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1. Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number

Author:
Werner, Arne
Source:
Nucleic acids research 2011 v.39 no.3 pp. e17
ISSN:
0305-1048
Subject:
RNA; diffusivity; hydrodynamics; models; molecular weight; nucleotides; polymers; prediction
Abstract:
... Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evoluti ...
DOI:
10.1093/nar/gkq808
PubMed:
21068070
PubMed Central:
PMC3035447

2. Correlating magnetic resonance findings with neuropathology and clinical signs in dogs and cats

Author:
VITE, CHARLES H.; CROSS, JOHNNY R.
Source:
Veterinary radiology & ultrasound 2011 v.52Suppls1 pp. S23
ISSN:
1058-8183
Subject:
cats; central nervous system; diffusivity; dogs; metabolites; myelination; spectroscopy
Abstract:
... The histologic characteristics that are the basis for diagnosis of central nervous system conditions cannot be visualized directly using magnetic resonance (MR) methods, but clinical diagnosis may be based on the frequency and pattern of MR imaging signs, which represent predominantly the gross morphologic features of lesions. Additional quantitative MR measures of myelination, cell swelling, glio ...
DOI:
10.1111/j.1740-8261.2010.01782.x
PubMed:
21392153
PubMed Central:
PMC3093660

3. Solid Loss of Carrots During Simulated Gastric Digestion

Author:
Kong, Fanbin; Singh, R. Paul
Source:
Food biophysics 2011 v.6 no.1 pp. 84-93
ISSN:
1557-1858
Subject:
acid hydrolysis; boiling; carrots; cooking; diffusivity; digestion; food matrix; foods; gastric juice; mass transfer; nutrients; pH; soaking; stomach; temperature; total soluble solids; viscosity
Abstract:
... The knowledge of solid loss kinetics of foods during digestion is crucial for understanding the factors that constrain the release of nutrients from the food matrix and their fate of digestion. The objective of this study was to investigate the solid loss of carrots during simulated gastric digestion as affected by pH, temperature, viscosity of gastric fluids, mechanical force present in stomach, ...
DOI:
10.1007/s11483-010-9178-8
PubMed:
21423328
PubMed Central:
PMC3034909

4. Effect of shrinkage on isothermal drying behavior of 2-phase olive mill waste

Author:
Milczarek, Rebecca R.; Dai, Annie A.; Otoni, Caio G.; McHugh, Tara H.
Source:
Journal of food engineering 2011 v.103 no.4 pp. 434
ISSN:
0260-8774
Subject:
diffusivity; microwave ovens; olives; shrinkage; temperature; thin-layer drying; wastes
Abstract:
... The objective of this study was to determine the drying behavior of 2-phase olive mill waste (2POMW) under isothermal microwave-convection drying conditions. 2POMW samples were dried in a thin layer in a variable-power pilot microwave oven with impinging air, using a feedback controller to maintain sample temperature at one of four levels. Moisture loss and shrinkage of the samples were recorded d ...
Handle:
10113/47510
DOI:
10.1016/j.jfoodeng.2010.11.013

5. Osmotic stress alters chromatin condensation and nucleocytoplasmic transport

Author:
Finan, John D.; Leddy, Holly A.; Guilak, Farshid
Source:
Biochemical and biophysical research communications 2011 v.408 no.2 pp. 230-235
ISSN:
0006-291X
Subject:
chromatin; cytoplasm; dextran; diffusivity; fluorescence; mathematical models; mechanism of action; nucleocytoplasmic transport; osmolality; osmotic stress; photobleaching; signal transduction
Abstract:
... Osmotic stress is a potent regulator of biological function in many cell types, but its mechanism of action is only partially understood. In this study, we examined whether changes in extracellular osmolality can alter chromatin condensation and the rate of nucleocytoplasmic transport, as potential mechanisms by which osmotic stress can act. Transport of 10kDa dextran was measured both within and ...
DOI:
10.1016/j.bbrc.2011.03.131
PubMed:
21463604
PubMed Central:
PMC3104296

6. Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins

Author:
Zhou, Huan-Xiang
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.21 pp. 8651-8656
ISSN:
0027-8424
Subject:
DNA; binding proteins; diffusivity; energy; enzymes; transcription factors
Abstract:
... We develop a theory for the rapid search of specific sites on DNA, via a mechanism in which a nonspecifically-bound protein can switch between two conformations. In the "inactive" conformation, the bound protein has favorable, nonspecific interactions with the DNA, but cannot be recognized by the target site. In the "active" conformation, the protein is recognized by the target site but has a very ...
DOI:
10.1073/pnas.1101555108
PubMed:
21543711
PubMed Central:
PMC3102365

7. Solute diffusion is hindered in the mitochondrial matrix

Author:
Dieteren, Cindy E.J.; Gielen, Stan C.A.M.; Nijtmans, Leo G.J.; Smeitink, Jan A.M.; Swarts, Herman G.; Brock, Roland; Willems, Peter H.G.M.; Koopman, Werner J.H.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.21 pp. 8657-8662
ISSN:
0027-8424
Subject:
chemical reactions; cytosol; diffusivity; endoplasmic reticulum; fluorescence recovery after photobleaching; fluorescent proteins; mathematical models; mitochondria; nanomaterials; solutes
Abstract:
... Intracellular chemical reactions generally constitute reaction-diffusion systems located inside nanostructured compartments like the cytosol, nucleus, endoplasmic reticulum, Golgi, and mitochondrion. Understanding the properties of such systems requires quantitative information about solute diffusion. Here we present a novel approach that allows determination of the solvent-dependent solute diffus ...
DOI:
10.1073/pnas.1017581108
PubMed:
21555543
PubMed Central:
PMC3102363

8. Electrokinetic trapping at the one nanometer limit

Author:
Fields, Alexander P.; Cohen, Adam E.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.22 pp. 8937-8942
ISSN:
0027-8424
Subject:
ambient temperature; diffusivity; electrophoresis; fluorescent dyes; hydrodynamics; molecular weight; proteins; single-stranded DNA; traps
Abstract:
... Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based anti-Brownian electrokinetic trap in which classical thermal noise is compen ...
DOI:
10.1073/pnas.1103554108
PubMed:
21562206
PubMed Central:
PMC3107292

9. Enhancement of biomixing by swimming algal cells in two-dimensional films

Author:
Kurtuldu, Hüseyin; Guasto, Jeffrey S.; Johnson, Karl A.; Gollub, J.P.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.26 pp. 10391-10395
ISSN:
0027-8424
Subject:
Chlamydomonas; algae; cell movement; diffusivity; hydrodynamics; microorganisms; mixing; models; probability distribution; stochastic processes
Abstract:
... Fluid mixing in active suspensions of microorganisms is important to ecological phenomena and presents a fascinating stochastic process. We investigate the mixing produced by swimming unicellular algal cells (Chlamydomonas) in quasi-two-dimensional liquid films by simultaneously tracking the motion of the cells and that of microscopic passive tracer particles advected by the fluid. The reduced spa ...
DOI:
10.1073/pnas.1107046108
PubMed:
21659630
PubMed Central:
PMC3127909

10. Gas uptake and chemical aging of semisolid organic aerosol particles

Author:
Shiraiwa, Manabu; Ammann, Markus; Koop, Thomas; Pöschl, Ulrich
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.27 pp. 11003-11008
ISSN:
0027-8424
Subject:
aerosols; air quality; climate; diffusivity; models; organic matter; oxidants; ozone; phase transition; public health; relative humidity; temperature; viscosity; water uptake
Abstract:
... Organic substances can adopt an amorphous solid or semisolid state, influencing the rate of heterogeneous reactions and multiphase processes in atmospheric aerosols. Here we demonstrate how molecular diffusion in the condensed phase affects the gas uptake and chemical transformation of semisolid organic particles. Flow tube experiments show that the ozone uptake and oxidative aging of amorphous pr ...
DOI:
10.1073/pnas.1103045108
PubMed:
21690350
PubMed Central:
PMC3131339

11. Protein self-diffusion in crowded solutions

Author:
Roosen-Runge, Felix; Hennig, Marcus; Zhang, Fajun; Jacobs, Robert M.J.; Sztucki, Michael; Schober, Helmut; Seydel, Tilo; Schreiber, Frank
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.29 pp. 11815-11820
ISSN:
0027-8424
Subject:
aqueous solutions; bovine serum albumin; diffusivity; hydrodynamics; models; translation (genetics)
Abstract:
... Macromolecular crowding in biological media is an essential factor for cellular function. The interplay of intermolecular interactions at multiple time and length scales governs a fine-tuned system of reaction and transport processes, including particularly protein diffusion as a limiting or driving factor. Using quasielastic neutron backscattering, we probe the protein self-diffusion in crowded a ...
DOI:
10.1073/pnas.1107287108
PubMed:
21730176
PubMed Central:
PMC3142006

12. Link between statistical equilibrium fidelity and forecasting skill for complex systems with model error

Author:
Majda, Andrew J.; Gershgorin, Boris
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.31 pp. 12599-12604
ISSN:
0027-8424
Subject:
climate change; diffusivity; models; tracer techniques; variance
Abstract:
... Understanding and improving the predictive skill of imperfect models for complex systems in their response to external forcing is a crucial issue in diverse applications such as for example climate change science. Equilibrium statistical fidelity of the imperfect model on suitable coarse-grained variables is a necessary but not sufficient condition for this predictive skill, and elementary example ...
DOI:
10.1073/pnas.1108132108
PubMed:
21768334
PubMed Central:
PMC3150900

13. Mobility in geometrically confined membranes

Author:
Domanov, Yegor A.; Aimon, Sophie; Toombes, Gilman E.S.; Renner, Marianne; Quemeneur, François; Triller, Antoine; Turner, Matthew S.; Bassereau, Patricia
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.31 pp. 12605-12610
ISSN:
0027-8424
Subject:
diffusivity; hydrodynamics; lipid bilayers; lipids; nanotubes; potassium channels; prediction; quantum dots
Abstract:
... Lipid and protein lateral mobility is essential for biological function. Our theoretical understanding of this mobility can be traced to the seminal work of Saffman and Delbrück, who predicted a logarithmic dependence of the protein diffusion coefficient (i) on the inverse of the size of the protein and (ii) on the "membrane size" for membranes of finite size [Saffman P, Delbrück M (1975) Proc Nat ...
DOI:
10.1073/pnas.1102646108
PubMed:
21768336
PubMed Central:
PMC3150897

14. Regulation of the MEX-5 Gradient by a Spatially Segregated Kinase/Phosphatase Cycle

Author:
Griffin, Erik E.; Odde, David J.; Seydoux, Geraldine
Source:
Cell 2011 v.146 no.6 pp. 955-968
ISSN:
0092-8674
Subject:
RNA-binding proteins; cytoplasm; dephosphorylation; diffusivity; mathematical models; phosphorylation; protein synthesis; tissues
Abstract:
... Protein concentration gradients encode spatial information across cells and tissues and often depend on spatially localized protein synthesis. Here, we report that a different mechanism underlies the MEX-5 gradient. MEX-5 is an RNA-binding protein that becomes distributed in a cytoplasmic gradient along the anterior-to-posterior axis of the one-cell C. elegans embryo. We demonstrate that the MEX-5 ...
DOI:
10.1016/j.cell.2011.08.012
PubMed:
21925318
PubMed Central:
PMC3201807

15. Regulation of hepatic stem/progenitor phenotype by microenvironment stiffness in hydrogel models of the human liver stem cell niche

Author:
Lozoya, Oswaldo A.; Wauthier, Eliane; Turner, Rachael A.; Barbier, Claire; Prestwich, Glenn D.; Guilak, Farshid; Superfine, Richard; Lubkin, Sharon R.; Reid, Lola M.
Source:
Biomaterials 2011 v.32 no.30 pp. 7389-7402
ISSN:
0142-9612
Subject:
bile ducts; culture media; diffusivity; genes; hepatocytes; humans; hydrocolloids; liver; mechanical properties; models; niches; phenotype; polyploidy; protein synthesis; stem cells
Abstract:
... Human livers have maturational lineages of cells within liver acini, beginning periportally in stem cell niches, the canals of Hering, and ending in polyploid hepatocytes pericentrally and cholangiocytes in bile ducts. Hepatic stem cells (hHpSCs) in vivo are partnered with mesenchymal precursors to endothelia (angioblasts) and stellate cells, and reside in regulated microenvironments, stem cell ni ...
DOI:
10.1016/j.biomaterials.2011.06.042
PubMed:
21788068
PubMed Central:
PMC3157321

16. Single-Molecule Analysis of PIP2;1 Dynamics and Partitioning Reveals Multiple Modes of Arabidopsis Plasma Membrane Aquaporin Regulation

Author:
Li, Xiaojuan; Wang, Xiaohua; Yang, Yong; Li, Ruili; He, Qihua; Fang, Xiaohong; Luu, Doan-Trung; Maurel, Christophe; Lin, Jinxing
Source:
The plant cell 2011 v.23 no.10 pp. 3780-3797
ISSN:
1040-4651
Subject:
Arabidopsis thaliana; aquaporins; clathrin; diffusivity; dispersions; permeability; plasma membrane; salt stress; sodium chloride; spectroscopy
Abstract:
... PIP2;1 is an integral membrane protein that facilitates water transport across plasma membranes. To address the dynamics of Arabidopsis thaliana PIP2;1 at the single-molecule level as well as their role in PIP2;1 regulation, we tracked green fluorescent protein–PIP2;1 molecules by variable-angle evanescent wave microscopy and fluorescence correlation spectroscopy (FCS). Single-particle tracking an ...
DOI:
10.1105/tpc.111.091454
PubMed:
22010034
PubMed Central:
PMC3229149

17. Spatial Distribution and Diffusive Motion of RNA Polymerase in Live Escherichia coli

Author:
Bratton, Benjamin P.; Mooney, Rachel A.; Weisshaar, James C.
Source:
Journal of bacteriology 2011 v.193 no.19 pp. 5138-5146
ISSN:
0021-9193
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; diffusivity; fluorescence; fluorescence microscopy; photobleaching
Abstract:
... By labeling the β' subunit of RNA polymerase (RNAP), we used fluorescence microscopy to study the spatial distribution and diffusive motion of RNAP in live Escherichia coli cells for the first time. With a 40-ms time resolution, the spatial distribution exhibits two or three narrow peaks of 300- to 600-nm full width at half-maximum that maintain their positions within 60 nm over 1 s. The intensit ...
DOI:
10.1128/JB.00198-11
PubMed:
21784927
PubMed Central:
PMC3187386

18. Light-Induced Conformational Changes in Full-Length Arabidopsis thaliana Cryptochrome

Author:
Kondoh, Masato; Shiraishi, Chiaki; Müller, Pavel; Ahmad, Margaret; Hitomi, Kenichi; Getzoff, Elizabeth D.; Terazima, Masahide
Source:
Journal of molecular biology 2011 v.413 no.1 pp. 128-137
ISSN:
0022-2836
Subject:
Arabidopsis thaliana; blue light; cryptochromes; diffusivity; electron transfer; energy; mutation; photoreceptors; protein conformation
Abstract:
... Cryptochromes (CRYs) are widespread flavoproteins with homology to photolyases (PHRs), a class of blue-light-activated DNA repair enzymes. Unlike PHRs, both plant and animal CRYs have a C-terminal domain. This cryptochrome C-terminal (CCT) domain mediates interactions with other proteins, while the PHR-like domain converts light energy into a signal via reduction and radical formation of the flavi ...
DOI:
10.1016/j.jmb.2011.08.031
PubMed:
21875594
PubMed Central:
PMC4451184

19. Inhibition of the transport of HIV in vitro using a pH-responsive synthetic mucin-like polymer system

Author:
Mahalingam, Alamelu; Jay, Julie I.; Langheinrich, Kristofer; Shukair, Shetha; McRaven, Mike D.; Rohan, Lisa C.; Herold, Betsy C.; Hope, Thomas J.; Kiser, Patrick F.
Source:
Biomaterials 2011 v.32 no.33 pp. 8343-8355
ISSN:
0142-9612
Subject:
Human immunodeficiency virus; active ingredients; animal models; crosslinking; diffusivity; drugs; explants; humans; modulus of elasticity; mucins; mucus; pH; polymers; semen; toxicity; virion
Abstract:
... In conjunction with the routine role of delivering the active ingredient, carefully designed drug delivery vehicles can also provide ancillary functions that augment the overall efficacy of the system. Inspired by the ability of the cervicovaginal mucus to impede the movement of HIV virions at acidic pH, we have engineered a pH-responsive synthetic polymer that shows improved barrier properties ov ...
DOI:
10.1016/j.biomaterials.2011.05.001
PubMed:
21875751
PubMed Central:
PMC3183097

20. Effect of β-sheet crystalline content on mass transfer in silk films

Author:
Karve, Kiran A.; Gil, Eun Seok; McCarthy, Stephen P.; Kaplan, David L.
Source:
Journal of membrane science 2011 v.383 no.1-2 pp. 44-49
ISSN:
0376-7388
Subject:
artificial membranes; crystal structure; diffusivity; drugs; fibroins; fluorescein; lysozyme; mass transfer; permeability; silk; silk proteins; vitamin B12
Abstract:
... The material properties of silk are favorable for drug delivery due to the ability to control material structure and morphology under ambient, aqueous processing conditions. Mass transport of compounds with varying physical–chemical characteristics was studied in silk fibroin films with control of β-sheet crystalline content. Two compounds, vitamin B12 and fluorescein isothiocynate (FITC) labeled ...
DOI:
10.1016/j.memsci.2011.08.032
PubMed:
22135474
PubMed Central:
PMC3224987