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Carvalho-Moore P, Borgato EA, Cutti L, Porri A, Meiners I, Lerchl J, Norsworthy JK, Patterson EL. A rearranged Amaranthus palmeri extrachromosomal circular DNA confers resistance to glyphosate and glufosinate. THE PLANT CELL 2025; 37:koaf069. [PMID: 40152451 PMCID: PMC11985328 DOI: 10.1093/plcell/koaf069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 02/07/2025] [Accepted: 02/22/2025] [Indexed: 03/29/2025]
Abstract
Some herbicide-resistant weeds become resistant by generating additional copies of specific loci. For example, amplification of the locus encoding chloroplastic glutamine synthetase (GS2) produces herbicide resistance in the glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession MSR2. Previously, overamplification of the glyphosate-resistant gene encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in Palmer amaranth was determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, we describe a rearranged eccDNA that confers resistance to both glyphosate and glufosinate ammonium due to the coduplication of the native chromosomal regions that contain the genes that encode for these herbicides target proteins. In addition to EPSPS, the replicon carries 2 GS2 isoforms (GS2.1 and GS2.2) and other genes. MSR2 samples harbored eccDNA carrying only EPSPS coexisting with eccDNAs harboring both EPSPS and GS2. A second glufosinate-resistant Palmer amaranth accession (MSR1) showed distinct GS2.1 and GS2.2 amplification patterns from MSR2, suggesting the existence of diverse replicons in Palmer amaranth. EPSPS copy number was correlated with both GS2 isoforms copy number in MSR2, further supporting the coexistence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.
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Affiliation(s)
- Pâmela Carvalho-Moore
- Crop, Soil and Environmental Science Department, University of Arkansas, Fayetteville, AR 72703, USA
| | - Ednaldo A Borgato
- Agronomy Department, West Florida Research and Education Center, University of Florida, Jay, FL 32565, USA
| | - Luan Cutti
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48823, USA
| | - Aimone Porri
- Global Research & Development Agricultural Solutions, BASF SE, Ludwigshafen 67063, Germany
| | - Ingo Meiners
- Agricultural Solutions North America, BASF Corporation, Research Triangle Park, NC 27709, USA
| | - Jens Lerchl
- Global Research & Development Agricultural Solutions, BASF SE, Ludwigshafen 67063, Germany
| | - Jason K Norsworthy
- Crop, Soil and Environmental Science Department, University of Arkansas, Fayetteville, AR 72703, USA
| | - Eric L Patterson
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48823, USA
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Raiyemo DA, Montgomery JS, Cutti L, Abdollahi F, Llaca V, Fengler K, Lopez AJ, Morran S, Saski CA, Nelson DR, Patterson EL, Gaines TA, Tranel PJ. Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70027. [PMID: 39994881 PMCID: PMC11850965 DOI: 10.1111/tpj.70027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/17/2024] [Accepted: 01/24/2025] [Indexed: 02/26/2025]
Abstract
Amaranthus palmeri (Palmer amaranth), Amaranthus retroflexus (redroot pigweed), and Amaranthus hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as "pigweeds," these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, RESTORER OF FERTILITY 1 (RF1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.
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Affiliation(s)
| | - Jacob S. Montgomery
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Luan Cutti
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Fatemeh Abdollahi
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Victor Llaca
- Genome Center of ExcellenceCorteva AgriscienceJohnstonIowaUSA
| | - Kevin Fengler
- Genome Center of ExcellenceCorteva AgriscienceJohnstonIowaUSA
| | | | - Sarah Morran
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Christopher A. Saski
- Department of Plant and Environmental SciencesClemson UniversityClemsonSouth CarolinaUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Eric L. Patterson
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Todd A. Gaines
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
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Abbasi AF, Asim MN, Ahmed S, Dengel A. Long extrachromosomal circular DNA identification by fusing sequence-derived features of physicochemical properties and nucleotide distribution patterns. Sci Rep 2024; 14:9466. [PMID: 38658614 PMCID: PMC11043385 DOI: 10.1038/s41598-024-57457-5] [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: 09/19/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Long extrachromosomal circular DNA (leccDNA) regulates several biological processes such as genomic instability, gene amplification, and oncogenesis. The identification of leccDNA holds significant importance to investigate its potential associations with cancer, autoimmune, cardiovascular, and neurological diseases. In addition, understanding these associations can provide valuable insights about disease mechanisms and potential therapeutic approaches. Conventionally, wet lab-based methods are utilized to identify leccDNA, which are hindered by the need for prior knowledge, and resource-intensive processes, potentially limiting their broader applicability. To empower the process of leccDNA identification across multiple species, the paper in hand presents the very first computational predictor. The proposed iLEC-DNA predictor makes use of SVM classifier along with sequence-derived nucleotide distribution patterns and physicochemical properties-based features. In addition, the study introduces a set of 12 benchmark leccDNA datasets related to three species, namely Homo sapiens (HM), Arabidopsis Thaliana (AT), and Saccharomyces cerevisiae (SC/YS). It performs large-scale experimentation across 12 benchmark datasets under different experimental settings using the proposed predictor, more than 140 baseline predictors, and 858 encoder ensembles. The proposed predictor outperforms baseline predictors and encoder ensembles across diverse leccDNA datasets by producing average performance values of 81.09%, 62.2% and 81.08% in terms of ACC, MCC and AUC-ROC across all the datasets. The source code of the proposed and baseline predictors is available at https://github.com/FAhtisham/Extrachrosmosomal-DNA-Prediction . To facilitate the scientific community, a web application for leccDNA identification is available at https://sds_genetic_analysis.opendfki.de/iLEC_DNA/.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, 67663, Kaiserslautern, Germany.
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany.
| | - Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany.
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany
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4
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Fu W, MacGregor DR, Comont D, Saski CA. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass ( Alopecurus myosuroides) Populations. Genes (Basel) 2023; 14:1905. [PMID: 37895254 PMCID: PMC10606437 DOI: 10.3390/genes14101905] [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: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
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Affiliation(s)
- Wangfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Dana R. MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - David Comont
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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Koo DH, Sathishraj R, Nakka S, Ju Y, Nandula VK, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-mediated spread of herbicide resistance in interspecific hybrids of pigweed. PLANT PHYSIOLOGY 2023; 193:229-233. [PMID: 37186777 PMCID: PMC10469533 DOI: 10.1093/plphys/kiad281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are found in many eukaryotic organisms. EccDNA-powered copy number variation plays diverse roles, from oncogenesis in humans to herbicide resistance in crop weeds. Here, we report interspecific eccDNA flow and its dynamic behavior in soma cells of natural populations and F1 hybrids of Amaranthus sp. The glyphosate-resistance (GR) trait is controlled by eccDNA-based amplification harboring the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (eccDNA replicon), the molecular target of glyphosate. We documented pollen-mediated transfer of eccDNA in experimental hybrids between glyphosate-susceptible Amaranthus tuberculatus and GR Amaranthus palmeri. Experimental hybridization and fluorescence in situ hybridization (FISH) analysis revealed that the eccDNA replicon in Amaranthus spinosus derived from GR A. palmeri by natural hybridization. FISH analysis also revealed random chromosome anchoring and massive eccDNA replicon copy number variation in soma cells of weedy hybrids. The results suggest that eccDNAs are inheritable across compatible species, contributing to genome plasticity and rapid adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Sridevi Nakka
- Heartland Plant Innovations Inc., Manhattan, KS 66506, USA
| | - Yoonha Ju
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Vijay K Nandula
- National Institute of Food and Agriculture, USDA, Kansas City, MO 64105, USA
- Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS 38776, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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Chitwood DG, Uy L, Fu W, Klaubert SR, Harcum SW, Saski CA. Dynamics of Amino Acid Metabolism, Gene Expression, and Circulomics in a Recombinant Chinese Hamster Ovary Cell Line Adapted to Moderate and High Levels of Extracellular Lactate. Genes (Basel) 2023; 14:1576. [PMID: 37628627 PMCID: PMC10454118 DOI: 10.3390/genes14081576] [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: 07/10/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
The accumulation of metabolic wastes in cell cultures can diminish product quality, reduce productivity, and trigger apoptosis. The limitation or removal of unintended waste products from Chinese hamster ovary (CHO) cell cultures has been attempted through multiple process and genetic engineering avenues with varied levels of success. One study demonstrated a simple method to reduce lactate and ammonia production in CHO cells with adaptation to extracellular lactate; however, the mechanism behind adaptation was not certain. To address this profound gap, this study characterizes the phenotype of a recombinant CHO K-1 cell line that was gradually adapted to moderate and high levels of extracellular lactate and examines the genomic content and role of extrachromosomal circular DNA (eccDNA) and gene expression on the adaptation process. More than 500 genes were observed on eccDNAs. Notably, more than 1000 genes were observed to be differentially expressed at different levels of lactate adaptation, while only 137 genes were found to be differentially expressed between unadapted cells and cells adapted to grow in high levels of lactate; this suggests stochastic switching as a potential stress adaptation mechanism in CHO cells. Further, these data suggest alanine biosynthesis as a potential stress-mitigation mechanism for excess lactate in CHO cells.
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Affiliation(s)
- Dylan G. Chitwood
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
| | - Lisa Uy
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
| | - Wanfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Stephanie R. Klaubert
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA;
| | - Sarah W. Harcum
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA;
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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7
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Ullah I, Dunwell JM. Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa ( Theobroma cacao L.) germplasm. Saudi J Biol Sci 2023; 30:103648. [PMID: 37131491 PMCID: PMC10149277 DOI: 10.1016/j.sjbs.2023.103648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 05/04/2023] Open
Abstract
Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.
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8
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Chitwood DG, Wang Q, Klaubert SR, Green K, Wu CH, Harcum SW, Saski CA. Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions. Sci Rep 2023; 13:1200. [PMID: 36681715 PMCID: PMC9862248 DOI: 10.1038/s41598-023-27962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Chinese hamster ovary (CHO) cell lines are widely used to manufacture biopharmaceuticals. However, CHO cells are not an optimal expression host due to the intrinsic plasticity of the CHO genome. Genome plasticity can lead to chromosomal rearrangements, transgene exclusion, and phenotypic drift. A poorly understood genomic element of CHO cell line instability is extrachromosomal circular DNA (eccDNA) in gene expression and regulation. EccDNA can facilitate ultra-high gene expression and are found within many eukaryotes including humans, yeast, and plants. EccDNA confers genetic heterogeneity, providing selective advantages to individual cells in response to dynamic environments. In CHO cell cultures, maintaining genetic homogeneity is critical to ensuring consistent productivity and product quality. Understanding eccDNA structure, function, and microevolutionary dynamics under various culture conditions could reveal potential engineering targets for cell line optimization. In this study, eccDNA sequences were investigated at the beginning and end of two-week fed-batch cultures in an ambr®250 bioreactor under control and lactate-stressed conditions. This work characterized structure and function of eccDNA in a CHO-K1 clone. Gene annotation identified 1551 unique eccDNA genes including cancer driver genes and genes involved in protein production. Furthermore, RNA-seq data is integrated to identify transcriptionally active eccDNA genes.
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Affiliation(s)
- Dylan G Chitwood
- Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Qinghua Wang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Stephanie R Klaubert
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Kiana Green
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Sarah W Harcum
- Department of Bioengineering, Clemson University, Clemson, SC, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.
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