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Cao J, Zhang R, Zhang Y, Wang Y. Combined screening analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. J Gastrointest Oncol 2022; 13:311-325. [PMID: 35284134 PMCID: PMC8899745 DOI: 10.21037/jgo-21-866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Methylation plays an important role in hepatocellular carcinoma (HCC) by altering the expression of key genes. The aim of this study was to screen the aberrantly methylated-differentially expressed genes (DEGs) in HCC and elucidate their underlying molecular mechanism. METHODS Gene expression microarrays (GSE101685) and gene methylation microarrays (GSE44909) were selected. DEGs and differentially methylated genes (DMGs) were screened. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the Database for Annotation, Visualization, and Integrated discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to analyze the functional protein-protein interaction (PPI) network. Molecular Complex Detection (MCODE) analysis was performed using the Cytoscape software. Hub genes were verified in The Cancer Genome Atlas (TCGA) database. RESULTS A total of 80 hypomethylation-high expression genes (Hypo-HGs) were identified. Pathway enrichment analysis showed DNA replication, cell cycle, viral carcinogenesis, and the spliceosome. The top 5 hub genes were minichromosome maintenance complex component 3 (MCM3), checkpoint kinase 1 (CHEK1), kinesin family member 11 (KIF11), PDZ binding kinase (PBK), and Rac GTPase activating protein 1 (RACGAP1). In addition, 189 hypermethylation-low expression genes (Hyper-LGs) were identified. Pathway enrichment analysis indicated enrichment in metabolic pathways, drug metabolism-other enzymes, and chemical carcinogenesis. The top 5 hub genes were leukocyte immunoglobulin like receptor B2 (LILRB2), formyl peptide receptor 1 (FPR1), S100 calcium binding protein A9 (S100A9), S100 calcium binding protein A8 (S100A8), and myeloid cell nuclear differentiation antigen (MNDA). The methylation status and mRNA expression of MCM3, CHEK1, KIF11, PBK, and S100A9 were consistent in the TCGA database and significantly correlated with the prognosis of patients. CONCLUSIONS Combined screening of aberrantly methylated-DEGs based on bioinformatic analysis may provide new clues for elucidating the epigenetic mechanism in HCC. Hub genes, including MCM3, CHEK1, KIF11, PBK, and S100A9, may serve as biomarkers for the precise diagnosis of HCC.
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Affiliation(s)
- Jisen Cao
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Ruiqiang Zhang
- Department of Orthopedics, General Hospital of Tianjin Medical University, Tianjin, China
| | - Ye Zhang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Yijun Wang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
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2
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Ugolini I, Halic M. Fidelity in RNA-based recognition of transposable elements. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0168. [PMID: 30397104 PMCID: PMC6232588 DOI: 10.1098/rstb.2018.0168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2018] [Indexed: 12/28/2022] Open
Abstract
Genomes are under constant threat of invasion by transposable elements and other genomic parasites. How can host genomes recognize these elements and target them for degradation? This requires a system that is highly adaptable, and at the same time highly specific. Current data suggest that perturbation of transcription patterns by transposon insertions could be detected by the RNAi surveillance pathway. Multiple transposon insertions might generate sufficient amounts of primal small RNAs to initiate generation of secondary small RNAs and silencing. At the same time primal small RNAs need to be constantly degraded to reduce the level of noise small RNAs below the threshold required for initiation of silencing. Failure in RNA degradation results in loss of fidelity of small RNA pathways and silencing of ectopic targets. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Ilaria Ugolini
- Department of Biochemistry and Gene Center, LMU Munich, 81377 Munich, Germany
| | - Mario Halic
- Department of Biochemistry and Gene Center, LMU Munich, 81377 Munich, Germany
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3
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Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA. The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Dev Cell 2017; 42:241-255.e6. [PMID: 28787591 PMCID: PMC5554785 DOI: 10.1016/j.devcel.2017.07.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/14/2017] [Accepted: 07/05/2017] [Indexed: 02/02/2023]
Abstract
Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in Caenorhabditis elegans. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
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Affiliation(s)
- Alper Akay
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Di Domenico
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Kin M Suen
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Amena Nabih
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Guillermo E Parada
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ragini Medhi
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ahmet C Berkyurek
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Christopher J Wedeles
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Konrad L M Rudolph
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstraße 16-18, Leipzig 04107, Germany
| | - Martin Hemberg
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
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Abstract
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom. However, an increasing number of fungal sRNAs with regulatory functions generated by specific RNAi pathways have been identified. Several mechanistic aspects of the biogenesis of these sRNAs are known, but their function in fungal development and physiology is scarce, except for remarkable examples such as Mucor circinelloides, in which specific sRNAs clearly regulate responses to environmental and endogenous signals. Despite the retention of RNAi in most species, some fungal groups and species lack an active RNAi mechanism, suggesting that its loss may provide some selective advantage. This article summarizes the current understanding of RNAi functions in the fungal kingdom.
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Tycowski KT, Shu MD, Steitz JA. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi. Cell Rep 2016; 15:1266-76. [PMID: 27134163 DOI: 10.1016/j.celrep.2016.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/25/2016] [Accepted: 03/28/2016] [Indexed: 01/08/2023] Open
Abstract
The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.
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Affiliation(s)
- Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
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Zheng M, Mitra RN, Filonov NA, Han Z. Nanoparticle-mediated rhodopsin cDNA but not intron-containing DNA delivery causes transgene silencing in a rhodopsin knockout model. FASEB J 2015; 30:1076-86. [PMID: 26564956 DOI: 10.1096/fj.15-280511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022]
Abstract
Previously, we compared the efficacy of nanoparticle (NP)-mediated intron-containing rhodopsin (sgRho) vs. intronless cDNA in ameliorating retinal disease phenotypes in a rhodopsin knockout (RKO) mouse model of retinitis pigmentosa. We showed that NP-mediated sgRho delivery achieved long-term expression and phenotypic improvement in RKO mice, but not NP housing cDNA. However, the protein level of the NP-sgRho construct was only 5-10% of wild-type at 8 mo postinjection. To have a better understanding of the reduced levels of long-term expression of the vectors, in the present study, we evaluated the epigenetic changes of subretinal delivering NP-cDNA vs. NP-sgRho in the RKO mouse eyes. Following the administration, DNA methylation and histone status of specific regions (bacteria plasmid backbone, promoter, rhodopsin gene, and scaffold/matrix attachment region) of the vectors were evaluated at various time points. We documented that epigenetic transgene silencing occurred in vector-mediated gene transfer, which were caused by the plasmid backbone and the cDNA of the transgene, but not the intron-containing transgene. No toxicity or inflammation was found in the treated eyes. Our results suggest that cDNA of the rhodopsin transgene and bacteria backbone interfered with the host defense mechanism of DNA methylation-mediated transgene silencing through heterochromatin-associated modifications.
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Affiliation(s)
- Min Zheng
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Rajendra N Mitra
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Nazar A Filonov
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Zongchao Han
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
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Kärblane K, Gerassimenko J, Nigul L, Piirsoo A, Smialowska A, Vinkel K, Kylsten P, Ekwall K, Swoboda P, Truve E, Sarmiento C. ABCE1 is a highly conserved RNA silencing suppressor. PLoS One 2015; 10:e0116702. [PMID: 25659154 PMCID: PMC4319951 DOI: 10.1371/journal.pone.0116702] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/12/2014] [Indexed: 01/15/2023] Open
Abstract
ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.
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Affiliation(s)
- Kairi Kärblane
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Centre for Cancer Research, Tallinn, Estonia
| | - Jelena Gerassimenko
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Centre for Cancer Research, Tallinn, Estonia
| | - Lenne Nigul
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Alla Piirsoo
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Agata Smialowska
- School of Life Sciences, Södertörn University College, S-14189, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, S-14183, Huddinge, Sweden
| | - Kadri Vinkel
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Per Kylsten
- School of Life Sciences, Södertörn University College, S-14189, Huddinge, Sweden
| | - Karl Ekwall
- School of Life Sciences, Södertörn University College, S-14189, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, S-14183, Huddinge, Sweden
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, S-14183, Huddinge, Sweden
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Centre for Cancer Research, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Centre for Cancer Research, Tallinn, Estonia
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Palazzo A, Moschetti R, Caizzi R, Marsano RM. The Drosophila mojavensis Bari3 transposon: distribution and functional characterization. Mob DNA 2014; 5:21. [PMID: 25093043 PMCID: PMC4120734 DOI: 10.1186/1759-8753-5-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/13/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon's family has been used as paradigm to investigate the complex dynamics underlying the persistence and structural evolution of transposable elements (TEs) within a genome. Three structural Bari variants have been identified so far and can be distinguished based on the organization of their terminal inverted repeats. Bari3 is the last discovered member of this family identified in Drosophila mojavensis, a recently emerged species of the Repleta group of the genus Drosophila. RESULTS We studied the insertion pattern of Bari3 in different D. mojavensis populations and found evidence of recent transposition activity. Analysis of the transposase domains unveiled the presence of a functional nuclear localization signal, as well as a functional binding domain. Using luciferase-based assays, we investigated the promoter activity of Bari3 as well as the interaction of its transposase with its left terminus. The results suggest that Bari3 is transposition-competent. Finally we demonstrated transposase transcript processing when the transposase gene is overexpressed in vivo and in vitro. CONCLUSIONS Bari3 displays very similar structural and functional features with its close relative, Bari1. Our results strongly suggest that Bari3 is an independent element that has generated genomic diversity in D. mojavensis. It can autonomously transcribe its transposase gene, which in turn can localize in the nucleus and bind the terminal inverted repeats of the transposon. Nevertheless, the identification of an unpredicted spliced form of the Bari3 transposase transcript allows us to hypothesize a control mechanism of its mobility based on mRNA processing. These results will aid the studies on the Bari family of transposons, which is intriguing for its widespread diffusion in Drosophilids coupled with a structural diversity generated during the evolution of Bari-like elements in their host genomes.
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Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
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