{"gene":"PF3D7_1446500","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2018,"finding":"NUP313 (PF3D7_1446500) was identified as a nucleoporin component of the nuclear pore complex (NPC) in Plasmodium parasites through bioinformatic and genetic methods; its ortholog was identified in P. falciparum based on homology to P. berghei Nups characterized in this study.","method":"Bioinformatic identification combined with genetic tagging and localization in P. berghei; ortholog identification in P. falciparum","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single study, bioinformatic identification with genetic tagging but no functional mechanistic dissection of NUP313 specifically","pmids":["30050042"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"NUP313 (PF3D7_1446500) localizes to the nuclear periphery in P. berghei blood-stage parasites, is evenly distributed around nuclei, and is organized in a rosette structure around the centriolar plaque during blood-stage asexual replication, as revealed by ultrastructure expansion microscopy (U-ExM).","method":"Ultrastructure expansion microscopy (U-ExM) of fluorescently tagged Nup313 throughout the 24-hour blood-stage replication cycle in P. berghei","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment with high-resolution imaging (U-ExM) providing spatial detail, single lab but specific to NUP313 with clear structural phenotype","pmids":["38405843"],"is_preprint":true,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2026,"finding":"PfNUP313 (PF3D7_1446500) in P. falciparum was successfully GFP-tagged using a sequential CRISPR/Cas9-based gene editing approach, demonstrating that the locus is accessible for genetic manipulation; no functional phenotype or localization data for PfNUP313 were reported beyond confirmation of successful tagging.","method":"CRISPR/Cas9-based endogenous GFP tagging in P. falciparum","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single study, tagging confirmed but no mechanistic or localization data for NUP313 reported in the abstract","pmids":["41885428"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"NUP313 (PF3D7_1446500) is a nucleoporin component of the nuclear pore complex in Plasmodium parasites; in P. berghei blood-stage parasites it localizes evenly around the nuclear periphery and forms a rosette structure at the centriolar plaque during asexual replication, while in P. falciparum it has been successfully GFP-tagged but no additional mechanistic function has been experimentally established beyond its NPC membership."},"narrative":{"mechanistic_narrative":"NUP313 (PF3D7_1446500) is a nucleoporin component of the Plasmodium nuclear pore complex, identified through bioinformatic analysis and genetic tagging of P. berghei Nups with the P. falciparum ortholog assigned by homology [PMID:30050042]. In P. berghei blood-stage parasites, ultrastructure expansion microscopy shows NUP313 distributed evenly around the nuclear periphery and organized into a rosette structure around the centriolar plaque during asexual replication [PMID:38405843]. In P. falciparum, the endogenous locus has been GFP-tagged by CRISPR/Cas9, establishing that it is genetically tractable, but no localization or functional phenotype has been reported for the P. falciparum protein [PMID:41885428]. Beyond its NPC membership and the P. berghei localization pattern, no substrates, interaction partners, or mechanistic function of NUP313 have been characterized in the available corpus.","teleology":[{"year":2018,"claim":"Establishing which Plasmodium proteins constitute the nuclear pore complex was needed to define parasite nuclear architecture, and this work placed NUP313 among the identified nucleoporins.","evidence":"Bioinformatic identification with genetic tagging in P. berghei and homology-based ortholog assignment in P. falciparum","pmids":["30050042"],"confidence":"Low","gaps":["Identification is bioinformatic/homology-based with no functional mechanistic dissection of NUP313 specifically","No interaction partners or sub-complex assignment within the NPC established","P. falciparum ortholog assigned by homology only, not experimentally validated in this study"],"attribution":[{"species":"Plasmodium berghei","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Whether NUP313 has a defined spatial organization during replication was unknown; high-resolution imaging revealed an even nuclear-periphery distribution and a rosette around the centriolar plaque, linking the protein to the replication machinery.","evidence":"Ultrastructure expansion microscopy (U-ExM) of tagged Nup313 across the 24-hour blood-stage cycle in P. berghei (preprint)","pmids":["38405843"],"confidence":"Medium","gaps":["Functional consequence of the centriolar-plaque rosette organization is not tested","Shown only in P. berghei; not demonstrated in P. falciparum","No interaction partners identified that mediate the rosette structure"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2026,"claim":"Genetic tractability of the P. falciparum locus was needed for future study; endogenous GFP tagging demonstrated the locus can be edited, though it yielded no functional or localization data.","evidence":"Sequential CRISPR/Cas9-based endogenous GFP tagging in P. falciparum","pmids":["41885428"],"confidence":"Low","gaps":["No localization or functional phenotype for the P. falciparum protein was reported","Whether the P. berghei rosette localization is conserved in P. falciparum is untested","No essentiality or knockdown analysis performed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The molecular function of NUP313 beyond NPC membership — its interaction partners, its role in nuclear transport, and the significance of its centriolar-plaque rosette during replication — remains unresolved.","evidence":"No experimental evidence in the available corpus addresses NUP313 molecular function","pmids":[],"confidence":"Low","gaps":["No substrates or cargo interactions identified","No physical interaction partners within the NPC established for NUP313","Functional role of the centriolar-plaque rosette during asexual replication untested"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Nuclear pore complex (NPC)"],"partners":[],"other_free_text":["Organized in a rosette structure around the centriolar plaque during P. berghei blood-stage asexual replication [#1]","P. falciparum locus is genetically tractable and has been endogenously GFP-tagged, but no localization or functional data reported [#2]","P. falciparum ortholog assigned by homology to P. berghei Nups [#0]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"30050042","id":"PMC_30050042","title":"Nuclear Pore Complex Components in the Malaria Parasite Plasmodium berghei.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30050042","citation_count":20,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38405843","id":"PMC_38405843","title":"Nuclear pore complexes undergo Nup221 exchange during blood stage asexual replication of Plasmodium parasites.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38405843","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["NUP313"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41885428","id":"PMC_41885428","title":"A heterologous marker-free selection approach for CRISPR/Cas9-based gene editing in the malaria parasite Plasmodium falciparum.","date":"2026","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/41885428","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfNUP313"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4701,"output_tokens":935,"usd":0.014064,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5637,"output_tokens":1823,"usd":0.03688,"stage2_stop_reason":"end_turn"},"total_usd":0.050944,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"NUP313 (PF3D7_1446500) was identified as a nucleoporin component of the nuclear pore complex (NPC) in Plasmodium parasites through bioinformatic and genetic methods; its ortholog was identified in P. falciparum based on homology to P. berghei Nups characterized in this study.\",\n      \"method\": \"Bioinformatic identification combined with genetic tagging and localization in P. berghei; ortholog identification in P. falciparum\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single study, bioinformatic identification with genetic tagging but no functional mechanistic dissection of NUP313 specifically\",\n      \"pmids\": [\"30050042\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NUP313 (PF3D7_1446500) localizes to the nuclear periphery in P. berghei blood-stage parasites, is evenly distributed around nuclei, and is organized in a rosette structure around the centriolar plaque during blood-stage asexual replication, as revealed by ultrastructure expansion microscopy (U-ExM).\",\n      \"method\": \"Ultrastructure expansion microscopy (U-ExM) of fluorescently tagged Nup313 throughout the 24-hour blood-stage replication cycle in P. berghei\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment with high-resolution imaging (U-ExM) providing spatial detail, single lab but specific to NUP313 with clear structural phenotype\",\n      \"pmids\": [\"38405843\"],\n      \"is_preprint\": true,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PfNUP313 (PF3D7_1446500) in P. falciparum was successfully GFP-tagged using a sequential CRISPR/Cas9-based gene editing approach, demonstrating that the locus is accessible for genetic manipulation; no functional phenotype or localization data for PfNUP313 were reported beyond confirmation of successful tagging.\",\n      \"method\": \"CRISPR/Cas9-based endogenous GFP tagging in P. falciparum\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single study, tagging confirmed but no mechanistic or localization data for NUP313 reported in the abstract\",\n      \"pmids\": [\"41885428\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"NUP313 (PF3D7_1446500) is a nucleoporin component of the nuclear pore complex in Plasmodium parasites; in P. berghei blood-stage parasites it localizes evenly around the nuclear periphery and forms a rosette structure at the centriolar plaque during asexual replication, while in P. falciparum it has been successfully GFP-tagged but no additional mechanistic function has been experimentally established beyond its NPC membership.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NUP313 (PF3D7_1446500) is a nucleoporin component of the Plasmodium nuclear pore complex, identified through bioinformatic analysis and genetic tagging of P. berghei Nups with the P. falciparum ortholog assigned by homology [#0]. In P. berghei blood-stage parasites, ultrastructure expansion microscopy shows NUP313 distributed evenly around the nuclear periphery and organized into a rosette structure around the centriolar plaque during asexual replication [#1]. In P. falciparum, the endogenous locus has been GFP-tagged by CRISPR/Cas9, establishing that it is genetically tractable, but no localization or functional phenotype has been reported for the P. falciparum protein [#2]. Beyond its NPC membership and the P. berghei localization pattern, no substrates, interaction partners, or mechanistic function of NUP313 have been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Establishing which Plasmodium proteins constitute the nuclear pore complex was needed to define parasite nuclear architecture, and this work placed NUP313 among the identified nucleoporins.\",\n      \"evidence\": \"Bioinformatic identification with genetic tagging in P. berghei and homology-based ortholog assignment in P. falciparum\",\n      \"pmids\": [\"30050042\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Identification is bioinformatic/homology-based with no functional mechanistic dissection of NUP313 specifically\",\n        \"No interaction partners or sub-complex assignment within the NPC established\",\n        \"P. falciparum ortholog assigned by homology only, not experimentally validated in this study\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether NUP313 has a defined spatial organization during replication was unknown; high-resolution imaging revealed an even nuclear-periphery distribution and a rosette around the centriolar plaque, linking the protein to the replication machinery.\",\n      \"evidence\": \"Ultrastructure expansion microscopy (U-ExM) of tagged Nup313 across the 24-hour blood-stage cycle in P. berghei (preprint)\",\n      \"pmids\": [\"38405843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of the centriolar-plaque rosette organization is not tested\",\n        \"Shown only in P. berghei; not demonstrated in P. falciparum\",\n        \"No interaction partners identified that mediate the rosette structure\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Genetic tractability of the P. falciparum locus was needed for future study; endogenous GFP tagging demonstrated the locus can be edited, though it yielded no functional or localization data.\",\n      \"evidence\": \"Sequential CRISPR/Cas9-based endogenous GFP tagging in P. falciparum\",\n      \"pmids\": [\"41885428\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No localization or functional phenotype for the P. falciparum protein was reported\",\n        \"Whether the P. berghei rosette localization is conserved in P. falciparum is untested\",\n        \"No essentiality or knockdown analysis performed\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular function of NUP313 beyond NPC membership — its interaction partners, its role in nuclear transport, and the significance of its centriolar-plaque rosette during replication — remains unresolved.\",\n      \"evidence\": \"No experimental evidence in the available corpus addresses NUP313 molecular function\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No substrates or cargo interactions identified\",\n        \"No physical interaction partners within the NPC established for NUP313\",\n        \"Functional role of the centriolar-plaque rosette during asexual replication untested\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0017056\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005643\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0034399\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\n      \"Nuclear pore complex (NPC)\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Organized in a rosette structure around the centriolar plaque during P. berghei blood-stage asexual replication [#1]\",\n      \"P. falciparum locus is genetically tractable and has been endogenously GFP-tagged, but no localization or functional data reported [#2]\",\n      \"P. falciparum ortholog assigned by homology to P. berghei Nups [#0]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1446500","name":null,"product":"nucleoporin NUP313, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1310200","name":null,"product":"nucleoporin NUP313","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1235700","name":null,"product":"nucleoporin NUP313, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NUP313","evaluation":null}