Independent Project

Deadlines

Feb 20th: Copy of paper to TA plus 1-2 paragraphs on why chosen. Hand in with homework. Counts as two homework problems.

March 6th: One page summary over what they are going to cover in project. Include a list of sources for paper. Handed in with homework. Counts as one homework grade.

April 13th: Final Paper is due in the homework box by 5pm. No exceptions unless Univ. approved.

Late April Evening(s) (pizza served): Oral presentation by each student to the class. 12 min. total (8 min. presentation, 4 minute questions). Should be at level that your fellow students can understand. Have 5 or so transparencies (or powerpoint slides) made -- lots of pictures rather than a lot of words make a more effective presentation. A few weeks before presentations, we will discuss in class about how to give a talk.

Each student must do his/her own independent project. This involves a 10 page (1.5 line spacing) written report and a 12 minute oral presentation to the class - 8 minute talk and 4 minutes for questions - including 3-5 transparencies. The ability to read, write, and verbally communicate is more important than any scientific fact you learn, and this is a good opportunity to gain some of these skills. Learning also comes from you doing - not listening to the prof - especially about a subject you're interested in.

The basic idea is to pick a topic you're interested in, find an important primary research article and explain the article at a level that your co-students can understand. For example... What is the article's main point? Why is it important? How does it fit into the larger scientific field? What techniques did they use? What are their limitations/uncertainties in their approach? What new questions/ avenues of research does the article raise?

The article should be from a high quality scientific journal like Science, Nature, Proceedings of the National Academy of Sciences USA, Physical Review Letters or other similar journals. In order to understand the article, it is expected that you will read and reference at least one review journal article from the scientific literature and several more general references, such as encyclopedia articles and scientific books.

Below are a list of some possible primary articles (an occasional review article is thrown in). Several have links to PDF files which you can look at or download. You will need Adobe Acrobat Reader, a free program to read the PDF files. Click here to download a free copy.

Possible Articles for Independent Project

Molecular Motors

The motor domain determines the large step of myosin-V
H TANAKA, K HOMMA, A H IWANE, E KATAYAMA, R IKEBE, J SAITO, T YANAGIDA & M IKEBE
Nature 415, 10 January 2002, 192 - 195 (PDF 250K)

The Way Things Move: Looking Under the Hood of Molecular Motor Proteins
Ronald D. Vale and Ronald A. Milligan
Science 2000 April 7; 288: 88-95 (PDF 426K)
[Review]

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase
Ryohei Yasuda, Hiroyuki Noji, Masasuke Yoshida, Kazuhiko Kinosita Jr & Hiroyasu Itoh
Nature 410, 19 April 2001, 898 - 904 (PDF 699K)

Doing a rotary two-step
Mark J. Schnitzer
Nature 410, 19 April 2001, 878 - 881 (PDF 633K)
[Review of previous]

Distinguishing Inchworm and Hand-Over-Hand Processive Kinesin Movement by Neck Rotation Measurements
Wei Hua, Johnson Chung, and Jeff Gelles
Science 2002 February 1; 295: 844-848. (PDF 234K)

Associated Commentary: Molecular Motors Move in Mysterious Ways.
Jennifer Couzin
Science 2002 295: 780-781. (in News of the Week) (PDF 126K)

Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase.
Harada, Y., ..., Kinosita, K.
Nature 409, 113-5 (2001). (PDF 264K)

Powering an inorganic nanodevice with a biomolecular motor
Soong, R. K., Bachand, G. D., Neves, H. P., Olkhovets, A. G., Craighead, H. G., and Montemagno, C. D.
Science 290, 1555-8 (2000). (PDF 1.23M)

A rotary molecular motor that can work at near 100% efficiency
Kinosita, K., Jr., Yasuda, R., Noji, H., and Adachi, K.
Philos Trans R soc Lond B Biol Sci 355, 473-89 (2000). (PDF 1.62M)

Mechanical disruption of individual nucleosomes revelas a reversible multistage release of DNA
Brower-Toland, B. D., SMith, C. L., Yeh, R. C., Lis, J. T., Peterson, C. L., and Wang, M. D.
Proc Natl Acad Sci USA 99, 1960-5 (2002). (PDF 506K)

Myosin V is a left-handed spiral motor on the right-handed actin helix,
Ali, M. Y., ...Kinosita, K., Jr., Ishiwata, S.,
Nature Structural Biology 9, 464-7 (2002). (PDF 1.76M)

The gated gait of the processive molecular motor, myosin V,
C. Veigel, F. Wang, M. L. Bartoo, J. R. Sellers, J. E. Molloy,
Nature Cell Biology 4, 59-65 (2002). (PDF 665K)

A crossbridge too far,
J. A. Spudich, R. S. Rock,
Nature Cell Biology 4, E8-10 (2002). (PDF 565K)
[Review of Veigel et al, "The gated gate...of myosin V".]

The speed of the flagellar rotary motor of Escherichia coli varies linearly with protonmotive force,
Gabel, C. V. & Berg, H. C.,
Proc Natl Acad Sci U S A 100, 8748-8751 (2003). (PDF 366K)

Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5 nm localization,
Ahmet Yildiz, Joseph N. Forkey, Sean A. McKinney, Taekjip Ha, Yale E. Goldman, Paul R. Selvin,
Science, 300, 2061-2065 (2003). (PDF 870K)
See also related Perspective:
Biophysics. Myosin motors walk the walk,
Molloy, J. E. & Veigel, C.,
Science 300, 2045-6 (2003). (PDF 138K)

DNA/RNA

Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna
K Hamad-Schifferli, , J J Schwartz, A T Santos, S Zhang & J M Jacobson
Nature 415, 10 January 2002, 152 - 155 (2002) (PDF 211K)

Reversible Unfolding of Single RNA Molecules by Mechanical Force
Jan Liphardt, Bibiana Onoa, Steven B. Smith, Ignacio Tinoco Jr., and Carlos Bustamante
Science 2001 April 27; 292: 733-737 (PDF 429K).

Vision

Visual systems: Predator and prey views of spider camouflage
M THÉRY & J CASAS
Nature 415, 10 January 2002, 133 (PDF 95K)
[This is a short article and could be used as part of a project.]

Single-photon detection by rod cells of the retina
F. Rieke, D. A. Baylor
Reviews of Modern Physics, Vol 70 No 3, July 1998 pgs 1027-1036. (PDF 669K).

Women with 4 color pigments:
http://www.redherring.com/mag/issue86/mag-mutant-86.html
(see also: Jordan, G; Mollon, J. D.; Vision Research 1993,33(11), 1495-1508 (fromWebOfScience))
(PDF 76K).

Imperfect optics may be the eye's defence against chromatic blur
JS MCLELLAN, S MARCOS, PM PRIETO & SA BURNS
Nature, 417, 174-176, 2002. (PDF 253K).

Ion Channels

Ion channels: From idea to reality
Bertil Hille, Clay M. Armstrong, Roderick MacKinnon
Nature Medicine 5:1101, 1999 (PDF 527K)
[Review]

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity
Declan A. Doyle, Joćo Morais Cabral, Richard A. Pfuetzner, Anling Kuo, Jacqueline M. Gulbis, Steven L. Cohen, Brian T. Chait, and Roderick MacKinnon
Science 1998 April 3; 280: 69-77. (PDF 6.7M)
[Probably the most important ion channel paper in last decade.]

See potassium run
Christopher Miller
Nature, 414, Nov 1, 2001 (PDF 94K)
[Review/commentary on Mackinnon's latest KcsA crystal structure in same issue, explaining how potassium ions can move quickly but selectively through ion channel pore.]

Energetic optimization of ion conduction rate by the K+ selectivity filter
H. Morais-Cabral, Yufeng Zhou, Roderick MacKinnon
Nature, 414, 37 - 42 (01 Nov 2001) (PDF 317K) (Note that first page is bad in PDF file)
[Summary: The K+ selectivity filter catalyses the dehydration, transfer and rehydration of a K+ ion in about ten nanoseconds. This physical process is central to the production of electrical signals in biology. Here we show how nearly diffusion-limited rates are achieved...]

Counting Channels: A Tutorial Guide on Ion Channel Fluctuation Analysis
Alvarez, O., Gonzalez, C., Latorre, R.
Adv. Physiol. Educ. 2002, 26, 327. (PDF 719K)

Putting ion channels to work: mechanoelectrical transduction, adaptation, and amplification by hair cells
A. J. Hudspeth, Y. Choe, A. D. Mehta, P. Martin
Proc Natl Acad Sci USA 97, 11765-72 (Oct 24, 2000). (PDF 337K)

Scaling

Effects of Size and Temperature on Metabolic Rate
James F. Gillooly, James H. Brown, Geoffrey B. West, Van M. Savage, and Eric L. Charnov
Science 2001 September 21; 293: 2248-2251 (PDF 454K)

All creatures great and small
J. Whitfield
Nature 413, 342 - 344 (27 Sep 2001) (PDF 1.1M)
[Nice Journalistic Review of Gillooly, Brown...scaling.]

A General Model for the Origin of Allometric Scaling Laws in Biology
B. West, James H. Brown, and Brian J. Enquist
Science 1997 April 4; 276: 122-126. (PDF 389K)

Re-examination of the 3/4 scaling law
P. H. Dodds, D.S. Rothman, J.S. Weitz
J. Theoretical Biology, 209:9 2001 (PDF 359K)
[Questions whether 3/4 power law derived by West, Brown, Enquist, is even experimentally correct.]

Scaling effects in caudal fin propulsion and speed in ichthyosaurus
Ryosuko Motani
Nature 415, 309-312 (17 Jan 2002) (PDF 182K)

Tyrannosaurus was not a fast runner
John R. Hutchinson and Mariano Garcia
Nature 415, 1018-1021 (28 Feb 2002) (PDF 225K)

Walking with tyrannosaurs
Andrew A. Biewener
Nature 415, 971-973 (28 Feb 2002) (PDF 82K)
[Review of Hutchinson and Garcia article]

Biomaterials

Science Round-up, June 30, 2006 (PDF)

Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites
BETTYE L. SMITH, PAUL K. HANSMA
Nature 399, 761 - 763 (1999) (PDF 296K)

Segmented nanofibers of spider dragline silk: Atomic force microscopy and single-molecule force spectroscopy,
E. Oroudjev, J. Soares, S. Arcdiacono, J. B. Thompson, S. A. Fossey, and H. G. Hansma
Proc Natl Acad Sci USA, vol. 16, pp. 16, 2002 (PDF 337K)

Materials: Surprising strength of silkworm silk,
Shao, Z. & Vollrath, F.
Nature 418, 741 (2002) (PDF 65K)

Liquid crystalline spinning of spider silk,
Vollrath, F. & Knight, D.P.
Nature 410, 541-548 (2001) (PDF 458K)
[Review]

Mammalian cells spin a spidery new yarn.
Service, R.F.
Science 295, 419-21 (2002). (PDF 164K)
[News Commentary]

The study of protein mechanics with the atomic force microscope.
T. E. Fisher, A. F. Oberhauser, M. Carrion-Vazquez, P. E. Marszalek, J. M. Fernandez
Trends Biochem Sci 24, 379-84 (Oct, 1999). (PDF 387K)
[Review]

Micromanipulation Techniques

Lights, action: optical tweezers
Molloy, J. E.; Padgett, M. J.
Contemporary Physics 2002, 43, 241 (PDF 1000K)

Light with a twist in its tail
Padgett, M. J.; Allen, L.
Contemporary Physics 2000, 41, 275. (PDF 951K)

Self-Assembly

Hierarchical self-assembly of F-actin and cationic lipid complexes: stacked three-layer tubule networks
Wong, G. C., Tang, J. X., Lin, A., Li, Y., Janmey, P. A., and Safinya, C. R.
Science 288, 2035-9 (2000) (PDF 590k)

Structure of DNA-cationic liposome complexes: DNA intercalation in multilamellar membranes in distinct interhelical packing regimes.
J. O. Radler, I. Koltover, T. Salditt, and C. R. Safinya.
Science 275, 810 (1997). (PDF 768k)

Gene Chips

Quantitative monitoring of gene expression patterns with a complementary DNA microarray
Schena, M., Shalon, D., Davis, R. W., and Brown, P. O.
Science 270, 467-70 (1995) (PDF 1.09M)

The transcriptional program in the response of human fibroblasts to serum
Iyer, V. R., Eisen, M. B., Ross, D. T., Schuler, G., Moore, T., Lee, J. C., Trent, J. M., Staudt, L. M., Hudson, J., Jr., Boguski, M. S., Lashkari, D., Shalon, D., Botstein, D., and Brown, P. O.
Science 283, 83-7.(1999) (PDF 318k)

Others

Macromolecular crowding: obvious but underappreciated
R. John Ellis
Trends Biochem Sci 26:597-604 (PDF 116k)

Sudhir Kumar and Sankar Subramanian
Mutation rates in mammalian genomes
Proceedings of the National Academy of Sciences, USA 2002 99: 803-808 (PDF 333k)

Biological Physics
Hans Frauenfelder, Peter G. Wolynes, Robert H. Austin
Reviews of Modern Physics -- March 1999 -- Volume 71, Issue 2 pp. S419-S430 (PDF 367K)
[Interesting review of connections between physics and biology. Can be used as a review article for one of many original research articles cited in paper.]

Olfactory search at high Reynolds number
Eugene Balkovsky and Boris I. Shraiman
Proceedings of the National Academy of Sciences, USA 2002 99: 12589-12593 (PDF 116k)

Stochastic Gene Expression in a Single Cell
Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia, and Peter S. Swain
Science 2002 August 16; 297: 1183-1186. (PDF 282k)

GENETIC NETWORKS: Small Numbers of Big Molecules
Nina Fedoroff and Walter Fontana
Science 2002 August 16; 297: 1129-1131. (PDF 220k)
[in Perspectives, commentary on above article]

Combinatorial Synthesis of Genetic Networks
Calin C. Guet, Michael B. Elowitz, Weihong Hsing, and Stanislas Leibler
Science 2002 May 24; 296: 1466-1470. (PDF 453k)


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