The DOI matches its Crossref record; 126 of the 179 references it cites were found in a registry or an index, and 48 are not checked yet; none of the 109 sources its claims cite is checked for support yet.
The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome
Open accessAbstract
Metazoan genomes contain large numbers of genes that participate in responses to environmental stressors. We surveyed the sea urchin Strongylocentrotus purpuratus genome for homologs of gene families thought to protect against chemical stressors; these genes collectively comprise the 'chemical defensome.' Chemical defense genes include cytochromes P450 and other oxidases, various conjugating enzymes, ATP-dependent efflux transporters, oxidative detoxification proteins, and transcription factors that regulate these genes. Together such genes account for more than 400 genes in the sea urchin genome. The transcription factors include homologs of the aryl hydrocarbon receptor, hypoxia-inducible factor, nuclear factor erythroid-derived 2, heat shock factor, and nuclear hormone receptors, which regulate stress-response genes in vertebrates. Some defense gene families, including the ABCC, the UGT, and the CYP families, have undergone expansion in the urchin relative to other deuterostome genomes, whereas the stress sensor gene families do not show such expansion. More than half of the defense genes are expressed during embryonic or larval life stages, indicating their importance during development. This genome-wide survey of chemical defense genes in the sea urchin reveals evolutionary conservation of this network combined with lineage-specific diversification that together suggest the importance of these chemical stress sensing and response mechanisms in early deuterostomes. These results should facilitate future studies on the evolution of chemical defense gene networks and the role of these networks in protecting embryos from chemical stress during development.
Checked 2026-10-06 · 48 references not checked yet
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The S. purpuratus genome includes a single predicted CNC-bZIP gene, designated Sp-Cnc (SPU_011174; Table 1).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative stress-responsive transcription factors
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The two HIF genes resemble vertebrate paralogs HIF-1α (HIF1A) and HIF-2α (EPAS1).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Receptors and signal transduction
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Some defense gene families, including the ABCC, the UGT, and the CYP families, have undergone expansion in the urchin relative to other deuterostome genomes”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In phylogenetic analyses (Fig. 2), Sp-Cnc occurs basal to the four human CNC-bZIP genes”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative stress-responsive transcription factors
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“AHR and HIF1α appear to have been duplicated in sea urchin, because single forms occur in protostomes and Ciona”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Receptors and signal transduction
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Together such genes account for more than 400 genes in the sea urchin genome.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“whereas the stress sensor gene families do not show such expansion.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“More than half of the defense genes are expressed during embryonic or larval life stages”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We have been unable to find a homolog of either human BACH gene in the current urchin assembly.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative stress-responsive transcription factors
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes- Rests on an assumption: The current sea urchin genome assembly and EST libraries are complete enough that failure to detect a homolog indicates its absence.
In the paper
“The main xenobiotic efflux in early embryos is an MK-571 sensitive MRP-like efflux activity (Hamdoun et al., 2004)”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
What the sources say
- Not checked yetcites Hamdoun et al., 2004 source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- It may state two separate claims as one. 90
- Probably not a substantial claim. 41
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sea urchin genome contains at least 14 predicted PAS genes representing 12 of the 14 known metazoan PAS subfamilies”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Receptors and signal transduction
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One of the AHR genes (Sp-Ahr) is most closely related to vertebrate AHRs, while the other (Sp-Ahrl/Sp-AHR-like) is a partial gene sequence that is more closely related to the Drosophila AHR homolog spineless (ss).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Receptors and signal transduction
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“One large Maf gene (Sp-Maf, SPU_025888) and one small Maf gene ( Sp-Mafs, SPU_030167) have been reported in urchin (Coolen et al., 2005) (Table 1); both possess the conserved extended homology region (EHR) and bZIP domains that characterize vertebrate Maf proteins.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative stress-responsive transcription factors
What the sources say
- Not checked yetcites Coolen et al., 2005
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The transcription factors include homologs of the aryl hydrocarbon receptor, hypoxia-inducible factor, nuclear factor erythroid-derived 2, heat shock factor, and nuclear hormone receptors”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The other three NR1H-like genes form a monophyletic group that may represent a new subfamily within the NR1 family”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“All of the complete CYP3-like sea urchin genes contain 12-13 exons, remarkably similar to the 12-13 exons in tunicate and vertebrate CYP3 genes, and distinctly different from the 1-6 exons in insect CYP6 and CYP9 genes.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sea urchin genome contains 16 FMO genes, divided among 4 of the 5 families of FMOs, FMO1, 2, 3, and 5, with the majority most closely related to FMO5.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Flavoprotein monooxygenases
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Eleven CYP1-like genes are present in the urchin genome, more than twice the five CYP1s in C. intestinalis or the 3-4 CYP1s in most vertebrates.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sea urchin genome contains 30 OATP genes, mostly (60%) members of the OATP4 subfamily.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Ion transporters
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One ABCC gene, Sp-ABCC9A, has been cloned from sea urchin eggs and encodes a protein of 1519 amino acids (SPU_025903; 33 exons spanning 24 kb of genomic DNA).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A second ABC gene cloned from eggs is Sp-ABCB1 (SPU_001752, 27 exons spanning 32 kb of genomic DNA).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Other stress-sensing genes present in the urchin genome include single homologs of the metal-responsive transcription factor MTF1 (Sp-Mtf, SPU_016490), and the heat shock factor HSF1 (Sp-Hsf, SPU_013409).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sea urchins have 65 ABC genes organized into 8 subfamilies (Supplemental Figs.S3-S9, Table S2) including the three multidrug transporter subfamilies (ABC B, C and G).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
In the paper
“Two partial CYP4C genes, CYP4C19 and CYP4C20, have been isolated from the white sea urchin, Lytechinus anamesis (Snyder, 1998), and orthologs of these exist in the S. purpuratus genome (SPU_002380 and SPU_012081, respectively).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
What the sources say
- Not checked yetcites Snyder, 1998
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One of these genes (SPU_027598, Sp-FXR) is related to both LXR and FXR, and is of particular interest because the ligand-binding domain clusters with the LXR in phylogenetic analyses, whereas the DNAbinding domain clusters with the FXR”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Half of the CYP4 genes exhibit embryonic or laval expression, with SPU_005931 exhibiting high expression and a subset expressed at lower levels”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“S. purpuratus also possesses homologs of RXR (NR2B) and HNF4 (NR2A)”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
None of the sources cited for this claim have been checked yet.
In the paper
“Sp-Shr2 exhibits ubiquitous expression throughout development (Howard-Ashby et al., 2006) but also appears to be upregulated in eggs in response to maternal estradiol treatment (Roepke et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
What the sources say
- Not checked yetcites Howard-Ashby et al., 2006
- Not checked yetcites Roepke et al., 2006
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There are four ABCG2-like genes in the urchin genome ( SPU_021184, SPU_014013, SPU_024785, and SPU_014007), the same number as in tunicates and zebrafish.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sea urchins posses a large number of xenobiotic-conjugating enzymes, including genes for 36 cytosolic sulfotransferase (SULT) genes, 49 distinct UGT genes, and 38 GST genes”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the sea urchin, the number of CYP2-like genes is expanded relative to most other known genomes, consisting of 73 predicted genes, more than 60% of the total CYP complement, in contrast to the 30-49% in vertebrate genomes”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sp-ABCB1 codes for a 1329-amino-acid protein and is detected in embryos shortly after fertilization.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the case of sea urchins, the ABCC family is about 25% larger than in other deuterostome genomes, with at least 30 genes, accounting for almost half of all the ABC transporters”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sea urchin genome contains 10 CYP4-like genes; Bayesian phylogenetic analysis shows that 3 of these genes cluster with the vertebrate and tunicate CYP4F genes, whereas 6 form a cluster with the vertebrate CYP4V genes (data not shown).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sea urchins posses 20 ALDH genes (Table 2; Supplemental Table S4), of which 5 are ALDH1-like (including three ALDH2 mitochondrial precursor-like genes) and 2 are ALDH3A-like.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Aldehyde dehydrogenases
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The majority of CYP2-like genes (51/73) exhibit embryonic or larval expression, with five genes (SPU_010576, SPU_016816, SPU_020753, SPU_020756, SPU_021087) exhibiting very high embryonic expression levels”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“S. purpuratus possesses two PPAR paralogs (SPU_021289 and SPU_019332; Table 1), but no ERs.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The current sea urchin genome assembly and EST libraries are complete enough that failure to detect a homolog indicates its absence.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The 38 urchin GSTs represent 6 of the major GST classes (alpha, pi, sigma, theta, zeta, omega; Supplemental Fig. S10, Table S5).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“All but one of the ALDH1 and ALDH3-like genes are expressed during development, the exception being one ALDH2-like gene (SPU_007284).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Aldehyde dehydrogenases
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sea urchin contains 120 CYP genes, and those related to CYP gene families 1-4 constitute a large proportion (80%) of the total”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“This gene is one of 12 ABCB genes present in the sea urchin and is orthologous to mammalian ABCB1/PGP.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
In the paper
“Although there are high levels of efflux activity in sea urchin embryos, the transcript is present at trace quantities, <1 copy/ cell”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
What the sources say
- Not checked yetcites Hamdoun et al., 2004
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Much of the expansion is in the Sp-ABCC5 and Sp-ABCC9 families, whereas orthologs of the vertebrate gene ABCC2 (also called MRP2) are absent.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The current sea urchin genome assembly and EST libraries are complete enough that failure to detect a homolog indicates its absence.
- Rests on an assumption: Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sea urchins possess 10 AKR-like genes but no NQO-like genes.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The current S. purpuratus genome assembly is complete enough that failure to find a homolog indicates absence from the genome.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Three sea urchin genes similar to mammalian epoxide hydrolase-related genes are also present; these genes do not have a known function.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
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In the paper
“HSP genes appear to be highly expressed during development, based on the tiling array data (Samanta et al., 2006); roughly 80% of the HSPs showed significant signals on the array.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Heat shock proteins
What the sources say
- Not checked yetcites Samanta et al., 2006
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The reducing and hydrolyzing Phase II enzymes are also represented in the sea urchin genome, and are slightly expanded relative to mammals (Table 2, Supplemental Fig. S12).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Embryonic and larval expression in untreated sea urchins varies among the toxicologically relevant GSTs, with 5 alpha class, 3 theta class, all 4 omega class, and both the zeta and pi GSTs expressed (Supplemental Table S5).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The urchin genome contains one homolog of both GCLC (SPU_026291) and GCLM (SPU_002909) which, along with GSS (SPU_000830), are expressed at high levels during developmental and larval stages (Table 3).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The 36 cytosolic SULT genes in the urchin genome are divided into two major divisions: 17 are SULT1-like and 19 are SULT3/ SULT4-like (Supplemental Fig. S11).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“A variety of peroxidases are present, including 4 glutathione peroxidase genes, one of which is a single exon gene (SPU_014373), and one that is expressed during development (SPU_014276).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Other metal-binding genes in the urchin genome include a homolog of the Cu and Fe-binding protein ceruloplasmin (SPU_027885, also know as ferroxidase), a homolog of the Febinding protein transferrin (SPU_026949), and both heavy and light chains of the Fe storage protein ferritin (SPU_004876 and SPU_024366).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nine are MGST1-like, only one is MGST2-like (SPU_008286), and the remaining two full and partially assembled genes are MGST3-like (SPU_016492 and SPU_023582).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Sea urchins also have at least 4 HSP90 genes and 2 small α-crystalline HSP20s.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Heat shock proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found only one GST-pi (SPU_024294) and one GSTzeta (SPU_025025); GST-pi has been related to carcinogenesis in humans and mice (Henderson et al., 1998), whereas GST-zeta deficiency causes oxidative stress in mice (Blackburn et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“At least three thioredoxin peroxidase genes are present (SPU_006211, SPU_014869, and SPU_022529), and expressed at high levels during normal development.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Three PCS genes are present in the urchin genome (SPU_004431, SPU_022493, and SPU_023132), four PCS homologs are present in the genome of the sea anemone Nematostella vectensis, and one PCS gene is present in the genome of the tunicate C. intestinalis.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The sea urchin genome possesses one vertebrate-like SOD2 gene (mitochondrial manganese SOD; SPU_024657; see Table 3) and one manganese SOD gene that is more similar to bacterial Mn/Fe SodM (SPU_021817).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Eleven full and one partially assembled MGST-like genes were found in the current urchin genome assembly (Table 2), representing all three classes of MGSTs (MGST1, MGST2, and MGST3).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The major family of heat shock proteins is the HSP70 family, containing at least 17 genes with at least 10 HSP40/DNAJ co-chaperones.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Heat shock proteins
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Interestingly, there are no ABCC2 genes in either urchins or tunicates; this gene subfamily may be specific to vertebrates.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The current S. purpuratus genome assembly is complete enough that failure to find a homolog indicates absence from the genome.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Orthologous relationships are discernable among the PAS proteins and among the ABC transporters.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Discussion
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The total number of ABCB genes is similar across deuterostomes, with most species containing 1 or 2 ABCB1-like genes.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Although far fewer in absolute numbers, both the CYP3-and the CYP1related genes in urchin show a similar, or even greater degree of expansion relative to the number of CYP3 or CYP1 genes in vertebrates.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For example, in urchins there are 73 CYP genes related to the vertebrate CYP2 family, larger than the 16 CYP2s known in humans or most other vertebrates (M.musculus: 51, R. rattus: 50, B. taurus: 23, T. rubripes: 17).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Urchins have two ABCB1 genes, the same as in fish and rodents.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Such distinct relationships are less evident among the CYP genes, or amongst the GST, SULT, and UGT genes.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Discussion
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“While there is general conformity in the presence of higher order gene groups across taxa, in most cases gene orthology is more difficult to determine.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Discussion
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In contrast to the apparent diversification in several active defense gene groups, PAS gene diversity in S. purpuratus is similar to that found in other invertebrate genomes, including the chordate C. intestinalis, but lower than that of vertebrates (Supplemental Table S1).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“indicating their importance during development.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“EST or cDNA evidence confirms a number of the genes presented here, as noted in the Results.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene annotation
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“reveals evolutionary conservation of this network combined with lineage-specific diversification”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“oxidation, N-acetylation, and sulfate or glutathione conjugation can lead to toxic and mutagenic metabolites in a cell and chemical specific manner”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Gamage et al., 2006
- Not checked yetcites Guengerich et al., 2003
- Not checked yetcites Hein et al., 1993
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Thus, there is a balance of protective and injurious processes, and between endogenous and exogenous functions”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Nebert, 1991
- Not checked yetcites Nebert and Russell, 2002
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Gene identities were confirmed by reciprocal BLAST of the predicted genes against Genbank or, where possible, by comparison to cloned cDNAs.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene annotation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Bioactivation to toxic intermediates is therefore a consequence of chemical structural diversity and the occasional necessity for the creation of chemically reactive sites for subsequent conjugation reactions.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The pregnane-X-receptor (PXR), constitutive androstane receptor (CAR), non-mammalian PXR homologs BXR and CXR, peroxisome proliferator-activated receptors (PPARs), liver-X-receptor (LXR), and farnesoid-Xreceptor (FXR) are activated by a variety of xenobiotic and endobiotic compounds and regulate a coordinated response involving various CYP2s, CYP3s, and CYP4s, conjugating enzymes, and transporters”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Bock and Kohle, 2004
- Not checked yetcites Klaassen and Slitt, 2005
- Not checked yetcites Xie and Evans, 2001
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“A third set of sensors includes nuclear factor erythroid-derived 2 (NFE2)-related factor 2 (NRF2, NFE2-like2) and related cap'n'collar (CNC)basic-leucine zipper (bZIP) family proteins, which are activated by oxidants and electrophiles and form heterodimers with small Maf proteins to stimulate transcription of genes encoding antioxidant enzymes such as GST, NQO, glutamate-cysteine ligase (GCL), SOD”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Nguyen et al., 2003b
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The primary member of this family that is a chemical sensor, but also has developmental roles, is the aryl hydrocarbon receptor (AHR), which is activated by planar aromatic hydrocarbons and a variety of other chemicals”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Denison and Nagy, 2003
- Not checked yetcites Nebert et al., 2004
- Not checked yetcites Whitlock, 1999
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Only one CYP2-like gene can be confidently assigned to a subfamily, CYP2U (SPU_008632), suggesting functional conservation in that subfamily.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These three adjacent genes exhibit very different embryonic and larval expression during normal development (SPU_010719 is weakly expressed, SPU_010720 is strongly expressed, and SPU_010721 does not show significant expression) suggesting different enzymatic roles in the organism”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“If this result holds, it would suggest that PTGS genes have been lost on the echinoderm lineage, because at least two PTGS genes are present in vertebrates, and two PTGS genes have been cloned from coral”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Other oxidases
What the sources say
- Not checked yetcites Jarving et al., 2004
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
- Rests on an assumption: The current sea urchin genome assembly and EST libraries are complete enough that failure to detect a homolog indicates its absence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Based on Bayesian analysis, the Lytechinus sequences cluster with the vertebrate CYP4Vs, suggesting a reconsideration of the Lytechinus sequence classification.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Alpha, pi, and mu GSTs in mammals are responsible for the conjugation of polycyclic aromatic hydrocarbon metabolites (Sundberg et al., 1997).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Sundberg et al., 1997
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nine of the urchin genes are single coding exon genes, and three of these are adjacent in the genome assembly, suggesting tandem duplication following reinsertion of a processed transcript.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“At least two of the FMO5 genes are located on the same scaffold, suggesting that urchin FMOs may be clustered, similar to the mammalian genomic FMO arrangement.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Flavoprotein monooxygenases
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Reactive oxygen species (ROS), including superoxide, hydrogen peroxide, and hydroxyl radicals, can be derived from a variety of cellular processes and can contribute to diseases and pathologies generally due to altered gene expression or damage to biomolecules, including proteins, lipids, and DNA (Halliwell and Gutteridge, 1999;Lesser, 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
What the sources say
- Not checked yetcites Halliwell and Gutteridge, 1999
- Not checked yetcites Lesser, 2006
Strength:plain· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“GST-pi has been related to carcinogenesis in humans and mice (Henderson et al., 1998), whereas GST-zeta deficiency causes oxidative stress in mice (Blackburn et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Henderson et al., 1998
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“There appear to be two membrane epoxide hydrolase (EPHX) genes similar to xenobiotic-inducible mammalian EPHX1, and three EPHX genes related to the vertebrate EPHX2 (soluble EPHX) genes (mammals have two EPHX genes (Barth et al., 2004a,b; fatty acid epoxides are the major physiological substrates of EPHX2).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Barth et al., 2004a,b
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Six of the urchin AKR-like genes are most closely related to the vertebrate AKR1 family genes (Supplemental Fig. S13), the products of which in mammals function as aldehyde and aldose reductases and dihydrodiol dehydrogenases, acting on PAH-diols formed by CYP and EPHX (Hyndman et al., 2003;Jez and Penning, 2001).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Hyndman et al., 2003
- Not checked yetcites Jez and Penning, 2001
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Three of the metal complexing genes found in the genome have previously been identified in sea urchins, the metallothioneins MTA, MTB1, and MTB2 (Nemer et al., 1991), which are active in response to excess metal stress but may also play roles in nutrient metal homeostasis and in apoptosis (reviewed in Vasak and Hasler, 2000).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
What the sources say
- Not checked yetcites Vasak and Hasler, 2000
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Only 3 MGSTs are present in the human genome (Pearson, 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Pearson, 2005
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“In mammals, expression of both GCLC and GCLM is dependent on NRF2 (Dickinson et al., 2004;Gong and Cederbaum, 2006;Yang et al., 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
What the sources say
- Not checked yetcites Dickinson et al., 2004
- Not checked yetcites Gong and Cederbaum, 2006
- Not checked yetcites Yang et al., 2005
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Vertebrate genomes do not contain a gene homologous to PCS, suggesting that phytochelatin synthesis ability was lost some time after the divergence of tunicates from the lineage leading to the vertebrates.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The expansion in MGST1-like genes in the urchin may be due to tandem duplication, because at least two gene clusters of MGST1-like genes (one of 4 genes and one of 2 genes) are present.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Urchins also posses a heme peroxidase important during fertilization, ovoperoxidase, which has superoxide dismutase activity (Heinecke and Shapiro, 1990;LaFleur et al., 1998) and is similar to human myeloperoxidase (Nomura et al., 1999).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
What the sources say
- Not checked yetcites Nomura et al., 1999
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Interestingly, sea urchins possess an SOD2-like gene (SPU_014006) that may be related to the molluscan metal-binding proteins cavortin and pernin, which are hemolymph proteins with binding affinity for Fe but also Cu, Ni, Co, and Zn (Huvet et al., 2004;Scotti et al., 2001).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
What the sources say
- Not checked yetcites Huvet et al., 2004
- Not checked yetcites Scotti et al., 2001
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“There appear to be two membrane epoxide hydrolase (EPHX) genes similar to xenobiotic-inducible mammalian EPHX1, and three EPHX genes related to the vertebrate EPHX2 (soluble EPHX) genes (mammals have two EPHX genes (Barth et al., 2004a,b; fatty acid epoxides are the major physiological substrates of EPHX2).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Barth et al., 2004a,b
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“In vertebrates, MGST2 may play an important role in tert-butylhydroperoxide resistance (Ma et al., 2004).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Ma et al., 2004
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“In vertebrates, arylamine NAT enzymes catalyze the addition of an acetyl group to aromatic amines and hydrazines, a reaction generally resulting in detoxification (Boukouvala and Fakis, 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Boukouvala and Fakis, 2005
Strength:plain· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Heat shock proteins (HSP) have been implicated in the response to various toxicants including heavy metals, such as cadmium and arsenic, and free radicals (Feder and Hofmann, 1999).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Heat shock proteins
What the sources say
- Not checked yetcites Feder and Hofmann, 1999
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“GST-pi has been related to carcinogenesis in humans and mice (Henderson et al., 1998), whereas GST-zeta deficiency causes oxidative stress in mice (Blackburn et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Blackburn et al., 2006
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“An oxidative stress response involving CNC-related proteins appears to be conserved in animals, although there are differences in the specific roles and mechanisms involved (An and Blackwell, 2003;Veraksa et al., 2000;Walker et al., 2000).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites An and Blackwell, 2003
- Not checked yetcites Veraksa et al., 2000
- Not checked yetcites Walker et al., 2000
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“resistance by stabilization of other proteins (Cowen and Lindquist, 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Heat shock proteins
What the sources say
- Not checked yetcites Cowen and Lindquist, 2005 source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“One of these AHR homologs (Sp-Ahr; SPU_013788) is more closely related to the vertebrate AHR, a ligand-activated transcription factor that regulates the expression of xenobioticmetabolizing enzymes such as CYPs in response to dioxins, polycyclic aromatic hydrocarbons, and a variety of other compounds (Nebert et al., 2004).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Nebert et al., 2004
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The connectivity, path-length, and interconnectivity of this stresssensing and response network are greater in humans than in yeast (Lee et al., 2002), an evolutionary distance bridged, in part, by sea urchins.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Lee et al., 2002
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Urchin embryos exposed to environmental levels of UV significantly upregulate SOD and undergo apoptosis (Lesser et al., 2003).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Lesser et al., 2003
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Those results indicate that transcription factors governing a stress response have greater regulatory influence, and that they regulate in simpler combinations.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Two important factors may be at work in defensome gene regulation: coregulation and redundancy.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Sp-Fxr is most closely related to vertebrate FXR and LXR, which are activated by oxysterols and bile acids, respectively (Eloranta and Kullak-Ublick, 2005;Handschin and Meyer, 2005), suggesting a role in endobiotic signaling.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Eloranta and Kullak-Ublick, 2005
- Not checked yetcites Handschin and Meyer, 2005
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The sea urchin embryo produces hydrogen peroxide at fertilization to facilitate the hardening of the fertilization envelope (Wong et al., 2004;Wong and Wessel, 2005), and their antioxidant mechanisms have been well studied (see Epel, 2003;Shapiro, 1991).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Wong et al., 2004
- Not checked yetcites Wong and Wessel, 2005
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Recent work has shown that, in yeast, environmental responses such as stress responses have shorter regulatory cascades than endogenous functions such as cell cycle control, implying faster signal propagation (Lunscombe et al., 2004).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Lunscombe et al., 2004
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“These small molecule antioxidants are present in eggs at high concentrations (GSH and ovothiol total ∼ 10 mM; Turner et al., 1986Turner et al., , 1988) ) and remain high throughout development (Schomer and Epel, 1998).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Turner et al., 1986
- Not checked yetcites Schomer and Epel, 1998
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similarly, many of the gene families or superfamilies that participate in the defensome in deuterostomes are found in protostomes, suggesting the origin of an orchestrated chemical defense in a bilaterian ancestor.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Discussion
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear? Based: unclearIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“HIF proteins mediate the response to low oxygen through a signaling mechanism that is evolutionarily conserved and required for development in most metazoans (Lavista-Llanos et al., 2002;Shen et al., 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Lavista-Llanos et al., 2002
- Not checked yetcites Shen et al., 2005
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“The delay between activation and response in transcriptional cascades is also shorter (fewer cell cycles) for sensory responses than for developmental patterning, perhaps reflecting the irreversibility of patterning (Rosenfeld and Alon, 2003).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Rosenfeld and Alon, 2003
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, gene orthologies may or may not be predictive of function, as seen with Sp-ABCC9A.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Discussion
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“However, unlike the vertebrate AHRs, the known invertebrate AHR homologs do not bind typical ligands of the vertebrate AHR (Butler et al., 2001;Powell-Coffman et al., 1998), suggesting an important distinction in AHR functions that is not well understood.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Butler et al., 2001
- Not checked yetcites Powell-Coffman et al., 1998
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Receptor activation by xenobiotic ligands may interfere with the endogenous ligand-dependent developmental signaling, particularly via AHR, bZIP-CNC, and NR proteins.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✗ Based: failsProbably not a substantial claim. The paper may give no reason why it holds.
In the paper
“Understanding the action of these genes in sea urchins should provide insights into the mechanisms that result in the lowered senescence and increased longevity (> 100 years) observed in adult sea urchins (Ebert and Southon, 2003).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Ebert and Southon, 2003
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“A similar relationship between defense genes and longevity genes has been seen in the C. elegans genes that control dauer formation, a whole organism stress response during development (Antebi et al., 2000;Yabe et al., 2005).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
What the sources say
- Not checked yetcites Antebi et al., 2000
- Not checked yetcites Yabe et al., 2005
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A special challenge in embryonic development may be the integration of the regulation of defensive genes with the gene programs that are active during differentiation.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The regulatory proteins governing the expression of many defensome genes are not known even in vertebrates, and thus there could be transcription factors yet to be described that are involved in regulation of the active stress defense genes in sea urchin.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper relies on this without support.
The current sea urchin genome assembly and EST libraries are complete enough that failure to detect a homolog indicates its absence.
“Orthologs of genes in the NR1I family (PXR, CAR, VDR) have not been detected in the current genome assembly, nor in EST libraries.”
“We have been unable to find a homolog of either human BACH gene in the current urchin assembly.”
“appear to be missing from the current genome assembly.”
The paper relies on this without support.
Predicted gene models from the GLEAN3 assembly correspond to actual genes, so gene counts reflect functional gene family sizes.
“Predicted genes are derived from the GLEAN3 predictions of the whole genome shotgun assembly”
“Many of these predicted genes are supported by expression data from a whole genome tiling array”
“Partial gene sequences may be pseudogenes or may be due to incomplete genome assembly.”
The paper relies on this without support.
The current S. purpuratus genome assembly is complete enough that failure to find a homolog indicates absence from the genome.
“we have not been able to find in the current genome assembly homologs of the important heme-detoxification enzyme heme oxygenase 1 (HMOX1) or biliverdin reductase (BLVR)”
“Sea urchins possess 10 AKR-like genes but no NQO-like genes.”
The paper relies on this without support.
Sea urchin embryos lack specialized tissues and organs that are integral to adult stress and toxicant response.
“Embryos lack specialized tissues and organs that are integral to adult stress and toxicant response.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The sea urchin genome also contains two peroxisome proliferator-activated receptor (PPAR, NR1C) homologs and an NR1H gene coorthologous to both liver X receptor (LXR) and farnesoid X receptor (FXR) (42).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“S. purpuratus has 65 ABC transporter genes in the eight major subfamilies of these genes [ABC A to H; (42)].”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“In several cases (CYPs, AHR, NF-E2), the evolution of pathways for chemical defense may have involved recruitment from developmental signaling pathways (42).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“These CYP genes in concert with additional expanded defensive gene families represent a large diversification of defense gene families by the sea urchin relative to mammals (42).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“Many of the defense genes are expressed during development (10,42)”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“The sea urchin has 120 CYP genes, and those related to CYP gene families 1 to 4 constitute 80% of the total, which suggests that there has been selective pressure to expand functionality in these gene families (42).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
In the citing paper
“Strongylocentrotus purpuratus has 32 nuclear receptor (NR) genes (20), two-thirds the number in humans, including several with potential roles in chemical defense (42).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [42]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
The Sp-FXR gene model differs between the text and Table 1
MinorThe text identifies SPU_027598 as Sp-FXR, while Table 1 assigns the corresponding Sp-Fxr/Lxr entry to SPU_011348. SPU_027598 is not among the four NR1H-related models listed in that table.
“One of these genes (SPU_027598, Sp-FXR) is related to both LXR and FXR, and is of particular interest because the ligand-binding domain clusters with the LXR in phylogenetic analyses, whereas the DNAbinding domain clusters with the FXR (Supplemental Figs.S1 and S2).”
“Sp-Fxr/Lxr NR1H SPU_011348 Vertebrate LXR”
The listed CYP1-CYP4 counts exceed the stated 80% share
MinorTable 2 lists 104 CYP1-CYP4 genes. Against the stated total of 120 CYP genes, that is 86.7%, not 80%; including the seven additional, incompletely assembled CYP3-like genes mentioned in the text would make the share higher still.
“The sea urchin contains 120 CYP genes, and those related to CYP gene families 1-4 constitute a large proportion (80%) of the total, suggesting pressure to expand functionality in these gene families.”
“| Oxidative | CYP1-like | 11 | 3 | | | CYP2-like | 73 | 16 | | | CYP3-like | 10 | 4 | | | CYP4-like | 10 | 12 |”
The Sp-Shr2 model number has two forms
MinorThe text gives the Sp-Shr2 model as SPU_00817, whereas Table 1 gives SPU_008117.
“a previously cloned NR, Sp-Shr2 (NR2B/C-like, SPU_00817; Kontrogianni-Konstantopoulos et al., 1996)”
“Sp-Shr2 NR2C2 SPU_008117 Vertebrate TR4”
Citations
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Flagged first, then by citations
5 of the 179 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Howard-Ashby, 2006, The identification and characterization of transcription factor families in early Strongylocentrotus purpuratus development, Dev. Biol.
Cited by
Sorted by citations
The oyster genome reveals stress adaptation and complexity of shell formation
Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., et al. (2012) · Nature · doi:10.1038/nature11413 · Cited by 2,241
The Genome of the Sea Urchin Strongylocentrotus purpuratus
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science · doi:10.1126/science.1133609 · Cited by 1,132
Self-citationGoldstone, J. V., McArthur, A. G., Kubota, A., Zanette, J., Parente, T. E., Jönsson, M. E., Nelson, D. R., & Stegeman, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-643 · Cited by 449
Self-citationThe UDP-Glycosyltransferase (UGT) Superfamily: New Members, New Functions, and Novel Paradigms
Meech, R., Hu, D. G., McKinnon, R. A., Mubarokah, S. N., Haines, A. Z., Nair, P. C., Rowland, A., & Mackenzie, P. I. (2019) · Physiological Reviews · doi:10.1152/physrev.00058.2017 · Cited by 379
Todgham, A. E., & Hofmann, G. E. (2009) · Journal of Experimental Biology · doi:10.1242/jeb.032540 · Cited by 269
Metadata
- Authors
- Goldstone, J. V., Hamdoun, A., Cole, B. J., Howard-Ashby, M., Nebert, D. W., Scally, M., Dean, M., Epel, D., Hahn, M. E., & Stegeman, J. J.
- Affiliations
- Woods Hole Oceanographic Institution (US)
- Hopkins Marine Station (US)
- University of Cincinnati (US)
- Frederick National Laboratory for Cancer Research (US)
- Corresponding author
- Goldstone, J.V.
- Hamdoun, A.
- Venue
- Developmental Biology
- Publisher
- Elsevier BV
- Published
- 2006-12
- Volume
- 300
- Issue
- 1
- Pages
- 366-384
- ISSN
- 0012-1606 (ISSN-L)
- PMC
- PMC3166225
- OpenAlex
- W2034298458
- Cited by
- 280
- References
- 179
- Citations by year
- 2026: 6 · 2025: 13 · 2024: 13 · 2023: 15 · 2022: 12 · 2021: 31 · 2020: 11 · 2019: 16 · 2018: 16 · 2017: 14 · 2016: 9 · 2015: 14 · 2014: 13 · 2013: 10 · 2012: 21
- FWCI
- 8.12
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Developmental Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation
- National Institutes of Health (1f32es012794-01)
- National Institute of Environmental Health Sciences (2-P42-ES-07381, R01ES006272, P30ES006096, P42ES007381, F32-ES012794, P30 ES-06096)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (F32HD047136, F32-HD-47136)
- Topics
- Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Environmental Toxicology and Ecotoxicology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Echinoderm biology and ecology
- Keywords
- environmental stress response, Strongylocentrotus purpuratus, sea urchin genome, cytochrome P450, aryl hydrocarbon receptor, hypoxia-inducible factor, heat shock transcription factor, nuclear receptors, gene family expansion, detoxification, embryonic development, deuterostome evolution
- MeSH terms
- Acclimatization, Animals, Environment, Humans, Inactivation, Metabolic, Phylogeny, Sea Urchins, Transcription Factors, Signal Transduction, Genome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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