Society of Toxicology Course Objectives--Draft June 25, 2018 Post-Feedback Draft

These objectives have been developed by the Learning Objectives Work Group of the SOT Education Committee’s Undergraduate Subcommittee. The group includes Joshua Gray (chair), Chris Curran, Vanessa Fitsanakis, Sid Ray, and Karen Stine.

For some items, a link to a case study or the PubMed unique identifier (PMID) or PubMed Central reference number (PMCID) for a relevant paper is provided.

Comments are encouraged. Please provide comments at this link.

Level One Objectives Evolution …………………………………………………………………... p. 1 Biological Information ………………………………………………..…… p. 4 Risk and Risk Management ……………………………………………... p. 12 Systems Toxicology ……………………………………………..……….. p. 18 Pathways and Transformations for Energy and Matter …………..….. p. 26

Evolution Second Third Level Fourth Level Level Model Describe • Explain how large numbers of offspring are beneficial for ideal model systems. Organisms features of • Explain how ease of manipulation is important for an ideal model system. for ideal model • Describe how use of a common model system contributes to reproducibility Toxicology systems. across laboratories. • Describe how ideal model systems have similarities to humans. • Explain how some model organisms are selected for organ-specific similarity to humans. For example, eyes of rabbits or skin of pigs. • Describe which ideal model organisms have similar xenobiotic metabolism systems to humans. • Explain why cost of maintenance, large number of offspring, and simplicity are characteristics of ideal model systems. Describe • Describe which model systems have similar metabolic pathways to humans. common model 28931683 systems, • Describe the historical importance of each common model system. including • Describe the advantages of simple animal model systems compared with cell Drosophila, C. culture or other in vitro approaches. elegans, • Describe how genetic similarities between Drosophila and humans make it a mouse, rat, and valuable model system. 29056683 non-human • Describe how Drosophila models metal toxicity in humans. 28684721 primate. • Describe the use of C. elegans as a model for viral host interactions. 28931683 • Discuss the history of the development of C. elegans as a model organism. 28326696

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Describe how • Describe the relationship between genetic phylogeny and similarity in evolution is physiology in terms of model systems for toxicology. fundamental to • Describe the role of evolution in comparisons of genes across species. the use of • Describe how evolution provides the rationale that animal studies are model systems translatable to humans. in toxicology. Describe • Describe how ethical issues impact the types of experiments that can be ethical reasons performed on humans. for using model • Describe how lack of data in humans supports the use of animals in research. organisms • Describe how reduction, refinement, and replacement (the three R's) ensure the best ethical treatment of animals used in research. • Describe the role of the Institutional Animal Care and Use Committee (IACUC) in guiding research at local institutions, ensuring the ethical treatment of animals. Evolution Contrast • Contrast a from a . of toxins and . • Know that many toxins are peptides or functional groups similar to amino acids. • Describe historical uses of toxins. • List and describe common toxins to which people are exposed on a regular basis. • Describe common uses for compounds classified as toxins. • Describe how toxins and toxicants are used in research settings. Explain the role • Contrast and . of toxins in • Describe the various ways animals and plants use toxins. 12179963 organismal • Describe common treatments used by clinical toxicologists to treat people defense. exposed to various toxins. • Distinguish between primary and secondary metabolites as defense molecules for various plants. • Discuss how animals and plants prevent intoxicating themselves with their own toxins. • Describe how quorum sensing affects the production of toxins in infectious microorganisms. Explain • Describe how prey detect toxins present in predators. mechanisms of • List common mechanisms associated with degradation/detoxification of toxins. avoidance of For example, many toxins are amino acid chains. poisoning by • Identify protective mechanisms (physical and chemical) used to prevent toxins. intoxication. • Discuss the role that taste, and smell may have in avoidance. • Evaluate the success of various protective mechanisms. • Describe one example of how seed lectin exhibits a toxin activity and a structural activity. 16441240 Explain the • Define the difference between a primary and secondary (or secondary and importance of tertiary) metabolite. secondary • Describe what additional protection and cost the production of a secondary metabolites. metabolite may provide the organism. • Case study: Describe the additional protection and cost incurred in oak trees responding to infestations with gypsy moths by induction of secondary metabolites in New York in the 1980s. • Compare and contrast the difference in toxicity caused by secondary metabolites. • List organisms that use secondary metabolites as deterrents (non-lethal chemicals) to predators. • List organisms that use secondary metabolites as lethal defenses against predators.

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Discuss how • List important toxins that are used in toxicology, pharmacology, neuroscience, important and other disciplines. toxins have • Describe the mechanism of research toxins and how they alter physiology of been helpful in the system being studied. characterizing • Describe the major advances in science associated with each toxin. basic biological • Case study: Describe how tetrodotoxin is used to investigate the role of properties. sodium channels by inhibiting the channel. • Case study: Describe how nicotine is used to investigate the role of nicotinic acetylcholine receptors. Evolution Discuss the • List common mechanisms of detoxification. of role of • Describe key enzymes that aid metabolism of toxic substances. xenobiotic xenobiotic • Compare and contrast general mechanisms of detoxicating toxins and defense defense toxicants. mechanism mechanisms in • List common toxins and toxicants and how they are specifically detoxicated s protection of • Discuss the difference between defense and detoxication. organisms from • Provide examples of how specific organisms deal with specific insults with toxicants and which they come into contact. toxins. Explain how • Describe how toxins and toxicants (such as pesticides or antibiotics) are evolution sources of selective pressure that drive evolutionary change. informs the • Discuss hypotheses regarding differences in the number of P450 enzymes in development of different species. http://drnelson.uthsc.edu/P450.evolution.2000.html the cytochrome • Describe the hypothesis that the cytochrome P450 gene superfamily evolved P450 from a single common ancestor. 22687468 superfamily of • Describe the evolution of transcription factors that regulate the cytochrome genes. P450 genes from the nuclear receptor family and bHLH-PAS family. 22687468 Explain how • Describe the micro-evolution of resistance to DDT. 21416112 evolution drives • Describe the example of evolution of sulfide spring fishes in response to resistance to environments rich in H2S. 29368386 toxicants, • Describe how application of low levels of pesticides can increase mutation toxins, metals, rates by inducing stress that lead to resistance. 21308950 and radiation. • Case study: Describe how exposure to polycyclic aromatic hydrocarbons in the Elizabeth River system of southeastern Virginia selected for resistance in Atlantic killifish. 26505693 Describe how • Describe the evolution of myoglobin and hemoglobin from a primordial globin knowledge of gene. genetic • Describe how the Basic Local Alignment Search Tool (BLAST) is used to information can provide regions of local similarity between protein or nucleotide sequences. predict function https://www.ncbi.nlm.nih.gov/books/NBK1734/ of similar genes • Analyze evolutionary trees to determine the relatedness of genes or protein within the same sequences. organism or in https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_interpretations other _02 organisms.

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Biological Information Chemical Describe the • Explain the development of genetic instability in cells undergoing neoplastic Carcinogene general conversion. PMC4274643 sis characteristics • Describe the changes in the cell cycle which are typically seen in neoplastic (genotoxic of cells that cells. and have • Describe the alterations in apoptotic susceptibility typically seen in neoplastic nongenotixic undergone cells. PMC4091735 ) and Cancer neoplastic • Explain the factors behind the tendency for local invasiveness in neoplastic conversion. cells. • Explain metastasis and describe the molecular changes behind the development of metastatic potential in neoplastic cells. PMC4071451, PMC3910084 Describe the • Describe the evidence for the link between mutagenesis and carcinogenesis mutational as generated by laboratory studies. theory of • Describe the evidence for the role of mutagenesis which derives from carcinogenesis observations of inheritability at both the cellular and organismal levels. and explain the • Describe the discovery of oncogenes and tumor suppressor genes and evidence that explain how this influenced the mutational theory. supports it. • Explain how evidence from DNA repair mechanism deficits supports the mutational theory. Explain the • Explain how missense, nonsense, insertion, deletion, frameshift, and repeat roles that proto- expansion mutations can affect proto-oncogenes. oncogenes can • Explain and give examples of proto-oncogene products (ras, PDGF, and play in normal others) with roles in ligand-receptor interactions and signal transduction. cell function; 26892781, PMC 4382731 then relate • Explain and give examples of proto-oncogene products (fos, jun, myc, and these, using others) with roles in regulation of gene expression (transcription factors). specific examples, to the role of proto- oncogenes in carcinogenesis. Describe the • Explain how missense, nonsense, insertion, deletion, frameshift, and repeat role of tumor expansion mutations can affect proto-oncogenes. suppressor • Describe the roles of tumor suppressor gene products (p53, Rb-1 and others) genes; using in regulation of cell growth cycle. PMC2773645 specific • Describe the roles of tumor suppressor gene products (BRCA-1 and others) in examples, DNA repair. explain how • Case study: Describe how polymorphisms in the APC gene increase the risk they can play a for colorectal neoplasia. 23896379 role in genetic predisposition to cancer.

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Identify the • Describe oxidative deamination of nucleotides. parts of the • Describe the alkylation of bases, including the discussion of “hot spots” in the DNA molecule genome. PMC5217664, PMC1856827 which are most • Explain the process of formation of DNA adducts, using examples (including vulnerable to nitrogen mustards, PAH). PMC5509823 damage by • Describe cross-linking and other mechanisms of damage to DNA. physical and PMC3755464 chemical agents and describe the mechanisms through which the damage occurs.

Explain the • Describe the metabolic activation of pro-, including examples differences such as nitrosamines and polycyclic aromatic hydrocarbons. 26652254, between pro- PMC4408964 carcinogens • Describe how cytochrome P450 enzymes play a prominent role in the and bioactivation of procarcinogens to create carcinogens. 9685642 carcinogens and be able to name examples of each. Explain the • Explain stimulation of cell division as a mechanism of promotion. concept of • Explain production of free radicals as a mechanism of promotion. promotion and • Explain alterations in biotransformation rates as a mechanism of promotion. discuss the • Explain inhibition of DNA repair as a mechanism of promotion. various • Explain the role of hormones (including estrogen, adipokines, and others) in mechanisms promotion. 25781552 through which toxicants can act as promoters. Compare and • Explain why a point mutation might or might not result in an alteration in contrast the protein structure and/or function. effects of point • Describe the potential consequences of point mutations in various regions of and frameshift DNA including genes (both exons and introns) and promoter regions. mutations on a • Describe the relationship between the position of a point mutation within a gene. codon and consequences for amino acid substitutions • Describe the significance of point mutations in terms of specific amino acid substitutions (e.g., nonpolar for polar, etc.). • Describe the significance of the location of point mutations/amino acid alterations in terms of primary structure of the protein. • Explain why frameshift mutations are often more severe than point mutations in terms of functional consequences. • Explain how either a point mutation or frameshift mutation could produce “stop” codon and the consequences of that on protein structure and function.

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Describe the • Describe the molecular mechanism of the excision repair systems. 28798238 excision repair • Describe the molecular mechanism of the mismatch repair system. 28927527 and mismatch • Describe the relationship between excision repair defects and xeroderma repair systems pigmentosum. PMC5556200 for repairing • Describe the relationship between mismatch repair and hereditary DNA damage. nonpolyposis colon cancer. 27315067

Compare and • Discuss the difficulties involved in generating data applicable to low human contrast the exposure levels. threshold vs. • Provide examples of policy decisions (including institution of the Delaney the non- Clause by the FDA) relating to the debate over cancer risk. threshold • Discuss how thresholds relate to regulatory definitions such as the “threshold models for risk of toxicological concern” (TTC). 15829616 following exposure to carcinogens and be able to discuss the public policy implications of both. Explain the • Explain how the Ames test is used to identify potential carcinogens and the concepts limitations of the Ames assay. behind in vitro • Compare and contrast the major in vitro bacterial testing systems with in vitro tests for mammalian systems. 22147568 mutagenic • Describe the role of the addition of microsomes to in vitro tests in terms of potential of identifying pro-carcinogens. toxicants and • Explain why in vitro tests are problematic in testing for epigenetic carcinogens compare and and promotion. contrast the • Explain why animal bioassay studies for carcinogenesis typically utilize high strengths and dose levels. weaknesses of these test versus animal bioassay studies. Gene/Envir Discuss the • Describe how SREBP-1c/SREBF regulate lipogenic genes as they relate to onment role that non-alcoholic fatty liver disease. 23545492 Interactions nutrition plays • Describe the role of inflammatory transcription factors and cytokines in (including in regulating lipogenesis. 16952562 epigenetics transcription • Describe the role of PPARγ in high-fat diet induced obesity and insulin ) factors. resistance. 1872365 • Explain the role of folic acid in preventing developmental toxicity. • Identify dietary factors that alter gene regulation. List the • Describe how aflatoxin reacts with DNA to induce mutations. changes that • Describe how ultraviolet light induces thymidine dimers in DNA. toxicants may • Describe how 4-hydroxynonenal is produced by lipid peroxidation and induces induce in the a lipid peroxidation chain reaction in the plasma membrane. protein • Describe how prions induce changes in protein structure that result in prion structure, disease. nucleic acid • Describe the effects of oxidizing agents on proteins and nucleic acids sequence, • Describe the effects of heavy metals on protein structure and function and/or fatty • Identify the common DNA changes induced by different toxicants acid • Identify compounds associated with fatty acid oxidation metabolites.

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Describe • Describe how DNA methylation, histone modification, and non-coding RNA mechanisms of (ncRNA)-associated gene silencing transmit epigenetic information. 15164071 epigenetic • Describe the role of CpG islands in promoters in regulating gene expression. transfer of • Describe how cancerous cells have altered DNA methylation patterns that information. result in altered gene expression. • Describe epigenetic mechanisms that increase or reduce gene expression • Explain how chromatin remodeling can affect gene expression. • Describe genetic imprinting and the importance of developmental timing in the inheritance of epigenetic information. Describe how • Describe environmental factors that can influence epigenetic mechanisms or toxicants can epigenetic marks. induce changes • Identify toxicants that can affect DNA methylation. in epigenetic • Identify toxicants that can affect chromatin remodeling. information that • Describe how benzene exposure affects methylation. 29370017 can be • Describe how aflatoxin B1, air pollution, arsenic, bisphenol A, cadmium, transferred to chromium, lead, mercury, polycyclic aromatic hydrocarbons, persistent subsequent organic pollutants, tobacco smoke, and nutritional factors influence DNA generations. methylation in humans. 29328878 Describe how • Identify critical windows of susceptibility to toxicant exposure. gene/environm • Identify allelic differences that affect susceptibility to developmental toxicant ent/time exposure. interactions • Describe how developmental exposures can lead to adult disease. affect • Interpret graphs of functional changes over the lifespan before/after toxicant developmental exposure to predict onset of disease/dysfunction. disorders and disorders of aging. Describe • Understand why transgenerational studies must include the F3 generation at features of a minimum. model systems • Case study: Describe transgenerational effects of diethylstilbestrol. 12902917 used to • Case study: Describe transgenerational effects of high fat diet. 25059803 examine • Describe the development of primordial germ cells and potential impacts of gene/environm toxicant exposures. ent • Describe the transgenerational effects of insulin resistance. interactions. Describe • Compare patterns of gene expression associated with toxicant exposure toxicant/toxin • Identify tissue-specific patterns of gene expression based on routes of effects on gene exposure. expression. • Describe how dioxin and other polycyclic aromatic hydrocarbons regulate transcription through the aryl hydrocarbon receptor (AhR). • Describe how fibrates regulate gene expression through the peroxisome proliferator-activated receptor alpha (PPARα). • Describe how phytoestrogens regulate gene expression through the estrogen receptor. • Describe how partial antagonists like tamoxifen alter gene expression through the estrogen receptor. Describe • Identify allelic differences associated with increased cancer risk following genetic toxicant exposure polymorphisms • Identify allelic differences associated with decreased antioxidant response that affect • Identify allelic differences that alter the response to heavy metals toxicokinetics • Identify allelic differences that alter susceptibility to arsenic and risk. • Identify allelic differences that alter susceptibility to morphine. • Describe how polymorphisms in alcohol dehydrogenase ADH1B result in higher sensitivity to ethanol toxicity in some populations. 17718397

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• Describe why polymorphism of CYP2D6, 2C19, and 2C9 account for variations in phase 1 metabolism 19514967 Biomarkers Describe how • Describe how tests/panels may be used to assess a wide variety of biomarkers can toxicities. be used to • Provide examples of the different kinds of biomarkers, such as direct indicate measurements (weight, body temperature, number of offspring), chemical exposure to a product, protein, mRNA, and DNA sequence. toxicant. • Describe how the comprehensive metabolic panel is used to provide a medical screen for kidney function, liver function, diabetic and parathyroid status, and electrolyte and fluid balance. List the types of • Describe how serum levels of aspartate transaminase (AST), alanine biomarkers that transaminase (ALT), and gamma-glutamyltransferase are used to quantify are currently organ toxicity. used. • Describe how the ratio of AST to ALT can be used to differentiate diseases. • Describe how cardiac troponin is used as a biomarker for cardiac function and health. • Case study: Describe how N-acetyl-beta-glucosaminidase is used as a biomarker for tubular injury of the kidney. PMC 2742480 • Case study: Describe neurotoxicity biomarkers. PMC4659531 Describe the • Case study: Review ongoing efforts in developing biomarkers for role of neurotoxicity. PMC4659531. validation in • Describe the important role of biomarkers in pharmaceutical development. evaluating 12364809 biomarkers. • Describe the importance of validation in determining the usefulness of a biomarker. 12364809 • Describe some features of biomarker validation, including: sensitivity, specificity, ease of bioanalytical assessment, rate of false negatives and false positives, and establishment of toxicokinetic parameters for the biomarker. 12364809 • Case study: Describe the process and challenges of biomarkers for cancer. PMC4511498 • Case study: Review ongoing efforts in developing biomarkers for cancer. 25458054 Differences Explain how • Describe how polymorphisms in cytochrome P450 enzymes (CYP2A6, 2B6, in differences in 2C9, 2C19, and 2D6) relate to differences in risks upon exposure to . susceptibili individuals 21149643 ty to result in • Know that there are genetic, epigenetic, environmental, and toxicants differences in pathophysiological reasons for individual's differences in response to (dose susceptibility of toxicants. response) a population to • Contrast the various P450 phenotypes, including poor metabolizers (two toxicants. defective alleles), intermediate metabolizers (heterozygous for a defective allele or carrying two alleles with decreased activity), extensive metabolizers (carrying two functional alleles), or ultra-rapid metabolizers (carrying more than two active gene copies). 21149643 • Case study: Describe how a rare defective allele in CYP1B1 results in elevated risk of glaucoma. 12624268 • Case study: Describe how a defective allele in CYP2C9 resulted in neurological signs of phenytoin intoxication. 11673755

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Explain why • Describe how inbreeding is performed to generate an inbred, or isogenic, inbred animals strain. are used in • Define the scientific term "inbred” and know that most laboratory animal many strains are inbred. toxicological • Contrast the benefits and risks of using inbred versus outbred strains of tests. laboratory animals. Know that while studies using inbred strains are more reproducible due to less genetic variability, they might not translate to outbred strains. • Know that inbred strains sometimes carry mutations that alter their susceptibility to toxicants when compared with wild type animals. • Know that breeding two inbred strains can generate a hybrid that may remove recessive genes. • Case study: Summarize the argument for using multiple inbred strains in place of outbred strains in toxicology, safety testing, and drug development. 20562325 • Provide the name of a first-generation cross of two inbred strains. For example, know that a first-generation cross of a female C57/BL6 and a male DBA/2 mouse is B6D2F1. 20562325 • Explain why the number of animals used in an experiment using outbred mice must be higher than an experiment using inbred mice. Contrast • Know that an immune reaction is one type of idiosyncratic response. idiosyncratic • Describe how a drug or its reactive metabolite may act as a hapten to induce reactions with an idiosyncratic adverse drug reaction. 18052104 other kinds of • Contrast intrinsic versus idiosyncratic toxicities. 20019161 variation in a • Case study: Describe the idiosyncratic reaction to penicillin. 16879083 population's • Case study: Describe the idiosyncratic hepatotoxic reaction to halothane. response to a 8989020 toxicant. Contrast • Contrast the formulas for Margin of Safety and Therapeutic Index. Margin of • Describe a situation in which Therapeutic Index may be less useful than Safety with Margin of Safety in determining the safety of a drug for a population. Therapeutic • Explain why cancer drugs often have a lower Therapeutic Index than other Index with approved drugs. regards to prediction of drug safety in a population. Explain the • Describe the interplay between exposure and rates of elimination. concept of • Describe how a slow excretion rate can contribute to cumulative toxicity. dose spacing in • Explain the rationale behind the FDA's recommendation that pregnant women terms of limit their intake of fish to a certain number of days per week, and why type of toxicity. fish matters. https://www.fda.gov/downloads/Food/FoodborneIllnessContaminants/Metals/ UCM537120.pdf Describe the • Describe why a hormetic dose response curve is called "U shaped" or concept of "biphasic" PMC2248601 hormesis as it • Contrast a typical dose response curve with a biphasic dose response curve. applies to • Describe the role of different mechanisms of action at different doses in toxicology. hormetic responses. • Case study: Describe how preconditioning ischemia protects cells against a subsequent more severe ischemia. • Case study: Review the history of hormesis and explain the controversy surrounding this topic. 2669125, 8523095. http://pubs.acs.org/doi/pdf/10.1021/es072436l

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Predisposin Describe how • Describe how endocrine disruptors exhibit different toxicities depending on g factors endocrine the time of exposure during development. (sex-, disruptors • Describe the use of laboratory animals as surrogates for developmental gender-, affect the toxicants. 2653734 and age- development • Describe how exposure to endocrine disruptors causes permanent changes related and function of due to alteration of development. toxicology) the • Case study: Describe how DDT administered to neonatal rats induces reproductive persistent estrus syndrome. 5105675 system. • Case study: Describe how diethylstilbesterol affects the development and function of female reproductive tissues depending on the timing of exposure during development. 11252812 and 7024873 • Case study: Describe how the anti-androgen flutamide and finasteride affects male sex organ differentiation during in utero development. 1324152 Describe how • Contrast agonists, antagonists, and partial antagonists. partial agonists • Describe how partial agonists can act as antagonists under some such as circumstances. tamoxifen • Case study: Describe how the thyroid hormone receptor antagonist NH3 function to affects thyroid signaling in rats. 17440037 block hormone • Case study: Describe how tamoxifen is used to treat estrogen-sensitive signaling cancers. pathways. Describe the • Describe the masculinizing effects of anabolic steroids, including effects of sex testosterone. http://www.pbs.org/wnet/secrets/the-state-sponsored-doping- hormones on program/52/ adolescents • Describe the effects of anti-estrogen treatment on the female reproductive and adults. system. • Describe the benefits and risks of hormone replacement therapy treatment. • Describe the effects of phytoestrogens on males and females. Relate the • Know that a teratogen is a chemical that causes toxicity to a developing fetus sequence of at a dose which does not cause toxicity to the mother. 20563928 human • Describe the critical windows concept, that certain stages of development development to offer heightened sensitivity to teratogenesis by a toxicant depending on its time periods in mechanism of action. which • Case study: Describe thalidomide-induced birth defects. teratogen • Case study: Describe fetal alcohol syndrome. exposure • Case study: Describe how consumption of Veratrum californicum (Liliaceae) results in causes differential teratogenesis depending on the timing of exposure during developmental pregnancy. 2218940 toxicity. • Case study: Describe how diethylstilbesterol affects the development and function of female and male reproductive tissues depending on the timing of exposure during development. 11252812, 7024873 • Case study: Describe how exposure to thalidomide during fetal development causes different teratological abnormalities depending on the timing of exposure during development 3067417 Explain why • Know that children express different levels of bio transformational enzymes. children may • Know that because children have a smaller mass overall, a fixed dose of be more toxicant will result in a higher mg/kg dose. susceptible to • Describe how differences in pH in the digestive system contribute to toxicants than differential toxicities in children versus adults. adults. • Describe features of the developing organism that make it more susceptible to perturbation by chemicals. • Case study: Describe the effect of lead exposure on neurological development.

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• Case study: Describe why neurotoxicants are more harmful to newborns than adults. • Know that for many toxicants a threshold exists below which a toxic response does not occur. Describe the • Explain how decreased gastrointestinal mobility during pregnancy results in effect of higher absorption of slowly absorbed drugs. pregnancy on • Explain how decreased plasma albumin results in an altered bound/unbound susceptibility of toxicant fraction. females to • Explain how increased renal elimination during pregnancy affects toxicants. toxicokinetics. • Know that pregnant females have inhibition of metabolic inactivation in the liver late in pregnancy. Explain how • Describe the mechanisms by which alteration in histones, methylation epigenetic patterns, and other epigenetic mechanisms can alter gene expression. mechanisms PMC2802667 can play a role • Explain the role of microRNAs in regulation of gene expression; also explain in DNA gene their potential role in carcinogenesis. 2844907, PMC3724248 expression and carcinogenesis

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Risk Assessment and Risk Management Epidemiolo Compare the • Compare the strengths and weaknesses of epidemiological study designs, gy strengths and including prospective, retrospective, cross-sectional, and case-control study weaknesses of versus cohort study. http://sphweb.bumc.bu.edu/otlt/MPH- different Modules/PH/Outbreak/Outbreak7.html epidemiological • Contrast prospective cohort studies, retrospective cohort studies, and study designs. ambidirectional studies. • Contrast internal, external, and general population comparison groups. Understand the • Describe how dose response studies are important in differentiating difference correlation and causation. between • Describe the difficulties in using epidemiological data to differentiate correlation and correlation and causation. causation and • Contrast incidence and prevalence for a given disease or toxic effect. incidence v prevalence. Be able to • Given a sample set of data, calculate “relative risk” for an epidemiological interpret relative study. 26231012 risk and odd • Given a sample set of data, calculate the “odds ratio” for an epidemiological ratios. study. 26231012 Understand the • Define “biological significance” and “statistical significance”. difference • Describe why a measured, statistically significant difference in an experiment between may not be biologically significant. statistical significance and biological significance. Understand the • Contrast selection bias, prevalence-incidence bias, Berkson’s biasm, and various forms of verification bias. bias and how to • Contrast positive and negative types of confounding bias. control for • Define a confounder variable in epidemiology. them. • Case study: describe how smoking is a confounding risk factor with alcohol consumption for coronary heart disease. https://www.healthknowledge.org.uk/e- learning/epidemiology/practitioners/chance-bias-confounding At-risk List the major • Describe how young children are at higher risk for toxicant exposure due to Populations at-risk the developmental state of their xenobiotic defense mechanisms. populations: • Case study: Describe how aging reduces xenobiotic defense in the mouse infants and model system. 17521389 young children, • Describe features of aging populations that cause higher risk from acute pregnant kidney injury. 25257519 women, older • Define the healthy worker effect. PMC2847330 adults, people • Describe how lung disease such as asthma, COPD, and fibrosis, contribute to with weakened increased risk. immune systems, and elderly. Environmen Describe the • Describe the distribution of inhaled gases and particulates in the human tal effects of respiratory system. Toxicology exposure to • Compare and contrast the types of physiological effects seen following acute carbon oxides, exposure to airborne toxicants with the effects seen following chronic sulfur oxides, exposures. and nitrogen • Explain the mechanisms of the greenhouse effect, discuss models of global oxides on warming human

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respiratory • Discuss potential impact of global warming on the environmental effects of function; also toxicants. 24480426, PMC3601420 describe the • Explain the mechanisms behind acid rain; describe the effects of acid rain on mechanisms aquatic and terrestrial communities; also describe the role of environmental behind the buffering capacity in terms of effects. contribution of carbon oxides to global warming and sulfur and nitrogen oxides to acid rain. Explain how • Describe the origin and composition of photochemical smog. incomplete • Describe the mechanism of action of particulate matter pollution. combustion of • Contrast the formation of ozone in the upper atmosphere versus lower organic material atmosphere. leads not only to the release of hydrocarbons and particulate matter, but also to the production of secondary pollutants such as ozone. Discuss the • Explain the effects of particulate matter on pulmonary function. findings linking PMC5343780, PMC4922809 exposure to • Explain the effects of particulate matter on neurological function. particulate PMC5544553, PMC4974252 matter to • Discuss the link between exposure to particulate matter and developmental adverse effects toxicology. PMC4917489 on human • Discuss the link between exposure to ultrafine/nanosized particles and blood health. clots leading to cardiovascular disease. Compare and • Provide examples of pollution by organic substances, including petroleum contrast point products, solvents, pesticides, polymers, pharmaceuticals. and nonpoint • Provide examples of pollution by inorganic substances, including heavy source water metals, nitrates, phosphates. pollution in terms of sources, typical content, and options for control. Describe some • Discuss effects of major oil spills including the Exxon Valdez and the of the options Deepwater Horizon. 14684812, 27301686 for responding • Describe the risks and benefits of bioremediation, including use of genetically to oil spills, modified organisms. 28511936 including the • Describe the risks and benefits of chemical dispersants. 25938731 risks and benefits to wildlife posed by those options.

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Explain the • Describe the role of fertilizers and waste in eutrophication. mechanisms • Explain the consequences of eutrophication on ecological community behind the structure. process of eutrophication, as well as the consequences for aquatic life. Compare and • Summarize the effects of organochlorine insecticides (DDT, chlordane, aldrin, contrast the and others). 26563787 major • Summarize the effects of organophosphate and carbamate insecticides. categories of 26563788 pesticides in • Summarize the effects of pyrethroid insecticides. 26563787 terms of their • Summarize the effects of chlorphenoxy acid herbicides (2,4-D and 2,4,5-T). mechanisms of 15578861 action, • Summarize the effects of bipyridyl herbicides (paraquat and diquat). persistence in 18161502 the environment, and risks to human health and the ecosystem Describe some • Describe the effects of lead on human health, including neurological and of the sources hematological effects. of heavy metal • Describe the physiological and ecological effects of cadmium. pollution in • Describe the physiological and ecological effects of arsenic. water and give • Describe the physiological and ecological effects of mercury, including examples of discussion of differences between different species of mercury. 28889024 effects of environmental exposure to heavy metals on human health and/or ecological function. Describe the • Describe the effects of microplastics in the environment. PMC5044952 hazards • Describe the effects of macroplastics in the environment. 27232963 associated with • Describe the release of dioxins caused by trash burning. the presence of • Describe the effects of microwaving plastics. plastics in the environment. Compare and • Evaluate the use of UV and chemical treatments for detoxification. contrast the • Evaluate the use of high temperature combustion and pyrrolysis; discuss the options of problem of the disposal of ash. incineration, • Describe strategies for landfill design and protection against leaching of detoxication, toxicants into the water supply. biodegradation, • Describe the three steps in a modern waste water treatment plant. and burial of hazardous waste in terms of the risks and benefits of each.

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Discuss the • Compare and contrast the risks and benefits of on-site storage vs. current issues reprocessing vs. central storage. involving safe • Case study: Explore the debate over Yucca Mountain as a long-term solution long-term for US spent nuclear fuel and high-level radioactive waste. 22569220 disposal of radioactive wastes. Regulatory Describe the • Contrast threshold and no-threshold responses to toxicants. Toxicology controversy of • Describe the controversy of the no-threshold relationship with regard to threshold ionizing radiation. 19332842 versus non- • Describe the rationale behind a no-threshold relationship for lead exposure. threshold 27837574 assumptions with regard to regulatory policy regarding toxicants. U.S. - Describe • Describe major historical events that led to the evolution of environmental the major laws, such as patent medicines, “The Jungle”, and the “Crying Indian environmental Commercial”. laws of the • Describe the Clean Air Act and Clean Water Act United States • Describe the Safe Drinking Water Act (and other • Describe the Comprehensive Environmental Response, Compensation, and nations). Liability Act (CERCLA) and its amendments; aka Superfund Act. Discuss the • Describe the role of the International Council for Harmonisation in terms of importance of drug development. Commented [JG1]: Need some fourth level bullets for regulatory this one. harmonization across various markets Describe how • Describe the National Toxicology Program and how it informs regulatory toxicology policy. testing is used • Describe the role of contract research organizations in producing toxicology to inform data to inform regulatory policy. regulatory policy. Concepts of • Describe how the three R’s (reduce, refine, and replace) are used to minimize reduce, refine, the use of animals in scientific research. and replace in • Describe how refinement of experimental design results in reduction of animal the concept of suffering and improves animal welfare. animal research • Describe how reduction balances reducing the number of animals used in an experiment with having enough animals for sufficient experimental statistical power. • Describe how models and tools replace the use of animals. https://www.nc3rs.org.uk/the-3rs Describe risk • Contrast risk assessment and risk management. assessment • Describe how risk management uses information from risk assessment to and risk make informed decisions. management. • Identify risk assessment examples under the classic paradigm of Hazard Identification, Exposure Assessment, Dose-Response, and Risk Characterization. List various • Identify the portals of entry for toxicants into the body. Managemen ways that • Case study: contrast absorption of the heavy metal lead via each major portal of entry into the body.

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t & poisons enter the body.

List signs and • Describe the relationship between the patient suffering from poisoning or symptoms overdose and airway management. associated with • Recognize the need for medical direction in caring for the patient with poisoning. poisoning or overdose. • Describe the signs of organophosphate exposure using the SLUDGE acronym. Describe the • Explain the rationale for administering activated charcoal. general • Describe the following strategies for treatment of : gastric treatment of lavage, emesis, activated charcoal, charcoal-resin hemoperfusion, drug overdose. , peritoneal dialysis, , pressor agents, cardiac monitoring, and support of the airway. Discuss the • Explain the rationale for contacting medical direction early in the prehospital emergency management of the poisoning or overdose patient. medical care for • Describe the role of Poison Control Centers in reducing morbidity and the patient with mortality from exposure to toxicants. possible over- dose and/or suspected poisoning. Describe the • Describe aflatoxin poisoning in terms of overdose, manifestation, and importance of prevention strategies. poisoning and • Describe saxitoxin poisoning in terms of overdose, manifestation, and overdose, their prevention strategies. manifestations, • Describe domoic acid (anemic shellfish poisoning) in terms of overdose, prevention manifestation, and prevention strategies. strategies utilized in the management of few prototype toxins. Explain the role • Describe federal, state, and other governmental Poison Control Centers and and function of how they function at each level of government. Poison Control • Describe the history of the Poison Control Center. Centers and https://www.wnycstudios.org/story/poison-control/ TESS (Toxic Exposure Surveillance system. Historical Workplace • Define "industrial hygiene". events and toxicology • Describe worker safety practices designed to prevent injury to workers. impact on • Describe "permissible exposure limits" as they relate to chemical substances regulation as defined by the Occupational Safety and Health Administration. • Describe the role of the Occupational Safety and Health Administration or equivalent governmental body in your country of residence. • Describe how time-weighted averages are used with both short-term exposure limits or ceiling limits.

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Describe the • Describe the history of the Love Canal as it relates to toxicology and public history as it policy. relates to public • Describe the history of the (methyl isocyanate) as it relates to policy of key toxicology and public policy. historical events • Describe the history of the disaster as it relates to in toxicology toxicology and public policy. and the • Describe the history of the Sevoso disaster as it relates to toxicology and mechanism of public policy. toxicity of the • Describe the history of Rachel Carson's publication of "Silent Spring," (DDT) toxicant behind as it relates to toxicology and public policy. the event. • Describe the history of “the radium girls” as it relates to toxicology and public policy. • Describe the history of Agent Orange (dioxin) as it relates to toxicology and public policy. • Describe the history of Times Beach, MO, and how it relates to toxicology and public policy. • Describe the history of the cleanup of the Hudson River by General Electric Corporation as it relates to toxicology and public policy. Describe what • Describe the legal definition of a brownfield. brownfields are. • Describe government's role in brownfield remediation. • Describe the Superfund program's history and current function.

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Systems Toxicology Cellular Describe the • Explain the differences between hydrogen bonding, ionic attraction, and Toxicology types of covalent bonding in terms of stability of a non-covalent versus covalent bond. chemical bonds • Describe how suicide inhibitors function. that can • Case study: Describe how nerve agents can undergo aging to prevent characterize the reaction of acetylcholinesterase by oximes. interaction of toxicants with the major classes of cellular macromolecule s. Explain the • Review the concepts of Vmax and KM. interaction of • Explain the use of Michaelis-Menten kinetics for making experimental toxicants with determination of competitive vs. noncompetitive binding of toxicants enzymes, • Cite examples of enzyme inhibition, including inhibition of including the acetylcholinesterase by organophosphates and role of aging in reversibility of differences inhibition. 28869561 between competitive and noncompetitive inhibition in terms of both sites of action and enzyme kinetics. Describe the • Describe the action of G protein-coupled receptors (including beta adrenergic major and muscarinic acetylcholine receptors), along with examples of drugs and categories of toxicants which interact with them (including beta blockers and atropine). receptors found • Describe the action of receptor tyrosine kinases, along with examples of in cells, and drugs and toxicants which interact with them. differentiate • Describe the action of ligand-gated ion channels (including the nicotinic between acetylcholine receptor and NMDA receptors), along with examples of drugs toxicants and toxicants which interact with them (including curare). classified as • Describe the action of intracellular receptors (including steroidal hormone agonists, receptors), along with examples of drugs and toxicants which interact with antagonists, them. and partial • Contrast the mechanism of action of botulinum toxin and tetanus toxin; agonists in explain why very similar mechanisms of action have opposite physiological terms of their effects. interactions with those receptors. Explain the • Describe how TRPV1 is affected by capsaicin and resinaferatoxin. potential impact • Describe how tetrodotoxin functions at the molecular level. of toxicants on • Describe how saxitoxin functions at the molecular level. voltage- activated ion channels in terms of membrane potentials. Describe the • Explain the concept and give examples of free radicals. sources and • Describe the formation of free radicals from biotransformation processes characteristics (chlorinated hydrocarbons).

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of free radicals • Describe the formation of free radicals (superoxide and hydrogen peroxide) and explain the as byproducts of oxidative phosphorylation. mechanisms • Describe the structure of biological membranes, noting the presence of behind the vulnerable unsaturated fatty acids process of lipid peroxidation. Explain what • Explain the alkylation of bases, including discussion of “hot spots” for adduct alkylating formation. agents are and • Describe examples of alkylating agents. discuss how • Case study: describe the mechanism of action of DNA alkylation by nitrogen they interact mustard. with DNA. Explain the • Describe the mechanism for induction of stress proteins (including discussion circumstances of the heat shock factor and heat shock element). 28852220 under which • Describe some examples of, and general roles of stress proteins in cellular cells produce protection (chaperones, regulation of receptor function). stress proteins • Describe examples of the roles of protein misfolding and stress proteins in and describe disease. MC5433227 examples of some of their protective mechanisms and effects (including the role of several stress proteins as chaperones). Compare and • Describe the fundamental steps in apoptosis, including discussion of extrinsic contrast the and intrinsic pathways. mechanisms • Explain the roles of mitochondria, cytochrome c, and the mitochondrial behind cell permeability transition in apoptosis. 28325213 death, including • Describe the effects of the regulators of apoptosis, including Bax, Bid, Bad, apoptosis, Bcl-2, Bcl-XL. necrosis, and • Compare and contrast apoptosis and necrosis, and discuss hypotheses autophagy. concerning what determines which path a cell will take. • Discuss the concept of autophagy as it relates to cell survival and cell death. 28866100 Organ- Identify and • List examples of prototype therapeutic (acetaminophen, doxorubicin, specific understand bleomycin, caffeine) & non-therapeutic toxins (aflatoxin, botulinum toxin, Toxicology toxic effects snake toxin, E. coli toxin etc.). emanating from • Explain how these toxins produce toxicity. therapeutic and • Understand how specific bioactivation pathway leads to specific form of non-therapeutic, toxicity. intentional and • List parameters that are tested to demonstrate toxicity. unintentional • Explain specific changes (biochemical, morphological, molecular) associated drug/chemical with toxicity. exposures. • Understand correlations between biochemical, morphological, molecular changes during development of toxicity. Recognize • List examples of organ specific hepatotoxins, neurotoxins, pulmonary toxins, system-specific nephrotoxins etc. and organ- • Identify unique ways how therapeutic agents cause specific organ toxicity. specific toxic • Discuss how specific bioactivation products (free radicals, BRIs etc.) produce effects on specific forms of toxicity to specific types of cells. humans and other

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experimental • List examples of organ specific parameters that are used to determine models. specific organ toxicity (ALT/AST for liver toxicity; BUN/Creatinine for nephrotoxicity; CK/Trponins for cardiotoxicity etc.). • Discuss specific morphological changes in specific areas of organs during toxicity. • Correlate biochemical (serum chemistry) parameters with histopathological changes. Explain adverse • List classes of adverse drug reactions and types of medication errors. reactions • List manifestations of adverse drug reactions and outcomes of medication originating from errors. toxic exposures • Discuss corrective actions after adverse reactions appear and how in any setting, medication errors can be avoided. and medication errors in healthcare setting. Predict/Explain • List pharmacogenetic options and pre-existing conditions that can lead to possible toxicity within safe limits. toxicological • Define possible toxicological interactions and drug interactions even after safe consequences limit exposures. after exposure • Understand synergism, antagonism, potentiation and additive reactions in to toxicology with examples. drugs/chemicals • Understand potential of toxicity after long-term exposures at safe levels. within safe • Explain how human microbiota can contribute to drug interactions and limits. adverse drug reactions. Describe the • List examples of Phase-I and Phase-II bioactivation reactions with specific importance of examples. the bioactivation • Understand how these reactions can lead to the production of useful (from a process for prodrug) and/or toxic free radical species and/or Biological Reactive prodrugs. Intermediates. • Discuss cellular targets of these reactive species, such as, plasma membranes, mitochondria, DNA, RNA, etc. • Discuss consequences of BRIs and macromolecules (Lipids, DNA, enzymes). • Discuss quantitative methods to determine toxic end points generated via free radicals (lipid peroxidation, DNA m=damage etc.). Decipher the • Explain differences in drug metabolism (biotransformation reactions) in in vivo mechanisms for and in vitro models. drug and • Understand the cause of the differences (such as the presence or absence of chemical- CYP450 isozymes) in drug metabolism. induced toxicity • Explain the advantages and disadvantages of using in vivo and in vitro in in vivo and in models for toxicity screenings. vitro models, • List all different types of clinical trials and understand how in vivo and in vitro and models are used in various phases of clinical trials. appropriately • Explain LD50, LC50, LD20, and related items for in vivo and in vitro systems. design and interpret drug screenings. Evaluate and • List toxicology literature sources that describe toxicological interactions and interpret provide information that can be used to prevent future exposures. relevant • Understand the importance of dose-response, cause and effect and time information from course relationships in toxicology. the toxicology • Explain how the above relationships can be extrapolated to determine safe literature, and toxic levels of exposure. understand • Explain drug interactions from perspectives of LD50, LC50, LD20 doses for in toxicological vivo and in vitro models.

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interactions and identify preventable causes. Discuss the • Describe the liver anatomy, lobule zonation, and list all types of cells found in important role the liver. the liver plays in • Explain which cells are responsible for xenobiotic metabolism and why. xenobiotic • Explain detoxification pathways that operate in liver cells. metabolism. • List different types of liver injuries (cirrhosis, necrosis, fatty liver, steatosis etc.) initiated by different types of xenobiotics. • List various biomarkers of different types of liver injuries. • Explain morphological, biochemical and molecular changes associated with different types of liver injuries. • Correlate biochemical changes (serum chemistry and tissue biochemistry) with morphological changes. List the • Describe the kidney anatomy and list all types of cells found in kidneys. characteristics • Understand the mechanism of excretion and different kidney structures that enable the coordinate fluid regulation. kidney to • Explain how kidneys can be vulnerable to toxicity at therapeutic doses of efficiently drugs. excrete • List different types of kidney injuries (acute kidney injury, chronic kidney xenobiotics. injury, kidney stone formation etc.) initiated by different types of xenobiotics • List various biomarkers of different types of kidney injuries . • Explain morphological, biochemical and molecular changes associated with different types of kidney injuries. • Correlate biochemical changes (serum chemistry and tissue biochemistry) with morphological changes. • Describe the differences between Acute and Chronic Renal Failure, as well as treatment options. • Describe the effect of the cardiovascular system on kidney function. System Recognize • Understand anatomy, physiology and pathophysiology of organ systems. Toxicology system-specific • List prototypical neurotoxicants, reproductive toxcants, cardiotoxicants, and organ- nephrotoxicants, pneumotoxicants, etc. specific toxic • List signs, symptoms, and assessment tools of neurotoxicity, reproductive effects on toxicity, nephrotoxicity, pulmonary toxicity, etc. humans and • Understand the similarities and differences between humans and other experimental models while assessing organ specific toxicities. experimental • Describe how data from animal studies can be extrapolated to humans. models. Explain adverse • List classes of adverse drug reactions and types of medication errors. reactions • List manifestations of adverse drug reactions and outcomes of medication originating from errors. toxic exposures • Discuss possible corrective actions after onset of adverse reactions and in any setting, devise ways to avoid of medication errors. and medication • Explain irreversible and reversible drug reactions. errors in a • Describe how medication errors can be minimized at every level of healthcare healthcare (doctors, pharmacists, nurses & other healthcare workers). setting.

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Predict/Explain • List pre-existing conditions such as pharmacogenetic issues that can lead to possible toxicity within safe limits. toxicological • Define possible toxicological interactions and drug interactions even after safe consequences limit exposures. after exposure • Understand synergism, antagonism, potentiation and additive reactions in to toxicology with examples. drugs/chemicals • Understand potential of toxicity after long-term exposures at safe levels. in safe and • Explain how human microbiota can contribute to drug interactions and unsafe limits. adverse drug reactions. Evaluate and • List toxicology literature sources (such as Medline, Pubmed, and NLM drug interpret interaction databases) that describe toxicological interactions and provide relevant information that can be used to prevent future exposures. information from • Understand the importance of dose-response, cause and effect, and time the toxicology course relationships in toxicology. literature, • Explain how the above relationships can be extrapolated to determine safe understand and toxic levels of exposure. toxicological • Understand the relationships in toxicology to explain mortality, lethality, acute, Commented [JG3]: What kind of relationships? Can interactions, chronic toxicity. you give an example or two? and identify • Describe how data from animal studies can be extrapolated to humans using preventable toxicology literature sources, dose-response, cause and effect, and time causes. course relationships. Commented [JG2]: Preventable causes of what? • Learn how the above principles can be applied in various phases of clinical trials. List various • Describe analytical tools used in toxicology, such as chromatographic analytical, procedures: liquid, ion-exchange, size exclusion, thin layer, and affinity molecular, and chromatography. computational • Describe molecular techniques used in toxicology, such as PCR, microarrays, tools used to MiRNA profiling, Western blot, electrophoresis, ELISA, norther blot, southern interpret blot, metabolomics, next generation sequencing, and chromatin information from immunoprecipitation. toxicology • Describe how instruments are used to detect free radicals or their biological studies, to derivatives in biological fluids including ESR, NMR, and IR. understand • List Computational tools such as PB-PK models, QSAR, Toxtree, Toxmatch, toxicological DART, CRAFT, PBPK models frequently used to determine toxicity or fate of interactions, toxic drugs and chemicals. and to describe preventable causes. Commented [JG4]: Preventable causes of what? This List and • Describe how genetic factors (pharmacogenetics) can influence xenobiotic is unclear. interpret the metabolism in the body). general • Understand how genetic factors can be used to customize drug exposure to principles of individuals with certain ethnic backgrounds. clinical • Explain how nutritional factors (high fat low fat diet, diets with insufficient or toxicology and excessive antioxidants or vitamins, diets rich in sugars, diets deficient in discuss factors proteins etc.) can considerably influence xenobiotic metabolism in the body. that influence • Describe how diet and nutrition are linked to body's defense system toxicity. (antioxidant imbalance oxidized/reduced glutathione ratios, ascorbate level, alpha-tocopherol level etc.) or cytoprotection mechanisms. • Understand how environmental factors are linked to diseases (exposure to high levels of CO, CO2, drinking water contaminants, air pollutants, radiation etc.).

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Discuss the • Case study: Describe how sewage effluent containing birth control downstream medications causes feminization of male fish. effects that • Describe how DES exposure at particular development points in development occur from has different effects. exposure to an endocrine disrupting compound. Describe the • Understand the complex anatomy of the nervous system (CNS and PNS). characteristics • Understand the structure and function of various cells of the CNS and PNS. of the nervous • Describe the role played by the blood brain barrier. system that • Understand the complexity of the structural & functional integration of the make it a nervous system. vulnerable • Describe how the limited repair ability of neurons makes the nervous system system for vulnerable to injury. many toxicants. • Explain the susceptibility of the nervous system to lipid-soluble toxicants. • Explain how heavy dependence on glucose makes the nervous system more vulnerable to toxicants. • Explain how ion channels, axonal transport and synaptic transmission are subjected to toxic effects by drugs and chemicals. Discuss the role • Describe anatomy, physiology and pathophysiology of the cardiovascular that the system. circulatory • Explain how the cardiovascular system plays a role in the systemic system plays in distribution of toxicants. exacerbating or • Explain how numerous factors found in the blood (different types of cells, limiting toxicity. glutathione, detoxifying enzymes) detoxify and facilitate elimination of toxicants from the body. • Understand how cardiovascular system works in coordination with the excretory system (renal) to exacerbate toxicity. • Describe the differential distribution of toxicants in the body due to differences in lipid solubility and plasma distribution. Developme Contrast the • Describe how the menstrual cycle can be affected through altered corpus ntal and four luteum function, fertilization, maintenance of implantation, or alteration of the Reproducti reproductive hypothalamus/pituitary system. ve endpoints: • Describe how the testis can be affected by modification of CNS function, Toxicology fertility, pituitary, testicular vasculature, nutrition, pineal, fertilization, or paternal menstrual cycle, development. sperm count • Case study: Describe the effect of m-dinitrobenzene on rat testis. 3341027 and viability, • Case study: describe the mechanism of action of abortifacients that induce and sexual pregnancy loss through reduction of progesterone. 2886593 behavior. • Case study: Describe how busulfan affects germ line development in rats. Contrast the • Contrast teratology, birth weight, growth, and neurobehavioral changes as primary primary developmental toxicological endpoints. development • Describe mechanisms of toxicants affecting onset of puberty. toxicological • Describe mechanisms of pheromones on affecting the onset of puberty. endpoints. • Describe how susceptibility of a fetus to teratogens differs depending on the stage of development of the fetus. Fate and Describe, using • Explain the fundamental concepts behind the process of natural selection. Transport, examples, the • Describe the effects of pesticides on both pest populations, and nontarget Population, role that populations. PMC5533829. community, toxicants can • Describe the effects of antibiotics on bacterial populations. PMC4567305 and play in exerting ecosystem selection

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systematic pressures on effects populations.

Contrast the • Define r strategists and K strategists. effects of • Contrast the relationships between population numbers and carrying capacity environmental for r strategists and K strategists. toxicants on r • Differentiate between density-dependent and density-independent action of strategists toxicants. PMC4921107 versus K strategists. Contrast the • Describe the characteristics of predator-prey kinetics. effects of • Provide examples of the impact of toxicants on predator-prey interactions. toxicants on PMC4935736 predator populations, prey populations, and the interactions between them. Discuss how • Provide examples of effects of toxicants on producers, potentially leading to toxicants can decreases in productivity. PMC5009500 alter ecosystem • Provide examples of effects of toxicants on detritivores, potentially leading to structure in decreases in release of nutrients. PMC5420384 terms of effects on energy flow and the trophic pyramid. Explain the • Compare average residence times for toxicants moving through ecological concept of compartments. residence times • Describe the factors that influence residence times for toxicants. for toxicants in the environment and compare and contrast the ways in which toxicants move through soil, atmosphere, and water. Explain the • Describe the chemical factors that influence the tendency for toxicants to concepts of bioaccumulate. MC5044975 bioavailability • Provide specific quantitative examples of of toxicants, such and as DDT or PCBs. bioconcentratio • Provide specific examples of biotransformation affecting bioconcentration n. (such as mercury, for example). PMC1797140 Discuss • Discuss the use of daphnids, fathead minnows, quail, and other species as examples of models for . PMC3764090, PMC4490443, PMC3744572, typical species PMC4388576 used in ecotoxicological

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single-species testing.

Compare and • Describe the strengths and weaknesses of microcosms and mesocosms in contrast the measuring toxic effects. strengths and • Compare and contrast flow-through versus static testing aquatic systems. limitations of the • Discuss the issues with locating appropriate control areas for comparison in most common assessing ecological disasters. methods of • Discuss the complexity of ecological models using examples of assumptions ecotoxicological and trade-offs made in ecological modeling. testing including microcosms, mesocosms, field studies, and mathematical modeling. Identify • Explain some of the complexities involved in assessing risk at population, important community, and ecosystem levels. PMC5141515 concepts in • Understand the concept of adverse outcome pathways in ecotoxicology. ecotoxicological 25439131, PMC3478868 risk assessment

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Pathways and Transformations for Energy and Matter Model Describe how • Identify homeostatic imbalances caused by toxicant exposure Organism toxicants disrupt • Identify physiological functions disturbed by toxicant exposure s for homeostasis. • Explain how a toxicant disrupts homeostasis in a specific target tissue or Toxicolog organ. y • Describe how organisms respond to toxicants by attempting to restore homeostasis. • Describe how the inability to maintain homeostasis leads to pathological responses. • Describe how organisms handle allostasis differently after toxicant exposure. Commented [JG5]: Eva recommended this one. She Describe the • Describe the function of the anti-oxidant response system in RedOx balance. said she was thinking of Lou Guillette’s gators in Lake role of • Describe the function of Phase I and Phase II enzymes in detoxification Apopka. Anyone know anything about that? xenobiotic pathways. defense • Identify key proteins involved in sequestration and excretion of heavy metals. mechanisms in • Describe unique features of plant metabolism and xenobiotic defense. maintaining homeostasis. Contrast a • Describe an antioxidant pathway that could lead to detoxification or physiological DNA/protein damage. versus a • Describe a metabolic pathway that could lead to detoxification or DNA adducts. pathological • Case study: describe how chronic exposure to testosterone causes adaptation to a pathological adaptations that result in dysfunction. stimulus. Contrast • Contrast the physiological and pathological adaptations of atrophy, physiological hypertrophy, hyperplasia, metaplasia, dysplasia, anaplasia, and neoplasia. and • Compare cellular and tissue changes following toxicant exposure. pathological • Describe how growth hormone induces physiological or pathological cellular adaptations depending on the timing of exposure. adaptations. • Case study: describe how opioids induce pathological adaptations. Dose Describe the • Describe the importance of modeling exposure. Response different kinds • Describe how route of exposure affects dose. of doses: • Define absorption, specific to the discipline of toxicology. exposure, • Describe the influence of age, nutrition, and genetic background on dose. administered, absorbed, internal, and delivered. Describe a dose • Describe the assumptions made if based on the mean of a population. response curve, • Describe the difference between individual response and population response labeling the for a dose response curve. axes and • Describe the importance of the linear portion of the dose response curve. identifying • Describe the difference between lethality, effect, and inhibition types of dose important response curves. regions of the • Describe the importance of defining an appropriate end point/response. plot. • Describe the difference between nutrient dose-response curves and toxicant dose-response curves. • Describe the importance of inflection points in the dose response curve. • Case study: Describe the controversy surrounding the linear no-threshold hypothesis. • Case study: Apply the dose response concept to homeopathic medicine. • Contrast threshold values versus NOAELs in a dose response curve. • Describe the importance of outliers or hypersensitive individuals to a dose response curve.

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• Describe how comparison of dose response curves allows interpretation of the relative toxicity of two compounds in a population. • Describe how a dose response curve is necessary to determine a causal relationship between exposure and effect. • Explain the statement “dose response curves do not allow determination of mechanism.” • Apply the Henderson-Hasselbach equation to dose response. Describe the • Define threshold dose. features of a • Describe the quantitative relationship between dose and response. dose-response • Describe whether a cause/effect relationship can be determined from a dose curve. response curve. • Relate the toxicity of two compounds in a population using dose response curves. • Contrast efficacy and potency. • Contrast threshold versus NOAELs • Describe the importance of outliers. • Explain the statement "dose response curves do not allow determination of mechanism" Explain • Apply population dose-response curves to individuals. differences in • Identify allelic variations that alter response following toxicant exposure dose responses • Identify non-genetic factors such as age, sex, weight, and diet, that affect in a population individual responses to toxicant exposures of individuals.

Describe why • Describe why it is important to perform toxicology tests in both males and individuals that females. have • Describe how differences in epigenetic methylation/acetylation can cause idiosyncratic idiosyncratic responses. responses • Describe the role of the immune system in generating idiosyncratic responses. (either • Describe how polymorphisms in cytochrome P450 enzymes can cause hypersensitive hypersensitivity or hyperresistance to toxicants. or hyper resistant to toxicants) are outliers and propose mechanisms for their differences. Describe how • Describe how pre-exposure to low doses of a toxicant can protect against a alterations in subsequent exposure to that toxicant or to other toxicants. homeostasis • Describe the role of mitochondria in energy homeostasis. can affect an • Describe the effect of nutritional status (lack of vitamins for enzyme cofactors, individual's for example), on homeostasis and response to xenobiotics. dose response. • Describe how age affects metabolism and homeostasis. • Describe how disease states affect homeostasis. • Describe how drugs of abuse alter homeostasis. Describe the • Define bioavailability as it relates to ADME. fundamental • Describe how vehicles affect ADME. basis of • Describe the primary importance of the liver and kidney in xenobiotic defense. xenobiotic • Describe how vascularization affects xenobiotic defense. defense through • Explain how the presence of Phase 1 and 2 enzymes affect ADME. ADME. • Contrast lipophilicity and hydrophilicity and how they affect ADME.

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• Explain how storage in the lipid or bone is one route of elimination. • Describe how remobilization of toxicants from lipids in times of starvation stress can cause toxicity. • Case study: Describe toxicant remobilization during starvation of Sarasota Bay dolphins during red tide in the 1990s. Commented [JG6]: Asked Eva Oberdorster for a citation for this.

Explain why • Contrast LD50 and LC50. LD50 is • Explain the importance in choosing an appropriate animal model to make commonly used useful comparisons to humans. as a measure of • Explain how LD50 is affected by route of exposure. toxicity of a • Explain the importance of length of exposure in determining LD50. compound. • Describe the use of uncertainty factors when extrapolating animal-derived LD50 data to humans. ADME Describe the • Know the words that make up the acronym ADME: absorption, distribution (or concept of disposition), metabolism, and excretion. ADME as it • Describe how characteristics of ADME change with dose. relates to • Contrast unsaturated with saturated elimination. toxicant • Apply the Henderson-Hasselbach equation to ADME. exposure. • Case study: Describe the ADME of ethanol. • Case study: Describe the ADME of acetaminophen. • List the five major processes of elimination: renal, fecal, pulmonary, biotransformation, and other means (sweat, milk, hair, nails) • Define biotransformation. Contrast the • Describe the three major portals of entry to the body: gastrointestinal, major sites of inhalational, and dermal. entry for • Describe how route of exposure affects the toxicity of a toxicant. toxicants and • Know the major sites of entry for toxicants and their surface areas in humans: how site of respiratory system (100 m2), gastrointestinal system (300 m2), and entry affects integumentary system (2 m2). dose and risk. • Describe percutaneous absorption and the effects of skin conditions (cuts, scratches, inflammation, and hair follicles) on penetration. Describe • Know the characteristics of chemicals that affect diffusion: size, molecular features of charge, ionization, water solubility, and concentration differences across chemicals and membranes. barriers that • Know that turbinates of the nose capture highly water-soluble gases and high affect reactive gases, preventing exposure of the lower lung. absorption of • Differentiate simple diffusion, active transport, facilitated diffusion, compounds phagocytosis, and pinocytosis. • Case study: Contrast aspirin and aniline for their relative absorbance in the stomach or intestines due to pH. • Know the sizes of particles that reach different parts of the respiratory system. • List the chemical disposition features of importance, including: duration and concentration at site of entry, rate of absorption, total amount of toxicant absorbed, distribution within the body and presence at specific sites, efficiency of biotransformation, toxicity of metabolites, storage of the toxicant and metabolites in the body, and rate and sites of elimination. • Describe iron as a case study for elimination. • Explain why a dose of a chemical given intravenously often results in a higher body burden than a chemical given orally.

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Describe • Describe the role of the blood brain barrier in preventing exposure to toxicants. barriers to • Describe the number of barriers through which a toxicant must travel before distribution, reaching target tissues. including the • Describe the controversy about the role of the placenta as a barrier to blood brain toxicants. barrier, blood- testis barrier, and placenta Contrast the • Contrast phase I and phase II metabolism. mechanisms of • Describe deposition in the skin or bone as a route of elimination elimination, • Describe how defects in excretion pathways affect toxicity of compounds in including sensitive populations. excretion, • List examples of where storage of toxicants can occur and the types of storage, and toxicants that get stored there: plasma proteins, adipose tissues, bones, liver biotransformatio • Know that renal excretion is good at eliminating molecules smaller than 60,000 n. MW and water-soluble compounds. • Know the fecal elimination includes bile, which is good at eliminating organic acids and bases, heavy metals, and nonionized chemicals. • Describe enterohepatic circulation. • Know that lipophilic gases are primarily eliminated via exhalation. Toxicodyn Define • Describe how the volume of distribution (VD) is used to help quantify exposure amics and toxicokinetics and body burden. Toxicokin and • Describe the three compartments of water in the body: plasma, interstitial, and etics pharmacokineti intracellular. cs. • Define body burden. Explain how • Identify standard tests that can be used to estimate the concentrations of the toxicokinetic parent compound and metabolites. studies are • Be able to interpret data on AUC, clearance, and half-life. used to • Understand the limitation of animal studies and computer models in predicting determine an individual human’s response. changes in concentration of a chemical and its metabolites over time in blood and other tissues. Explain several • Describe the use of radiolabeled chemicals in toxicokinetic studies. methods of • Describe how toxicokinetics is used to identify persistence, half-life, and toxicokinetic potential for toxicants. analysis. Describe how • Explain the assumptions of the one compartment model. Explain why a one one-, two-, or compartment model is often sufficient despite its simplicity. multi- • Describe how the nervous system acts as a separate compartment from the compartment rest of the body. models are • Describe how binding to plasma proteins can affect the distribution of a used to toxicant. approximate • case studies on all three types of compounds Commented [JG7]: Find case studies for all three. toxicokinetics. • Explain the difference between a one compartment and two compartment models Describe how • Case study: Describe how ethanol is eliminated from the body. saturation • Case study: Describe the mechanism by which ethanol protects against affects the methanol toxicity.

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elimination of a compound.

Contrast zero- • Know that one-compartment model systems typically eliminate a chemical in a order versus first-order manner (first order means that the half-life remains constant first-order throughout elimination). kinetics of • Create a graph showing elimination of a chemical using one-compartment elimination. model kinetics (time is x axis, log of concentration is y axis). • Know that zero-order kinetics become more important when a saturable system is involved. • Case study: Describe how ethanol is eliminated from the body primarily via zero-order kinetics. • Draw a 2-compartment model, illustrating rates of entry, metabolism, and excretion. Describe how • Describe why the placenta as a barrier to toxicants is controversial. barriers such as • Describe the structure of the blood brain barrier and how active transport is the blood brain used to prevent diffusion of lipophilic compounds into the CSF. barrier or • Know that most toxic chemicals pass the placenta via passive diffusion. placenta alter • drugs in the brain slow rate of BB diffusion toxicokinetics. • Case study: Describe how P-gp null mice are more sensitive to neurotoxicity in response to vinblastine. Pharmacol Contrast • Contrast margin of safety with therapeutic index for a drug. ogy measurements • Describe why chemotherapeutics have a smaller therapeutic index and margin of drug safety. of safety than other drugs. • Define the maximum tolerated dose. Explain the • Case study: Describe the effect of large doses of acetaminophen given at once concept of dose versus over time on phase 2 metabolic pathways. spacing • Describe how slow rates of excretion or metabolism can cause accumulation of a toxicant over time through frequent low-dose exposures. • Case study: describe how limitations on fish in the diet relate to fractional dosing and mercury exposure.

Describe the • Describe the process of drug development. role of • Describe the Ames assay and its use in determining potential . toxicology in the • Describe resorufin-based cellular viability assays. drug • Describe how high throughput screens using high content data are used to development screen drug candidates for toxicity. process, including preclinical studies and clinical trials. Redox Describe free • Contrast the toxicity of hydroxyl radicals versus hydrogen peroxide. Biology radical forms of • Describe how free radicals can serve as signaling molecules. oxygen and • Describe the role of free radicals in the immune system. nitrogen • Describe the role of nitric oxide in neurotransmission • Describe how free radicals are produced by mitochondria.

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Describe the • Describe the role of the cell membrane in lipid peroxidation. mechanism of • Describe how lipid peroxidation can affect mitochondria and the nucleus. lipid • Describe how homeostasis is disrupted by loss of membrane integrity. peroxidation. • Describe how protein structures are affected by protein structures. • Describe membrane repair. • Contrast lipid peroxidation repair and protein/DNA repair mechanisms. • Describe how lipid peroxidation products act as signaling molecules. • Describe how lipid peroxidation is used as a strategy for killing bacteria. Describe the • Contrast mitochondrial versus cytosolic defense pathways against free defenses radicals. organisms have • Describe the role of vitamins and essential metals in defense against oxidative against free stress. radicals. • Describe the role of melanin in defense from oxidative stress. • Describe how antioxidant molecules defend against oxidative stress. • Describe the balance between oxidants and antioxidants in defense against free radicals. Describe the • Describe the role of transcription factors in the nrf2 signaling pathway. NRF2 pathway • Contrast the roles of nrf2 in different tissues. and it signals • Contrast inducible versus constitutively active enzymes. defense against • Explain how antioxidant enzymes are controlled by multiple transcription and oxidative stress. signaling pathways. Energy Discuss the role • Contrast aerobic and anaerobic metabolism. that glycolysis • Describe the implications of cytoplasmic acidification plays in energy • Describe the importance of metabolic phosphorylation for sequestering production. molecules in the cell. • Describe the long-term effects of shifting to glycolysis for energy production. • Contrast respiratory capacity of model organisms versus humans. Describe the • Describe the role of phosphorylation in production of ATP importance of • Contrast how kinase and phosphatase activity are balanced. ATP in cellular • Explain how apoptosis requires energy. homeostasis. • Explain how the maintenance of concentration gradients requires energy. • Describe the importance of ATP in cell cycle control. • Describe how mitochondrial inhibitors affect cellular function. List the • Describe the importance of carbohydrates in metabolism. implications of a • Describe the role of cholesterol in membrane integrity. high-fat/high- • Describe the necessity of cholesterol in steroid synthesis. energy diet. • Explain how high-fat/high-energy diets disrupt cellular metabolism • Explain how lipophilic xenobiotics can be stored in adipose tissue. • Contrast catabolism of PUFA's and saturated fatty acids • Discuss the importance of omega 3 fatty acids • Describe the role of Krebs cycle anabolism in carbohydrate catabolism. Describe the • Discuss the implications of inhibiting Complex 1. central role of • Describe diseases associated with mitochondrial inhibitors oxidative • Explain mechanisms for monitoring redox potential in the cell. phosphorylation • Describe the importance of NAD+/NADH balance in energy • Discuss implications of inhibiting Complex IV. generation. • Contrast proton (electrical) gradient and pH gradient across the mitochondrial inner membrane. • Discuss the importance of mitochondrial energy coupling.

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