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Biophysical Phenomena (4):
Recent article
Biophysical Phenomena
Scientific American (305)1 2011
Abstract
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Abstract
We developed a directed weighted graph, the topology graph, to represent the secondary structure assignment problem. We prove that the problem of finding the valid topology with the minimum cost is NP hard. We developed an O(N(2)2(N)) dynamic programming algorithm to identify the topology with the m...
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PMID: 21714133
PDF is available here.
PDF is available here.
Klinichna khirurhiia / Ministerstvo okhorony zdorov'ia Ukrainy, Naukove tovarystvo khirurhiv Ukrainy ()4 2011
Abstract
Brief historical review of drainage procedures of the wounds and abdominal cavity was adduced. The main mechanisms of the drainage process, from the hydrodynamics laws point, were discussed. There was shown, that drainage occurs due to hydrostatic tissue of liquid and the capillarity laws. The main m...
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PMID: 21698932
PDF is available here.
PDF is available here.
Abstract
We now report a novel tetrameric PilZ domain structure of XCC6012 from the plant pathogen Xanthomonas campestris pv. campestris (Xcc). It is one of the four PilZ domain proteins essential for Xcc pathogenicity. Although the monomer adopts a structure similar to those of the PilZ domains with very we...
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PMID: 21760949
PDF is available here.
PDF is available here.
Abstract
We focus here on the question of initial adhesion, the mechanisms of which are still far from being fully understood. Recently, the frontier between microbiologists and physicists has become increasingly permeable, boosting implementation of new methodological approaches for better elucidating the i...
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PMID: 21557073
PDF is available here.
PDF is available here.
Abstract
In flat-panel detector-based cone beam CT breast imaging (CBCTBI) systems, scattering is an important factor that degrades image quality. It is not practical to measure the scattering profiles of a breast for all view angles in a patient study, but it is possible to develop a method to estimate the s...
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PMID: 21422591
PDF is available here.
PDF is available here.
Abstract
Abstract
We investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (...
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PMID: 20974927
PDF is available here.
PDF is available here.
Biophysical Journal (99)4 2010
Abstract
We present a model for microtubule-cortex anchoring and collision-based interactions between microtubules, based on a competition between cross-linker bonding, microtubule bending, and microtubule polymerization. Our model predicts a higher probability of entrainment at smaller collision angles and...
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PMID: 20712991
PDF is available here.
PDF is available here.
Abstract
We show that full ligand-induced activation appears already with only two ligands bound to the tetrameric channel. Kinetic analysis of channel activation and ligand binding suggests direct interaction between the voltage sensor and the cyclic nucleotide-binding domain, bypassing the pore. By exploit...
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PMID: 20624593
PDF is available here.
PDF is available here.
Homeopathy (99)3 2010
Abstract
Abstract
We use existing MSMs for the villin headpiece and NTL9, which were constructed from atomistic simulations, to accomplish this goal. In addition, we provide simpler, humanly comprehensible networks that capture the essence of molecular kinetics and reproduce qualitative phenomena like the apparent tw...
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PMID: 20534497
PDF is available here.
PDF is available here.
Abstract
We demonstrate that edge direction has profound effects on assortativity. We define a set of four directed assortativity measures and assign statistical significance by comparison to randomized networks. We apply these measures to three network classes--online/social networks, food webs, and word-ad...
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PMID: 20505119
PDF is available here.
PDF is available here.
Abstract
We constructed a Calpha-trace model of the membrane region. The model structure, supported by mutagenesis data, was used to investigate global dynamics through elastic network models. Identified as dominant hinge regions, hCTR1's MxxxM and GxxxG motifs were shown to have significant roles in functio...
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PMID: 20534491
PDF is available here.
PDF is available here.
Abstract
We seek a quantitative relationship between the geometry of conical stromatolites and the biophysical processes that control their growth. We note that all modern conical stromatolites and many that formed in the last 2.8 billion years display a characteristic centimeter-scale spacing between neighb...
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PMID: 20479268
PDF is available here.
PDF is available here.
Abstract
We quantify the straightening of curved Caulobacter crescentus cells after disruption of the cell-curving crescentin structure. We observe that cells straighten at a rate that is about half (57%) the cell growth rate. Next we show that in the absence of other effects there exists a mathematical rela...
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PMID: 20479277
PDF is available here.
PDF is available here.
Biophysical Journal (98)8 2010
Abstract
A dynamical biophysical model for the functioning of an epithelium is presented. This model integrates the electrical and osmotic behaviors of the epithelium, taking into account intracellular conditions. The specific tissue modeled is the human bronchial epithelium, which is of particular interest,...
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PMID: 20409466
PDF is available here.
PDF is available here.
Abstract
We examined the in vivo usefulness of porous bodies as scaffolds combined with an atelocollagen hydrogel, and investigated the suitable conditions for atelocollagen and seeding cells within the engineered tissues. We made tissue-engineered constructs using a collagen sponge (CS) or porous poly(L-lac...
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PMID: 19536835
PDF is available here.
PDF is available here.
Abstract
We observed that (i) bundles of flagella on swarmer cells remain cohesive during frequent collisions with neighboring cells, (ii) flagella on nonmotile swarmer cells at the leading edge of the colony protrude in the direction of the uncolonized agar surface and are actively rotated in a thin layer o...
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PMID: 20023074
PDF is available here.
PDF is available here.
Abstract
We report on the realization of an effective pumping device that mimics a ciliated surface and imitates its motion to generate fluid flow. The artificial biomimetic cilia are constructed as long chains of spherical superparamagnetic particles, which self-assemble in an external magnetic field. Magne...
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PMID: 19934055
PDF is available here.
PDF is available here.
Abstract
We considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway f...
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PMID: 20080561
PDF is available here.
PDF is available here.
Abstract
We investigate the effects of ubiquitination on the folding thermodynamics and mechanism of various substrates using computational tools and find that ubiquitination changes the thermal stability of modified proteins in a manner relevant to cellular processes. These changes depend on the substrate m...
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PMID: 20080694
PDF is available here.
PDF is available here.
Abstract
We probe the architecture and dynamics of complexes formed between an oligomeric sHSP and client by employing unique mass spectrometry strategies. We observe over 300 different stoichiometries of interaction, demonstrating that an ensemble of structures underlies the protection these chaperones conf...
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PMID: 20133845
PDF is available here.
PDF is available here.
Abstract
We directly extract the full free energy landscape of a single molecule of the GCN4 leucine zipper using dual beam optical tweezers. To this end, we use deconvolution force spectroscopy to follow an individual molecule's trajectory with high temporal and spatial resolution. We find a heterogeneous e...
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PMID: 20133846
PDF is available here.
PDF is available here.
Abstract
In this study, a comparison was made between a plastic scintillator (BC400), a Faraday Cup (FC) and an ionization chamber (IC) used for routine proton dosimetry. Thin scintillators can be applied to proton dosimetry and consequently to proton therapy as relative dosimeters because of their water-equ...
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PMID: 20679742
PDF is available here.
PDF is available here.
Abstract
Evidence has consistently indicated that activation of sphingomyelinases and/or ceramide synthases and the resulting accumulation of ceramide mediate cellular responses to stressors such as lipopolysaccharide, interleukin 1beta, tumor necrosis factor alpha, serum deprivation, irradiation and various...
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PMID: 20919648
PDF is available here.
PDF is available here.
Abstract
The objective of this work was to evaluate the physical properties and in vivo circulation of chitosan (CH)-coated liposomes of mitoxantrone (MTO). Changes in particle size and zeta potential confirmed the existence of a coating layer on the surface of liposomes. The in vitro release of adsorbed CH...
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PMID: 20957162
PDF is available here.
PDF is available here.
Abstract
Abstract
Biochemistry (Washington) (48)38 2009
Abstract
We utilized a computational approach to generate a hypothetical structure for Manduca sexta EH. The de novo algorithm exploited the restricted conformational space of disulfide bonds (Cys14-Cys38, Cys18-Cys34, and Cys21-Cys49) and predicted secondary structure elements to generate a thermodynamicall...
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PMID: 19670911
PDF is available here.
PDF is available here.
Abstract
We now explore the effects of NS1 upon the biophysical properties of human airway epithelial cells. Transient expression of NS1 depolarized electrically isolated cells maintained in glucocorticoid-free medium by activating a cation conductance identical to the glucocorticoid-induced conductance seen...
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PMID: 19403603
PDF is available here.
PDF is available here.
Abstract
We showed that HeLa cells expressing Cx57 and C-terminally fused with enhanced green fluorescent protein (Cx57-EGFP) form junctional plaques (JPs) and that only cell pairs exhibiting at least one JP demonstrate cell-to-cell electrical coupling and transfer of negatively and positively charged dyes w...
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PMID: 19433576
PDF is available here.
PDF is available here.
Journal of Neurophysiology (102)1 2009
Abstract
We investigate the characteristics of rNST neurons sending information rostrally to the parabrachial nucleus (PBN). Afferent connections to these rNST-PBN projection neurons were identified by anterograde labeling of the chorda tympani (CT), glossopharyngeal (IX), and lingual (LV) nerves. We used vo...
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PMID: 19439671
PDF is available here.
PDF is available here.
Neurobiology of Disease (35)1 2009
Abstract
We generated a bacterial artificial chromosome (BAC) transgenic mouse model that expresses the human SCN1A GEFS+ mutation, R1648H. Mice with the R1648H mutation exhibit a more severe response to the proconvulsant kainic acid compared with mice expressing a control Scn1a transgene. Electrophysiologic...
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PMID: 19409490
PDF is available here.
PDF is available here.
Abstract
We introduce a novel rescaling procedure by which we speed all dynamical processes related to actin polymerization and depolymerization up by the same factor. In general, the actin protomers within a filament can attain three different states corresponding to a bound adenosine triphosphate (ATP), ad...
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PMID: 19586123
PDF is available here.
PDF is available here.
Analytical Biochemistry (392)1 2009
Abstract
We studied the interaction of this series with ADP-Eg5 complexes using a thermal shift assay. We measured up to a 7 degrees C increase in the thermal melting (T(m)) of Eg5 for an inhibitor that produced IC(50) values of 60 and 130 nM in microtubule-dependent adenosine triphosphatase (ATPase) and cel...
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PMID: 19497292
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
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PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology....
|
PMID: 19416726
PDF is available here.
PDF is available here.