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Skalny M, Rokowska A, Szuwarzynski M, Gajewska M, Dziewit L, Bajda T. Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates. CHEMOSPHERE 2024; 362:142602. [PMID: 38871190 DOI: 10.1016/j.chemosphere.2024.142602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m2/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca2+ and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca2+, and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca2+ led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.
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Affiliation(s)
- Mateusz Skalny
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland.
| | - Anna Rokowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Michal Szuwarzynski
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Marta Gajewska
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Bajda
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
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Lu Y, Elrod J, Herrmann M, Knopf J, Boettcher M. Neutrophil Extracellular Traps: A Crucial Factor in Post-Surgical Abdominal Adhesion Formation. Cells 2024; 13:991. [PMID: 38891123 PMCID: PMC11171752 DOI: 10.3390/cells13110991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Post-surgical abdominal adhesions, although poorly understood, are highly prevalent. The molecular processes underlying their formation remain elusive. This review aims to assess the relationship between neutrophil extracellular traps (NETs) and the generation of postoperative peritoneal adhesions and to discuss methods for mitigating peritoneal adhesions. A keyword or medical subject heading (MeSH) search for all original articles and reviews was performed in PubMed and Google Scholar. It included studies assessing peritoneal adhesion reformation after abdominal surgery from 2003 to 2023. After assessing for eligibility, the selected articles were evaluated using the Critical Appraisal Skills Programme checklist for qualitative research. The search yielded 127 full-text articles for assessment of eligibility, of which 7 studies met our criteria and were subjected to a detailed quality review using the Critical Appraisal Skills Programme (CASP) checklist. The selected studies offer a comprehensive analysis of adhesion pathogenesis with a special focus on the role of neutrophil extracellular traps (NETs) in the development of peritoneal adhesions. Current interventional strategies are examined, including the use of mechanical barriers, advances in regenerative medicine, and targeted molecular therapies. In particular, this review emphasizes the potential of NET-targeted interventions as promising strategies to mitigate postoperative adhesion development. Evidence suggests that in addition to their role in innate defense against infections and autoimmune diseases, NETs also play a crucial role in the formation of peritoneal adhesions after surgery. Therefore, therapeutic strategies that target NETs are emerging as significant considerations for researchers. Continued research is vital to fully elucidate the relationship between NETs and post-surgical adhesion formation to develop effective treatments.
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Affiliation(s)
- Yuqing Lu
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Julia Elrod
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Martin Herrmann
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Michael Boettcher
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
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3
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Palomba E, Chiusano ML, Monticolo F, Langella MC, Sanchez M, Tirelli V, de Alteriis E, Iannaccone M, Termolino P, Capparelli R, Carteni F, Incerti G, Mazzoleni S. Extracellular Self-DNA Effects on Yeast Cell Cycle and Transcriptome during Batch Growth. Biomolecules 2024; 14:663. [PMID: 38927066 PMCID: PMC11201494 DOI: 10.3390/biom14060663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of (heterologous) nonself-DNA. The self-DNA treatment determined a reduction in the growth rate and a major elongation of the diauxic lag phase, as well as a significant delay in the achievement of the stationary phase. This was associated with significant changes in the cell cycle dynamics, with slower exit from the G0 phase, followed by an increased level of cell percentage in the S phase, during the cultivation. Comparatively, the exposure to heterologous DNA did not affect the growth curve and the cell cycle dynamics. The transcriptomic analysis showed that self-DNA exposure produced a generalized downregulation of transmembrane transport and an upregulation of genes associated with sulfur compounds and the pentose phosphate pathway. Instead, in the case of the nonself treatment, a clear response to nutrient deprivation was detected. Overall, the presented findings represent further insights into the complex functional mechanisms of self-DNA inhibition.
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Affiliation(s)
- Emanuela Palomba
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici, Italy; (E.P.); (P.T.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Maria Chiara Langella
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (V.T.)
| | - Valentina Tirelli
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (V.T.)
| | - Elisabetta de Alteriis
- Department of Biology, University of Naples “Federico II”, Via Cinthia 26, 80126 Naples, Italy;
| | - Marco Iannaccone
- Laboratory of Bioproducts and Bioprocesses ENEA, Piazzale Enrico Fermi 1, 80055 Portici, Italy;
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici, Italy; (E.P.); (P.T.)
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Guido Incerti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy;
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
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Ratsoma FM, Mokoena NZ, Santana QC, Wingfield BD, Steenkamp ET, Motaung TE. Characterization of the Fusarium circinatum biofilm environmental response role. J Basic Microbiol 2024; 64:e2300536. [PMID: 38314962 DOI: 10.1002/jobm.202300536] [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: 09/15/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/07/2024]
Abstract
The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum, can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our research shows F. circinatum's ability to adapt to environmental changes by assuming a biofilm-like lifestyle. This was demonstrated by varying metabolic activities exhibited by the biofilms in response to factors like temperature and pH. Further analysis revealed that while planktonic cells produced small amounts of ECM per unit of the biomass, heat- and azole-exposed biofilms produced significantly more ECM than nonexposed biofilms, further demonstrating the adaptability of F. circinatum to changing environments. The increased synthesis of ECM triggered by these abiotic factors highlights the link between ECM production in biofilm and resistance to abiotic stress. This suggests that ECM-mediated response may be one of the key survival strategies of F. circinatum biofilms in response to changing environments. Interestingly, azole exposure also led to biofilms that were resistant to DNase, which typically uncouples biofilms by penetrating the biofilm and degrading its extracellular DNA; we propose that DNases were likely hindered from reaching target cells by the ECM barricade. The interplay between antifungal treatment and DNase enzyme suggests a complex relationship between eDNA, ECM, and antifungal agents in F. circinatum biofilms. Therefore, our results show how a phytopathogen's sessile (biofilm) lifestyle could influence its response to the surrounding environment.
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Affiliation(s)
- Francinah M Ratsoma
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nthabiseng Z Mokoena
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Quentin C Santana
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Agricultural Research Council (ARC) Biotechnology Platform, Private Bag X5 Onderstepoort, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Thabiso E Motaung
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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de Alteriis E, Incerti G, Cartenì F, Chiusano ML, Colantuono C, Palomba E, Termolino P, Monticolo F, Esposito A, Bonanomi G, Capparelli R, Iannaccone M, Foscari A, Landi C, Parascandola P, Sanchez M, Tirelli V, de Falco B, Lanzotti V, Mazzoleni S. Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:292-295. [PMID: 38053574 PMCID: PMC10695634 DOI: 10.15698/mic2023.12.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.
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Affiliation(s)
- Elisabetta de Alteriis
- Department of Biology, University of Naples “Federico II”, Via Cinthia 26, 80126 Naples, Italy
| | - Guido Incerti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Fabrizio Cartenì
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Emanuela Palomba
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alfonso Esposito
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Marco Iannaccone
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Laboratory of Biotechnological Processes for Energy and Industry, ENEA, Via Anguillarese, 301, - 00123 Rome, Italy
| | - Alessandro Foscari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Carmine Landi
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Palma Parascandola
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valentina Tirelli
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Bruna de Falco
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Virginia Lanzotti
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
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Shirakawa M, Matsushita N, Fukuda K. Visualization of root extracellular traps in an ectomycorrhizal woody plant (Pinus densiflora) and their interactions with root-associated bacteria. PLANTA 2023; 258:112. [PMID: 37935872 PMCID: PMC10630192 DOI: 10.1007/s00425-023-04274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
MAIN CONCLUSION Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants.
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Affiliation(s)
- Makoto Shirakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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Zárate-López MA, Quintana-Rodríguez E, Orona-Tamayo D, Aguilar-Hernández V, Araujo-León JA, Brito-Argáez L, Molina-Torres J, Hernández-Flores JL, Loyola-Vargas VM, Lozoya-Pérez NE, Lozoya-Gloria E. Metabolic Responses of the Microalga Neochloris oleoabundans to Extracellular Self- and Nonself-DNA. Int J Mol Sci 2023; 24:14172. [PMID: 37762475 PMCID: PMC10531809 DOI: 10.3390/ijms241814172] [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: 07/13/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Stressed organisms identify intracellular molecules released from damaged cells due to trauma or pathogen infection as components of the innate immune response. These molecules called DAMPs (Damage-Associated Molecular Patterns) are extracellular ATP, sugars, and extracellular DNA, among others. Animals and plants can recognize their own DNA applied externally (self-exDNA) as a DAMP with a high degree of specificity. However, little is known about the microalgae responses to damage when exposed to DAMPs and specifically to self-exDNAs. Here we compared the response of the oilseed microalgae Neochloris oleoabundans to self-exDNA, with the stress responses elicited by nonself-exDNA, methyl jasmonate (MeJA) and sodium bicarbonate (NaHCO3). We analyzed the peroxidase enzyme activity related to the production of reactive oxygen species (ROS), as well as the production of polyphenols, lipids, triacylglycerols, and phytohormones. After 5 min of addition, self-exDNA induced peroxidase enzyme activity higher than the other elicitors. Polyphenols and lipids were increased by self-exDNA at 48 and 24 h, respectively. Triacylglycerols were increased with all elicitors from addition and up to 48 h, except with nonself-exDNA. Regarding phytohormones, self-exDNA and MeJA increased gibberellic acid, isopentenyladenine, and benzylaminopurine at 24 h. Results show that Neochloris oleoabundans have self-exDNA specific responses.
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Affiliation(s)
- Mónica A. Zárate-López
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Unidad Irapuato, Km 9.6 Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico; (M.A.Z.-L.); (J.M.-T.); (J.L.H.-F.)
- Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), Omega # 201 Col. Industrial Delta, León 37545, Guanajuato, Mexico; (D.O.-T.); (N.E.L.-P.)
| | - Elizabeth Quintana-Rodríguez
- Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), Omega # 201 Col. Industrial Delta, León 37545, Guanajuato, Mexico; (D.O.-T.); (N.E.L.-P.)
| | - Domancar Orona-Tamayo
- Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), Omega # 201 Col. Industrial Delta, León 37545, Guanajuato, Mexico; (D.O.-T.); (N.E.L.-P.)
| | - Víctor Aguilar-Hernández
- Centro de Investigación Científica de Yucatán, A.C. (CICY), Calle 43 # 130, Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico; (V.A.-H.); (J.A.A.-L.); (L.B.-A.); (V.M.L.-V.)
| | - Jesús A. Araujo-León
- Centro de Investigación Científica de Yucatán, A.C. (CICY), Calle 43 # 130, Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico; (V.A.-H.); (J.A.A.-L.); (L.B.-A.); (V.M.L.-V.)
| | - Ligia Brito-Argáez
- Centro de Investigación Científica de Yucatán, A.C. (CICY), Calle 43 # 130, Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico; (V.A.-H.); (J.A.A.-L.); (L.B.-A.); (V.M.L.-V.)
| | - Jorge Molina-Torres
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Unidad Irapuato, Km 9.6 Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico; (M.A.Z.-L.); (J.M.-T.); (J.L.H.-F.)
| | - José Luis Hernández-Flores
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Unidad Irapuato, Km 9.6 Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico; (M.A.Z.-L.); (J.M.-T.); (J.L.H.-F.)
| | - Víctor M. Loyola-Vargas
- Centro de Investigación Científica de Yucatán, A.C. (CICY), Calle 43 # 130, Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico; (V.A.-H.); (J.A.A.-L.); (L.B.-A.); (V.M.L.-V.)
| | - Nancy E. Lozoya-Pérez
- Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), Omega # 201 Col. Industrial Delta, León 37545, Guanajuato, Mexico; (D.O.-T.); (N.E.L.-P.)
| | - Edmundo Lozoya-Gloria
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Unidad Irapuato, Km 9.6 Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico; (M.A.Z.-L.); (J.M.-T.); (J.L.H.-F.)
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8
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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9
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Oberemok VV, Useinov RZ, Skorokhod OA, Gal’chinsky NV, Novikov IA, Makalish TP, Yatskova EV, Sharmagiy AK, Golovkin IO, Gninenko YI, Puzanova YV, Andreeva OA, Alieva EE, Eken E, Laikova KV, Plugatar YV. Oligonucleotide Insecticides for Green Agriculture: Regulatory Role of Contact DNA in Plant-Insect Interactions. Int J Mol Sci 2022; 23:ijms232415681. [PMID: 36555325 PMCID: PMC9779641 DOI: 10.3390/ijms232415681] [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: 10/31/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Insects vastly outnumber us in terms of species and total biomass, and are among the most efficient and voracious consumers of plants on the planet. As a result, to preserve crops, one of the primary tasks in agriculture has always been the need to control and reduce the number of insect pests. The current use of chemical insecticides leads to the accumulation of xenobiotics in ecosystems and a decreased number of species in those ecosystems, including insects. Sustainable development of human society is impossible without useful insects, so the control of insect pests must be effective and selective at the same time. In this article, we show for the first time a natural way to regulate the number of insect pests based on the use of extracellular double-stranded DNA secreted by the plant Pittosporum tobira. Using a principle similar to one found in nature, we show that the topical application of artificially synthesized short antisense oligonucleotide insecticides (olinscides, DNA insecticides) is an effective and selective way to control the insect Coccus hesperidum. Using contact oligonucleotide insecticide Coccus-11 at a concentration of 100 ng/μL on C. hesperidum larvae resulted in a mortality of 95.59 ± 1.63% within 12 days. Green oligonucleotide insecticides, created by nature and later discovered by humans, demonstrate a new method to control insect pests that is beneficial and safe for macromolecular insect pest management.
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Affiliation(s)
- Volodymyr V. Oberemok
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
- Laboratory of Entomology and Phytopathology, Dendrology and Landscape Architecture, Nikita Botanical Gardens—National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Crimea
- Correspondence: ; Tel.: +7-(978)-814-68-66
| | - Refat Z. Useinov
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Oleksii A. Skorokhod
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
| | - Nikita V. Gal’chinsky
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Ilya A. Novikov
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Tatyana P. Makalish
- S.I. Georgievsky Medical Academy, V.I. Vernadsky Crimean Federal University, Simferopol 295015, Crimea
| | - Ekaterina V. Yatskova
- Laboratory of Entomology and Phytopathology, Dendrology and Landscape Architecture, Nikita Botanical Gardens—National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Crimea
| | - Alexander K. Sharmagiy
- Laboratory of Entomology and Phytopathology, Dendrology and Landscape Architecture, Nikita Botanical Gardens—National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Crimea
| | - Ilya O. Golovkin
- S.I. Georgievsky Medical Academy, V.I. Vernadsky Crimean Federal University, Simferopol 295015, Crimea
| | - Yuri I. Gninenko
- All-Russian Research Institute for Silviculture and Mechanization of Forestry, Pushkino 141200, Russia
| | - Yelizaveta V. Puzanova
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Oksana A. Andreeva
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Edie E. Alieva
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Emre Eken
- Department of Molecular Genetics and Biotechnologies, Institute of Biochemical Technologies, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Crimea
| | - Kateryna V. Laikova
- S.I. Georgievsky Medical Academy, V.I. Vernadsky Crimean Federal University, Simferopol 295015, Crimea
| | - Yuri V. Plugatar
- Department of Natural Ecosystems, Nikita Botanical Garden—National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Crimea
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10
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Lanzotti V, Grauso L, Mangoni A, Termolino P, Palomba E, Anzano A, Incerti G, Mazzoleni S. Metabolomics and molecular networking analyses in Arabidopsis thaliana show that extracellular self-DNA affects nucleoside/nucleotide cycles with accumulation of cAMP, cGMP and N6-methyl-AMP. PHYTOCHEMISTRY 2022; 204:113453. [PMID: 36174718 DOI: 10.1016/j.phytochem.2022.113453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Extracellular DNA (exDNA) widely occurs in the environment due to release by either cell lysis or active secretion. The role of exDNA in plant-soil interactions has been investigated and inhibitory effects on the growth of conspecific individuals by their self-DNA have been reported. Transcriptome analysis in the model plant Arabidopsis thaliana showed a clear recognition by the plant roots of self- and nonself-exDNA, with inhibition occurring only after exposure to the former. In this study, an untargeted metabolomics approach was used to assess at molecular level the plant reactions to exDNA exposure. Thus, the effects on the metabolites profile of A. thaliana after exposure to self- and nonself-exDNA from plants and fish, were studied by NMR, LC-MS, chemometrics and molecular networking analyses. Results show that self-DNA significantly induces the accumulation of RNA constituents (nucleobases, ribonucleosides, dinucleotide and trinucleotide oligomers). Interestingly, AMP and GMP are found along with their cyclic analogues cAMP and cGMP, and in form of cyclic dimers (c-di-AMP and c-di-GMP). Also methylated adenosine monophosphate (m6AMP) and the dimeric dinucleotide N-methyladenylyl-(3'→5') cytidine (m6ApC) increased only in the self-DNA treatment. Such striking evidence of self-DNA effects highlights a major role of exDNA in plant sensing of its environment.
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Affiliation(s)
- Virginia Lanzotti
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Laura Grauso
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Alfonso Mangoni
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy.
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), 80055, Portici, Italy.
| | - Emanuela Palomba
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), 80055, Portici, Italy.
| | - Attilio Anzano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Guido Incerti
- Department of Agri-Food, Animal and Environmental Sciences, University of Udine, 33100, Udine, Italy.
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
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11
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González-Plaza JJ, Furlan C, Rijavec T, Lapanje A, Barros R, Tamayo-Ramos JA, Suarez-Diez M. Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Front Microbiol 2022; 13:1006946. [PMID: 36519168 PMCID: PMC9744117 DOI: 10.3389/fmicb.2022.1006946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 08/31/2023] Open
Abstract
The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.
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Affiliation(s)
- Juan José González-Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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12
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Huang L, Lu W, Ning Y, Liu J. Reverse effects of Streptococcus mutans physiological states on neutrophil extracellular traps formation as a strategy to escape neutrophil killing. Front Cell Infect Microbiol 2022; 12:1023457. [PMID: 36439223 PMCID: PMC9687095 DOI: 10.3389/fcimb.2022.1023457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/25/2022] [Indexed: 03/07/2024] Open
Abstract
Bacteria in nature are present in different lifestyles with distinct characteristics. Streptococcus mutans is the etiologic pathogen of dental caries and could easily gain access into the bloodstream after oral surgery and adopt a biofilm lifestyle, resulting in infective endocarditis. A growing amount of evidence have revealed that the large web-like structure composed of extracellular DNA and antimicrobial proteins released by neutrophils, named Neutrophil Extracellular Traps (NETs), play an active role in the defense against bacterial invasion. The present study demonstrated that NETs formation was discriminatively affected by S. mutans biofilm and its planktonic counterpart. The free-floating planktonic S. mutans exhibited an active NETs response, whereas the biofilm community exhibited a reverse negative NETs response. Besides, impaired biofilm killing correlated with the decrease in NETs production. Unlike planktonic cells, biofilm avoided the burst of reactive oxygen species (ROS) when co-culture with neutrophils, and the NADPH-oxidase pathway was partially involved. A mice infection model also supported the distinguishing response of neutrophils challenged by different lifestyles of S. mutans. In conclusion, different bacterial physiological states can affect the distinct response of the host-microbe interaction, thus contributing to the anti-pathogen immune response activation and immune surveillance survival.
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Affiliation(s)
- Lijia Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
| | - Wenhua Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangdong, Guangzhou, China
| | - Yang Ning
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
- Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
| | - Jia Liu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangdong, Guangzhou, China
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13
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Palomba E, Chiaiese P, Termolino P, Paparo R, Filippone E, Mazzoleni S, Chiusano ML. Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111436. [PMID: 35684209 PMCID: PMC9183124 DOI: 10.3390/plants11111436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.
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Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Rosa Paparo
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Edgardo Filippone
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
- Correspondence: ; Tel.: +39-81-2539492
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14
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Cayetano RDA, Kim GB, Park J, Yang YH, Jeon BH, Jang M, Kim SH. Biofilm formation as a method of improved treatment during anaerobic digestion of organic matter for biogas recovery. BIORESOURCE TECHNOLOGY 2022; 344:126309. [PMID: 34798247 DOI: 10.1016/j.biortech.2021.126309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The efficiency of anaerobic digestion could be increased by promoting microbial retention through biofilm development. The inclusion of certain types of biofilm carriers has differentiated existing AD biofilm reactors through their respective mode of biofilm growth. Bacteria and archaea engaged in methanogenesis during anaerobic processes potentially build biofilms by adhering or attaching to biofilm carriers. Meta-analyzed results depicted varying degrees of biogas enhancement within AD biofilm reactors. Furthermore, different carrier materials highly induced the dynamicity of the dominant microbial population in each system. It is suggested that the promotion of surface contact and improvement of interspecies electron transport have greatly impacted the treatment results. Modern spectroscopy techniques have been and will continue to give essential information regarding biofilm's composition and structural organization which can be useful in elucidating the added function of this special layer of microbial cells.
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Affiliation(s)
- Roent Dune A Cayetano
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Gi-Beom Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungsu Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Min Jang
- Department of Environmental Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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15
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Driouich A, Gaudry A, Pawlak B, Moore JP. Root cap-derived cells and mucilage: a protective network at the root tip. PROTOPLASMA 2021; 258:1179-1185. [PMID: 34196784 DOI: 10.1007/s00709-021-01660-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/27/2021] [Indexed: 05/06/2023]
Abstract
Root cap-derived cells and mucilage provide the first line of defense of the plant against soil microbial pathogens. These cells form a mucilaginous root extracellular trap (RET), which also harbors a range of molecules including exDNA and defensive peptides and proteins much like the neutrophil extracellular trap (NET) of mammalians. Plant RETs resemble mucus structures found in mammalian systems and are rich in arabinogalactan proteins that have similarities to highly glycosylated human mucins. Human mucus and mucins regulate the intestinal flora microbiome through recruiting certain species of microbes and it is plausible that the arabinogalactan protein-rich mucilage found in plant roots fulfills a similar function by attracting specific microbes to the rhizosphere. The role of RETs in root defense functioning is highlighted.
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Affiliation(s)
- Azeddine Driouich
- UNIROUEN, Normandie Université, Laboratoire Glycobiologie Et Matrice Extracellulaire Végétale EA 4358, Université de Rouen Normandie, 76000, Rouen, France.
- UNIROUEN, Fédération de Recherche, Normandie Université, Normandie Végétal-FED 4277, Université de Rouen Normandie, 76000, Rouen, France.
| | - Alexia Gaudry
- UNIROUEN, Normandie Université, Laboratoire Glycobiologie Et Matrice Extracellulaire Végétale EA 4358, Université de Rouen Normandie, 76000, Rouen, France
- UNIROUEN, Fédération de Recherche, Normandie Université, Normandie Végétal-FED 4277, Université de Rouen Normandie, 76000, Rouen, France
| | - Barbara Pawlak
- UNIROUEN, Normandie Université, Laboratoire Glycobiologie Et Matrice Extracellulaire Végétale EA 4358, Université de Rouen Normandie, 76000, Rouen, France
- UNIROUEN, Fédération de Recherche, Normandie Université, Normandie Végétal-FED 4277, Université de Rouen Normandie, 76000, Rouen, France
| | - John P Moore
- Department of Viticulture and Oenology, Faculty of AgriSciences, South African Grape and Wine Research Institute, Stellenbosch University, Matieland, 7602, South Africa
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16
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Chiusano ML, Incerti G, Colantuono C, Termolino P, Palomba E, Monticolo F, Benvenuto G, Foscari A, Esposito A, Marti L, de Lorenzo G, Vega-Muñoz I, Heil M, Carteni F, Bonanomi G, Mazzoleni S. Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081744. [PMID: 34451789 PMCID: PMC8400022 DOI: 10.3390/plants10081744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023]
Abstract
The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.
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Affiliation(s)
- Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
- Correspondence: (M.L.C.); (S.M.)
| | - Guido Incerti
- Department of Agri-Food, Animal and Environmental Sciences, University of Udine, 33100 Udine, Italy;
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine, via campi Flegrei, 34 Pozzuoli, 80078 Napoli, Italy;
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), 80055 Portici, Italy;
| | - Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giovanna Benvenuto
- Biology and Evolution of Marine Organisms Department (BEOM), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Alessandro Foscari
- Dipartimento di Scienze della Vita, University of Trieste, 34127 Trieste, Italy;
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Lucia Marti
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Giulia de Lorenzo
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Isaac Vega-Muñoz
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Martin Heil
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Correspondence: (M.L.C.); (S.M.)
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Bednarek PT, Pachota KA, Dynkowska WM, Machczyńska J, Orłowska R. Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System. Int J Mol Sci 2021; 22:7546. [PMID: 34299165 PMCID: PMC8304781 DOI: 10.3390/ijms22147546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.
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Affiliation(s)
- Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.A.P.); (W.M.D.); (J.M.); (R.O.)
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18
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Meitha K, Esyanti RR, Iriawati, Hanisia RH, Rohyani. Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA. Noncoding RNA Res 2021; 6:42-50. [PMID: 33778217 PMCID: PMC7970063 DOI: 10.1016/j.ncrna.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.
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Affiliation(s)
- Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rizkita Rachmi Esyanti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Iriawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Ristag Hamida Hanisia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rohyani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
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19
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Kamino LN, Gulden RH. The effect of crop species on DNase-producing bacteria in two soils. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Extracellular deoxyribonucleases (exDNases) from microbial origin contribute substantially to the restriction of extracellular DNA (exDNA) in the soil. Hence, it is imperative to understand the diversity of bacterial species capable of performing this important soil function and how crop species influence their dynamics in the soil. The present study investigates the occurrence of DNase-producing bacteria (DPB) in leachate samples obtained from soils in which the crop species of alfalfa (Medicago sativa L.), canola (Brassica napus L.), soybean (Glycine max [L.] Merr.) and wheat (Triticum aestivum L.) were raised in a growth room.
Methods
Selective media containing methyl green indicator was used to screen for DPB from leachate samples, whereas the 16S rRNA sequence analysis was employed to identify the isolates.
Results
The proportion of culturable DPB ranged between 5.72 and 40.01%; however, we did observe specific crop effects that shifted throughout the growing period. In general, higher proportions of exDNase producers were observed when the soils had lower nutrient levels. On using the 16S rRNA to classify the DPB isolates, most isolates were found to be members of the Bacillus genera, while other groups included Chryseobacterium, Fictibacillus, Flavobacterium, Microbacterium, Nubsella, Pseudomonas, Psychrobacillus, Rheinheimera, Serratia and Stenotrophomonas. Five candidate exDNase/nuclease-encoding proteins were also identified from Bacillus mycoides genomes using online databases.
Conclusion
Results from this study showed that crop species, growth stage and soil properties were important factors shaping the populations of DPB in leachate samples; however, soil properties seemed to have a greater influence on the trends observed on these bacterial populations. It may be possible to target soil indigenous bacteria that produce exDNases through management to decrease potential unintended effects of transgenes originating from genetically modified organisms (GMOs) or other introduced nucleic acid sequences in the environment.
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Barbero F, Guglielmotto M, Islam M, Maffei ME. Extracellular Fragmented Self-DNA Is Involved in Plant Responses to Biotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:686121. [PMID: 34381477 PMCID: PMC8350447 DOI: 10.3389/fpls.2021.686121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/05/2021] [Indexed: 05/17/2023]
Abstract
A growing body of evidence indicates that extracellular fragmented self-DNA (eDNA), by acting as a signaling molecule, triggers inhibitory effects on conspecific plants and functions as a damage-associated molecular pattern (DAMP). To evaluate early and late events in DAMP-dependent responses to eDNA, we extracted, fragmented, and applied the tomato (Solanum lycopersicum) eDNA to tomato leaves. Non-sonicated, intact self-DNA (intact DNA) was used as control. Early event analyses included the evaluation of plasma transmembrane potentials (Vm), cytosolic calcium variations (Ca2+ cy t), the activity and subcellular localization of both voltage-gated and ligand-gated rectified K+ channels, and the reactive oxygen species (ROS) subcellular localization and quantification. Late events included RNA-Seq transcriptomic analysis and qPCR validation of gene expression of tomato leaves exposed to tomato eDNA. Application of eDNA induced a concentration-dependent Vm depolarization which was correlated to an increase in (Ca2+)cyt; this event was associated to the opening of K+ channels, with particular action on ligand-gated rectified K+ channels. Both eDNA-dependent (Ca2+)cyt and K+ increases were correlated to ROS production. In contrast, application of intact DNA produced no effects. The plant response to eDNA was the modulation of the expression of genes involved in plant-biotic interactions including pathogenesis-related proteins (PRPs), calcium-dependent protein kinases (CPK1), heat shock transcription factors (Hsf), heat shock proteins (Hsp), receptor-like kinases (RLKs), and ethylene-responsive factors (ERFs). Several genes involved in calcium signaling, ROS scavenging and ion homeostasis were also modulated by application of eDNA. Shared elements among the transcriptional response to eDNA and to biotic stress indicate that eDNA might be a common DAMP that triggers plant responses to pathogens and herbivores, particularly to those that intensive plant cell disruption or cell death. Our results suggest the intriguing hypothesis that some of the plant reactions to pathogens and herbivores might be due to DNA degradation, especially when associated to the plant cell disruption. Fragmented DNA would then become an important and powerful elicitor able to trigger early and late responses to biotic stress.
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Affiliation(s)
- Francesca Barbero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Michela Guglielmotto
- Neuroscience Institute of Cavalieri Ottolenghi Foundation, University of Turin, Turin, Italy
| | - Monirul Islam
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Massimo E. Maffei
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- *Correspondence: Massimo E. Maffei,
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