Ranking the Relative Importance of Toxicological Observations Based on Subject Matter Expertise

<p>Toxicological investigations provide key observations for establishing potential impacts of chemicals and other materials in environmental exposures. The specific evaluation of chemical toxicity can be drawn from numerous lines of evidence, including, but, not limited to: lethality, sub-lethal impacts, toxicokinetics, critical tissue residues, molecular toxicology, reproductive impacts, mutation, carcinogenesis, decreased genetic diversity in populations and decreased species diversity. Despite this richness of potential observations, many predictive toxicological models, such as those included in life cycle impact assessment (LCIA), generally rely on one or a few ecotoxicity measures including median lethal concentrations (LC50) and no observed effects concentrations (NOECs). By excluding all but these composite effects metrics, such models often fail to accurately and/or robustly capture potential adverse outcomes that may negatively affect individual health, biological fitness and/or population sustainability. Although each has the potential to add value to chemical risk assessment, the relative importance of the various toxicological observations available for characterizing and assessing environmental impact has not been established. Therefore, we sought to establish the importance of multiple ecotoxicological lines of evidence for assessing environmental impacts. “Importance” in this context is a subjective valuation based on perceived utility within an assessment, therefore we developed and administered a survey to query subject matter experts (SMEs) in the fields of toxicology, ecotoxicology and risk assessment on the importance of a broad array of ecotoxicological measurements. This scoping study focused on SME opinions from Department of Defense scientists and risk assessors where 61 surveys were distributed and 21 returned and analyzed. Overall, observations from chronic exposures and reproductive endpoints were ranked the highest among SMEs while lines of evidence from in vivo studies outranked both in vitro and in silico observations.</p

Appendix A. Estimating bioenergetic model parameters from synthesized literature data.

Estimating bioenergetic model parameters from synthesized literature data

Appendix B. Supplementary figures on the dynamics and predictions of the bioenergetic model.

Supplementary figures on the dynamics and predictions of the bioenergetic model

Appendix C. Literature summary of papers investigating global transcript expression in Daphnia.

Literature summary of papers investigating global transcript expression in Daphnia

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

<div><p>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 <em>de novo</em> 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 <em>de novo</em> 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.</p> </div

The extent of common protein sequences in different assemblies and parameters from Japanese quail datasets against chicken proteome database.

<p>Panel A represents the intra-assembling parameterization of PAVE at 80% and 90% identity and Panel B represents the inter-assembling comparison among PAVE, MIRA and CAPRG. Panel C represents the intra-assembling parameterization of PAVE at 80% and 90% identity and Panel D represents the inter-assembling comparison among PAVE, MIRA and CAPRG.</p

A Systems Toxicology Approach to Elucidate the Mechanisms Involved in RDX Species-Specific Sensitivity

Interspecies uncertainty factors in ecological risk assessment provide conservative estimates of risk where limited or no toxicity data is available. We quantitatively examined the validity of interspecies uncertainty factors by comparing the responses of zebrafish (<i>Danio rerio</i>) and fathead minnow (<i>Pimephales promelas</i>) to the energetic compound 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), a known neurotoxicant. Relative toxicity was measured through transcriptional, morphological, and behavioral end points in zebrafish and fathead minnow fry exposed for 96 h to RDX concentrations ranging from 0.9 to 27.7 mg/L. Spinal deformities and lethality occurred at 1.8 and 3.5 mg/L RDX respectively for fathead minnow and at 13.8 and 27.7 mg/L for zebrafish, indicating that zebrafish have an 8-fold greater tolerance for RDX than fathead minnow fry. The number and magnitude of differentially expressed transcripts increased with increasing RDX concentration for both species. Differentially expressed genes were enriched in functions related to neurological disease, oxidative-stress, acute-phase response, vitamin/mineral metabolism and skeletal/muscular disorders. Decreased expression of collagen-coding transcripts were associated with spinal deformity and likely involved in sensitivity to RDX. Our work provides a mechanistic explanation for species-specific sensitivity to RDX where zebrafish responded at lower concentrations with greater numbers of functions related to RDX tolerance than fathead minnow. While the 10-fold interspecies uncertainty factor does provide a reasonable cross-species estimate of toxicity in the present study, the observation that the responses between ZF and FHM are markedly different does initiate a call for concern regarding establishment of broad ecotoxicological conclusions based on model species such as zebrafish

Runtime for each program.

<p>Assembly times represent execution on a computer with a duo 2.26 GHz Quad core Intel Xeon processor, 16 GB of RAM and 64 bit Snow Leopard v1.6 operating system.</p

Assembly comparison for <i>Coturnix japonica</i> with various assembler programs and parameter spaces.

<p><i>E-value</i> cutoff for all database searches was <10E-05. The abbreviation “nr” represents non-redundant protein database from NCBI and “K” represents K-mer size. CAPRG* are assembly of reads that mapped to reference genome singly or failed to assemble by windowing against chromosome.</p

Distribution of contigs per chromosome for Japanese quail and Northern bobwhite against the chicken reference genome.

<p>Distribution of contigs per chromosome for Japanese quail and Northern bobwhite against the chicken reference genome.</p