Questions 2008/09

BIOLOGY DEPARTMENT
INTEGRATIVE EXERCISE QUESTIONS
2008-09

Faculty available to advise comps: Hougen-Eitzman, Jaramillo, McKone, Rand, Singer, Tymoczko, Walser-Kuntz, Wolff, and Zweifel

1. (Tymoczko) Resveratrol is a phytoalexin, a class of antibiotic compounds produced as a part of a plant's defense system against disease. Resveratrol is found in a variety of sources, most notably the skin of red grapes. The apparent effects of resveratrol are wide-ranging. Evidence exits that resveratrol can modulates a number of biochemical systems, and there is research showing the resveratrol protects against heart disease, cancer, diabetes, aging and inflammation. Review the literature on resveratrol and suggest a biochemical basis for its effects.

Prevaiz, S. (2003). Resveratrol: from grapevines to mammalian biology. The FASEB Journal. 17, 1975-1985

Baur, J.A., and Sinclair, D.A. (2006) Therapeutic potential of resveratrol: the in vivo evidence. Nature Reviews. Drug Discovery. 5, 493-506.

2. (Tymoczko) The polycystic ovarian syndrome (PCOS), a common endocrine disorder in premenopausal woman, is defined as a condition meeting two of the three following criteria: hyperandrogenism, infrequent or irregular ovulation and polycystic ovary as detected by ultrasound. PCOS is has a number of reproductive and metabolic consequences, including a proclivity toward insulin resistance. Investigate the biochemical basis of this condition and how PCOS exerts it metabolic effects.

Special issue of Trends In Endocrinology and Metabolism. (2007). 18, 259-290.

3. (Wolff and Walser-Kuntz) Tissues and organs of the immune system are formed during embryonic development, and cells of the immune system continuously renew from stem cells throughout the life of a vertebrate. Explain the signaling and gene expression networks involved in the development of an organ or cell type in the immune system.

Dzierzak, E., and Speck, N.A. (2008). Of lineage and legacy: the development of mammalian hematopoietic stem cells. Nature Immunology 9, 129-136.

Boehm, T., and Bleul, C.C. (2006). Thymus-homing precursors and the thymic microenvironment. Trends in Immunology 27, 477-484.

Suda, T. et al. (2005). Hematopoietic stem cells and their niche. Trends in Immunology 26, 426-433.

4. (Rand and Zweifel) Through careful analysis of most behaviors, one can show that environmental factors can induce behavioral differences. However, one can also argue that behavioral traits are directly, or indirectly, influenced by genetics. Examine the evidence that illustrates the relationship between an organism's genetic makeup and a specific behavioral pattern. Include a discussion of the mechanism by which gene products influence the physiology of behavior.

Robinson, G.E., Grozinger, C.M., and Whitfield, C.W. (2005). Sociogenomics: social life in molecular terms. Nature Reviews Genetics 6, 257-270.

5. (Rand) It is well established that gonadotropin-releasing hormone (GnRH) plays a fundamental role in the regulation of fertility, sexual maturation, and reproductive behavior. However, the upstream neuroendocrine mechanisms that integrate internal physiological states and environmental conditions remain less well understood. Newly discovered neuroendocrine signals such as kisspeptin and the RF amide peptides are currently being investigated as potential regulators of the hypothalamic-pituitary-gonad axis. Investigate the experimental evidence that describes the upstream mechanisms that stimulate and/or inhibit a specific reproductive function.

Mason, A.O., Greives, T.J., Scotti, M.L., Levine, J., Frommeyer, S., Ketterson, E.D., Demas, G.E., Kriegsfeld, L.J. (2007). Suppression of kisspeptin expression and gonadotropic axis sensitivity following exposure to inhibitory day lengths in female Siberian hamsters. Horm Behav. 52, 492-498.

Mead, E.J., Maguire, J.J., Kuc, R.E., and Davenport, A.P. (2007). Kisspeptins: a multifunctional peptide system with a role in reproduction, cancer and the cardiovascular system. Brit. J. Pharmacol. 151, 1143-1153.

Tsutsuia, K., and Ukena, K. (2006). Hypothalamic LPXRF-amide peptides in vertebrates: Identification, localization and hypophysiotropic activity. Peptides 27, 1121-1129.

6. (Zweifel) Alternative splicing is the process by which the exons of primary transcripts can be spliced in different arrangements to produce structurally and functionally distinct mRNA and protein variants. Genome-wide microarray studies have suggested that alternative splicing plays a major role in the generation of proteomic diversity in metazoan organisms, and disruption of the alternative splicing mechanism has a determinative role in disease. Examine the mechanisms of alternative splicing, and the role of transcription variants in normal and disease physiology. In addition, discuss how alternative splicing is coordinated to achieve cell and tissue specific functions.

Blencowe, B.J. (2006). Alternative splicing: new insights from global analysis. Cell 126, 37-47.

Wang, G-S., and Cooper, T.A. (2007). Splicing and disease: disruption of the splicing code and the decoding machinery. Nature Rev. Genet. 8, 749-760.

7. (Wolff and Jaramillo) The development of many organs, including the lungs, kidneys, pancreas, mammary glands, and heart depends on the processes of tube formation (tubulogenesis) and, in some cases, the branching of tubes into elaborate tree-like structures (branching morphogenesis). Abnormal tubulogenesis and branching morphogenesis can lead to disorders like polycystic kidney disease, in which enlarged tubules interfere dramatically with normal kidney function. Discuss how regulation of tubulogenesis and branching morphogenesis contributes to organogenesis during development of a tubular structure or organ.

Swanson, L.E., and Beitel, G.J. (2006). Tubulogenesis: an inside job. Curr Biol. Jan 24; 16(2), R51-3.

Davies, J.A. (2005). Watching tubules glow and branch. Curr Opin Genet Dev. Aug; 15(4), 364-70

“Tubes, Branches and Pumps in Development” is the title of the 2008 Developmental Biology Symposium at the University of Minnesota on September 24th and 25th, 2008. This scientific conference will include talks from leaders in the field, and is FREE to undergraduate students.

8. (Hougen-Eitzman and Singer) Plants have been releasing volatile organic compounds for millions of years. We humans especially appreciate them in our cooking and perfumes. However, it has only been in the last decade that the ecological role and biochemical basis for these chemicals have been examined. Many of these chemicals are important in mobilizing a plant's defense against attack. Furthermore, many animals respond to plant volatiles, with the chemicals acting as attractants, repellants, or even as cues for finding food or mates. Plant volatiles have even been implicated as a medium for plant-to-plant communication, and as a method for plants to ”call in” predators to protect the plants from herbivory. Evaluate the ecological or physiological significance of one or more plant volatile compounds at the heirarchical level of your choice (e.g., genetic, biochemical, ecological, evolutionary). You may choose a plant or animal perspective.

Baldwin, I., Halitschke, R., Paschold, A, von Dahl, C., and Preston, C. (2006). Volatile signaling in plant-plant interactions: "Talking trees" in the genomics era. Science 311, 812-815.

Bruce, T.J. A. et al. (2008). cis-Jasmone induces Arabidopsis genes that affect the chemical ecology of multitrophic interactions with aphids and their parasitoids. Proceedings of the National Academy of Sciences 105, 4553-4558.

Heil, M., and Bueno, J.C.S. (2007). From the Cover: Within-plant signaling by volatiles leads to induction and priming of an indirect plant defense in nature. Proceedings of the National Academy of Sciences 104, 5467-5472.

Schroeder, R., and Hilker, M. (2008). The relevance of background odor in resource location by insects: A behavioral approach. Bioscience 58, 308-316.

9. (Jaramillo) The presence of noise in the nervous system is ubiquitous. In some cases, noise is viewed as detrimental to information processing, whereas in others the evidence points to a beneficial role. Explore the causes of noise's diverse effects on neural function.

Faisal et al. (2008). Noise in the nervous system. Nature Reviews Neuroscience 9, 292-303.

Murphy, G.J., and Rieke, F. (2008). Signals and noise in an inhibitory interneuron diverge to control activity in nearby retinal ganglion cells. Nature Neuroscience 11, 318-326.

Butson, C.R., and Clark, G.A. (2008). Mechanisms of noise-induced improvement in light-intensity encoding in Hermissenda photoreceptor network. J. Neurophysiol. 2008 vol. 99 (1), 155-65.

10. (Jaramillo and Wolff) During development of the nervous system, billions of neurons must find and connect to their targets, forming trillions of synapses. How can neurons navigate the complex maze of the nervous system to reach these targets? Explore recent developments in our understanding of axonal guidance during neural development.

Farrar, N., and Spencer, G. (2008). Pursuing a 'turning point' in growth cone research. Dev. Biol. (in press).

Makita, T. et al. (2008). Endothelins are vascular-derived axonal guidance cues for developing sympathetic neurons. Nature 452, 759-763.

Vizard, Y. et al. (2008). Regulation of axonal and dendritic growth by the extracellular calcium-sensing receptor. Nature Neuroscience 11, 285-291.

11. (McKone) Evolution by natural selection is sometimes simplistically conceived as the substitution of one allele by another at a locus that controls a single phenotypic trait. In reality, the relationship between genotype and phenotype is more complex. Some genes have impact on multiple phenotypic traits (pleiotropy), while some particular traits are influenced by multiple genes (epistasis). How does the genetic correlation introduced by these factors influence the outcome of natural selection?

Gratten, J., Wilson, A.J., McRae, A.F., Beraldi, D., Visscher, P.M., Pemberton, J.M., and Slate, J. (2008). A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science 319, 318-320.

Linksvayer, T.A. (2007). Ant species differences determined by epistasis between brood and worker genomes. PLoS ONE 2, e994.

Mank, J. E., Hultin-Rosenberg, L., Zwahlen, M., and Ellegren, H. (2008). Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. American Naturalist 171, 35-43.

12. (Hougen-Eitzman and McKone) In attempting to understand interspecific interactions, ecologists often focus their investigations on a small number of directly interacting species. However, there is a growing body of evidence that indirect effects among species (effects via intermediate species) can have a major impact on distribution and abundance. Compare the importance of direct and indirect effects in ecological communities.

Berger, K. J., Gese, E. M., and, Berger, J. (2008). Indirect effects and traditional trophic cascades: a test involving wolves, coyotes, and pronghorn. Ecology 89, 818-828.

Hansen, D. M., Kiesbüy, H.C., Jones, C.G., and Müller, C.B. (2007). Positive indirect interactions between a neighboring plant species via a lizard pollinator. American Naturalist 169, 534-542.

Palmer, T.M., Stanton, M.L., Young, T.P., Goheen, J.R., Pringle, R.M., and Karban, R. (2008). Breakdown of an ant-plant mutualism follows the loss of large herbivores from an African savanna. Science 319, 192-195.

13. (Hougen-Eitzman and McKone) In industrialized regions of the world, the forest nitrogen cycle has been disrupted by inputs of nitrogenous airborne pollution, such as acid rain. In some regions, such as the northeastern US, ecologists believe that forest ecosystems have become N saturated. Unfortunately, much of the basic science about the nitrogen cycle was formulated in this human-dominated region, so our basic understanding of the N cycle may be biased. Examine the literature to determine the ecological effects of N pollution and saturation on terrestrial ecosystems. To what extent does N saturation alter the N cycle compared to unpolluted regions?

Aber, J.D., Nadelhoffer, K.J., Steudler, P. et al. (1989). Nitrogen saturation in northern forest ecosystems. BioScience 39, 378-386.

Aber J., McDowell, W. Nadelhoffer, K., et al. (1998). Nitrogen saturation in temperate forest ecosystems - Hypotheses revisited. BioScience 48, 921-934.

Hedin, L.O., Armesto, J.J., and Johnson, A.H. (1995). Patterns of nutrient loss from unpolluted, old-growth temperate forests - evaluation of biogeochemical theory. Ecology 76, 493-509.