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Carvajal-Yepes M, Ospina JA, Aranzales E, Velez-Tobon M, Correa Abondano M, Manrique-Carpintero NC, Wenzl P. Identifying genetically redundant accessions in the world's largest cassava collection. Front Plant Sci 2024; 14:1338377. [PMID: 38304449 PMCID: PMC10830726 DOI: 10.3389/fpls.2023.1338377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava (Manihot esculenta) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT's cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions.
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Affiliation(s)
- Monica Carvajal-Yepes
- Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | | | | | | | | | - Peter Wenzl
- Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Carvajal-Yepes M, Jimenez J, Belalcazar J, Cuasquer JB, Lozano I, Olaya CA, Cuellar WJ. Genome Analysis and Pathobiology of Cassava-Infecting Torradoviruses Containing a Putative Maf/HAM1 Pyrophosphatase Domain. Plant Dis 2022; 106:2808-2816. [PMID: 35471077 DOI: 10.1094/pdis-11-21-2520-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Next generation sequencing has been used to identify and characterize the full genome sequence of a cassava-infecting torradovirus, revealing the presence of a Maf/HAM1 domain downstream of the RNA-dependent RNA-polymerase (RdRp) domain in RNA1 in all isolates sequenced. A similar domain is also found in unrelated potyvirids infecting Euphorbiaceae hosts in the Americas and cassava in Africa. Even though cassava torrado-like virus (CsTLV) could not be mechanically transmitted to a series of herbaceous hosts, it can be efficiently transmitted by bud graft-inoculation to different cassava landraces. Our bioassays show that CsTLV has a narrow host range. Crystal-like structures of isometric virus-like particles were observed in cells of plants with single infection by CsTLV, and consistently induced chlorotic leaf spots and affected root yields significantly. Moreover, CsTLV infection induces changes in the accumulation of total sugars in storage roots. Field surveys indicated the presence of CsTLV in the main cassava growing regions of Colombia, and the occurrence of two different cassava-infecting torradovirus species. Profiles of small RNAs of 21 to 24 nucleotides in length, derived from CsTLV RNAs targeted by cassava RNA silencing defense mechanisms, are also reported.
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Affiliation(s)
| | - Jenyfer Jimenez
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia (UNAL), Palmira, Colombia
| | - John Belalcazar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Juan B Cuasquer
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ivan Lozano
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Cristian A Olaya
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
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Prasanna BM, Carvajal-Yepes M, Kumar PL, Kawarazuka N, Liu Y, Mulema AA, McCutcheon S, Ibabao X. Sustainable management of transboundary pests requires holistic and inclusive solutions. Food Secur 2022. [DOI: 10.1007/s12571-022-01301-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractGlobalization and changing climates are aggravating the occurrence and impacts of transboundary pests, and driving the emergence of new threats. Most of the low- and middle-income countries in Africa, Asia and Latin America are not fully prepared in terms of surveillance, diagnostics, and deployment of plant health solutions due to several factors: adequate investment is lacking; knowledge is inadequate; and connections from the local to global, and global to local are insufficient. Effectively countering the current and emerging threats to plant health requires a holistic approach that includes: 1) globally coordinated diagnostic and surveillance systems; 2) epidemiological modelling, risk assessment, forecasting and preparedness for proactive management and containment; and 3) implementation of context-sensitive, eco-friendly, gender-responsive and socially inclusive integrated disease and pest management approaches to reduce the impacts of devastating transboundary pests and diseases. Despite several success stories where major pests and diseases have been brought to control through integrated approaches, further multi-institutional and multi-disciplinary efforts are necessary. Plant health management requires stronger interface between the biophysical and social sciences, and empowerment of local communities. These reflections derive from the proceedings of a webinar on “Transboundary Disease and Pest Management,” organized by CGIAR (Consultative Group on International Agricultural Research) on March 3, 2021, in recognition of the United Nations designated International Year of Plant Health.
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Carvajal-Yepes M, Cardwell K, Nelson A, Garrett KA, Giovani B, Saunders DGO, Kamoun S, Legg JP, Verdier V, Lessel J, Neher RA, Day R, Pardey P, Gullino ML, Records AR, Bextine B, Leach JE, Staiger S, Tohme J. A global surveillance system for crop diseases. Science 2020; 364:1237-1239. [PMID: 31249049 DOI: 10.1126/science.aaw1572] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - K Cardwell
- Oklahoma State University, Stillwater, OK, USA
| | - A Nelson
- Department of Natural Resources, Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Enschede, Netherlands
| | | | - B Giovani
- European and Mediterranean Plant Protection Organization-Euphresco, Paris, France
| | | | - S Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - J P Legg
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | - V Verdier
- French National Research Institute for Sustainable Development (IRD), CIRAD, University of Montpellier, Interactions Plantes Microorganismes Environnement, Montpellier, France
| | - J Lessel
- Gro Intelligence, New York, NY, USA
| | - R A Neher
- University of Basel, Basel, Switzerland
| | - R Day
- Centre for Agriculture and Biosciences International, Wallingford, UK
| | - P Pardey
- University of Minnesota, Minneapolis, MN, USA
| | | | - A R Records
- United States Agency for International Development, Washington, DC, USA
| | - B Bextine
- University of Texas, Austin, TX, USA
| | - J E Leach
- Colorado State University, Fort Collins, CO, USA
| | - S Staiger
- International Center of Tropical Agriculture, Cali, Colombia
| | - J Tohme
- International Center of Tropical Agriculture, Cali, Colombia.
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Lozano I, Leiva AM, Jimenez J, Fernandez E, Carvajal-Yepes M, Cuervo M, Cuellar WJ. Resolution of cassava-infecting alphaflexiviruses: Molecular and biological characterization of a novel group of potexviruses lacking the TGB3 gene. Virus Res 2017; 241:53-61. [PMID: 28365210 DOI: 10.1016/j.virusres.2017.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/24/2017] [Accepted: 03/25/2017] [Indexed: 10/19/2022]
Abstract
Several potexviruses (Family Alphaflexiviridae) have been reported infecting cassava (Manihot esculenta Crantz) in the Americas. They were isolated from severely diseased plants during the last 30-40 years and include: Cassava common mosaic virus (CsCMV), Cassava Caribbean mosaic virus (CsCaMV), Cassava Colombian symptomless virus (CsCSV) and Cassava virus X (CsVX). However, their definitive classification as distinct species remains unresolved for several reasons, including the lack of sequence data and unavailability of samples from original isolates. This complicates disease diagnostics, cassava germplasm exchange certification, evaluation of virus cleaning protocols and epidemiological studies. Furthermore, a recently detected novel alphaflexivirus, indicates that cassava-infecting potexviruses may be more diverse. To solve the identity of these viruses, we started indexing samples from different parts of Colombia using different sets of PCR primers, antisera available and inoculation to indicator plants. Results show that there are three major phylogenetic groups of potexviruses infecting cassava, and they correspond to CsCMV, CsVX and the newly identified Cassava new alphaflexivirus (CsNAV). Bioassays and sequence analysis established that isolates of CsNAV and CsVX cause latent infections in different cassava landraces, they are not efficiently transmitted to the indicator plant Nicotiana benthamiana and they lack the gene 3 of the conserved potexviral 'triple gene block' (TGB). In contrast, all isolates of CsCMV (which have a characteristic potexvirus genome arrangement) caused Cassava Common Mosaic Disease (CCMD) in single infections and were efficiently transmitted to N. benthamiana. Although phylogenetic analysis of the replicase sequence placed CsNAV and CsVX as members of the Potexvirus genus, their distinct genome arrangement and biological characteristics suggest they can be considered as members of a separate taxonomic group.
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Affiliation(s)
- Ivan Lozano
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ana M Leiva
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia; Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira, Colombia
| | - Jenyfer Jimenez
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia; Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira, Colombia
| | - Elizabeth Fernandez
- Sub-Dirección de Recursos Genéticos, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Monica Carvajal-Yepes
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Maritza Cuervo
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer J Cuellar
- Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia.
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Carvajal-Yepes M, Zambrano L, Bueno JM, Raatz B, Cuellar WJ. Complete genome sequence of bean leaf crumple virus, a novel begomovirus infecting common bean in Colombia. Arch Virol 2017; 162:1773-1776. [PMID: 28188374 DOI: 10.1007/s00705-017-3271-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/31/2017] [Indexed: 11/30/2022]
Abstract
A copy of the complete genome of a novel bipartite begomovirus infecting common bean (Phaseolus vulgaris L.) in Colombia was obtained by rolling-circle amplification (RCA), cloned, and sequenced. The virus is associated with leaf crumple symptoms and significant yield losses in Andean and Mesoamerican beans. Such symptoms have been reported increasingly in Colombia since at least 2002, and we detected the virus in leaf material collected since 2008. Sequence analysis showed that the virus is a member of a distinct species, sharing 81% and 76% nucleotide (nt) sequence identity (in DNA-A and DNA-B, respectively) to other begomoviruses infecting common bean in the Americas. The data obtained support the taxonomic status of this virus (putatively named 'bean leaf crumple virus', BLCrV) as a member of a novel species in the genus Begomovirus.
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Affiliation(s)
- Monica Carvajal-Yepes
- Virology Laboratory, Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Leidy Zambrano
- Virology Laboratory, Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Juan M Bueno
- Bean Genetics Laboratory and CGIAR Research Program on Legumes, CIAT, Cali, Colombia
| | - Bodo Raatz
- Bean Genetics Laboratory and CGIAR Research Program on Legumes, CIAT, Cali, Colombia
| | - Wilmer J Cuellar
- Virology Laboratory, Agrobiodiversity Research Area (AgBio), International Center for Tropical Agriculture (CIAT), Cali, Colombia.
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Carvajal-Yepes M, Sporer KRB, Carter JL, Colvin CJ, Coussens PM. Enhanced production of human influenza virus in PBS-12SF cells with a reduced interferon response. Hum Vaccin Immunother 2015; 11:2296-304. [PMID: 26090991 DOI: 10.1080/21645515.2015.1016677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Influenza is one of the most important infectious diseases in humans. The best way to prevent severe illness caused by influenza infection is vaccination. Cell culture-derived influenza vaccines are being considered in addition to the widely used egg-based system in order to support the increasing seasonal demand and to be prepared in case of a pandemic. Cell culture based systems offer increased safety, capacity, and flexibility with reduced downstream processing relative to embryonated eggs. We have previously reported a chick embryo cell line, termed PBS-12SF, that supports replication of human and avian influenza A viruses to high titers (>10(7) PFU/ml) without the need for exogenous proteases or serum proteins. Viral infections in cells are limited by the Interferon (IFN) response typified by production of type I IFNs that bind to the IFNα/β receptor and activate an antiviral state. In this study, we investigated how neutralizing the interferon (IFN) response in PBS-12SF cells, via shRNA-mediated knock-down of IFNAR1 mRNA expression, affects influenza virus production. We were successful in knocking down ∼90% of IFNAR1 protein expression by this method, resulting in a significant decrease in the response to recombinant chIFNα stimulation in PBS-12SF cells as shown by a reduction in expression of interferon-responsive genes when compared to control cells. Additionally; IFNAR1-knock-down cells displayed enhanced viral HA production and released more virus into cell culture supernatants than parental PBS-12SF cells.
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Affiliation(s)
- Monica Carvajal-Yepes
- a Molecular Pathogenesis Laboratory; Department of Animal Science; Michigan State University ; East Lansing , MI USA
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Carvajal-Yepes M, Himmelsbach K, Schaedler S, Ploen D, Krause J, Ludwig L, Weiss T, Klingel K, Hildt E. Hepatitis C virus impairs the induction of cytoprotective Nrf2 target genes by delocalization of small Maf proteins. J Biol Chem 2011; 286:8941-51. [PMID: 21216956 DOI: 10.1074/jbc.m110.186684] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The expression of a variety of cytoprotective genes is regulated by short cis-acting elements in their promoters, called antioxidant response elements (AREs). A central regulator of ARE-mediated gene expression is the NF-E2-related factor 2 (Nrf2). Nrf2/ARE-regulated genes are crucial for the maintenance of cellular integrity. Hepatitis C virus inhibits the induction of ARE-regulated genes, but neither induction nor inhibition of ARE-regulated gene expression affects HCV replication directly. In HCV-replicating cells the core protein triggers the delocalization of sMaf proteins from the nucleus to the replicon complex. Here sMafs bind to NS3. The extranuclear sMaf proteins prevent Nrf2 from entry in the nucleus and thereby inhibit the induction of Nrf2/ARE-regulated genes. This results in the decreased expression of cytoprotective genes. Consistent with this finding, the elimination of ROI is impaired in HCV-replicating cells as demonstrated by elevated protein oxidation or 8-OH-dG formation, reflecting DNA damage. In conclusion, these data identified a novel mechanism of Nrf2 regulation and suggest that the HCV-dependent inhibition of Nrf2/ARE-regulated genes confers to the HCV-associated pathogenesis by elevation of intracellular ROI that affect integrity of the host genome and regenerative processes.
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Affiliation(s)
- Monica Carvajal-Yepes
- Institute of Infection Medicine, Molecular Medical Virology, University of Kiel, D-24105 Kiel, Germany
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Schaedler S, Krause J, Himmelsbach K, Carvajal-Yepes M, Lieder F, Klingel K, Nassal M, Weiss TS, Werner S, Hildt E. Hepatitis B virus induces expression of antioxidant response element-regulated genes by activation of Nrf2. J Biol Chem 2010; 285:41074-86. [PMID: 20956535 DOI: 10.1074/jbc.m110.145862] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The expression of a variety of cytoprotective genes is regulated by short cis-acting elements in their promoters, called antioxidant response elements (AREs). A central regulator of ARE-mediated gene expression is the NF-E2-related factor 2 (Nrf2). Human hepatitis B virus (HBV) induces a strong activation of Nrf2/ARE-regulated genes in vitro and in vivo. This is triggered by the HBV-regulatory proteins (HBx and LHBs) via c-Raf and MEK. The Nrf2/ARE-mediated induction of cytoprotective genes by HBV results in a better protection of HBV-positive cells against oxidative damage as compared with control cells. Furthermore, there is a significantly increased expression of the Nrf2/ARE-regulated proteasomal subunit PSMB5 in HBV-positive cells that is associated with a decreased level of the immunoproteasome subunit PSMB5i. In accordance with this finding, HBV-positive cells display a higher constitutive proteasome activity and a decreased activity of the immunoproteasome as compared with control cells even after interferon α/γ treatment. The HBV-dependent induction of Nrf2/ARE-regulated genes might ensure survival of the infected cell, shape the immune response to HBV, and thereby promote establishment of the infection.
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Affiliation(s)
- Stephanie Schaedler
- Institute of Infection Medicine, Molecular Medical Virology, University of Kiel, D-24105 Kiel, Germany
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Lan L, Gorke S, Rau SJ, Zeisel MB, Hildt E, Himmelsbach K, Carvajal-Yepes M, Huber R, Wakita T, Schmitt-Graeff A, Royer C, Blum HE, Fischer R, Baumert TF. Hepatitis C virus infection sensitizes human hepatocytes to TRAIL-induced apoptosis in a caspase 9-dependent manner. J Immunol 2008; 181:4926-35. [PMID: 18802096 DOI: 10.4049/jimmunol.181.7.4926] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Apoptosis of infected cells represents a key host defense mechanism against viral infections. The impact of apoptosis on the elimination of hepatitis C virus (HCV)-infected cells is poorly understood. The TRAIL has been implicated in the death of liver cells in hepatitis-infected but not in normal liver cells. To determine the impact of TRAIL on apoptosis of virus-infected host cells, we studied TRAIL-induced apoptosis in a tissue culture model system for HCV infection. We demonstrated that HCV infection sensitizes primary human hepatocytes and Huh7.5 hepatoma cells to TRAIL induced apoptosis in a dose- and time-dependent manner. Mapping studies identified the HCV nonstructural proteins as key mediators of sensitization to TRAIL. Using a panel of inhibitors targeting different apoptosis pathways, we demonstrate that sensitization to TRAIL is caspase-9 dependent and mediated in part via the mitochondrial pathway. Sensitization of hepatocytes to TRAIL-induced apoptosis by HCV infection represents a novel antiviral host defense mechanism that may have important implications for the pathogenesis of HCV infection and may contribute to the elimination of virus-infected hepatocytes.
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Affiliation(s)
- Lin Lan
- Department of Medicine II, University of Freiburg, Germany
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