DEPARTMENT OF BIOLOGY
INTEGRATIVE EXERCISE QUESTIONS
Faculty available to advise comps: Hernández, Hougen-Eitzman, McKone, Mitra, Moore, Rand, Tymoczko, and Wolff
1. Dan Hernández
Ecological stoichiometry is the balance of multiple chemical substances in ecological processes and interactions. Stoichiometric balances (and imbalances) influence all levels of ecology, including the growth and maintenance of homeostasis in individual organisms, the structure of communities, trophic interactions, and ecosystem processes like carbon and nutrient cycling. In this question, consider the stoichiometric controls on the structure and/or function of an ecological system at any level of organization, from individuals to ecosystems.
Finzi A. C. et al. (2011). Responses and feedbacks of coupled biogeochemical cycles to climate change: examples from terrestrial ecosystems. Front. Ecol. Environ. 9, 61-67.
Hall E. K. et al. (2011). Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches. Ecosystems 14, 261-273.
Persson J. et al. (2010). To be or not to be what you eat: regulation of stoichiometric homeostasis among autotrophs and heterotrophs. Oikos 119, 741-751.
Taylor P.G. and Townsend A. R.(2010). Stoichiometric control of organic carbon-nitrate relationship from soils to the sea. Nature 464, 1178-1181.
Weber T. S. and Deutsch C. (2010). Ocean nutrient ratios governed by plankton biogeography. Nature 467, 550-554.
2. Dan Hernández and Mark McKone
Ecological communities worldwide are experiencing accelerated rates of both species loss and species gain. Evaluate the empirical evidence for the consequences of such changes in ecological diversity on the ecological function of communities.
Reich, P. B., Tilman, D., Isbell, F., Mueller, K., Hobbie, S. E., Flynn, D. F. B., and Eisenhauer, N. (2012). Impacts of biodiversity loss escalate through time as redundancy fades. Science 336, 589-592.
Wardle, D. A., Bardgett, R. D., Callaway, R. M., and Van der Putten, W. H. (2011). Terrestrial ecosystem responses to species gains and losses. Science 332, 1273-1277.
3. David Hougen-Eitzman
Genetically modified (GM) crops are a recent addition to the plants that farmers grow. The first modified plant was produced in 1982, and since then the use of GM crops has become widespread, including such major crops as maize (corn), soybeans, cotton, canola, sugarbeets, alfalfa and potatoes. Most of these crops were modified to provide resistance to pests or certain herbicides, with some spectacular results. However, as with many things that humans do, there could be a host of unknown and unintended effects on organisms and communities in or near these crop fields. Discuss the ecological impacts of GM crop use.
Ahrens, C. W., and Auer, C. A. (2012). Annual glyphosate treatments alter growth of unaffected bentgrass (Agrostis) weeds and plant community composition. PLOS One 7, e50643Carriere, Y., Ellers-Kirk, C., Hartfield, K., et al. (2012). Large-scale, spatially-explicit test of the refuge strategy for delaying insecticide resistance. Proc. Natl. Acad. Sci., USA 109, 775-780.
Dutra, C. C., Koch, R. L., Burkness, E. C., et al. (2012). Harmonia axyridis (Coleoptera: Coccinellidae) exhibits preference between Bt and non-Bt maize fed Spodoptera frugiperda (Lepidoptera: Noctuidae). PLOS ONE 7, e44867
Hagenbucher, S., Wackers, F. L., Wettstein, F. E. et al. (2013). Pest trade-offs in technology: reduced damage by caterpillars in Bt cotton benefits aphids. Proc. R. Soc. B 280, 20130042
4. Mark McKone
The origin of eukaryotic cells was one of the most fundamental changes in the evolutionary history of life on Earth. Discuss recent research about how complex eukaryotic structures or genomes evolved.
Alvarez-Ponce D., Lopez, P., Bapteste, E., and McInerney J.O. (2013). Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc. Natl. Acad. Sci., USA 110, 1594-1603.
Vesteg, M., Ŝándorová, Z., and Krajčovič. J. (2012). Selective forces for the origin of
spliceosomes. J. Mol. Evol. 74, 226-231.
Wickstead, B., and Gull. K. (2011). The evolution of the cytoskeleton. J. Cell
5. Jalean Petricka
Selecting Items for the Garbage? Protein degradation by the ubiquitin-proteasome system (UPS) is integral to hormonal signaling in plants and to cell proliferation and carcinogenesis in mammalian systems. In UPS, E3 ubiquitin ligases select specific protein targets for degradation. In many eukaryotic organisms, the selection and timing of protein degradation is carefully orchestrated to ensure proper activation and repression of transcriptional targets, hormonal responses, and cellular signaling events. Select one hormonal or cellular process regulated by this protein degradation pathway in an organism and explore the genetic and molecular evidence linking the process you selected and protein destruction.
Kelley, D.R. and Estelle, M. (2012). Ubiquitin-mediated control of plant hormone signaling. Plant Physiol.160, 47-55.
Zhou, W., Wei, W., Sun, Y. (2013) Genetically engineered mouse models for functional studies of SKP1-CUL1-F-box-protein (SCF) E3 ubiquitin ligases. Cell Research, 1-21. doi: 10.1038/cr.2013.44
Husniak, K. and Dikic, I. (2012). Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu. Rev. Biochem. 81, 291-322.
Tomko, Jr., R.J. and Hochstrasser, M. (2013) Molecular architecture and assembly of the eukaryotic proteasome. Annu. Rev. Biochem 82, 13.1-13.31.
6. John Tymoczko
Nutrients are key regulators of cell and tissue growth. Nutrient sensing regulates the metabolism of the cells in response to extracellular and intracellular conditions. A rapid and efficient response to changes in nutrient levels and types is crucial for the survival of all organisms. Describe the molecular pathways that can sense nutrient concentrations and investigate how they are regulated to respond to any changes.
Jewell, J. L., and Guan, K.-.L. (2013). Nutrient signaling to mTOR and cell growth.
Trends Biochem. Sci. 38, 233—242.
Laplante, M., and Sabati, D. M. (2012). mTOR Signaling in growth control and disease. Cell 149, 274—293.
7. Jennifer Wolff
Development depends on a series of epic journeys, among them the sperm’s quest for the egg, the gonad-bound expedition of primordial germ cells, the trails forged by the neural crest, and the radial paths of cortical neurons. Migrating cells’ ability to senseand respond to directional cues is essential to the morphogenetic processes that shape the embryo. Trace the extracellular and intracellular molecular events that govern a migrating cell’s (or group of cells’) journey from a site of origin to its destination in the embryo, and explore the consequences of failure to successfully execute this migration.
Ayala, R., Shu, T., and Tsai, L.-H. (2007). Trekking across the Brain: The Journey Neuronal Migration. Cell 128, 29–43.
Kaupp, U. B., Kashikar, N. D., and Weyand, I. (2008). Mechanisms of Sperm Chemotaxis. Annu. Rev. Phys. 70, 93–117.
Rørth, P. (2009). Collective Cell Migration. Annu. Rev. Cell Dev. Biol. 25(1), 407–429.
Solnica-Krezel, L., and Sepich, D. S. (2012). Gastrulation: Making and Shaping Germ Layers. Annu. Rev. Cell Dev. Biol. 28, 687–717.
Tarbashevich, K., and Raz, E. (2010). The nuts and bolts of germ-cell migration. Curr. Opin. Cell Biol. 22(6), 715–721.
Theveneau, E., and Mayor, R. (2012). Neural crest delamination and migration: From epithelium-to-mesenchyme transition to collective cell migration. Dev. Biol. 366, 34–54.
8. Raka Mitra
Stem cells can divide indefinitely and differentiate into specialized cell types in order to build organisms or replenish tissues. Thus, these cells hold great promise for modern medicine. While most adult stem cells can only differentiate into a select number of cell types, pluripotent stem cells, which typically originate from the embryo, can differentiate into nearly all cell types. Explore the nature of pluripotency examining the current level of understanding about the mechanisms that maintain this state and the process by which a cell chooses to exit pluripotency and differentiate into a particular cell type.
Dalton, S. (2013). Signaling networks in human pluripotent stem cells. Curr. Opin. Cell Biol. 25, 241-246.
Fong, Y.W., Cattoglio, C., Yamaguchi, T., and Tjian, R. (2012). Transcriptional regulation by coactivators in embryonic stem cells. Trends Cell Biol. 22, 292-298.
Betschinger, J., Nichols, J., Dietmann, S., Corrin, P.D., Paddison, P.J., and Smith, A. (2013). Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3. Cell 153, 335-347.
Takahashi, K., and Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676.
9. Matt Rand
Vertebrate placentae are diverse across taxa and diverse in function. Starting with implantation and ending with the regulation of parturition, the placenta is involved with complex developmental and physiological functions from gas and nutrient exchange to fetal-maternal endocrine signaling. In addition, the interactions between the extra embryonic membranes and maternal tissue present unique immunological challenges. Uncompromised fetal development is dependent upon proper placental function and certain complications during pregnancy are thought to arise through placental signaling or metabolic errors. Choose one of the many placental functions and describe our current understanding of the mechanisms involved in producing the normal and/or pathological state.
Carter, A.M. (2012) Evolution of placental function in mammals: the molecular basis of gas and nutrient transfer, hormone secretion, and immune responses. Physiol. Rev. 92, 1543-1576.
Christiansen, O.B. (2013) Reproductive immunology. Mol. Immunol. 55, 8–15.
Miehle, K., Stepan, H., Fasshauer, M. (2012) Leptin, adiponectin and other adipokines in gestational diabetes mellitus and pre-eclampsia. Clin. Endocrinol. 76, 2–11.
Redman, C.W.G., and Sargent. I.L. (2009) Placental Stress and Pre-eclampsia: A Revised View. Placenta 30, 38–42 Suppl.
10. Amy Moore
Gut microbes have long been recognized as crucial in maintaining intestinal health. However, accumulating evidence suggests that intestinal microbiota are also influential in normal neural development and neural plasticity. Describe the physiological mechanisms associated with bidirectional communication of this “gut-brain axis”, highlighting molecular events in specific brain regions and their potential role in pathological conditions.
Collins, S.M., Surette, M., Bercik, P. (2012) The interplay between the intestinal microbiota and the brain. Nat. Rev. Microbiol. 10, 735-742.
Cryan, J.F., Dinan T.G. (2012) Mind-altering microorganisms: the impact of the gut microbiota on brain and behavior. Nat Rev Neurosci. 13, 701-712.