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At least 613 records · Page 34Linked to original sources

PubMed2006

Macroporous bioactive glass-ceramic scaffolds for tissue engineering.

Highly bioactive scaffolds for tissue engineering were synthesized using a glass belonging to the SiO2-CaO-K2O (SCK) system. The glass SCK was prepared by a traditional melting-quenching route and its bioactivity was assessed by in vitro tests in a simulated body fluid (SBF). The glass was ground and sieved to obtain powders of specific size that were subsequently mixed with polyethylene particles of two different dimensions. The powders were then uniaxially pressed to obtain a crack free green compact that was thermally treated to remove the organic component and to sinter the inorganic phase. The obtained biomaterial was characterised by means of X-ray Diffraction, SEM equipped with EDS, mercury intrusion porosimetry, density measurements, image analysis, mechanical tests and in vitro evaluations. A glass-ceramic macroporous scaffold with a homogenously distributed and highly interconnected porosity was obtained. The amount and size of the introduced porosity could be tailored using various amounts of polyethylene powders of different size.

Biocompatible Materials↗

PubMed1994

Improvements to the quality of MRI cluster analysis.

Cluster analysis techniques are gaining widespread use for segmentation of MRI data, especially for volume measurement and 3-D display purposes. This paper describes four improvements to such techniques: (1) The use of intensity simulations to model cluster plots; (2) Correction of image nonuniformity; (3) Anisotropic smoothing of data; and (4) Automatic isolation of tissues of interest. Simulation of cluster plots allows an informed choice of pulse sequence(s) and acquisition parameters to be made. Correction of image nonuniformity and anisotropic smoothing reduce the spread of signal intensity from a single tissue thus producing significantly more compact clusters, whilst the isolation of tissues of interest prevents overlap of clusters from the tissues of interest with those not under consideration. These techniques may be used to improve the results of cluster analysis or traded off, for example to allow lower signal-to-noise images, shorter repetition time images, or fewer images to be used for segmentation.

Cluster Analysis↗

PubMed1994

Solution structure of a peptide fragment of human alpha-lactalbumin in trifluoroethanol: a model for local structure in the molten globule.

BACKGROUND: At low pH, human alpha-lactalbumin forms a partly folded molten globule state that contains a non-native clustering of the side chains of Tyr103, Trp104 and His107. In order to understand the conformation of this region of the protein in the molten globule state, we investigated the structure of a peptide corresponding to residues 101-110 of human alpha-lactalbumin in trifluoroethanol. RESULTS: We determined the structure of the 101-110 peptide from an NMR data set of 145 nuclear Overhauser effects and nine 3JHN alpha coupling constants, using an ensemble calculation approach to take into account the possibilities of conformational averaging of the data. The backbone of residues 3-10 in the peptide adopts a series of turns, that involving residues 5-8 being the best defined, while the side chains of residues 1, 3, 4, 5, 6 and 7 form a hydrophobic cluster. CONCLUSIONS: The peptide conformation differs from that previously determined for residues 101-110 in crystal structures of native alpha-lactalbumin determined at both high and low pH, particularly in the relative orientations of the side chains. The series of turns seen in the peptide could, however, be related to the alpha-helical structure seen for residues 104-111 in crystals at high pH, and may be important in the molten globule state for bringing the peptide chain into a compact conformation where favourable interactions between the side chains can occur.

Amino Acid Sequence↗

PubMed2000

Quantification and macroscopic modeling of the nonlinear viscoelastic behavior of strained gels with varying fibrin concentrations.

The mechanical properties of fibrin gels under uniaxial strains have been analyzed for low fibrin concentrations using a free-floating gel device. We were able to quantify the viscous and elastic moduli of gels with fibrin concentration ranging from 0.5 to 3 mg/ml, reporting significant differences of biogels moduli and dynamical response according to fibrin concentration. Furthermore, considering sequences of successively imposed step strains has revealed the strain-hardening properties of fibrin gels for strain amplitude below 5%. This nonlinear viscoelastic behavior of the gels has been precisely analyzed through numerical simulations of the overall gel response to the strain steps sequences. Phenomenological power laws relating the instantaneous and relaxed elasticity moduli to fibrin concentration have been validated, with concentration exponent in the order of 1.2 and 1.0, respectively. This continuous description of strain-dependent mechanical moduli was then used to simulate the biogel behavior when continuously time-varying strains are applied. We discuss how this experimental setup and associated macroscopic modeling of fibrin gels enable a further quantification of cell traction forces and mechanotransduction processes induced by biogel compaction or stretching.

Biomedical Engineering↗

PubMed2003

Simulating the hydrodynamic conditions in the United States Pharmacopeia paddle dissolution apparatus.

The objective of this work was to examine the feasibility of developing a high-performance computing software system to simulate the United States Pharmacopeia (USP) dissolution apparatus 2 (paddle apparatus) and thus aid in characterizing the fluid hydrodynamics in the method. The USP apparatus was modeled using the hydrodynamic package Fluent. The Gambit program was used to create a "wireframe" of the apparatus and generate the 3-dimensional grids for the computational fluid dynamics solver. The Fluent solver was run on an IBM RS/6000 SP distributed memory parallel processor system, using 8 processors. Configurations with and without a tablet present were developed and examined. Simulations for a liquid-filled vessel at a paddle speed of 50 rpm were generated. Large variations in fluid velocity magnitudes with position in the vessel were evident. Fluid velocity predictions were in good agreement with those previously published, using laser Doppler velocity measurements. A low-velocity domain was evident directly below the center of the rotating paddle. The model was extended to simulate the impact of the presence of a cylindrical tablet in the base of the dissolution vessel. The presence of the tablet complicated the local fluid flow, and large fluid shear rates were evident at the base of the compact. Fluid shear rates varied depending on the tablet surface and the location on the surface and were consistent with the reported asymmetrical dissolution of model tablets. The approach has the potential to explain the variable dissolution results reported and to aid in the design/prediction of optimal dissolution conditions for in vitro--in vivo correlations.

Chemistry, Pharmaceutical↗

PubMed1994

Deep heating using a movable applicator phased array hyperthermia system. A preclinical feasibility study.

A preclinical evaluation of the 'movable applicator phased array hyperthermia system' was performed. The system employs four coherent applicators enabling power steering by amplitude and phase control. This concept has already been used in other systems, but the combination with a compact applicator design and easy movement of applicators has not been used before. The paper contains a description of the system and a verification of its performance using quality assurance tests with scanned E-field measurements. A clinical simulation was performed in pig to address the clinical feasibility of the system. The target volume was the left kidney. Two heating sessions, with and without occluded blood-flow to the kidney, were performed. In the low-flow experiments a temperature of 48 degrees C and 46 degrees C was obtained in the upper and lower pole of the kidney respectively. For the high-flow experiment the temperature in the upper pole was 48 degrees C.

Animals↗

PubMed2006

Water mediated attraction between repulsive ions: a cluster-based simulation approach.

Could two like ions be attractive to each other in the presence of water? To address this question and to further interrogate the intriguing solvent effects at a molecular level on multiply charged species, a "bottom-up" simulation approach was formulated, from which the inter-ionic potential of mean force and other properties were monitored closely with the gradual addition of the water molecules. This approach was first tested on a commonly studied ion pair (namely, Na+ and Cl-), where excellent agreement with the published bulk-phase data was found. Further application of this approach to the like-ion pair indicated that an attractive interaction between two anions or two cations can be induced by the addition of an appropriate number of water molecules. This result corroborates a recent experimental report of an intriguing folding of a dianionic polymer into a more compact structure with the addition of water molecules in gas phase as well as previous theoretical findings of possible attraction between like-ion pairs in bulk aqueous phases.

Chlorides↗

PubMed1994

Probing the microenvironments of tryptophan residues in the monomeric crystallins of the bovine lens.

Tryptophan microenvironments have been examined in bovine beta s-, gamma II-, gamma IIIa-, gamma IIIb-, gamma IVa- and gamma IVb-crystallins by fluorescence methods. The proteins could be divided into two groups on the basis of the accessibilities of their tryptophan residues. The first group, comprising beta s, gamma II and gamma IIIb, appeared to have a compact structure with none of the tryptophans accessible to KI and only moderately so to acrylamide. By contrast in gamma IIIa, gamma IVa and gamma Vb, all tryptophans were readily accessible to acrylamide and 70% of the fluorescence could be quenched with KI. Spectral analysis, before and after quenching, time-resolved spectroscopy and simulations of the quenching curves suggested that gamma IIIa, gamma IVa and gamma IVb contain two classes of tryptophan residues. One class (tau 0 = 0.52 ns, fa = 0.3, lambda max = 324 nm) which was completely inaccessible to KI and relatively inaccessible to acrylamide (Ksv = 0.25 M-1), was assigned to the topologically equivalent residues in positions 42 and 131. The other class (tau 0 = 2.1-3.4 ns, fa = 0.7, lambda max = 330 nm) was accessible to both quenchers (Ksv = 5.00-5.15 M-1 and 2.47-2.60 M-1, for acrylamide and KI, respectively) and corresponded to the tryptophan residues in positions 68 and 157. The same classes may be present in the other low molecular weight proteins (tau 0 = 0.47-0.55 and 1.55-1.74) but the lower emission and low accessibilities to quenchers prevented their distinction and suggested that these proteins had more compact structures.

Acrylamide↗

PubMed2003

Myosin head configuration in relaxed insect flight muscle: x-ray modeled resting cross-bridges in a pre-powerstroke state are poised for actin binding.

Low-angle x-ray diffraction patterns from relaxed insect flight muscle recorded on the BioCAT beamline at the Argonne APS have been modeled to 6.5 nm resolution (R-factor 9.7%, 65 reflections) using the known myosin head atomic coordinates, a hinge between the motor (catalytic) domain and the light chain-binding (neck) region (lever arm), together with a simulated annealing procedure. The best head conformation angles around the hinge gave a head shape that was close to that typical of relaxed M*ADP*Pi heads, a head shape never before demonstrated in intact muscle. The best packing constrained the eight heads per crown within a compact crown shelf projecting at approximately 90 degrees to the filament axis. The two heads of each myosin molecule assume nonequivalent positions, one head projecting outward while the other curves round the thick filament surface to nose against the proximal neck of the projecting head of the neighboring molecule. The projecting heads immediately suggest a possible cross-bridge cycle. The relaxed projecting head, oriented almost as needed for actin attachment, will attach, then release Pi followed by ADP, as the lever arm with a purely axial change in tilt drives approximately 10 nm of actin filament sliding on the way to the nucleotide-free limit of its working stroke. The overall arrangement appears well designed to support precision cycling for the myogenic oscillatory mode of contraction with its enhanced stretch-activation response used in flight by insects equipped with asynchronous fibrillar flight muscles.

Actins↗

PubMedDate not supplied

Comparison between denaturant- and temperature-induced unfolding pathways of protein: a lattice Monte Carlo simulation.

Denaturant-induced unfolding of protein is simulated by using a Monte Carlo simulation with a lattice model for protein and denaturant. Following the binding theory for denaturant-induced unfolding, the denaturant molecules are modeled to interact with protein by nearest-neighbor interactions. By analyzing the conformational states on the unfolding pathway of protein, the denaturant-induced unfolding pathway is compared with the temperature-induced unfolding pathway under the same condition; that is, the free energies of unfolding under two different pathways are equal. The two unfoldings show markedly different conformational distributions in unfolded states. From the calculation of the free energy of protein as a function of the number fraction (Q0) of native contacts relative to the total number of contacts, it is found that the free energy of the largely unfolded state corresponding to low Q0 (0.1 < Q0 < 0.5) under temperature-induced unfolding is lower than that under denaturant-induced unfolding, whereas the free energy of the unfolded state close to the native state (Q0 > 0.5) is lower in denaturant-induced unfolding than in temperature-induced unfolding. A comparison of two unfolding pathways reveals that the denaturant-induced unfolding shows a wider conformational distribution than the temperature-induced unfolding, while the temperature-induced unfolding shows a more compact unfolded state than the denaturant-induced unfolding especially in the low Q0 region (0.1 < Q0 < 0.5).

Algorithms↗

PubMed2002

Scaling exponents of rough surfaces generated by the Domany-Kinzel cellular automaton.

The critical behavior at the frozen-active transition in the Domany-Kinzel stochastic cellular automaton is studied via a surface growth process in (1+1) dimensions. At criticality, this process presents a kinetic roughening transition; we measure the critical exponents in simulations. Two update schemes are considered: in the symmetric scheme, the growth surfaces belong to the directed percolation (DP) universality class, except at one terminal point. At this point, the phase transition is discontinuous and the surfaces belong to the compact directed percolation universality class. The relabeling of space-time points in the nonsymmetric scheme alters significantly the surface growth, changing the values of the critical exponents. The critical behavior of rough surfaces at the nonchaotic-chaotic transition is also studied using the damage spreading technique; the exponents confirm DP values for the symmetric scheme.

Journal Article↗

PubMed2001

Ultrafast folding of WW domains without structured aromatic clusters in the denatured state.

Ultrafast-folding proteins are important for combining experiment and simulation to give complete descriptions of folding pathways. The WW domain family comprises small proteins with a three-stranded antiparallel beta-sheet topology. Previous studies on the 57-residue YAP 65 WW domain indicate the presence of residual structure in the chemically denatured state. Here we analyze three minimal core WW domains of 38-44 residues. There was little spectroscopic or thermodynamic evidence for residual structure in either their chemically or thermally denatured states. Folding and unfolding kinetics, studied by using rapid temperature-jump and continuous-flow techniques, show that each domain folds and unfolds very rapidly in a two-state transition through a highly compact transition state. Folding half-times were as short as 17 micros at 25 degrees C, within an order of magnitude of the predicted maximal rate of loop formation. The small size and topological simplicity of these domains, in conjunction with their very rapid two-state folding, may allow us to reduce the difference in time scale between experiment and theoretical simulation.

Amino Acid Sequence↗

PubMed1992

Molecular dynamics simulations of a monofucosylated biantennary glycan of the N-acetyllactosamine type: the human lactotransferrin glycan.

Molecular dynamics simulations were carried out to explore the conformational flexibility of the antennae of N-linked glycans. They were performed over 200 ps in vacuo on the complete disialylated monofucosylated biantennary glycan of the N-acetyllactosaminic type. Starting from a bird-conformation, the 3-D-structure evolved through 9 successive transitional states to a new, compact and energetically favorable conformation which had never been previously described. In this conformation, both antennae are organized in two coplanar loops rolled in a contrary direction and oriented perpendicularly to the plane of the di-N-acetyl chitobiose residue leading to a 'lobster conformation'. All the glycosidic linkages of the disialylated monofucosylated biantennary glycan, except the Fuc(alpha 1-6)GlcNAc(beta 1-), were modified by a phase transition. Particularly, the Man(beta 1-4) GlcNAc(beta 1-) linkage, which was previously described by NMR and X-ray diffraction as a rigid one, was involved in numerous conformational changes during 83 ps, even before the first transition phase. The freedom of mobility of the torsional angles of the Man(alpha 1-6)Man(beta 1-) linkage was limited, under these simulation conditions, to the angle psi which took three values: 30 degrees, 90 degrees and 180 degrees. Moreover, from 150 ps up to the end of the simulation, the value of the torsional angle omega of the NeuAc(alpha 2-6)Gal(beta 1-) linkage of the alpha-1,6-antenna continuously swung between 60 degrees and -60 degrees. Finally, we observed that the values of the torsional angles of the three linkages: NeuAc(alpha 2-6)Gal(beta 1-), Gal(beta 1-4)GlcNAc(beta 1-) and GlcNAc(beta 1-2)Man(beta 1-) of each of the two antennae were different, demonstrating their asymmetric conformation.

Amino Sugars↗

PubMed2003

Improved prediction-based ovarian follicle detection from a sequence of ultrasound images.

A new algorithm is presented for ovarian follicle recognition from a sequence of ultrasound images. The basic version of the prediction-based algorithm is upgraded by means of two improvements. The negative influence brought by the gross measurement errors is suppressed, and the locality of the treated process is considered. The basis for both improvements is the Kalman filter. The proposed algorithm is a combination of three mutually dependent Kalman filters: a global one whose parameters are then modified by two additional ones, firstly detecting the gross measurement errors and secondly, regarding the recognised contour of the object. The obtained results show that the follicles recognised using the final prediction algorithm are about 2% more compact and about 6% more accurate, on average, when compared to the values obtained using the basic prediction-based algorithm.

Algorithms↗

PubMed1996

Molecular dynamics simulations of synthetic peptide folding.

Because the time scale of protein folding is much greater than that of the widely used simulations of native structures, a detailed report of molecular dynamics simulations of folding has not been available. In this study, we included the average solvent effect in the potential functions to simplify the calculation of the solvent effect and carried out long molecular dynamics simulations of the alanine-based synthetic peptides at 274 K. From either an extended or a randomly generated conformation, the simulations approached a helix-coil equilibrium in about 3 ns. The multiple minima problem did not prevent helix folding. The calculated helical ratio of Ac-AAQ-AAAAQAAAAQAAY-NH2 was 47%, in good agreement with the circular dichroism measurement (about 50%). A helical segment with frayed ends was the most stable conformation, but the hydrophobic interaction favored the compact, distorted helix-turn-helix conformations. The transition between the two types of conformations occurred in a much larger time scale than helix propagation. The transient hydrogen bonds between the glutamine side chain and the backbone carbonyl group could reduce the free energy barrier of helix folding and unfolding. The substitution of a single alanine residue in the middle of the peptide with valine or glycine decreased the average helical ratio significantly, in agreement with experimental observations.

Alanine↗

PubMed2005

Fast gas-phase hydrogen/deuterium exchange observed for a DNA G-quadruplex.

The gas-phase hydrogen/deuterium (H/D) exchange kinetics of DNA G-quadruplexes has been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The quadruplex [(TGGGGT)4 . 3NH4+] undergoes very fast H/D exchange, in both the positive and in the negative ion modes, compared to DNA duplexes and other quadruplexes tested, and compared to the corresponding single-stranded TGGGGT. Substitution of NH4+ for K+ did not alter this fast H/D exchange, indicating that the hydrogens of the ammonium ions are not those exchanged. However, stripping of the interior cations of the quadruplex by source collision-induced dissociation (CID) in the positive ion mode showed that the presence of the inner cations is essential for the fast exchange to be possible. Molecular dynamics simulations show that the G-quadruplex is very rigid in the gas phase with NH4+ ions inside the tetrads. We suggest that the fast H/D exchange is favored by this rigid quadruplex conformation. This example illustrates that the concept that compact DNA structures exchange H for D slower than unfolded ones is a misconception.

DNA↗

PubMed1996

Accurate velocity mapping with FAcE.

Spin dislocation between the slice selection, phase encoding, and frequency encoding is a source of image distortions. Two strategies can be pursued to improve the appearance of moving spins in an image. Either the sequence is made equally sensitive to velocity-dependent dislocation artifacts for all spatial directions or the sensitivity is reduced with a shorter echo time. The first approach increases the dislocation for the phase-encoding direction and is therefore not useful if velocity maps with minimal distortion are the goal. FAcE (FID acquired echoes) is a sequence with separate sampling of the left and right k-space half-planes that allows for very short echo times. It was applied for velocity mapping of flow in the slice select direction. Special attention was paid to a compact design of the velocity-encoding select gradient to achieve short echo times even with high velocity sensitivity. Artifacts introduced by in-plane motion were studied for FAcE and conventional gradient-echo sequences, both in phantom experiments and simulation. FAcE allows for very short echo times with inherent motion compensation of the frequency-encoding gradient. Thus, both motion-related dislocation artifacts and signal voids due to coherence loss in regions with irregular flow are minimal.

Artifacts↗

PubMed2006

Electron tunneling chains of mitochondria.

The single, simple concept that natural selection adjusts distances between redox cofactors goes a long way towards encompassing natural electron transfer protein design. Distances are short or long as required to direct or insulate promiscuously tunneling single electrons. Along a chain, distances are usually 14 A or less. Shorter distances are needed to allow climbing of added energetic barriers at paired-electron catalytic centers in which substrate and the required number of cofactors form a compact cluster. When there is a short-circuit danger, distances between shorting centers are relatively long. Distances much longer than 14 A will support only very slow electron tunneling, but could act as high impedance signals useful in regulation. Tunneling simulations of the respiratory complexes provide clear illustrations of this simple engineering.

Animals↗