2018–19 Comps Questions

1. Top-down approaches to understanding early life (Rika Anderson)

In exploring the likely characteristics of the earliest organisms on Earth, scientists tend to use both “top-down” and “bottom up” methods. “Bottom up” methods rely on geological and chemical analyses that attempt to recreate the likeliest conditions and characteristics for early organisms. In contrast, “top down” methods rely on analysis of modern life, often using bioinformatics approaches, to make inferences about what life on Earth looked like several billion years ago. For example, this can include better understanding the likely habitat of our last universal common ancestor, how multicellularity originated, or tracing the timing and spread of metabolisms on the early Earth. Evaluate the literature using top-down approaches to better understand a specific aspect of early life on Earth.

Recommended courses: Genomics & Bioinformatics and/or The Origin & Early Evolution of Life

Brunet, T., and N. King. 2017. The origin of animal multicellularity and cell differentiation. Developmental Cell 43:124–140.

David, L. A., and E. J. Alm. 2011. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469:93–6.

Hsiao, C., S. Mohan, B. K. Kalahar, and L. D. Williams. 2009. Peeling the onion: Ribosomes are ancient molecular fossils. Molecular Biology and Evolution 26:2415–2425.

Weiss, M. C., F. L. Sousa, N. Mrnjavac, S. Neukirchen, M. Roettger, S. Nelson-Sathi, and W. F. Martin. 2016. The physiology and habitat of the last universal common ancestor. Nature Microbiology 1:16116. 

2. Ecological controls on greenhouse gas fluxes (Dan Hernández)

Natural ecosystems have a large influence on the exchange of greenhouse gases (CO2, CH4, and N20) in the biosphere. The flux of greenhouse gases from ecosystems is controlled by both abiotic and biotic factors. Explore the drivers of greenhouse gas fluxes for a given ecosystem type and the potential impacts of changes in these drivers on net greenhouse gas exchange.

Recommended courses: Global Change Biology and/or Ecosystem Ecology

O’Connell, C., Ruan, L., and Silver, W.L. 2018. Drought drives rapid shifts in tropical rainforest soil biogeochemistry and greenhouse gas emissions. Nature Communications 9: 1348-1357.

Tian, H., Lu, C., Ciais, P., et al. 2016. The terrestrial biosphere as a net source of greenhouse gases to the atmosphere. Nature 531: 225-228.

Schmitz, O., Raymond P.A., Estes J., et al. 2014. Animating the carbon cycle. Ecosystems 17: 344-359.

Yvon-Durocher, G., Allen, A.P., Bastviken, D., Conrad, R., Gudasz, C., St. Pierre, A., Nguyen, T., and del Giorgio, P.A. 2014. Methane fluxes show consistent temperature dependence across microbial to ecosystem scales. Nature 507: 488-491. 

3. Non-endemic species and ecosystem structure/function (David Hougen-Eitzman)

Individual organisms often move from one area to another, providing important sources of genetic diversity and replacement stocks to local populations.  However, when individuals of a species visit a “new” habitat (not containing conspecific individuals), this non-native species can become established.  Discuss the effects of non-endemic species on ecosystem structure and function. 

Recommended courses: Population Ecology and/or Ecosystem Ecology and/or Conservation Biology

Gallardo, B. Clavero, M. Sanchez, M.I. et al.  2016.  Global ecological impacts of invasive species in aquatic ecosystems.  Global Change Biology 22: 151-163

Lesk, C., Coffel, E., D’Amato, A.W. et al.  2017.  Threats to North American forests from southern pine beetle with warming winters.  Nature Climate Change 7: 713-717.

Nabors, A.J., Cen, H.J., Hung, K.L., et al.  2018.  The effect of removing numerically dominant, non-native honey bees on seed set of a native plant.  Oecologia 186: 281-289.

Simberloff, D., Martin, J.L., Genovesi, P., et al.  2013.  Impacts of biological invasions: what’s what and the way forward.  Trends in Ecology and Evolution  28: 58-66. 

4. Cheating and deception in ecological interactions (Mark McKone)

Most types of ecological interactions are vulnerable to exploitation by cheating or deception, either by one of the interacting individuals or by other species.  Discuss the evolutionary or ecological consequences of cheating and deception. 

Recommended courses: Evolution and/or Population Ecology

Goodrich, K.R., and Jürgens, A.  (2018).  Pollination systems involving floral mimicry of fruit: aspects of their ecology and evolution.  New Phytologist 217, 74-81.

Scantlebury, D.M., Mills, M.G.L., Wilson, R.P., Wilson, J.W., Mills, M.E.J., Durant, N.C., Bradford, P., Marks, N.J., and Speakman, J.R. (2014). Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism. Science 346, 79-81.

Schiebold, J.M.-I., Bidartondo, M.I., Lenhard, F., Makiola, A. and Gebauer, G. (2018).  Exploiting mycorrhizas in broad daylight: Partial mycoheterotrophy is a common nutritional strategy in meadow orchids.  Journal of Ecology 106, 168-178.

York, J.E., and Davies, N.B.  (2017).  Female cuckoo calls misdirect host defences towards the wrong enemy.  Nature Ecology & Evolution 1, 1520–1525. 

5. Nuclear lamina (Raka Mitra)

The nucleus of the eukaryotic cell was the first organelle to be discovered, likely because of its prominent structure within the cell.  This structure is maintained by the nuclear lamina: a protein scaffold lining the nuclear envelope.  The nuclear lamina has been implicated in nuclear structure and mechanics, tethering of heterochromatin and the cytoplasmic cytoskeleton to the nuclear envelope, and regulation of signaling and gene expression. Additionally, mutations in the genes encoding proteins of the nuclear lamina cause a spectrum of human diseases. Choose a biological process that is regulated by the nuclear lamina and explore the mechanisms that control this process on a cellular, molecular and biochemical level.

Recommended courses: Cell Biology and/or Genetics

de Leeuw, R., Gruenbaum, Y., and Medalia, O. (2018). Nuclear Lamins: Thin Filaments with Major Functions. Trends Cell Biol 28, 35-45.

Gerace, L., and Tapia, O. (2018). Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. Curr Opin Cell Biol 52, 14-21.

Naetar, N., Ferraioli, S., and Foisner, R. (2017). Lamins in the nuclear interior – life outside the lamina. J Cell Sci 130, 2087-2096. 

6. Mechanisms and outcomes of metabolic reprogramming (Rou-Jia Sung)

Metabolism can be defined as the ‘chemical processes that occur within a living organism in order to maintain life.’ It is an incredible set of processes subject to a variety of regulatory mechanisms that can dictate how much of any molecule is converted into specific products via a particular set of pathway(s). Prolonged changes to the metabolic state of a system can be found under both healthy circumstances (such as during cellular differentiation) as well as in disease states (such as during tumor development or diabetes). Exactly how and when these prolonged changes occur remains an active area of research. For this question, explore both the potential molecular mechanism(s) and outcomes (at both the cellular and organismal level) underlying significant prolonged alterations to metabolic pathways.

Recommended courses: Biochemistry, Cell Biology, and/or Biological Chemistry

Bantug GR, et al. 2017. The spectrum of T cell metabolism in health and disease. Nature Reviews Immunology, 18: 19-34.

Ryall JG, et al. 2015. Metabolic reprogramming of stem cell epigenetics. Cell Stem Cell, 17: 651-662.

Agathocleous M and Harris WA. 2013. Metabolism in physiological proliferation and differentiation. Trends in Cell Biology, 23: 484-492.

DeBeraridinis RJ, et al. 2008. Biology of cancer: Metabolic reprogramming fuels cell growth and proliferation. Cell Metabolism, 7: 11-20. 

7. Antiviral immunity (Debby Walser-Kuntz)

The vertebrate immune system has evolved multiple mechanisms for anti-viral defense, which include antibodies, natural killer cells, T cells, and innate host restriction molecules. Several viruses, including HIV and influenza, invade via a mucosal surface and others, such as Zika or herpes, are able to cross the placenta. Explore antiviral immunity in a mucosal surface or the placenta. You may choose to examine how immune function differs depending on the microenvironment or how viruses evade the immune response in either of these locations.

Recommended courses: Immunology and/or Topics on Virology

Beachboard, D. 2016. Innate immune evasion strategies of DNA and RNA viruses. Current Opinion in Microbiology 32: 113-119.

Desai. S., 2017. Zika Virus (ZIKV): a review of proposed mechanisms of transmission and associated congenital abnormalities. American Journal of Stem Cells 6: 13-22.

Iwasaki, A. 2016. Exploiting mucosal immunity for antiviral vaccines. Annual Review of Immunology 34: 575-608.

Openshaw, P.J.M. et al. 2017. Protective and harmful immunity to RSV infection. Annual Review of Immunology 35: 501-532. 

8. Neuroepigenetics (Jennifer Wolff or Fernán Jaramillo)

While we have long understood the connection between gene sequence and phenotype, environment can also profoundly shape traits and behaviors. Recent advances in genome-level analysis have shed light on the molecular details of these environmental, or epigenetic, effects.  It is now clear that environmental influences can lead to biochemical changes to DNA and histones that affect phenotype and function without altering gene sequence.  These epigenetic changes can persist through a cell’s functional lifetime and can be inherited across generations of cells and organisms. The field of neuroepigenetics has begun to highlight the importance of epigenetics in almost every aspect of nervous system function, including development, learning and memory, behavior, addiction, and disease.  Review the mechanisms and consequences of epigenetic control of gene expression in nervous system development, function, or pathology.  

Recommended courses: Cell Biology, Genetics, and/or Neurobiology

Azpurua, J., and Eaton, B.A. (2015). Neuronal epigenetics and the aging synapse. Front. Cell. Neurosci. 9, 947.

Iwase, S., Bérubé, N.G., Zhou, Z., Kasri, N.N., Battaglioli, E., Scandaglia, M., and Barco, A. (2017). Epigenetic Etiology of Intellectual Disability. J Neurosci 37, 10773–10782.

McCarthy, M.M., Nugent, B.M., and Lenz, K.M. (2017). Neuroimmunology and neuroepigenetics in the establishment of sex differences in the brain. Nat Rev Neurosci 18, 471–484.

Nestler, E.J. (2014). Epigenetic Mechanisms of Drug Addiction. Neuropharmacology 76, 259–268.

Sweatt, J.D. (2013). The Emerging Field of Neuroepigenetics. Neuron 80, 624–632. 

9. Meiotic Drive (Mark McKone or Jennifer Wolff)

A premise of Mendel’s law of segregation is that after homologous chromosomes pair in the first meiotic division, they segregate to produce gametes with equal numbers of each.  However, this is not necessarily so: there are cases of meiotic drive (or segregation distortion) that lead to greater representation of one of the homologues.  Review meiotic drive from one or more of the following perspectives: (a) evolutionary consequences; (b) molecular mechanisms; (c) potential use as a tool to manage human pathogens or their intermediate hosts.

Recommended courses: Genetics and/or Evolution

Hammond, A.M., Kyrou, K., Bruttini, M., North, A., Galizi, R., Karlsson, X., Kranjc, N., Carpi, F.M., D’Aurizio, R., Crisanti, A., and Nolan, T. (2017) The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito. PLoS Genet 13, e1007039.

Lindholm, A.K., Dyer, K.A., Firman, R.C., Fishman, L., Forstmeier, W., Holman, L., Johannesson, H., Knief, U., Kokko, H., Larracuente, A.M., et al. (2016). The ecology and evolutionary dynamics of meiotic drive. Trends in Ecology & Evolution 31, 315–326.

Núñez, M.A.B., Nuckolls, N.L., and Zanders, S.E. (2018). Genetic villains: killer meiotic drivers. Trends Genet, in press.