← All .science files
pmid:30666240
Diallyl Disulfide From Garlic Oil Inhibits Pseudomonas aeruginosa Quorum Sensing Systems and Corresponding Virulence Factors.
Wen-Ru Li · Yong-Kai Ma · Xiao-Bao Xie · Qing-Shan Shi · Xia Wen · Ting-Li Sun · Hong Peng
Frontiers in microbiology · 2018 doi:10.3389/fmicb.2018.03222
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 7 items
claims array · 2 items
[0] object · 6 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[1] object · 6 fields
evidence array · 2 items
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 6 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 4 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
evidence object · 3 fields
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30666240", "kind": "science-record", "revision": 8, "content_hash": "sha256:d05791b54f5dabf36fa40360233879eb8cefd81f703fcfbc051fe83d12c9223a", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:43:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Diallyl Disulfide From Garlic Oil Inhibits Pseudomonas aeruginosa Quorum Sensing Systems and Corresponding Virulence Factors.", "doi": "10.3389/fmicb.2018.03222", "pmid": "30666240", "authors": ["Wen-Ru Li", "Yong-Kai Ma", "Xiao-Bao Xie", "Qing-Shan Shi", "Xia Wen", "Ting-Li Sun", "Hong Peng"], "journal": "Frontiers in microbiology", "year": 2018, "abstract": "Previously, we determined that diallyl disulfide (DADS) from garlic oil can inhibit Pseudomonas aeruginosa PAO1 pathogenic factors by inactivating the transcription of key genes from three quorum sensing (QS) systems (las, rhl, and pqs) based on the effects of DADS on growth, virulence factor production (elastase, pyocyanin, biofilm, and swarming motility), and RNA transcription (real-time q-PCR). To further investigate the mechanisms underlying the inhibition of the three P. aeruginosa QS systems by DADS, high-throughput RNA and proteome sequencing techniques were used to study differences in the transcriptional and proteome expression of P. aeruginosa PAO1 following treatment with DADS. The RNA-seq and proteomic data are available via NCBI Gene Expression Omnibus database with accession number GSE118801 and ProteomeXchange with identifier PXD011144, respectively. The experimental results indicated that all key genes of the three QS systems (las, rhl, and pqs) of P. aeruginosa PAO1 as well as the virulence factors (including exoprotease LasA, elastase LasB, lectin LecA and LecB, pyocyanin biosynthesis, and biofilm formation) regulated by these three QS systems were inhibited. This is consistent with our previous studies on the physiology, biochemistry, and RNA expression of P. aeruginosa treated with DADS. Additionally, our results also indicated that bacterial motility, chemotaxis, and two-component systems were inhibited by DADS treatment. All these changes abolish the sensitivity of P. aeruginosa PAO1 to environmental stimuli and cause the cells to be in a state of passivation. Further research is needed to determine how QS systems regulate these functions. Our findings could potentially contribute to the treatment and control of P. aeruginosa infection, virulence, and pathogenicity.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis of the two groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using Benjamini and Hochberg’s method for controlling the false discovery rate. The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30666240", "locator": "sections[8] \"Differential Expression Analysis and GO and KEGG Enrichment Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "Differential expression analysis of the two groups was performed using the DESeq R package (1.18.0)."}, {"asset": "source:pmid:30666240", "locator": "sections[8] \"Differential Expression Analysis and GO and KEGG Enrichment Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "The resulting P-values were adjusted using Benjamini and Hochberg’s method for controlling the false discovery rate."}, {"asset": "source:pmid:30666240", "locator": "sections[9] \"Accession Number\" paragraph 2", "quote": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30666240", "locator": "sections[9] \"Accession Number\" paragraph 2", "quote": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801."}, {"asset": "source:pmid:30666240", "locator": "sections[15] \"Accession Number\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144."}], "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:30666240"], "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:GSE118801"], "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:GSE118801"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30666240", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmicb.2018.03222", "sha256": "sha256:c7529d674e0cda98e1c4b18c360eefbfe64904eec814568d71cb7dae0dbb6573", "bytes": 42875, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmicb.2018.03222", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6330763", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE118801", "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=GSE118801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118801", "version": null, "note": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3347985", "GSM3347986", "GSM3347987", "GSM3347988", "GSM3347989", "GSM3347990"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "19430", "taxon": "Pseudomonas aeruginosa PAO1", "title": "Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and diallyl disulphide-treated P. aeruginosa PAO1 Transcriptomes", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD011144", "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=PXD011144", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD011144", "version": null, "note": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "iTRAQ dataset of Pseudomonas aeruginosa PAO1 following dially disulfide treatment", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE118801 not downloaded", "asset:data:geo:GSE118801 licence not read", "asset:data:geo:PXD011144 not downloaded", "asset:data:geo:PXD011144 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Differential expression analysis of the two groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using Benjamini and Hochberg’s method for controlling the false discovery rate. The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801."}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "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": ["GSE118801", "PXD011144"], "resolved_accessions": ["GSE118801", "PXD011144"], "statements": ["The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011144."], "basis": "The paper names GSE118801, PXD011144 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30666240", "data:geo:GSE118801"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE118801"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:28Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "reordered"}, "calls": 3, "usage": {"prompt_tokens": 34185, "completion_tokens": 1345, "cached_tokens": 656}}, "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:30666240", "type": "paper", "label": "pmid:30666240"}, {"id": "source:pmid:30666240", "type": "manuscript", "label": "PMID 30666240 full text"}, {"id": "data:geo:GSE118801", "type": "dataset", "label": "GEO GSE118801"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30666240", "type": "paper", "label": "pmid:30666240"}, {"id": "source:pmid:30666240", "type": "manuscript", "label": "PMID 30666240 full text"}, {"id": "data:geo:GSE118801", "type": "dataset", "label": "GEO GSE118801"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30666240", "type": "extraction", "used": ["source:pmid:30666240"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE118801", "type": "accession_resolution", "used": ["data:geo:GSE118801"], "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:30666240", "parent_hash": "sha256:bb5580e666a1623e389d86b0dc82098fb01e1929894b68d01075d41b2a8dc57b", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE118801 licence not read", "asset:data:geo:GSE118801 not downloaded", "asset:data:geo:PXD011144 licence not read", "asset:data:geo:PXD011144 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nosa PAO1 following treatment with DADS. The RNA-seq and proteomic data are available via NCBI Ge", "aeruginosa PAO1 vs. control groups based on RNA-seq analysis.Click here for additional data file"], "order_basis": "paper_text_order:783", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differential expression analysis of the two groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using Benjamini and Hochberg’s method for controlling the false discovery rate. The RNA-seq datasets are available at the NCBI Gene Expression Omnibus (GEO) database under accession number GSE118801."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}