{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34022944", "kind": "science-record", "revision": 8, "content_hash": "sha256:8cf011d09cf47280c2fe4e93758118c1c4f291d4d6fc6c91edb33c9af5d01bd0", "created_at": "2026-11-01T15:41:36Z", "updated_at": "2026-11-01T22:46:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources.", "doi": "10.1186/s13068-021-01970-6", "pmid": "34022944", "authors": ["E Hounslow", "C A Evans", "J Pandhal", "T Sydney", "N Couto", "T K Pham", "D James Gilmour", "P C Wright"], "journal": "Biotechnology for biofuels", "year": 2021, "abstract": "BACKGROUND: Chlamydomonas reinhardtii is a model green alga strain for molecular studies; its fully sequenced genome has enabled omic-based analyses that have been applied to better understand its metabolic responses to stress. Here, we characterised physiological and proteomic changes between a low-starch C. reinhardtii strain and the snow alga Chlamydomonas nivalis, to reveal insights into their contrasting responses to salinity stress.\nRESULTS: Each strain was grown in conditions tailored to their growth requirements to encourage maximal fatty acid (as a proxy measure of lipid) production, with internal controls to allow comparison points. In 0.2 M NaCl, C. nivalis accumulates carbohydrates up to 10.4% DCW at 80 h, and fatty acids up to 52.0% dry cell weight (DCW) over 12 days, however, C. reinhardtii does not show fatty acid accumulation over time, and shows limited carbohydrate accumulation up to 5.5% DCW. Analysis of the C. nivalis fatty acid profiles showed that salt stress improved the biofuel qualities over time. Photosynthesis and respiration rates are reduced in C. reinhardtii relative to C. nivalis in response to 0.2 M NaCl. De novo sequencing and homology matching was used in conjunction with iTRAQ-based quantitative analysis to identify and relatively quantify proteomic alterations in cells exposed to salt stress. There were abundance differences in proteins associated with stress, photosynthesis, carbohydrate and lipid metabolism proteins. In terms of lipid synthesis, salt stress induced an increase in dihydrolipoyl dehydrogenase in C. nivalis (1.1-fold change), whilst levels in C. reinhardtii remained unaffected; this enzyme is involved in acetyl CoA production and has been linked to TAG accumulation in microalgae. In salt-stressed C. nivalis there were decreases in the abundance of UDP-sulfoquinovose (- 1.77-fold change), which is involved in sulfoquinovosyl diacylglycerol metabolism, and in citrate synthase (- 2.7-fold change), also involved in the TCA cycle. Decreases in these enzymes have been shown to lead to increased TAG production as fatty acid biosynthesis is favoured. Data are available via ProteomeXchange with identifier PXD018148.\nCONCLUSIONS: These differences in protein abundance have given greater understanding of the mechanism by which salt stress promotes fatty acid accumulation in the un-sequenced microalga C. nivalis as it switches to a non-growth state, whereas C. reinhardtii does not have this response.", "claims": [{"id": "claim-method", "statement": "Proteins that were statistically different in abundance using ANOVA (p < 0.05) across the treatments are summarised in Tables 2 and 3 for C. reinhardtii and C. nivalis, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34022944", "locator": "sections[5] \"Proteomic study in C. reinhardtii and C. nivalis\" paragraph 4", "quote": "Proteins that were statistically different in abundance using ANOVA (p < 0.05) across the treatments are summarised in Tables 2 and 3 for C. reinhardtii and C. nivalis, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [83] partner repository with the dataset identifier PXD018148.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34022944", "locator": "sections[28] \"notes\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [83] partner repository with the dataset identifier PXD018148."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34022944"], "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:PXD018148"], "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:PXD018148"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34022944", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13068-021-01970-6", "sha256": "sha256:cea47f2cec0f29885d7253b33ccbeef727400c2332affd37878919c32e6e9b15", "bytes": 81812, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13068-021-01970-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8141184", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD018148", "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=PXD018148", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018148", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [83] partner repository with the dataset identifier PXD018148.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [83] partner repository with the dataset identifier PXD018148.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "¬¬Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered lipid accumulation via reallocation of carbon resources", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34022944:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2bbf570066b79956e61d95c41cd0a2b387f46e77af26a73ba0415ee0425c17f8", "bytes": 1469, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Biofuel properties of C. nivalis samples (n = 3)", "structure": {"pmcid": "PMC8141184", "section_index": 3, "section_title": "The impact of salt stress on the physiology of Chlamydomonas reinhardtii and Chlamydomonas nivalis", "row_count": 12, "column_count": 8}, "table": {"label": "Table 1", "caption": "Biofuel properties of C. nivalis samples (n = 3)", "rows": [["Sample", "Saponification number (mg KOH g−1 oil)", "Iodine number (g I2 100 g−1 oil)", "Cetane number", "Degree of unsaturation (wt. %)", "Long chain saturation factor (LCSF) (°C)", "Cold filter plugging point (CFPP) (°C)"], ["Time (hours)", "NaCl concentration (M)", "", "", "", ""], ["0", "0", "193.6 ± 0.1", "144.5 ± 0.4", "42.0 ± 0.1", "117.2 ± 0.4", "12.2 ± 0.5", "21.9 ± 1.7"], ["0", "0.2", "193.5 ± 0.0", "143.8 ± 0.2", "42.1 ± 0.1", "115.7 ± 0.2", "13.1 ± 0.1", "24.6 ± 0.3"], ["24", "0", "193.8 ± 0.2", "145.5 ± 0.5", "41.7 ± 0.1", "117.2 ± 0.8", "12.5 ± 0.4", "22.7 ± 1.2"], ["24", "0.2", "193.8 ± 0.1", "131.5 ± 1.2", "44.9 ± 0.3", "110.6 ± 1.1", "11.0 ± 0.2", "18.2 ± 0.8"], ["80", "0", "193.6 ± 0.1", "144.2 ± 0.7", "42.0 ± 0.1", "117.9 ± 0.3", "11.6 ± 0.3", "20.0 ± 0.8"], ["80", "0.2", "192.4 ± 0.1", "115.9 ± 0.8", "48.6 ± 0.2", "107.2 ± 0.4", "6.8 ± 0.2", "4.8 ± 0.7"], ["168", "0", "194.1 ± 0.1", "132.1 ± 0.5", "44.7 ± 0.1", "113.0 ± 0.3", "10.1 ± 0.1", "15.2 ± 0.5"], ["168", "0.2", "191.8 ± 0.1", "104.9 ± 0.4", "51.2 ± 0.1", "104.1 ± 0.1", "4.2 ± 0.1", "− 3.4 ± 0.4"], ["291", "0", "193.6 ± 0.3", "115.5 ± 1.5", "48.5 ± 0.4", "107.2 ± 0.7", "6.3 ± 0.3", "3.4 ± 0.9"], ["291", "0.2", "191.6 ± 0.1", "98.8 ± 0.8", "52.6 ± 0.2", "101.1 ± 0.7", "3.5 ± 0.2", "− 5.4 ± 0.8"]], "row_count": 12, "column_count": 8, "numeric_cells": 82, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34022944:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d2ec8d920e34dfba22637e23000a6aed44fb998b8b1871d8a77c522ee4c4b57c", "bytes": 557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#Tab2", "version": null, "note": "Summary of protein changes detected between sample groups in C. reinhardtii iTRAQ experiment", "structure": {"pmcid": "PMC8141184", "section_index": 5, "section_title": "Proteomic study in C. reinhardtii and C. nivalis", "row_count": 5, "column_count": 4}, "table": {"label": "Table 2", "caption": "Summary of protein changes detected between sample groups in C. reinhardtii iTRAQ experiment", "rows": [["Comparison", "Number of proteins changed", "Number of proteins increased", "Number of proteins decreased"], ["0 h and 11 h salt conditions", "171", "91", "80"], ["11 h and 18 h salt conditions", "217", "94", "123"], ["0 h and 18 h salt conditions", "212", "76", "136"], ["18 h control and 18 h salt conditions", "337", "113", "224"]], "row_count": 5, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34022944:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6a879397bb54be01c38598082e2c3dba07f6291cf1541cc2c29445b6d282a954", "bytes": 555, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#Tab3", "version": null, "note": "Summary of protein changes detected between sample groups in C. nivalis iTRAQ experiment", "structure": {"pmcid": "PMC8141184", "section_index": 5, "section_title": "Proteomic study in C. reinhardtii and C. nivalis", "row_count": 5, "column_count": 4}, "table": {"label": "Table 3", "caption": "Summary of protein changes detected between sample groups in C. nivalis iTRAQ experiment", "rows": [["Comparison", "Number of proteins changed", "Number of proteins increased", "Number of proteins decreased"], ["0 h and 80 h salt conditions", "143", "115", "28"], ["80 h and 168 h salt conditions", "22", "12", "10"], ["0 h and 168 h salt conditions", "155", "26", "129"], ["168 h control and 168 h salt conditions", "231", "43", "188"]], "row_count": 5, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[5]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:34022944:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a02f1973347649b36ea91d5a595b12e82c48ec59f7d77dd8a5c18f5f83b1b8af", "bytes": 11680, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[3]#Tab4", "version": null, "note": "Summary of protein changes in each strain during salt stress", "structure": {"pmcid": "PMC8141184", "section_index": 5, "section_title": "Proteomic study in C. reinhardtii and C. nivalis", "row_count": 74, "column_count": 11}, "table": {"label": "Table 4", "caption": "Summary of protein changes in each strain during salt stress", "rows": [["Protein accession ID", "Protein name", "Pathway/role", "Salt stress treatment comparisons with relative protein changes (values indicate fold change)"], ["", "", "", "C. reinhardtii", "C. nivalis"], ["", "", "", "0–11 h salt", "11–18 h salt", "0–18 h salt", "18 h control–18 h salt", "0–80 h salt", "80–168 h salt", "0–168 h salt", "168 h control–168 h salt"], ["Stress proteins"], ["A8HYV3/ Q39603", "Heat shock protein 70B", "Chloroplast localised heat shock protein protecting against photoinhibition [84]", "↑ 1.073", "→", "↑ 1.077", "→", "↓ -1.340", "→", "↓ -1.363", "↓ -1.708"], ["A8J3P5", "Heat shock protein 70E", "Cytosolic heat shock protein [84]", "→", "→", "→", "↓ -1.172", "→", "→", "→", "→"], ["A8JEU4", "Heat shock protein 70A", "Cytosolic heat shock protein [84]", "→", "→", "→", "→", "↓ -1.358", "→", "↓ -1.334", "↓ -1.880"], ["A8IZU0", "Heat shock protein 70C", "Mitochondrial heat shock protein [84]", "→", "→", "→", "→", "↓ -1.336", "→", "↓ -1.386", "↓ -1.731"], ["A8J1U1", "Heat shock protein 90A", "Cytosolic heat shock protein [85]", "→", "→", "→", "→", "→", "→", "↓ -1.189", "↓ -1.848"], ["Q66T67", "Heat shock protein 90C", "Chloroplastic heat shock protein [85]", "→", "→", "→", "→", "→", "→", "↓ -1.543", "↓ -1.868"], ["A8I7T1", "Heat shock protein 90B (Fragment)", "ER localised heat shock protein [86]", "→", "→", "→", "→", "→", "→", "→", "↓ -1.771"], ["Q1RS84", "Aldehyde-alcohol dehydrogenase", "Aldehyde scavenging (during lipid peroxidation) [42]", "↑ 1.134", "→", "↑ 1.106", "→", "→", "→", "→", "→"], ["A8JHR9/ A8JHS0/ P49644", "Glyceraldehyde-3-phosphate dehydrogenase", "Glycolysis (and carbohydrate metabolism)", "→", "↑ 1.155", "↑ 1.284", "→", "↑ 2.166", "→", "↑ 2.200", "→"], ["A8HXA6", "Glutathione reductase", "Reduction of glutathione disulphide [45]", "↓ -1.195", "↑ 1.201", "→", "→", "→", "↑ 1.277", "→", "→"], ["A8JG06", "Programmed cell death protein 6-interacting protein", "Protein self-association and ubiquitin binding", "→", "→", "→", "→", "→", "↑ 1.208", "→", "→"], ["A8J1C1", "Ubiquitin-activating enzyme E1", "Ubiquitin conjugation cascade", "↓ -1.088", "↑ 1.169", "→", "→", "→", "↑ 1.254", "↑ 1.198", "↑ 1.097"], ["A8J5Z8", "Aldehyde dehydrogenase", "Aldehyde detoxification, ROS scavenging, inhibits lipid peroxidation", "→", "↑ 1.180", "↑ 1.274", "↑ 1.271", "→", "→", "↑ 1.306", "→"], ["A8JB85", "Autophagy-related protein", "Autophagy", "↑ 1.385", "→", "↑ 1.274", "→", "→", "→", "↑ 1.352", "→"], ["A8J431", "Stress-related chlorophyll a/b binding protein 2", "Non-photochemical quenching, protect photosynthetic apparatus from photo-oxidative damage", "→", "→", "→", "↑ 1.776", "→", "→", "↑ 1.572", "→"], ["Photosynthesis proteins"], ["Q39588", "Carbonic anhydrase, alpha type", "Carbon dioxide fixation [87]", "→", "→", "↓ -1.202", "↓ -1.135", "→", "→", "→", "→"], ["Q8S567", "Chlorophyll a/b-binding protein", "Photosynthesis and light harvesting", "↓ -1.190", "→", "↓ -1.191", "→", "→", "→", "→", "→"], ["A8J270", "Chlorophyll a-b binding protein of LHCII", "Light harvesting in photosystem I", "→", "→", "→", "↑ 1.144", "→", "→", "→", "→"], ["Q8S3T9", "Chlorophyll a-b binding protein of LHCII", "Light harvesting in photosystem I", "→", "→", "→", "↑ 1.171", "→", "→", "→", "→"], ["A8HP84/ P50362", "Glyceraldehyde-3-phosphate dehydrogenase", "Photosynthesis, Calvin cycle", "→", "→", "→", "→", "↓ -1.529", "→", "↓ -1.682", "↓ -2.147"], ["Q75VY7", "Light-harvesting chlorophyll-a/b protein of photosystem I", "Chlorophyll binding, light harvesting in photosystem I", "↓ -1.240", "→", "→", "↓ -1.347", "→", "→", "→", "→"], ["A8ITV3", "Light-harvesting protein of photosystem I", "Chlorophyll binding, light harvesting in photosystem I", "↓ -1.190", "→", "↓ -1.191", "→", "→", "→", "→", "→"], ["Q93VE0", "Light-harvesting chlorophyll-a/b binding protein LhcII-4", "Chlorophyll binding, light harvesting in photosystem I", "→", "→", "→", "↑ 1.147", "→", "→", "→", "→"], ["A8J0B1", "Low-CO2-inducible protein", "Inorganic carbon uptake [52]", "↓ -1.161", "→", "→", "→", "→", "→", "→", "→"], ["A8J225", "Low-CO2-inducible protein (Fragment)", "Inorganic carbon uptake [52]", "↑ 1.285", "→", "↑ 1.240", "↑ 1.385", "→", "→", "→", "→"], ["Q75NZ1", "Low-CO2 inducible protein", "Inorganic carbon uptake [52]", "→", "↑ 1.067", "→", "→", "→", "→", "→", "→"], ["A8IT08", "Low-CO2-inducible chloroplast envelope protein", "L-orthinine transmembrane transport activity", "→", "→", "↑ 1.268", "↑ 1.390", "→", "→", "→", "→"], ["A8JEV1", "Oxygen evolving enhancer protein 3", "Photosynthetic electron transfer chain, calcium ion binding", "→", "↓ -1.150", "↓ -1.141", "↓ -1.226", "↓ -1.495", "→", "↓ -1.674", "→"], ["A8J0E4", "Oxygen-evolving enhancer protein 1 of photosystem II", "Photosystem II assembly and stability, oxygen evolving activity", "→", "↓ -1.094", "↓ -1.145", "↓ -1.290", "↓ -1.864", "→", "↓ -2.186", "↓ -2.300"], ["A8IYH9", "Oxygen-evolving enhancer protein 2 of photosystem II", "Photosynthesis, calcium ion binding", "→", "→", "↓ -1.136", "↓ -1.108", "↓ -1.520", "→", "↓ -1.626", "↓ -2.072"], ["P12852", "Oxygen-evolving enhancer protein 3, chloroplastic", "Photosynthesis, calcium ion binding", "→", "↓ -1.150", "↓ -1.141", "↓ -1.226", "↓ -1.495", "→", "↓ -1.674", "→"], ["Q00914", "Photosystem I iron-sulphur centre", "Photosynthetic electron transport in photosystem I", "→", "→", "→", "→", "↓ -1.672", "→", "↓ -1.932", "→"], ["P13352", "Photosystem I reaction centre subunit VI, chloroplastic", "Photosynthesis", "→", "→", "→", "→", "→", "→", "→", "↓ -2.285"], ["Q5NKW4", "Photosystem I reaction centre subunit II, 20 kDa", "Photosynthesis", "→", "↓ -1.177", "→", "→", "→", "→", "→", "→"], ["Q39615", "Photosystem I reaction centre subunit II, chloroplastic", "Photosynthesis", "→", "↓ -1.177", "→", "→", "→", "→", "→", "→"], ["P12154", "Photosystem I P700 chlorophyll a apoprotein A1", "Photosynthesis, electron transfer, chlorophyll binding", "→", "→", "↓ -1.261", "→", "↓ -1.823", "→", "↓ -1.864", "→"], ["P09144", "Photosystem I P700 chlorophyll a apoprotein A2", "Photosynthesis, electron transfer, chlorophyll binding", "→", "→", "↓ -1.200", "→", "↓ -1.643", "→", "↓ -1.614", "→"], ["P10898", "Photosystem II CP43 reaction centre protein", "Photosynthetic electron transport in photosystem II, chlorophyll binding", "→", "→", "→", "→", "↓ -1.623", "→", "↓ -1.824", "↓ -1.469"], ["P37255", "Photosystem II CP47 reaction centre protein", "Photosynthetic electron transport in photosystem II, chlorophyll binding", "→", "→", "→", "→", "↓ -1.583", "→", "↓ -1.693", "→"], ["P06007", "Photosystem II D2 protein", "Photosynthetic electron transport in photosystem II, chlorophyll binding", "→", "→", "→", "→", "↓ -1.611", "→", "↓ -1.634", "→"], ["P07753", "Photosystem II protein D1", "Photosynthetic electron transport in photosystem II, chlorophyll binding", "→", "→", "→", "→", "↓ -1.840", "→", "↓ -1.727", "↓ -1.445"], ["A8J4S1", "Photosystem I reaction centre subunit III", "Photosynthesis, protein domain specific binding", "→", "↓ -1.255", "↓ -1.289", "↓ -1.461", "→", "→", "→", "→"], ["P12356", "Photosystem I reaction centre subunit III, chloroplastic", "Photosynthesis, protein domain specific binding", "→", "↓ -1.255", "↓ -1.289", "↓ -1.461", "→", "→", "→", "→"], ["A8HVJ9", "Photosystem II stability/assembly factor HCF136 fragment", "Photosystem II biogenesis", "→", "→", "→", "↓ -1.190", "→", "→", "→", "→"], ["A8JGP9", "Ribulose bisphosphate carboxylase small chain", "Carbon fixation, photorespiration, photosynthesis", "↓ -1.213", "→", "↓ -1.356", "→", "→", "→", "→", "→"], ["P00873", "Ribulose bisphosphate carboxylase small chain 1, chloroplastic", "Carbon fixation, photorespiration, photosynthesis", "↓ -1.213", "→", "↓ -1.356", "→", "→", "→", "→", "→"], ["P08475", "Ribulose bisphosphate carboxylase small chain 2, chloroplastic", "Carbon fixation, photorespiration, photosynthesis", "↓ -1.219", "→", "↓ -1.357", "→", "→", "→", "→", "→"], ["P00877", "Ribulose bisphosphate carboxylase large chain", "Photorespiration, reductive pentose-phosphate cycle", "→", "↓ -1.078", "↓ -1.154", "↓ -1.110", "↓ -1.810", "→", "↓ -1.991", "↓ -2.751"], ["P23489", "Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic", "Photosynthesis regulation", "→", "↓ -1.107", "↓ -1.108", "↓ -1.186", "→", "→", "↓ -1.555", "↓ -2.809"], ["Q6SA05", "Rubisco activase", "Photosynthesis regulation", "→", "↓ -1.107", "↓ -1.108", "→", "→", "→", "↓ -1.555", "↓ -2.809"], ["Carbohydrate proteins"], ["Q2VA40", "Alpha-1,4 glucan phosphorylase", "Starch degradation [88]", "↑ 1.123", "↑ 1.105", "↑ 1.240", "↑ 1.122", "↑ 1.237", "↑ 1.158", "↑ 1.433", "↓ -1.688"], ["Q2VA41/ A8IYK1", "Alpha-1,4 glucan phosphorylase", "Starch degradation [88]", "↑ 1.096", "→", "↑ 1.147", "→", "→", "→", "→", "→"], ["A2PZC2", "UDP-glucose:protein transglucosylase", "Polysaccharide biosynthesis", "→", "→", "→", "→", "↓ -1.535", "→", "↓ -1.713", "↓ -2.510"], ["A8HW52", "Starch branching enzyme", "Starch biosynthesis", "→", "→", "→", "→", "→", "→", "→", "↓ -2.318"], ["A8IHX1", "Starch branching enzyme", "Starch biosynthesis", "→", "→", "↑ 1.207", "→", "→", "→", "→", "→"], ["A8J914", "UDP-glucose 6-dehydrogenase", "Starch catabolism for glycolysis [58]", "↑ 1.263", "↑ 1.239", "↑ 1.562", "↑ 1.478", "→", "→", "→", "→"], ["A2PZC3", "UDP-glucose 6-dehydrogenase", "Starch catabolism for glycolysis [58]", "↑ 1.298", "↑ 1.231", "↑ 1.595", "↑ 1.461", "→", "→", "→", "↑ 2.008"], ["Lipid proteins"], ["A8HNN4/ A0A0B5KTL4", "Glycerol-3-phosphate dehydrogenase", "Glycerol metabolism, link between carbohydrate and lipid metabolism", "↑ 1.675", "↑ 1.169", "↑ 1.959", "↑ 1.959", "↑ 2.135", "↑ 1.192", "↑ 2.544", "↑ 2.648"], ["A0A0B5KYA7", "Glycerol-3-phosphate dehydrogenase", "Glycerol metabolism, link between carbohydrate and lipid metabolism", "↑ 1.719", "↑ 1.179", "↑ 2.027", "↑ 2.064", "→", "→", "→", "→"], ["A8HNN6", "Glycerol-3-phosphate dehydrogenase (fragment)", "Glycerol metabolism, link between carbohydrate and lipid metabolism", "↑ 1.744", "↑ 1.189", "↑ 2.073", "↑ 2.109", "→", "→", "→", "→"], ["A8J6J6", "Acetyl-CoA acyltransferase", "Catabolic beta-oxidation of fatty acids [63]", "↑ 1.162", "→", "↑ 1.181", "↑ 1.209", "→", "→", "↑ 1.250", "↑ 1.375"], ["A8J2S0", "Citrate synthase", "Tricarboxylic acid cycle", "→", "→", "→", "→", "→", "→", "→", "↓ -2.725"], ["Q6DN05", "Betaine lipid synthase", "Betaine lipid synthesis, including DGTS synthesis", "→", "↓ -1.093", "→", "→", "→", "→", "→", "→"], ["A8HXT4", "Pyruvate carboxylase", "Pyruvate metabolism, gluconeogenesis, links carbohydrate and lipid metabolism", "→", "↓ -1.047", "↓ -1.100", "→", "→", "→", "→", "→"], ["A8JGF4", "Biotin carboxylase, acetyl-CoA carboxylase component", "Malonyl-CoA biosynthesis, lipid metabolism", "→", "→", "→", "↓ -1.113", "↓ -1.479", "→", "↓ -1.482", "↓ -1.860"], ["Q763T6", "UDP-sulfoquinovose synthase", "Glycerolipid metabolism, sulfoquinovosyl diacylglycerol (SQDG) metabolism", "→", "→", "→", "→", "↓ -1.275", "→", "↓ -1.289", "↓ -1.770"], ["A8J1T4", "Dihydrolipoyl dehydrogenase", "Acetyl CoA production, cell redox homeostasis", "→", "→", "→", "→", "↑ 1.110", "→", "→", "↑ 1.149"]], "row_count": 74, "column_count": 11, "numeric_cells": 285, "header_rows": 3, "locator": "section[5]/table-wrap[3]#Tab4"}}], "gaps": ["asset:data:geo:PXD018148 not downloaded", "asset:data:geo:PXD018148 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Proteins that were statistically different in abundance using ANOVA (p < 0.05) across the treatments are summarised in Tables 2 and 3 for C. reinhardtii and C. nivalis, respectively."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD018148"], "resolved_accessions": ["PXD018148"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [83] partner repository with the dataset identifier PXD018148."], "basis": "The paper names PXD018148 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:34022944", "data:geo:PXD018148", "asset:table:pmid:34022944:1", "asset:table:pmid:34022944:2", "asset:table:pmid:34022944:3", "asset:table:pmid:34022944:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD018148"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 61588, "completion_tokens": 978, "cached_tokens": 20744}}, "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:34022944", "type": "paper", "label": "pmid:34022944"}, {"id": "source:pmid:34022944", "type": "manuscript", "label": "PMID 34022944 full text"}, {"id": "data:geo:PXD018148", "type": "dataset", "label": "GEO PXD018148"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34022944", "type": "paper", "label": "pmid:34022944"}, {"id": "source:pmid:34022944", "type": "manuscript", "label": "PMID 34022944 full text"}, {"id": "data:geo:PXD018148", "type": "dataset", "label": "GEO PXD018148"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34022944", "type": "extraction", "used": ["source:pmid:34022944"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD018148", "type": "accession_resolution", "used": ["data:geo:PXD018148"], "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:34022944", "parent_hash": "sha256:7d5349e5f7cfb6c4ab2538fc4bb7977462716bd135dfb5f1d0fa3de1a22e1e8d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD018148 licence not read", "asset:data:geo:PXD018148 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Proteins that were statistically different in abundance using ANOVA (p < 0.05) across the treatments are summarised in Tables 2 and 3 for C. reinhardtii and C. nivalis, respectively."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:35:42+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}