Chemotyping and identification of protected Dalbergiatimber using gas chromatography quadrupole time of flight mass spectrometry.

The international trade in illegally logged and environmentally endangered timber has spurred enforcement agencies to seek additional technical procedures for the identification of wood species. All Dalbergia species are listed under the Convention on International Trade in Endangered Species (CITES) which is the reason this genus was chosen for study. Multiple sources of the heartwood from different Dalbergia species were extracted and chromatographic profiles collected by gas chromatography with high resolution quadrupole Time of Flight mass spectrometry (GC/QToF). The collected data was mined to select peaks and mass ions representative of the investigated Dalbergia species, and used to develop a Microsoft Excel® template offering immediate graphical representation of the results. Using wood specimens sourced from different xylaria, this graphical fingerprint proved adept at definitive identification of Dalbergia species. The CITES Appendix I species, D. nigra, was easily distinguished from D. melanoxylon and look-alike species of other genera. Similarly, a number of other Dalbergia species were differentiated using this current approach. Kernel discrimination analysis (KDA) was applied to increase the confidence of the species identification. The mislabeling of specimens appears to be common, and the emerging technique of GC/QToF in combination with other techniques, offers improved confidence in identification. GC/QToF further provides automation, the dimension of chromatography to avoid interferences, and production of reproducible electron impact positive (EI+) spectra. The prospect of building an EI+ spectral database for future wood identification is an important feature considering the limited accessibility of authenticated wood species specimens.

Ecotoxicogenomics: Microarray interlaboratory comparability.

Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.

Gene expression pattern in the liver during recovery from an acute stressor in rainbow trout.

The physiological response to stressors, including hormonal profiles and associated tissue responsiveness, has been extensively studied with salmonid fish, but less is known about the molecular basis of this adaptive response. As liver is the major target organ for metabolic adjustments, we exploited a selective transcriptomics approach to address molecular response in this tissue during acute stress adaptation in rainbow trout. The stressor consisted of a standardized 3 min handling disturbance of trout, and plasma and liver samples were collected either prior to or 1 and 24 h after stressor exposure. We developed a low density custom cDNA array consisting of 147 rainbow trout genes designed specifically to represent stress-responsive and endocrine-related pathways in fish. The acute stress response and recovery was confirmed by the transient elevation in plasma cortisol concentration at 1 h, which returned to pre-stress levels over a 24 h period. This was accompanied by significant upregulation of 40 genes at 1 h, and 15 genes at 24 h after stressor exposure in trout liver. Many of these genes were involved in energy metabolism, implicating a rapid liver molecular reprogramming as critical for the metabolic adjustments to an acute stressor. Several other transcripts not previously implicated in the stress response process in fish, including genes involved in immune function and protein degradative pathways, were found to be stress-responsive in trout. A large number of these stress-responsive transcripts were also shown previously to be glucocorticoid-responsive in fish. Together, our results suggest a role for stressor-mediated genomic cortisol signaling in the liver molecular programming associated with stress in fish. Overall, the study demonstrates the complex nature of the adaptive stress response at the molecular level and underscores the utility of targeted gene expression studies for identifying stress coping mechanisms.