Cited by 280Environmental Toxicology and EcotoxicologyDevelopmental Biology and Gene RegulationEchinoderm biology and ecology

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 access

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.·2006·Developmental Biology

DOI 10.1016/j.ydbio.2006.08.066PMC PMC3166225

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Abstract

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.

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Crossref · 10.1016/j.ydbio.2006.08.066

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Claims the paper makes

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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 calibrated
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
“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
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
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
“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 calibrated
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
“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 calibrated
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
“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 calibrated
Tests✓ 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“As one indication of their functional importance, 25 of these 30 genes show significant levels of expression at some stage of development”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
What the sources say
- Not checked yetcites Samanta et al., 2006 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“However, an estrogen receptor-related receptor (ERR; NR3B) homolog (SPU_004723) was identified.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ 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
“we also found an urchin homolog of the vertebrate gene KEAP1”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative stress-responsive transcription factors
Load-bearingStrength:plain· not yet calibrated
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
“Ten complete and seven incompletely assembled CYP3-like genes were identified in the sea urchin genome.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Oxidative biotransformation Cytochromes P450
Load-bearingStrength:plain· not yet calibrated
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
“We also found 46 members of the SLC22 branch, which includes both OAT and OCT genes.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Ion transporters
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ 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
“Homologs of another important dioxygenase/peroxidase gene, prostaglandin-endoperoxide synthase (PTGS; also known as cycloxygenase, COX), appear to be missing from the current genome assembly.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Other oxidases
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ 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.
None of the sources cited for this claim have been checked yet.
In the paper
“However, ligands of mammalian LXR and FXR that have been shown to upregulate mammalian ABCC (MRP) genes (Kast et al., 2002;Kullak-Ublick and Becker, 2003) also induce ABCC9A in sea urchin (Hamdoun et al., unpublished data).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
What the sources say
- Not checked yetcites Kast et al., 2002 source
- Not checked yetcites Kullak-Ublick and Becker, 2003
- Not checked yetcites Hamdoun et al., unpublished data
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“By contrast, orthologs of genes in the NR1I family (PXR, CAR, VDR) have not been detected in the current genome assembly, nor in EST libraries.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Nuclear receptors
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ 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
“Based on inhibition characteristics, Sp-ABCB1 accounts for less of the embryo's observed calcein efflux activity than Sp-ABCC9A (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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 urchin UGT enzymes are principally divided among the UGT1-like and UGT2-like families (13 UGT1-like and 29 UGT2-like).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ 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.
None of the sources cited for this claim have been checked yet.
In the paper
“This represents a very large diversification in these gene families relative to those in mammals: the human genome contains 13 SULT, 13 UGT and 17 GST genes”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Gamage et al., 2006 source
- Not checked yetcites Mackenzie et al., 2005 source
- Not checked yetcites Nebert and Vasiliou, 2004
Load-bearingStrength:plain· not yet calibrated
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.
In the paper
“Thirty-three predicted NR genes were identified in the S. purpuratus genome”
§ 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
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ 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.
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 Nemer et al., 1991 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“The six urchin theta-class GST genes are most closely related to vertebrate theta-class GSTs, rather than to the insect thetaclass GSTs, aiding the phylogenetic resolution of this widespread GST-family (Nebert and Vasiliou, 2004;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 Nebert and Vasiliou, 2004
- Not checked yetcites Pearson, 2005 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“GSR (SPU_025989) is also expressed at high levels during development, as has been known for some time (Ichio, 1977;Ii and Sakai, 1974a,b).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
What the sources say
- Not checked yetcites Ichio, 1977 source
- Not checked yetcites Ii and Sakai, 1974a,b
Strength:boosted· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“Given the expansion of the ABCC8 and 9 subfamilies in urchins, we were surprised to find that these families appear to be absent in tunicates (Annilo et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Annilo et al., 2006 source
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“The first line of cellular defense, against amphipathic or slightly lipophilic compounds in particular, is the active expulsion of these compounds by efflux proteins known as ATP Binding Cassette (ABC) or multidrug efflux transporters”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Introduction
What the sources say
- Not checked yetcites Dean et al., 2001 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“Many of these predicted genes are supported by expression data from a whole genome tiling array”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene annotation
What the sources say
- Not checked yetcites Samanta et al., 2006 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“These gene counts represent significant expansions of the SLC22 family, which consists of only 5 genes in humans and mice”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Ion transporters
What the sources say
- Not checked yetcites Sweet, 2005 source
Load-bearingStrength:plain· not yet calibrated
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.
In the paper
“Four omega-class GSTs are present in the urchin genome, closely related to vertebrate and insect omega GSTs with dehydroascorbate reductase, thioltransferase, and monomethylarsenate reductase activities (Whitbread et al., 2003).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Reductive and conjugative biotransformation
What the sources say
- Not checked yetcites Whitbread et al., 2003 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“Although there is considerable variation in the total number of ABC genes within eukaryotic genomes (Annilo et al., 2006), the relative proportion of each family has tended to stay constant”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Efflux transporter proteins
What the sources say
- Not checked yetcites Annilo et al., 2006 source
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“a previously cloned NR, Sp-Shr2 (NR2B/C-like, SPU_00817; Kontrogianni-Konstantopoulos et al., 1996), has recently been shown to bind estradiol (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 Roepke et al., 2006 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
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 Heinecke and Shapiro, 1990
- Not checked yetcites LaFleur et al., 1998 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“although there is no significant change in the overall GSH and GSSG concentrations during fertilization and early development (Fahey et al., 1976)”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Antioxidant proteins
What the sources say
- Not checked yetcites Fahey et al., 1976 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“This latter finding is in line with the observed lack of NQO genes in the worm, fly, sea squirt, or plants (Vasiliou 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 Vasiliou et al., 2006 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“S. purpuratus may possess alternative mechanisms of heme turnover and detoxification.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The current S. purpuratus genome assembly is complete enough that failure to find a homolog indicates absence from the genome.
None of the sources cited for this claim have been checked yet.
In the paper
“Both SLC22 and ABC efflux proteins (see above) export metals directly or as glutathione (GSH) conjugates (Leslie et al., 2001;Sweet, 2005), and the urchin genome contains multiple genes in the subfamilies known to be involved in resistance to heavy metal toxicity.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Metal detoxification
What the sources say
- Not checked yetcites Leslie et al., 2001 source
- Not checked yetcites Sweet, 2005 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 source
- Not checked yetcites Scotti et al., 2001 source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“Therefore, chemical defense genes may be especially critical for resilience and survival of these early stages.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Load-bearingStrength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: Sea urchin embryos lack specialized tissues and organs that are integral to adult stress and toxicant response.
None of the sources cited for this claim have been checked yet.
In the paper
“In vertebrate animals, genes in the NR1 family (PXR, CAR, LXR, FXR), regulate xenobiotic-and endobiotic-inducible adaptive responses involving CYP, ABC, and other genes encoding biotransformation enzymes and transporters (Bock and Kohle, 2004;Klaassen and Slitt, 2005;Krasowski et al., 2005;Xie and Evans, 2001).”
§ 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 Bock and Kohle, 2004
- Not checked yetcites Klaassen and Slitt, 2005
- Not checked yetcites Krasowski et al., 2005 source
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“The presence of three SOD genes and an unusual peroxidase, ovoperoxidase, with SOD-like activity (Heinecke and Shapiro, 1990), provides further evidence that ROS may be an important stressor to sea urchins.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Heinecke and Shapiro, 1990
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Sea urchins posses antioxidants such as glutathione (Sakai and Dan, 1959), carotenoids (Griffiths, 1966;Griffiths and Perrott, 1976), tocopherols, ascorbic acid (Backstrom, 1957), and a unique embryo-specific thiol named ovothiol (Shapiro and Hopkins, 1991;Turner et al., 1986Turner et al., , 1988)).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Sakai and Dan, 1959
- Not checked yetcites Griffiths, 1966 source
- Not checked yetcites Backstrom, 1957 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Some defense gene products may be packaged into eggs during oogenesis to provide adequate defense during early cleavage stages when divisions are rapid and nucleus:cytoplasm ratios are low (Epel, 2003;Giudice et al., 1999;Hamdoun et al., 2004), a period in which gene expression is unlikely to result in efficient upregulation of protein concentration.”
§ 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 Epel, 2003 source
- Not checked yetcites Giudice et al., 1999 source
- Not checked yetcites Hamdoun et al., 2004 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Coordinate regulation of defensome genes, such as AHR regulation of CYPs and UGTs or the coregulation of CYP3A4, UGT1As, and ABCC2 by CAR/PXR in mammals (Bock and Kohle, 2004;Xu et al., 2005), may be a method of accelerating the response to toxicant exposure.”
§ 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 Bock and Kohle, 2004
- Not checked yetcites Xu et al., 2005
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“The PAS gene family has undergone expansion in vertebrates, with two or three paralogs for each of the genes found in the genomes of D. melanogaster, C. elegans, and C. intestinalis (Hahn, 2002;Hahn et al., 2006).”
§ 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 Hahn, 2002 source
- Not checked yetcites Hahn et al., 2006 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 apparent absence of urchin genes related to NR1I genes (PXR, CAR), which are key xenobiotic sensors in vertebrates, suggests an important difference in sensor repertoire between these deuterostome groups.”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Diversity and conservation in signaling
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The current S. purpuratus genome assembly is complete enough that failure to find a homolog indicates absence from the genome.
In the paper
“In contrast, in tunicates there are 5 ABCB1 (PGP) subfamily genes (Annilo et al., 2006).”
§ The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome > Gene family diversification
What the sources say
- Not checked yetcites Annilo et al., 2006 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Despite the fact that the individual genes within the network may vary across organisms, this network may be comprised of evolutionarily conserved modules,”
§ 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 Davidson and Erwin, 2006 source
- Not checked yetcites von Dassow et al., 2000 source
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“For example, in humans, ABCB1 is induced by a large variety of cues, including protein denaturing stressors, ensuring virtually ubiquitous inducibility (Shtil and Azare, 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 Shtil and Azare, 2005
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
- 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 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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.
- 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It 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
Load-bearingStrength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably 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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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
Load-bearingStrength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
Load-bearingStrength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.

113 of 113

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.”

4 of 4

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?

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
Minor
The 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.
The listed CYP1-CYP4 counts exceed the stated 80% share
Minor
Table 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 Sp-Shr2 model number has two forms
Minor
The text gives the Sp-Shr2 model as SPU_00817, whereas Table 1 gives SPU_008117.

3 of 3

MUSCLE: multiple sequence alignment with high accuracy and high throughput
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PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
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Tumour stem cells and drug resistance
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Self-citation
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Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956
Free radicals in biology and medicine
Halliwell, B. B., & Gutteridge, J. M. C. (1985) · Journal of Free Radicals in Biology & Medicine · doi:10.1016/0748-5514(85)90140-0 · Cited by 2,938

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Show all 179 references

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.

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-citation
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Goldstone, 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-citation
The 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
Transcriptomic response of sea urchin larvaeStrongylocentrotus purpuratusto CO2-driven seawater acidification
Todgham, A. E., & Hofmann, G. E. (2009) · Journal of Experimental Biology · doi:10.1242/jeb.032540 · Cited by 269

See all 280

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.
ORCID: Goldstone, J.V.
Hamdoun, A.
Dean, M.
Hahn, M.E.
Stegeman, J.J.
Venue: Developmental Biology
Publisher: Elsevier BV
Published: 2006-12
Volume: 300
Issue: 1
Pages: 366-384
ISSN: 0012-1606 (ISSN-L)
DOI: 10.1016/j.ydbio.2006.08.066
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: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 2420 d)
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

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The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome

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