Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.

Environmental RNA: A Revolution in Ecological Resolution?

Developmental models for skin exist in terrestrial and amphibious vertebrates but there is a lack of information in aquatic vertebrates. We have analysed skin epidermal development of a bony fish (teleost), the most successful group of extant vertebrates. A specific epidermal type I keratin cDNA (hhKer1), which may be a bony-fish-specific adaptation associated with the divergence of skin development (scale formation) compared with other vertebrates, has been cloned and characterized. The expression of hhKer1 and collagen 1α1 in skin taken together with the presence or absence of keratin bundle-like structures have made it possible to distinguish between larval and adult epidermal cells during skin development. The use of a flatfish with a well-defined larval to juvenile transition as a model of skin development has revealed that epidermal larval basal cells differentiate directly to epidermal adult basal cells at the climax of metamorphosis. Moreover, hhKer1 expression is downregulated at the climax of metamorphosis and is inversely correlated with increasing thyroxin levels. We suggest that, whereas early mechanisms of skin development between aquatic and terrestrial vertebrates are conserved, later mechanisms diverge.

Molecular, cellular and histological changes in skin from a larval to an adult phenotype during bony fish metamorphosis

Thyroid hormones (THs) are vital in the maintenance of homeostasis and in the control of development. One postembryonic developmental process that is principally regulated by THs is amphibian metamorphosis. This process has been intensively studied at the genomic level yet very little information at the proteomic level exists. In addition, there is increasing evidence that changes in the phosphoproteome influence TH action. Here we identify components of the proteome and phosphoproteome in the tail fin that changed within 48 h of exposure of premetamorphic Rana catesbeiana tadpoles to 10 nM 3,5,3'-triiodothyronine (T3). To this end, we developed a cell and protein fractionation method combined with two-dimensional gel electrophoresis and phosphoprotein-specific staining. Altered proteins were identified using mass spectrometry (MS). We identified and cloned a novel Rana larval type I keratin, RLK I, which may be a target for caspase-mediated proteolysis upon exposure to T3. In addition, the RLK I transcript is reduced during T3-induced and natural metamorphosis which is consistent with a larval keratin. Furthermore, GILT, a protein involved in the immune system, is changed in phosphorylation state which is linked to its activation. Using a complementary MS technique for the analysis of differentially-expressed proteins, isobaric tags for relative and absolute quantitation (iTRAQ) revealed 15 additional proteins whose levels were altered upon T3 treatment. The success of identifying proteins whose levels changed upon T3 treatment with iTRAQ was enhanced through de novo sequencing of MS data and homology database searching. These proteins are involved in apoptosis, extracellular matrix structure, immune system, metabolism, mechanical function, and oxygen transport. We have demonstrated the ability to derive proteomics-based information from a model species for postembryonic development for which no genome information is currently available. The present study identifies proteins whose levels and/or phosphorylation states are altered within 48 h of the induction of tadpole tail regression prior to overt remodeling of the tail. In particular, we have identified a novel keratin that is a target for T3-mediated changes in the tail that can serve as an indicator of early response to this hormone.

/pdf/analysis-of-the-rana-catesbeiana-tadpole-tail-fin-proteome-1of5dtu13a.pdf

Analysis of the Rana catesbeiana tadpole tail fin proteome and phosphoproteome during T3-induced apoptosis: identification of a novel type I keratin

Amphibian body skin provides an opportunity to investigate the molecular mechanism of thyroid hormone (TH)-dependent organ remodeling during metamorphosis. Global gene expression changes in the TH-dependent body skin remodeling were studied with microarray analysis. We identified 401 genes that were differentially expressed more than fourfold for 7 days after TH-treatment. As expected, larval- and adult-type keratin genes were significantly inactivated and activated, respectively. The expression changes of the Gene Ontology annotated genes demonstrated significant correlation with the morphological and physiological changes in body skin metamorphosis. The 'transcription and proteolysis' category genes were first upregulated 1 day after TH-treatment. Subsequently, the 'cell cycle' category genes were activated at 3 days. The 'defense response' and 'immune response' category genes were the late TH-response genes, which were downregulated and upregulated at 5 and 7 days, respectively. From these genes, adult-type keratin-c (xak-c) gene was selected as a suitable gene to visually monitor the emergence of adult-type epidermal cells during skin remodeling, because the gene is specifically expressed in adult epidermal basal cells. We generated enhanced green fluorescent protein (EGFP)-transgenic Xenopus laevis driven by the promoter of xak-c gene. The keratin promoter faithfully expressed the EGFP gene in adult-type basal cells. Spatial and temporal EGFP-fluorescence patterns of filial 1 (F1)-offspring tadpoles visually demonstrated an event of sequential replacement of larval keratinocytes with the newly generated adult counterparts.

Molecular features of thyroid hormone-regulated skin remodeling in Xenopus laevis during metamorphosis

Proteome analysis of abundant proteins in two age groups of early Atlantic cod (Gadus morhua) larvae.

Anuran larvae transform their epidermis to the adult counterpart during metamorphosis. The major event of this process is the proliferation of larval epidermal basal cells and their differentiation into adult ones. The present study isolated novel type I keratin cDNA dubbed xak-c (Xenopus adult keratin-c) that was exclusively expressed in adult epidermal basal cells. The gene started its expression in the larval epidermis at the onset of metamorphosis. Thyroid hormone (TH) induced the precocious expression of the gene in the epidermis of premetamorphic tadpoles. To study the transcriptional regulation of this gene in relation to epidermal metamorphosis, a 2.8 kb 5'-flanking region of xak-c was cloned and its promoter activity was investigated. Gene constructs were made so as to contain the xak-c promoter region and gene of EGFP or luciferase as a reporter gene and were transfected into various types of cells, which revealed that the 5'-flanking region had an epidermal cell-specific transcriptional activity in both anurans and mammals. Larval skin tissues of Xenopus were transfected with the constructs and cultured in the presence and absence of TH, which showed that the promoter region is responsive to TH, although the region did not contain the consensus TH response element-like sequence. In sharp contrast, the promoter region did not respond to TH in the adult skin, clearly indicating that the cloned region contains specific sequences that respond to metamorphosis-dependent transcription factor(s).

https://anatomypubs.onlinelibrary.wiley.com/doi/pdf/10.1002/dvdy.10196

Metamorphosis-dependent transcriptional regulation of xak-c, a novel Xenopus type I keratin gene

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Metamorphosis-dependent transcriptional regulation of xak-c, a novel Xenopus type I keratin gene