-specific oxidation of mitochondrial genome in mtDNA replication, we overexpressed mitochondria-targeted 8-oxoguanine glycosylase Ogg1 in rat pulmonary artery endothelial cells, enhancing the mtDNA repair capacity of transfected cells. Overexpression of Ogg1 resulted in suppression of hypoxia-induced mtDNA oxidation in the D-loop region and attenuation of hypoxia-induced mtDNA replication. Ogg1 overexpression also reduced binding of mitochondrial transcription factor A (TFAM) to both regulatory and coding regions of the mitochondrial genome without altering total abundance of TFAM in either control or hypoxic cells. These observations suggest that oxidative DNA modifications in the D-loop region during hypoxia are important for increased TFAM binding and ensuing replication of the mitochondrial genome.
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Affiliation(s)
- Viktor M Pastukh
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Olena M Gorodnya
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Mark N Gillespie
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Mykhaylo V Ruchko
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
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29
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André M, Reghin S, Boussard E, Lempereur L, Maisonneuve S. Universal real-time PCR assay for quantitation and size evaluation of residual cell DNA in human viral vaccines. Biologicals 2016; 44:139-49. [DOI: 10.1016/j.biologicals.2016.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/26/2015] [Accepted: 03/05/2016] [Indexed: 12/15/2022] Open
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30
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Datta S, Budhauliya R, Chatterjee S, Veer V, Chakravarty R. Enhancement of PCR Detection Limit by Single-Tube Restriction Endonuclease-PCR (RE-PCR). Mol Diagn Ther 2016; 20:297-305. [PMID: 26993322 DOI: 10.1007/s40291-016-0195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Polymerase chain reaction (PCR) is widely used in biological research and diagnostics because of its high sensitivity and specificity. However, the sensitivity of PCR is strongly influenced by topological characteristics of the template. Supercoiled templates are known to inhibit PCR, whereas linearized forms of the same supercoiled templates facilitate PCR. OBJECTIVES This study was conducted to compare the PCR efficiency of circular supercoiled DNA templates to their restriction endonuclease (RE)-mediated linearized forms. Additionally, we also evaluated the possibility of RE digestion of the circular supercoiled templates within the complete PCR buffer. METHODS Following a systematic approach, we demonstrated that circular supercoiled templates could be efficiently linearized by RE in the complete PCR buffer itself. This allowed linearization of circular supercoiled templates and their subsequent amplification in the PCR buffer in a single-tube format. RESULTS Using this extremely simple RE-PCR approach, we documented up to tenfold increases in detection efficiency of PCR with two different circular supercoiled templates of clinical origin, including an international calibration standard. CONCLUSIONS This inexpensive and easy approach to increasing PCR sensitivity can be easily adapted to any standard PCR protocol aimed at amplifying circular supercoiled genomes. Apart from its application in the development of sensitive clinical diagnostic PCR assays for a large number of organisms, this method could also prove to be very useful in simplifying the existing protocols for other applications where pre-PCR restriction digestion is required, such as mutation detection, genotyping, and selective template amplification.
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Affiliation(s)
- Sibnarayan Datta
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India.
| | - Raghvendra Budhauliya
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Soumya Chatterjee
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Vijay Veer
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Runu Chakravarty
- Hepatitis Research Laboratory, ICMR Virus Unit, Kolkata (ICMR), Kolkata, 700010, West Bengal, India
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31
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Barkallah M, Gharbi Y, Hmani M, Mallek Z, Gautier M, Gdoura R, Fendri I. Locked nucleic acid probe-based real-time PCR for the diagnosis of Listeria monocytogenes in ruminants. Mol Cell Probes 2016; 30:138-45. [PMID: 26921518 DOI: 10.1016/j.mcp.2016.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 11/27/2022]
Abstract
Because of its high fatality rate, listeriosis ranks among the most important infectious diseases worldwide. Although ruminants are known as natural reservoirs for Listeria monocytogenes and a possible source of human listeriosis, studies of the prevalence and risk factors associated with ruminant listeriosis are limited to some developed countries. Therefore, this report describes the development of a real-time PCR targeting the hly gene for the absolute quantification of L. monocytogenes based on circular and linear DNA standards. Results show that the PCR that uses circular plasmid as a template gave a 2.6-7.89 greater threshold cycle number than did equimolar linear standards. No cross-amplification was observed when bacteria commonly found in bovine and ovine diseases were tested. The PCR achieved good intra and inter-run reproducibility and a detection limit of 6.1 copies of linear plasmid per reaction. This PCR was then applied to 1134 samples taken from 378 Tunisian ruminants. Based on the test sensitivity (90%) and specificity (100%), the true individual animal prevalence of listeriosis was 5.7% in cattle and 10.2% in sheep. In addition, the true herd-level prevalence was 50.1% in cattle and 26.7% in sheep. A multivariable logistic regression analysis at the animal-population level indicated that for cattle, the variables strata and mastitis were important risk factors, whereas for sheep, the variables strata, age and abortion were found to be associated with listeriosis. At the herd level, risk factors for Listeria test-positivity they were: abortion, herd composition and silage storage for cattle, whereas for sheep were: management system, cleaning frequency, silage storage and floor type. Animal hygiene, food quality and sanitary practices on the farm should be applied as strategies to control this pathogen in ruminant herds.
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Affiliation(s)
- Mohamed Barkallah
- Toxicology-Microbiology and Environmental Health Unit (UR11ES70), Faculty of Sciences, University of Sfax, Tunisia.
| | - Yaakoub Gharbi
- Toxicology-Microbiology and Environmental Health Unit (UR11ES70), Faculty of Sciences, University of Sfax, Tunisia
| | - Mariam Hmani
- Toxicology-Microbiology and Environmental Health Unit (UR11ES70), Faculty of Sciences, University of Sfax, Tunisia
| | | | - Michel Gautier
- Equipe Microbiologie de l'œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Radhouane Gdoura
- Toxicology-Microbiology and Environmental Health Unit (UR11ES70), Faculty of Sciences, University of Sfax, Tunisia
| | - Imen Fendri
- Toxicology-Microbiology and Environmental Health Unit (UR11ES70), Faculty of Sciences, University of Sfax, Tunisia
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32
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Yadav N, Kumar S, Kumar R, Srivastava P, Sun L, Rapali P, Marlowe T, Schneider A, Inigo JR, O'Malley J, Londonkar R, Gogada R, Chaudhary AK, Yadava N, Chandra D. Mechanism of neem limonoids-induced cell death in cancer: Role of oxidative phosphorylation. Free Radic Biol Med 2016; 90:261-71. [PMID: 26627937 PMCID: PMC4734361 DOI: 10.1016/j.freeradbiomed.2015.11.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/01/2015] [Accepted: 11/23/2015] [Indexed: 12/17/2022]
Abstract
We have previously reported that neem limonoids (neem) induce multiple cancer cell death pathways. Here we dissect the underlying mechanisms of neem-induced apoptotic cell death in cancer. We observed that neem-induced caspase activation does not require Bax/Bak channel-mediated mitochondrial outer membrane permeabilization, permeability transition pore, and mitochondrial fragmentation. Neem enhanced mitochondrial DNA and mitochondrial biomass. While oxidative phosphorylation (OXPHOS) Complex-I activity was decreased, the activities of other OXPHOS complexes including Complex-II and -IV were unaltered. Increased reactive oxygen species (ROS) levels were associated with an increase in mitochondrial biomass and apoptosis upon neem exposure. Complex-I deficiency due to the loss of Ndufa1-encoded MWFE protein inhibited neem-induced caspase activation and apoptosis, but cell death induction was enhanced. Complex II-deficiency due to the loss of succinate dehydrogenase complex subunit C (SDHC) robustly decreased caspase activation, apoptosis, and cell death. Additionally, the ablation of Complexes-I, -III, -IV, and -V together did not inhibit caspase activation. Together, we demonstrate that neem limonoids target OXPHOS system to induce cancer cell death, which does not require upregulation or activation of proapoptotic Bcl-2 family proteins.
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Affiliation(s)
- Neelu Yadav
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
| | - Sandeep Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Rahul Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Pragya Srivastava
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Leimin Sun
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA; Gastroenterology Department, Sir Run Run Shaw Hospital, Zhejiang University Medical School, Hangzhou 310016, China
| | - Peter Rapali
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Timothy Marlowe
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Andrea Schneider
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Joseph R Inigo
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Jordan O'Malley
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Ramesh Londonkar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Raghu Gogada
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Ajay K Chaudhary
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Nagendra Yadava
- Pioneer Valley Life Sciences Institute, Springfield, MA 01107, USA
| | - Dhyan Chandra
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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33
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Oxidative phosphorylation-dependent regulation of cancer cell apoptosis in response to anticancer agents. Cell Death Dis 2015; 6:e1969. [PMID: 26539916 PMCID: PMC4670921 DOI: 10.1038/cddis.2015.305] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 08/24/2015] [Accepted: 09/09/2015] [Indexed: 01/04/2023]
Abstract
Cancer cells tend to develop resistance to various types of anticancer agents, whether they adopt similar or distinct mechanisms to evade cell death in response to a broad spectrum of cancer therapeutics is not fully defined. Current study concludes that DNA-damaging agents (etoposide and doxorubicin), ER stressor (thapsigargin), and histone deacetylase inhibitor (apicidin) target oxidative phosphorylation (OXPHOS) for apoptosis induction, whereas other anticancer agents including staurosporine, taxol, and sorafenib induce apoptosis in an OXPHOS-independent manner. DNA-damaging agents promoted mitochondrial biogenesis accompanied by increased accumulation of cellular and mitochondrial ROS, mitochondrial protein-folding machinery, and mitochondrial unfolded protein response. Induction of mitochondrial biogenesis occurred in a caspase activation-independent mechanism but was reduced by autophagy inhibition and p53-deficiency. Abrogation of complex-I blocked DNA-damage-induced caspase activation and apoptosis, whereas inhibition of complex-II or a combined deficiency of OXPHOS complexes I, III, IV, and V due to impaired mitochondrial protein synthesis did not modulate caspase activity. Mechanistic analysis revealed that inhibition of caspase activation in response to anticancer agents associates with decreased release of mitochondrial cytochrome c in complex-I-deficient cells compared with wild type (WT) cells. Gross OXPHOS deficiencies promoted increased release of apoptosis-inducing factor from mitochondria compared with WT or complex-I-deficient cells, suggesting that cells harboring defective OXPHOS trigger caspase-dependent as well as caspase-independent apoptosis in response to anticancer agents. Interestingly, DNA-damaging agent doxorubicin showed strong binding to mitochondria, which was disrupted by complex-I-deficiency but not by complex-II-deficiency. Thapsigargin-induced caspase activation was reduced upon abrogation of complex-I or gross OXPHOS deficiency whereas a reverse trend was observed with apicidin. Together, these finding provide a new strategy for differential mitochondrial targeting in cancer therapy.
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Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC. Current and future resources for functional metagenomics. Front Microbiol 2015; 6:1196. [PMID: 26579102 PMCID: PMC4625089 DOI: 10.3389/fmicb.2015.01196] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/14/2015] [Indexed: 11/18/2022] Open
Abstract
Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries—physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.
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Affiliation(s)
- Kathy N Lam
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Jiujun Cheng
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo Waterloo, ON, Canada
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Werling NJ, Satkunanathan S, Thorpe R, Zhao Y. Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products. Hum Gene Ther Methods 2015; 26:82-92. [PMID: 25953194 PMCID: PMC4492554 DOI: 10.1089/hgtb.2015.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/26/2015] [Indexed: 01/17/2023] Open
Abstract
Adeno-associated viral (AAV) vectors show great promise for gene therapy because of their excellent safety profile; however, development of robust dose-determining assays for AAV has presented a significant challenge. With the ultimate goal of future harmonization and standardization of AAV dose determination assays, we systematically analyzed the influence of key variables, including sample preparation procedure, the choice of primers, and real-time quantitative PCR (qPCR) target sequences and calibration DNA conformation on the qPCR quantitation of AAV products. Our results emphasize the importance of designing qPCR primers and conducting sample preparation and demonstrate the need for extensive characterization, vigorous control, and use of reference materials in clinical dose determination.
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Affiliation(s)
- Natalie Jayne Werling
- Division of Advanced Therapies, NIBSC/Medicines and Healthcare Products Regulatory Agency , Potters Bar, Hertfordshire, EN6 3QG United Kingdom
| | - Stifani Satkunanathan
- Division of Advanced Therapies, NIBSC/Medicines and Healthcare Products Regulatory Agency , Potters Bar, Hertfordshire, EN6 3QG United Kingdom
| | - Robin Thorpe
- Division of Advanced Therapies, NIBSC/Medicines and Healthcare Products Regulatory Agency , Potters Bar, Hertfordshire, EN6 3QG United Kingdom
| | - Yuan Zhao
- Division of Advanced Therapies, NIBSC/Medicines and Healthcare Products Regulatory Agency , Potters Bar, Hertfordshire, EN6 3QG United Kingdom
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DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials. Anal Bioanal Chem 2015; 407:1831-40. [PMID: 25600685 PMCID: PMC4336415 DOI: 10.1007/s00216-015-8458-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 01/31/2023]
Abstract
The value assignment for properties of six certified reference materials (ERM-AD623a–f), each containing a plasmid DNA solution ranging from 1 million to 10 copies per μL, by using digital PCR (dPCR) with the BioMark™ HD System (Fluidigm) has been verified by applying droplet digital PCR (ddPCR) using the QX100 system (Bio-Rad). One of the critical factors in the measurement of copy number concentrations by digital PCR is the partition volume. Therefore, we determined the average droplet volume by optical microscopy, revealing an average droplet volume that is 8 % smaller than the droplet volume used as the defined parameter in the QuantaSoft software version 1.3.2.0 (Bio-Rad) to calculate the copy number concentration. This observation explains why copy number concentrations estimated with ddPCR and using an average droplet volume predefined in the QuantaSoft software were systematically lower than those measured by dPCR, creating a significant bias between the values obtained by these two techniques. The difference was not significant anymore when the measured droplet volume of 0.834 nL was used to estimate copy number concentrations. A new version of QuantaSoft software (version 1.6.6.0320), which has since been released with Bio-Rad’s new QX200 systems and QX100 upgrades, uses a droplet volume of 0.85 nL as a defined parameter to calculate copy number concentration. Monolayer of droplets generated by the droplet generator and observed under an optical microscope ![]()
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Yadav N, Pliss A, Kuzmin A, Rapali P, Sun L, Prasad P, Chandra D. Transformations of the macromolecular landscape at mitochondria during DNA-damage-induced apoptotic cell death. Cell Death Dis 2014; 5:e1453. [PMID: 25299778 PMCID: PMC4649512 DOI: 10.1038/cddis.2014.405] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/08/2014] [Accepted: 08/14/2014] [Indexed: 12/18/2022]
Abstract
Apoptosis is a dynamic process regulated by mitochondrion critical for cellular respiration and survival. Execution of apoptosis is mediated by multiple protein signaling events at mitochondria. Initiation and progression of apoptosis require numerous apoptogenic factors that are either released from or sequestered in mitochondria, which may transform the biomolecular makeup of the organelle. In this communication, using Raman microspectroscopy, we demonstrate that transformation in biomolecular composition of mitochondrion may be used as apoptosis marker in an individual cell. For the first time, we show that significant changes occur in the concentrations of RNA, DNA, protein, and lipid constituents of mitochondria during apoptosis. The structural analysis of proteins on mitochondria demonstrated a decrease in α-helix secondary structure content, and an increase in the levels of random coils and β-sheets on mitochondria. This may represent an additional hallmark of apoptosis. Strikingly, we observed nearly identical changes in macromolecular content of mitochondria both in the presence and absence of a key proapoptotic protein, Bax (Bcl-2-associated X protein). Increased DNA level in mitochondria corresponded with higher mitochondrial DNA (mtDNA), cellular reactive oxygen species (ROS), and mitochondrial ROS production. Upregulation of polymerase-γ (POLG), mitochondrial helicase Twinkle, and mitochondrial transcription factor A (Tfam) in response to DNA damage correlated with increased mtDNA and RNA synthesis. Elevated activity of oxidative phosphorylation complexes supports functional mitochondrial respiration during apoptosis. Thus, we define previously unknown dynamic correlation of macromolecular structure of mitochondria and apoptosis progression in the presence and absence of Bax protein. These findings open up a new approach for monitoring physiological status of cells by non invasive single-cell method.
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Affiliation(s)
- N Yadav
- Department of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, USA
| | - A Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - A Kuzmin
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - P Rapali
- Department of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, USA
| | - L Sun
- 1] Department of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, USA [2] Gastrointestinal Division, Sir Run Run Shaw Hospital, Zhejiang University Medical School, Hangzhou, China
| | - P Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - D Chandra
- Department of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, USA
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Efficient diagnosis and treatment follow-up of human brucellosis by a novel quantitative TaqMan real-time PCR assay: a human clinical survey. J Clin Microbiol 2014; 52:4239-43. [PMID: 25275001 DOI: 10.1128/jcm.01819-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and effective diagnosis of brucellosis is a challenge for clinicians. Even when diagnosis is on time and therapy is initiated, meticulous follow-up appointments are crucial for ensuring the efficacy of the treatment. Due to shortcomings of serological methods, molecular diagnosis, especially real-time PCR, is becoming a main approach in laboratory diagnostics. Thus, the development of efficient procedures and standardization of the PCR tests will have a great impact on the precise detection and quantification of bacterial DNA loads, which is valuable for the medical management of brucellosis patients. We developed a new TaqMan real-time PCR directed to bcsp31, a shared gene of the brucellae. The bcsp31 gene fragment was cloned into pJET1.2. Recombinant pJET1.2-bcsp31 was linearized by HindIII digestion, and the product was used for the preparation of a standard curve. A panel of Brucella spp. and non-Brucella pathogens was tested. No bacterial genomes other than those of the brucellae were detected. According to the results, specificity of the method was 100%. In a clinical assessment, the positive-control group comprised 37 patients with microbiologically confirmed brucellosis, and 25 healthy individuals served as the negative-control group. By the end of the treatment period, there was a significant decrease in the DNA load of the 37 brucellosis patients, which persisted for the 4 weeks of monitoring after treatment, suggesting that our proposed method is an efficient monitoring tool. Serum samples prior to any treatment were collected from the 25 serologically suspicious patients and assessed by our method; 72% of these patients tested positive for brucellosis.
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Strand JM, Scheffler K, Bjørås M, Eide L. The distribution of DNA damage is defined by region-specific susceptibility to DNA damage formation rather than repair differences. DNA Repair (Amst) 2014; 18:44-51. [PMID: 24685126 DOI: 10.1016/j.dnarep.2014.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 01/20/2023]
Abstract
The cellular genomes are continuously damaged by reactive oxygen species (ROS) from aerobic processes. The impact of DNA damage depends on the specific site as well as the cellular state. The steady-state level of DNA damage is the net result of continuous formation and subsequent repair, but it is unknown to what extent heterogeneous damage distribution is caused by variations in formation or repair of DNA damage. Here, we used a restriction enzyme/qPCR based method to analyze DNA damage in promoter and coding regions of four nuclear genes: the two house-keeping genes Gadph and Tbp, and the Ndufa9 and Ndufs2 genes encoding mitochondrial complex I subunits, as well as mt-Rnr1 encoded by mitochondrial DNA (mtDNA). The distribution of steady-state levels of damage varied in a site-specific manner. Oxidative stress induced damage in nDNA to a similar extent in promoter and coding regions, and more so in mtDNA. The subsequent removal of damage from nDNA was efficient and comparable with recovery times depending on the initial damage load, while repair of mtDNA was delayed with subsequently slower repair rate. The repair was furthermore found to be independent of transcription or the transcription-coupled repair factor CSB, but dependent on cellular ATP. Our results demonstrate that the capacity to repair DNA is sufficient to remove exogenously induced damage. Thus, we conclude that the heterogeneous steady-state level of DNA damage in promoters and coding regions is caused by site-specific DNA damage/modifications that take place under normal metabolism.
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Affiliation(s)
- Janne M Strand
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Norway
| | - Katja Scheffler
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Norway.
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Integrated three-dimensional system-on-chip for direct quantitative detection of mitochondrial DNA mutation in affected cells. Biosens Bioelectron 2013; 48:6-11. [DOI: 10.1016/j.bios.2013.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/05/2013] [Accepted: 02/12/2013] [Indexed: 01/14/2023]
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Manente AG, Valenti D, Pinton G, Jithesh PV, Daga A, Rossi L, Gray SG, O'Byrne KJ, Fennell DA, Vacca RA, Nilsson S, Mutti L, Moro L. Estrogen receptor β activation impairs mitochondrial oxidative metabolism and affects malignant mesothelioma cell growth in vitro and in vivo. Oncogenesis 2013; 2:e72. [PMID: 24061575 PMCID: PMC3816222 DOI: 10.1038/oncsis.2013.32] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/27/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022] Open
Abstract
Estrogen receptor (ER)-β has been shown to possess a tumor suppressive effect, and is a potential target for cancer therapy. Using gene-expression meta-analysis of human malignant pleural mesothelioma, we identified an ESR2 (ERβ coding gene) signature. High ESR2 expression was strongly associated with low succinate dehydrogenase B (SDHB) (which encodes a mitochondrial respiratory chain complex II subunit) expression. We demonstrate that SDHB loss induced ESR2 expression, and that activated ERβ, by over-expression or by selective agonist stimulation, negatively affected oxidative phosphorylation compromising mitochondrial complex II and IV activity. This resulted in reduced mitochondrial ATP production, increased glycolysis dependence and impaired cell proliferation. The observed in vitro effects were phenocopied in vivo using a selective ERβ agonist in a mesothelioma mouse model. On the whole, our data highlight an unforeseen interaction between ERβ-mediated tumor suppression and energy metabolism that may be exploited to improve on the therapy for clinical management of malignant mesothelioma.
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Affiliation(s)
- A G Manente
- Department Pharmaceutical Sciences, University of Piemonte Orientale 'A. Avogadro', Novara, Italy
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Koochekpour S, Marlowe T, Singh KK, Attwood K, Chandra D. Reduced mitochondrial DNA content associates with poor prognosis of prostate cancer in African American men. PLoS One 2013; 8:e74688. [PMID: 24086362 PMCID: PMC3781126 DOI: 10.1371/journal.pone.0074688] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
Reduction or depletion of mitochondrial DNA (mtDNA) has been associated with cancer progression. Although imbalanced mtDNA content is known to occur in prostate cancer, differences in mtDNA content between African American (AA) and Caucasian American (CA) men are not defined. We provide the first evidence that tumors in AA men possess reduced level of mtDNA compared to CA men. The median tumor mtDNA content was reduced in AA men. mtDNA content was also reduced in normal prostate tissues of AA men compared to CA men, suggesting a possible predisposition to cancer in AA men. mtDNA content was also reduced in benign prostatic hyperplasia (BPH) tissue from AA men. Tumor and BPH tissues from patients ≥ 60 years of age possess reduced mtDNA content compared to patients <60 years of age. In addition, mtDNA content was higher in normal tissues from patients with malignant T3 stage disease compared to patients with T2 stage disease. mtDNA levels in matched normal prostate tissues were nearly doubled in Gleason grade of >7 compared to ≤ 7, whereas reduced mtDNA content was observed in tumors of Gleason grade >7 compared to ≤ 7. Together, our data suggest that AA men possess lower mtDNA levels in normal and tumor tissues compared to CA men, which could contribute to higher risk and more aggressive prostate cancer in AA men.
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Affiliation(s)
- Shahriar Koochekpour
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Department of Urology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Timothy Marlowe
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Keshav K. Singh
- Departments of Genetics, Pathology, and Environmental Health, UAB Comprehensive Cancer Center and Center for Free Radical Biology, School of Medicine, University of Alabama, Birmingham, Alabama, United States of America
| | - Kristopher Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Dhyan Chandra
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
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Ledeker BM, De Long SK. The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants. J Microbiol Methods 2013; 94:224-31. [PMID: 23806694 DOI: 10.1016/j.mimet.2013.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/14/2013] [Accepted: 06/15/2013] [Indexed: 11/19/2022]
Abstract
Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences.
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Affiliation(s)
- Brett M Ledeker
- Department of Civil and Environmental Engineering, Colorado State University, 1372 Campus Delivery, Fort Collins, CO 80523, USA.
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Lin YJ, Huang LH, Huang CT. Enhancement of heterologous gene expression in Flammulina velutipes using polycistronic vectors containing a viral 2A cleavage sequence. PLoS One 2013; 8:e59099. [PMID: 23516605 PMCID: PMC3597617 DOI: 10.1371/journal.pone.0059099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 02/12/2013] [Indexed: 01/06/2023] Open
Abstract
Agrobacterium tumefaciens-mediated transformation for edible mushrooms has been previously established. However, the enhancement of heterologous protein production and the expression of multi-target genes remains a challenge. In this study, heterologous protein expression in the enoki mushroom Flammulina velutipes was notably enhanced using 2A peptide-mediated cleavage to co-express multiple copies of single gene. The polycistronic expression vectors were constructed by connecting multi copies of the enhanced green fluorescent protein (egfp) gene using 2A peptides derived from porcine teschovirus-1. The P2A peptides properly self-cleaved as shown by the formation of the transformants with antibiotic resistant capacity and exciting green fluorescence levels after introducing the vectors into F. velutipes mycelia. The results of western blot analysis, epifluorescent microscopy and EGFP production showed that heterologous protein expression in F. velutipes using the polycistronic strategy increased proportionally as the gene copy number increased from one to three copies. In contrast, much lower EGFP levels were detected in the F. velutipes transformants harboring four copies of the egfp gene due to mRNA instability. The polycistronic strategy using 2A peptide-mediated cleavage developed in this study can not only be used to express single gene in multiple copies, but also to express multiple genes in a single reading frame. It is a promising strategy for the application of mushroom molecular pharming.
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Affiliation(s)
- Yu-Ju Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Li-Hsin Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ching-Tsan Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- * E-mail:
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Ball HC, Holmes RK, Londraville RL, Thewissen JGM, Duff RJ. Leptin in whales: validation and measurement of mRNA expression by absolute quantitative real-time PCR. PLoS One 2013; 8:e54277. [PMID: 23342116 PMCID: PMC3546977 DOI: 10.1371/journal.pone.0054277] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/10/2012] [Indexed: 12/17/2022] Open
Abstract
Leptin is the primary hormone in mammals that regulates adipose stores. Arctic adapted cetaceans maintain enormous adipose depots, suggesting possible modifications of leptin or receptor function. Determining expression of these genes is the first step to understanding the extreme physiology of these animals, and the uniqueness of these animals presents special challenges in estimating and comparing expression levels of mRNA transcripts. Here, we compare expression of two model genes, leptin and leptin-receptor gene-related product (OB-RGRP), using two quantitative real-time PCR (qPCR) methods: "relative" and "absolute". To assess the expression of leptin and OB-RGRP in cetacean tissues, we first examined how relative expression of those genes might differ when normalized to four common endogenous control genes. We performed relative expression qPCR assays measuring the amplification of these two model target genes relative to amplification of 18S ribosomal RNA (18S), ubiquitously expressed transcript (Uxt), ribosomal protein 9 (Rs9) and ribosomal protein 15 (Rs15) endogenous controls. Results demonstrated significant differences in the expression of both genes when different control genes were employed; emphasizing a limitation of relative qPCR assays, especially in studies where differences in physiology and/or a lack of knowledge regarding levels and patterns of expression of common control genes may possibly affect data interpretation. To validate the absolute quantitative qPCR methods, we evaluated the effects of plasmid structure, the purity of the plasmid standard preparation and the influence of type of qPCR "background" material on qPCR amplification efficiencies and copy number determination of both model genes, in multiple tissues from one male bowhead whale. Results indicate that linear plasmids are more reliable than circular plasmid standards, no significant differences in copy number estimation based upon background material used, and that the use of ethanol precipitated, linearized plasmid preparation produce the most reliable results.
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Affiliation(s)
- Hope C. Ball
- Department of Biology, The University of Akron, Akron, Ohio, United States of America
| | - Robert K. Holmes
- Department of Biology, The University of Akron, Akron, Ohio, United States of America
| | | | - Johannes G. M. Thewissen
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
| | - Robert Joel Duff
- Department of Biology, The University of Akron, Akron, Ohio, United States of America
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Simultaneous quantification of mitochondrial DNA damage and copy number in circulating blood: a sensitive approach to systemic oxidative stress. BIOMED RESEARCH INTERNATIONAL 2012; 2013:157547. [PMID: 23484085 PMCID: PMC3591215 DOI: 10.1155/2013/157547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 11/12/2012] [Accepted: 11/13/2012] [Indexed: 12/25/2022]
Abstract
Systemic oxidative stress is associated with a wide range of pathological conditions. Oxidative DNA damage is frequently measured in circulating lymphocytes. Mitochondrial DNA (mtDNA) is known to be more sensitive to oxidative damage than nuclear DNA but is rarely used for direct measurement of DNA damage in clinical studies. Based on the supercoiling-sensitive real-time PCR method, we propose a new approach for the noninvasive monitoring of systemic oxidative stress by quantifying the mtDNA structural damage and copy number change in isolated lymphocytes in a single test. We show that lymphocytes have significantly less mtDNA content and relatively lower baseline levels of damage than cancer cell lines. In an ex vivo challenge experiment, we demonstrate, for the first time, that exogenous H2O2 induces a significant increase in mtDNA damage in lymphocytes from healthy individuals, but no repair activity is observed after 1 h recovery. We further demonstrate that whole blood may serve as a convenient alternative to the isolated lymphocytes in mtDNA analysis. Thus, the blood analysis with the multiple mtDNA end-points proposed in the current study may provide a simple and sensitive test to interrogate the nature and extent of systemic oxidative stress for a broad spectrum of clinical investigations.
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Han Y, Chen JZ. Oxidative stress induces mitochondrial DNA damage and cytotoxicity through independent mechanisms in human cancer cells. BIOMED RESEARCH INTERNATIONAL 2012; 2013:825065. [PMID: 23509785 PMCID: PMC3591153 DOI: 10.1155/2013/825065] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 01/21/2023]
Abstract
Intrinsic oxidative stress through increased production of reactive oxygen species (ROS) is associated with carcinogenic transformation, cell toxicity, and DNA damage. Mitochondrial DNA (mtDNA) is a natural surrogate to oxidative DNA damage. MtDNA damage results in the loss of its supercoiled structure and is readily detectable using a novel, supercoiling-sensitive real-time PCR method. Our studies have demonstrated that mtDNA damage, as measured by DNA strand breaks and copy number depletion, is very sensitive to exogenous H2O2 but independent of endogenous ROS production in both prostate cancer and normal cells. In contrast, aggressive prostate cancer cells exhibit a more than 10-fold sensitivity to H2O2-induced cell toxicity than normal cells, and a cascade of secondary ROS production is a critical determinant to the differential response. We propose a new paradigm to account for different mechanisms governing cellular oxidative stress, cell toxicity, and DNA damage with important ramifications in devising new techniques and strategies in prostate cancer prevention and treatment.
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Affiliation(s)
- Yue Han
- Division of Urology, Department of Surgery, Research Institute of McGill University Health Center, Room R1-107, 1650 Cedar Avenue, Montreal, QC, Canada H3G 1A4
| | - Junjian Z. Chen
- Division of Urology, Department of Surgery, Research Institute of McGill University Health Center, Room R1-107, 1650 Cedar Avenue, Montreal, QC, Canada H3G 1A4
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Resveratrol depletes mitochondrial DNA and inhibition of autophagy enhances resveratrol-induced caspase activation. Mitochondrion 2012; 13:493-9. [PMID: 23088850 DOI: 10.1016/j.mito.2012.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 10/08/2012] [Accepted: 10/11/2012] [Indexed: 01/06/2023]
Abstract
We recently demonstrated that resveratrol induces caspase-dependent apoptosis in multiple cancer cell types. Whether apoptosis is also regulated by other cell death mechanisms such as autophagy is not clearly defined. Here we show that inhibition of autophagy enhanced resveratrol-induced caspase activation and apoptosis. Resveratrol inhibited colony formation and cell proliferation in multiple cancer cell types. Resveratrol treatment induced accumulation of LC3-II, which is a key marker for autophagy. Pretreatment with 3-methyladenine (3-MA), an autophagy inhibitor, increased resveratrol-mediated caspase activation and cell death in breast and colon cancer cells. Inhibition of autophagy by silencing key autophagy regulators such as ATG5 and Beclin-1 enhanced resveratrol-induced caspase activation. Mechanistic analysis revealed that Beclin-1 did not interact with proapoptotic proteins Bax and Bak; however, Beclin-1 was found to interact with p53 in the cytosol and mitochondria upon resveratrol treatment. Importantly, resveratrol depleted ATPase 8 gene, and thus, reduced mitochondrial DNA (mtDNA) content, suggesting that resveratrol induces damage to mtDNA causing accumulation of dysfunctional mitochondria triggering autophagy induction. Together, our findings indicate that induction of autophagy during resveratrol-induced apoptosis is an adaptive response.
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Gabriel MS, Chan SW, Alhathal N, Chen JZ, Zini A. Influence of microsurgical varicocelectomy on human sperm mitochondrial DNA copy number: a pilot study. J Assist Reprod Genet 2012; 29:759-64. [PMID: 22562241 DOI: 10.1007/s10815-012-9785-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 04/24/2012] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND There is good evidence to show that varicocele repair can improve conventional sperm parameters, as well as, sperm DNA integrity, in infertile men with a clinical varicocele. OBJECTIVE To examine the effect of varicocelectomy on sperm quality, specifically, sperm nuclear chromatin integrity and sperm mitochondrial DNA (mtDNA) copy number. DESIGN, SETTING, AND PARTICIPANTS A prospective study done between March 2007 and January 2008. We evaluated a consecutive series of infertile men (n = 14) presenting to Ovo clinic with one year or more history of infertility, a clinically palpable varicocele and poor motility (<25 % rapid progressive and <50 % progressive). SURGICAL PROCEDURE Microsurgical sub-inguinal varicocelectomy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Conventional sperm parameters, sperm mtDNA copy number (by real time PCR) and sperm chromatin structure assay (SCSA) parameters (%DFI,% HDS) before and 4 months after microsurgical varicocelectomy. RESULTS AND LIMITATIONS Sperm concentration and SCSA parameters (%DFI and %HDS) improved significantly after surgery (P < 0.05). Sperm mitochondrial DNA copy number decreased significantly after surgery (27 ± 30 to 9 ± 6 copies per sperm, respectively, P = 0.032). There was a significant negative correlation between mitochondrial DNA copy number and sperm motility (r = - 0.71, P = 0.002). CONCLUSION These findings support the concept that correction of a varicocele can improve spermatogenesis and sperm function, as mitochondrial DNA copy number has been suggested to reflect the efficiency of spermatogenesis and has been inversely related to sperm motility.
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Affiliation(s)
- Maria San Gabriel
- Division of Urology, Department of Surgery, McGill University, Montreal, QC, Canada
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Ling X, Wen L, Zhou Y. Role of mitochondrial translocation of telomerase in hepatocellular carcinoma cells with multidrug resistance. Int J Med Sci 2012; 9:545-54. [PMID: 22991493 PMCID: PMC3444975 DOI: 10.7150/ijms.4648] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/19/2012] [Indexed: 11/28/2022] Open
Abstract
Multidrug resistance (MDR) is a major obstacle of cancer chemotherapy. This study aimed to investigate the role of mitochondrial translocation of telomerase (hTERT) in MDR of human hepatocellular carcinoma (HCC) cells. In this study, three HCC cell lines (SK-Hep1/CDDP1 cells, SK-Hep1/CDDP2 cells and SK-Hep1/CDDP3 cells) with differential resistance index (RI) to cisplatin (CDDP) were induced by pulse treatment of SK-Hep1 (human hepatocellular cell line) with CDDP in vitro. The RI of SK-Hep1/CDDP1 cells, SK-Hep1/CDDP2 cells and SK-Hep1/CDDP3 cells was 5.14, 8.66, and 14.25, respectively, and all the cell lines showed cross-resistance to Doxorubicin (DOX) and 5-Fuorouracil (5-FU). The apoptosis rates in drug-resistant cells were significantly reduced. Cell cycle analysis revealed the ratio of drug-resistant cells in G2/M and S phases increased, while that in G1 phase decreased. Immunofluorescence staining and Western blot assay demonstrated, with the gradual elevation in RI, increasing hTERT translocated from the nuclei to the mitochondria, while real-time PCR indicated the shortening of telomere length in drug-resistant cells under the chemotherapeutic stress and the reduction of damaged mtDNA with the increase in RI. Furthermore, JC-1 staining also indicated the reduction of mitochondrial membrane potential in drug-resistant cells. The mitochondrial translocation of hTERT increases in multidrug-resistant cells and exerts protective effect on mitochondrial function. Drug-resistant tumor cells escape from apoptosis through hTERT-mediated mitochondrial protection. Mitochondrial translocation of hTERT may serve as an underlying mechanism of MDR.
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Affiliation(s)
- Xianlong Ling
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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