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

A broader take on DNA
Aaron M. Leconte and Floyd E. Romesberg
Nature 444, 553-5 (30 November 2006) (PDF 374K)

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, João 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.]

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

Design of Superior Spider Silk: From Nanostructure to Mechanical Properties
Ning Du,Xiang Yang Liu, Janaky Narayanan, Lian Li, Matthew Lek Min Lim, and Daiqin Liy
Biophysical Journal 91,4528–4535 (December 2006) (PDF 673K)

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)

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)

General Biology

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TOC.html

http://www.dnaftb.org/dnaftb/

Nicholas D. Kristof
The Hubris of the Humanities
NY Times (December 6, 2005) (PDF 66K)

Rasmus Nielsen
Why Sex?
Science 311:960 (February 17, 2006) (PDF 1M)

Michael Andreeff and Daniel Pinkel, editors. 1999.
Introduction to fluorescence in situ hybridization: principles and clinical applications
New York: Wiley-Liss (Chapter 1) (Chapter 2)

F. Rieke, D. Baylor
Single-photon detection by rod cells of the retina
Reviews of Modern Physics 70:1027-1036 (July 1998) (PDF 914K)

DNA as a Material

Nadrian C. Seeman
DNA in a material world
Nature 421: 427-431 (January 23, 2003) (PDF 316K)

DNA: Basics & Sequencing

How DNA is sequenced. (PDF 2M)

G. Kolata
Slowly, Cancer Genes Tender Their Secrets
NY Times (December 27, 2005) (PDF 85K)

Scientists find unusual lung cancer tumour-suppressor gene
Pharmabiz.com (January 21, 2006) (PDF 157K)

A.K. Raap
Overview of Fluorescence In Situ Hybridization Techniques for Molecular Cytogenetics
Current Protocols in Cytometry 8.1.1-8.1.6 (1997) (PDF 186K)

DNA Forensics

Greg Hampikian
The Future of Forensic DNA
Canadian Journal of Police & Security Services 3: 5-16 (2005) (PDF 2M)

Andre A. Moenssens
A Mistaken DNA Identification?What Does It Mean?
Forensic Evidence.com (October 2000) (PDF 56K)

S. Dewan, B. Goodman
After 24 Years in Prison, Man Has a Reason to Smile
NY Times (December 8, 2005) (PDF 68K)

N. Wade
Scientist at Work/Kary Mullis; After the 'Eureka,' a Nobelist Drops Out
NY Times (September 15, 1998) (PDF 42K)

N. Wade
Dog's Genome Could Provide Clues to Disorders in Humans
NY Times (December 8, 2005) (PDF 218K)

N. Wade
DNA Offers New Insight Concerning Cat Evolution
NY Times (January 6, 2006) (PDF 241K)

Darren Nesbeth
Humans 1 Neanderthals 0
London Student (PDF 18K) (Web: http://www.londonstudent.org.uk/7issue/futures/neanderthal.htm)

Neanderthals not human ancestors
BBC News (March 29, 2000) (PDF 112K)

DNA clues to Neanderthals
BBC News (October 11, 2000) (PDF 104K)

Ann Gibbons
New Methods Yield Mammoth Samples
Science 310, 1889 (December 23, 2005) (PDF 189K)

Alexandra Witze
Mammoth cave yields most recent animals
Nature.com (October 20, 2005) (PDF 95K)

Palaeogenomics
Nature 7, 82 (February 2006) (PDF 94K)

Johannes Krause, et. al.
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae
Nature.com (December 18, 2005) (PDF 763K)

DNA Stiffness & Twisting

Paul R. Selvin, David N. Cook, Ning G. Pon, William R. Bauer, Melvin P. Klein, John E. Hearst.
Torsional Rigidity of Positively and Negatively Supercoiled DNA.
Science 255, 82-85 (1992).

Carlos Bustamante, Jed C.Macosko, Gijs J. L.Wuite
Grabbing the Cat by the Tail: Manipulating Molecules One by One
Nature 1, 130 (November 2000) (PDF 1M)

Carlos Bustamante, Zev Bryant, Steven B. Smith
Ten years of tension: single-molecule DNA mechanics
Nature 421, 423 (January 23, 2003) (PDF 2M)

Zev Bryant, et. alt.
Structural transitions and elasticity from torque measurements on DNA
Nature 424:338-341 (July 17, 2003) (PDF 644K)

DNA, Haplotyping, & SNP

David B. Goldstein,Gianpiero L. Cavalleri.
Genomics: Understanding human diversity
Nature 437, 1241-1242 (27 October 2005) News and Views(PDF 704K) , Editor's Comment (PDF 30K)

Jennifer Couzin
New Mapping Project Splits the Community
Science 296(24 May 2002) (PDF 145K)

Gene Chips

Patrick O. Brown, David Botstein
Exploring the new world of the genome with DNA microarrays
Nature Genetics Supplement 21:33-37 (January 1999) (PDF 1M)

Pat Brown, Time Mag. Feb. 17, 2002: Brief Biography. (PDF 68K)

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

Chang, H.Y., D.S. Nuyten, J.B. Sneddon, T. Hastie, R. Tibshirani, T. Sorlie, H. Dai, Y.D. He, L.J. van't Veer, H. Bartelink, M. van de Rijn, P.O. Brown, and M.J. van de Vijver
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival.
Proc Natl Acad Sci U S A, 2005. 102(10): p. 3738-43. (PDF 513K)

Chang, H.Y., J.B. Sneddon, A.A. Alizadeh, R. Sood, R.B. West, K. Montgomery, J.T. Chi, M. van de Rijn, D. Botstein, and P.O. Brown
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.
PLoS Biol, 2004. 2(2): p. E7. (PDF 4.41M)

Aging

Univ. Utah: Aging and Telomere Shortening Press Release: Jan. 2003 (PDF 75K)
Univ. Utah: Are Telomeres the Key to Aging and Cancer? (PDF 793K)

Andrea G. Bodnar et. alt.
Extension of Life-Span by Introduction of Telomerase into Normal Human Cells
Science 279, 349-352 (January 16, 1998) (PDF 590K)

Lawrence K. Altman
Studying Rare Disorder, Scientists Find Gene Affecting Aging
NY Times (April 12, 1996) (PDF 27K)

Helicase

P.H. von Hippel.
Helicases become mechanistically simpler and functionally more complex.
Nat Struct Mol Biol. 2004 Jun;11(6):494-6. News & Views (PDF 131K)

Eckhard Jankowsky
Helicase snaps back.
Nature 437, 1245 (27 October 2005) News & View of Ha. et al.(PDF 85K)

Sua Myong, Ivan Rasnik, Chirlmin Joo, Timothy M. Lohman, Taekjip Ha
Repetitive shuttling of a motor protein on DNA
Nature 437, 1321(27 October 2005) (PDF 678K)

Planaria, C. Elegans and Regeneration

P. A. Newmark and A.S. Alvarado
Not Your Father's Planarian: A Classic Model Enters the Era of Funcitonal Genomics
Nature 3, 210 (March 2002) (PDF 2M)

P. A. Newmark and A.S. Alvarado
Regeneration in Planaria
Encyclopedia of Life Sciences (2001) (PDF 1M)

Jeremy P. Brockes and Anoop Kumar
Appendage Regeneration in Adult Vertebrates and Implications for Regenerative Medicine
Science 310: 1919 (December 23, 2005) Review Article (PDF 382K)

Elizabeth Pennisi
RNAi Takes Evo-Devo World by Storm
Science 304: 384 (April 16, 2004) General News Article (PDF 75K)

Xantha Karp and Victor Ambros
Encountering MicroRNAs in Cell Fate Signaling
Science 310: 1288 (November 25, 2005) Perspective (PDF 1M)

P. W. Reddien and A. S. Alvarado
Fundamentals of Planarian Regeneration
Annu. Rev. Cell Dev. Biol. 20:725–57 (2004) Review (PDF 665K)

HHMI Commentary on Tesseria
Simple Chemical Switches Steer Migrating Neurons
Science (1998) (PDF 92K)

Mehmet Fatih Yanik,Hulusi Cinar,Hediye Nese Cinar, Andrew D. Chisholm,Yishi Jin, Adela Ben-Yakar
Functional regeneration after laser axotomy
Nature 432:822 (December 14, 2004) (PDF 203K)

Marc Tessier-Lavigne and Corey S. Goodman
The Molecular Biology of Axon Guidance
Science 274:1123-1133 (November 15, 1996) (PDF 1208K)

Pico Caroni
Perspectives NEUROSCIENCE:Driving the Growth Cone
Science 281:1465-1466 (November 15, 1996) (PDF 214K)

Micromanipulation Techniques

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

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

K. Svoboda and S. M. Block
Biological Applications of Optical Forces
Ann. Rev. Biophys. Biomol. Struct. 23; 247-85 (1994) (PDF 4M)

M.C. Williams
Optical Tweezers: Measuring Piconewton Forces
[http://www.biophysics.org/education/williams.pdf] (1992)

M.C. Williams and I. Rouzina
Force spectroscopy of single DNA and RNA molecules
Current Opinion in Structural Biology 2002, 12:330–336 (PDF 212K)

Keir C. Neuman and Steven M. Block
Optical trapping
Rev. Sci. Inst. 75, 2787-2809 (2004) (PDF 1M)

Bryant et al
Direct observation of base-pair stepping by RNA polymerase
Nature 438:460-465 (November 24, 2005) (PDF 1M)

Molecular Motors

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

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

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

Ahmet Yildiz, Joseph N. Forkey, Sean A. McKinney, Taekjip Ha, Yale E. Goldman, Paul R. Selvin.
Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5 nm localization.
Science, 300 (5628) 2061-2065 (online June 5, 2003; in print June 27, 2003).
{supporting online materials}, {movie}, {perspective}, {cover illustration}{UIUC Physics link}

Ahmet Yildiz, Michio Tomishige, Ronald D. Vale, Paul R. Selvin.
Kinesin Walks Hand-Over-Hand.
Science, 303, 676-678 (2004).
{UIUC Physics Link}, {supporting online materials}

Asbury, C.L., A.N. Fehr, and S.M. Block,
Kinesin moves by an asymmetric hand-over-hand mechanism.
Science, 2003. 302(5653): p. 2130-4.

NY Times--Steve Block (PDF 43K)

Ion Channels

C. Armstrong
A One-Domain Voltage-Gated Sodium Channel in Bacteria
Science 294:2306-2308 (December 14, 2001) (PDF 428K)

C. Armstrong
Voltage-Gated K Channels
Sci. STKE, 2003: re10 (June 24, 2003) (PDF 612K)

Anthony Auerbach
Life at the Top: The Transition State of AChR Gating
Sci. STKE, 2003: re11 (June 24, 2003) (PDF 522K)

Maria L. Garcia and Gregory J. Kaczorowski
Potassium Channels as Targets for Therapeutic Intervention
Sci. STKE, 2005: pe46 (September 20, 2005) (PDF 251K)

Eduardo Perozo, D. Marien Cortes, Luis G. Cuello
Structural Rearrangements Underlying K1-Channel Activation Gating
Science 285: 73-78 ( July 2, 1999) (PDF 595K)

Random Web Sites

Hearing -- http://www.bcm.edu/oto/research/cochlea/Volta/index.html

"Speach" --The evolution of speech: a comparative review, W. Tecumseh Fitch, Trends in Cognitive Sciences- Vol.4, No.7, July 2000

Carlos Bustamante, Jan Liphardt, and Felix Ritort
The Nonequilibrium Thermodynamics of Small Systems
Physics Today (July 2005) (PDF 3M)

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Updated: 11/28/06