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PubMed2005

Molecular dynamics simulations of a nucleosome and free DNA.

All atom molecular dynamics simulations (10ns) of a nucleosome and of its 146 basepairs of DNA free in solution have been conducted. DNA helical parameters (Roll, Tilt, Twist, Shift, Slide, Rise) were extracted from each trajectory to compare the conformation, effective force constants, persistence length measures, and fluctuations of nucleosomal DNA to free DNA. The conformation of DNA in the nucleosome, as determined by helical parameters, is found to be largely within the range of thermally accessible values obtained for free DNA. DNA is found to be less flexible on the nucleosome than when free in solution, however such measures are length scale dependent. A method for disassembling and reconstructing the conformation and dynamics of the nucleosome using Fourier analysis is presented. Long length variations in the conformation of nucleosomal DNA are identified other than those associated with helix repeat. These variations are required to create a proposed tetrasome conformation or to qualitatively reconstruct the 1.75 turns of the nucleosome's superhelix. Reconstruction of free DNA using selected long wavelength variations in conformation can produce either a left-handed or a right-handed superhelix. The long wavelength variations suggest 146 basepairs is a natural length of DNA to wrap around the histone core.

Base Pairing↗
PubMed2006

A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: Contribution of conformational flexibility to inhibitory activity.

In this study, we investigated by linear regression model the SAR data of the 15 HIV-1 protease inhibitors possessing structurally diverse scaffolds. First, a regression model was developed only using the enzyme-inhibitor interaction energy as a term of the model, but did not provide a good correlation with the inhibitory activity (R2 = 0.580 and Q2 = 0.500). Then, we focused on the conformational flexibility of the inhibitors which may represent the diversity of the inhibitors, and added two conformational parameters into the model, respectively: the number of rotatable bonds of ligands (deltaSrot) and the distortion energy of ligands (deltaElig). The regression model by adding deltaElig successfully improved the quality of the model (R2 = 0.771 and Q2 = 0.713) while the model with deltaSrot was unsuccessful. The prediction for a training inhibitor by the deltaElig model also showed good agreement with experimental activity. These results suggest that the conformational flexibility of HIV-1 protease inhibitors directly contributes to the enzyme inhibition.

Aspartic Acid↗
PubMed2004

Increased shoe bending stiffness increases sprint performance.

The purposes of this investigation were to determine if increasing the bending stiffness of sprint shoes increases sprinting performance and to determine whether simple anthropometric factors can be used to predict shoe bending stiffness for optimal performance. Thirty-four athletes were tested using four different shoe conditions--a standard condition consisting of their currently used footwear and three conditions where the bending stiffness was increased systematically. The sprinters performed maximal effort 40 m sprints and their sprint times were recorded from 20 to 40 m. On average, increasing the shoe bending stiffness increased sprint performance. The stiffness each athlete required for his or her maximal performance was subject specific but was not related to subject mass, height, shoe size or skill level. It is speculated that individual differences in the force-length and force-velocity relationships of the calf muscles may influence the appropriate shoe stiffness for each athlete to obtain their maximal performance.

Anthropometry↗
PubMed2004

The human cervical spine in tension: effects of frame and fixation compliance on structural responses.

There is little data available on the responses of the human cervical spine to tensile loading. Such tests are mechanistically and technically challenging due to the variety of end conditions that need to be imposed and the difficulty of strong specimen fixation. As a result, spine specimens need to be tested using fairly complex, and potentially compliant, apparati in order to fully characterize the mechanical responses of each specimen. This, combined with the relatively high stiffness of human spine specimens, can result in errors in stiffness calculations. In this study, 18 specimen preparations were tested in tension. Tests were performed on whole cervical spines and on spine segments. On average, the linear stiffness of the segment preparations was 257 N/mm, and the stiffness of the whole cervical spine was 48 N/mm. The test frame was found to have a stiffness of 933 N/mm. Assembling a whole spine from a series combination of eight segments with a stiffness of 257 N/mm results in an estimated whole spine stiffness of 32.1 N/mm (32% error). The segment stiffnesses were corrected by assuming that the segment preparation stiffness is a series combination of the stiffnesses of the segment and the frame. This resulted in an average corrected segment stiffness of 356 N/mm. Taking the frame compliance into account, the whole spine stiffness is 51 N/mm. A series combination of eight segments using the corrected stiffnesses results in an estimated whole spine stiffness of 45.0 N/mm (12% error). We report both linear and nonlinear stiffness models for male spines and conclude that the compliance of the frame and the fixation must be quantified in all tension studies of spinal segments. Further, reported stiffness should be adjusted to account for frame and fixation compliance.

Aged↗
PubMed2005

Intervertebral neck injury criterion for simulated frontal impacts.

OBJECTIVE: The Intervertebral Neck Injury Criterion (IV-NIC) is based on the hypothesis that dynamic intervertebral motion beyond physiological limits may injure soft tissues. In contrast, the Neck Injury Criterion (NIC) hypothesizes that sudden change in spinal fluid pressure may cause neural injuries. The goals of this study, using the biofidelic whole human cervical spine model with muscle force replication, were to determine the IV-NIC injury threshold due to frontal impact at each intervertebral level, and to compare the IV-NIC and NIC in determining injury. METHODS: Using a bench-top apparatus, frontal impacts were simulated at 4, 6, 8, and 10 g horizontal accelerations of the T1 vertebra. Pre- and post-trauma flexibility testing measured the soft tissue injury; that is, a significant increase (p < 0.05) in neutral zone or range of motion at any intervertebral level, above the corresponding physiological limit. RESULTS: Results indicated that the soft tissue injury occurred due to flexion mode of injury and its threshold was 8 g. The average IV-NIC injury threshold (95% confidence interval) was 2.0 (1.2-2.8) at C4-C5 and 2.3 (1.6-3.0) at C6-C7, while the average NIC injury threshold was 18.4 (17.9-19.0) m(2)/s(2). The NIC injury threshold was reached significantly earlier than all the IV-NIC injury thresholds, demonstrating that the NIC may be unable to predict facet and soft tissue injury caused by non-physiologic inververtebral rotation. CONCLUSIONS: Present results suggest that IV-NIC is an effective tool for determining soft tissue neck injuries by identifying the intervertebral level, mode, time, and severity of injury.

Acceleration↗
PubMedDate not supplied

Recreational sports participation is associated with enhanced physical fitness in children.

The purpose of this study was to examine the association between seasonal participation in recreational sports and its influence on physical fitness measures in children. A total of 44 children (20 boys and 24 girls) all in the fifth grade (11.2 +/- 0.3 yr) were tested for flexibility, upper body strength, upper body power, and lower body power. Activity questionnaires examined seasonal participation rates in recreational sports. Spearman rank correlations showed significant correlations between sport participation rates and performance on selected physical fitness tests (p range between 0.34 and 0.55). Subjects participating in recreational sport programs throughout the year (fall, winter, and spring) performed significantly better in tests of upper body strength, upper body power, and lower body power than subjects who did not participate in any sport or subjects who participated in only one sport. These findings suggest that regular participation in recreational sports throughout the year may be associated with higher levels of muscular strength and anaerobic power in children.

Anaerobic Threshold↗
PubMed2003

Pain, trunk muscle strength, spine mobility and disability following lumbar disc surgery.

OBJECTIVE: To study associations between pain, trunk muscle strength, flexibility and disability in patients with lumbar disc herniation 2 months after surgery. DESIGN: Clinical cross-sectional survey. PARTICIPANTS: 172 operated lumbar disc herniation patients. METHODS: Back and leg pain on Visual Analogue Scale, Oswestry Disability Index and Brief Depression Scale were applied to assess the subjectively perceived outcome. Isometric and dynamic strength of trunk muscles and mobility of the lumbar spine were measured to mirror physical impairment. RESULTS: Two months after the operation median leg pain had decreased by 87% and back pain by 81%, respectively. However, moderate or severe leg pain was still reported by 25% and back pain by 20% of the patients. Approximately 30% of the patients perceived moderate or severe disability measured by the Oswestry index. Decreased muscle strength and spine mobility caused functional disability, especially in older patients and patients with postoperative pain. Furthermore, the ratio of trunk extension/flexion strength had changed in favour of the flexion muscles, being 0.98. Greater age and depression were associated with poorer postoperative recovery. CONCLUSION: Pain, decreased trunk muscle strength and decreased mobility still remained in a considerable proportion of patients with lumbar disc herniation 2 months after surgery. Early identification of those patients with restrictions is essential in order to commence rehabilitation.

Adolescent↗
PubMed2001

Sorption of parabens by flexible tubings.

Flexible tubings are extensively used in pharmaceuticals, food industry, and in hospitals. This study was undertaken to compare various flexible tubings to determine their sorption characteristics, using methyl and propyl parabens. After 24 h, some tubings showed 100% sorption of propylparaben and over 40% for methylparaben. Significant losses were observed within a few hours using several tubings. For methylparaben, the losses were in the following decreasing order of sorption: Tygon, Clearflo, silicone, Nylotube, and Newtex. For propylparaben, the losses were in the following order: Tygon, Clearflo, silicone, Newtex, and Nylotube. Teflon, Zelite, and Vitube showed little to no losses of methyl and propylparaben over 120 h of study. The silicone tubing, refilled after 120 h with fresh methylparaben or propylparaben solutions, again showed significant losses within a few hours. The tubings show slow desorption when filled with the buffer vehicle. For Silastic tubing, increase in temperature from 25 to 40 degrees C, increase in pH from 3.5 to 6.5, tubing lot to lot variation, or curing with peroxide or platinum had little or no effect on paraben sorption. As expected, the sorption of parabens increased with increasing surface area of Silastic tubing. Results provided can be used to select the best tubings and to minimize paraben losses during production and filling of liquid pharmaceuticals andfood products containing these antimicrobial preservatives.

Adsorption↗
PubMed1995

Rigidity of microtubules is increased by stabilizing agents.

Microtubules are rigid polymers that contribute to the static mechanical properties of cells. Because microtubules are dynamic structures whose polymerization is regulated during changes in cell shape, we have asked whether the mechanical properties of microtubules might also be modulated. We measured the flexural rigidity, or bending stiffness, of individual microtubules under a number of different conditions that affect the stability of microtubules against depolymerization. The flexural rigidity of microtubules polymerized with the slowly hydrolyzable nucleotide analogue guanylyl-(alpha, beta)-methylene-diphosphonate was 62 +/- 9 x 10(-24) Nm2 (weighted mean +/- SEM); that of microtubules stabilized with tau protein was 34 +/- 3 x 10(-24) Nm2; and that of microtubules stabilized with the antimitotic drug taxol was 32 +/- 2 x 10(-24) Nm2. For comparison, microtubules that were capped to prevent depolymerization, but were not otherwise stabilized, had a flexural rigidity of 26 +/- 2 x 10(-24) Nm2. Decreasing the temperature from 37 degrees C to approximately 25 degrees C, a condition that makes microtubules less stable, decreased the stiffness of taxol-stabilized microtubules by one-third. We thus find that the more stable a microtubule, the higher its flexural rigidity. This raises the possibility that microtubule rigidity may be regulated in vivo. In addition, the high rigidity of an unstabilized, GDP-containing microtubule suggests that a large amount of energy could be stored as mechanical strain energy in the protein lattice for subsequent force generation during microtubule depolymerization.

Animals↗
PubMed2001

An atomic model of actin filaments cross-linked by fimbrin and its implications for bundle assembly and function.

Actin bundles have profound effects on cellular shape, division, adhesion, motility, and signaling. Fimbrin belongs to a large family of actin-bundling proteins and is involved in the formation of tightly ordered cross-linked bundles in the brush border microvilli and in the stereocilia of inner ear hair cells. Polymorphism in these three-dimensional (3D) bundles has prevented the detailed structural characterization required for in-depth understanding of their morphogenesis and function. Here, we describe the structural characterization of two-dimensional arrays of actin cross-linked with human T-fimbrin. Structural information obtained by electron microscopy, x-ray crystallography, and homology modeling allowed us to build the first molecular model for the complete actin-fimbrin cross-link. The restriction of the arrays to two dimensions allowed us to deduce the spatial relationship between the components, the mode of fimbrin cross-linking, and the flexibility within the cross-link. The atomic model of the fimbrin cross-link, the cross-linking rules deduced from the arrays, and the hexagonal packing of actin bundles in situ were all combined to generate an atomic model for 3D actin-fimbrin bundles. Furthermore, the assembly of the actin-fimbrin arrays suggests coupling between actin polymerization, fimbrin binding, and crossbridge formation, presumably achieved by a feedback between conformational changes and changes in affinity.

Actin Cytoskeleton↗
PubMed2005

Counting out to the flexibility of molecules.

We outline the mathematical models, and the related counting algorithms, that are the basis for fast computations to predict biomolecular flexibility and rigidity. Within these mathematical models, we describe the snap-shot flexibility (instantaneous motions) of biomolecules, extracted from a single snap-shot of the molecule and the connection to larger finite motions. We illustrate the results and techniques with direct analysis of simple secondary structures. Understanding these basic ideas clarifies both the limits and the power of the algorithms, as well as the prospects for extensions and refinements of these algorithms.

Algorithms↗
PubMed2001

Ureteral access for upper urinary tract disease: the access sheath.

Ureteral access with the flexible ureteroscope remains a challenge for the urologist. The routine use of a newly developed, site-specific ureteral access sheath facilitates entry into the ureter for fragmentation and basket extraction of ureteral and renal calculi. The step-by-step technique of ureteral access with the Access Sheath is described.

Equipment Design↗
PubMed2001

Flexible cystoscopy: is the volume and content of the urethral gel critical?

PURPOSE: To determine whether volume (10 or 20mL) or the presence of 2% lidocaine (lignocaine) in the gel used for urethral lubrication alters the discomfort felt during flexible cystoscopy. PATIENTS AND METHODS: A randomized double-blind trial was performed in men attending for flexible cystoscopy. Patients were assigned to one of four groups: 10 mL of gel with or without lidocaine and 20 mL with or without lidocaine. Gel was retained for 10 minutes prior to cystoscopy. Pain felt during both the instillation of the gel and the cystoscopy itself was evaluated using a visual analog scale (0-10). RESULTS: Interim analysis after 147 patients had been recruited revealed a significant difference between the groups in terms of the pain felt on instillation of the gel, leading to an early termination of the trial. There was a significant reduction in pain on cystoscopy in patients receiving 20 mL of gel if this contained lidocaine. CONCLUSION: The least pain on cystoscopy occurred in patients receiving 20 mL of gel containing lidocaine.

Aged↗
PubMed1997

Flexible endoscope deflectability: changes using a variety of working instruments and laser fibers.

To measure the effects of different working instruments and holmium laser fibers on the deflectability in a variety of actively deflectable flexible endoscopes, a benchtop study was performed. The endoscopes studied were the Storz 7.5 flexible ureteroscope, the AUR-7 and AUR-9 flexible ureteroscopes (Circon-ACMI), a prototype Mitsubishi flexible ureteroscope (Mitsubishi Optics, Inc.), the ACN flexible cystoscope (Circon-ACMI), and the Storz flexible cystoscope. Working instruments included 1.6F (Wolf) and 1.9F (Microvasive) electrohydraulic lithotripsy (EHL) probes, 1.9F two-prong graspers and Bagley baskets, 2.4F Segura and helical baskets (Microvasive), 3.0F Segura basket, and 200- and 365-micron holmium laser fibers (Xintec). In ureteroscopes, the effect of 1.6F and 1.9F EHL probes ranged from having no effect in the Xintec 6,000, to decreasing deflection by 30 degrees in the AUR-7. Working instruments that were 2.4F or greater reduced deflection from 33 degrees to 93 degrees. Better deflectability was noted with the 200-micron holmium laser fiber than with the 365-micron fiber. The diameter of the working instrument did not affect deflectability as severely in cystoscopes. No significant differences in deflection existed between the 365-micron and 200-micron fibers in the flexible nephroscopes tested. In general, working instruments less than 2.4F and the 200-micron laser fiber have little effect on deflectability compared with working instruments 2.4F or larger and the 365-micron fiber. Flexible cystoscopes, with their larger working channels and stronger deflection cables, are affected less by working instrument diameter than are flexible ureteroscopes.

Cystoscopes↗
PubMed2006

Durability of working channel in flexible ureteroscopes when inserting ureteroscopic devices.

PURPOSE: We studied the physical damage to the working channel of flexible ureteroscopes caused by insertion of various accessories. A procedure was developed to avoid channel damage. MATERIALS AND METHODS: An experimental model representing a flexible ureteroscope was prepared, and damage to its working channel was evaluated by inserting instruments through it. Deflection angles of the channel were changed from 0 degrees to 120 degrees, and each device was inserted and removed 100 times for each selected angle of the channel. Any induced pinholes were identified by an air-leak test. Also, the inside of the channel was inspected with an extremely fine fiberscope. RESULTS: Insertions of 3F biopsy forceps or a 2.4F Nitinol stone-retrieval device caused only slight damage to the model channel, even when the deflection angle was 120 degrees. However, the tips of 200- or 250-microm holmium laser fibers shaved the inner surface of the channel at 60 degrees of deflection, and at 120 degrees, the laser fiber either penetrated the channel or could not be advanced because of resistance by the channel wall. When the laser fiber was inserted within a protective tube, the channel was never damaged, even when the deflection angle was 120 degrees. CONCLUSIONS: When devices are inserted into the working channel of a flexible ureteroscope, damage to the wall depends on the kind of device and deflection angle. Harm could be avoided by inserting the devices, especially laser probes, within a protective tube.

Equipment Design↗
PubMed2006

Alteration in irrigant flow and deflection of flexible ureteroscopes with nitinol baskets.

BACKGROUND AND PURPOSE: Introduction of an instrument into the working channel of ureteroscopes adversely affects flow and deflection. We evaluated the alterations in ureteroscope channel flow and deflection caused by available Nitinol(R) baskets. MATERIALS AND METHODS: We compared the effects of 11 Nitinol baskets on irrigation flow and deflection of three flexible ureteroscopes (Olympus P3, ACMI DUR8, and ACMI DUR8 Elite). ANOVA was used to compare the loss of flow and deflection for each basket, with P values adjusted for multiple comparisons by the Tukey method. RESULTS: Ureteroscope flow and deflection were progressively adversely affected by all baskets as their diameter increased. The average baseline irrigant flow (46.6 mL/min) was decreased significantly: by 78.5% (to 9.9 mL/min), with the smaller baskets (Microvasive 1.9F and Cook 2.2F) and by 99.1% (to 0.4 mL/min) with the larger baskets (ACMI 3.0F and Microvasive 3.0F). Similarly, the mean baseline upward deflection (162 degrees) decreased by 2 degrees (1.2%) for the Cook 2.4F N-Compass and by 20 degrees (12.3%) for the ACMI 3.0F. Loss of downward deflection from baseline (170 degrees) ranged from 6 degrees (3.5%) for the Microvasive 1.9F to 17 degrees (10%) for the Microvasive 2.6F grasping forceps. The least deterioration in flow and deflection occurred with the two smallest baskets (Microvasive 1.9F and Cook 2.2F). CONCLUSION: Ureteroscope irrigation flow and deflection deteriorate progressively with larger-caliber Nitinol baskets. The Microvasive 1.9F and Cook 2.2F baskets resulted in the least deterioration of irrigation and deflection metrics. However, basket size is not the only factor responsible for changes in flow and ureteroscope deflection.

Alloys↗
PubMed2006

Direct adenoviral transfer of bone morphogenetic protein-2 cDNA enhances fracture healing in osteoporotic sheep.

Osteoporosis, a major public health burden, is associated with increased fracture risk. Fracture healing in osteoporosis is delayed, with reduced callus formation and impaired biomechanical properties of newly formed bone leading to high risk of fixation failure. Adenoviral gene transfer of bone morphogenetic protein-2 (BMP-2) has been shown to enhance fracture healing. This study evaluated the ability of gene transfer to enhance bone healing in osteoporosis. An established sheep model of osteoporosis with well-characterized alterations in fracture healing was used. Osteotomies were created surgically in the tibias of adult female sheep and monitored for 8 weeks, using radiographic, biomechanical, and histological methods. For pilot experiments, primary ovine osteoblasts and mesenchymal stem cells were transduced with a recombinant adenovirus carrying BMP-2 cDNA (Ad.BMP-2). Large increases in alkaline phosphatase production and mineralization confirmed the ability of human BMP-2 to stimulate osteoblastic differentiation in sheep. In vivo bending stiffness measurements during fracture healing as well as ex vivo torsional stiffness measurements demonstrated stiffer callus tissue after treatment with Ad.BMP-2. The differences were found mainly in the early fracture-healing period. Computed tomography demonstrated that animals receiving the BMP-2 cDNA had larger cross-sectional callus area and higher callus density. Histological examination of the tibias confirmed enhanced callus formation. Direct, local adenoviral delivery of an osteogenic gene thus led to enhanced healing of fractures in an ovine model of osteoporosis. These promising data encourage the further development of genetic approaches to enhance bone healing in patients suffering osteoporosis-associated fractures.

Adenoviridae↗
PubMed1999

Structural basis for triplet repeat disorders: a computational analysis.

MOTIVATION: Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases? RESULTS: Using several different computational models of DNA structure, we show that the triplets involved in the pathological repeats generally fall into extreme classes. Thus, CAG/CTG repeats are particularly flexible, whereas GCC, CGG and GAA repeats appear to display both flexible and rigid (but curved) characteristics depending on the method of analysis. The fact that (1) trinucleotide repeats often become increasingly unstable when they exceed a length of approximately 50 repeats, and (2) repeated 12-mers display a similar increase in instability above 13 repeats, together suggest that approximately 150 bp is a general threshold length for repeat instability. Since this is about the length of DNA wrapped up in a single nucleosome core particle, we speculate that chromatin structure may play an important role in the expansion mechanism. We furthermore suggest that expansion of a dodecamer repeat, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA). CONTACT: pfbaldi@ics.uci.edu, yves@netid.com, brunak@cbs.dtu.dk, gorm@cbs.dtu.dk.

Anticipation, Genetic↗