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Barbieri P, Zupin L, Licen S, Torboli V, Semeraro S, Cozzutto S, Palmisani J, Di Gilio A, de Gennaro G, Fontana F, Omiciuolo C, Pallavicini A, Ruscio M, Crovella S. Molecular detection of SARS-CoV-2 from indoor air samples in environmental monitoring needs adequate temporal coverage and infectivity assessment. Environ Res 2021; 198:111200. [PMID: 33901446 PMCID: PMC8065246 DOI: 10.1016/j.envres.2021.111200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/03/2021] [Accepted: 04/09/2021] [Indexed: 05/18/2023]
Abstract
The relevance of airborne exposure to SARS-CoV-2 in indoor environments is a matter of research and debate, with special importance for healthcare low-risk settings. Experimental approaches to the bioaerosol sampling are neither standardized nor optimized yet, leading in some cases to limited representativity of the temporal and spatial variability of viral presence in aerosols. Airborne viral viability moreover needs to be assessed. A study has been conducted collecting five 24-h PM10 samples in a COVID-19 geriatric ward in late June 2020, and detecting E and RdRp genes by RT-qPCR with a Ct between 36 and 39. The viral RNA detection at Ct = 36 was related to the maximal numerosity of infected patients hosted in the ward. Lacking a direct infectivity assessment for the collected samples an experimental model has been defined, by seeding twelve nasopharyngeal swab extracts from COVID-19 positive patients on Vero E6 cells; only the four extracts with a viral load above E+10 viral copies (approximately Ct<24) have been able to establish a persistent infection in vitro. Therefore, the cytopathic effect, a key feature of residual infectivity, could be considered unlikely for the environmental PM10 samples showing amplification of viral RNA at Ct = 36 or higher. A standardization of airborne SARS-CoV-2 long-term monitoring and of environmental infectivity assessment is urgently needed.
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Affiliation(s)
- Pierluigi Barbieri
- Dept. of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy; INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9 50121, Firenze, Italy.
| | - Luisa Zupin
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Via Dell'Istria 65/1, 34137, Trieste, Italy.
| | - Sabina Licen
- Dept. of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy; INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9 50121, Firenze, Italy.
| | - Valentina Torboli
- Dept. of Life Sciences, University of Trieste, Via L. Giorgieri 8, 34127, Trieste, Italy.
| | - Sabrina Semeraro
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9 50121, Firenze, Italy.
| | - Sergio Cozzutto
- ARCO Solutions Srl, C/o BIC Incubatori FVG S.p.A. Via Flavia 23/1, 34148, Trieste, Italy.
| | - Jolanda Palmisani
- Dept. of Biology, University of Bari "Aldo Moro", Via Via E. Orabona, 4 70124, Bari, Italy.
| | - Alessia Di Gilio
- Dept. of Biology, University of Bari "Aldo Moro", Via Via E. Orabona, 4 70124, Bari, Italy.
| | - Gianluigi de Gennaro
- Dept. of Biology, University of Bari "Aldo Moro", Via Via E. Orabona, 4 70124, Bari, Italy.
| | - Francesco Fontana
- Azienda Sanitaria Universitaria Giuliano Isontina - Ospedale San Polo Via Luigi Galvani 1, 34074, Monfalcone (GO), Italy.
| | - Cinzia Omiciuolo
- Azienda Sanitaria Universitaria Giuliano Isontina - Ospedale Maggiore Piazza Dell'Ospitale 1, 34129, Trieste (TS), Italy.
| | - Alberto Pallavicini
- Dept. of Life Sciences, University of Trieste, Via L. Giorgieri 8, 34127, Trieste, Italy.
| | - Maurizio Ruscio
- Azienda Sanitaria Universitaria Giuliano Isontina - Ospedale Maggiore Piazza Dell'Ospitale 1, 34129, Trieste (TS), Italy.
| | - Sergio Crovella
- Department of Biological and Environmental Sciences, College of Arts and Sciences, University of Qatar, Doha, 2713, Qatar.
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Ansaloni F, Gerdol M, Torboli V, Fornaini NR, Greco S, Giulianini PG, Coscia MR, Miccoli A, Santovito G, Buonocore F, Scapigliati G, Pallavicini A. Cold Adaptation in Antarctic Notothenioids: Comparative Transcriptomics Reveals Novel Insights in the Peculiar Role of Gills and Highlights Signatures of Cobalamin Deficiency. Int J Mol Sci 2021; 22:ijms22041812. [PMID: 33670421 PMCID: PMC7918649 DOI: 10.3390/ijms22041812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/13/2023] Open
Abstract
Far from being devoid of life, Antarctic waters are home to Cryonotothenioidea, which represent one of the fascinating cases of evolutionary adaptation to extreme environmental conditions in vertebrates. Thanks to a series of unique morphological and physiological peculiarities, which include the paradigmatic case of loss of hemoglobin in the family Channichthyidae, these fish survive and thrive at sub-zero temperatures. While some of the distinctive features of such adaptations have been known for decades, our knowledge of their genetic and molecular bases is still limited. We generated a reference de novo assembly of the icefish Chionodraco hamatus transcriptome and used this resource for a large-scale comparative analysis among five red-blooded Cryonotothenioidea, the sub-Antarctic notothenioid Eleginops maclovinus and seven temperate teleost species. Our investigation targeted the gills, a tissue of primary importance for gaseous exchange, osmoregulation, ammonia excretion, and its role in fish immunity. One hundred and twenty genes were identified as significantly up-regulated in Antarctic species and surprisingly shared by red- and white-blooded notothenioids, unveiling several previously unreported molecular players that might have contributed to the evolutionary success of Cryonotothenioidea in Antarctica. In particular, we detected cobalamin deficiency signatures and discussed the possible biological implications of this condition concerning hematological alterations and the heavy parasitic loads typically observed in all Cryonotothenioidea.
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Affiliation(s)
- Federico Ansaloni
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- International School for Advanced Studies, 34136 Trieste, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Correspondence:
| | - Valentina Torboli
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Nicola Reinaldo Fornaini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Department of Cell Biology, Charles University, 12800 Prague, Czech Republic
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Piero Giulio Giulianini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, 80131 Naples, Italy;
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | | | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Anton Dohrn Zoological Station, 80122 Naples, Italy
- National Institute of Oceanography and Experimental Geophysics, 34010 Trieste, Italy
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Setti L, Passarini F, De Gennaro G, Barbieri P, Perrone MG, Borelli M, Palmisani J, Di Gilio A, Torboli V, Fontana F, Clemente L, Pallavicini A, Ruscio M, Piscitelli P, Miani A. SARS-Cov-2RNA found on particulate matter of Bergamo in Northern Italy: First evidence. Environ Res 2020; 188:109754. [PMID: 32526492 DOI: 10.1101/2020.04.15.20065995] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND The burden of COVID-19 was extremely severe in Northern Italy, an area characterized by high concentrations of particulate matter (PM), which is known to negatively affect human health. Consistently with evidence already available for other viruses, we initially hypothesized the possibility of SARS-CoV-2 presence on PM, and we performed a first experiment specifically aimed at confirming or excluding this research hyphotesys. METHODS We have collected 34 PM10 samples in Bergamo area (the epicenter of the Italian COVID-19 epidemic) by using two air samplers over a continuous 3-weeks period. Filters were properly stored and underwent RNA extraction and amplification according to WHO protocols in two parallel blind analyses performed by two different authorized laboratories. Up to three highly specific molecular marker genes (E, N, and RdRP) were used to test the presence of SARS-CoV-2 RNA on particulate matter. RESULTS The first test showed positive results for gene E in 15 out of 16 samples, simultaneously displaying positivity also for RdRP gene in 4 samples. The second blind test got 5 additional positive results for at least one of the three marker genes. Overall, we tested 34 RNA extractions for the E, N and RdRP genes, reporting 20 positive results for at least one of the three marker genes, with positivity separately confirmed for all the three markers. Control tests to exclude false positivities were successfully accomplished. CONCLUSION This is the first evidence that SARS-CoV-2 RNA can be present on PM, thus suggesting a possible use as indicator of epidemic recurrence.
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Affiliation(s)
- Leonardo Setti
- Dept. Industrial Chemistry, University of Bologna, Viale Del Risorgimento - 4, I-40136, Bologna, Italy.
| | - Fabrizio Passarini
- Interdepartmental Centre for Industrial Research "Renewable Sources, Environment, Blue Growth, Energy", University of Bologna, Rimini, Italy.
| | | | - Pierluigi Barbieri
- Dept. of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
| | | | - Massimo Borelli
- Dept. of Life Sciences - University of Trieste, Trieste, Italy.
| | | | | | | | - Francesco Fontana
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | - Libera Clemente
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Maurizio Ruscio
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Alessandro Miani
- Italian Society of Environmental Medicine (SIMA), Milan, Italy; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
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4
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Setti L, Passarini F, De Gennaro G, Barbieri P, Perrone MG, Borelli M, Palmisani J, Di Gilio A, Torboli V, Fontana F, Clemente L, Pallavicini A, Ruscio M, Piscitelli P, Miani A. SARS-Cov-2RNA found on particulate matter of Bergamo in Northern Italy: First evidence. Environ Res 2020; 188:109754. [PMID: 32526492 DOI: 10.1016/j.envres.2020.109754.b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND The burden of COVID-19 was extremely severe in Northern Italy, an area characterized by high concentrations of particulate matter (PM), which is known to negatively affect human health. Consistently with evidence already available for other viruses, we initially hypothesized the possibility of SARS-CoV-2 presence on PM, and we performed a first experiment specifically aimed at confirming or excluding this research hyphotesys. METHODS We have collected 34 PM10 samples in Bergamo area (the epicenter of the Italian COVID-19 epidemic) by using two air samplers over a continuous 3-weeks period. Filters were properly stored and underwent RNA extraction and amplification according to WHO protocols in two parallel blind analyses performed by two different authorized laboratories. Up to three highly specific molecular marker genes (E, N, and RdRP) were used to test the presence of SARS-CoV-2 RNA on particulate matter. RESULTS The first test showed positive results for gene E in 15 out of 16 samples, simultaneously displaying positivity also for RdRP gene in 4 samples. The second blind test got 5 additional positive results for at least one of the three marker genes. Overall, we tested 34 RNA extractions for the E, N and RdRP genes, reporting 20 positive results for at least one of the three marker genes, with positivity separately confirmed for all the three markers. Control tests to exclude false positivities were successfully accomplished. CONCLUSION This is the first evidence that SARS-CoV-2 RNA can be present on PM, thus suggesting a possible use as indicator of epidemic recurrence.
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Affiliation(s)
- Leonardo Setti
- Dept. Industrial Chemistry, University of Bologna, Viale Del Risorgimento - 4, I-40136, Bologna, Italy.
| | - Fabrizio Passarini
- Interdepartmental Centre for Industrial Research "Renewable Sources, Environment, Blue Growth, Energy", University of Bologna, Rimini, Italy.
| | | | - Pierluigi Barbieri
- Dept. of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
| | | | - Massimo Borelli
- Dept. of Life Sciences - University of Trieste, Trieste, Italy.
| | | | | | | | - Francesco Fontana
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | - Libera Clemente
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Maurizio Ruscio
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Alessandro Miani
- Italian Society of Environmental Medicine (SIMA), Milan, Italy; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
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5
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Setti L, Passarini F, De Gennaro G, Barbieri P, Perrone MG, Borelli M, Palmisani J, Di Gilio A, Torboli V, Fontana F, Clemente L, Pallavicini A, Ruscio M, Piscitelli P, Miani A. SARS-Cov-2RNA found on particulate matter of Bergamo in Northern Italy: First evidence. Environ Res 2020; 188:109754. [PMID: 32526492 PMCID: PMC7260575 DOI: 10.1016/j.envres.2020.109754] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND The burden of COVID-19 was extremely severe in Northern Italy, an area characterized by high concentrations of particulate matter (PM), which is known to negatively affect human health. Consistently with evidence already available for other viruses, we initially hypothesized the possibility of SARS-CoV-2 presence on PM, and we performed a first experiment specifically aimed at confirming or excluding this research hyphotesys. METHODS We have collected 34 PM10 samples in Bergamo area (the epicenter of the Italian COVID-19 epidemic) by using two air samplers over a continuous 3-weeks period. Filters were properly stored and underwent RNA extraction and amplification according to WHO protocols in two parallel blind analyses performed by two different authorized laboratories. Up to three highly specific molecular marker genes (E, N, and RdRP) were used to test the presence of SARS-CoV-2 RNA on particulate matter. RESULTS The first test showed positive results for gene E in 15 out of 16 samples, simultaneously displaying positivity also for RdRP gene in 4 samples. The second blind test got 5 additional positive results for at least one of the three marker genes. Overall, we tested 34 RNA extractions for the E, N and RdRP genes, reporting 20 positive results for at least one of the three marker genes, with positivity separately confirmed for all the three markers. Control tests to exclude false positivities were successfully accomplished. CONCLUSION This is the first evidence that SARS-CoV-2 RNA can be present on PM, thus suggesting a possible use as indicator of epidemic recurrence.
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Affiliation(s)
- Leonardo Setti
- Dept. Industrial Chemistry, University of Bologna, Viale Del Risorgimento - 4, I-40136, Bologna, Italy.
| | - Fabrizio Passarini
- Interdepartmental Centre for Industrial Research "Renewable Sources, Environment, Blue Growth, Energy", University of Bologna, Rimini, Italy.
| | | | - Pierluigi Barbieri
- Dept. of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
| | | | - Massimo Borelli
- Dept. of Life Sciences - University of Trieste, Trieste, Italy.
| | | | | | | | - Francesco Fontana
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | - Libera Clemente
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Maurizio Ruscio
- Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy.
| | | | - Alessandro Miani
- Italian Society of Environmental Medicine (SIMA), Milan, Italy; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
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Savi T, Casolo V, Dal Borgo A, Rosner S, Torboli V, Stenni B, Bertoncin P, Martellos S, Pallavicini A, Nardini A. Drought-induced dieback of Pinus nigra: a tale of hydraulic failure and carbon starvation. Conserv Physiol 2019; 7:coz012. [PMID: 31198559 PMCID: PMC6541882 DOI: 10.1093/conphys/coz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/22/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Ongoing climate change is apparently increasing tree mortality rates, and understanding mechanisms of drought-induced tree decline can improve mortality projections. Differential drought impact on conspecific individuals within a population has been reported, but no clear mechanistic explanation for this pattern has emerged. Following a severe drought (summer 2012), we monitored over a 3-year period healthy (H) and declining (D) Pinus nigra trees co-occurring in a karstic woodland to highlight eventual individual-specific physiological differences underlying differential canopy dieback. We investigated differences in water and carbon metabolism, and xylem anatomy as a function of crown health status, as well as eventual genotypic basis of contrasting drought responses. H and D trees exploited the same water pools and relied on similar hydraulic strategies to cope with drought stress. Genetic analyses did not highlight differences between groups in terms of geographical provenance. Hydraulic and anatomical analyses showed conflicting results. The hydraulic tracheid diameter and theoretical hydraulic conductivity were similar, but D trees were characterized by lower water transport efficiency, greater vulnerability to xylem conduit implosion and reduced carbohydrate stores. Our results suggest that extreme drought events can have different impacts on conspecific individuals, with differential vulnerability to xylem embolism likely playing a major role in setting the fate of trees under climate change.
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Affiliation(s)
- Tadeja Savi
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
- Division of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 24, Tulln, Austria
| | - Valentino Casolo
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, Università di Udine, Via delle Scienze 91, Udine, Italia
| | - Anna Dal Borgo
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
| | - Sabine Rosner
- Institute of Botany, University of Natural Resources and Life Sciences, Gregor Mendel Strasse 33, Vienna, Austria
| | - Valentina Torboli
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
| | - Barbara Stenni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Via Torino 155, Venezia Mestre, Italia
| | - Paolo Bertoncin
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
| | - Stefano Martellos
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
| | - Alberto Pallavicini
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
| | - Andrea Nardini
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 10, Trieste, Italia
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7
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Aloisio M, Licastro D, Caenazzo L, Torboli V, D'Eustacchio A, Severini GM, Athanasakis E. A technical application of quantitative next generation sequencing for chimerism evaluation. Mol Med Rep 2016; 14:2967-74. [PMID: 27499173 PMCID: PMC5042788 DOI: 10.3892/mmr.2016.5593] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/12/2016] [Indexed: 11/24/2022] Open
Abstract
At present, the most common genetic diagnostic method for chimerism evaluation following hematopoietic stem cell transplantation is microsatellite analysis by capillary electrophoresis. The main objective was to establish, through repeated analysis over time, if a complete chimerism was present, or if the mixed chimerism was stable, increasing or decreasing over time. Considering the recent introduction of next generation sequencing (NGS) in clinical diagnostics, a detailed study evaluating an NGS protocol was conducted, coupled with a custom bioinformatics pipeline, for chimerism quantification. Based on the technology of Ion AmpliSeq, a 44-amplicon custom chimerism panel was designed, and a custom bioinformatics pipeline dedicated to the genotyping and quantification of NGS data was coded. The custom chimerism panel allowed identification of an average of 16 informative recipient alleles. The limit of detection of the protocol was fixed at 1% due to the NGS background (<1%). The protocol followed the standard Ion AmpliSeq library preparation and Ion Torrent Personal Genome Machine guidelines. Overall, the present study added to the scientific literature, identifying novel technical details for a possible future application of NGS for chimerism quantification.
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Affiliation(s)
| | - Danilo Licastro
- Cluster in Biomedicine, CBM S.c.r.l., Bioinformatic Services, Area Science Park, I‑34149 Basovizza, Italy
| | - Luciana Caenazzo
- Department of Molecular Medicine, University of Padova, I‑35121 Padova, Italy
| | - Valentina Torboli
- Department of Life Sciences, University of Trieste, I‑34127 Trieste, Italy
| | - Angela D'Eustacchio
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
| | - Giovanni Maria Severini
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
| | - Emmanouil Athanasakis
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
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8
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Gerdol M, Puillandre N, De Moro G, Guarnaccia C, Lucafò M, Benincasa M, Zlatev V, Manfrin C, Torboli V, Giulianini PG, Sava G, Venier P, Pallavicini A. Identification and Characterization of a Novel Family of Cysteine-Rich Peptides (MgCRP-I) from Mytilus galloprovincialis. Genome Biol Evol 2015. [PMID: 26201648 PMCID: PMC4558851 DOI: 10.1093/gbe/evv133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis. These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Italy
| | - Nicolas Puillandre
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), Paris, France
| | | | - Corrado Guarnaccia
- Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | | | - Ventislav Zlatev
- Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Italy
| | | | | | - Gianni Sava
- Department of Life Sciences, University of Trieste, Italy
| | - Paola Venier
- Department of Biology, University of Padova, Italy
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Agostini C, Albaladejo RG, Aparicio A, Arthofer W, Berrebi P, Boag PT, Carbone I, Conroy GC, Cortesero AM, Costa Gonçalves E, Costa D, Couto A, Girolamo MI, Du H, Fu S, Garrido‐Garduño T, Gettová L, Gilles A, Guerreiro Hamoy I, Herrera CM, Heussler C, Isidro E, Josso C, Krapf P, Lamont RW, Ralec A, Lopes S, Luís C, Luo H, Mahéo F, Marino IAM, Mieuzet L, Murray BW, Ogbourne SM, Pallavicini A, Parejo‐Farnés C, Patarnello T, Paty C, Pereira C, Pinho C, Pinto P, Poinsot D, Powell A, Putman AI, Santoro A, Santos S, Schlick‐Steiner BC, Scott C, Silvanira Barbosa M, Šimková A, Simon J, Solé‐Cava A, Steiner FM, Sun Z, Torboli V, Tredway LP, Coeverden de Groot PJ, Vasconcellos A, Vázquez‐Domínguez E, Wang D, Wang Y, Wei Q, Zane L, Zhang S. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2013–31 May 2013. Mol Ecol Resour 2013; 13:966-8. [DOI: 10.1111/1755-0998.12140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gerdol M, De Moro G, Torboli V, Manfrin C, Rosani U, Venier P, Pallavicini A. Genomics in bivalve aquaculture. Commun Agric Appl Biol Sci 2013; 78:153-156. [PMID: 25141653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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