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PubMedDate not supplied

Developmental system drift and flexibility in evolutionary trajectories.

The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.

Animals↗

PubMed1993

Open-loop and closed-loop control of posture: a random-walk analysis of center-of-pressure trajectories.

A new conceptual and theoretical framework for studying the human postural control system is introduced. Mathematical techniques from statistical mechanics are developed and applied to the analysis and interpretation of stabilograms. This work was based on the assumption that the act of maintaining an erect posture could be viewed, in part, as a stochastic process. Twenty-five healthy young subjects were studied under quite-standing conditions. Center-of-pressure (COP) trajectories were analyzed as one-dimensional and two-dimensional random walks. This novel approach led to the extraction of repeatable, physiologically meaningful parameters from stabilograms. It is shown that although individual stabilograms for a single subject were highly variable and random in appearance, a consistent, subject-specific pattern emerged with the generation of averaged stabilogram-diffusion plots (mean square COP displacement vs time interval). In addition, significant inter-subject differences were found in the calculated results. This suggests that the steady-state behavior of the control mechanisms involved in maintaining erect posture can be quite variable even amongst a population of age-matched, anthropometrically similar, healthy individuals. These posturographic analyses also demonstrated that COP trajectories could be modelled as fractional Brownian motion and that at least two control systems-a short-term mechanism and a long-term mechanism-were operating during quit standing. More specifically, the present results suggest that over short-term intervals open-loop control schemes are utilized by the postural control system, whereas over long-term intervals closed-loop control mechanisms are called into play. This work strongly supports the position that much can be learned about the functional organization of the postural control system by studying the steady-state behavior of the human body during periods of undisturbed stance.

Adult↗

PubMed2003

Developmental typology of trajectories to nighttime bladder control: epidemiologic application of longitudinal latent class analysis.

The authors aimed to characterize developmental trajectories to nighttime continence by applying two latent class models-longitudinal latent class analysis (LLCA) and latent class growth analysis (LCGA)-to data on nighttime bed-wetting from a population-based birth cohort, the Medical Research Council 1946 National Survey of Health and Development cohort. Data on a binary outcome (wetting in the past month vs. not wetting) were available for children at six ages (4, 6, 8, 9, 11, and 15 years) assessed in 1950, 1952, 1954, 1955, 1957, and 1961. For 3,272 children with complete data (62.5% of the cohort), results of sequential model comparisons (T classes vs. T + 1 classes) and chi-square goodness-of-fit tests were evaluated using parametric bootstrapping. At least four trajectory classes (LLCA and LCGA) were identified. Associations between class membership and the prevalence of related measures were examined using a confirmatory latent class analysis approach. Inclusion of 1,483 children with partially incomplete data (n = 4,755; 90.9% of the cohort) enabled the authors to refine trajectories further: normal development (prevalence = 84.0%); delayed acquisition of bladder control ("transient" (8.7%) and "persistent" (1.8%)), capturing primary enuresis; chronic bed-wetting (2.6%), or experiencing night wetting until age 15 years; and a final trajectory (relapse = 2.9%) capturing secondary or onset enuresis. This empirically based, typologic approach to analysis of extensive longitudinal data in a general population sample provides an alternative perspective to that offered by traditional diagnostic criteria.

Adolescent↗

PubMed2004

Dot trajectories in the superposition of random screens: analysis and synthesis.

Moiré effects that occur in the superposition of aperiodic layers such as correlated random dot screens are known as Glass patterns. One of the most interesting properties of such moiré effects, which clearly distinguish them from their periodic counterparts, is undoubtedly the appearence in the superposition of intriguing microstructure dot alignments, also known as dot trajectories. These dot trajectories may have different geometric shapes, depending on the transformations undergone by the superposed layers. In the case of simple linear transformations such as layer rotations or layer scalings, the resulting dot trajectories are rather simple (circular, radial, spiral, elliptic, hyperbolic, linear, etc.); but in more complex layer transformations the dot trajectories can have much more interesting and surprising shapes. A full mathematical analysis of the dot trajectories, their morphology, and their various properties is provided. Furthermore, it is shown how the approach also allows us to synthesize correlated random screens that give in their superposition dot trajectories having any desired geometric shapes. Finally, it is also explained why such dot trajectories are visible only in superpositions of aperiodic screens but not in superpositions of periodic screens.

Journal Article↗

PubMed2005

Spatiotemporal consistency of trajectories in gymnastics: a three-dimensional analysis of flic-flac.

Sport performance during the execution of closed skills combines specific body and limb movements into codified patterns where stability and consistency may be more important than variability. Repeated sport movements can be investigated to assess the consistency of body trajectories. More consistent trajectories will result in more repeatable movements. The present study quantified the short-term consistency of body trajectories during the performance of the backward flic-flac, a technique of floor gymnastics. Nine experienced gymnasts (six men, three women), all of national level, performed 10 repetitions of backward flic-flac. An optoelectronic instrument was used for the detection of the three-dimensional movement of 13 body landmarks. The spatiotemporal consistency of repeated landmark trajectories was measured by the standard deviation between standardized trajectories. The results showed smaller standard deviation (larger consistency between landmark trajectories) in female than in male gymnasts. The analysis of the consistency of landmark trajectories could help gymnasts indicating which parts of the body do not repeat a selected movement with sufficient accuracy.

Adolescent↗

PubMed2000

The development of heavy drinking and alcohol-related problems from ages 18 to 37 in a U.S. national sample.

OBJECTIVE: The purpose of this study is to add to the understanding of the development of heavy alcohol use and alcohol-related problems by examining data from the National Longitudinal Survey of Youth (NLSY), a general population sample that contains information on alcohol use for the ages 18-37. A key question in this study is how background characteristics of the individual influence this development and whether the influence of these background characteristics changes over time. METHOD: The data used in this study are a general population sample (N = 7,859) from the National Longitudinal Survey of Youth (NLSY). This study uses a multivariate outcome approach that focuses on individual variation in trajectories over age. The statistical analysis uses random coefficients in a latent variable framework. Across-age changes in the importance of the influence of background variables on the outcomes are modeled using varying centering points. RESULTS: A key finding is that dropping out of high school has no effect on alcohol-related problems for individuals in their mid-twenties, but is associated with significantly increased levels of alcohol-related problems for individuals in their mid-thirties. In contrast, going on to college is associated with lower levels of heavy drinking when individuals reach their late twenties and their thirties. Strong gender and ethnicity effects seen in the twenties diminish when individuals reach their thirties. CONCLUSIONS: The trajectory analysis expands the knowledge of problematic alcohol development for individuals in their late twenties and thirties. The increasing detrimental effect of dropping out of high school up to the age 37 endpoint of the study raises questions about the effects in later life of dropping out of high school.

Achievement↗

PubMedDate not supplied

Bayesian model based clustering analysis: application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core.

This work describes the application of a Bayesian method for clustering protein conformations sampled during a molecular dynamics simulation of the HIV-1 integrase catalytic core. A clustering analysis is carried out under the assumption of normal distribution without fixing the number of clusters in advance. Some performance measures, such as posterior probability and class cross entropy, are used to determine the most probable set of clusters. The Bayesian clustering method results in meaningful groups identifying transitions between conformational ensembles. The dihedral angles involved in such transitions are also examined in detail. The conformations in high dimensional space are projected into 3D space employing a multidimensional scaling technique to provide a visual inspection.

Algorithms↗

PubMed1997

Classification of organelle trajectories using region-based curve analysis.

A method based on analysis of the region of movement and the functioning of the acto-myosin cytoskeleton has been elaborated to quantify and classify patterns of organelle movement in tobacco pollen tubes. The trajectory was dilated to the region of movement, which was then reduced to give a one-pixel-wide skeleton, represented by a graph structure. The longest line in this skeleton was hypothesized to represent the basic track of the organelle along a single actin filament. Quantitative features were derived from the graph structure, direction of movement on the longest skeletal line, and distance between skeletal line and particle. These features corresponded to biological events like the amount of linear movement or the probability of attachment of an organelle to the actin filament. From 81 analyzed organelle trajectories, 17 had completely linear, 17 had completely non-linear, and 47 had alternating linear and non-linear movement. Selected features were employed for classification and ranking of the movement patterns of a representative sample of the population of organelles moving in the cell tip. The presented methods can be applied to any field where analysis and classification of particle motion are intended.

Actin Cytoskeleton↗

PubMed1991

Single particle tracking. Analysis of diffusion and flow in two-dimensional systems.

Analysis of the trajectories of small particles at high spatial and temporal resolution using video enhanced contrast microscopy provides a powerful approach to characterizing the mechanisms of particle motion in living cells and in other systems. We present here the theoretical basis for the analysis of these trajectories for particles undergoing random diffusion and/or systematic transport at uniform velocity in two-dimensional systems. The single particle tracking method, based on observations of the trajectories of individual particles, is compared with methods that characterize the motions of a large collection of particles such as fluorescence photobleaching recovery. Determination of diffusion coefficients or transport velocities either from correlation of positions or of velocities of the particles is discussed. A result of practical importance is an analysis of the dependence of the expected statistical uncertainty of these determinations on the number of position measurements. This provides a way of judging the accuracy of the diffusion coefficients and transport velocities obtained using this approach.

Diffusion↗

PubMed2025

The cost and cost trajectory of genome sequencing and bioinformatics analysis for Indigenous children with suspected rare diseases.

PURPOSE: Indigenous peoples are underrepresented in reference genome libraries. Consequently, rare disease diagnosis may require bespoke bioinformatics analyses of genome sequences. Establishing diagnostic cost is crucial to support policy development for equitable diagnosis of rare diseases. We estimated the cost and cost trajectory of diagnostic genome sequencing and bioinformatics for Indigenous participants with suspected rare diseases. METHODS: We conducted a microcosting study of Indigenous children and their families receiving genome sequencing through Canada's Silent Genomes Project. Invoice data informed the costs of genome sequencing. We conducted a time-and-motion study for bioinformatics analyses, including labor, computing, and data storage costs. RESULTS: With standard bioinformatics, costs ranged from C$3645 (SD: 455) for singletons to C$7402 (SD: 566) for trios. With advanced, bespoke bioinformatics, costs ranged from C$5344 (SD: 634) for singletons to C$9760 (SD: 822) for trios. Genome sequencing was a primary cost driver; however, sequencing costs decreased by 61% over 4 years. Bioinformatics costs ranged from 21.3% to 58.3% of the total costs. The time required for bioinformatics ranged from 71 hours to 215 hours for standard and advanced analyses, respectively. CONCLUSION: Genome sequencing costs decreased over time. Bioinformatics is a significant cost driver, particularly for bespoke analyses arising from nonrepresentative reference libraries.

Humans↗

PubMed2000

Molecular dynamics of the anticodon domain of yeast tRNA(Phe): codon-anticodon interaction.

We have studied the effect of codon-anticodon interaction on the structure and dynamics of transfer RNAs using molecular dynamics simulations over a nanosecond time scale. From our molecular dynamical investigations of the solvated anticodon domain of yeast tRNA(Phe) in the presence and absence of the codon trinucleotides UUC and UUU, we find that, although at a gross level the structures are quite similar for the free and the bound domains, there are small but distinct differences in certain parts of the molecule, notably near the Y37 base. Comparison of the dynamics in terms of interatomic or inter-residual distance fluctuation for the free and the bound domains showed regions of enhanced rigidity in the loop region in the presence of codons. Because fluorescence experiments suggested the existence of multiple conformers of the anticodon domain, which interconvert on a much larger time scale than our simulations, we probed the conformational space using five independent trajectories of 500 ps duration. A generalized ergodic measure analysis of the trajectories revealed that at least for this time scale, all the trajectories populated separate parts of the conformational space, indicating a need for even longer simulations or enhanced sampling of the conformational space to give an unequivocal answer to this question.

Anticodon↗

PubMed2005

Molecular dynamics simulation of folding of a short helical peptide with many charged residues.

A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.

Amino Acids↗

PubMed1993

Kinematic description of variability of fast movements: analytical and experimental approaches.

Analysis of variability of fast aimed movements predicts the properties of trajectory variance. The analysis is based on a kinematic model with nonlinear changes in "internal time". The purpose of the work was to identify different sources of variability and their influence on the trajectory variance. An analytical expression for the speed-accuracy trade-off is introduced. Experiments were performed with subjects making single-joint elbow flexion movements over different distances as fast as possible with their eyes closed to memorized targets. Standard deviation of movement trajectory increased during the first part of the movement and subsequently decreased. The variance peaked after the time of peak velocity, close to the time of peak deceleration. A dependence of the trajectory variance on movement distance (speed-accuracy trade-off) was seen during the movement (at times of peak velocity and peak deceleration) but not after the movement termination. We conclude that the previously reported drop in the variability of movement trajectory during the deceleration phase does not necessarily mean a compensation by the control system but may result from purely kinematic properties of the movement. The importance of the time of measurement for analysis of the speed-accuracy trade-offs is emphasized.

Biomechanical Phenomena↗

PubMed2006

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

The mechanism of protein folding remains largely a mystery in molecular biology, despite the enormous effort from many groups in the past decades. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates such as the fraction of native contacts, the radius of gyration and so on. In this paper, we present an integrated approach towards understanding the folding process via visual analysis of patterns of these reaction coordinates. The three disparate processes (1) protein folding simulation, (2) pattern elicitation and (3) visualization of patterns, work in tandem. Thus as the protein folds, the changing landscape in the pattern space can be viewed via the visualization tool, PROTERAN, a program we developed for this purpose. We first present an incremental (on-line) trie-based pattern discovery algorithm to elicit the patterns and then describe the terrain metaphor based visualization tool. Using two example small proteins, a beta-hairpin and a designed protein Trp-cage, we next demonstrate that this combined pattern discovery and visualization approach extracts crucial information about protein folding intermediates and mechanism.

Algorithms↗

PubMed2003

Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.

Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical calculations and a Generalized Born continuum solvent model. Starting from its fully extended conformation, our simulation has produced a final structure resembling that of NMR native structure to within 1A main-chain root mean square deviation. Remarkably, the simulated structure stayed in the native state for most part of the simulation after it reached the state. Of greater significance is that our simulation has not only reached the correct main-chain conformation, but also a very high degree of accuracy in side-chain packing conformation. This feat has traditionally been a challenge for ab initio simulation studies. In addition to characterization of the trajectory, comparison of our results to experimental data is also presented. Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain.

Biophysical Phenomena↗

PubMed2005

Self-consistent Lagrangian study of nonlinear Landau damping.

The electric field computed by numerically solving the one-dimensional Vlasov-Poisson system is used to calculate Lagrangian trajectories of particles in the wave-particle resonance region. The analysis of these trajectories shows that, when the initial amplitude of the electric field is above some threshold, two populations of particles are present: a first one located near the separatrix, which performs flights in the phase space and whose trajectories become ergodic and chaotic, and a second population of trapped particles, which displays a nonergodic dynamics. The complex, nonlinear interaction between these populations determines the oscillating long-time behavior of solutions.

Journal Article↗

PubMed2005

Development of Caenorhabditis elegans pharynx, with emphasis on its nervous system.

The Caenorhabditis elegans pharynx is a neuromuscular tube of which the function is to pump and crush bacteria, and inject them into the intestine. The 80-cell pharynx develops via the morphogenesis and differentiation of the cells that compose its semi-spherical primordium, and requires the activity of several evolutionarily conserved genes, such as pha-4 (the homolog to the Drosophila forkhead and vertebrate FoxA), ceh-22 (the homolog to the Drosophila tinman and vertebrate Nkx2.5), and pha-2 (the homolog to the vertebrate Hex). There are 20 neurons in the pharynx, each with a reproducible unique trajectory. Developmental genetic analysis of axon guidance in the pharynx indicates that some axon trajectories are in part established without growth cones, whereas other parts necessitate growth cone function and guidance. Here we provide an overview of the developmental genetics of the Caenorhabditis elegans pharynx, with an emphasis on its nervous system.

Animals↗

PubMed2000

The effects of visual input on postural control mechanisms: an analysis of center-of-pressure trajectories using the auto-regressive model.

New measures to characterize center-of-pressure (COP) trajectories during quiet standing were proposed and then utilized to investigate changes in postural control with respect to visual input. Eleven healthy male subjects (aged 20-27 years) were included in this study. An instrumented force platform was used to measure the time-varying displacements of the COP under each subject's feet during quiet standing. The subjects were tested under eyes-open and eyes-closed conditions. The COP time series were separately analyzed for the medio-lateral and antero-posterior directions. The proposed measures were obtained from the parameter estimation of auto-regressive (AR) models. The percentage contributions and geometrical moment of AR coefficients showed statistically significant differences between vision conditions. The present COP displacements under the eyes-open condition showed higher correlation with the past COP displacements at longer lag times, when compared to the eyes-closed condition. In contrast, no significant differences between vision conditions were found for conventional summary statistics, e.g., the total length of the COP path. These results suggest that the AR parameters are useful for the evaluation of postural stability and balance function, even for healthy young individuals. The role of visual input in the postural control system and implications of the findings were discussed.

Adult↗