Chris Holland : Teaching

All tutorials should be emailed to me by 4pm on the day before the tutorial. Handwritten essays may be placed in the 'H' pigeonhole on D level in Zoology.

All essays must include at least one recent reference additional to the reading list from a peer reviewed journal (i.e. no websites).

If you have any specific questions whilst writing the essay or require something explained in greater depth please make a note of this on your tute so that we can get to it during the tutorial.

Cells and Development Class Year 2 HT

Most proteins have evolved to perform inside the body or attached to it. A few however, have evolved to perform fully independently and outside this highly controlled environment. Ecto-secretions are used throughout nature both for their material properties and catalytic ability, from locomotion and protection to digestion. For these proteins to perform in an external and fluctuating environment, Natural Selection has endowed them with specialised processing routes and unique adaptations to maintain their structure and function.

Scientifically ecto-secretions are a unique and underexploited resource. For testing purposes their proteins are high yield, inexpensive, non-invasive and require the bare minimum of preparatory (and potentially denaturing) steps. Thus removing the restrictions of sample availability and quality allows the biologist to adopt tools and techniques usually reserved for the physical sciences to investigate their natural function.

Instructions:

Please read all of the following carefully:

This class will divide you into pairs and focus on invertebrate ecto-secretions.

If you wish to be paired with a specific person both sign up to the class first and then email me at least 1 week prior to the class otherwise you will be paired arbitrarily.

Each pair will be assigned one of three ecto-secretions and asked to discuss two papers in depth (1 provided, one of their choosing):

Pairs are required to read the relevant review paper and together select a single experimental paper that has contributed wards understanding the secretion’s natural function. The choice of this paper is up to the individual pair, although it must be a significant physcial experimental paper and not a modelling paper or review.

Please remember to bring copies of the experimental paper to the class for us to look at.

During the class each pair should be prepared to give a brief oral overview of their group of ecto-secretions. This will require discussing what it is produced by, what it is used for, what is it made of and how is it produced/processed, alongside any other points of interest you wish. (5-10 minutes including questions).

Then each pair will focus on discussing the experimental paper they have chosen. This will require describing the purpose of the study, what questions it addresses, what techniques have been used and the papers conclusions. (5-10 minutes including questions).

You will be expected to justify why you chose this paper (why is it interesting? why is it important?) and what are its strengths and weaknesses (experimental design, does the evidence support their claims?). Ensure you broadly understand and are able to explain to the rest of the class the techniques used in the study (as they are unlikely to be ones you have encountered before, however a well-known online encyclopedia is a good source for information).

In searching for an appropriate experimental paper, scopus is an excellent place to start.

Review papers (once pairs have been decided):
Pair 1: Saliva
Pair 2: Slime
Pair 3: Silk

The meeting room D31 is the last door on the left at the far end of the admin corridor on D level in Zoology.

Human Sciences

Tutorial 1.

Biodiversity

You are not expected to reference all reading listed below you can provide a general overiew or pick a particlar aspect (hotspots, measurement, management) that interests you.

Potential reading

Thomas, C. D. (1990). "Fewer species." Nature 347(6290): 237-237. access

** Ghilarov, A. (1996). "What does biodiversity' mean -- scientific problem or convenient myth?" Trends in Ecology & Evolution 11(7): 304-306. access

Courtillot, V. and Y. Gaudemer (1996). "Effects of mass extinctions on biodiversity." Nature 381(6578): 146-148. access

Wilson, E. O. and F. M. Peters (1998). Biodiversity. Washington DC, National Academy Press.

Vézquez, D. P. and J. L. Gittleman (1998). "Biodiversity conservation: Does phylogeny matter?" Current Biology 8(11): R379-R381. access

** Chapin Iii, F. S., E. S. Zavaleta, et al. (2000). "Consequences of changing biodiversity." Nature 405(6783): 234-242. access

** McCann, K. S. (2000). "The diversity-stability debate." Nature 405(6783): 228-233. access

Kassen, R., A. Buckling, et al. (2000). "Diversity peaks at intermediate productivity in a laboratory microcosm." Nature 406(6795): 508-12. access

Tilman, D. (2000). "Causes, consequences and ethics of biodiversity." Nature 405(6783): 208-211. access

** Purvis, A. and A. Hector (2000). "Getting the measure of biodiversity." Nature 405(6783): 212-9. access

Loreau, M., S. Naeem, et al. (2001). "Biodiversity and ecosystem functioning: current knowledge and future challenges." Science 294(5543): 804-8. access

** Pereira, H.M. Cooper, D.H. (2006) Towards the global monitoring of biodiversity change. Trends in Ecology & Evolution, 21 (3), 123-129. access

** Green, J. Bohannan, B.J.M. (2006) "Spatial Scaling of Microbial Biodiversity" Trends In Ecology & Evolution 21 (9): 501-7 access

Willis, K. J. and H. J. B. Birks (2006). "What Is Natural? The Need for a Long-Term Perspective in Biodiversity Conservation." Science 314(5803): 1261-1265. access

Renema, W., D. R. Bellwood, et al. (2008). "Hopping Hotspots: Global Shifts in Marine Biodiversity." Science 321(5889): 654-657. access

Valentini, A., F. Pompanon, et al. (2009). "DNA barcoding for ecologists." Trends in Ecology & Evolution 24(2): 110-117. access

Petchey, O.L. and K.J. Gaston,(2002) Functional diversity (FD), species richness and community composition. Ecology Letters,5(3): p. 402-411. access

Myers, N. (1988) Mass extinction—profound problem, splendid opportunity, Oryx 22 (4) 205-210 access

Tutorial 2.

What role does competition play in the definition of an organism’s niche?

This will require some initial textbook/lecture notes reading first but please find some examples from the scientific literature to illustrate your examples.

Textbooks RSL Link

Ricklefs, R.E. Miller, G.L. (1999). Ecology, 4th Edition, Freeman, New York

Begon, M. Harper, J.L. Townsend, C.R. (1996). Ecology, 3rd edn. Blackwell, Oxford

Krebs, C. (2001). Ecology, The Experimental Analysis of Distribution and Abundance 5th edn. Benjamin Cummings, San Fransisco.

Papers

Hardin, G. (1960). The Competitive Exclusion Principle. Science 131 (3409): 1292-1297. access

Hutchinson, G. E., (1961). The paradox of the plankton. American Naturalist 95, 137–145. access

MacArthur, Robert. 1958. Population ecology of some warblers of northeastern coniferous forests. Ecology 39 (4): 599-619. access

Tilman, D. (1977). Resource Competition between Plankton Algae: An Experimental and Theoretical Approach. Ecology 58(2): 338-348. access

Goldberg, D. E. and Barton, A. M. (1992). Patterns and Consequences of Interspecific Competition in Natural Communities: A Review of Field Experiments with Plants. The American Naturalist 139(4): 771-801. access

Bonsall, M. B. and Hassell, M. P. (1997). Apparent competition structures ecological assemblages. Nature 388(6640): 371-373. access

Banks, W. E., d'Errico, F., et al. (2008). Neanderthal Extinction by Competitive Exclusion. PLoS ONE 3(12): e3972. access

Sommer, U. (1999). Ecology: Competition and coexistence. Nature 402(6760): 366-367. access

Lenski, R. E. (2004). Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Plant Breeding Reviews 24:225-265 access

Barrick, J.E., et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1247. access

Moll, J.D. & Brown, J.S.(2008) Competition and Coexistence with Multiple Life-History Stages. The American Naturalist 171, 839-843. access

Biological Sciences

Animal Behaviour Tutorial 1.

Kin Recognition; why has it evolved and how is it achieved?

Potential reading

Bateson, P. Preferences for cousins in Japanese quail. Nature 295, 236-237 (1982). access

Brown, J.L. & Eklund, A. Kin Recognition and the Major Histocompatibility Complex: An Integrative Review. The American Naturalist 143, 435 (1994). access

Grafen, A. Do animals really recognize kin? Animal Behaviour 39, 42-54 (1990). access

Sherman et al Recognition Systems (1997) Ch 4 in Krebs, J.R. and Davies, N.B. Behavioural Ecology. in RSL (useful article)

Mateo, J.M. & Johnston, R.E. Kin recognition and the 'armpit effect': Evidence of self-referent phenotype matching. Proceedings of the Royal Society B: Biological Sciences 267, 695-700 (2000). access

Hepper, P. & Cleland, J. Developmental aspects of kin recognition. Genetica 104, 199-205 (1998). access

Hain, T. J. A. and B. D. Neff (2006). "Promiscuity Drives Self-Referent Kin Recognition." Current Biology 16(18): 1807-1811. access

Zelano, B. & Edwards, Scott V. An Mhc Component to Kin Recognition and Mate Choice in Birds: Predictions, Progress, and Prospects. The American Naturalist 160, S225-S237 (2002). access

Nakagawa, S. & Waas, J.R. 'O sibling, where art thou?' - A review of avian sibling recognition with respect to the mammalian literature. Biological Reviews of the Cambridge Philosophical Society 79, 101-119 (2004). access

Frommen, J. G., Luz, C., et al. (2007). Kin discrimination in sticklebacks is mediated by social learning rather than innate recognition. Ethology 113(3): 276-282. access

Gerlach, G., Hodgins-Davis, A., et al. (2008). Kin recognition in zebrafish: A 24-hour window for olfactory imprinting. Proceedings of the Royal Society B: Biological Sciences 275(1647): 2165-2170. access

Hauber, M. E. and Safran, R. (2006). Behavioural Ecology: Promiscuous Fathers Sire Young that Recognize True Family. Current Biology 16(18): R797-R800. access

Mehlis, M., Bakker, T. C. M., et al. (2008). Smells like sib spirit: Kin recognition in three-spined sticklebacks (Gasterosteus aculeatus) is mediated by olfactory cues. Animal Cognition 11(4): 643-650. access

Thunken, T., Bakker, T. C. M., et al. (2007). Active Inbreeding in a Cichlid Fish and Its Adaptive Significance. Current Biology 17(3): 225-229. access