Characterization of genome-reduced fission yeast strains.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23563150", "kind": "science-record", "revision": 4, "content_hash": "sha256:65e0f02df20f267b4cec5ee0b8b45866bb15e221e2c110257fb3fceb0e93de91", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T21:19:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of genome-reduced fission yeast strains.", "doi": "10.1093/nar/gkt233", "pmid": "23563150", "authors": ["Mayumi Sasaki", "Hiromichi Kumagai", "Kaoru Takegawa", "Hideki Tohda"], "journal": "Nucleic acids research", "year": 2013, "abstract": "The Schizosaccharomyces pombe genome is one of the smallest among the free-living eukaryotes. We further reduced the S. pombe gene number by large-scale gene deletion to identify a minimal gene set required for growth under laboratory conditions. The genome-reduced strain has four deletion regions: 168.4 kb in the left arm of chromosome I, 155.4 kb in the right arm of chromosome I, 211.7 kb in the left arm of chromosome II and 121.6 kb in the right arm of chromosome II. The deletions corresponded to a loss of 223 genes of the original ~5100. The quadruple-deletion strain, with a total deletion size of 657.3 kb, showed a decreased ability to uptake glucose and some amino acids in comparison with the parental strain. The strain also showed increased gene expression of the mating pheromone M-factor precursor and the nicotinamide adenine dinucleotide phosphate -specific glutamate dehydrogenase. There was also a 2.7-fold increase in the concentration of cellular adenosine triphosphate, and levels of the heterologous proteins, enhanced green fluorescent protein and secreted human growth hormone were increased by 1.7- and 1.8-fold, respectively. The transcriptome data from this study have been submitted to the Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE38620 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=vjkxjewuywgcovc&acc=GSE38620).", "claims": [{"id": "claim-method", "statement": "In addition, ASP3894 showed a slight but significant decrease in glucose consumption (P = 0.0080, t-test, n = 5) and ethanol production (P = 0.0046) compared with ASP3880 in the late logarithmic phase (Figure 3B, Supplementary Figure S4 and Supplementary Table S3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23563150", "locator": "sections[22] \"Glucose uptake efficiency is decreased during late logarithmic phase in the quadruple-deletion strain\" paragraph 2", "quote": "In addition, ASP3894 showed a slight but significant decrease in glucose consumption (P = 0.0080, t-test, n = 5) and ethanol production (P = 0.0046) compared with ASP3880 in the late logarithmic phase (Figure 3B, Supplementary Figure S4 and Supplementary Table S3)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary Data are available at NAR Online: Supplementary Tables 1–4, Supplementary Figures 1–5 and Supplementary Sequences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23563150", "locator": "sections[29] \"SUPPLEMENTARY DATA\" paragraph 2", "quote": "Supplementary Data are available at NAR Online: Supplementary Tables 1–4, Supplementary Figures 1–5 and Supplementary Sequences."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used a t-test for statistical comparison, and the transcriptome source data are available through GEO under accession GSE38620.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23563150", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcriptome data from this study have been submitted to the Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE38620 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=vjkxjewuywgcovc&acc=GSE38620)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used a t-test for statistical comparison, and the transcriptome source data are available through GEO under accession GSE38620.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:23563150"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE38620"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE38620"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:23563150", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/nar/gkt233", "sha256": "sha256:51caa6b0377b6068b5c64e583c12a2e80ae77d2289736a09a937b950eb43471f", "bytes": 68774, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/nar/gkt233", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3664816", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE38620", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38620", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38620", "version": null, "note": "Supplementary Data are available at NAR Online: Supplementary Tables 1–4, Supplementary Figures 1–5 and Supplementary Sequences.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supplementary Data are available at NAR Online: Supplementary Tables 1–4, Supplementary Figures 1–5 and Supplementary Sequences.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM946275", "GSM946276", "GSM946277"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "15627", "taxon": "Schizosaccharomyces pombe", "title": "Transcriptional profiling of a genome-reduced strain in Schizosaccharomyces pombe", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:23563150:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a0176ed0b4289950f0a1da3b6c4f9d2e69713028a2c414507f3538d748986f97", "bytes": 2220, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#gkt233-T1", "version": null, "note": "Genome-reduced strains and heterologous protein production strains", "structure": {"pmcid": "PMC3664816", "section_index": 3, "section_title": "Strains and culture conditions", "row_count": 28, "column_count": 4}, "table": {"label": "Table 1.", "caption": "Genome-reduced strains and heterologous protein production strains", "rows": [["Strain", "Genotype", "Source", "NBRP IDa"], ["ARC010", "h− leu1-32 ura4-D18", "JY743", ""], ["ARC001", "h− leu1-32", "ATCC38399", ""], ["ARC032", "h−", "JY1", ""], ["IGF719", "h− leu1-32 ura4-D18 int::SPAC1F8.07cb ALT-D1797", "This study", ""], ["IGF718", "h− leu1-32 ura4-D18 int::SPAC1F8.07cb ALT-D1684", "This study", "FY21635"], ["IGF524", "h− leu1-32 ura4-D18 ART-D1554", "This study", "FY21636"], ["IGF525", "h− leu1-32 ura4-D18 BLT-D2117", "This study", "FY21637"], ["IGF526", "h− leu1-32 ura4-D18 BRT-D1216", "This study", "FY21638"], ["IGF740", "h− leu1-32 ura4-D18 int::SPAC1F8.07cb ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216", "This study", "FY21649"], ["IGF725", "h− leu1-32 ura4 int::SPAC1F8.07cc ALT-D1797", "This study", ""], ["IGF724", "h− leu1-32 ura4 int::SPAC1F8.07cc ALT-D1684", "This study", "FY21650"], ["IGF628", "h− leu1-32 ART-D1554", "This study", "FY21651"], ["IGF629", "h− leu1-32 BLT-D2117", "This study", "FY21652"], ["IGF630", "h− leu1-32 BRT-D1216", "This study", "FY21653"], ["IGF742", "h− leu1-32 ura4 int::SPAC1F8.07cc ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216", "This study", "FY21664"], ["IGF816", "h− leu1 int::SPBC1683.05d ura4-D18 BLT-D2117", "This study", ""], ["IGF817", "h− leu1 int::SPBC1683.06ce ura4-D18 BLT-D2117", "This study", ""], ["ASP3880", "h− leu1 int::EGFPf", "This study", ""], ["ASP3881", "h− leu1 int::EGFPf ura4 int::SPAC1F8.07cc ALT-D1684", "This study", ""], ["ASP3882", "h− leu1 int::EGFPf ART-D1554", "This study", ""], ["ASP3883", "h− leu1 int::EGFPf BLT-D2117", "This study", ""], ["ASP3884", "h− leu1 int::EGFPf BRT-D1216", "This study", ""], ["ASP3894", "h− leu1 int::EGFPf ura4 int::SPAC1F8.07cc ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216", "This study", ""], ["ASP3341", "h− leu1 int::hGHf", "This study", ""], ["ASP4187", "h− leu1 int::hGHf ura4 int::SPAC1F8.07cc ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216", "This study", ""], ["ASP3895", "h− leu1 int::hTFf", "This study", ""], ["ASP3909", "h− leu1 int::hTFf ura4 int::SPAC1F8.07cc ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216", "This study", ""]], "row_count": 28, "column_count": 4, "numeric_cells": 62, "header_rows": 1, "locator": "section[3]/table-wrap[1]#gkt233-T1"}}, {"id": "asset:table:pmid:23563150:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eccad8627808c303f3036ecb77ffe92944ccbabc7aabebe9c2e0ac9520eb8707", "bytes": 1919, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#gkt233-T2", "version": null, "note": "Summary of deletion genes", "structure": {"pmcid": "PMC3664816", "section_index": 18, "section_title": "Deletion of large-scale regions from the termini of chromosomes I and II", "row_count": 29, "column_count": 7}, "table": {"label": "Table 2.", "caption": "Summary of deletion genes", "rows": [["Name", "Term", "ALT", "ART", "BLT", "BRT", "Subtotal"], ["Transmembrane transport", "GO:0055085", "8", "10", "20", "3", "41"], ["Cellular amino acid metabolic process", "GO:0006520", "4", "5", "4", "1", "14"], ["Generation of precursor metabolites and energy", "GO:0006091", "3", "3", "2", "0", "8"], ["Protein glycosylation", "GO:0006486", "3", "0", "0", "4", "7"], ["Carbohydrate metabolic process", "GO:0005975", "0", "2", "2", "2", "6"], ["Cell adhesion", "GO:0007155", "2", "1", "2", "1", "6"], ["Regulation of transcription, DNA-dependent", "GO:0006355", "2", "0", "4", "0", "6"], ["DNA recombination", "GO:0006310", "2", "0", "0", "1", "3"], ["Vitamin metabolic process", "GO:0006766", "2", "0", "0", "1", "3"], ["Lipid metabolic process", "GO:0006629", "1", "0", "1", "0", "2"], ["Meiosis", "GO:0007126", "2", "0", "0", "0", "2"], ["Nucleobase-containing small molecule metabolic process", "GO:0055086", "0", "0", "2", "0", "2"], ["Transcription, DNA-dependent", "GO:0006351", "1", "1", "0", "0", "2"], ["DNA replication", "GO:0006260", "0", "0", "0", "1", "1"], ["Cellular cell wall organization or biogenesis", "GO:0070882", "0", "1", "0", "0", "1"], ["Chromosome segregation", "GO:0007059", "1", "0", "0", "0", "1"], ["Cofactor metabolic process", "GO:0051186", "0", "0", "1", "0", "1"], ["Conjugation with cellular fusion", "GO:0000747", "0", "1", "0", "0", "1"], ["Cytoskeleton organization", "GO:0007010", "0", "0", "0", "1", "1"], ["Nitrogen cycle metabolic process", "GO:0071941", "0", "0", "0", "1", "1"], ["Protein targeting", "GO:0006605", "0", "1", "0", "0", "1"], ["Signaling", "GO:0023052", "0", "1", "0", "0", "1"], ["Other", "", "23", "22", "16", "13", "74"], ["Conserved unknown", "", "5", "1", "2", "3", "11"], ["Sequence orphan", "", "6", "1", "3", "3", "13"], ["Pseudogene", "", "5", "0", "4", "4", "13"], ["Dubious", "", "0", "1", "0", "0", "1"], ["Total deletion genes", "", "70", "51", "63", "39", "223"]], "row_count": 29, "column_count": 7, "numeric_cells": 162, "header_rows": 1, "locator": "section[18]/table-wrap[1]#gkt233-T2"}}, {"id": "asset:table:pmid:23563150:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:486b5015f00a275dfd6204fdb34f3789a4f5684fc9e0cb5b1d83f6689c36b426", "bytes": 501, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#gkt233-T3", "version": null, "note": "Cell size of genome-reduced strains", "structure": {"pmcid": "PMC3664816", "section_index": 21, "section_title": "The quadruple-deletion slightly affects growth rate and cell size", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3.", "caption": "Cell size of genome-reduced strains", "rows": [["Strain", "Deletion region", "Cell length (μm)", "SD(±)", "P-value"], ["ARC001", "", "14.0", "0.8", ""], ["IGF724", "ALT", "12.7", "0.9", "1.5E-10"], ["IGF628", "ART", "11.8", "1.1", "6.2E-19"], ["IGF629", "BLT", "12.8", "1.1", "2.5E-07"], ["IGF630", "BRT", "12.0", "1.2", "1.2E-15"], ["IGF742", "ALT BRT BLT BRT", "10.9", "1.1", "1.0E-27"]], "row_count": 7, "column_count": 5, "numeric_cells": 23, "header_rows": 1, "locator": "section[21]/table-wrap[1]#gkt233-T3"}}], "gaps": ["asset:data:geo:GSE38620 not downloaded", "asset:data:geo:GSE38620 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In addition, ASP3894 showed a slight but significant decrease in glucose consumption (P = 0.0080, t-test, n = 5) and ethanol production (P = 0.0046) compared with ASP3880 in the late logarithmic phase (Figure 3B, Supplementary Figure S4 and Supplementary Table S3)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE38620"], "resolved_accessions": ["GSE38620"], "statements": ["Supplementary Data are available at NAR Online: Supplementary Tables 1–4, Supplementary Figures 1–5 and Supplementary Sequences."], "basis": "The paper names GSE38620 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:23563150", "data:geo:GSE38620", "asset:table:pmid:23563150:1", "asset:table:pmid:23563150:2", "asset:table:pmid:23563150:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE38620"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:23Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 143588, "completion_tokens": 4167, "cached_tokens": 107776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:23563150", "type": "paper", "label": "pmid:23563150"}, {"id": "source:pmid:23563150", "type": "manuscript", "label": "PMID 23563150 full text"}, {"id": "data:geo:GSE38620", "type": "dataset", "label": "GEO GSE38620"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:23563150", "type": "paper", "label": "pmid:23563150"}, {"id": "source:pmid:23563150", "type": "manuscript", "label": "PMID 23563150 full text"}, {"id": "data:geo:GSE38620", "type": "dataset", "label": "GEO GSE38620"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-23563150", "type": "extraction", "used": ["source:pmid:23563150"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE38620", "type": "accession_resolution", "used": ["data:geo:GSE38620"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:23563150", "parent_hash": "sha256:7ac372eb4ef59d3b7e8cd4aaaad7a9283618d765a7271f51bdebdb0234b54039", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE38620 licence not read", "asset:data:geo:GSE38620 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}