Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics.

The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.

Cytochrome P450 and Glutathione-S-Transferase Activity are Altered Following Environmentally Relevant Atrazine Exposures in Crayfish (Faxoniusvirilis).

The herbicide atrazine is heavily applied in the U.S. Midwest to control broadleaf weeds. It enters local streams and rivers through runoff and seepage, and exposure can affect non-target aquatic organisms, like crayfish. We examined sublethal effects of atrazine on the expression and activity of the detoxification enzymes cytochrome P450 (CYP450) and glutathione-S-transferase (GST) in crayfish. Crayfish were exposed to 0, 10, 40, 80, 100 and 300 ppb atrazine for 1, 2, 4, 7 and 10 days. Their hepatopancreas was collected and CYP450 expression and GST activity was analyzed. Atrazine exposure caused differential expression and activity of CYP450 and GST. CYP450 expression varied over exposure concentrations and time. Further, GST activity significantly increased following a 2 day, 10 ppb exposure to atrazine and a 300 ppb atrazine exposure for all days tested. We found that atrazine detoxification is a dynamic process that changes with the length and intensity of atrazine exposure.

Diminished Conspecific Odor Recognition in the Rusty Crayfish (Orconectes rusticus) Following a 96-h Exposure to Atrazine.

The presence of agricultural contaminants has been shown to disrupt olfactory-mediated behaviors in aquatic animals. We assessed the effects of atrazine on the ability of reproductively active (form I), male crayfish (Orconectes rusticus) to identify and respond to conspecific chemical signals involved in mating. Male crayfish were exposed to atrazine (80 ppb) and water (control) for 96 h. We analyzed odor localization and locomotor behaviors of herbicide-treated and control male crayfish to two different odor sources: female odor or water (control) delivered from the proximal end of a test arena. Control crayfish spent more time in the proximal region of the test arena and at the odor source. Atrazine-exposed crayfish showed no preference for the proximal region of the test arena and odor source when female odor was delivered. Atrazine exposure did not affect locomotor behaviors. Overall, atrazine-mediated chemosensory deficits have the potential to disrupt mating and affect population size.

Developing Undergraduate Scientists by Scaffolding the Entry into Mentored Research.

For many college students, joining a research group is a critical step toward developing strong mentor-mentee relationships that help shape their science identities and research self-efficacy. ReBUILDetroit, a program that seeks to diversify the biomedical research workforce, uses a scaffolded process to help its scholars transition into research. The first-year curriculum includes a research methods course and a course-based undergraduate research experience that prepare ReBUILDetroit Scholars for entering a research group. Curricular and cocurricular elements prepare scholars for faculty interactions and diminish barriers that might otherwise prevent diverse students from obtaining these research experiences. The program facilitates research placements through student coaching and speed-pairing events. Quantitative and qualitative data on the scholars show strong perceived gains in science identity, enhanced research self-efficacy, and greater research preparedness.