Matt Gethers/20.310 Term Paper

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20.310 Term Paper

Sickle Cell Anemia

Treatments exist for preventive and palliative treatment of sickle cell episodes, but no treatment has yet been developed to mitigate the effects of an attack once it has started. We need a way of dealing with Hbs fibers once they have polymerized. We feel we can develop a treatment for an ongoing attack by addressing the biomechanical basis of the pathology.


  1. Galkin O, Pan W, Filobelo L, Hirsch RE, Nagel RL, and Vekilov PG. Two-step mechanism of homogeneous nucleation of sickle cell hemoglobin polymers. Biophys J 2007 Aug 1; 93(3) 902-13. doi:10.1529/biophysj.106.103705 pmid:17449671. PubMed HubMed [Galkin]
  2. Carragher B, Bluemke DA, Gabriel B, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. I. Sickle hemoglobin fibers. J Mol Biol 1988 Jan 20; 199(2) 315-31. pmid:3351926. PubMed HubMed [Carragher]
  3. Bluemke DA, Carragher B, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. II. Sickle hemoglobin macrofibers. J Mol Biol 1988 Jan 20; 199(2) 333-48. pmid:3351927. PubMed HubMed [Carragher2]
  4. Carragher B, Bluemke DA, Becker M, McDade WA, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. III. Fibers within fascicles. J Mol Biol 1988 Jan 20; 199(2) 383-8. pmid:3351930. PubMed HubMed [Carragher3]
  5. Jones CW, Wang JC, Ferrone FA, Briehl RW, and Turner MS. Interactions between sickle hemoglobin fibers. Faraday Discuss 2003; 123 221-36; discussion 303-22, 419-21. pmid:12638863. PubMed HubMed [Turner]
  6. Wang JC, Turner MS, Agarwal G, Kwong S, Josephs R, Ferrone FA, and Briehl RW. Micromechanics of isolated sickle cell hemoglobin fibers: bending moduli and persistence lengths. J Mol Biol 2002 Jan 25; 315(4) 601-12. doi:10.1006/jmbi.2001.5130 pmid:11812133. PubMed HubMed [Wang]
All Medline abstracts: PubMed HubMed

DNApol processivity as a function of tension in the strand of template DNA

Processivity

  1. Von Hippel PH, Fairfield FR, and Dolejsi MK. On the processivity of polymerases. Ann N Y Acad Sci 1994 Jul 29; 726 118-31. pmid:8092670. PubMed HubMed [Hippel]
  2. López de Saro FJ, Georgescu RE, and O'Donnell M. A peptide switch regulates DNA polymerase processivity. Proc Natl Acad Sci U S A 2003 Dec 9; 100(25) 14689-94. doi:10.1073/pnas.2435454100 pmid:14630952. PubMed HubMed [Lopez]
  3. McClure WR and Chow Y. The kinetics and processivity of nucleic acid polymerases. Methods Enzymol 1980; 64 277-97. pmid:6990186. PubMed HubMed [McClure]
  4. Washington MT, Johnson RE, Prakash S, and Prakash L. Fidelity and processivity of Saccharomyces cerevisiae DNA polymerase eta. J Biol Chem 1999 Dec 24; 274(52) 36835-8. pmid:10601233. PubMed HubMed [Washington]
  5. Williams MC, Rouzina I, and Karpel RL. Quantifying DNA-protein interactions by single molecule stretching. Methods Cell Biol 2008; 84 517-40. doi:10.1016/S0091-679X(07)84017-9 pmid:17964942. PubMed HubMed [Williams]
  6. Xiang Y, Goodman MF, Beard WA, Wilson SH, and Warshel A. Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins 2008 Jan 1; 70(1) 231-47. doi:10.1002/prot.21668 pmid:17671961. PubMed HubMed [Xiang]
  7. Yang J, Zhuang Z, Roccasecca RM, Trakselis MA, and Benkovic SJ. The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci U S A 2004 Jun 1; 101(22) 8289-94. doi:10.1073/pnas.0402625101 pmid:15148377. PubMed HubMed [Yang]
All Medline abstracts: PubMed HubMed

DNA Stretching

  1. Bustamante C, Smith SB, Liphardt J, and Smith D. Single-molecule studies of DNA mechanics. Curr Opin Struct Biol 2000 Jun; 10(3) 279-85. pmid:10851197. PubMed HubMed [Bustamante]
  2. Pope LH, Bennink ML, and Greve J. Optical tweezers stretching of chromatin. J Muscle Res Cell Motil 2002; 23(5-6) 397-407. pmid:12785093. PubMed HubMed [Pope]
  3. Wang MD, Yin H, Landick R, Gelles J, and Block SM. Stretching DNA with optical tweezers. Biophys J 1997 Mar; 72(3) 1335-46. pmid:9138579. PubMed HubMed [Wang2]
All Medline abstracts: PubMed HubMed

Miscellaneous

  1. Gromiha MM. Influence of DNA stiffness in protein-DNA recognition. J Biotechnol 2005 May 4; 117(2) 137-45. doi:10.1016/j.jbiotec.2004.12.016 pmid:15823403. PubMed HubMed [Grohima]
  2. Hogan ME and Austin RH. Importance of DNA stiffness in protein-DNA binding specificity. Nature 1987 Sep 17-23; 329(6136) 263-6. doi:10.1038/329263a0 pmid:3627268. PubMed HubMed [Hogan]
  3. Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, and Block SM. Force and velocity measured for single molecules of RNA polymerase. Science 1998 Oct 30; 282(5390) 902-7. pmid:9794753. PubMed HubMed [Wang3]
  4. Yin H, Wang MD, Svoboda K, Landick R, Block SM, and Gelles J. Transcription against an applied force. Science 1995 Dec 8; 270(5242) 1653-7. pmid:7502073. PubMed HubMed [Yin]
All Medline abstracts: PubMed HubMed

Phage-based Artificial ECM

Synthetic ECM References

http://dx.doi.org

Development of biocompatible synthetic extracellular matrices for tissue engineering

Byung-Soo Kima and David J. Mooneya, b, doi:10.1016/S0167-7799(98)01191-3

Static and dynamic mechanical properties of extracellular matrix synthesized by cultured chondrocytes

Shogo Miyata a, Corresponding Author Contact Information, E-mail The Corresponding Author, Katsuko S. Furukawa a, Takashi Ushida a, Yasuo Nitta a and Tetsuya Tateishi b doi:10.1016/j.msec.2003.11.007

Stability of hydrogels used in cell encapsulation: An in vitro comparison of alginate and agarose Molly S. Shoichet *, Rebecca H. Li, Melissa L. White, Shelley R. Winn

Transport characterization of hydrogel matrices for cell encapsulation Biotechnology and Bioengineering Volume 50, Issue 4, Date: 20 May 1996, Pages: 365-373 Rebecca H. Li, David H. Altreuter, Frank T. Gentile

26. V.C. Mow, S.C. Kuei, W.M. Lai and C.G. Armstrong. J. Biomech. Eng. 102 (1980), pp. 73–84. View Record in Scopus | Cited By in Scopus (637)

27. C.G. Armstrong, W.M. Lai and V.C. Mow. J. Biomech. Eng. 106 (1984), pp. 165–173. View Record in Scopus | Cited By in Scopus (147)

  • Combinatorial and high-throughput measurements of the modulus of thin polymer films

Rev. Sci. Instrum. 76, 062207 (2005); DOI:10.1063/1.1906085 Published 18 May 2005

  • High-throughput mechanical characterization of free-standing polymer films

Rev. Sci. Instrum. 76, 062214 (2005); DOI:10.1063/1.1926967 Published 20 May 2005

  • Nanomechanical property screening of combinatorial thin-film libraries by nanoindentation

OL Warren, TJ Wyrobek - Measurement Science and Technology, 2005 - iop.org

  • Techniques and Instrumentation for Combinatorial and High-Throughput Polymer Research: Recent Developments

Stefan Schmatloch, Ulrich S. Schubert *

  • Microrheology as a tool for high-throughput screening V. Breedveld1 and D. J. Pine
  • Multi-sample Couette viscometer for

polymer formulations∗ Howard J Walls1,3, Robert F Berg2 and Eric J Amis1

  • Combinatorial studies of mechanical properties of Ti–Al thin films using nanoindentation

Seung Min Hana, Corresponding Author Contact Information, E-mail The Corresponding Author, R. Shaha, R. Banerjeeb, G.B. Viswanathanb, B.M. Clemensa and W.D. Nixa

  • Elastic modulus and hardness of cortical and trabecular bone lamellae measured by nanoindentation in the human femur

Philippe K. ZyssetCorresponding Author Contact Information, E-mail The Corresponding Author, X. Edward Guo, C. Edward Hoffler, Kristin E. Moore and Steven A. Goldstein

  • Characterization of viscoelastic properties of polymeric materials through nanoindentation G. M. Odegard1 Contact Information, T. S. Gates2 and H. M. Herring2
  • Chondrocytes in agarose culture synthesize a mechanically functional extracellular matrix

Michael D. Buschmann 1, Yehezkiel A. Gluzband 1, Dr. Alan J. Grodzinsky 1 *, James H. Kimura 2, Ernst B. Hunziker 3

  • Streaming potentials during the confined compression creep test of normal and proteoglycan-depleted cartilage Albert C. Chen2, 1, Tara T. Nguyen2, 1 and Robert L. Sah2, 1
  • Depth- and strain-dependent mechanical and electromechanical properties of full-thickness bovine articular cartilage in confined compression

A. C. Chen, W. C. Bae, R. M. Schinagl and R. L. SahCorresponding Author Contact Information, E-mail The Corresponding Author


  1. Akizuki S, Mow VC, Müller F, Pita JC, Howell DS, and Manicourt DH. Tensile properties of human knee joint cartilage: I. Influence of ionic conditions, weight bearing, and fibrillation on the tensile modulus. J Orthop Res 1986; 4(4) 379-92. doi:10.1002/jor.1100040401 pmid:3783297. PubMed HubMed [Akizuki]
  2. Gildner CD, Lerner AL, and Hocking DC. Fibronectin matrix polymerization increases tensile strength of model tissue. Am J Physiol Heart Circ Physiol 2004 Jul; 287(1) H46-53. doi:10.1152/ajpheart.00859.2003 pmid:15001442. PubMed HubMed [Gildner]
  3. Hsu S, Jamieson AM, and Blackwell J. Viscoelastic studies of extracellular matrix interactions in a model native collagen gel system. Biorheology 1994 Jan-Feb; 31(1) 21-36. pmid:8173042. PubMed HubMed [Hsu]
  4. Krishnan L, Weiss JA, Wessman MD, and Hoying JB. Design and application of a test system for viscoelastic characterization of collagen gels. Tissue Eng 2004 Jan-Feb; 10(1-2) 241-52. doi:10.1089/107632704322791880 pmid:15009949. PubMed HubMed [Krishnan]
  5. Mow VC, Kuei SC, Lai WM, and Armstrong CG. Biphasic creep and stress relaxation of articular cartilage in compression? Theory and experiments. J Biomech Eng 1980 Feb; 102(1) 73-84. pmid:7382457. PubMed HubMed [Mow]
  6. Oberhauser AF, Marszalek PE, Erickson HP, and Fernandez JM. The molecular elasticity of the extracellular matrix protein tenascin. Nature 1998 May 14; 393(6681) 181-5. doi:10.1038/30270 pmid:9603523. PubMed HubMed [Oberhauser]
  7. Parekh A and Velegol D. Collagen gel anisotropy measured by 2-D laser trap microrheometry. Ann Biomed Eng 2007 Jul; 35(7) 1231-46. doi:10.1007/s10439-007-9273-2 pmid:17380393. PubMed HubMed [Parekh]
  8. Pryse KM, Nekouzadeh A, Genin GM, Elson EL, and Zahalak GI. Incremental mechanics of collagen gels: new experiments and a new viscoelastic model. Ann Biomed Eng 2003 Nov; 31(10) 1287-96. pmid:14649502. PubMed HubMed [Pryse]
  9. Saddiq ZA, Barbenel JC, and Grant MH. The mechanical strength of collagen gels containing glycosaminoglycans and populated with fibroblasts. J Biomed Mater Res A 2008 Apr 28. doi:10.1002/jbm.a.32007 pmid:18442115. PubMed HubMed [Saddiq]
  10. Wu CC, Ding SJ, Wang YH, Tang MJ, and Chang HC. Mechanical properties of collagen gels derived from rats of different ages. J Biomater Sci Polym Ed 2005; 16(10) 1261-75. pmid:16268252. PubMed HubMed [Wu]
All Medline abstracts: PubMed HubMed
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