PMC:7019868 / 7390-9327 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"138","span":{"begin":44,"end":51},"obj":"Chemical"},{"id":"139","span":{"begin":56,"end":63},"obj":"Chemical"},{"id":"140","span":{"begin":69,"end":76},"obj":"Chemical"},{"id":"141","span":{"begin":88,"end":95},"obj":"Chemical"},{"id":"154","span":{"begin":429,"end":436},"obj":"Species"},{"id":"155","span":{"begin":1470,"end":1474},"obj":"Species"},{"id":"156","span":{"begin":1820,"end":1826},"obj":"Species"},{"id":"157","span":{"begin":1843,"end":1849},"obj":"Species"},{"id":"158","span":{"begin":140,"end":151},"obj":"Chemical"},{"id":"159","span":{"begin":233,"end":243},"obj":"Chemical"},{"id":"160","span":{"begin":285,"end":296},"obj":"Chemical"},{"id":"161","span":{"begin":1123,"end":1129},"obj":"Chemical"},{"id":"162","span":{"begin":1130,"end":1140},"obj":"Chemical"},{"id":"163","span":{"begin":1419,"end":1444},"obj":"Chemical"},{"id":"164","span":{"begin":1446,"end":1449},"obj":"Chemical"},{"id":"165","span":{"begin":1625,"end":1634},"obj":"Chemical"}],"attributes":[{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"Tax:562"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Tax:28295"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"Tax:3724"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"Tax:3724"},{"id":"A161","pred":"tao:has_database_id","subj":"161","obj":"MESH:D019800"},{"id":"A162","pred":"tao:has_database_id","subj":"162","obj":"MESH:D002725"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.3. Generation and Recovery of Recombinant iPEDVPT-P5, iPEDVPT-P96, iPEDVPT-P5-96S and iPEDVPT-P96-5S Viruses\nThe strategy used to recover iPEDVPT-P96 has been described previously [19]. The approach to constructing a cDNA clone of iPEDVPT-P5 was technically identical to that of the iPEDVPT-P96. However, we split the plasmid B into two fragments because the sequence remained toxic to the One Shot™ TOP10 Chemically Competent E. coli cells (Invitrogen, Carlsbad, USA) despite propagation in LB broth supplemented with 10% SOC medium and being incubated at 30 °C. To generate chimeric viruses carrying heterologous spike (S) genes, namely the iPEDVPT-P5-96S and iPEDVPT-P96-5S, cDNA clones of iPEDVPT-P5 and iPEDVPT-P96, respectively, were used as the backbones. The sequences covering the complete S gene of each virus were exchanged without disruption to the remaining genomic structure. Sequence differences in the S genes of iPEDVPT-P5 and iPEDVPT-P96 viruses are summarized in Table 1. Each plasmid was digested with corresponding type-IIS restriction enzymes as designated in Figure S1, gel-purified, assembled and phenol-chloroform extracted to generate the full-length cDNAs. The cDNAs were then in vitro transcribed to the full-length RNA transcripts using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA, USA) and immediately electroporated into 800 μL of 107 cells/mL Vero cells in RNase-free phosphate buffered saline (PBS) along with 5 μg of PEDV nucleocapsid (N) transcripts. After electroporation, the cells were allowed to recover in growth medium for approximately 16 h and then maintained in PI-medium until cytopathic effects involved over 90% of cell monolayers. The whole flasks were subjected to one freeze-and-thaw cycle and the rescued viruses were passaged once to generate viral stocks (P1). The viral stocks were titrated on Vero cells in 96-well plates to determine the viral titer (see below)."}

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T38","span":{"begin":437,"end":442},"obj":"Body_part"},{"id":"T39","span":{"begin":754,"end":763},"obj":"Body_part"},{"id":"T40","span":{"begin":803,"end":807},"obj":"Body_part"},{"id":"T41","span":{"begin":1246,"end":1249},"obj":"Body_part"},{"id":"T42","span":{"begin":1385,"end":1390},"obj":"Body_part"},{"id":"T43","span":{"begin":1399,"end":1404},"obj":"Body_part"},{"id":"T44","span":{"begin":1532,"end":1537},"obj":"Body_part"},{"id":"T45","span":{"begin":1681,"end":1685},"obj":"Body_part"},{"id":"T46","span":{"begin":1872,"end":1877},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma13478"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"2.3. Generation and Recovery of Recombinant iPEDVPT-P5, iPEDVPT-P96, iPEDVPT-P5-96S and iPEDVPT-P96-5S Viruses\nThe strategy used to recover iPEDVPT-P96 has been described previously [19]. The approach to constructing a cDNA clone of iPEDVPT-P5 was technically identical to that of the iPEDVPT-P96. However, we split the plasmid B into two fragments because the sequence remained toxic to the One Shot™ TOP10 Chemically Competent E. coli cells (Invitrogen, Carlsbad, USA) despite propagation in LB broth supplemented with 10% SOC medium and being incubated at 30 °C. To generate chimeric viruses carrying heterologous spike (S) genes, namely the iPEDVPT-P5-96S and iPEDVPT-P96-5S, cDNA clones of iPEDVPT-P5 and iPEDVPT-P96, respectively, were used as the backbones. The sequences covering the complete S gene of each virus were exchanged without disruption to the remaining genomic structure. Sequence differences in the S genes of iPEDVPT-P5 and iPEDVPT-P96 viruses are summarized in Table 1. Each plasmid was digested with corresponding type-IIS restriction enzymes as designated in Figure S1, gel-purified, assembled and phenol-chloroform extracted to generate the full-length cDNAs. The cDNAs were then in vitro transcribed to the full-length RNA transcripts using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA, USA) and immediately electroporated into 800 μL of 107 cells/mL Vero cells in RNase-free phosphate buffered saline (PBS) along with 5 μg of PEDV nucleocapsid (N) transcripts. After electroporation, the cells were allowed to recover in growth medium for approximately 16 h and then maintained in PI-medium until cytopathic effects involved over 90% of cell monolayers. The whole flasks were subjected to one freeze-and-thaw cycle and the rescued viruses were passaged once to generate viral stocks (P1). The viral stocks were titrated on Vero cells in 96-well plates to determine the viral titer (see below)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T24","span":{"begin":1123,"end":1129},"obj":"Chemical"},{"id":"T25","span":{"begin":1130,"end":1140},"obj":"Chemical"},{"id":"T26","span":{"begin":1419,"end":1428},"obj":"Chemical"},{"id":"T30","span":{"begin":1625,"end":1627},"obj":"Chemical"},{"id":"T34","span":{"begin":1828,"end":1830},"obj":"Chemical"}],"attributes":[{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_15882"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_35255"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_18367"},{"id":"A27","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_26020"},{"id":"A28","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_35780"},{"id":"A29","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_43474"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_28874"},{"id":"A31","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_53806"},{"id":"A32","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_61484"},{"id":"A33","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_74790"},{"id":"A34","pred":"chebi_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/CHEBI_60949"}],"text":"2.3. Generation and Recovery of Recombinant iPEDVPT-P5, iPEDVPT-P96, iPEDVPT-P5-96S and iPEDVPT-P96-5S Viruses\nThe strategy used to recover iPEDVPT-P96 has been described previously [19]. The approach to constructing a cDNA clone of iPEDVPT-P5 was technically identical to that of the iPEDVPT-P96. However, we split the plasmid B into two fragments because the sequence remained toxic to the One Shot™ TOP10 Chemically Competent E. coli cells (Invitrogen, Carlsbad, USA) despite propagation in LB broth supplemented with 10% SOC medium and being incubated at 30 °C. To generate chimeric viruses carrying heterologous spike (S) genes, namely the iPEDVPT-P5-96S and iPEDVPT-P96-5S, cDNA clones of iPEDVPT-P5 and iPEDVPT-P96, respectively, were used as the backbones. The sequences covering the complete S gene of each virus were exchanged without disruption to the remaining genomic structure. Sequence differences in the S genes of iPEDVPT-P5 and iPEDVPT-P96 viruses are summarized in Table 1. Each plasmid was digested with corresponding type-IIS restriction enzymes as designated in Figure S1, gel-purified, assembled and phenol-chloroform extracted to generate the full-length cDNAs. The cDNAs were then in vitro transcribed to the full-length RNA transcripts using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA, USA) and immediately electroporated into 800 μL of 107 cells/mL Vero cells in RNase-free phosphate buffered saline (PBS) along with 5 μg of PEDV nucleocapsid (N) transcripts. After electroporation, the cells were allowed to recover in growth medium for approximately 16 h and then maintained in PI-medium until cytopathic effects involved over 90% of cell monolayers. The whole flasks were subjected to one freeze-and-thaw cycle and the rescued viruses were passaged once to generate viral stocks (P1). The viral stocks were titrated on Vero cells in 96-well plates to determine the viral titer (see below)."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T26","span":{"begin":1291,"end":1304},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T27","span":{"begin":1565,"end":1571},"obj":"http://purl.obolibrary.org/obo/GO_0040007"}],"text":"2.3. Generation and Recovery of Recombinant iPEDVPT-P5, iPEDVPT-P96, iPEDVPT-P5-96S and iPEDVPT-P96-5S Viruses\nThe strategy used to recover iPEDVPT-P96 has been described previously [19]. The approach to constructing a cDNA clone of iPEDVPT-P5 was technically identical to that of the iPEDVPT-P96. However, we split the plasmid B into two fragments because the sequence remained toxic to the One Shot™ TOP10 Chemically Competent E. coli cells (Invitrogen, Carlsbad, USA) despite propagation in LB broth supplemented with 10% SOC medium and being incubated at 30 °C. To generate chimeric viruses carrying heterologous spike (S) genes, namely the iPEDVPT-P5-96S and iPEDVPT-P96-5S, cDNA clones of iPEDVPT-P5 and iPEDVPT-P96, respectively, were used as the backbones. The sequences covering the complete S gene of each virus were exchanged without disruption to the remaining genomic structure. Sequence differences in the S genes of iPEDVPT-P5 and iPEDVPT-P96 viruses are summarized in Table 1. Each plasmid was digested with corresponding type-IIS restriction enzymes as designated in Figure S1, gel-purified, assembled and phenol-chloroform extracted to generate the full-length cDNAs. The cDNAs were then in vitro transcribed to the full-length RNA transcripts using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA, USA) and immediately electroporated into 800 μL of 107 cells/mL Vero cells in RNase-free phosphate buffered saline (PBS) along with 5 μg of PEDV nucleocapsid (N) transcripts. After electroporation, the cells were allowed to recover in growth medium for approximately 16 h and then maintained in PI-medium until cytopathic effects involved over 90% of cell monolayers. The whole flasks were subjected to one freeze-and-thaw cycle and the rescued viruses were passaged once to generate viral stocks (P1). The viral stocks were titrated on Vero cells in 96-well plates to determine the viral titer (see below)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T52","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T53","span":{"begin":5,"end":110},"obj":"Sentence"},{"id":"T54","span":{"begin":111,"end":187},"obj":"Sentence"},{"id":"T55","span":{"begin":188,"end":297},"obj":"Sentence"},{"id":"T56","span":{"begin":298,"end":565},"obj":"Sentence"},{"id":"T57","span":{"begin":566,"end":764},"obj":"Sentence"},{"id":"T58","span":{"begin":765,"end":891},"obj":"Sentence"},{"id":"T59","span":{"begin":892,"end":992},"obj":"Sentence"},{"id":"T60","span":{"begin":993,"end":1185},"obj":"Sentence"},{"id":"T61","span":{"begin":1186,"end":1504},"obj":"Sentence"},{"id":"T62","span":{"begin":1505,"end":1697},"obj":"Sentence"},{"id":"T63","span":{"begin":1698,"end":1832},"obj":"Sentence"},{"id":"T64","span":{"begin":1833,"end":1937},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.3. Generation and Recovery of Recombinant iPEDVPT-P5, iPEDVPT-P96, iPEDVPT-P5-96S and iPEDVPT-P96-5S Viruses\nThe strategy used to recover iPEDVPT-P96 has been described previously [19]. The approach to constructing a cDNA clone of iPEDVPT-P5 was technically identical to that of the iPEDVPT-P96. However, we split the plasmid B into two fragments because the sequence remained toxic to the One Shot™ TOP10 Chemically Competent E. coli cells (Invitrogen, Carlsbad, USA) despite propagation in LB broth supplemented with 10% SOC medium and being incubated at 30 °C. To generate chimeric viruses carrying heterologous spike (S) genes, namely the iPEDVPT-P5-96S and iPEDVPT-P96-5S, cDNA clones of iPEDVPT-P5 and iPEDVPT-P96, respectively, were used as the backbones. The sequences covering the complete S gene of each virus were exchanged without disruption to the remaining genomic structure. Sequence differences in the S genes of iPEDVPT-P5 and iPEDVPT-P96 viruses are summarized in Table 1. Each plasmid was digested with corresponding type-IIS restriction enzymes as designated in Figure S1, gel-purified, assembled and phenol-chloroform extracted to generate the full-length cDNAs. The cDNAs were then in vitro transcribed to the full-length RNA transcripts using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA, USA) and immediately electroporated into 800 μL of 107 cells/mL Vero cells in RNase-free phosphate buffered saline (PBS) along with 5 μg of PEDV nucleocapsid (N) transcripts. After electroporation, the cells were allowed to recover in growth medium for approximately 16 h and then maintained in PI-medium until cytopathic effects involved over 90% of cell monolayers. The whole flasks were subjected to one freeze-and-thaw cycle and the rescued viruses were passaged once to generate viral stocks (P1). The viral stocks were titrated on Vero cells in 96-well plates to determine the viral titer (see below)."}