DEPARTMENT OF BIOLOGY
INTEGRATIVE EXERCISE QUESTIONS
Faculty available to advise comps: Hernández, Hougen-Eitzman, McKone, Mitra, Petricka, Walser-Kuntz, Wolff, and Zweifel
1. Human-Altered Ecosystems – Dan Hernández, David Hougen-Eitzman, Mark McKone
Ecologists traditionally have focused their research in systems with relatively low impacts of human activity. Recently there has been expanded investigation of ecological communities with a large human footprint, including agricultural systems, urban areas, restored areas, and novel combinations of species outside their native range. Discuss one of the following aspects of ecosystems altered by humans: 1) What has research in such human-influenced ecosystems revealed about fundamental ecological processes? 2) How do human altered ecosystems interact with natural systems to influence ecological processes? 3) How do the drivers of ecological processes, or relative importance of different drivers, change under human alteration of ecosystems?
Fischer, J. D., S. H. Cleeton, T. P. Lyons, and J. R. Miller. 2012. Urbanization and the predation paradox: the role of trophic dynamics in structuring vertebrate communities. BioScience 62:809-818.
Hobbs, R. J., E. S. Higgs, and C. Holl. 2013. Novel ecosystems: intervening in the new ecological world order. Wiley-Blackwell.
Power, A. 2010. Ecosystem services and agriculture: tradeoffs and synergies. Philosophical Transactions of the Royal Society B 365:2959-2971.
2. Key Innovations in Macroevolution – Mark McKone
The rate of evolutionary diversification differs dramatically among related lineages. Some groups radiate rapidly to produce large numbers of species while their sister groups remain small. Recent advances in phylogenetic information have helped to test hypotheses about the causes of diversification. Review current ideas about key innovations that may cause rapid diversification in successful clades.
Price, T. D., D. M. Hooper, C. D. Buchanan, U. S. Johansson, D. T. Tietz, et al. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509:222-225.
Pyron, R. A., and F. T. Burbrink. 2012. Extinction, ecological opportunity, and the origins of global snake diversity. Evolution 66:163-178.
Vamosi, J. C., and S. M. Vamosi. 2011. Factors influencing diversification in angiosperms: at the crossroads of intrinsic and extrinsic traits. American Journal of Botany 98:460-471.
3. Cellular Homeostasis in Microbes – Raka Mitra
Cellular homeostasis is defined as the ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes. Homeostasis is an essential capability of all living cells and is mediated by complex and diverse regulatory networks. Homeostatic mechanisms are particularly important for microbes, which need to adapt to changing environmental conditions or coordinate cooperative activities. A few examples of homeostatic processes are listed below.
· Escherichia coli opens mechanosensitive ion channels when transferred from high to low osmolarity environments in order to prevent structural perturbations to the membrane.
· Aspergillus fumigatus adapts to iron limitation by upregulating iron uptake mechanisms and downregulating iron-consuming pathways.
· Caulobacter crescentus modulates the cell division cycle according to the needs of the environment.
Identify a situation in which a microbe must employ cellular homeostatic pathways, and explore the mechanisms involved including signal sensing, regulation and physiological outputs.
Booth, I.R. (2014). Bacterial mechanosensitive channels: progress towards an understanding of their roles in cell physiology. Curr. Opin. Microbiol. 18C, 16-22.
Jonas, K. (2014). To divide or not to divide: control of the bacterial cell cycle by environmental cues. Curr. Opin. Microbiol. 18C, 54-60.
Schrettl, M., and Haas, H. (2011). Iron homeostasis–Achilles’ heel of Aspergillus fumigatus? Curr. Opin. Microbiol. 14, 400-405.
4. Protein Glycosylation – Raka Mitra, Jalean Petricka
For years, the study of carbohydrates was considered less exciting than many if not most topics of biochemistry. Carbohydrates were recognized as important fuels and structural components but were thought to be peripheral to most key activities of the cell. This view has changed dramatically in the past few years. We have learned that cells of all organisms are coated in a dense and complex coat of carbohydrates. Secreted proteins are often extensively decorated with carbohydrates essential to a protein’s function. The extracellular matrix in higher eukaryotes—the environment in which the cells live—is rich in secreted carbohydrates central to cell survival and cell-to-cell communication. Carbohydrates, carbohydrate-containing proteins, and specific carbohydrate binding proteins are required for interactions that allow cells to form tissues, are the basis of human blood groups, and are used by a variety of pathogens to gain access to their hosts.
Glycosylation of proteins is now known to play an important regulatory role in nutrient sensing, gene expression and a host of other biochemical processes. Defects in glycosylation are a cause of wide array of diseases, including cancer.
Describe the role of a specific glycosylation pathway and examine the biochemical results of malfunction of the pathway.
Cummings, R. D., and Pierce, J. M. (2014). The challenge and promise of glycomics. Chem. Biol. 21, 1-15.
Freeze, H. H. (2013). Understanding human glycosylation disorders: biochemistry leads the charge. J. Biol. Chem. 288, 6936-6946.
5. Branching Processes in Growth and Development – Jalean Petricka
Branching is a common mechanism by which cells, tissues, and organisms develop and/or explore their environment. Many organisms, including humans, plants, and fungi have branching processes that are regulated by hormones and/or signaling dictated by genetic and molecular programs. Investigate and review the mechanisms underlying a specific branching process in an organism of your choice.
Harris, S. D. (2008). Branching of fungal hyphae: regulation, mechanisms and comparison with other branching systems. Mycologia 100, 823-832.
Herriges M., Morrisey E.E. (2014). Lung development: orchestrating the generation and regeneration of a complex organ. Development 141, 502-513.
Lewis, T. L., Jr., Courchet, J., and Folleux, F. (2013). Cellular and molecular mechanisms underlying axon formation, growth, and branching. J. Cell Biol. 202, 837-848.
Zhang, D., and Yuan, Z. (2014). Molecular control of grass inflorescence development. Annu. Rev. Plant Biol. 65, 553-578.
6. Function of Natural Killer Cells – Debby Walser-Kuntz
Natural killer (NK) cells play a role in antiviral and antitumor immunity, but our understanding of their function has lagged behind that of B and T cells. Initially described as part of the innate branch of the immune system – our first line of defense – recent work suggests that NK cells are capable of memory responses. In addition to lysing target cells, NK cells secrete cytokines and likely modulate the overall immune response through a complex balancing act between activating and inhibitory receptors. Explore the function of NK cells and their receptors in the context of viral infections, cancer surveillance, vaccine development, or immune regulation.
Jost, S., and Altfeld, M. (2013). Control of human viral infections by natural killer cells. Annu. Rev. Immunol. 31, 163-194.
Rölle, A., Pollmann, J., and Cerwenka, A. (2013). Memory of infections: an emerging role for natural killer cells. PLoS Pathog. 9, e1003548.
7. Morphogenesis in Development – Jennifer Wolff
Morphogenesis, the development of shape, requires the orchestration of cellular processes such as adhesion, cell shape changes, migration, and death. As advances in stem cell technology have begun to provide a renewable source of cells to repair damaged tissues and organs, the problem of how to sculpt those cells into functional three-dimensional structures has become increasingly significant. Several recent studies have succeeded in growing organ-like structures in tissue culture. These breakthroughs highlight both the promises of in vitro morphogenesis and the importance of understanding in vivo morphogenesis during embryonic development.
Discuss advances in our understanding of how the three-dimensional structure of an organ or tissue develops, with an emphasis on implications and possibilities for in vitro tissue engineering.
Ali, R.R., and Sowden, J.C. (2011). Regenerative medicine: DIY eye. Nature 472, 42–43.
Bedzhov, I., and Zernicka-Goetz, M. (2014). Self-organizing properties of mouse pluripotent cells initiate morphogenesis upon implantation. Cell 156, 1032–1044.
Gjorevski, N., Ranga, A., and Lutolf, M.P. (2014). Bioengineering approaches to guide stem cell-based organogenesis. Development 141, 1794–1804.
Maher, B. (2013). Tissue engineering: how to build a heart. Nature 499, 20–22.
Sato, T., and Clevers, H. (2013). Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications. Science 340, 1190–1194.
Shih, H.P., Wang, A., and Sander, M. (2013). Pancreas organogenesis: from lineage determination to morphogenesis. Annu. Rev. Cell Dev. Biol. 29, 81–105.
8. Dosage Compensation in Sex Chromosomes – Stephan Zweifel
The genetic control of sex determination is often associated with dimorphic sex chromosomes. In the XY system, females are homogametic (XX), whereas the males are heterogametic (XY). The Y chromosome has considerably less genetic information than the X chromosome, creating an imbalance in X-linked gene products between the two sexes. Dosage compensation mechanisms have evolved to equalize X-linked gene expression between males and females, thereby ensuring the appropriate balance of X chromosome and autosomal gene products in the cells of each sex. Three well-studied systems of dosage compensation are worms, flies, and mammals. Examine the mechanisms of gene regulation that ensure an equal amount of X-linked gene products in the two sexes.
Ferrari, F. (2014). Transcriptional control of a whole chromosome: emerging models for dosage compensation. Nat. Struct. Mol. Biol. 21, 118-125.
Mank, J. (2013). Sex chromosome dosage compensation: definitely not for everyone. Trends Genet. 29, 677-683.