• Practical Skills in Ecology and Evolution, full course 

  Snyder, Amelia (2017-04-25)

  This three-credit, discussion-based course will help students develop skills necessary to succeed in the area of evolutionary and ecological biology as an independent researcher. They will learn how to a) Comprehend and ...
• Supplementary Electronic Appendix, accompanying article: Physiological Predictors of Leptin Vary During Menses and Ovulation in Healthy Women, by K.E. Sylvia, T.K. Lorenz, J.R. Heiman & G.E. Demas; under consideration. 

  Sylvia, Kristyn; Lorenz, Tierney; Heiman, Julia; Demas, Gregory
• Supplementary Electronic Appendix, accompanying article: Physiological Predictors of Leptin Vary Across the Menstrual Cycle in Healthy Women, by K.E. Sylvia, T.K. Lorenz, J.R. Heiman, & G. E. Demas; under consideration at The American Journal of Human Biology. 

  Sylvia, Kristyn; Lorenz, Tierney; Heiman, Julia; Demas, Gregory
• List of base-pair substitutions found in Mutation Accumulation lines of Escherichia coli K-12 PFM2 and its derivative strains (DNA repair) 

  Foster, Patricia L; Lee, Heewook; Popodi, Ellen M; Towns, Jesse P; Tang, Haixu

  List of base-pair substitutions found in mutation accumulation of the following E. coli strains: 1. K12 PFM2 (LB) 2. K12 PFM2 (minimal) 3. ED1a 4. IAI1 5. PFM101 6. PFM133 7. PFM35 8. PFM40 9. PFM88 10. PFM180 11. ...
• List of base-pair substitutions found in 21 mutation accumulation lines of Wild-type 6K (E. coli PFM2) 

  Lee, Heewook; Popodi, Ellen; Tang, Haixu; Foster, Patricia L (2012-09-19)

  List of base-pair substitutions found in 21 mutation accumulation lines of Wild-type 6K (E. coli PFM2)
• Assortative mating and self-fertilization differ in their contributions to reinforcement, cascade speciation, and diversification. 

  Castillo, DM; Gibson, AK; Moyle, LC (Current Zoology, )

  Cascade speciation and reinforcement can evolve rapidly when traits are pleiotropic and act as both signal/cue in non-random mating. Reproductive isolation due to these traits can be rapid, facilitating cascade speciation ...
• Conspecific plant-soil feedbacks of temperate tree species in the southern Appalachians, USA 

  Reinhart, K.O.; Johnson, D.; Clay, K. (PLOS ONE, 2012)

  Many tree species have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify ...
• Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila 

  Smibert, P.; Miura, P.; Westholm, J.O.; Shenker, S.; May, G.; Duff, M.O.; Zhang, D.; Eads, B.D.; Carlson, J.; Brown, J.B.; Eisman, R.C.; Andrews, J.; Kaufman, T.; Cherbas, P.; Celniker, S.E.; Graveley, B.R.; Lai, E.C. (Cell Reports, 2012)

  We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in $\textit{Drosophila melanogaster}$ by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond ...
• Tissue Damage Disrupts Developmental Progression and Ecdysteroid Biosynthesis in Drosophila 

  Hackney, J.F.; Zolali-Meybodi, O.; Cherbas, P. (PLOS ONE, 2012)

  In humans, chronic inflammation, severe injury, infection and disease can result in changes in steroid hormone titers and delayed onset of puberty; however the pathway by which this occurs remains largely unknown. Similarly, ...
• Cryptocephal, the Drosophila melanogaster ATF4, Is a Specific Coactivator for Ecdysone Receptor Isoform B2 

  Gauthier, S.A.; VanHaaften, E.; Cherbas, L.; Cherbas, P.; Hewes, R.S. (PLoS Genetics, 2012)

  The ecdysone receptor is a heterodimer of two nuclear receptors, the Ecdysone receptor (EcR) and Ultraspiracle (USP). In $\textit{Drosophila melanogaster}$, three EcR isoforms share common DNA and ligand-binding domains, ...
• Analysis of model replication origins in Drosophila reveals new aspects of the chromatin landscape and its relationship to origin activity and the prereplicative complex 

  Liu, J.; Mconnell, K.; Dixon, M.; Calvi, B.R. (The American Society for Cell Biology, 2012)

  Epigenetic regulation exerts a major influence on origins of DNA replication during development. The mechanisms for this regulation, however, are poorly defined. We showed previously that acetylation of nucleosomes regulates ...
• TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction 

  Doyle, E.L.; Booher, N.J.; Standage, D.S.; Voytas, D.F.; Brendel, V.P.; Vandyk, J.K.; Bogdanove, A.J. (Oxford University Press, 2012)

  Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the ...
• ParsEval: Parallel comparison and analysis of gene structure annotations 

  Standage, D.S.; Brendel, V.P. (BioMed Central Ltd., 2012)

  Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, ...
• Primary and Secondary siRNAs in Geminivirus-induced Gene Silencing 

  Aregger, M.; Borah, B.K.; Seguin, J.; Rajeswaran, R.; Gubaeva, E.G.; Zvereva, A.S.; Windels, D.; Vazquez, F.; Blevins, T.; Farinelli, L.; Pooggin, M.M. (Public Library of Science, 2012)

  In plants, RNA silencing-based antiviral defense is mediated by Dicer-like (DCL) proteins producing short interfering (si)RNAs. In $\textit{Arabidopsis}$ infected with the bipartite circular DNA geminivirus $\textit{Cabbage ...
• Functional Consequences of Subunit Diversity in RNA Polymerases II and V 

  Tan, E.H.; Blevins, T.; Ream, T.S.; Pikaard, C.S. (Elsevier (Cell Press), 2012)

  Multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved as specialized forms of Pol II that mediate RNA-directed DNA methylation (RdDM) and transcriptional silencing of transposons, viruses, and endogenous repeats ...
• Natal-host environmental effects on juvenile size, transmission success, and operational sex ratio in the entomopathogenic nematode Steinernema carpocapsae 

  Therese, M.O.; Bashey, F. (American Society of Parasitologists, 2012)

  Trans-host effects can alter the ecological and evolutionary dynamics of parasite and host populations. Here, we examine whether resource limitation within a parasite's natal host affects propagule size and influences ...
• Adaptation, Exaptation, and Constraint: A Hormonal Perspective 

  Ketterson, Ellen D.; Nolan, Val Jr (American Society of Naturalists, 1999-07)

  We approach conceptual issues in evolutionary biology from an endocrinological perspective, noting that single hormones typically act on several target tissues and thereby mediate suites of correlated phenotypic traits. ...
• Testosterone and Avian Life Histories: Effects of Experimentally Elevated Testosterone on Behavior and Correlates of Fitness in the Dark-Eyed Junco (Junco hyemalis) 

  Ketterson, Ellen D.; Nolan, Val Jr; Wolf, Licia; Ziegenfus, Charles (American Society of Naturalists, 1992-12)

  Hormones influence many aspects of organismal behavior, physiology, and morphol- ogy, and thus hormones may lie at the root of many life-history trade-offs. By manipulating hormones we can create novel phenotypes (i.e., ...
• Hormones and Life Histories: An Integrative Approach 

  Ketterson, Ellen D.; Nolan, Val Jr (American Society of Naturalists, 1992-11)

  Because of their role in mediating life‐history trade‐offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation ...
• Ordinary Extraordinary Junco 

  Ketterson, Ellen (Indiana University Department of Biology, 2013)

  The Ordinary Extraordinary Junco is a documentary film project designed to engage, entertain, and inspire student and adult audiences of all backgrounds. The feature-length film (88 min.) is comprised of eight shorter video ...

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