{"gene":"PF3D7_1135600","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2020,"finding":"In Plasmodium falciparum, condensin II complex (which includes CAPD3/PF3D7_1135600 as a subunit) forms during mature schizogony and male gametogenesis, but not during early schizogony when SMC2/SMC4 localize to centromeres without forming condensin I or II complexes.","method":"Co-immunoprecipitation and fluorescence microscopy (SMC2/SMC4 localization with NDC80 marker, ChIP-seq for centromere identification)","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal complex formation established by Co-IP and ChIP-seq in a single lab; CAPD3 is identified as a condensin II subunit but the abstract does not describe direct experiments on CAPD3 itself beyond complex membership","pmids":["32049018"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"CAPD3 (PF3D7_1135600) transcript is expressed at an advanced stage of development in the mosquito midgut, corresponding to late zygote/early ookinete progression, consistent with a role in meiotic chromosome condensation during this stage.","method":"Single-cell transcriptomics with pseudotime analysis of P. falciparum development in the mosquito midgut","journal":"Microbiology spectrum","confidence":"Low","confidence_rationale":"Tier 4 / Weak — transcriptomic expression profiling only, no direct functional or biochemical experiment performed on CAPD3/PF3D7_1135600","pmids":["36847501"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1135600 (CAPD3) is a subunit of the condensin II complex in Plasmodium falciparum, which assembles during mature schizogony and male gametogenesis (but not early schizogony), and its transcript is expressed during late zygote/early ookinete development in the mosquito midgut, suggesting a role in meiotic chromosome condensation; beyond its membership in the condensin II complex, no direct mechanistic experiments on CAPD3 itself have been reported."},"narrative":{"mechanistic_narrative":"CAPD3 (PF3D7_1135600) is a subunit of the condensin II complex in Plasmodium falciparum, a complex that assembles specifically during mature schizogony and male gametogenesis but not during early schizogony, when SMC2/SMC4 instead localize to centromeres without forming condensin I or II [PMID:32049018]. This developmental restriction places CAPD3-containing condensin II in stages associated with chromosome condensation. Consistent with such a role, the CAPD3 transcript is expressed during late zygote/early ookinete progression in the mosquito midgut, a timing compatible with meiotic chromosome condensation [PMID:36847501]. Beyond its membership in the condensin II complex [PMID:32049018], no direct mechanistic experiments on CAPD3 itself have been reported in the available corpus.","teleology":[{"year":2020,"claim":"Establishing when condensin II assembles resolved whether P. falciparum uses distinct condensin complexes at different points in its cell cycle, and placed CAPD3 as a subunit active only in specific stages.","evidence":"Co-immunoprecipitation, fluorescence microscopy of SMC2/SMC4 with an NDC80 centromere marker, and ChIP-seq in P. falciparum","pmids":["32049018"],"confidence":"Medium","gaps":["No direct experiment on CAPD3 itself beyond identifying it as a condensin II subunit","The chromosomal targets and condensation activity attributable specifically to CAPD3 are not defined","Loss-of-function phenotype for CAPD3 is not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Mapping the developmental timing of CAPD3 transcription tested whether the gene is expressed at a stage consistent with meiotic condensation in the mosquito.","evidence":"Single-cell transcriptomics with pseudotime analysis of P. falciparum development in the mosquito midgut","pmids":["36847501"],"confidence":"Low","gaps":["Transcriptomic profiling only; no functional or biochemical assay of CAPD3 was performed","Protein-level expression and localization at this stage were not shown","A causal link between CAPD3 and meiotic chromosome condensation was not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct biochemical function, essential interactions, and loss-of-function phenotype of CAPD3 remain uncharacterized independently of the condensin II complex.","evidence":"No direct experiment on CAPD3 protein reported in the corpus","pmids":[],"confidence":"Low","gaps":["No CAPD3-specific knockout or knockdown phenotype","No structural or biochemical characterization of CAPD3 within condensin II","No demonstration that CAPD3 is required for chromosome condensation in any stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["condensin II complex"],"partners":[],"other_free_text":["Identified as a subunit of the P. falciparum condensin II complex, which assembles during mature schizogony and male gametogenesis but not early schizogony [#0]","CAPD3 transcript expressed at late zygote/early ookinete stage in the mosquito midgut, consistent with meiotic chromosome condensation [#1]","No direct mechanistic experiments on CAPD3 itself reported beyond complex membership"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"32049018","id":"PMC_32049018","title":"Plasmodium Condensin Core Subunits SMC2/SMC4 Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32049018","citation_count":30,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36847501","id":"","title":"Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.","date":"2023","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/36847501","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAPD3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4393,"output_tokens":677,"usd":0.011667,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5276,"output_tokens":1395,"usd":0.030627,"stage2_stop_reason":"end_turn"},"total_usd":0.042294,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"In Plasmodium falciparum, condensin II complex (which includes CAPD3/PF3D7_1135600 as a subunit) forms during mature schizogony and male gametogenesis, but not during early schizogony when SMC2/SMC4 localize to centromeres without forming condensin I or II complexes.\",\n      \"method\": \"Co-immunoprecipitation and fluorescence microscopy (SMC2/SMC4 localization with NDC80 marker, ChIP-seq for centromere identification)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal complex formation established by Co-IP and ChIP-seq in a single lab; CAPD3 is identified as a condensin II subunit but the abstract does not describe direct experiments on CAPD3 itself beyond complex membership\",\n      \"pmids\": [\"32049018\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CAPD3 (PF3D7_1135600) transcript is expressed at an advanced stage of development in the mosquito midgut, corresponding to late zygote/early ookinete progression, consistent with a role in meiotic chromosome condensation during this stage.\",\n      \"method\": \"Single-cell transcriptomics with pseudotime analysis of P. falciparum development in the mosquito midgut\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — transcriptomic expression profiling only, no direct functional or biochemical experiment performed on CAPD3/PF3D7_1135600\",\n      \"pmids\": [\"36847501\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1135600 (CAPD3) is a subunit of the condensin II complex in Plasmodium falciparum, which assembles during mature schizogony and male gametogenesis (but not early schizogony), and its transcript is expressed during late zygote/early ookinete development in the mosquito midgut, suggesting a role in meiotic chromosome condensation; beyond its membership in the condensin II complex, no direct mechanistic experiments on CAPD3 itself have been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CAPD3 (PF3D7_1135600) is a subunit of the condensin II complex in Plasmodium falciparum, a complex that assembles specifically during mature schizogony and male gametogenesis but not during early schizogony, when SMC2/SMC4 instead localize to centromeres without forming condensin I or II [#0]. This developmental restriction places CAPD3-containing condensin II in stages associated with chromosome condensation. Consistent with such a role, the CAPD3 transcript is expressed during late zygote/early ookinete progression in the mosquito midgut, a timing compatible with meiotic chromosome condensation [#1]. Beyond its membership in the condensin II complex [#0], no direct mechanistic experiments on CAPD3 itself have been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Establishing when condensin II assembles resolved whether P. falciparum uses distinct condensin complexes at different points in its cell cycle, and placed CAPD3 as a subunit active only in specific stages.\",\n      \"evidence\": \"Co-immunoprecipitation, fluorescence microscopy of SMC2/SMC4 with an NDC80 centromere marker, and ChIP-seq in P. falciparum\",\n      \"pmids\": [\"32049018\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct experiment on CAPD3 itself beyond identifying it as a condensin II subunit\",\n        \"The chromosomal targets and condensation activity attributable specifically to CAPD3 are not defined\",\n        \"Loss-of-function phenotype for CAPD3 is not established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mapping the developmental timing of CAPD3 transcription tested whether the gene is expressed at a stage consistent with meiotic condensation in the mosquito.\",\n      \"evidence\": \"Single-cell transcriptomics with pseudotime analysis of P. falciparum development in the mosquito midgut\",\n      \"pmids\": [\"36847501\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Transcriptomic profiling only; no functional or biochemical assay of CAPD3 was performed\",\n        \"Protein-level expression and localization at this stage were not shown\",\n        \"A causal link between CAPD3 and meiotic chromosome condensation was not tested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct biochemical function, essential interactions, and loss-of-function phenotype of CAPD3 remain uncharacterized independently of the condensin II complex.\",\n      \"evidence\": \"No direct experiment on CAPD3 protein reported in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No CAPD3-specific knockout or knockdown phenotype\",\n        \"No structural or biochemical characterization of CAPD3 within condensin II\",\n        \"No demonstration that CAPD3 is required for chromosome condensation in any stage\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\"condensin II complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Identified as a subunit of the P. falciparum condensin II complex, which assembles during mature schizogony and male gametogenesis but not early schizogony [#0]\",\n      \"CAPD3 transcript expressed at late zygote/early ookinete stage in the mosquito midgut, consistent with meiotic chromosome condensation [#1]\",\n      \"No direct mechanistic experiments on CAPD3 itself reported beyond complex membership\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1135600","tier":"GROUNDING","verdict":"Evidence-grounding concern","subtype":"uncited_synthesis","uniprot_band":"empty","rules_fired":"R8","issue":"R8: 1/3 claims uncited (33%)"},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1135600","name":null,"product":"condensin-2 complex subunit D3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0913000","name":null,"product":"condensin-2 complex subunit D3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0933800","name":null,"product":"condensin-2 complex subunit D3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CAPD3","evaluation":null}