A501: Techniques in Reproductive Diversity Common Themes in Reproductive Diversity Indiana University Fall 2006

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On this page you will find many materials and readings needed for this class. Some of these pages are password protected; please contact Danielle Whittaker (djwhitta at indiana dot edu) if you need help. Files are in PDF format. This page will be updated as necessary, so check back regularly. Syllabus/Schedule Tuesday, August 29 Ellen Ketterson: Working with wild animals Class at Kent Farm Bird Observatory. Lab #1: Working with wild animals Feather Tract Diagram August 31 and September 5, 7 Amy Poehlman and Danielle Whittaker: Hormone and DNA extractions Required readings: DNA and Hormone Extraction Lab Testosterone EIA Protocol Clotfelter et al. 2004. Consequences of elevating plasma testosterone in females of a socially monogamous songbird: evidence of constraints on male evolution? Hormones and Behavior 46: 171-178. DNA Extraction Protocol: will be handed out in class. Reference: Moore, D.D. and D. Dowhan. 2002. In: Current protocols in molecular biology.  F. M. Ausubel, R. Brent; R. E. Kingston, D. D. Moore; J.G. Seidman, J. A. Smith, K. Struhl, eds. New York: John Wiley and Sons. Pp. 2.0.1-2.0.3, 2.1.1- 2.1.3, 2.1.9-2.1.10. Taberlet, P. and G. Luikart (1999). Non-invasive genetic sampling and individual identification. Biological Journal of the Linnaean Society 68: 41-55. Additional readings: Extraction of hormones from egg yolks: Lipar, J. L., E. D. Ketterson, V. Nolan, Jr., and J. M. Casto (1999). Egg yolk layers vary in the concentration of steroid hormones in two avian species. General and Comparative Endocrinology 115: 220-227. Extraction of hormones from feces: Hirschenhauser, K,, E. Mostl, P. Peczely, B. Wallner, J. Dittami, and K. Kotrschal (2000).  Seasonal relationships between plasma and fecal testosterone in response to GnRH in domestic ganders.  Gen. Comp. Endocrin. 118:262-272. RIA: Wingfield and Farner 1975. The determination of five steroids in avian plasma by radioimmunoassay and competitive protein-binding. Steroids 26: 311-327. This is the original protocol. Lecture: Hormone and DNA extractions (Powerpoint file) Tuesday, September 12 Lynn Siefferman: Measuring Colorful Phenotypes Readings: 2 chapters from the book: Bird Coloration Vol 1 Mechanisms and Measurements. 2006. G. E. Hill and K. J. McGraw (eds), Harvard University Press. This book will be on reserve in the Biology library, other chapters will be helpful for those interested in measuring and analyzing coloration. Chapter 2 Chapter 3 (part 1) Chapter 3 (part 2) Lecture: Animal Coloration (Powerpoint file, 35 MB) Spectrometer protocol, with links to programs. (MS Word document with embedded links) September 14 and 19 Amy Poehlman: Assessing Relatedness with Microsatellite Genotyping Microsatellite Lab (Word document; note there are links to readings embedded in the document!) Reading: Selkoe, K. A., and R. J. Toonen (2006). Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9: 615-629. Thursday, September 21: Analyze genotypes; Intro to Hormone Assays Required: Instructions for GeneMapper (please bring with you) Supplemental information: Instructions for the ABI 3730 Tuesday, September 26 Danielle Whittaker: Hormone Assays. Hormone Assay Lab Producing the Standard Curve Steroid extractions from Egg Yolks Chromatography Columns Sept 28-Oct 3 Curt Lively: Modeling the evolution of sex These worksheets are intended to serve as an introduction to Mathematica and as preliminary problems in anticipation of the work we will do on Tuesday October 3rd.  Please bring your computers equipped with Mathematica and ready to roll. CISAB worksheet LMC.8(CSS) The Limit October 5th and 10th Dale Sengelaub: Employing neuroanatomical techniques to study sex differences Class will meet at CISAB on the 5th and at Dale's lab in the Psychology Building on the 10th street on the 10th - PYA408. Readings: Isgor, C. and D. R. Sengelaub (1998). Prenatal gonadal steroids affect adult spatial behavior, CA1 and CA3 pyramidal cell morphology in rats. Hormones and Behavior 34: 183-198. Isgor, C. and D. R. Sengelaub (2003). Effects of neonatal gonadal steroids on adult CA3 pyramidal neuron dendritic morphology and spatial memory in rats. October 12 and 17 Stephanie Sanders: Designing questionnaires to study human sexual behavior Meet at the Kinsey Institute on both days. Enter Morrison Hall by the front door (the door that faces the interior of the quadrangle that consists of Memorial, Goodbody, Morrison, and Sycamore); you will find an elevator to your left, take it to the second floor, then follow signs that will be put up by Stephanie Sanders. Reading for October 12: Reinisch, J. M., S. A. Sanders, and M. Ziemba-Davis (1988). The study of sexual behavior in relation to the transmission of human immunodeficiency virus: caveats and recommendations. American Psychologist 43: 921-927. (Which was reprinted in 1997 in JM Notterman (Ed.) The Evolution of Psychology: Fifty Years of the American Psychologist, pp. 677-692, American Psychological Association, Washington, D.C.)   Readings for October 17: Wiederman, MW (2002) Reliability and validity of measurement. In MW Wiederman & BE Whitley, Jr. (Eds.), Handbook for Conducting Sexuality Research (2nd Ed.), pp. 25-50. Mahwah, NJ: Lawrence Erlbaum Associates. Turner CF, Miller, HG, & Rogers, SM (1997) Survey measurement of sexual behavior: Problems and progress. In J Bancroft (Ed.), Researching Sexual Behavior: Methodological Issues,  pp. 37-60. Bloomington,IN: Indiana University Press. October 19 and 24 Heather Rupp: Imaging brains using fMRI Reading: Ramsey, N. F., H. Hoogduin, J. M. Jansma (2002). Functional MRI experiments: acquisition, analysis and interpretation of data. European Neuropsychopharmacology 12: 517-526. Lectures (Powerpoint files): Introduction Scan session October 26 and 31 Greg Demas: Analyzing immune function in birds and mammals October 26 powerpoint file: Measuring immunity Protocols (powerpoint files): KLH and ELISA PHA wing swelling Readings: Smits, J. E., G. R. Bortolotti, and J. L. Tella (1999). Simplyfing the phytohaemagglutinin skin-testing technique in studies of avian immunocompetence. Functional Ecology 13: 567-572. Voller, A., A. Bartlett, and D. E. Bidwell (1978). Enzyme immunoassays with special reference to ELISA techniques. Journal of Clinical Pathology 31: 507-520. November 2 and 7 Milos Novotny and Helena Soini: Analyzing volatile metabolites in biological specimens using GC-MS techniques Thursday, November 2, we will meet in the chemistry faculty lounge C127 (1st floor, next to the chairman’s office).   Tuesday, November 7, we’ll start at Chemistry A500 (5th floor north side) and continue in the Novotny lab C105 (need to divide into 2 groups). For this lab, students will need to bring their protective laboratory eye glasses. Readings: Burger, B. V. (2005). Mammalian Semiochemicals. Topics in Current Chemistry 240: 231-278. Dulac, C. and A. T. Torello (2003). Molecular detection of pheromone signals in mammals: from genes to behaviour. Nature Reviews: Neuroscience 4: 551-562. Hurst, J. L. and R. J. Beynon (2004). Scent wars: the chemobiology of competitive signalling in mice. BioEssays 26: 1288-1298. Novotny, M. K. (2003). Pheromones, binding proteins and receptor responses in rodents. Biochemical Society Transactions 31: 117-122. Soini, H. A. et al (2005). Stir bar sorptive extractions: a new quantitative and comprehensive sampling technique for determination of chemical signal profiles from biological media. Journal of Chemical Ecology 31(2): 377-392. Soini, H. A. et al (2006). In situ surface sampling of biological objects and preconcentration of their volatiles for chromatographic analysis. Anal. Chem. 76: 7161-7168 Lectures - files too large for web access (email djwhitta if you would like the files) Lecture 1 (53MB Powerpoint file) Lecture 2 (30MB Powerpoint file) November 9 and 14 Emilia Martins: Understanding evolution using the comparative method Readings: Felsenstein, J. 1985. Phylogenies and the Comparative Method. Am. Nat. 125: 1-15. Losos, J.B. & R.E. Glor. 2003. Phylogenetic comparative methods and the geography of speciation. TREE 18: 220-227. Martins, E.P. 2000. Adaptation and the comparative method. TREE, 15: 295-299. For Tuesday, if you have a laptop computer, go to http://compare.bio.indiana.edu, and download the local executable version of COMPARE. Unzip it and open "startForm.html" to make sure that it runs. You may need to download and install Java Virtual Machine (http://java.com/en/) to get it to work. November 16 and 21 Armin Moczek: Employing comparative anatomy, immunostaining, in situ hybridization, and RNAi to study the evolution of development Readings for Tuesday: Moczek, AP (2006). Integrating micro- and macroevolution of development through the study of horned beetles. Heredity 97: 168-178. Moczek, AP, D Rose, W Sewell, and BR Kesselring (2006). Conservation, innoveation, and the evolution of horned beetle diversity. Dev. Genes Evol. Lectures: Powerpoint 1 (Thursday) Powerpoint 2 (Tuesday) November 28 Christine Quirk: Using molecular techniques, particularly gene arrays, to study reproduction Please bring your lab coats to class. We will meet in the Alumni Room (JH102) for lecture and quickly move up to my lab (JH209/211) for the bench work. ***Please note: the lab is typically very warm - you may want to wear light clothing!*** Please read the RNA Isolation Protocol before class, and bring it with you. Material Safety Data Sheets for chemicals we will be using in lab. Links to helpful websites: http://www.affymetrix.com/corporate/outreach/educator.affx (info on Affymetrix GeneChips) http://www.ambion.com/ (general info on RNA) http://www.invitrogen.com/content.cfm?pageid=1&ix=1 (info on TRIzol reagent and RNA isolation) Powerpoint presentation: Measuring Gene Expression (7 MB) November 30 and December 5 Troy Smith: Recording electrical behavior in animals and cells to study sex differences Readings: Axon Guide.  This book contains lots of useful tips for electrophysiological recordings. Because it is published by a company that sells equipment for electrophysiology, some of it has a commercial bias, but it is still a good reference for the beginning electrophysiologist.  Students should focus on the following chapters/pages: Chapter 1; Chapter 2, pp. 18-21; Chapter 3, pp. 27-37, 42-44 Zhou and Smith (in press).  Focus on the Methods and Results.   December 7 Ellen Ketterson: Overview and retrospective Final presentations: Male satin bowerbird painting and female choice, by Jef Akst, Christy Bergeon, and Emily Chester Effects of maternal care on spinal cord development and reproductive behavior in male rats, by Joy Garrett, Katy Lenz, and Aaron Wilber The influence of mating systems on morphological and physiological divergence in bats (Chiroptera), by Karen Acree, Jacqueline Ho, Harald Parzer, and Mayte Ruiz Physiological and genetic mechanisms underlying population divergence across an altitudinal gradient, by Jonathan Atwell, Tim Greives, and Dawn O'Neal All of the Ketterson Laboratory Protocols are available here (password protected). Return to Ketterson Laboratory Home Page.

Page last updated: December 14, 2006
Maintained by Danielle Whittaker