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Coastal waters of Lake Superior are generally inhospitable to the establishment of invasive Dreissena spp. mussels (both Dreissena polymorpha and Dreissena bugensis). Dreissena have inhabited the Saint Louis River estuary (SLRE; largest commercial port in the Laurentian Great Lakes) for over three decades, but only in the last few years have small colonies been found in the Apostle Islands National Lakeshore (APIS, an archipelago situated 85 km to the east of SLRE) A 2017 survey determined a low abundance Dreissena spatial distribution in APIS, with the largest colonies on the north and west islands which suggested potential veliger transport from the SLRE via longshore currents. Our objective in this study was to determine if Dreissena veligers are transported by currents at low densities along the south shore of Lake Superior from the SLRE to APIS. To do so, we used both eDNA (water and passive substrate samples) and zooplankton collection methods at eight sites evenly spaced between the SLRE and APIS with three sampling times over five weeks. Dreissena veligers were consistently detected along the south shore, although at low abundances (veligers per m3 range = 0-690, median = 8), and for every 1 km increase in distance from the SLRE, both veliger counts and water eDNA copy numbers decreased on average by 5 and 7%, respectively. D. polymorpha (suited to estuary habitats) was detected two times more than D. bugensis (better suited to deep-lake habitats). There was not a trend in the veliger size distribution along the south shore, and temperature and calcium concentrations fluctuated around the threshold for Dreissena veliger and adult development, averaging 11.0°C and 14.8 ppm, respectively. Three zooplankton taxa representative of the estuary community-Daphnia retrocurva, Diaphanosoma birgei, and Mesocyclops copepodites-decreased as the distance from the SLRE increased mirroring Dreissena veliger abundance patterns. Findings represent multiple sources of evidence of a propagule "conveyor belt" for Dreissena along the south shore of Lake Superior. We conclude that veligers are functioning as a propagule, using coastal currents to spread from the point of invasion, thereby traversing coastal habitat previously reported as inhospitable to distant habitats suitable for colonization.

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BACKGROUND: Bioinformaticians collaborating with life scientists need software that allows them to involve their collaborators in the process of data analysis. RESULTS: We have developed a web application that allows researchers to publish and execute data analysis scripts. Within the platform bioinformaticians are able to deploy data analysis workflows (recipes) that their collaborators can execute via point and click interfaces. The results generated by the recipes are viewable via the web interface and consist of a snapshot of all the commands, printed messages and files that have been generated during the recipe run. A demonstration version of our software is available at https://www.bioinformatics.recipes/ . Detailed documentation for the software is available at: https://bioinformatics-recipes.readthedocs.io . The source code for the software is distributed through GitHub at https://github.com/ialbert/biostar-central . CONCLUSIONS: Our software platform supports collaborative interactions between bioinformaticians and life scientists. The software is presented via a web application that provides a high utility and user-friendly approach for conducting reproducible research. The recipes developed and shared through the web application are generic, with broad applicability and may be downloaded and executed on other computing platforms.

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The toxicity of waterborne retene (7-isopropyl-1-methyl phenanthrene) to post-hatch embryos of rainbow trout (Oncorhynchus mykiss) was assessed at 5 and 11 °C. Survival times of retene-exposed embryos were 70 % longer at 5 °C than at 11 °C, but survival times and LC50 s did not vary when time was expressed as degree-days (thermal units), i.e., at a common stage of development. The size of survivors decreased with increasing retene concentrations, but not with temperature. Retene did not bioconcentrate to any extent (bioconcentration factors < 2) at either temperature, indicating effective biotransformation by embryos. However, concentrations of retene metabolites were slightly higher at 5 °C, suggesting slower excretion rates than at 11 °C. The relative expression of cytochrome P450 proteins (CYP1A) did not vary with temperature but increased with retene concentration, as indicated by cyp1a mRNA concentrations. The induction of CYP1A protein by retene exposure was evident in the vasculature of eye, brain, heart, kidney, liver, gill, mouth, intestine, muscle, and yolk-sac. However, immunohistochemical staining was greater at 5 than at 11 °C for all tissues except liver and muscle. Overall, temperature effects on retene toxicity disappeared when the duration of embryo development and retene exposure were expressed as thermal units (degree-days). Temperature controlled the rate of embryo development and the rate of toxicity (time to a toxic endpoint), but not the concentrations that were toxic.

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Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp movement, hydrography, spawning and eDNA on the Wabash River, IN, USA. We found positive relationships between eDNA and movement and eDNA and hydrography. We did not find a relationship between eDNA and spawning activity in the form of drifting eggs. Our first finding demonstrates how eDNA may be used to monitor species abundance, whereas our second finding illustrates the need for additional research into eDNA methodologies. Current applications of eDNA are widespread, but the relatively new technology requires further refinement.

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The suppressor of cytokine signaling (SOCS) proteins are a family of intracellular proteins that are centrally involved with vertebrate growth, development and immunity via their effects as negative feed-back regulators of cytokine (and hormone) signaling. The genes for SOCS-1 & -3 were cloned, sequences analyzed and expression patterns examined in the commercially-important teleost, yellow perch (Perca flavescens). The deduced (mature) proteins for yellow perch (yp)SOCS-1 and (yp)SOCS-3 consist of 211 and 205 amino acids, respectively. Functional domains such as the Src homology-2 (SH2) and SOCS-box were present in ypSOCS-1 and ypSOCS-3 and these domains were well conserved between teleost species. Sequence analysis showed that ypSOCS-1 & -3 share highest homology (among similar teleost sequences), to the stickleback (Gasterosteus aculatus) SOCS-1 & -3 protein homologs. To investigate sex-specific expression of the ypSOCS-1 and ypSOCS-3 mRNAs, juvenile male and female yellow perch were immunologically challenged with a single injection (10 µg/g bw) of lipopolysaccharide (LPS) and tissues (gill, head kidney, kidney, liver and spleen) were sampled over a 48-h time-course. Quantitative real-time PCR analysis showed that ypSOCS-1 & -3 were expressed in all tissues examined and at all sampling time-points. LPS injection significantly induced ypSOCS-1 & -3 mRNA levels in gill, head kidney, liver, kidney and spleen, with maximal induction occurring at 6 h post-injection in each tissue. By 48-h post-injection, expression levels for ypSOCS-1 & -3 mRNAs approached, or reached, control levels in all tissues examined. While there were statistical interactions among variables (treatment, time and sex) for ypSOCS-1, we only found a main effect of sex on SOCS-3 mRNA expression in head kidney with higher copy numbers occurring in males than in females treated with LPS. Sexually-dimorphic expression of SOCS-1 or -3 mRNA has not been examined, or described, in a teleost. Our findings suggest the involvement of the SOCS genes in the yellow perch immune response and that differences among the sexes are evident and should be explored further.

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BACKGROUND: Methylmercury (MeHg) is a known neurotoxic agent, but the mechanisms by which MeHg may act on reproductive pathways are relatively unknown. Several studies have indicated potential changes in hormone levels as well as declines in vertebrates with increasing dietary MeHg exposure. OBJECTIVES: The purpose of this study was to identify alterations in gene expression associated with MeHg exposure, specifically those associated with previously observed changes in reproduction and reproductive biomarkers. Fathead minnows, Pimephales promelas, were fed one of three diets that were similar to documented concentrations of MeHg in the diets of wild invertivorous and piscivorous fish. We used a commercial macroarray in conjunction with quantitative polymerase chain reaction to examine gene expression in fish in relation to exposure to these environmentally relevant doses of MeHg. RESULTS: Expression of genes commonly associated with endocrine disruption was altered with Hg exposure. Specifically, we observed a marked up-regulation in vitellogenin mRNA in individual Hg-exposed males and a significant decline in vitellogenin gene expression in female fish with increasing Hg concentrations. Other genes identified by the macroarray experiment included those associated with egg fertilization and development, sugar metabolism, apoptosis, and electron transport. We also observed differences in expression patterns between male and female fish not related to genes specifically associated with reproduction, indicating a potential physiological difference in the reaction of males and females to MeHg. CONCLUSION: Gene expression data may provide insight into the mechanisms by which MeHg affects reproduction in fish and indicate how MeHg differs in its effect from other heavy metals and endocrine-disrupting compounds.

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Expression of cytochrome P4501A (CYP1A) has been used as a biomarker for possible exposure to contaminants such as PCBs and dioxins in teleost fish. Using a quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) and a non-lethal gill biopsy, we estimated levels of CYP1A mRNA expression in Atlantic salmon (Salmo salar). Groups of ten Atlantic salmon juveniles (48-76 g) received an intraperitoneal injection of 50 microg g(-1) beta-naphthoflavone (BNF) or vehicle. Their gill tissues were repeatedly sampled by non-lethal biopsies on day 0, 1, 2 and 7. Control fish expressed basal levels of CYP1A over the duration of sampling. BNF-treated salmon demonstrated similar levels of CYP1A to control fish at day 0 and higher levels over the course of each additional sampling point. Gill biopsies from wild salmon sampled from Millers River (South Royalston, Worcester County, MA, USA), known to contain PCBs, showed significantly higher CYP1A levels over an uncontaminated reference stream, Fourmile Brook (Northfield, Franklin County, MA, USA). We conclude that gill biopsies coupled with Q-RT-PCR analysis is a valuable tool in environmental assessment of wild Atlantic salmon populations and has the potential to be applied to other populations of fish as well.

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The expression of CYP1A (cytochrome P4501A) can be induced by a large array of aromatic and organic compounds in teleost fishes. We developed a real-time quantitative PCR assay useful for measuring beta-naphthoflavone (BNF) induction of liver CYP1A mRNA in four salmonid species. First, to obtain necessary information for the design of a cRNA standard, full-length CYP1A cDNA sequences were determined for two Salvelinus species, lake trout (S. namaycush) and brook trout (S. fontinalis). Each cDNA was found to share the same characteristics with known CYP1A sequences of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss): a start codon, conserved heme-binding region, putative poly-adenylation signal, stop codon, relatively long 3'-untranslated region (UTR; >1 kb), and a protein length of 523 amino acid residues. The brook trout and lake trout CYP1A cDNA's were 2636 and 2672 base pairs (bp) in length and shared greater than 97% coding region sequence identity with Atlantic salmon and rainbow trout CYP1A's. Next, using the generated sequence information, we developed a CYP1A-specific real-time quantitative PCR assay. Primers and a fluorescent-labeled probe were designed from a 68 bp region that was found to be conserved among salmonid CYP1A genes. The assay was designed to allow for simultaneous comparison of CYP1A expression among each experimental group. Finally, groups (n = 4-8) of hatchery-raised Atlantic salmon, brook trout, lake trout, and rainbow trout were given an intraperitoneal injection of a corn oil control, 25 mg kg(-1) BNF, or 50 mg kg(-1) BNF and sacrificed after 48 h. Liver tissue was collected and CYP1A mRNA levels were estimated. In all species, BNF treated fish showed 1.8-3.0 orders of magnitude higher CYP1A than control fish. The CYP1A induction levels were not different in fish treated with both dosages. Mean base levels of CYP1A expression ranged from 7.24 x 10(6) (rainbow trout) to 1.05 x 10(7) (brook trout) transcripts microg(-1) total RNA. Mean induced levels of CYP1A expression ranged from 1.07 x 10(8) (lake trout) to 1.05 x 10(9) (brook trout) trancripts microg(-1) total RNA.

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Many environmental pollutants induce expression of the cytochrome P450 (CYP) 1A subfamily of genes. We integrated cellular and molecular biological techniques to examine the effects of beta-naphthoflavone (BNF) exposure in lake trout brain CYP1A distribution and dynamics. Over a 32-day time-course, real time quantitative reverse transcription polymerase chain reaction (Q-RT-PCR) results showed that CYP1A mRNA induction in response to BNF exposure occurred rapidly and continued to rise in the BNF-treated lake trout after 4 h, with a peak at or after 2 days. Messenger RNA levels fell after 4 days, and this trend continued after 16 days of exposure. In situ hybridization indicated that CYP1A mRNA was universally elevated in the brain of BNF-exposed fish and was mainly expressed in the endothelia and occasionally in the glial cells. CYP1A immunoreactivity was induced in the olfactory bulb and valvula cerebelli of BNF-treated fish. Other brain areas showed constitutive CYP1A immunoreactivity in both control and BNF-treated fish. Some BNF-treated fish contained multifocal hemorrhages in the brain tissue, and these fish had overall depressed CYP1A immunoreactivity in the brain. The relationship between transcriptional and translational effects of BNF exposure in the brain of juvenile lake trout is discussed.

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