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At least 1,729 records · Page 96Linked to original sources
PubMed2006

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

Reconstructing the evolutionary history of protein sequences will provide a better understanding of divergence mechanisms of protein superfamilies and their functions. Long-term protein evolution often includes dynamic changes such as insertion, deletion, and domain shuffling. Such dynamic changes make reconstructing protein sequence evolution difficult and affect the accuracy of molecular evolutionary methods, such as multiple alignments and phylogenetic methods. Unfortunately, currently available simulation methods are not sufficiently flexible and do not allow biologically realistic dynamic protein sequence evolution. We introduce a new method, indel-Seq-Gen (iSG), that can simulate realistic evolutionary processes of protein sequences with insertions and deletions (indels). Unlike other simulation methods, iSG allows the user to simulate multiple subsequences according to different evolutionary parameters, which is necessary for generating realistic protein families with multiple domains. iSG tracks all evolutionary events including indels and outputs the "true" multiple alignment of the simulated sequences. iSG can also generate a larger sequence space by allowing the use of multiple related root sequences. With all these functions, iSG can be used to test the accuracy of, for example, multiple alignment methods, phylogenetic methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein family classification methods. We empirically evaluated the performance of iSG against currently available methods by simulating the evolution of the G protein-coupled receptor and lipocalin protein families. We examined their true multiple alignments, reconstruction of the transmembrane regions and beta-strands, and the results of similarity search against a protein database using the simulated sequences. We also presented an example of using iSG for examining how phylogenetic reconstruction is affected by high indel rates.

Carrier Proteins↗
PubMed2003

Decoding of complex isothermal chromatograms recovered from space missions. Identification of molecular structure.

A chemometric approach, based on the study of the autocovariance function, is described to study isothermal GC chromatograms of multicomponent mixtures: isothermal GC analysis is the method of choice in space missions since it is, to date, the only method compatible with flight constraints. Isothermal GC chromatograms look inhomogeneous and disordered with peak density decreasing at higher retention times: a time axis transformation is proposed to make retention an homogeneous process so that CH2 addition in terms of an homologous series yields a constant retention increment. The time axis is transformed into a new scale based on the retention times of n-alkanes, as they are the basis of the universal Kovats indices procedure. The order introduced into the chromatogram by retention time linearization can be simply singled out by the experimental autocorrelation function (EACF) plot: if constant inter-distances are repeated in different regions of the chromatogram, well-shaped peaks are evident in the EACF plot. By comparison, with a standard mixture it is possible to identify peaks diagnostic of specific molecular structures: study of the EACF plot provides information on sample chemical composition. The procedure was applied to standard mixtures containing compounds representative of the planetary atmospheres that will be investigated in the near future: in particular, those related to Titan's atmosphere (Cassini-Huygens mission) and cometary's nucleus (Rosetta mission). The employed experimental conditions simulated those applied to GC instruments installed on space probes and landers in space missions. The method was applied to two specific investigations related to space research, i.e., a comparison of retention selectivity of different GC columns and identification of the chemical composition of an unknown mixture.

Chromatography, Gas↗
PubMedDate not supplied

Vestibularly evoked potentials (VESTEPs) of the horizontal semicircular canals under different body positions in space.

We recorded vestibularly evoked potentials (VESTEPs) using natural vestibular stimuli simulating the form of a normal head movement ("raised cosine"). Its smooth course was designed to minimize all possible sources of artifacts of mechanical, electrical, and physiological origin. This motion profile was applied to subjects (Ss) sitting upright, thus stimulating the horizontal semicircular canals alone, as well as when they were tilted in different positions in steps of 30 degrees about the interaural y-axis, which had the effect of modulating the otolithic contribution to the horizontal VESTEP. The transient bell-shaped VESTEP recorded in the upright sitting S was more and more superimposed or replaced by a sustained negativity the more the S was tilted toward a horizontal position. Thus, the VESTEP gradually changes from a velocity response in the upright S (canals only) to a position response in the lying S (canals plus otoliths). Differences in the VESTEPs obtained for clockwise (cw) and counterclockwise (ccw) turns in the tilted S were found. The reason for this is not clear at present and requires further experimentation. However, the VESTEPs obtained under conditions involving backward tilts and cw turns corresponded to those obtained with forward tilts and ccw turns. A similar relationship was found for the VESTEPs obtained with backward tilts and ccw turns and those obtained with forward tilts and cw turns. The physiological basis of this is discussed.

Adolescent↗
PubMed2004

Simulations of a membrane-anchored peptide: structure, dynamics, and influence on bilayer properties.

A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at different applied surface tensions by molecular dynamics simulations. The lipid membrane environment influences the conformational space explored by the peptide. The overall secondary structure of the anchored peptide is found to deviate at times from its structure in aqueous solution through reversible conformational transitions. The peptide is, despite the anchor, highly mobile at the membrane surface with the peptide motion along the bilayer normal being integrated into the collective modes of the membrane. Peptide anchoring moderately alters the lateral compressibility of the bilayer by changing the equilibrium area of the membrane. Although membrane anchoring moderately affects the elastic properties of the bilayer, the model peptide studied here exhibits conformational flexibility and our results therefore suggest that peptide acylation is a feasible way to reinforce peptide-membrane interactions whereby, e.g., the lifetime of receptor-ligand interactions can be prolonged.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2000

Accuracy of deadspace free ventilatory measurements for lung function testing in ventilated newborns: a simulation study.

OBJECTIVE: A deadspace free method based on simultaneous ventilatory measurements in the inspiratory and expiratory limb of the ventilator circuit was compared to the conventional endotracheal method where the flow is measured between ETT and Y-Piece. The aim of our study was to find out how the arrangement of this setup affects the measuring accuracy of 1) the ventilatory and 2) the lung mechanical parameters by means of a computer simulation. METHOD: The system consisting of ventilator tubes and lung was described in state space and the flow signals of endotracheal method, of deadspace free method and the pressure at the Y-piece were simulated in the time domain. To investigate the influence of the position of the pneumotachographs (PNTs) in the ventilator circuit on measuring accuracy, the distance d0 of the PNT from the Y-piece was varied between 0 and 900 mm. The respiratory compliance C, resistance R and inertance I were calculated by least square method using the simulated flow and pressure signals of both methods. RESULTS: Compared to the endotracheal method, with increasing d0, the tidal volume measured with the deadspace free method rose linearly, depending on the ratio between the compliance of the ventilator tubes to the respiratory compliance. The differences of C and R for both methods were acceptable (< 10%) if the distance between each PNT and the y-piece didn't exceed 200 mm and the shorter do the higher the measuring accuracy. The inertance could not be measured by this method with satisfactory accuracy if d0 was higher than 100 mm. IN CONCLUSION: The dead space free method can be used for accurate ventilatory measurements during mechanical ventilation. However, for lung mechanic measurements in very low birth weight infants the position of the PNTs must be as short as possible.

Airway Resistance↗
PubMed2002

Improved Monte Carlo sampling in a real space approach to the crystallographic phase problem.

A real space approach has been proposed to solve the x-ray phase problem formulated as a minimization problem. The cost function consists of two parts: one represents the usual crystallographical residual while the other enforces the probability distribution of the invariant phase triplets. Starting from a random real space structure, the atoms are moved one by one to gradually reduce the cost function (simulated annealing). In addition, the atoms are encouragd to preferentially sample the high density regions in space determined by an approximate density map which in turn is updated and modified by averaging and Fourier synthesis. Such a reduction of the configurational space has led to considerable improvement of the algorithm compared to an earlier version. Trial calculations for structures including hexadecaisoleucinomycin (HEXIL) and a collagenlike peptide (PPG) are presented.

Journal Article↗
PubMed1999

Head-out immersion in the non-human primate: a model of cardiovascular deconditioning during microgravity.

BACKGROUND: Orthostatic intolerance is a common complication associated with spaceflight. It has been speculated that this is due to changes in blood volume and alterations in cardiovascular reflexes. The objective of the current study was to develop a model that would allow us to study the cardiovascular system and the regulation of blood volume during short-term microgravity exposure in the primate with the intent of eventually being able to elucidate those factors responsible for the orthostatic intolerance. HYPOTHESIS: Head-out water immersion in the conscious non-human primate simulates the cardiovascular and volume regulatory responses observed in astronauts during exposure to microgravity. METHODS: Four monkeys were chronically instrumented for measuring BP and heart rate and then conditioned to the primate restraint chair. They were then subjected to 72 h of head-out water immersion (two immersions in three monkeys and one immersion in the fourth) in order to simulate the cardiovascular and renal effects of the microgravity environment. RESULTS: During the immersion, there was an increase in arterial BP (ABP) and central venous pressure (CVP) and a reflex decrease in heart rate (HR). Urine flow (UV) increased and water intake decreased, producing a negative water balance. This was not associated with an alteration in food intake. CVP and UV decreased following de-immersion. There was also resetting of the arterial baroreflex control of HR. Significant tachycardia occurred after the immersion that was associated with a decrease in ABP. CONCLUSION: These results are similar to those observed in astronauts during and after spaceflight, suggesting that head-out water immersion of the non-human primate provides a good model for studying cardiovascular and renal adaptations to spaceflight.

Animals↗
PubMed1999

Effects of microgravity on c-fos gene expression in osteoblast-like MC3T3-E1 cells.

The paper summarizes the data on proliferation and gravity-related gene expression of osteoblasts that were obtained from an experiment conducted under simulated and real microgravity conditions. Simulated microgravity conditions obtained in a clinostat depress proliferation of both osteoblast-like MC3T3-E1 and HeLa carcinoma cells. This depression of proliferation occurs in a collagen gel culture in which the flow of culture medium by rotation may be reduced. Interestingly, MC3T3-E1 cells which are probably one of target cells to microgravity are more sensitive than the HeLa cells. Simulated microgravity inhibited the epidermal growth factor (EGF)-induced c-fos gene expression in the MC3T3-El cells. To examine in detail the effect of real microgravity on the EGF signal transduction cascade in osteoblasts, MC3T3-E1 cells were cultured in the Cell Culture Experiment Module of the sounding rocket TR-1A6. The EGF-induced c-fos expression in cells was depressed under short-term microgravity conditions in the sounding rocket, while the phosphorylation of mitogen-activated protein kinase (MAPK) was not affected compared with the controls grown on the ground. These results suggest that an action site of microgravity in the signal transduction pathway may be downstream of MAPK.

Animals↗
PubMed2003

A computational model of direct interstitial infusion of macromolecules into the spinal cord.

Convection-enhanced interstitial infusion can deliver macromolecular drugs to large tissue volumes of the central nervous system. To characterize infusion into the spinal cord, an image-based three-dimensional finite element model of the rat spinal cord was developed. The model incorporated convection and diffusion through white and gray matter, including anisotropic transport due to alignment of white matter tracts. Spatial and temporal distribution of the marker substance albumin within the interstitial space was determined. Consistent with previous experiments, predicted distribution was highly anisotropic. Infusing into the dorsal column, albumin was primarily confined to, white matter with limited penetration into adjacent gray matter. Distribution was determined primarily by the ratio of fiber-parallel to fiber-perpendicular hydraulic conductivity tensor components (k(wm-z)/k(wm-x)), the ratio of transverse white and gray matter hydraulic conductivity (k(wm-x)/k(gm)), and tissue porosity. Fits to previous experimental measures of axial and transverse spread, distribution volume, and protein recovery yielded an optimum k(wm-z)/k(wm-x) of approximately 20 at 0.1 microl/min. k(wm-x)/k(gm) of 100 was sufficient to match experimental transverse distribution data. Best fits to data at 0.1 microl/min were achieved by porosities characteristic of moderate edema (e.g., 0.26). Distribution also varied with catheter placement with more medial placement resulting in greater distribution volumes.

Albumins↗
PubMed1997

In-shoe force measurements from locomotion in simulated zero gravity during parabolic flight.

INTRODUCTION:: No effective countermeasure for space-induced bone loss has yet been identified. It has been hypothesized that an effective exercise regimen would elicit loads on the lower extremity which resemble those encountered on Earth. Although a treadmill has been used on shuttle flights, the loads to which the lower extremity was exposed have not yet been quantified. It is believed that these loads are much less than the loads experienced in 1G. The purpose of this study was to determine the magnitude of lower extremity loading during tethered treadmill exercise in a 0G environment. METHODS:: Data were collected on five subjects (avg. ht. 177.3+/-10.1 cm, avg. mass 78.3+/-18.0 kg) onboard the KC-135, a NASA airplane used to simulate periods of zero gravity through parabolic flight. Subjects ambulated at 4 speeds: a walk (1.56m/sec), fast walk (2.0m/sec) slow jog (2.75m/sec), and jog (3.35m/sec) on the NASA treadmill operated in either a passive or motorized mode. Each subject wore a harness connected to the Subject Load Device (SLD) to tether them to the treadmill. The tension in the SLD was subjectively adjusted for comfort by each subject. Force data were collected at 60 Hz using Pedar insoles. The number of parabolas per subject was variable due to motion sickness and hardware problems. RESULTS:: Analysis of the insole data showed that the average SLD load was only 35.2% BW, although the values ranged from 20.1% to 56.6%. Maximum ground reaction force values increased with increasing speed and were not affected by treadmill mode. The impulse was higher during walking with the treadmill in the passive mode than in the active mode, but this difference diminished with increasing speed. Subjects tended to run on their forefeet, as shown from the extremely small heel impulse values. At higher speeds, heel contact was absent, while forefoot impulse became more pronounced. DISCUSSION:: All force values were lower than those reported from 1G studies, where typical peak ground reaction forces are 1.2xBW and 2.5xBW for walking and running, respectively. At every speed, the ratio of the rearfoot to forefoot impulse was much lower than reported from 1G studies, and this ratio decreased with increasing speed. CONCLUSIONS:: If the exposure to forces similar to those in 1G is a requirement for countermeasures against space-induced osteoporosis, the loads in the SLD must be greatly increased and should be directly measured before exercise.

Journal Article↗
PubMed1999

[Volume kinetics--a new method to control intravenous fluid infusion].

The body's handling of fluid given by intravenous infusion can be analysed and simulated by means of volume kinetics, in which pharmacokinetic principles are applied to dilution-time profiles obtained during fluid therapy. In volume kinetics, the emphasis is on the distribution of fluid to body fluid spaces which accordingly become expanded. These spaces do not always correspond to known anatomical or physiological fluid compartments. The time course of the effect of volume fluid distribution to these spaces may be investigated by means of computer-assisted simulation, or a nomogram based on values for volume kinetic variables obtained from infusion experiments.

Computer Simulation↗
PubMed2003

Comparing zonal and CFD model predictions of isothermal indoor airflows to experimental data.

It is inappropriate to use the assumption of instantaneously well-mixed zones to model airflows and pollutant transport in large indoor spaces. We investigate two approaches for describing the details of airflows in large indoor spaces, for accuracy and suitability for integration with multi-zone infiltration models. One approach, called the zonal method, was developed over the last 15 years to provide an improvement over the well-mixed assumption. The second approach is the use of a computational fluid dynamics simulation using a coarse grid model of the large indoor space. We compare velocity predictions from different formulations of zonal methods and coarse-grid k-epsilon computational fluid dynamics (CFD) models, to measurements, in a 2D mechanically ventilated isothermal room. Our results suggest that, when airflow details are required, coarse-grid CFD is a better-suited method to predict airflows in large indoor spaces coupled with complex multi-zone buildings, than are the zonal methods. Based on the comparison of pressure predictions from different models, we offer guidance regarding the coupling of a model of detailed airflow in large spaces to algebraic multi-zone infiltration models.

Air Movements↗
PubMed2000

Weak beam under convergent beam illumination

The weak beam technique is now used widely for the determination of stacking fault energies, in particular for intermetallic alloys, and the accuracy of the approach is critically dependent upon the reliability of the relationship between the image and the actual position of the dissociated dislocations. Examining as a model case a dislocation dissociated into two Shockley partial dislocations in Cu at 100 kV for orientations ranging through the g(3g) weak beam condition, image simulations are used to explore the accuracy to which the true spacing between the partial dislocations can be determined from the spacing measured on the image as a function of the dislocation character, the foil thickness, the dislocation depth in the foil, the diffraction condition and the beam convergence. It appears that for image simulations and for the given conditions a beam convergence of about 5 mrad allows to greatly improve the accuracy, and that beam convergence must be taken into account quantitatively when deducing the true partial dislocation spacing as it is the principal parameter controlling the precision in this type of measurement.

Journal Article↗
PubMed1995

Measurement of serum isopropanol and the acetone metabolite by proton nuclear magnetic resonance: application to pharmacokinetic evaluation in a simulated overdose model.

The purpose of this investigation was to 1) compare the performance of proton nuclear magnetic resonance spectroscopy to gas chromatography head-space analysis in the measurement of serum isopropanol and its metabolite, acetone, obtained during a simulated overdose, and 2) compare pharmacokinetic parameters obtained using the two analytical techniques. Three healthy volunteers ingested 0.6 mL/kg of 70% isopropanol and blood samples were obtained at baseline, 0.16, 0.33, 0.66, 1.0, 1.5, 2.0, 3.0, 4.0, 6.0, 8.0, 12.0, and 24.0 hours post-ingestion. Resulting sera were analyzed by gas chromatography head-space analysis and proton nuclear magnetic resonance spectroscopy for determination of isopropanol and acetone concentrations. A correlation between concentrations quantitated by gas chromatography head-space analysis versus proton nuclear magnetic resonance spectroscopy was determined using linear regression. Pharmacokinetic disposition parameters were determined from serum concentration-time data and compared using analysis of variance. For isopropanol, the linear regression equation which describes the relationship between gas chromatography head-space analysis and proton nuclear magnetic resonance spectroscopy was y = 1.041x - 2.180 (r2 = 0.995, p < 0.0001); for acetone, y = 1.022x - 0.946 (r2 = 0.984, p < 0.0001). Pharmacokinetic disposition parameters derived from the two analytical methods were comparable. Proton nuclear magnetic resonance spectroscopy can be used to rapidly quantitate serum isopropanol and acetone concentrations in the same sample when gas chromatography head-space analysis is unavailable. Also, proton nuclear magnetic resonance spectroscopy can be used to follow serial serum concentrations during an ingestion for the purpose of pharmacokinetic analysis.

1-Propanol↗
PubMed2006

Bifurcation and singularity analysis of a molecular network for the induction of long-term memory.

Withdrawal reflexes of the mollusk Aplysia exhibit sensitization, a simple form of long-term memory (LTM). Sensitization is due, in part, to long-term facilitation (LTF) of sensorimotor neuron synapses. LTF is induced by the modulatory actions of serotonin (5-HT). Pettigrew et al. developed a computational model of the nonlinear intracellular signaling and gene network that underlies the induction of 5-HT-induced LTF. The model simulated empirical observations that repeated applications of 5-HT induce persistent activation of protein kinase A (PKA) and that this persistent activation requires a suprathreshold exposure of 5-HT. This study extends the analysis of the Pettigrew model by applying bifurcation analysis, singularity theory, and numerical simulation. Using singularity theory, classification diagrams of parameter space were constructed, identifying regions with qualitatively different steady-state behaviors. The graphical representation of these regions illustrates the robustness of these regions to changes in model parameters. Because persistent protein kinase A (PKA) activity correlates with Aplysia LTM, the analysis focuses on a positive feedback loop in the model that tends to maintain PKA activity. In this loop, PKA phosphorylates a transcription factor (TF-1), thereby increasing the expression of an ubiquitin hydrolase (Ap-Uch). Ap-Uch then acts to increase PKA activity, closing the loop. This positive feedback loop manifests multiple, coexisting steady states, or multiplicity, which provides a mechanism for a bistable switch in PKA activity. After the removal of 5-HT, the PKA activity either returns to its basal level (reversible switch) or remains at a high level (irreversible switch). Such an irreversible switch might be a mechanism that contributes to the persistence of LTM. The classification diagrams also identify parameters and processes that might be manipulated, perhaps pharmacologically, to enhance the induction of memory. Rational drug design, to affect complex processes such as memory formation, can benefit from this type of analysis.

Algorithms↗
PubMed2004

Estimation of critical behavior from the density of states in classical statistical models.

We present a simple and efficient approximation scheme which greatly facilitates the extension of Wang-Landau sampling (or similar techniques) in large systems for the estimation of critical behavior. The method, presented in an algorithmic approach, is based on a very simple idea, familiar in statistical mechanics from the notion of thermodynamic equivalence of ensembles and the central limit theorem. It is illustrated that we can predict with high accuracy the critical part of the energy space and by using this restricted part we can extend our simulations to larger systems and improve the accuracy of critical parameters. It is proposed that the extensions of the finite-size critical part of the energy space, determining the specific heat, satisfy a scaling law involving the thermal critical exponent. The method is applied successfully for the estimation of the scaling behavior of specific heat of both square and simple cubic Ising lattices. The proposed scaling law is verified by estimating the thermal critical exponent from the finite-size behavior of the critical part of the energy space. The density of states of the zero-field Ising model on these lattices is obtained via a multirange Wang-Landau sampling.

Journal Article↗
PubMed1997

Weightlessness simulations for cardiovascular and muscle systems: validity of rat models.

Animal models are widely used to evoke responses comparable to those obtained during weightlessness. Two models are reviewed; one examines cardiovascular responses and cephalad fluid shifts in head down tilting (HDT), and the other examines atrophy in load bearing muscles by unloading the hind limbs. Cephalad fluid shifts result in diuresis, natriuresis, and kaliuresis. Reversals are rapid, within one week. Reports of cardiovascular responses are not similar among various laboratories, probably due to variations in protocols. Blood pressures (MAP, SP and DP) and heart rates measured with direct aorta cannulations become elevated as early as one and three days of HDT; recovery occurs within several hours; the response is a transient hypertension. The role of central and peripheral sympathetic nervous activity in flight and suspended rats is examined. Rats show little or no evidence of cardiac deconditioning. Direct blood pressures have not been made in flight rats, precluding direct comparisons with earth side experiments. Muscle atrophy and load bearing (slow twitch fibers) and non-load bearing (fast twitch fibers) muscle responses with hind limb unloading and recovery are compared with flight animal responses. Soleus muscle in response to whole body suspension (WBS), tail suspension (TS) or flight exposure consistently shows significant weight loss. In contrast, the extensor digitorum longus and vastus medialis show less marked responses. More specifically, slow twitch fibers in all these muscles show the greatest loss in mass (e.g. cross sectional areas). The conclusion is that both WBS or TS systems are useful in predicting and comparing changes due to weightless flight.

Animals↗