GoEnrich: creating high quality genomic DNA resources from limited voucher specimen tissues or museum specimens of at-risk species for conservation-friendly use in the validation of environmental DNA assays.

Objective: Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible.

Effects of storage conditions on the stability of qPCR reagents: implications for environmental DNA detection.

Objective: Environmental DNA (eDNA) detection is a transformative tool for ecological surveys which in many cases offers greater accuracy and cost-effectiveness for tracking low-density, cryptic species compared to conventional methods. For the use of targeted quantitative PCR (qPCR)-based eDNA detection, protocols typically require freshly prepared reagents for each sample, necessitating systematic evaluation of reagent stability within the functional context of eDNA standard curve preparation and environmental sample evaluation. Herein, we assessed the effects of long-term storage and freeze-thaw cycles on qPCR reagents for eDNA analysis across six assays.

De novo synthetic antimicrobial peptide design with a recurrent neural network.

Antibiotic resistance is recognized as an imminent and growing global health threat. New antimicrobial drugs are urgently needed due to the decreasing effectiveness of conventional small-molecule antibiotics. Antimicrobial peptides (AMPs), a class of host defense peptides, are emerging as promising candidates to address this need.

Salmonid smolt caudal fin and liver transcriptome responses to low sulfur marine diesel and high sulfur fuel oil water accommodated fractions for assessing oil spill effects in marine environments.

The environmental impact of oil spills is a critical concern, particularly pertaining to low sulfur marine diesel (LSMD) and high sulfur fuel oil (HSFO) that are commonly involved in coastal spills. Although transcriptomic biomonitoring of sentinel animals can be a powerful tool for assessing biological effects, conventional methods utilize lethal sampling to examine the liver. As a non-lethal alternative, we have previously shown salmonid caudal fin cyp1a1 is significantly responsive to LSMD-derived toxicants.

Transcriptomic profiling of Rana [Lithobates] catesbeiana back skin during natural and thyroid hormone-induced metamorphosis under different temperature regimes with particular emphasis on innate immune system components.

As amphibians undergo thyroid hormone (TH)-dependent metamorphosis from an aquatic tadpole to the terrestrial frog, their innate immune system must adapt to the new environment. Skin is a primary line of defense, yet this organ undergoes extensive remodelling during metamorphosis and how it responds to TH is poorly understood. Temperature modulation, which regulates metamorphic timing, is a unique way to uncover early TH-induced transcriptomic events.

Utilization of temperature-mediated activation of thyroid hormone-induced molecular memory to evaluate early signaling events in the olfactory epithelium of Rana [Lithobates] catesbeiana tadpoles.

The amphibian olfactory system is highly distinct between aquatic tadpole and terrestrial frog life stages and therefore must remodel extensively during thyroid hormone (TH)-dependent metamorphosis. Developmentally appropriate functioning of the olfactory epithelium is critical for survival. Previous studies in other Rana [Lithobates] catesbeiana premetamorphic tadpole tissues showed that initiation of TH-induced metamorphosis can be uncoupled from execution of TH-dependent programs by holding tadpoles in the cold rather than at warmer permissive temperatures.

Relationship between serum thyroid hormones and their associated metabolites, and gene expression bioindicators in the back skin of tadpoles and frogs during metamorphosis.

Anuran metamorphosis is characterized by profound morphological changes including remodeling of tissues and organs. This transition is initiated by thyroid hormones (THs). However, the current knowledge of changing levels of THs during metamorphosis relies on pooled samples using methods known for high variability with sparse reporting of measured variation.

Dynamic cyp1a1 transcript responses in the caudal fin of coho salmon (Oncorhynchus kisutch) smolts to low sulfur marine diesel water accommodated fraction exposures and depuration.

Oil spills that occur in high traffic coastal environments can have profound consequences for the health of marine ecosystems and the commercial and social interests that are dependent upon these habitats. Given that the global reliance on marine fuels is not abating, it is imperative to develop sensitive and robust tools to monitor oil contamination and remediation in a timely manner. Such tools are increasingly important for ascertaining the immediate and long-term effects of oil contamination on species of interest and local habitats as water-soluble components of oils, such as polycyclic aromatic hydrocarbons (PAHs), can persist post-remediation.

Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects.

Antimicrobial peptides (AMPs) are a diverse class of short, often cationic biological molecules that present promising opportunities in the development of new therapeutics to combat antimicrobial resistance. Newly developed in silico methods offer the ability to rapidly discover numerous novel AMPs with a variety of physiochemical properties. Herein, using the rAMPage AMP discovery pipeline, we bioinformatically identified 51 AMP candidates from amphibia and insect RNA-seq data and present their in-depth characterization.

Comparison of transcriptome responses of the liver, tail fin, and olfactory epithelium of Rana [Lithobates] catesbeiana tadpoles disrupted by thyroid hormones and estrogen.

Thyroid hormones (THs) are important developmental regulators in vertebrates, including during the metamorphosis of a tadpole into a frog. Metamorphosis is a post-embryonic developmental period initiated by TH production in the tadpole thyroid gland. The two main bioactive forms of TH are L-thyroxine (T) and 3,5,3'-triiodothyronine (T); these hormones have overlapping but distinct mechanisms of action.

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage.

Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics.

Advancement in oil forensics through the addition of polycyclic aromatic sulfur heterocycles as biomarkers in diagnostic ratios.

In current oil spill forensics, diagnostic ratios of hydrocarbon biomarker responses are commonly used to compare oil spill samples to source materials in order to determine the identity of the oil. This well recognized procedure was developed by the European Committee for Standardization (CEN) with corresponding published EN 15522-2 Oil Spill Identification guidelines. However, it is further recognized that weathering can have a negative effect on some of the biomarkers used in the analysis, leading to decreased confidence in the result.

A rapid gas chromatography quadrupole time-of-flight mass spectrometry method for the determination of polycyclic aromatic hydrocarbons and sulfur heterocycles in spilled crude oils.

Spilled crude oil samples contain various toxic compounds including polycyclic aromatic hydrocarbons (PAHs) as well as sulfur heterocycles (PASHs) and their related alkylated forms (APAHs and APASHs). In this study, a method was successfully developed employing a gas chromatography quadrupole time-of-flight (GC-QToF) mass spectrometer to quantitatively analyze both PAHs/APAHs and PASHs/APASHs in these samples. With GC-QToF, the monoisotopic mass of the compounds is distinguished, allowing the PASHs/APASHs to be extracted separately from the PAHs/APAHs in crude oil.

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens.

Background: Antibiotic resistance is a growing global health concern prompting researchers to seek alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are attracting attention again as therapeutic agents with promising utility in this domain, and using in silico methods to discover novel AMPs is a strategy that is gaining interest. Such methods can sift through large volumes of candidate sequences and reduce lab screening costs.

Disruption by stealth - Interference of endocrine disrupting chemicals on hormonal crosstalk with thyroid axis function in humans and other animals.

Thyroid hormones (THs) are important regulators of growth, development, and homeostasis of all vertebrates. There are many environmental contaminants that are known to disrupt TH action, yet their mechanisms are only partially understood. While the effects of Endocrine Disrupting Chemicals (EDCs) are mostly studied as "hormone system silos", the present critical review highlights the complexity of EDCs interfering with TH function through their interactions with other hormonal axes involved in reproduction, stress, and energy metabolism.

Mechanism of copper nanoparticle toxicity in rainbow trout olfactory mucosa.

Chemosensory perception is crucial for fish reproduction and survival. Direct contact of olfactory neuroepithelium to the surrounding environment makes it vulnerable to contaminants in aquatic ecosystems. Copper nanoparticles (CuNPs), which are increasingly used in commercial and domestic applications due their exceptional properties, can impair fish olfactory function.

Sucralose Affects Thyroid Hormone Signaling in American Bullfrog [Rana (Lithobates) catesbeiana] Tadpoles.

Nonnutritive sweeteners used in food and beverage products are widespread, persistent aquatic pollutants. Despite this, their impact on aquatic organisms, particularly vertebrates, is not well-studied. Recent findings in rodents suggest sucralose, a chlorinated disaccharide, alters thyroid hormone (TH) metabolism.

Dioctyl Sodium Sulfosuccinate as a Potential Endocrine Disruptor of Thyroid Hormone Activity in American bullfrog, Rana (Lithobates) catesbeiana, Tadpoles.

The thyroid hormones, thyroxine (T) and triiodothyronine (T), are required to regulate complex developmental processes in vertebrates and are highly sensitive to endocrine-disrupting compounds. Previous studies demonstrate that dioctyl sodium sulfosuccinate (DOSS), a common constituent of pharmaceuticals, cosmetics, and food products, disrupts canonical signaling of adipocyte differentiation by binding a nuclear hormone receptor in the same superfamily as thyroid hormone (TH) receptors. The present study was designed to determine whether DOSS is capable of disrupting TH signaling using the American bullfrog, Rana (Lithobates) catesbeiana-a cosmopolitan frog species that undergoes TH-dependent metamorphosis to transition from an aquatic tadpole to a terrestrial juvenile frog.

The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA.

Objective: Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published.

Enhanced analysis of weathered crude oils by gas chromatography-flame ionization detection, gas chromatography-mass spectrometry diagnostic ratios, and multivariate statistics.

Artificially weathered crude oil "spill" samples were matched to unweathered suspect "source" oils through a three-tiered approach as follows: Tier 1 gas chromatography-flame ionization detection (GC/FID), Tier 2 gas chromatography-mass spectrometry (GC/MS) diagnostic ratios, and Tier 3 multivariate statistics. This study served as proof of concept for a promising and new method of crude oil forensics that applies principal component analysis (PCA) and partial least squares discriminant analysis (PLSDA) in tandem with traditional forensic oil fingerprinting tools to confer additional confidence in challenging oil spill cases. In this study, weathering resulted in physical and chemical changes to the spilled oils, thereby decreasing the reliability of GC/FID and GC/MS diagnostic ratios in source attribution.

Corrigendum: Contaminant and Environmental Influences on Thyroid Hormone Action in Amphibian Metamorphosis.

[This corrects the article DOI: 10.3389/fendo.2019.

Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs.

Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization.

Contaminant and Environmental Influences on Thyroid Hormone Action in Amphibian Metamorphosis.

Aquatic and terrestrial environments are increasingly contaminated by anthropogenic sources that include pharmaceuticals, personal care products, and industrial and agricultural chemicals (i. e., pesticides).

Expansion of the known distribution of the coastal tailed frog, Ascaphus truei, in British Columbia, Canada, using robust eDNA detection methods.

The coastal tailed frog (Ascaphus truei) is endemic to the Pacific Northwest of North America and is listed as a species of Special Concern under the Canadian Species at Risk Act. Its range is limited to British Columbia where it occurs widely west of the Coast Mountain Ranges extending north almost to the Alaskan Panhandle. The present study focused on surveying within the Cayoosh, Bridge (Shulaps), Seton, Anderson, Carpenter, and Downton Lake drainages.

Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles.

Antimicrobial peptides (AMPs) exhibit broad-spectrum antimicrobial activity, and have promise as new therapeutic agents. While the adult North American bullfrog (Rana [Lithobates] catesbeiana) is a prolific source of high-potency AMPs, the aquatic tadpole represents a relatively untapped source for new AMP discovery. The recent publication of the bullfrog genome and transcriptomic resources provides an opportune bridge between known AMPs and bioinformatics-based AMP discovery.