Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

Background: In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings: We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43uN, 63–71uW, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance: The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists

Loss of liver-specific and sexually dimorphic gene expression by aryl hydrocarbon receptor activation in C57BL/6 mice

<div><p>The aryl hydrocarbon receptor (AhR) is a highly conserved transcription factor that mediates a broad spectrum of species-, strain-, sex-, age-, tissue-, and cell-specific responses elicited by structurally diverse ligands including 2,3,7,8-tetrachlorodibenzo-<i>p</i>-dioxin (TCDD). Dose-dependent effects on liver-specific and sexually dimorphic gene expression were examined in male and female mice gavaged with TCDD every 4 days for 28 or 92 days. RNA-seq data revealed the coordinated repression of 181 genes predominately expressed in the liver including albumin (3.7-fold), α-fibrinogen (14.5-fold), and β-fibrinogen (17.4-fold) in males with corresponding AhR enrichment at 2 hr. Liver-specific genes exhibiting sexually dimorphic expression also demonstrated diminished divergence between sexes. For example, male-biased <i>Gstp1</i> was repressed 3.0-fold in males and induced 4.5-fold in females, which were confirmed at the protein level. Disrupted regulation is consistent with impaired GHR-JAK2-STAT5 signaling and inhibition of female specific CUX2-mediated transcription as well as the repression of other key transcriptional regulators including <i>Ghr</i>, <i>Stat5b</i>, <i>Bcl6</i>, <i>Hnf4a</i>, <i>Hnf6</i>, <i>Foxa1/2/3</i>, <i>and Zhx2</i>. Attenuated liver-specific and sexually dimorphic gene expression was concurrent with the induction of fetal genes such as alpha-fetoprotein. The results suggest AhR activation causes the loss of liver-specific and sexually dimorphic gene expression producing a functionally “de-differentiated” hepatic phenotype.</p></div

2,3,7,8-Tetrachlorodibenzo-p-dioxin abolishes circadian regulation of hepatic metabolic activity in mice

Abstract Aryl hydrocarbon receptor (AhR) activation is reported to alter the hepatic expression of circadian clock regulators, however the impact on clock-controlled metabolism has not been thoroughly investigated. This study examines the effects of AhR activation on hepatic transcriptome and metabolome rhythmicity in male C57BL/6 mice orally gavaged with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) every 4 days for 28 days. TCDD diminished the rhythmicity of several core clock regulators (e.g. Arntl, Clock, Nr1d1, Per1, Cry1, Nfil3) in a dose-dependent manner, involving either a ≥ 3.3-fold suppression in amplitude or complete loss of oscillation. Accordingly, protein levels (ARNTL, REV-ERBα, NFIL3) and genomic binding (ARNTL) of select regulators were reduced and arrhythmic following treatment. As a result, the oscillating expression of 99.6% of 5,636 clock-controlled hepatic genes was abolished including genes associated with the metabolism of lipids, glucose/glycogen, and heme. For example, TCDD flattened expression of the rate-limiting enzymes in both gluconeogenesis (Pck1) and glycogenesis (Gys2), consistent with the depletion and loss of rhythmicity in hepatic glycogen levels. Examination of polar hepatic extracts by untargeted mass spectrometry revealed that virtually all oscillating metabolites lost rhythmicity following treatment. Collectively, these results suggest TCDD disrupted circadian regulation of hepatic metabolism, altering metabolic efficiency and energy storage

Lipidomic Evaluation of Aryl Hydrocarbon Receptor-Mediated Hepatic Steatosis in Male and Female Mice Elicited by 2,3,7,8-Tetrachlorodibenzo‑<i>p</i>‑dioxin

The environmental contaminant 2,3,7,8-tetrachlorodibenzo-<i>p</i>-dioxin (TCDD) induces hepatic steatosis mediated by the aryl hydrocarbon receptor. To further characterize TCDD-elicited hepatic lipid accumulation, mice were gavaged with TCDD every 4 days for 28 days. Liver samples were examined using untargeted lipidomics with structural confirmation of lipid species by targeted high-resolution MS/MS, and data were integrated with complementary RNA-Seq analyses. Approximately 936 unique spectral features were detected, of which 379 were confirmed as unique lipid species. Both male and female samples exhibited similar qualitative changes (lipid species) but differed in quantitative changes. A shift to higher mass lipid species was observed, indicative of increased free fatty acid (FFA) packaging. For example, of the 13 lipid classes examined, triglycerides increased from 46 to 48% of total lipids to 68–83% in TCDD treated animals. Hepatic cholesterol esters increased 11.3-fold in male mice with moieties consisting largely of dietary fatty acids (FAs) (i.e., linolenate, palmitate, and oleate). Phosphatidylserines, phosphatidylethanolamines, phosphatidic acids, and cardiolipins decreased 4.1-, 5.0-, 5.4- and 7.4-fold, respectively, while ceramides increased 6.6-fold. Accordingly, the integration of lipidomic data with differential gene expression associated with lipid metabolism suggests that in addition to the repression of <i>de novo</i> fatty acid synthesis and β-oxidation, TCDD also increased hepatic uptake and packaging of lipids, while inhibiting VLDL secretion, consistent with hepatic fat accumulation and the progression to steatohepatitis with fibrosis

Immunohistochemical evaluation of hepatic AFP.

<p>Representative photomicrographs for AFP stained liver sections of (A) sesame oil vehicle treated females, (B) sesame oil vehicle treated males, (C) 30 μg/kg TCDD treated females, and (D) 30 μg/kg TCDD treated males. Scale bar represents 50 μm. The portal vein is designated by the letter V, bile ducts with the letter b, and AFP positive stained regions by solid black arrows.</p

Gene expression changes of liver related genes.

<p>Gene set enrichment analysis (GSEA) of 181 liver specific-genes in (A) male and (B) female mice gavaged with 30 μg/kg TCDD every 4 days for 28 days, or (C) female mice gavaged with 30 μg/kg TCDD every 4 days for 92 days. The 181 liver-specific genes were identified using published microarray datasets representing 96 tissues/cell types [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184842#pone.0184842.ref034" target="_blank">34</a>]. Identification of liver-specific genes is described in materials and methods. TCDD elicited gene expression changes were ranked from most induced (left—red) to most repressed (right). Vertical black line represents identified liver-specific genes. The top panel (green line) represents a running-sum statistic (enrichment score) based on the lower panel, increasing when a gene is a member of the liver-specific gene set and decreasing when it is not. Enrichment scores increased most dramatically on the right indicating most of the liver-specific genes were repressed by TCDD. (D) Heat map of liver-specific gene expression changes elicited by TCDD. (E) Heatmap of TCDD-elicited repression of hepatokines. For heatmaps (D and E) blue indicates repression while red represents induction. The presence of pDREs (MSS ≥ 0.856) and hepatic AhR enrichment peaks (FDR ≤ 0.05) at 2h are shown as green boxes. Read count represents the maximum raw number of aligned reads to each transcript where yellow represents a lower level of expression (≤ 500 reads) and pink represents a higher level of expression (≥ 10,000).</p

Albuminoid genomic region.

<p>Albuminoid genomic region including <i>Alb</i>, <i>Afp</i>, and <i>Afm</i>. UCSC genome browser tracks show (1) the scale, (2) male AhR ChIP-seq peaks at 2 h, (3) male AhR enriched sites (FDR ≤ 0.05), (4) female AhR ChIP-seq peaks, (5) female AhR enriched sites (FDR ≤ 0.05), (6) location of pDREs (diagonal line indicates pDREs with a matrix similarity score ≥0.85), and (7) location of <i>Alb</i>, <i>Afp</i> and <i>Afm</i> genes within the albuminoid genomic region. <i>Gc</i>, the fourth albuminoid, is located 1 Mb upstream of <i>Alb</i> (not shown). Tracks are available for visualization at <a href="http://dbzach.fst.msu.edu/index.php/publications/supplementary-data/" target="_blank">http://dbzach.fst.msu.edu/index.php/publications/supplementary-data/</a>.</p