Ecotoxicology of metal-hydrocarbon mixtures in benthic invertebrates

Metal-hydrocarbon mixtures are becoming increasingly prevalent in natural environments due to expanding industrial activity and urbanization. The ecotoxicology of metal-hydrocarbon mixtures in benthic environments is of particular concern because both classes of contaminants partition to sediments and can thereby exert toxic effects in benthic organisms. Mixtures of dissimilar chemicals (including metals and hydrocarbons) are broadly hypothesized to elicit independent toxic effects however; this hypothesis has little supporting data. The purpose of this dissertation was to test this hypothesis for metal-hydrocarbon mixtures using environmentally relevant exposures and to determine mechanisms for observed interactive effects. Sediment and water-only bioassays were conducted employing the toxic heavy metal cadmium (Cd) and the polynuclear aromatic hydrocarbon phenanthrene (Phen) as model toxicants. Lethal and sublethal effects of singular and combined contaminants were examined in two freshwater species, the epibenthic amphipod Hyalella azteca and the bulk deposit-feeding benthic oligochaete Ilyodrilus templetoni. When interactive toxicity was observed, mixture effects on contaminant bioavailability, bioaccumulation and elimination were tested. As well, mixture effects on bioenergetics parameters were investigated and kinetic modeling was conducted to establish the source of mixture-mediated changes in contaminant bioaccumulation in I. templetoni. Cadmium-Phen mixtures caused independent effects in water-only exposures, but when incorporated into sediments, elicited synergistic lethal effects in H. azteca and antagonistic lethal effects in I. templetoni. Interactive effects were likely caused by Phen-mediated alterations in Cd bioaccumulation that resulted from changes in exposure via feeding. The current basis for assessing ecotoxicological effects of contaminant mixtures in natural environments relies heavily on models derived from dosage-based mixture toxicology with considerably less emphasis on environmental science and biology. Understanding how contaminants interact toxicologically is important, but does not provide all the information necessary for assessing effects in natural populations that encounter contaminant mixtures in a diversity of natural environments. My experiments indicate that exposure source may be more important than dosage-based toxicological interactions in determining contaminant mixture effects in sediment environments. If this trend is widespread, understanding how species are exposed, determining the route of uptake and understanding how environmental characteristics affect exposure may be more important in determining mixture effects than mixture toxicology

CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms

Our goal is to introduce and describe the utility of a new pipeline “Contigs Assembly Pipeline using Reference Genome” (CAPRG), which has been developed to assemble “long sequence reads” for non-model organisms by leveraging a reference genome of a closely related phylogenetic relative. To facilitate this effort, we utilized two avian transcriptomic datasets generated using ROCHE/454 technology as test cases for CAPRG assembly. We compared the results of CAPRG assembly using a reference genome with the results of existing methods that utilize de novo strategies such as VELVET, PAVE, and MIRA by employing parameter space comparisons (intra-assembling comparison). CAPRG performed as well or better than the existing assembly methods based on various benchmarks for “gene-hunting.” Further, CAPRG completed the assemblies in a fraction of the time required by the existing assembly algorithms. Additional advantages of CAPRG included reduced contig inflation resulting in lower computational resources for annotation, and functional identification for contigs that may be categorized as “unknowns” by de novo methods. In addition to providing evaluation of CAPRG performance, we observed that the different assembly (inter-assembly) results could be integrated to enhance the putative gene coverage for any transcriptomics study

Quail Genomics: a knowledgebase for Northern bobwhite

<p>Abstract</p> <p>Background</p> <p>The Quail Genomics knowledgebase (<url>http://www.quailgenomics.info</url>) has been initiated to share and develop functional genomic data for Northern bobwhite (<it>Colinus virginianus</it>). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank.</p> <p>Description</p> <p>A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A normalized MySQL relational database was established to provide comprehensive search parameters where meta-data can be retrieved using functional and structural information annotation such as gene name, pathways and protein domain. Additionally, blast hit cutoff levels and microarray expression data are available for batch searches. A Gene Ontology (GO) browser from Amigo is locally hosted providing 8,825 unigenes that are putative orthologs to chicken genes. In an effort to address over abundance of Northern bobwhite unigenes (71,384) caused by non-overlapping contigs and singletons, we have built a pipeline that generates scaffolds/supercontigs by aligning partial sequence fragments against the indexed protein database of chicken to build longer sequences that can be visualized in a web browser. </p> <p>Conclusion</p> <p>Our effort provides a central repository for storage and a platform for functional interrogation of the Northern bobwhite sequences providing comprehensive GO annotations, meta-data and a scaffold building pipeline. The Quail Genomics knowledgebase will be integrated with Japanese quail (<it>Coturnix coturnix</it>) data in future builds and incorporate a broader platform for these avian species. </p

Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative of Phenotypic Outcomes in Western Fence Lizard

Background The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizards (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays. Results Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms linking transcript expression and toxicological phenotypes. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses and adverse decreases in lizard growth at high doses. Functional enrichment results were indicative of inhibited potential for lipid mobilization and catabolism in TNT exposures which corresponded with increased inguinal fat weights and was suggestive of a decreased overall energy budget. Malaria infection elicited enriched expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune responses consistent with a decrease in WBC levels. Conclusions Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bio-energetic constraints. Interestingly, both TNT and malaria individually increased transcriptional expression of immune-related genes and increased overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated

Exposure to cadmium-phenanthrene mixtures elicits complex toxic responses in the freshwater tubificid oligochaete, Ilyodrilus templetoni

The joint toxicity of metal-hydrocarbon mixtures in sediments was investigated using cadmium (Cd) and phenanthrene (Phen) as model contaminants. Sediment bioassays were utilized to quantify effects of individual and combined contaminants in the bulk-deposit feeding oligochaete Ilyodrilus templetoni. Combined contaminants elicited antagonistic lethal effects and independent responses for feeding rate (measured as sediment ingestion). The 10-d LC(50) for Cd alone was 1375 mg kg(-1) (95% C.I. 1340-1412), whereas Phen elicited no mortality even when loaded to sediment saturation. The presence of Phen decreased Cd lethality, increasing the LC(50) of Cd by as much as 40%. Regression analyses indicated that Phen was nearly 10 times more potent than Cd in eliciting feeding rate reductions. Exposure to Cd-Phen mixtures resulted in feeding rate reductions equivalent to those caused by Phen alone. The marked reduction in sediment ingestion induced by the co-pollutant Phen reduced exposure to Cd via ingestion. We suggest that this Phen-induced reduction in Cd exposure decreased Cd bioaccumulation and subsequent lethality. More generally, we suggest that even if the toxicological effects among dissimilarly acting chemicals (including metals and hydrocarbons) are independent, contaminant mixtures may elicit unexpected interactive effects facilitated by modifying exposure

Exposure-related effects on Cd bioaccumulation explain toxicity of Cd-phenanthrene mixtures in Hyalella azteca

Little is known regarding mixture effects of metals and polynuclear aromatic hydrocarbon (PAHs) under environmentally relevant exposure regimes. Standard U.S. Environmental Protection Agency (U.S. EPA) procedures were applied and extended to test effects of phenanthrene (Phen) on sediment-Cd uptake, aqueous-Cd uptake, and Cd-elimination kinetics in the amphipod Hyalella azteca. In sediment exposures, Phen increased the projected equilibrium-tissue concentration of Cd from 47.2 (36.2-58.3) to 221.1 microg/g ([117.8-324.3], 95% confidence intervals [CI] in parentheses). Although Cd bioaccumulation increased markedly in sediment exposures, dissolved Cd concentrations and physical-chemical parameters indicative of Cd bioavailability were unaffected by Phen. Further, in water-only exposures, Phen had no effect on Cd bioaccumulation or Cd-elimination kinetics. These results indicate that increased Cd bioaccumulation in Cd-Phen mixtures occurred via a sediment-mediated process and was likely a function of increased uptake associated with feeding (i.e., Phen-induced alterations in ingestion and/or digestive processes). Observed increases in H. azteca lethality when exposed to Cd-Phen mixtures in sediment, but not in water-only exposures, likely resulted from increased Cd bioaccumulation rate rather than a true toxicological synergism. Thus, apparent synergisms and antagonisms may result from exposure-mediated effects in sediment that are unrelated to toxicological interactions. Implications of these findings regarding sediment-quality assessment and suggestions for future studies are discussed

Mixtures of metals and polynuclear aromatic hydrocarbons elicit complex, nonadditive toxicological interactions in meiobenthic copepods

The acute toxicity of metal-polynuclear aromatic hydrocarbon (PAH) mixtures (i.e., Cd, Hg, Pb, fluoranthene, and phenanthrene) associated with sediments was assessed in two benthic copepods. Schizopera knabeni was exposed to sediment amended with single contaminants and mixtures. Adult S. knabeni were highly tolerant of single-contaminant exposures to phenanthrene, Cd, Hg, and Pb as well as a mixture of Cd, Hg, and Pb. Binary experiments revealed that although phenanthrene was synergistic with Cd and Hg, the phenanthrene-Cd synergism was much stronger (2.8 times more lethal than predicted). When a mixture of Cd, Hg, and Pb was combined with phenanthrene, a synergistic response was observed, eliciting 1.5 times greater lethality than predicted. A Cd-phenanthrene synergism in S. knabeni was also observed in aqueous exposures, suggesting that the interaction was related to a pharmacological insult rather than a sediment-related exposure effect. An antagonism between Cd, Hg, and Pb was indicated, and this antagonism may have moderated the Cd-phenanthrene synergism in mixtures containing Cd, Hg, Pb, and phenanthrene. Experiments with Amphiascoides atopus revealed that phenanthrene and fluoranthene were each synergistic with Cd in aqueous exposures. Our studies suggest that interactive toxicity among metal-PAH mixtures may be common among benthic copepods and that strong synergistic effects observed in binary mixtures may be moderated in more diverse contaminant mixtures. However, the strength of the observed synergisms raises concerns that established sediment quality criteria may not be protective for organisms jointly exposed to PAH and metals, especially Cd-PAH mixtures

Genome Scale Inference of Transcriptional Regulatory Networks Using Mutual Information On Complex Interactions

Inferring the genetic network architecture in cells is of great importance to biologists as it can lead to the understanding of cell signaling and metabolic dynamics underlying cellular processes, onset of diseases, and potential discoveries in drug development. The focus today has shifted to genome scale inference approaches using information theoretic metrics such as mutual information over the gene expression data. In this paper, we propose two classes of inference algorithms using scoring schemes on complex interactions which are primarily based on information theoretic metrics. The central idea is to go beyond pair-wise interactions and utilize more complex structures between any node (gene or transcription factor) and its possible multiple regulators (only transcription factors). While this increases the network inference complexity over pair-wise interaction based approaches, it achieves much higher accuracy. We restricted the complex interactions considered in this paper to 3-node structures (any node and its two regulators) to keep our schemes scalable to genome-scale inference and yet achieve higher accuracy than other state of the art approaches. Detailed performance analyses based on benchmark precision and recall metrics over the known Escherichia coli transcriptional regulatory network, indicated that the accuracy of the proposed algorithms (sCoIn, aCoIn and its variants) is consistently higher in comparison to popular algorithms such as context likelihood of relatedness (CLR), relevance networks (RN) and GEneNetwork Inference with Ensemble of trees (GENIE3)