Difference between revisions of "Molecule"
Line 11: | Line 11: | ||
** monomers or very small oligomers of nucleic acids, proteins, and polysaccharides | ** monomers or very small oligomers of nucleic acids, proteins, and polysaccharides | ||
** "Large collections of small molecules (molecular weight about 600 or less), of similar or diverse nature which are used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, or other chemical interactions." (from [http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?mode=&index=24714&field=all&HM=&II=&PA=&form=&input= nlm.nih.gov] and [http://en.wikipedia.org/wiki/Small_molecule wikipedia]) | ** "Large collections of small molecules (molecular weight about 600 or less), of similar or diverse nature which are used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, or other chemical interactions." (from [http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?mode=&index=24714&field=all&HM=&II=&PA=&form=&input= nlm.nih.gov] and [http://en.wikipedia.org/wiki/Small_molecule wikipedia]) | ||
+ | |||
+ | ==Model changes== | ||
+ | ===Changes for WS250/1=== | ||
+ | ?Molecule Name ?Text | ||
+ | Public_name ?Text | ||
+ | Formula | ||
+ | Monoisotopic_mass | ||
+ | IUPAC | ||
+ | SMILES | ||
+ | InChi | ||
+ | Synonym ?Text | ||
+ | DB_info Database ?Database ?Database_field ?Text | ||
+ | Status Detected #Evidence | ||
+ | Predicted #Evidence | ||
+ | Range UNIQUE Int UNIQUE Int #Evidence | ||
+ | Class Carbohydrate | ||
+ | Sugar | ||
+ | Polysaccharide | ||
+ | Lipid | ||
+ | Protein | ||
+ | Amino_acid | ||
+ | Nucleic_acid | ||
+ | Toxin | ||
+ | Source Endogenous ?Species #Evidence | ||
+ | Exogenous | ||
+ | Pharmaceutical | ||
+ | Receptor ?Gene | ||
+ | ?Molecule | ||
+ | ?Protein | ||
+ | Pathway Database ?Database ?Database_field ?Text //for importing KEGG pathways | ||
+ | Role Essential | ||
+ | Nonessential | ||
+ | Metabolite | ||
+ | Regulatory | ||
+ | Structural | ||
+ | Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule | ||
+ | WBProcess ?WBProcess XREF Molecule | ||
+ | Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence | ||
+ | Strain ?Strain ?Phenotype #Evidence | ||
+ | Transgene ?Transgene ?Phenotype #Evidence | ||
+ | RNAi ?RNAi ?Phenotype #Evidence | ||
+ | Rearrangement ?Rearrangement ?Phenotype #Evidence | ||
+ | Interaction ?Interaction XREF Molecule_interactor | ||
+ | Molecule_use ?Text #Evidence | ||
+ | Reference ?Paper XREF Molecule | ||
+ | Remark ?Text #Evidence | ||
==Approved model== | ==Approved model== |
Revision as of 15:55, 18 June 2015
links to relevant pages
Caltech documentation
Example molecule pages
Contents
Molecule Curation
Molecule curation captures chemical and drug entities that have been shown to effect the biology of the worm. We provide links to other databases that deal with these molecule entities in greater detail.
- What we mean by small molecule
- drug
- metabolite (primary and secondary)
- monomers or very small oligomers of nucleic acids, proteins, and polysaccharides
- "Large collections of small molecules (molecular weight about 600 or less), of similar or diverse nature which are used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, or other chemical interactions." (from nlm.nih.gov and wikipedia)
Model changes
Changes for WS250/1
?Molecule Name ?Text Public_name ?Text Formula Monoisotopic_mass IUPAC SMILES InChi Synonym ?Text DB_info Database ?Database ?Database_field ?Text Status Detected #Evidence Predicted #Evidence Range UNIQUE Int UNIQUE Int #Evidence Class Carbohydrate Sugar Polysaccharide Lipid Protein Amino_acid Nucleic_acid Toxin Source Endogenous ?Species #Evidence Exogenous Pharmaceutical Receptor ?Gene ?Molecule ?Protein Pathway Database ?Database ?Database_field ?Text //for importing KEGG pathways Role Essential Nonessential Metabolite Regulatory Structural Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule WBProcess ?WBProcess XREF Molecule Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Rearrangement ?Rearrangement ?Phenotype #Evidence Interaction ?Interaction XREF Molecule_interactor Molecule_use ?Text #Evidence Reference ?Paper XREF Molecule Remark ?Text #Evidence
Approved model
///////////////////////////small molecule/chemical/drug //////////////////////////// // // ?Molecule // * metabolites: precursors, intermediates, or end products of a metabolic pathway // * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats?? // * chemicals/drugs // * minerals, ions, salts // //////////////////////////////////////////////////////////////////////////////////// ?Molecule Name ?Text Public_name ?Text Synonym ?Text DB_info Database ?Database ?Database_field Text Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Wen WS228 WBProcess ?WBProcess XREF Molecule Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad] Interaction ?Interaction XREF Molecule_regulator Molecule_use ?Text #Evidence Reference ?Paper XREF Molecule Remark ?Text #Evidence ///////////////////////////////////////////////////////////////////////////////////
Corresponding changes in touched models
///// ?Phenotype_info Affected_by Molecule ?Molecule #Evidence /////
///// ?Gene_regulation Regulator Molecule_regulator ?Molecule XREF Gene_regulator #Boolean /////
Model elements
- Name-> WBMol:ID
- originally, this field contained the MeSH ID, when no MeSH ID was available, a WBMol ID was assigned, which was supposed to be replaced by the MeSH ID when available. Unfortunately, Names are scripted to be used in URL constructions for MeSH and CTD database links resulting in WBMol_id name based URLs would have to be suppressed or, result in bad URLs. Also, the increased use of Molecule annotation in other curation pipelines resulted in confusion with object creation. These points of confusion prompted a move to change the Name field change from MeSH default IDs to WBMol IDs for all objects.
- Public name -> common name in elegans literature
- Synonym -> other names used in papers, case sensitivity. Many other names can be taken in from CTD pages. Other names need to be pipe separated
- DB_info -> links to entity in other database. Database URLs need to be added to github external URL file.
Molecule curation
Drug-phenotype curation
Molecules will be linked to genes based on their influence on gene activity altered by variation, overexpression, and RNAi-based knockdown.
Drug-gene interactions
Molecules will also be linked to genes through their influence on gene activity directly through gene regulation interactions.
Molecule databases
Molecule IDs will be provided, when available, for the following databases:
- Database "NLM_MeSH" "UID"
- Database "CTD" "ChemicalID"
- Database "ChemIDplus" using the CasRN
- Database "ChEBI" "CHEBI_ID"
- Database "KEGG COMPOUND" "ACCESSION_NUMBER"
- Database "SMID-DB"
--kjy 20:03, 16 December 2011 (UTC)
syncing with ChEBI
--kjy (talk) 20:21, 30 April 2014 (UTC) Script identifies any molecule in the mop tables with no mop_chebi id but has been used in curation through paper tables of either mop, app, grg, pro, or rna tables.
/home/acedb/karen/molecule/chebi_missing/find_missing_chebi_in_other_oa.pl checks molecule entries without chebi that have data for any of : app_molecule grg_moleculeregulator pro_molecule rna_molecule mop_paper print out mop_publicname mop_molecule mop_chemi mop_paper mop_smmid as well as corresponding papers from other OAs. aggregate all papers for a given molecule objects, convert to PMID if pmid exists. Output at file 'out' output looks like this: WBMol:00000139 Oxamniquine mop 139 mop_chemi 21738-42-1 mop_molecule D010073 mop_paper "WBPaper00038322","WBPaper00031181" aggregatedWBPapers WBPaper00031181, WBPaper00038322 aggregatedWBPmids pmid17988075, pmid21500322 WBMol:00000155 icariin mop 155 mop_chemi 489-32-7 mop_molecule C056599 mop_paper "WBPaper00040566" aggregatedWBPapers WBPaper00040566 aggregatedWBPmids pmid22216122
ChEBI terms and IDs are pulled from the chebi.obo on the ChEBI ftp server. This file is updated monthly (first Monday of the month except in the case of a Bank Holiday when it becomes the Tuesday). The ChEBI website is updated daily.
Molecule OA
For entering, editing, and storing information about molecule objects.
on tazendra or mangolassi:
~postgres/public_html/cgi-bin/oa/wormOA.pm
&initWormFields is like a switch to load a specific OA, each of them has a 3 letter code that corresponds to the postgres table name. so 'mop' is for the molecule oa and the 'mop_'
s in postgres mop then calls &initWormMopFields.currently around line 1200 there are sets of hashes like :
$fields{mop}{id}{type} = 'text'; $fields{mop}{id}{label} = 'pgid'; $fields{mop}{id}{tab} = 'all'; $fields{mop}{paper}{type} = 'multiontology'; $fields{mop}{paper}{label} = 'WBPaper'; $fields{mop}{paper}{tab} = 'all'; $fields{mop}{paper}{ontology_type} = 'WBPaper'; $fields{mop}{name}{type} = 'text'; $fields{mop}{name}{label} = 'Name'; $fields{mop}{name}{tab} = 'all';
most of these correspond to a postgres table. the first one is the
exception, which is the pgid. so excluding that in the example above,
there are 2 postgres tables, mop_paper and mop_name
- {type} is the type of data they hold
- text
- bigtext
- ontology
- dropdown
- toggle
- multiontology
- multidropdown
- {label} is the field name in the OA
- {tab} is which tab number it should show in. 'all' shows up in
all tabs, but is mostly used in OAs with no numbered tabs
- {ontology_type} if {type} is ontology / multiontology, ontology_type
refers to the type of values that go there for the autocomplete and validation.
- {ontology_table} if the type is ontology / multiontology
$fields{mop}{chebi}{type} = 'ontology'; $fields{mop}{chebi}{label} = 'ChEBI_ID'; $fields{mop}{chebi}{tab} = 'all'; $fields{mop}{chebi}{ontology_type} = 'obo'; $fields{mop}{chebi}{ontology_table} = 'chebi';
which corresponds to the obo_ tables that are updates via cronjob or populated just once. in this case mapping to obo_<name|data|syn>_chebi
- {dropdown_type} if the {type} is dropdown, which refers to the type of data like the {ontology_type}, but the values are hardcoded further down in the code instead of stored in postgres for querying.
mop_tables
Model tag | table | type | OA label | tab | ontology_type | ontology_table | cross table population script | comment |
pgonly | mop_id | not a table | pgid | all* | - | - | - | WBMol: $molId = &pad8Zeros($newPgid) |
pgonly | mop_timestamp | not a table | none | - | - | - | - | |
pgonly | mop_curator | dropdown | Curator | all | - | - | - | same values in all OA curation tables |
Name | mop_name | text | Name | all | - | - | - | WBMolID -added after tables were built |
Public_name | mop_publicname | bigtext | Public_name | all | - | - | - | |
Synonym | mop_synonym | bigtext | Synonyms | all | - | - | - | |
DB_info | mop_molecule | text | MeSH / CTD or default | all | - | - | - | use MeSh ID here originally used as Name |
DB_info | mop_chemi | text | CasRN | all | - | - | - | |
DB_info | mop_chebi | ontology | ChEBI_id | all | obo | chebi | downloaded from ChEBI server, which is updated monthly, ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo | |
DB_info | mop_kegg | text | Kegg compound (Acc#) | all | - | - | - | |
Remark | mop_remark | bigtext | Remark | all | - | - | - | |
Reference | mop_paper | multiontology | WBPaper | all | WBPaper | pap_tables | - | |
Molecule_use | mop_moleculeuse | bigtext | Molecule use | all | - | - | - | |
Not in model | mop_gotarget | multiontology | GO target | all | obo | goid | - | |
Not in model | mop_genetarget | multiontology | Gene target | all | WBGene | gin_tables | - | |
DB_info | mop_smmid | text | SMID-DB | all | - | - | - | |
Gene_regulation | grg_moleculeregulator | multiontology | Molecule Regulator | GENEREG tab3 | Molecule | mop_tables | - | |
WBProcess | pro_molecule | multiontology | Molecule | PROCESS tab1 | Molecule | mop_tables | - | |
Phenotype | app_molecule | multiontology | Molecule | PHENOTYPE tab2 | Molecule | mop_tables | - | |
RNAi | rna_molecule | multiontology | Molecule | RNAi tab2 | Molecule | mop_ tables | - | |
Interaction | int_moleculenondir int_moleculeone int_moleculetwo |
Molecule | Effected molecule Affected molecule Nondirectional molecule |
INTERACTION tab3 | Molecule | mop_tables | - | Molecule were initially curated through a/effected_other fields and stored as text in a field in tab4. |
- "all" can mean all tabs, but also is used for OA's that only have one tab.
Molecule list
Molecule names have changed to WBMoleculeIDs
Initially, we will be using MeSH UIDs, assigned by the NLM, as IDs for the molecules in our database. Due to the more comprehensive coverage of the NLM molecules, and the fact that it is more stably funded, this source was thought to be a good starting point for this project. The list we are starting with has been pared down and was created by the Comparative Toxicogenomic Database (CTD), which contains over 130,000 terms. For each term, this list contains a term name, CTD ID, MeSH UID, and where available CAS Registry Numbers. Using the CasRNs, we extracted the ChEBI ID from the Chemical Entities of Biological Interest database entity list, where it existed, along with any KEGG Compound accession number.
A sample molecule.ace record:
Molecule : "C009687" Public_name "wortmannin" Database "NLM_MeSH" "UID" "C009687" Database "CTD" "ChemicalID" "C009687" Database "ChemIDplus" "19545-26-7" Database "ChEBI" "CHEBI_ID" "52289" Database "KEGG COMPOUND" "ACCESSION_NUMBER" "C15181"
To make a working list of reference molecules for the various curation efforts, we used Textpresso to scan for all terms on the list that have been published in the C. elegans corpus. The resulting list is less than 6000 terms. The terms that have been identified in the corpus and available
based on frequency in corpus and
concatenated into one file
This last file is being used as a starting file for molecule look-up by WB curators.
Caveats and notes:
- The list is now small enough that if we wanted to load it into WB at least we know that every term has some relevance to the literature (although unverified).
- The list is small enough to be amenable to editing through ontology editors like OBOedit (even though it is not an ontology).
- We do not have definitions of the terms, nor are the terms arranged in any hierarchical manner; however other databases do, and we provide links to those websites if an ID is available.
- Terms and synonyms of terms, will be added as needed, this curation effort still needs to be worked out, ideally the list will be incorporated as a selection list for whatever curation tool a curator is using.
Molecule Curation Pipeline
Molecule upload
- Molecule.ace made from karen/Molecule/dump_molecule_ace.pl
- Database info for the chemical/small molecule database links needs to be manually edited on github in the external_urls file whenever there are changes to the databases associated with molecule data.
During each upload a molecule.ace file will be made in citace by Wen. This file will contain all the molecule cross references from within the RNAi and Variation Phenotype curation, merging them with the molecule data from the molecule list.
Papers flagged for chemical/molecule curation
WBPaperID | Comment |
461 | tetramisole |
464 | Yes |
484 | Yes |
493 | enhanced sensitivity of flu-2 mutants to EMS |
536 | pharmacological analysis of cell function (spermatozoan motility) not gene function |
1001 | Vanadate, AMP-PNP, ATP-gamma-S. NEM, Triton X-100, Taxol, analysis on unknown motor protein |
1010 | |
1524 | forskolin, NaF, AlCl3, GTPgammaS, GppNHp, GDPbetaS, pertussis toxin, cholera toxin |
2029 | campthothecin, berenil, trypanocidal drug, magnesium ion on DNA relaxation, and isolated topoisomerase, no gene product mentioned |
2116 | |
3137 | sodium arsenite, mercuric choride |
3150 | ouabain |
13430 | hematin, benzimidazole, Albendazole Diethylcarbamazine Fenbendazole Hematin Imidazole Ivermectin Levamisole Mebendazole Methimazole Morantel tartrate Oxibendazole Piperazine Pyrantel tartrate Thiabendazole: only tested in vitro on H. contortus GST activity. |
24940 | aldicarb |
24950 | diacetyl |
25017 | fig 4 |
25173 | Fig 5, Fig 7. |
28357 | yes |
28562 | octopamine |
28879 | serotonin |
28900 | fig.3 |
29114 | yes |
29130 | fig.3, fig.4 |
30726 | isoamyl alcohol |
30928 | fig.2 d) Exogenous serotonin and fluoxetine suppress 100G-induced DAF- 16TGFP nuclear accumulation. |
31225 | yes |
31321 | Figure 3. High NaCl accelerates aging of C. elegans |
31336 | nitrogen mustard |
31342 | yes |
31419 | yes |
31424 | fig.7 |
31427 | vitamin E |
31428 | yes |
31456 | tunicamycin |
31464 | yes |
31468 | fig.3 |
31474 | yes |
31482 | FUDR |
31483 | mPyrazine |
31490 | yes |
31509 | yes |
31530 | yes |
31535 | yes |
31571 | yes |
31593 | yes |
31604 | nicotine |
31626 | yes |
31627 | yes |
31644 | yes |
31657 | yes |
31667 | yes |
31669 | ethanol |
31672 | yes |
31682 | yes |
31683 | yes |
31690 | yes |
31694 | yes |
31703 | haem |
31810 | yes |
31824 | yes |
31834 | yes |
31850 | fluorathene |
31857 | yes |
31866 | yes |
31871 | DHP |
31872 | aldicarb |
31873 | arsenite |
31882 | 8-Br-cGMP |
31895 | Figure 4. Responses of wild-type (N2) and slo-1 mutant worms to aldicarb and levamisole |
31897 | fig.4 |
31915 | yes |
31924 | yes |
31939 | table 2 |
31941 | paraquat |
31959 | yes |
31977 | imipramine |
31982 | glutamate |
31991 | Flavone (2-phenyl chromone) |
31992 | NaCl |
31994 | arsenite |
31996 | fig.1 |
31999 | diltiazem |
32000 | arecoline |
32007 | levamisole |
32008 | aldicarb |
32011 | aldicarb |
32031 | NaCl |
32033 | yes |
32035 | yes |
32050 | yes |
32072 | amiloride |
32077 | C17ISO |
32079 | Dextran-HCC |
32093 | Quercetin |
32101 | cadmium, chlorpyrifos, nickel, prochloraz, diuron |
32103 | yes |
32125 | imidacloprid, thiacloprid |
32131 | yes |
32142 | phosphine, FCCP (carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone), PCP (2,3,4,5,6pentachlorophenol), DNP (2,4-dinitrophenol), sodium azide |
32143 | yes |
32181 | Table S2. Activity of the ascarosides in Daf-c and Daf-d strain backgrounds in the dauer formation assay |
32192 | tunicamycin |
32207 | 1NA-PP1 |
32215 | butanone, benzaldehyde |
32232 | paraquat |
32237 | paraquat |
32241 | paraquat |
32243 | ceramide |
32252 | aldicarb |
32255 | H2O2 |
32259 | 3-methyladenine |
32266 | metaboilte DA dafachronic acid, steroids |
32271 | ethanol aldicarb |
32286 | root exudate |
32295 | Ethosuximide |
32319 | NaCl and isoamyl alcohol (chemoattractants). |
32335 | serotonin |
32336 | benzaldehyde |
32358 | aldicarb |
32359 | ivermectin |
32366 | levamisole, nicotine |
32390 | flavonoid quercetin |
32427 | volatile anesthetic, halothane |
32429 | 1-octanol |
32470 | Species specificity of dauer pheromone extracts between elegans and Pristionchus. Response of Pristionchus and Strongyloides to different dafachronic acids. |
32475 | mianserin methiothepin |
32478 | levamisole |
32491 | amino acids |
32494 | AgNO3, CdCl2,CrCl2, CoCl2, CuSO4, HgCl2, MnCl2, NiSO4, Pb(NO3)2,and ZnCl2 |
32508 | chlorpyrifos oxon; cadmium chloride); hexachlorophene; neurotoxicants; chlorpyrifos, methyl mercury, chlordiazepoxide, tebuconazol; Cocaine; metals, ethanol, solvents, organophosphate; carbamate pesticides |
32517 | Fig 1.The structures of the dauer pheromone components, ascaroside C6 (1), ascaroside C9 (2), ascaroside C3 (3), and the less active ascaroside C7 (4). Fig 2. The chemical structures of the long-chain ascarosides from conditioned medium extracts from long-term dhs-28 cultures. The structural assignment of long-chain ascaroside 17 is tentative |
32522 | Sulfonamide CA inhibitors (CAIs) such as acetazolamide AZA, methazolamide MZA or ethoxzolamide EZA, many new sulfonamides (such as GUZ |
32878 | NaN3, benzaldehyde |
32880 | hydrogen peroxide |
32881 | 5-HT; Octanol, DiD |
32884 | paraquat, juglone |
32886 | dafachronic acids; Supp. New compounds reported in this study are: III, S-III, S-V, S-XV, S-XVI, S-XXII, XXIII, S-XXIII, XXIV, XXVII. |
32887 | |
32888 | dichlorvos,an organophosphorus insecticide, acetylcholinesterase, cadmium chloride |
32889 | sulfonamides; CAIs; 2-(hydrazinocarbonyl)-3-substituted-phenyl-1H-indole-5-sulfonamides possessing various 2-,3- or 4-substituted phenyl groups with methyl-, halogeno- and methoxy-functionalities, as well as the perfluorophenyl moiety; AZA and EZA |
32901 | CO2 |
32903 | paraquat |
32918 | Thus, (25R)-D7-dafachronic acid (2a) is one order of magnitude more active than (25R)-D4-dafachronic acid (1a). Similar to a previous study,5 little or no activity was detected with (25R)-cholestenoic acid (3a) |
32925 | cycloheximide |
32932 | resveratrol peptone |
32949 | Paraquat, tunicamycin |
32956 | These chemicals used on Pratylenchus penetrans: Acetic acid Propionic acid Isobutyric acid n-Butyric acid Isovaleric acid n-Valeric acid n-Caproic acid These chemicals used on C. elegans Acetic acid n-Caproic acid |
32958 | Fe-exposure |
32968 | tetramisole |
32989 | The levels of superoxide radical (.0^2-), in both mitochondria and cytosol, are increased in sod-1(tm776) and sod-1(tm783) mutants. |
32997 | dauer pheromone |
33002 | aldicarb levamisole |
33004 | electrically evoked and light evoked pharyngeal cholinergic post synaptic potentials reduced in amplitude by nicotinic antagonists benzoquinonium chloride and d-tubocurarine. Effect dose dependent. |
33009 | checked |
33024 | chloramine-T (CHT), DTT, H^20^2: tested for effects on both KVS-1 activity in vitro and on chemotaxis in vivo. |
33037 | dauer pheromone; 8-bromo-cGMP |
33040 | paraquat, excess O^2 |
33049 | Carbamate, Aldicarb, Carbofuran, Oxamyl, Neostigmine, Eserine, Organophosphates, Fenomiphos, Ethoprop, Parathion, Paraoxon, Phorate, Terbufos, meta-chlorperbenzoic acid, m-CPBA, diotioate |
33051 | identification of new daf-22 dependent dauer pheromone and mating pheromones ascr#7, ascr#8, and ascr#6.1 |
33060 | green tea polyphenol epigallocatechin gallate (EGCG) - |
33077 | flavopiridol olomoucine II |
33086 | hyperosmotic, sodium chloride, anoxia |
33094 | PMA induces the pnlp-29::gfp transgene |
33099 | dichlorvos fenamiphos organophosphates organophosphorous pesticides, neurotoxicant, mefloquine, |
33115 | low oxygen, lactacystn |
33126 | tunicamycin, glucose, deoxyglucose, sorbitol, glucose analog |
33130 | D-ribose affect larval growth |
33158 | Yes. Response to Diacetyl. |
33162 | The uncoupler CCCP (carbonylcyanide- 3-chlorophenylhydrazone) extends lifespan. |
33166 | dietary zinc |
33168 | Antipsychotic drugs, cyclosporin A |
33189 | Iron, PQS, PQS+Fe3 |
33433 | copper |
33441 | Pb, Hg, Cd, and Cr metals CdCl2, CrCl2, HgCl2, and Pb(NO3)2 in solution were used here: 2.5M, 50M, and 100M. |
33448 | Catechin Hydrogen peroxide catechin hydrate |
33456 | 8-bromo cGMP, paraquat, vinpocetine, zaprinast, EHNA (erythro-9-[2-hydroxy-3-nonyl] adenine) |
34686 | CdCl2, CrCl2, HgCl2, Pb(NO3)2 |
34687 | Screened ~54,000 chemicals from various libraries: Bioactives, natural product extracts, Analyticon purified natural product compounds, Diversity-oriented synthesis, ChemBridge kinases, ChemDiv, TimTec, MayBridge, ChemBridge. note: screened on glp-4(bn2);sek-1(km4) mutant worms Anti-infective hits that cure C. elegans of an E. faecalis infection at a concentration lower than the in vitro MIC with E. faecalis are grouped into 6 structural classes (representative structures shown). |
34688 | Bis-[4-methoxy-3- [3-(4-fluorophenyl)-6-(4-methylphenyl)-2(aryl)-tetrahydro-2Hpyrazolo[ 3,4-d]thiazol-5-yl]phenyl]methanes nematicidal activity |
34706 | Exposure to examined metals caused severe lethality toxicities in L1- and L2-larvae... |
34717 | fig 1, 40um juglone caused a significant increase in lifespan |
34757 | juglone, paraquat |
34758 | Rotenone, paraquat |
34766 | Cry5B toxin |
35074 | tribendimidine, levamisole, pyrantel |
35082 | drugs: muscimol and serotonin |
35083 | myxothiazol, FCCP |
35098 | Rib1P, 2-deoxy-a-d-ribose 1-phosphate (dRib1P), uridine, UMP, UDP, UTP, ATP, 2-deoxyuridine, 5-FU, 5dFUR, orotidine 5¢-phosphate, PPRP and 5-FU |
35114 | Pcm-1 mutant dauer larvae exposed to juglone develop into adults with a defect in egg-laying (Egl). Pcm-1 mutant eggs exposed to the oxidizing agents paraquat, homocysteine, and homocysteine thiolactone undergo a developmental delay more pronounced than that observed in wild-type animals. Pcm-1 mutant eggs exposed to homocysteine develop in to adults with a defect in egg-laying. |
35522 | 2-nonanone |