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Yang L, Jia S, Sun S, Wang L, Zhao B, Zhang M, Yin Y, Yang M, Fulano AM, Shen X, Pan J, Wang Y. A pyocin-like T6SS effector mediates bacterial competition in Yersinia pseudotuberculosis. Microbiol Spectr 2024:e0427823. [PMID: 38712967 DOI: 10.1128/spectrum.04278-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Within the realm of Gram-negative bacteria, bacteriocins are secreted almost everywhere, and the most representative are colicin and pyocin, which are secreted by Escherichia coli and Pseudomonas aeruginosa, respectively. Signal peptides at the amino terminus of bacteriocins or ABC transporters can secrete bacteriocins, which then enter bacteria through cell membrane receptors and exert toxicity. In general, the bactericidal spectrum is usually narrow, killing only the kin or closely related species. Our previous research indicates that YPK_0952 is an effector of the third Type VI secretion system (T6SS-3) in Yersinia pseudotuberculosis. Next, we sought to determine its identity and characterize its toxicity. We found that YPK_0952 (a pyocin-like effector) can achieve intra-species and inter-species competitive advantages through both contact-dependent and contact-independent mechanisms mediated by the T6SS-3 while enhancing the intestinal colonization capacity of Y. pseudotuberculosis. We further identified YPK_0952 as a DNase dependent on Mg2+, Ni2+, Mn2+, and Co2+ bivalent metal ions, and the homologous immune protein YPK_0953 can inhibit its activity. In summary, YPK_0952 exerts toxicity by degrading nucleic acids from competing cells, and YPK_0953 prevents self-attack in Y. pseudotuberculosis.IMPORTANCEBacteriocins secreted by Gram-negative bacteria generally enter cells through specific interactions on the cell surface, resulting in a narrow bactericidal spectrum. First, we identified a new pyocin-like effector protein, YPK_0952, in the third Type VI secretion system (T6SS-3) of Yersinia pseudotuberculosis. YPK_0952 is secreted by T6SS-3 and can exert DNase activity through contact-dependent and contact-independent entry into nearby cells of the same and other species (e.g., Escherichia coli) to help Y. pseudotuberculosis to exert a competitive advantage and promote intestinal colonization. This discovery lays the foundation for an in-depth study of the different effector protein types within the T6SS and their complexity in competing interactions. At the same time, this study provides a new development for the toolbox of toxin/immune pairs for studying Gram-negative bacteriocin translocation.
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Affiliation(s)
- Leilei Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuangkai Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Sihuai Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Bobo Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengsi Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanling Yin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Mingming Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Alex M Fulano
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Junfeng Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Hendrix P, Witsch J, Spalart V, Schneider H, Oertel J, Geisel J, Martinod K, Hemmer S. Neutrophil extracellular trap biomarkers in aneurysmal subarachnoid hemorrhage: early decline of DNase 1 activity associated with delayed cerebral ischemia. Front Neurol 2024; 15:1354224. [PMID: 38708000 PMCID: PMC11066163 DOI: 10.3389/fneur.2024.1354224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/26/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction High-mobility group box 1 (HMGB1) protein is a critical mediator of neutrophil extracellular trap (NET) formation (NETosis). Myeloperoxidase (MPO)-DNA complexes, a biomarker of NETs, and HMGB1 have been associated with delayed cerebral ischemia (DCI) after aneurysmal subarachnoid hemorrhage (aSAH). Additional mechanistic NET-related biomarkers and their role in the neuroinflammatory cascade surrounding DCI remain to be explored. Methods A post-hoc analysis of a prospective, blinded, single-center biomarker observational study was performed. De novo measurements of serum citrullinated histone H3-DNA complexes (H3Cit-DNA), peptidylarginine deiminase 4 (PAD4), cell-free DNA (cf-DNA), and DNase 1 activity were conducted on admission (D0) and day 4 (D4). Delayed cerebral infarction (DCI) was defined as new cerebral infarction on CT head not present on the post-treatment scan. Results H3Cit-DNA, PAD4, cf-DNA, and DNase 1 activity were within quantifiable ranges in all serum samples analyzed at D0 and D4. Admission biomarker levels were not associated with DCI development. From D0 to D4, in both the DCI and the non-DCI groups, H3Cit-DNA levels significantly decreased, cf-DNA levels significantly increased, and PAD4 levels remained stable. In contrast, DNase 1 activity significantly decreased from D0 to D4 in the DCI group (p < 0.001) but not in the non-DCI group. Conclusion This exploratory analysis demonstrated NET-related biomarkers such as H3Cit-DNA, PAD4, cf-DNA, and DNase 1 activity in all aSAH patients. A decline of systemic DNase 1 activity in the early phase might increase the risk of delayed cerebral ischemia.
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Affiliation(s)
- Philipp Hendrix
- Department of Neurosurgery, Saarland University Medical Center, Homburg, Germany
- Department of Neurosurgery, Geisinger Medical Center, Danville, PA, United States
| | - Jens Witsch
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Valérie Spalart
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Hauke Schneider
- Department of Neurology, University Hospital Augsburg, Augsburg, Germany
| | - Joachim Oertel
- Department of Neurosurgery, Saarland University Medical Center, Homburg, Germany
| | - Jürgen Geisel
- Department of Clinical Chemistry and Laboratory Medicine, Saarland University Medical Center, Homburg, Germany
| | - Kimberly Martinod
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Sina Hemmer
- Department of Neurosurgery, Saarland University Medical Center, Homburg, Germany
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Chimienti G, Russo F, Bianco A, Maqoud F, De Virgilio C, Galeano G, Orlando A, Riezzo G, D’Attoma B, Ignazzi A, Linsalata M, Prospero L, Franco I, Bagnato CB, Curci R, Coletta S. Effect of a 12-Week Walking Program Monitored by Global Physical Capacity Score (GPCS) on Circulating Cell-Free mtDNA and DNase Activity in Patients with Irritable Bowel Syndrome. Int J Mol Sci 2024; 25:4293. [PMID: 38673878 PMCID: PMC11050617 DOI: 10.3390/ijms25084293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Irritable bowel syndrome (IBS) involves low-grade mucosal inflammation. Among the various approaches capable of managing the symptoms, physical activity is still under investigation. Despite its benefits, it promotes oxidative stress and inflammation. Mitochondria impacts gut disorders by releasing damage-associated molecular patterns, such as cell-free mtDNA (cf-mtDNA), which support inflammation. This study evaluated the effects of a 12-week walking program on the cf-mtDNA and DNase in 26 IBS and 17 non-IBS subjects. Pro- and anti-inflammatory cytokines were evaluated by ELISA. Digital droplet PCR was used to quantify cf-mtDNA; DNase activity was assessed using a single radial enzyme diffusion assay. PCR-RFLP was used to genotype DNASE1 rs1053874 SNP. Significantly lower IL-10 levels were found in IBS than in non-IBS individuals. Exercise reduced cf-mtDNA in non-IBS subjects but not in IBS patients. DNase activity did not correlate with the cf-mtDNA levels in IBS patients post-exercise, indicating imbalanced cf-mtDNA clearance. Different rs1053874 SNP frequencies were not found between groups. The study confirms the positive effects of regular moderate-intensity physical activity in healthy subjects and its role in cf-mtDNA release and clearance. Walking alone might not sufficiently reduce subclinical inflammation in IBS, based on imbalanced pro- and anti-inflammatory molecules. Prolonged programs are necessary to investigate their effects on inflammatory markers in IBS.
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Affiliation(s)
- Guglielmina Chimienti
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Francesco Russo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Bianco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Fatima Maqoud
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Caterina De Virgilio
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Grazia Galeano
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Orlando
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Giuseppe Riezzo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Benedetta D’Attoma
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonia Ignazzi
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Michele Linsalata
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Laura Prospero
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Isabella Franco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Claudia Beatrice Bagnato
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Ritanna Curci
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Sergio Coletta
- Core Facility Biobank, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy;
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Gosálvez J, Bartolomé-Nebreda J, Tvrdá E, López-Fernández C, Fernández JL, Johnston S. Bacterial DNase activity as a putative inductor of sperm DNA fragmentation in infected bull frozen-thawed semen samples. Theriogenology 2023; 197:224-231. [PMID: 36525861 DOI: 10.1016/j.theriogenology.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
The aim of this study was to investigate the relationship between DNase activity associated with bacterial contamination of incubated bovine frozen-thawed spermatozoa and elevated sperm DNA fragmentation. Electrophoresis analysis of plasmid PBR322 incubated for 30 min at 37 °C with the supernatant of the diluent of frozen-thawed centrifuged bovine semen straws infected with bacteria showed clear evidence of DNase activity when compared to plasmid incubated in similarly prepared non-infected bovine diluent supernatant (Experiment 1). This DNase activity was subsequently found to be time dependent (0-60 min) and its activity prevented in the presence of EDTA (10 and 20 mM; Experiment 2). Semen straws infected (n = 10) and not infected (n = 10) with bacteria where incubated at 37 °C for up to 48h post-thaw. Semen infected with bacteria showed an exponential increase in bacterial growth and a corresponding increase in sperm DNA fragmentation. Non-infected semen samples showed no change in the incidence of sperm DNA fragmentation over the same period of incubation (Experiment 3). Our experiments reinforce the idea that exogenous DNases present in the semen should be considered as one of the primary contributing causes of sperm DNA fragmentation post ejaculation. In the case of the bull, post-thaw incubation of commercial straws contaminated with bacteria, resulted in increased levels of sperm DNA fragmentation, most likely associated with DNase activity (potentially restriction endonucleases) derived from the bacteria. Such adverse changes in sperm DNA fragmentation, as described here in vitro, may be also operative after insemination in the female reproductive tract (in vivo) and highlight the importance of implementing high levels of hygiene practice during semen processing, especially in light of future trends of bacterial resistance to the common antibiotics used in semen diluents.
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Affiliation(s)
- Jaime Gosálvez
- Unit of Genetics, Department of Biology, Universidad, Autónoma de Madrid, Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Javier Bartolomé-Nebreda
- Unit of Genetics, Department of Biology, Universidad, Autónoma de Madrid, Madrid, Campus de Cantoblanco, 28049, Madrid, Spain; Halotech DNA, PCM Parque Científico de Madrid, C/ Faraday, 7. Planta 1. Oficina 1.08. Campus de Cantoblanco, 28049, Madrid, Spain
| | - Eva Tvrdá
- Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, Nitra, 94976, Slovakia
| | - Carmen López-Fernández
- Unit of Genetics, Department of Biology, Universidad, Autónoma de Madrid, Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - José Luís Fernández
- Molecular Genetics and Radiobiology Laboratory, Centro Oncológico de Galicia, 15009, A Coruña, Spain; Genetics Unit, INIBIC-Complejo Hospitalario Universitario A Coruña (CHUAC), Spain
| | - Stephen Johnston
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Australia.
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Ondracek AS, Aszlan A, Schmid M, Lenz M, Mangold A, Artner T, Emich M, Fritzer-Szekeres M, Strametz-Juranek J, Lang IM, Sponder M. Physical Exercise Promotes DNase Activity Enhancing the Capacity to Degrade Neutrophil Extracellular Traps. Biomedicines 2022; 10:2849. [PMID: 36359376 PMCID: PMC9717727 DOI: 10.3390/biomedicines10112849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/24/2022] [Accepted: 10/29/2022] [Indexed: 10/17/2023] Open
Abstract
(1) Background: An unhealthy lifestyle is a significant contributor to the development of chronic diseases. Physical activity can benefit primary and secondary prevention. Higher DNase activity is associated with favourable outcomes after cardiovascular (CV) events. In this study, we aimed to investigate the influence of consequent endurance exercise on DNase activity. (2) Methods: 98 subjects with at least one CV risk factor but the physical ability to perform endurance training were included. Individuals performed a bicycle stress test at the beginning and after 8 months to assess physical performance. In between, all participants were instructed to engage in guideline-directed physical activity. Blood samples were drawn in two-month intervals to assess routine laboratory parameters, cell-free DNA (cfDNA), and DNase activity. (3) Results: Prevailing CV risk factors were overweight (65.9%), a positive family history (44.9%), hypertension (32.7%) and smoking (20.4%). Performance changed by 7.8 ± 9.1% after 8 months. Comparison of baseline to 8 months revealed a decrease in cfDNA and an increase in DNase activity. This effect was driven by participants who achieved a performance gain. (4) Conclusions: Regular physical activity might improve CV health by increasing DNase activity and thereby, the capacity to lower pro-inflammatory signalling, complementing measures of primary and secondary prevention.
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Affiliation(s)
- Anna S. Ondracek
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Adrienne Aszlan
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Martin Schmid
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Max Lenz
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Andreas Mangold
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Tyler Artner
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Michael Emich
- Austrian Federal Ministry of Defence, Austrian Armed Forces, 1090 Vienna, Austria;
| | | | | | - Irene M. Lang
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
| | - Michael Sponder
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria; (A.S.O.); (A.A.); (M.S.); (M.L.); (A.M.); (T.A.); (I.M.L.)
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Gosálvez J, Vargas-Baquero E, López-Fernández C, Bartolomé-Nebreda J, Fernández JL, Johnston S. Sperm DNA damage in men with spinal cord injury: the relative incidence of single- and double-strand DNA breaks. Andrology 2022; 10:1292-1301. [PMID: 35716146 DOI: 10.1111/andr.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Men with spinal cord injury (SCI) show a high proportion of sperm DNA damage in their ejaculate but the underlying pathology remains elusive. OBJECTIVE To investigate the relative incidence of single (SSBs) and double-strand DNA breaks (DSBs) and DNase activity in men with SCI. MATERIALS AND METHODS This study included ejaculates of 20 men with SCI and 27 normozoospermic (sperm donors). A TwoTails comet assay (TTComet) allowed visualization of three categories of sperm DNA damage corresponding to SSBs, DSBs and those with a combination of SSBs and DSBs, facilitating accurate calculation of the total proportion of SSBs and DSBs. A subset of 15 individuals (sperm donors and SCI patients) was used to test for DNase activity in the seminal plasma. RESULTS While the proportion of DSBs in men with SCI (median-57.5%) was higher (P = 0.000) than normozoospermic samples (median-4.6%), the proportion of SSBs was higher (P = 0.022) in the normozoospermic ejaculates (median-6.0%) compared to men with SCI (median-2.5%). The relative proportion of the total DSBs with respect to the total SSBs was 3.3× in men with SCI but 0.9× in normozoospermic samples. We further confirmed the high DNase activity in the seminal plasma of men with SCI. DISCUSSION The TTComet assay provided new insights to the pathology of sperm DNA in men with SCI and may have diagnostic value in developing sperm selection methodologies to reduce DSBs prior to ART. CONCLUSION Men with SCI are characterized by a high proportion of sperm with DSBs and high levels of DNase activity in the seminal plasma compared to normozoospermic men.
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Affiliation(s)
- Jaime Gosálvez
- Unit of Genetics, Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | | | - José Luís Fernández
- INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), Genetics Unit, Coruña, Spain
| | - Stephen Johnston
- School of Agriculture and Food Sciences, University of Queensland, Gatton, Australia
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Aslan E, Arslanyolu M. Discovery of deoxyribonuclease II-like proteins in bacteria. Mol Phylogenet Evol 2022; 174:107554. [PMID: 35714926 DOI: 10.1016/j.ympev.2022.107554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 12/01/2022]
Abstract
Deoxyribonuclease II (DNase II) is one of the earliest enzymes discovered in the history of biochemistry. Its role in apoptosis and development has been documented with great detail in eukaryotes. Prior in silico analyses showed its complete absence in bacterial genomes, with the exception of single bacterial genus: Burkholderia. It is therefore considered to be a eukaryotic enzyme. Here we show that the presence of DNase II is not limited to Burkholderia, as we find over one hundred DNase II-like sequences spanning 90 bacteria species belonging to 54 different genera and seven phyla. The majority of the significant hits (85%) come from Bacteroidetes and Proteobacteria phyla. Sequence analyses reveal that bacterial DNase II-like proteins possess a signature catalytic motif of eukaryotic DNase II. In phylogenetic analyses, we find that bacterial DNase II-like proteins are divided into two distinct clades. Our structural analyses reveal high levels of similarity between experimentally determined crystal structures of recombinant Burkholderia thailandensis DNase II and candidate bacterial DNase II-like proteins. We also biochemically show that Chromobacterium violaceum cell lysate possesses acidic DNase II-like activities. Collectively, our results indicate that DNase II has deeper evolutionary roots than previously thought. We argue that either some prokaryotic lineages have undergone losses of DNase II genes, resulting in rare conservation, or some lineages have acquired DNase II genes from eukaryotes through lateral gene transfer. We also discuss the possible involvement of DNase II as a part of an anti-phage defense system in bacteria.
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Affiliation(s)
- Erhan Aslan
- Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Iki Eylul Campus, 26555 Eskisehir, Turkey.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunus Emre Campus, 26470 Eskisehir, Turkey
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Bartolomé J, Romeo SC, Dorado-Silva M, García de la Vega C, López C, Sánchez-Martín P, Johnston S, Gosálvez J. DNase activity in human seminal plasma and follicular fluid and its inhibition by follicular fluid chelating agents. Reprod Biomed Online 2021:S1472-6483(21)00474-0. [PMID: 34753679 DOI: 10.1016/j.rbmo.2021.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
RESEARCH QUESTION What is the mechanism by which human follicular fluid inhibits seminal plasma DNase activity? DESIGN Human genomic DNA was incubated with human follicular fluid and seminal plasma (reaction mixture) under different experimental conditions; increasing volumes of human follicular fluid; proteinase K digested or heat inactivated human follicular fluid; and the addition of Ca2+ or Mg2+ to the reaction mixture. RESULTS Increasing volume of human follicular fluid resulted in a dose-dependent inhibition of seminal plasma DNase activity. Inhibition was not caused by proteins in the human follicular fluid as digestion with proteinase K or heat inactivation of human follicular fluid failed to abolish its inhibitory effect. Addition of divalent cations resulted in a reversion of the inhibitory effect, providing evidence that human follicular fluid inhibition of seminal plasma DNase activity seems to be mediated by a compound with chelating activity. Furthermore, incubation of genomic DNA with human follicular fluid in the presence of divalent cations served to elicit the existence of DNase activity. CONCLUSIONS Human follicular fluid seems to contain a molecule or molecules with chelating capacity that inhibits DNase activity of both follicular fluid and seminal plasma. Our findings provide new insight to understanding sperm preservation and the physiology of fertilization biology.
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Kostrikina IA, Buneva VN, Granieri E, Nevinsky GA. Extreme Diversity of IgGs Against Histones, DNA, and Myelin Basic Protein in the Cerebrospinal Fluid and Blood of Patients with Multiple Sclerosis. Biomolecules 2020; 10:biom10040630. [PMID: 32325782 PMCID: PMC7226582 DOI: 10.3390/biom10040630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/03/2020] [Accepted: 04/17/2020] [Indexed: 01/23/2023] Open
Abstract
It was recently shown that IgGs from sera of multiple sclerosis (MS) patients are active in the hydrolysis of DNA and myelin basic protein (MBP). We first analyzed the relative concentration of antibodies against five histones (H1, H2a, H2b, H3, and H4) in the cerebrospinal fluid (CSF) and serum of patients with MS. The relative concentrations of blood and CSF IgGs against histones and their activity in the hydrolysis of five histones varied greatly from patient to patient. However, all 28 IgG preparations were hydrolyzed from one to five histones. Relative activities and correlation coefficients among the activities of IgGs from serum and CSF in the hydrolysis of five histones (H1, H2a, H2b, H3, and H4), DNA, and MBP were calculated. It was shown that auto-IgGs from CSF and sera of MS patients are extremely heterogeneous in their affinity to histones, MBP, and DNA. The heterogeneity of IgG-abzymes hydrolyzing DNA, MBP, and histones from CSF and sera was also demonstrated using their isoelectrofocusing. The isofocusing profiles DNase, MBP-, and histone-hydrolyzing activities of IgGs may be very different for various individuals, but the total IgG subfractions with all their activities are distributed from pH 3 to 10.
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Affiliation(s)
- Irina A. Kostrikina
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Division, 630090 Novosibirsk, Russia; (I.A.K.); (V.N.B.)
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Division, 630090 Novosibirsk, Russia; (I.A.K.); (V.N.B.)
| | - Enrico Granieri
- Multiple Sclerosis Center, Department of Neurology, Ferrara University, 44121 Ferrara, Italy;
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Division, 630090 Novosibirsk, Russia; (I.A.K.); (V.N.B.)
- Correspondence: ; Tel.: +7-383-363-51-26
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Wojnicka M, Szczepanska A, Kurzynska-Kokorniak A. Unknown Areas of Activity of Human Ribonuclease Dicer: A Putative Deoxyribonuclease Activity. Molecules 2020; 25:E1414. [PMID: 32244942 DOI: 10.3390/molecules25061414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/03/2022] Open
Abstract
The Dicer ribonuclease plays a crucial role in the biogenesis of small regulatory RNAs (srRNAs) by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. Dicer-generated srRNAs can control gene expression by targeting complementary transcripts and repressing their translation or inducing their cleavage. Human Dicer (hDicer) is a multidomain enzyme comprising a putative helicase domain, a DUF283 domain, platform, a PAZ domain, a connector helix, two RNase III domains (RNase IIIa and RNase IIIb) and a dsRNA-binding domain. Specific, ~20-base pair siRNA or miRNA duplexes with 2 nucleotide (nt) 3’-overhangs are generated by Dicer when an RNA substrate is anchored within the platform-PAZ-connector helix (PPC) region. However, increasing number of reports indicate that in the absence of the PAZ domain, binding of RNA substrates can occur by other Dicer domains. Interestingly, truncated variants of Dicer, lacking the PPC region, have been found to display a DNase activity. Inspired by these findings, we investigated how the lack of the PAZ domain, or the entire PPC region, would influence the cleavage activity of hDicer. Using immunopurified 3xFlag-hDicer produced in human cells and its two variants: one lacking the PAZ domain, and the other lacking the entire PPC region, we show that the PAZ domain deletion variants of hDicer are not able to process a pre-miRNA substrate, a dsRNA with 2-nt 3ʹ-overhangs, and a blunt-ended dsRNA. However, the PAZ deletion variants exhibit both RNase and DNase activity on short single-stranded RNA and DNAs, respectively. Collectively, our results indicate that when the PAZ domain is absent, other hDicer domains may contribute to substrate binding and in this case, non-canonical products can be generated.
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Li B, Yan J, Zhang Y, Li W, Zeng C, Zhao W, Hou X, Zhang C, Dong Y. CRISPR-Cas12a Possesses Unconventional DNase Activity that Can Be Inactivated by Synthetic Oligonucleotides. Mol Ther Nucleic Acids 2020; 19:1043-1052. [PMID: 32045875 PMCID: PMC7015830 DOI: 10.1016/j.omtn.2019.12.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a (CRISPR-Cpf1) was reported to have multiple types of cleavage activities. Without the assistance of CRISPR RNA (crRNA), we investigated DNase activity and substrate specificity of Cas12a orthologs in the presence of diverse divalent metal ions. Cas12a from different species are capable of degrading single-stranded DNA (ssDNA) and/or double-stranded DNA (dsDNA), depending on the metal ions used. In spite of sharing high sequence similarity and functional domains among diverse Cas12a orthologs, only Acidaminococcus sp. Cas12a (AsCas12a) showed a predominant preference for cleaving ssDNA, but no detectable activity toward dsDNA substrate in the presence of magnesium (II) ions. In addition, we found that both AsCas12a and Francisella novicida Cas12a (FnCas12a) caused substantial dsDNA cleavage in the presence of manganese (II) ion. More importantly, the DNase activities can be inhibited by synthetic DNA oligonucleotides with phosphorothioate linkage modifications. Overall, ssDNase activity of the Cas12a orthologs uncovered a distinct approach for DNA cleavage compared with crRNA-guided dsDNA breaks, and provided insights into potential biological and therapeutic applications.
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Affiliation(s)
- Bin Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; Department of Infectious Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Jingyue Yan
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Youxi Zhang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Wenqing Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chunxi Zeng
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Weiyu Zhao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Xucheng Hou
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chengxiang Zhang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA; The Center for Clinical and Translational Science, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA.
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Barkhojasteh M, Abdolhay HA, Gorjipoor E, Amini H, Salahi MM, Eghbalsaied S. Robust DNase activity of the ooplasm can act as a gametic transfection barrier in rainbow trout. Theriogenology 2020; 142:62-6. [PMID: 31574402 DOI: 10.1016/j.theriogenology.2019.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/21/2019] [Accepted: 09/18/2019] [Indexed: 11/23/2022]
Abstract
In this study, we evaluated DNase activity of rainbow trout oocyte using an in vitro and in vivo study. First, synthetic single strand and natural double strand DNA from Eukaryotic and prokaryotic sources as well as naked DNA were in vitro incubated with the oocyte cytoplasm. Results showed that the DNase activity of rainbow trout oocyte is strong enough to degrade any type of DNA at the onset of the incubation. Then, we evaluated if similar to the mammalian species, dead spermatozoa from rainbow trout can protect exogenous DNA from oocyte DNases. A series of dead spermatozoa was incubated with pDB2, carrying EGFP transgene, for 30 min followed by the ooplasm treatment for an additional 30 min. Not only did oocyte DNases completely degrade the exogenous DNA, but also it degraded the compact genome of spermatozoa. In conclusion, in vitro results clearly showed that strong DNase activity of ooplasm could degrade any types of foreign DNAs including oligonucleotides and intensively compact sperm genome. The strong DNase activity of rainbow trout ooplasm could be a stumbling block for genetic modification using plasmids in salmonids.
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Dorado-Silva M, Bartolomé-Nebreda J, Sánchez-Martín P, Johnston S, Gosálvez J. Co-incubation of spermatozoa with human follicular fluid reduces sperm DNA fragmentation by mitigating DNase activity in the seminal plasma. J Assist Reprod Genet 2020; 37:63-9. [PMID: 31808045 DOI: 10.1007/s10815-019-01643-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE To examine the effect of co-incubating spermatozoa with human follicular fluid (HFF) on the rate of sperm DNA fragmentation. METHODS This prospective study used semen (n = 23) and HFF from oocyte donors (n = 23). Liquified semen was divided into four aliquots: (1) neat semen (NEAT), (2) seminal plasma removed and replaced with sperm media (HTF) containing 0% (FF0), (3) 20% (FF20), or (4) 50% (FF50) HFF. Sperm motility and DNA fragmentation (SDF) were assessed following 24 h of incubation at 37 °C. Pro-oxidant capacity of HFF and seminal plasma and the effect of HFF on seminal plasma DNase activity was assessed in a sub-sample of 10 ejaculates. RESULTS Sperm motility was higher after 3 h of incubation in media that contained HFF compared to the NEAT sample or when sperm was diluted in media without HFF. r-SDF (increase of SDF per time unit) values after 24 h of incubation for NEAT, FF0, FF20 and FF50 were 0.91, 0.69, 0.25 and 0.36, respectively. While pro-oxidant capacity of seminal plasma samples showed large variation (mean: 94.6 colour units; SD 65.4), it was lower and more homogeneous in FF samples (mean: 29.9 colour units; SD: 6.3). Addition of HFF to seminal plasma appeared to inhibit DNase activity. CONCLUSION While differences exist in the pro-oxidant capacity of seminal plasma of patients, sperm DNA integrity was preserved with addition of HFF to sperm media, irrespective of the level of pro-oxidant capacity. DNase activity in the original seminal plasma was abolished after HFF co-incubation.
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Cortés-Gutiérrez EI, De La Vega CG, Bartolomé-Nebreda J, Gosálvez J. Characterization of DNA cleavage produced by seminal plasma using leukocytes as a cell target. Syst Biol Reprod Med 2019; 65:420-429. [PMID: 31539284 DOI: 10.1080/19396368.2019.1645236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Numerous studies have shown the presence of DNA lesions in human spermatozoa affecting sperm quality. However, the nature of this anomaly and its relationship with patient etiology are poorly understood since different mechanisms can be involved in the formation of these novel DNA configurations including the action of a seminal plasma nuclease activity. The objective of this study was to assess the capacity of seminal plasma for producing endogenous DNA cleavage using nuclei of peripheral blood leukocytes as external targets. For this purpose, we used seminal plasma from fertile males with normal semen parameters to produce DNA cleavage in a sample of leukocytes. Three different tests were performed to visualize DNA cleavage: (a) DNase activity detection, (b) DNA Breakage Detection-Fluorescence In Situ Hybridization (DBD-FISH), and (c) Two-dimensional comet assay (Two-tail comet assay). Our results demonstrate that: (i) the seminal plasma is able to cleave DNA compacted with histones in the leukocytes; (ii) this DNA cleavage can be associated with DNase activity and (iii) DNA damage mainly corresponds to single-strand DNA breaks. In conclusion, capacity of seminal plasma for producing DNA cleavage represents a solid contribution to expand the analysis of the standard seminal profile and could constitute a putative diagnostic tool for evaluating male infertility.Abbreviations: ALS: alkali labile sites; ART: Assisted Reproduction Technologies; DBD-FISH: DNA Breakage Detection-Fluorescence In Situ Hybridization; DNA: deoxyribonucleic acid; DSBs-DNA: double-strand DNA; FITC: Fluorescein IsoThioCyanate; GEDA: Gravity Enforced Diffusion Assays; PBS: phosphate-buffered saline; ROS: Reactive Oxigen Species; SSBs-DNA: single-strand DNA; SSC: saline-sodium citrate.
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Affiliation(s)
- Elva I Cortés-Gutiérrez
- Faculty of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, México
| | | | | | - Jaime Gosálvez
- Department of Biology, Universidad Autónoma de Madrid (UAM), Madrid, Spain
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Tamkovich S, Laktionov P. Cell-surface-bound circulating DNA in the blood: Biology and clinical application. IUBMB Life 2019; 71:1201-1210. [PMID: 31091350 DOI: 10.1002/iub.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023]
Abstract
Cell-surface-bound extracellular DNA (csbDNA) is present on the outer membrane of blood cells, including both red blood cells and leukocytes. Although less well characterized than cell-free DNA (cfDNA) in plasma and serum, leukocyte and red blood cell csbDNA form a considerable fraction of the blood extracellular nucleic acids pool, with typically at least comparable amount of DNA occurring bound to the outer surface of cells as compared with circulating free DNA in plasma. The cellular origin of csbDNA is not clear; however, as with cfDNA, in patients with cancer a proportion is derived from the tumor, thus making it potentially a useful source of DNA for cancer diagnosis, prognosis, and monitoring. © 2019 IUBMB Life, 71(9):1201-1210, 2019.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
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Abstract
INTRODUCTION Cell-free DNA (cfDNA) was first detected in human plasma in the 1940s, but the knowledge on its regulation and rate of release is incomplete. CfDNA can originate from both normal and tumour cells. AIM Our aims were to investigate the rate of cfDNA's release in SHO mice/HT-29 colorectal adenocarcinoma cell line xenograft model and to define the decay of methylated and non-methylated DNA fragments in C57BL/6 bloodstream. METHOD SHO mice were xenografted with human HT-29 cells, than blood samples were collected over 2 months. CfDNA was isolated, then quantified by real-time PCR with highly specific genomic and mitochondrial human and mouse primer sets. This method permitted to define the ratio of human/mouse DNA. To assess the degradation rate of cfDNA, 3000 bp sized methylated and non-methylated DNA fragments were injected into healthy and C38 tumour-cell vaccinated C57BL/6 mice's bloodstream. The decay of amplicons was measured with 19 PCR assays. RESULTS The amount of human DNA until the 2nd week was below the limit of detection. From the third week, a continuous growth was experienced, which reached 18.26% by the 8th week. Moreover, it was found that in healthy animals the non-methylated DNA disappears from the plasma after 6 hours, while the methylated fragment was detectable even after 24 hours. In animals with tumour, both amplicons were detectable after 24 hours. CONCLUSION The examination of the role and mechanism of cfDNA shows an increasing level of interest. This work can contribute to a better understanding of the release and degradation of cfDNA. Orv Hetil. 2018; 159(6): 223-233.
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Affiliation(s)
- Barbara Kinga Barták
- II. Belgyógyászati Klinika, Molekuláris Gasztroenterológiai Laboratórium, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Szentkirályi u. 46., 1088
| | - Zsófia Brigitta Nagy
- II. Belgyógyászati Klinika, Molekuláris Gasztroenterológiai Laboratórium, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Szentkirályi u. 46., 1088
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts, USA
| | - Zsolt Tulassay
- II. Belgyógyászati Klinika, Molekuláris Gasztroenterológiai Laboratórium, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Szentkirályi u. 46., 1088.,Molekuláris Medicina Kutatócsoport, Magyar Tudományos Akadémia Budapest
| | - Magdolna Dank
- Onkológiai Központ, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest
| | - Péter Igaz
- II. Belgyógyászati Klinika, Molekuláris Gasztroenterológiai Laboratórium, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Szentkirályi u. 46., 1088.,Molekuláris Medicina Kutatócsoport, Magyar Tudományos Akadémia Budapest
| | - Béla Molnár
- II. Belgyógyászati Klinika, Molekuláris Gasztroenterológiai Laboratórium, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Szentkirályi u. 46., 1088.,Molekuláris Medicina Kutatócsoport, Magyar Tudományos Akadémia Budapest
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McCall J, Smith JJ, Marquardt KN, Knight KR, Bane H, Barber A, DeLong RK. ZnO Nanoparticles Protect RNA from Degradation Better than DNA. Nanomaterials (Basel) 2017; 7:nano7110378. [PMID: 29117135 PMCID: PMC5707595 DOI: 10.3390/nano7110378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 11/25/2022]
Abstract
Gene therapy and RNA delivery require a nanoparticle (NP) to stabilize these nucleic acids when administered in vivo. The presence of degradative hydrolytic enzymes within these environments limits the nucleic acids’ pharmacologic activity. This study compared the effects of nanoscale ZnO and MgO in the protection afforded to DNA and RNA from degradation by DNase, serum or tumor homogenate. For double-stranded plasmid DNA degradation by DNase, our results suggest that the presence of MgO NP can protect DNA from DNase digestion at an elevated temperature (65 °C), a biochemical activity not present in ZnO NP-containing samples at any temperature. In this case, intact DNA was remarkably present for MgO NP after ethidium bromide staining and agarose gel electrophoresis where these same stained DNA bands were notably absent for ZnO NP. Anticancer RNA, polyinosinic-polycytidylic acid (poly I:C) is now considered an anti-metastatic RNA targeting agent and as such there is great interest in its delivery by NP. For it to function, the NP must protect it from degradation in serum and the tumor environment. Surprisingly, ZnO NP protected the RNA from degradation in either serum-containing media or melanoma tumor homogenate after gel electrophoretic analysis, whereas the band was much more diminished in the presence of MgO. For both MgO and ZnO NP, buffer-dependent rescue from degradation occurred. These data suggest a fundamental difference in the ability of MgO and ZnO NP to stabilize nucleic acids with implications for DNA and RNA delivery and therapy.
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Affiliation(s)
- Jayden McCall
- Nanotechnology Innovation Center Kansas State (NICKS), Department of Anatomy and Physiology, College of Veterinary Medicine, Manhattan, KS 66506, USA.
| | - Joshua J Smith
- Department of Biomedical Sciences, College of Health and Human Services, Missouri State University, Springfield, MO 65897, USA.
| | - Kelsey N Marquardt
- Department of Biomedical Sciences, College of Health and Human Services, Missouri State University, Springfield, MO 65897, USA.
| | - Katelin R Knight
- Department of Biomedical Sciences, College of Health and Human Services, Missouri State University, Springfield, MO 65897, USA.
| | - Hunter Bane
- Department of Biomedical Sciences, College of Health and Human Services, Missouri State University, Springfield, MO 65897, USA.
| | - Alice Barber
- Department of Biomedical Sciences, College of Health and Human Services, Missouri State University, Springfield, MO 65897, USA.
| | - Robert K DeLong
- Nanotechnology Innovation Center Kansas State (NICKS), Department of Anatomy and Physiology, College of Veterinary Medicine, Manhattan, KS 66506, USA.
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Willett JL, Gucinski GC, Fatherree JP, Low DA, Hayes CS. Contact-dependent growth inhibition toxins exploit multiple independent cell-entry pathways. Proc Natl Acad Sci U S A 2015; 112:11341-6. [PMID: 26305955 DOI: 10.1073/pnas.1512124112] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems function to deliver toxins into neighboring bacterial cells. CDI+ bacteria export filamentous CdiA effector proteins, which extend from the inhibitor-cell surface to interact with receptors on neighboring target bacteria. Upon binding its receptor, CdiA delivers a toxin derived from its C-terminal region. CdiA C-terminal (CdiA-CT) sequences are highly variable between bacteria, reflecting the multitude of CDI toxin activities. Here, we show that several CdiA-CT regions are composed of two domains, each with a distinct function during CDI. The C-terminal domain typically possesses toxic nuclease activity, whereas the N-terminal domain appears to control toxin transport into target bacteria. Using genetic approaches, we identified ptsG, metI, rbsC, gltK/gltJ, yciB, and ftsH mutations that confer resistance to specific CdiA-CTs. The resistance mutations all disrupt expression of inner-membrane proteins, suggesting that these proteins are exploited for toxin entry into target cells. Moreover, each mutation only protects against inhibition by a subset of CdiA-CTs that share similar N-terminal domains. We propose that, following delivery of CdiA-CTs into the periplasm, the N-terminal domains bind specific inner-membrane receptors for subsequent translocation into the cytoplasm. In accord with this model, we find that CDI nuclease domains are modular payloads that can be redirected through different import pathways when fused to heterologous N-terminal "translocation domains." These results highlight the plasticity of CDI toxin delivery and suggest that the underlying translocation mechanisms could be harnessed to deliver other antimicrobial agents into Gram-negative bacteria.
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Barra GB, Santa Rita TH, de Almeida Vasques J, Chianca CF, Nery LFA, Santana Soares Costa S. EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples. Clin Biochem 2015; 48:976-81. [PMID: 25746148 DOI: 10.1016/j.clinbiochem.2015.02.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
OBJETIVES The extracellular DNA occurring in plasma-EDTA and serum is a biomarker of growing interest, especially in prenatal diagnosis and oncology. The objectives of the present study were to compare the DNase activity in these specimens and to investigate its ex-vivo impact over the circulating cell-free DNA yield (ccfDNA), using the circulating cell-free fetal DNA (ccffDNA) as a tool. DESIGN AND METHODS EDTA-plasma and serum from women bearing male fetus were submitted to an endogenous DNase activity assay based on qPCR hydrolysis probe degradation, they were treated with DNAse I to investigate the action of an exogenous nuclease and also submitted to different temperature conditions to investigate the temperature-dependent degradation of the ccffDNA. In all instances, all male ccffDNA were quantified by qPCR targeting the Y chromosome-specific sequence DYS-14. Moreover, a serial dilution of EDTA was added to nonanticoagulated plasma and serum before the endogenous DNAse activity assay, to investigate the EDTA-mediated inhibition of the blood's DNase. RESULTS The endogenous nuclease activity was 14.9-fold higher in serum compared to EDTA-plasma. The DNAse I treatment did not alter the ccffDNA yields in EDTA-plasma, but completely degraded it in serum. The addition of increasing doses of EDTA to nonanticoagulated plasma and serum resulted in a stepwise inhibition of their nucleases activity. Finally, we observed a much more pronounced temperature-mediated decrease on the ccffDNA amount in serum compared to EDTA-plasma. CONCLUSION The exogenous and endogenous DNases are more active in serum, the anticoagulant EDTA indirectly inhibits blood DNases, and consequently ccfDNA is protected from the blood's DNase preanalytical impact in EDTA-plasma.
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Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
| | - Júlia de Almeida Vasques
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
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Bryzgunova OE, Tamkovich SN, Cherepanova AV, Yarmoshchuk SV, Permyakova VI, Anykeeva OY, Laktionov PP. Redistribution of Free- and Cell-Surface-Bound DNA in Blood of Benign and Malignant Prostate Tumor Patients. Acta Naturae 2015; 7:115-8. [PMID: 26085953 PMCID: PMC4463421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A direct correlation between the concentration of cell-free and cell-surface-bound circulating DNA (cfDNA and csbDNA, respectively) was demonstrated. Based on an inverse correlation between blood plasma DNase activity and the cfDNA concentration, blood DNases are supposed to regulate the cfDNA concentration. However, no correlation was found between the DNase activity in blood plasma and the csbDNA concentration, indicating that blood DNases are not involved in csbDNA dissociation from the cell surface. The possibility of DNA redistribution between cfDNA and csbDNA indicates that the total pool of circulating DNA (cfDNA + csbDNA) should be used for a correct analysis of marker DNA concentrations and data standardization.
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Affiliation(s)
- O. E. Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva, 8, 630090, Novosibirsk, Russia
| | - S. N. Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva, 8, 630090, Novosibirsk, Russia,Novosibirsk State University, Pirogova Str., 2, 630090, Novosibirsk, Russia
| | - A. V. Cherepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva, 8, 630090, Novosibirsk, Russia
| | - S. V. Yarmoshchuk
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Rechkunovskaya Str., 15, 630055, Novosibirsk, Russia
| | - V. I. Permyakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva, 8, 630090, Novosibirsk, Russia
| | - O. Y. Anykeeva
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Rechkunovskaya Str., 15, 630055, Novosibirsk, Russia
| | - P. P. Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva, 8, 630090, Novosibirsk, Russia,Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Rechkunovskaya Str., 15, 630055, Novosibirsk, Russia
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Vogel B, Frantz S. Determination of DNase activity by degradation of ethidium bromide-DNA complexes using a fluorescence plate reader. Anal Biochem 2014; 471:73-9. [PMID: 25433147 DOI: 10.1016/j.ab.2014.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/13/2014] [Accepted: 11/19/2014] [Indexed: 11/29/2022]
Abstract
The long known toxicity of free chromatin mediated by histones regained attention after discovery of neutrophil extracellular traps (NETs). Free histones from necrotic cells or NETs can damage prokaryotic and eukaryotic cells and are responsible for the aggravation of a growing list of diseases. DNases degrade the toxic chromatin polymer to nucleosomes and efficiently reduce local high histone concentrations. Therefore, DNase activity as a biomarker is of growing interest in basic and clinical research. Here a detailed one-step protocol is presented that allows rapid and sensitive detection of DNases down to 400 fg/μl per reaction based on the detection of fluorescent ethidium bromide/DNA complexes in a 96-well plate reader. The flexible protocol uses an internal standard for background correction and allows convenient and reliable data analysis using common laboratory equipment and chemicals without elaborate preparations. The DNase activity of a sample is clearly defined by substrate amount, incubation time, and (if appropriate) a DNase standard for absolute quantification in Kunitz units per milligram sample protein. Quantitative kinetic determination is possible within less than 1h down to 5 pg DNases/μl per reaction.
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Affiliation(s)
- Benjamin Vogel
- Comprehensive Heart Failure Center (CHCF), Universitätsklinikum Würzburg, 97078 Würzburg, Germany; Medizinische Klinik und Poliklinik I, Universitätsklinikum Würzburg, 97078 Würzburg, Germany.
| | - Stefan Frantz
- Universitätsklinik und Poliklinik für Innere Medizin III, Universitätsklinikum Halle (Saale), 06120 Halle (Saale), Germany
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Kostrikina IA, Odintsova ES, Buneva VN, Nevinsky GA. Systemic lupus erythematosus: molecular cloning and analysis of recombinant DNase monoclonal κ light chain NGK-1. Int Immunol 2014; 26:439-50. [PMID: 24919596 DOI: 10.1093/intimm/dxu047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Because DNase antibodies are cytotoxic, enter the nucleus and cause DNA fragmentation inducing cell death by apoptosis, they can play an important role in the pathogenesis of different autoimmune pathologies and especially systemic lupus erythematosus (SLE). The interesting goal of catalytic antibodies research is not only to study a possible biological role of such antibodies, but also to develop in future new human and animal therapies that use the advantages offered by abzymes. An immunoglobulin κ light chain library from SLE patients was cloned into a phagemid vector. Phage particles displaying recombinant monoclonal antibody light chains (MLChs) capable of binding DNA were isolated by affinity chromatography on DNA-cellulose. Sixteen of the 46 MLChs efficiently hydrolyzed DNA; one MLCh (approximately 27-28kDa) was expressed in Escherichia coli and purified by metal chelating and gel filtration. MLCh NGK-1 was electrophoretically homogeneous and demonstrated a positive answer with mouse IgGs against light chains of human antibodies after western blotting. SDS-PAGE in a gel containing DNA demonstrated that the MLCh hydrolyzes DNA and is not contaminated by canonical DNases. The DNase MLCh was activated by several metal ions. The protein sequence of the DNase MLCh has homology with mammalian DNases I and shares with them several identical or similar (with the same side chain functionality) important amino acid residues, which are necessary for DNA hydrolysis and binding of Mg(2+) and Ca(2+) ions. The affinity of DNA for this first example of a MLCh (K(M) = 0.3 microM) was 150- to 200-fold higher than for human DNase I.
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Affiliation(s)
- Irina A Kostrikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Odintsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Valentina N Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
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Zarringhalam M, Zaringhalam J, Shadnoush M, Safaeyan F, Tekieh E. Inhibitory Effect of Black and Red Pepper and Thyme Extracts and Essential Oils on Enterohemorrhagic Escherichia coli and DNase Activity of Staphylococcus aureus. Iran J Pharm Res 2013; 12:363-369. [PMID: 24250643 PMCID: PMC3813290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this study, extracts and essential oils of Black and Red pepper and Thyme were tested for antibacterial activity against Escherichia coli O157: H7 and Staphylococcus aureus. Black and Red pepper and Thyme were provided from Iranian agricultural researches center. 2 g of each plant powder was added to 10 cc ethanol 96°. After 24 h, the crude extract was separated as an alcoholic extract and concentrated by distillation method. Plants were examined for determining their major component and essential oils were separated. Phytochemical analyses were done for detection of some effective substances in extracts. The antibacterial activity against Escherichia coli O157: H7 and Staphylococcus aureus was tested and the results showed that all extracts and essential oils were effective and essential oils were more active. The extracts and oils that showed antimicrobial activity were later tested to determine the Minimum Inhibitory Dilution (MID) for those bacteria. They were also effective on the inhibition of DNase activity. This study was indicated that extracts and essential oils of Black and Red pepper and Thyme can play a significant role in inhibition of Escherichia coli O157: H7 and Staphylococcus aureus.
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Affiliation(s)
- Maryam Zarringhalam
- Department of Microbiology, International Branch of Shahid Beheshti Medical University, Tehran, Iran.
| | - Jalal Zaringhalam
- Department of Physiology, Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Shadnoush
- Food Science and Technology Department, Nutritional Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Firouzeh Safaeyan
- Department of Microbiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elaheh Tekieh
- Department of Physiology, Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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