Department of Biology

Integrative Exercise Questions


Faculty available to advise comps:  Dan Hernández, David Hougen-Eitzman, Mark McKone, Raka Mitra, Matt Rand, Debby Walser-Kuntz and Stephan Zweifel

1. Ecological consequences of resource “hot spots” and “hot moments” Dan Hernández and David Hougen-Eitzman

Resource availability is an important constraint on ecological patterns and processes. The availability of resources is often determined by the regular cycling and flow of energy, water, and nutrients. However, recent research has suggested that irregular pulses of resources can also have a substantial influence on ecological processes in many ecosystems. Discuss the ecological consequences of transient resource pulses in an ecosystem, or the characteristics of a system that determines its response to resource pulses. Topics may explore the short-term and long-term impacts of resources pulses at any ecological scale.

McClain M., et al. 2003. Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems 6:301-312.

Yang, L.H., J.L. Bastow, K.O. Spence, and A.N. Wright. 2008.  What can we learn from resource pulses? Ecology 89621-634.

Yang L., K.F. Edwards, J.E. Bynres, J.L. Bastow, A.N. Wright, and K.O. Spence. 2010. A meta-analysis of resource pulse-consumer interactions. Ecological Monographs 80:125-151.

Collins S.L, et al. 2014. A multiscale, hierarchial model of pulse dynamics in arid-land ecosystems. Annual Review of Ecology, Evolution, and Systematics 45:397-419.

2. Evolutionary ecology of specialists versus generalists Mark McKone and David Hougen-Eitzman

Ecological interactions between species range from highly specific to broadly generalized.  For instance, consider the mutualism between pollinators and plants.  The hundreds of species of fig trees (Ficus spp) are each pollinated by a single species of agaonid wasp, and each of these wasps pollinates only a single species of fig.  In contrast, honeybees (Apis mellifera) can pollinate hundreds of different plant species, many of which are visited by multiple other generalist insect pollinators.  Such variation in specialization occurs widely, including in host-pathogen, plant-herbivore, and predator-prey interactions.  Discuss the evolutionary tradeoffs that determine whether a species becomes a generalist or a specialist in ecological interactions; or, alternatively, discuss the impact of generalists versus specialists on the structure and function of ecological communities.

Bruns, E., M. L. Carson, and G. May. 2014. The jack of all trades is master of none: a pathogen’s ability to infect a greater number of host genotypes comes at a cost of delayed reproduction. Evolution 68:2453-2466.

Nylin, S., J. Slove, and N. Janz. 2014. Host plant utilization, host range oscillations and diversification in nymphalid butterflies: a phylogenetic investigation. Evolution 68:105-124.

Suweis, S., F. Simini, J. R. Banavar, and A. Maritan. 2013. Emergence of structural and dynamical properties of ecological mutualistic networks. Nature 500:449-452.

Thornhill, D. J., A. M. Lewis, D. C. Wham, and T. C. LaJeunesse. 2014. Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts. Evolution 68:352-367.

3. Mechanisms of cellular movement – Raka Mitra

Cellular movement is critical in a number of biological processes, whether for microbial chemotaxis, embryonic development, or response to infection.  The process of movement involves force generation, directional control and dynamic adjustment.  Choose a biological process involving cell migration and examine the cellular, molecular and biochemical mechanisms involved in the coordination of movement in this context.

Burrows, L.L. (2012). Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu Rev Microbiol 66, 493-520.

Gardel, M.L., Schneider, I.C., Aratyn-Schaus, Y., and Waterman, C.M. (2010). Mechanical integration of actin and adhesion dynamics in cell migration. Annu Rev Cell Dev Biol 26, 315-333.

Pollard, T.D., and Cooper, J.A. (2009). Actin, a central player in cell shape and movement. Science 326, 1208-1212.

Ridley, A.J. (2011). Life at the leading edge. Cell 145, 1012-1022.

4. Mechanisms of muscle fatigue Matt Rand

Intense exercise can lead to diminished muscle performance known as muscle fatigue. Several biochemical and physiological changes occur during fatigue that involve neural and muscular excitation, neural feedback loops, extracellular and intracellular ion concentrations, and an accumulation of intracellular metabolites. Much of our understanding of fatigue is a result of studies in isolated animal tissue preparations. This presents a challenge to our understanding of the mechanisms of fatigue in intact muscles and certain disease states. Review the range of possible causes thought to contribute to observed declines in muscle performance and choose one or two of these cellular and/or biochemical mechanisms to argue which series of events is best supported by the current literature.

Ball, D (2015) Metabolic and endocrine response to exercise: sympathoadrenal integration with skeletal muscle.  J Endocrinol. 224:R79-95.

Laurin, J., V. Pertici, E. Dousset, T. Marqueste, P. Decherchi (2015) Group III and IV muscle afferents: role on central motor drive and clinical implications.  Neuroscience 290:543-51.

Miller, K.C. and J.A. Burne (2014) Golgi tendon organ reflex inhibition following manually applied acute static stretching.  J Sports Sci. 32:1491-7.

5. Gut immunity – Debby Walser-Kuntz

Commensal microbes colonize every surface of multicellular animals, including humans. The particular composition of microbes in the gut is influenced by breastfeeding, diet, and other environmental factors. Explore how the gut microbiota contributed to the evolution of the adaptive immune system, how host-microbe crosstalk impacts immune system development and function, how diet and breastfeeding alter microbe-host immune system crosstalk, and/or the links between the gut microbes and immune disorders, such as allergies, celiac disease, or Crohn’s.

Caballero, S. & E. Pamer. 2015. Microbiota-mediated inflammation and antimicrobial defense in the intestine. Annual Review of Immunology. 33: 227-256.

Shapiro H., C. Thaiss, M. Levy, & E. Elinav. 2014. The cross talk between microbiota and the immune system: metabolites take center stage. Current Opinion in Immunology 30:54–62.

Dishaw, L., J. Cannon, G. Litman, & W. Parker. 2014. Immune-directed support of rich microbial communities in the gut has ancient roots. Developmental & Comparative Immunology. 47: 36–51.

Geuking M., Y. Köller, S. Rupp & K. McCoy. 2014. The interplay between the gut microbiota and the immune system. Gut Microbes. 5: 411-418.

Jain, N. & W.A. Walker. 2015. Diet and host–microbial crosstalk in postnatal intestinal immune homeostasis. Nature Reviews. Gastroenterology & Hepatology: 12: 14-25.

6. Functional degeneracy of the genetic code – Stephan Zweifel

Because of the degeneracy of the genetic code, synonymous codon changes (base pair mutations which do not alter amino acid sequence) were initially thought to have no functional consequence with regards to protein expression.  In fact, many genetic textbooks still refer to synonymous mutations as “silent mutations”.  However, in most genomes that have been sequenced, synonymous codons are not used in equal frequency. This phenomenon, termed codon-usage bias has been proposed as a crucial evolutionary mechanism influencing cellular function through its effects on diverse processes, ranging from RNA processing to protein translation and protein folding.  Examine the biochemical, genetic, and evolutionary mechanisms by which codon bias is exploited by the cell to control gene expression.

Dauna, Z. E., and Kimchi-Sarfaty, C. (2011). Understanding the contribution of synonymous mutations to human disease. Nature Reviews Genetics, 12, 683-691.

Hunt, R.C, Simhadri, V.L., Iandoli, M., Sauna, Z.E., Kimchi-Sarfaty, C. (2014). Exposing synonymous mutations. Trends in Genetics, 30, 308-321.

Plotkin, J.B., Kudla, G. (2011). Synonymous but not the same: the causes and consequences of codon bias.  Nature Reviews Genetics, 12, 32-42.