INTEGRATIVE EXERCISE QUESTIONS

Faculty available to chair comps committees: Camill, Jarámillo, McKone, Reinke, Singer, Tymoczko, Wagenbach and Walser-Kuntz

1. (Walser-Kuntz) The vertebrate immune system is one of the most complex systems known. How did it evolve? Provide evidence for the evolution of one aspect of the vertebrate innate or adaptive immune system.

Van den Berg, T et al. (2004). On the origins of adaptive immunity: innate immune receptors join the tale. Trends in Immunology 25, 11-16.

Kasahara, M et al. (2004). On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates. Trends in Immunology 25, 105-111.

2. (Tymoczko) Cholesterol is a fundamental molecule of animal systems. It is crucial to membrane function, to food absorption and is a precursor to the steroid hormones and vitamin D. On the other hand, excess cholesterol plays a prominent role in the development of heart disease. Review the regulation of cholesterol synthesis, its role in heart disease and suggest means by which the biochemistry and cell biology of cholesterol can be altered to mitigate the pathological effects of cholesterol excess.

Hampton, R.Y. (2002). Proteolysis and sterol regulation. Annual Review of Cell and Developmental Biology 18, 345-78.

Shimano, H. (2001). Sterol regulatory element-binding protein family as global regulators of lipid synthetic genes in energy metabolism. Vitamins and Hormones 65, 167-94.

Kelley, R.I. and Herman, G.E. (2001). Inborn erros of sterol biosynthesis. Annual Review of Genomics and Human Genetics 2, 299-341.

3. (Tymoczko) Reactive oxygen species (ROS) are an inevitable by-product of aerobic metabolism. Inability to cope with these species has been implicated in a number of pathological conditions, including cancer, muscular dystrophy, alcoholic liver disease and diabetes. ROS have also been implicated in the aging process. It has been suggested that one of the long-term benefits of exercise is the enhancement of biochemical defense mechanisms against ROS. Examine how ROS are produced, the biochemical mechanisms that exist to protect against ROS and review the evidence supporting their role as chemical pathogens.

Cooke, M.S., Evans, M.D., Dizdaroglu, M., and Lunec, J. (2003). Oxidative DNA damage: mechanisms, mutation, and disease. The FASEB journal 17(10), 1195-214.

Overmyer, K., Brosche, M., and Kangasjarvi, J. (2003). Reactive oxygen species and hormonal control of cell death. Trends in Plant Science 8(7), 335-42.

Genova, M.L., Pich, M.M., Biondi, A., Bernacchia, A., Falasca, A., Bovina, C., Formiggini, G., Castelli, G.P., Lenaz, G. (2003). Mitochondrial production of oxygen radical species and the role of Coenzyme Q as an antioxidant. Experimental Biology and Medicine 228(5), 506-13.

4. (Jaramillo) The formation of synapses, the specialized junctions that allow neurons to communicate, is one of the central processes for the development of the nervous system. Describe how synaptic vesicles my be recruited for the construction of the presynaptic terminal.

Matteoli, M.N., et al. (2004). Vesicle Turnover in developing neurons: how to build a presynaptic terminal. Trends in Cell Biology 14, 133-140.

Goda, Y., and Davis, G.W. (2003). Mechanisms of synapse assembly and disassembly.

5. (Jaramillo) In the previous year students explored the origin of auditory hallucinations in schizophrenic patients. Auditory illusions are also remarkable, although not always understood, neurobiological phenomena. A recent study suggests that patterns of subthreshold cortical activity may be related to visual illusions. Explore the neural basis of illusion.

Jancke, D., et al. (2004). Imaging cortical correlates of illusion in early visual cortex. Nature 428, 423-426.

6. (Wagenbach) A traditional explanation for plague (black-death) in Medieval Europe is that a bacterium, Yersinia pestis, killed humans after being introduced into the body by the bite of a flea. This paradigm is being challenged and other infectious agents are being considered. Evaluate causality by presenting a critical analysis of the question using the best recent literature.

Gilbert, M.T.P., Cuccui, J, White, W., Lynnerup, N., Titball, R.W., Cooper, A., Prentice, M.B. (2004). Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology-SGM 150, 341-354 Part 2.

Wood, J.W., Ferrell R.J., Dewitte-Avina, S.N. (2003). The temporal dynamics of the fourteenth-century Black Death : New evidence from English ecclesiastical records. Human Biology 75 (4), 427-448.

7. (McKone) Organisms of a particular genotype sometimes have the potential to develop quite different phenotypes, depending on the environment they experience during their lives. Review the importance of phenotypic plasticity in determining the ecological characteristics of organisms, including interspecific interactions.

Agrawal, A. A. (2001). Phenotypic plasticity in the interaction and evolution of species. Science 284, 321-326.

Pecl, G.T., Moltschaniwskyj, N.A., Tracey, S.R., and Jordan, A.R. (2004). Inter-annual plasticity of squid life history and population structure: ecological and management implications. Oecologia 515-524.

Relyea, R. A. (2003). How prey respond to combined predators: a review and an empirical test. Ecology 84, 1827-1839.

8. (McKone) The origin of species has been a focus of evolutionary biology since Darwin. New species usually arise when there is reproductive isolation between populations, but such barriers to hybridization may not be complete early in the process of speciation. Which mechanisms are most important in the origin of reproductive isolation during the process of speciation? What prevents hybridization between newly forming species? Does hybridization play a role in the origin of genetically unique lineages?

Bordenstein, S. R., O’Hara, F. P., and Werren, J. H. (2001). Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia. Nature 409, 707-710.

Litjmaer, D.A., Mahler, B., and Tubaro, P.L. (2003). Hybridization and postzygotic patterns in pigeons and doves. Evolution 57, 1411-1418.

Robertson, A., Newton, A.C., and Ennos, R.A. (2004). Multiple hybrid origins, genetic diversity and population genetic structure of two endemic Sorbus taxa on the Isle of Arran, Scotland. Molecular Ecology 13, 123-134.

9. (Hougen-Eitzman) (Hougen-Eitzman) Biological control is the use of one biological organism to control another species, usually a pest. Even though it is considered to be one of the cornerstones of integrated pest management systems (whose primary goal is to reduce the use of pesticides in pest control), there have been both successes and failures. Examine the ecological basis of control, invasiveness of biological control agents, or nontarget effects of biological control agents.

Callaway, R. M., Thelen, G.C., Rodriguez, A., and Holben, W.E. (2004). Soil biota and exotic plant invasion. Nature 427, 731-733.

Michaud, J. P. (2002). Classical Biological Control: A Critical Review of Recent Programs Against Citrus Pests in Florida. Annals of the Entomological Society of America 95, 531-540.

Pearson, D. E. and Callaway, R.M. (2003). Indirect effects of host-specific biological control agents. Trends in Ecology and Evolution 18, 456-461.

Secord, D. (2003). Biological control of marine invasive species: cautionary tales and land-based lessons. Biological Invasions 5, 117-131.

10. (Camill) To paraphrase Rob Jackson in a recent article, “Ultimately what we seek as ecologists is a better understanding of ecology as an integrated science. Dichotomies of ‘belowground and aboveground’ are conveniences, allowing processes to be broken down conceptually. Reassembling the parts is eventually necessary – be it combining root and shoot functioning, the exchange of material among plants, the soil, and the atmosphere, or other convenient divisions.” With global change, the possible effects on changes in aboveground vegetation are becoming clear. What is less clear is the contribution of belowground processes on how ecosystems may respond to global change. There is increasing evidence that soil- and root-level processes, such as respiration, nutrient cycling, water relations, and interactions with microbes, can all affect the dynamics of ecosystems as a whole in ways that are not easily predictable by examining aboveground vegetation only. Evaluate this literature and identify how belowground ecosystem processes may affect the response of ecosystems during global change.

Norby R.J. and Jackson, R.B. (2000). Root dynamics and global change: seeking an ecosystem perspective. New Phytologist 147 (1), 3-12.

Woodward, F.I. and Osborne, C.P. (2000). The representation of root processes in models addressing the responses of vegetation to global change. New Phytologist 147(1), 223-232.

Jackson, R.B. (2000). Below ground processes and global change. Ecological Applications 10 (2), 397-398.

Zak, D.R. et al. (2003). Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology 84 (8), 2042-2050.

van Noordwijk M. et al. (1998). Global change and root function. Global Change Biology 4(7), 759-772.

Luo, Y.Q. et al. (2001). Acclimatization of soil respiration to warming in a tall grass prairie. Nature 413(6856), 622-625.

11. (Singer) The commonalities of developmental gene families among organisms and the limited number of these families lead to fascinating evolutionary questions. How can organisms share such similar developmental genes and yet have such distinct morphologies (e.g. the HOX and MADS box paradox)? Focus on a subset of one developmental gene family and explore this paradoxical situation. How is orthology between genes determined? How can orthologous genes contribute to distinct morphologies in different species? Consider how advances in genomics, proteomics and phylogenetics can aid in addressing this question.

Nam, J. et al. (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proceedings of the National Academy of Sciences 101, 1910-1915.

Kramer, E.M., et al. (2003) Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. International Journal of Plant Science 164, 1-11.

12. (Singer, Camill) Phytoremediation shows promise for removing toxic waste, including heavy metals and organics, from soils. Genetic modification of biochemical pathways in plants can enhance their value as phytoremediators. Investigate how plants can be used to remove toxins from the soil. What aspects of physiology, cell biology, genetics, and biochemistry are critical in effective phytoremediation.

Tong, Y. et al. (2004) Vacuolar compartmentalization: a second-generation approach to engineering plants for phytoremediation. Trends in Plant Science 9, 7-9

Clemens, S. et al. (2002) A long way ahead: understanding and engineering plant metal accumulation. Trends in Plant Science 7, 309-315

13. (Reinke) The inheritance of the cellular machinery is as essential to life as the inheritance of genetic information. The information necessary to construct a membrane-bound organelle does not reside solely in the cell’s DNA. During cell division, each new daughter cell must eventually inherit a minimal number of cytoplasmic organelles to maintain viability. In general, a cell cannot rely on an organelle simply “floating into” a new daughter cell. Different cell types use unique cellular and molecular mechanisms to partition organelles such as the endoplasmic reticulum, the Golgi apparatus, vacuoles, mitochondria and chloroplasts. Critically examine and discuss the work that leads to our current understanding of the cellular and molecular mechanisms of organelle inheritance.

Catlett, N.L. and Weismann, L.S. (2000). Divide and Multiply: organelle partitioning in yeast. Current Opinion in Cell Biology 12, 509-516.

Barr, F.A. (2002). Inheritance of the endoplasmic reticulum and Golgi apparatus. Current Opinion in Cell Biology 14, 496-499.

Cox, R.T. and Spradling, A.C. (2003). A Balbiani body and the fusome mediate mitochondrial inheritance during Drosophila oogenesis. Development 130, 1579-1590.

Sheahan, M.B. et al. (2004). Organelle inheritance in plant cell division: the actin cytoskeleton is required for unbiased inheritance of chloroplasts, mitochondria and endoplasmic reticulum in dividing protoplasts. The Plant Journal 37, 379-390.