biophysical phenomena

Summary

Summary: The physical characteristics and processes of biological systems.

Top Publications

  1. Ye L, Lv C, Man G, Song S, Elias P, Man M. Abnormal epidermal barrier recovery in uninvolved skin supports the notion of an epidermal pathogenesis of psoriasis. J Invest Dermatol. 2014;134:2843-2846 pubmed publisher
  2. Aik W, Lin M, Tan D, Tripathy A, Marzluff W, Dominski Z, et al. The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3'-end processing. PLoS ONE. 2017;12:e0186034 pubmed publisher
    ..Using solution light scattering, we characterized the stoichiometry of the FLASH NTD-Lsm11 NTD complex and found that it is a 2:1 heterotrimer, which is supported by observations from analytical ultracentrifugation and crosslinking. ..
  3. Roy A, Lim L, Srivastava S, Lu Y, Song J. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants. PLoS ONE. 2017;12:e0180632 pubmed publisher
  4. Friedman M, Hutchins G, Bargeron C, Deters O, Mark F. Correlation between intimal thickness and fluid shear in human arteries. Atherosclerosis. 1981;39:425-36 pubmed
    ..Sudanophilia also correlated negatively with PSR (P less than 0.01). These results suggest that large excursions of interfacial shear, at levels too low to cause damage, may inhibit intimal thickening. ..
  5. Model M, Omann G. Ligand-receptor interaction rates in the presence of convective mass transport. Biophys J. 1995;69:1712-20 pubmed
    ..Our results are expressed in a simple analytical form and can be used for the design and interpretation of experimental data. ..
  6. Amabile N, Renard J, Caussin C, Boulanger C. Circulating immune complexes do not affect microparticle flow cytometry analysis in acute coronary syndrome. Blood. 2012;119:2174-5; author reply 2175-6 pubmed publisher
  7. Abdellah M, Bilgili A, Eilemann S, Shillcock J, Markram H, Schürmann F. Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation. BMC Bioinformatics. 2017;18:62 pubmed publisher
    ..The pipeline is applied to analyze and validate simulation data generated from neuroscientific in silico experiments. ..
  8. Vazquez Anderson J, Mihailovic M, Baldridge K, Reyes K, Haning K, Cho S, et al. Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions. Nucleic Acids Res. 2017;45:5523-5538 pubmed publisher
    ..Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA-mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs. ..
  9. Cannell M, Cheng H, Lederer W. Spatial non-uniformities in [Ca2+]i during excitation-contraction coupling in cardiac myocytes. Biophys J. 1994;67:1942-56 pubmed

More Information

Publications62

  1. Gelbart W, Knobler C. Virology. Pressurized viruses. Science. 2009;323:1682-3 pubmed publisher
  2. Hopyan S. Biophysical regulation of early limb bud morphogenesis. Dev Biol. 2017;429:429-433 pubmed publisher
    ..A combination of quantitative biophysical experimentation and modelling will likely advance this field. ..
  3. Pinker F, Schelcher C, Fernández Millán P, Gobert A, Birck C, Thureau A, et al. Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding. J Biol Chem. 2017;292:13904-13913 pubmed publisher
    ..Altogether, this work provides a refined model of the PRORP-tRNA complex that illustrates how protein-only RNase P enzymes specifically bind tRNA and highlights the contribution of protein dynamics to achieve this specific interaction. ..
  4. Stabeno P, Duffy Anderson J, Eisner L, Farley E, Heintz R, Mordy C. Return of warm conditions in the southeastern Bering Sea: Physics to fluorescence. PLoS ONE. 2017;12:e0185464 pubmed publisher
    ..During years with no sea ice on the southern shelf (e.g. 2001-2005, 2014-2016), the depth-averaged temperature there was correlated to the previous summers ocean temperature. ..
  5. Meek K, Fullwood N, Cooke P, Elliott G, Maurice D, Quantock A, et al. Synchrotron x-ray diffraction studies of the cornea, with implications for stromal hydration. Biophys J. 1991;60:467-74 pubmed
    ..In both cases, it is possible to postulate a second set or population of fibrils that are more widely and irregularly separated and therefore do not contribute significantly to the diffraction pattern. ..
  6. HALLS A, Travill A. TRANSMISSION OF PRESSURES ACROSS THE ELBOW JOINT. Anat Rec. 1964;150:243-7 pubmed
  7. Guyton A. INTERSTITIAL FLUID PRESURE. II. PRESSURE-VOLUME CURVES OF INTERSTITIAL SPACE . Circ Res. 1965;16:452-60 pubmed
  8. Bizzarri M, Monici M, van Loon J. How microgravity affects the biology of living systems. Biomed Res Int. 2015;2015:863075 pubmed publisher
  9. Wen D, Laursen R. A model for binding of an antifreeze polypeptide to ice. Biophys J. 1992;63:1659-62 pubmed
  10. Tian F, Sui Y, Zhu L, Shu C, Sung H. Computational Methods and Models in Circulatory and Reproductive Systems. Comput Math Methods Med. 2016;2016:9028409 pubmed publisher
  11. Bayer A, Schmitt S, Gunther M, Haeufle D. The influence of biophysical muscle properties on simulating fast human arm movements. Comput Methods Biomech Biomed Engin. 2017;20:803-821 pubmed publisher
    ..To this end, further experiments systematically varying the initial muscular activity would be needed. ..
  12. Foley M, Magilligan F, Torgersen C, Major J, Anderson C, Connolly P, et al. Landscape context and the biophysical response of rivers to dam removal in the United States. PLoS ONE. 2017;12:e0180107 pubmed publisher
    ..To address the inconsistencies across dam-removal studies, we provide suggestions for prioritizing and standardizing data collection associated with dam removal activities. ..
  13. Carrell S, O Connell M, Jacobsen T, Pomeroy A, Hayes S, Reeves G. A facilitated diffusion mechanism establishes the Drosophila Dorsal gradient. Development. 2017;144:4450-4461 pubmed publisher
    ..Given that this mechanism has been found in other, independent, systems, we suggest that it might be more prevalent than previously thought. ..
  14. Tricarico D, Petruzzi R, Camerino D. Changes of the biophysical properties of calcium-activated potassium channels of rat skeletal muscle fibres during aging. Pflugers Arch. 1997;434:822-9 pubmed
    ..These findings indicate that, in skeletal muscle, the activity of KCa2+ channels increases with advancing age. ..
  15. Daghighian F, Mazziotta J, Hoffman E, Shenderov P, Eshaghian B, Siegel S, et al. Intraoperative beta probe: a device for detecting tissue labeled with positron or electron emitting isotopes during surgery. Med Phys. 1994;21:153-7 pubmed
  16. JAGER G, Westerhof N, Noordergraaf A. OSCILLATORY FLOW IMPEDANCE IN ELECTRICAL ANALOG OF ARTERIAL SYSTEM: REPRESENTATION OF SLEEVE EFFECT AND NON-NEWTONIAN PROPERTIES OF BLOOD. Circ Res. 1965;16:121-33 pubmed
  17. Möcks J. Topographic components model for event-related potentials and some biophysical considerations. IEEE Trans Biomed Eng. 1988;35:482-4 pubmed
  18. Heller G, Aprile F, Bonomi M, Camilloni C, De Simone A, Vendruscolo M. Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide. J Mol Biol. 2017;429:2772-2779 pubmed publisher
    ..These results suggest that the binding mechanism that we report may create novel opportunities to discover drugs that target disordered proteins in their monomeric states in a specific manner. ..
  19. Bhatia T, Cornelius F, Ipsen J. Capturing suboptical dynamic structures in lipid bilayer patches formed from free-standing giant unilamellar vesicles. Nat Protoc. 2017;12:1563-1575 pubmed publisher
    ..The protocol opens up a new avenue for quantitative biophysical studies of suboptical dynamic structures in biomembranes, which are local and short-lived. Preparation of GUVs, PLB patches and their imaging takes <24 h. ..
  20. An K, Takahashi K, Harrigan T, Chao E. Determination of muscle orientations and moment arms. J Biomech Eng. 1984;106:280-2 pubmed
    ..Advantages and disadvantages associated with each of the techniques are reviewed and compared based on our extensive experience. ..
  21. Fratzl P, Daxer A. Structural transformation of collagen fibrils in corneal stroma during drying. An x-ray scattering study. Biophys J. 1993;64:1210-4 pubmed
    ..The coating appears as a three-dimensional fractal network with fractal dimension of 2.7 +/- 0.1. ..
  22. Otto M, Lillo M, Beechem J. Resolution of multiphasic reactions by the combination of fluorescence total-intensity and anisotropy stopped-flow kinetic experiments. Biophys J. 1994;67:2511-21 pubmed
    ..The data analysis methodologies described allow characterization of multiphasic reactions in terms of internally consistent kinetic rates, quantum yields, and steady-state anisotropies. ..
  23. Gashev A. [The mechanism of the formation of a reverse fluid filling in the lymphangions]. Fiziol Zh SSSR Im I M Sechenova. 1991;77:63-9 pubmed
    ..The data obtained suggest absence of the isometric contraction phase in bovine mesenteric lymphangion's systole in reversed output. ..
  24. Ridge M, Wright V. Mechanical properties of skin: a bioengineering study of skin structure. J Appl Physiol. 1966;21:1602-6 pubmed
  25. Yang N, Kauke M, Sun F, Yang L, Maass K, Traxlmayr M, et al. Cytosolic delivery of siRNA by ultra-high affinity dsRNA binding proteins. Nucleic Acids Res. 2017;45:7602-7614 pubmed publisher
    ..The two-agent delivery system presented here possesses notable biophysical properties and potency, and provide a platform for the cytosolic delivery of nucleic acids. ..
  26. Echave J, Wilke C. Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence. Annu Rev Biophys. 2017;46:85-103 pubmed publisher
    ..We also propose future research directions to develop this nascent field. ..
  27. Aibara S, Gordon J, Riesterer A, McLaughlin S, Stewart M. Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae. Nucleic Acids Res. 2017;45:1529-1538 pubmed publisher
    ..The dimerization of Nab2 induced by RNA binding provides a basis for understanding its function in both poly(A) tail length regulation and in the compaction of mature transcripts to facilitate nuclear export. ..
  28. Berry R, Berg H. Torque generated by the flagellar motor of Escherichia coli while driven backward. Biophys J. 1999;76:580-7 pubmed
  29. Penuelas J, Rutishauser T, Filella I. Ecology. Phenology feedbacks on climate change. Science. 2009;324:887-8 pubmed publisher
  30. Knight C, Driggers E, DeVries A. Adsorption to ice of fish antifreeze glycopeptides 7 and 8. Biophys J. 1993;64:252-9 pubmed
    ..The sharing of polar groups with the ice crystal, rather than hydrogen-bonding to the ice surface, may be a general requirement for adsoprtion-inhibition of freezing. ..
  31. Wang Z, Messi M, Delbono O. L-Type Ca(2+) channel charge movement and intracellular Ca(2+) in skeletal muscle fibers from aging mice. Biophys J. 2000;78:1947-54 pubmed
    ..These data support the concept that the reduction in the peak intracellular [Ca(2+)] results from a larger number of ryanodine receptors uncoupled to DHPRs in skeletal muscle fibers from aging mammals. ..
  32. Bak B, Andreassen T. Reduced energy absorption of healed fracture in the rat. Acta Orthop Scand. 1988;59:548-51 pubmed
  33. Sasidharan V, Marepally S, Elliott S, Baid S, Lakshmanan V, Nayyar N, et al. The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea. Development. 2017;144:3211-3223 pubmed publisher
    ..Together, our results reveal a role for miR-124 in regulating the regeneration of a functional brain and visual system. ..
  34. Simpson C, Kohl M, Essenpreis M, Cope M. Near-infrared optical properties of ex vivo human skin and subcutaneous tissues measured using the Monte Carlo inversion technique. Phys Med Biol. 1998;43:2465-78 pubmed
    ..The transport scattering coefficient for all biological samples showed a monotonic decrease with increasing wavelength. The method was calibrated using solid tissue phantoms and by comparison with a temporally resolved technique. ..
  35. Hirschhorn J. Genomewide association studies--illuminating biologic pathways. N Engl J Med. 2009;360:1699-701 pubmed publisher
  36. Barnard A, Hunt W, Timlake W, Varley E. A theory of fluid flow in compliant tubes. Biophys J. 1966;6:717-24 pubmed
    ..A method of numerical solution of the set of equations is indicated, and the application to cases of interest is discussed. ..
  37. Livingstone D, Smith K, Lange B. Scuba diving and otology: a systematic review with recommendations on diagnosis, treatment and post-operative care. Diving Hyperb Med. 2017;47:97-109 pubmed
    ..We created a set of succinct evidence-based recommendations on each topic that should inform clinical decisions by otolaryngologists, dive medicine specialists and primary care providers when faced with diving-related patient pathology. ..
  38. Wang Q, Irobalieva R, Chiu W, Schmid M, Fogg J, Zechiedrich L, et al. Influence of DNA sequence on the structure of minicircles under torsional stress. Nucleic Acids Res. 2017;45:7633-7642 pubmed publisher
    ..Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy. ..
  39. Chalacheva P, Khaleel M, SUNWOO J, Shah P, Detterich J, Kato R, et al. Biophysical markers of the peripheral vasoconstriction response to pain in sickle cell disease. PLoS ONE. 2017;12:e0178353 pubmed publisher
    ..0167). This marked difference in BMn-v suggests that it is the most sensitive marker for quantifying combined alterations in autonomic and vascular function in SCD in response to heat-induced pain. ..
  40. Benton D, Wharton S, Martin S, McCauley J. Role of Neuraminidase in Influenza A(H7N9) Virus Receptor Binding. J Virol. 2017;91: pubmed publisher
    ..This could have implications for understanding human-to-human transmission of these viruses. ..
  41. Tong X, López Soto E, Li L, Liu H, Nedelcu D, Lipscombe D, et al. Retrograde Synaptic Inhibition Is Mediated by ?-Neurexin Binding to the ?2? Subunits of N-Type Calcium Channels. Neuron. 2017;95:326-340.e5 pubmed publisher
    ..2 reconstituted with ?2?-1 and ?2?-2. Collectively, these results suggest that ?-Neurexin binding to ?2? is a conserved mechanism for regulating synaptic transmission. ..
  42. Olejnik J, Sonar S, Krzymanska Olejnik E, Rothschild K. Photocleavable biotin derivatives: a versatile approach for the isolation of biomolecules. Proc Natl Acad Sci U S A. 1995;92:7590-4 pubmed
    ..Photocleavable biotins should be useful in numerous applications involving the isolation of proteins, nucleic acids, lipids, and cells. ..
  43. Sönnichsen C. Physics. Detecting intruders on the nanoscale. Science. 2011;332:1389-90 pubmed publisher
  44. Shen H, Tauzin L, Baiyasi R, Wang W, Moringo N, Shuang B, et al. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev. 2017;117:7331-7376 pubmed publisher
    ..We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT. ..
  45. Usery R, Enoki T, Wickramasinghe S, Weiner M, Tsai W, Kim M, et al. Line Tension Controls Liquid-Disordered + Liquid-Ordered Domain Size Transition in Lipid Bilayers. Biophys J. 2017;112:1431-1443 pubmed publisher
    ..We find that other properties of the coexisting Ld and Lo phases do not change significantly in the vicinity of the abrupt domain size transition. ..
  46. Ogawa S, Menon R, Tank D, Kim S, Merkle H, Ellermann J, et al. Functional brain mapping by blood oxygenation level-dependent contrast magnetic resonance imaging. A comparison of signal characteristics with a biophysical model. Biophys J. 1993;64:803-12 pubmed
  47. Sonntag R, Braun S, Al Salehi L, Reinders J, Mueller U, Kretzer J. Three-dimensional friction measurement during hip simulation. PLoS ONE. 2017;12:e0184043 pubmed publisher
    ..It should be considered in future pre-clinical testing protocols given by international organizations of standardization. ..
  48. Belcher D, Banerjee U, Baehr C, Richardson K, Cabrales P, Berthiaume F, et al. Mixtures of tense and relaxed state polymerized human hemoglobin regulate oxygen affinity and tissue construct oxygenation. PLoS ONE. 2017;12:e0185988 pubmed publisher
    ..These results show the effect of varying the T/R-state PolyhHb mole fraction on oxygenation of tissue-engineered constructs and their potential to oxygenate tissues...
  49. Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis H. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Res. 2017;45:5437-5448 pubmed publisher
    ..Overall, our results provide precise quantification of the rules governing translation initiation at N-terminal coding regions, improving the predictive design of post-transcriptional regulatory elements that regulate translation rate. ..
  50. Berg H, Turner L. Torque generated by the flagellar motor of Escherichia coli. Biophys J. 1993;65:2201-16 pubmed
    ..These results are consistent with a tightly coupled ratchet mechanism, provided that elastic deformation of force-generating elements is limited by a stop and that mechanical components yield at high applied torques. ..
  51. Berger F, Hudspeth A. Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms. PLoS Comput Biol. 2017;13:e1005566 pubmed publisher
    ..Changing the binding probabilities and myosin's stiffness under a constant force results in a mechanical relaxation which is large enough to account for fast adaptation in hair cells. ..
  52. Chang F. Forces that shape fission yeast cells. Mol Biol Cell. 2017;28:1819-1824 pubmed publisher
    ..Studies in yeast can help to illuminate approaches and mechanisms to study the mechanobiology of the cell surface in other cell types, including animal cells. ..
  53. Souli M, Klonos P, Fragopoulou A, Mavragani I, Pateras I, Kostomitsopoulos N, et al. Applying Broadband Dielectric Spectroscopy (BDS) for the Biophysical Characterization of Mammalian Tissues under a Variety of Cellular Stresses. Int J Mol Sci. 2017;18: pubmed publisher