Arsenic Reduces Gene Expression Response to Changing Salinity in Killifish

ESKAPE Act Plus: Pathway Activation Analysis for Bacterial Pathogens

The last 20 years have witnessed an explosion in publicly available gene expression and proteomic data and new tools to help researchers analyze these data. Tools typically include statistical approaches to identify differential expression, integrate prior knowledge, visualize results, and suggest how differential expression relates to changes in phenotype. Here, we provide a simple web-based tool that bridges some of the gaps between the functionality available to those studying eukaryotes and those studying prokaryotes. Specifically, our Shiny web application ESKAPE Act PLUS allows researchers to upload results of high-throughput bacterial gene or protein expression experiments from 13 species, including the six ESKAPE pathogens, to our system and receive (i) an analysis of which KEGG pathways or GO terms are significantly activated or repressed, (ii) visual representations of the magnitude of activation or repression in each category, and (iii) detailed diagrams showing known relationships between genes in each regulated KEGG pathway and fold changes of individual genes. Importantly, our statistical approach does not require users to identify which genes or proteins are differentially expressed. ESKAPE Act PLUS provides high-quality statistics and graphical representations not available using other web-based systems to assess whether prokaryotic biological functions are activated or repressed by experimental conditions. To our knowledge, ESKAPE Act PLUS is the first application that provides pathway activation analysis and pathway-level visualization of gene or protein expression for prokaryotes. IMPORTANCE ESKAPE pathogens are bacteria of concern because they develop antibiotic resistance and can cause life-threatening infections, particularly in more susceptible immunocompromised people. ESKAPE Act PLUS is a user-friendly web application that will advance research on ESKAPE and other pathogens commonly studied by the biomedical community by allowing scientists to infer biological phenotypes from the results from high-throughput bacterial gene or protein expression experiments. ESKAPE Act PLUS currently supports analysis of 23 strains of bacteria from 13 species and can also be used to re-analyze publicly available data to generate new findings and hypotheses for follow-up experiments.

Environmentally relevant arsenic exposure affects morphological and molecular endpoints associated with reproduction in the Western mosquitofish, Gambusia affinis

Arsenic (As) exposure, even at low environmentally relevant levels, may cause detrimental health outcomes through developmental toxicity and by acting as an endocrine disrupting compound (EDC). Although several studies indicate that wildlife bioaccumulate As, few evaluate the health impact on fish species in their natural environment. In the U.S., As has a drinking water regulatory limit of 10 μg/L. In many parts of Arizona, surface water and groundwater have naturally elevated levels of As from geologic deposits and contamination is exacerbated by anthropogenic activity. In aquatic environments, the Western mosquitofish, Gambusia affinis, is a good bioindicator for EDC exposure because of the distinct androgen-related development of an intromittent organ, the gonapodium, in males. We evaluated morphological and reproductive outcomes in mosquitofish exposed to As. In a laboratory experiment, juvenile male mosquitofish were exposed to sodium arsenite (0 μg/L, 0.75 μg/L, 7.50 μg/L, and 75 μg/L) for 30 days, and in a field study, populations of adult male mosquitofish were collected in Arizona waterways with As levels above and below the World Health Organization's regulatory limit. In both studies, higher As exposure was significantly associated with altered hepatosomatic indices, altered fish morphology, shortened gonopodia, and lower gonopodia-somatic indices. In the field experiment, populations from surface water with higher As concentrations exhibited lower condition factors, lower gonadal-somatic indices, distinct gonopodia shapes, and altered estrogen receptor alpha and vitellogenin gene expression; androgen receptor expression was unchanged. Together, laboratory and field results suggest that As exposure at environmentally-relevant levels affects general growth and reproductive development in mosquitofish. Observed effects may further influence individual health, mobility, or reproductive function, and because G. affinis is a species known to tolerate and adapt to a wide range of environments, it serves as a local bioindicator species as well as a model organism for parallel field and laboratory studies.

Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus)

Salinity is a major ecological factor in the marine environment, and extremely important for the survival, development, and growth of fish. In this study, gill transcriptomes were examined by high-throughput sequencing at three different salinities (12 ppt as low salinity, 22 ppt as control salinity, and 32 ppt as high salinity) in an importantly economical fish silvery pomfret. A total of 187 genes were differentially expressed, including 111 up-regulated and 76 down-regulated transcripts in low-salinity treatment group and 107 genes differentially expressed, including 74 up-regulated and 33 down-regulated transcripts in high-salinity treatment group compared with the control group, respectively. Some pathways including NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, Toll-like receptor pathway, cardiac muscle contraction, and vascular smooth muscle contraction were significantly enriched. qPCR analysis further confirmed that mRNA expression levels of immune (HSP90A, IL-1β, TNFα, TLR2, IP-10, MIG, CCL19, and IL-11) and ion transport-related genes (WNK2, NPY2R, CFTR, and SLC4A2) significantly changed under salinity stress. Low salinity stress caused more intensive expression changes of immune-related genes than high salinity. These results imply that salinity stress may affect immune function in addition to regulating osmotic pressure in silvery pomfret.

Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress

The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model as a result of its ability to acclimate to rapid environmental changes and adapt to polluted habitats. MicroRNAs (miRNAs) are highly conserved small RNAs that regulate gene expression and play critical roles in stress responses in a variety of organisms. Global miRNA expression in killifish and the potential roles miRNA have in environmental acclimation have yet to be characterized. Accordingly, we profiled miRNA expression in killifish gill for the first time and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms. Killifish respond to large fluctuations in salinity with rapid changes in gene expression and protein trafficking to maintain osmotic balance, followed by a secondary phase of gene and protein expression changes that enable remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit gene expression responses in killifish gill, as well the ability of killifish to acclimate to a rapid increase in salinity. Thus, we examined the individual and combined effects of salinity and arsenic on miRNA expression in killifish gill. Using small RNA sequencing, we identified 270 miRNAs expressed in killifish, and found that miR-135b was differentially expressed in response to arsenic and at 24 h following transfer to salt water. Predicted targets of miR-135b are involved in ion transport, cell motility and migration, GTPase mediated signal transduction and organelle assembly. Consistent with previous studies of these two environmental stressors, we found a significant interaction (i.e., arsenic dependent salinity effect), whereby killifish exposed to arsenic exhibited an opposite response in miR-135b expression at 24 h post hyperosmotic challenge compared to controls. By examining mRNA expression of predicted miRNA targets during salinity acclimation and arsenic exposure, we found that miR-135b targets were significantly more likely to decrease during salinity acclimation than non-targets. Our identification of a significant interaction effect of arsenic and salinity on miR-135b expression supports the hypothesis that arsenic alters upstream regulators of stress response networks, which may adversely affect the killifish response to osmotic stress. The characterization of miRNAs in this ecotoxicological model will be a valuable resource for future studies investigating the role of miRNAs in response to environmental stress.