Hidden Stochastic Nature of a Single Bacterial Motor

The rotary flagellar motor of Escherichia coli bacterium switches stochastically between the clockwise (CW) and counterclockwise (CCW) direction. We found that the CW and CCW intervals could be described by a gamma distribution, suggesting the existence of hidden Markov steps preceding each motor switch. Power spectra of time series of switching events exhibited a peaking frequency instead of the Lorentzian profile expected from standard kinetic two-state models. Our analysis indicates that the number of hidden steps may be a key dynamical parameter underlying the switching process in a single bacterial motor as well as in large cooperative molecular systems.Molecular and Cellular BiologyPhysic

Noise Underlies Switching Behavior of the Bacterial Flagellum

We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions.Molecular and Cellular Biolog

Fine-Tuning of Chemotactic Response in E. coli Determined by High-Throughput Capillary Assay

In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to l-aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio.Molecular and Cellular Biolog

Critical behavior of an absorbing phase transition in an interacting monomer-dimer model

We study a monomer-dimer model with repulsive interactions between the same species in one dimension. With infinitely strong interactions the model exhibits a continuous transition from a reactive phase to an inactive phase with two equivalent absorbing states. Static and dynamic Monte Carlo simulations show that the critical behavior at the transition is different from the conventional directed percolation universality class but is consistent with that of the models with the mass conservation of modulo 2. The values of static and dynamic critical exponents are compared with those of other models. We also show that the directed percolation universality class is recovered when a symmetry-breaking field is introduced.Comment: 9 pages, latex, 1 figure (one PS figure file upon request) (appear in Physica A (1995): Proceeding of Statphys-Taipei-1995

Gambaran Pelaksanaan Problem-Based Learning Pada Mahasiswa Program Studi Pendidikan Dokter Fakultas Kedokteran Dan Ilmu Kesehatan Universitas Jambi

Background: Problem-Based Learning (PBL) is a new learning strategy that is focused on students, where they learn based on problems. Faculty of Medicine and Health Sciences UNJA (FKIK UNJA) have implemented PBL as a learning strategy in the Competence based Curriculum since 2007, however, there are no studies that measure the implementation of PBL based on its four theories in FKIK UNJA. Methods: This descriptive cross-sectional study design was conducted in April-May 2014 in FKIK UNJA. The number of respondents are 184 students from the class of 2010, 2011 and 2012. This research employed a questionnaire developed by Romauli et al. Then the average analysis is utilized to obtain the level of implementation of PBL based on the four theories. Results: The implementation level of PBL in FKIK UNJA that based on learning constructive, independent, collaborative and contextual was moderate (1,94). The implementation level of constructive learning process based on class of 2010, 2012 was high (2,02 and 2,13) and the class of 2011 was moderate (1,98). The implementation level of self-learning process based on the class of 2010, 2011 and 2012 was moderate (1,89; 1,87; 1,96). The implementation level of collaborative learning based on the class of 2010, 2011 was high (2,16 and 2,09) and the class of 2011 was moderate (1,97). The implementation level of contextual learning based on the class of 2010, 2011, and 2012 was moderate (1,78; 1,80; 1,82). Conclusions: The implementation of PBL on students of Medical Education FKIK UNJA in each class and all students, have stimulated students to develop their knowledge, stimulate control of the learning process in the student itself, stimulate the interaction between students and stimulate the learning process which reflects the situation and environment, where the knowledge will be used

Critical phenomena of nonequilibrium dynamical systems with two absorbing states

We study nonequilibrium dynamical models with two absorbing states: interacting monomer-dimer models, probabilistic cellular automata models, nonequilibrium kinetic Ising models. These models exhibit a continuous phase transition from an active phase into an absorbing phase which belongs to the universality class of the models with the parity conservation. However, when we break the symmetry between the absorbing states by introducing a symmetry-breaking field, Monte Carlo simulations show that the system goes back to the conventional directed percolation universality class. In terms of domain wall language, the parity conservation is not affected by the presence of the symmetry-breaking field. So the symmetry between the absorbing states rather than the conservation laws plays an essential role in determining the universality class. We also perform Monte Carlo simulations for the various interface dynamics between different absorbing states, which yield new universal dynamic exponents. With the symmetry-breaking field, the interface moves, in average, with a constant velocity in the direction of the unpreferred absorbing state and the dynamic scaling exponents apparently assume trivial values. However, we find that the hyperscaling relation for the directed percolation universality class is restored if one focuses on the dynamics of the interface on the side of the preferred absorbing state only.Comment: 11 pages, 21 figures, Revtex, submitted to Phy. Rev.

Inverted translational control of eukaryotic gene expression by ribosome collisions.

The canonical model of eukaryotic translation posits that efficient translation initiation increases protein expression and mRNA stability. Contrary to this model, we find that increasing initiation rate can decrease both protein expression and stability of certain mRNAs in the budding yeast Saccharomyces cerevisiae. These mRNAs encode a stretch of polybasic residues that cause ribosome stalling. Our computational modeling predicts that the observed decrease in gene expression at high initiation rates occurs when ribosome collisions at stalls stimulate abortive termination of the leading ribosome or cause endonucleolytic mRNA cleavage. Consistent with this prediction, the collision-associated quality-control factors Asc1 and Hel2 (orthologs of human RACK1 and ZNF598, respectively) decrease gene expression from stall-containing mRNAs only at high initiation rates. Remarkably, hundreds of S. cerevisiae mRNAs that contain ribosome stall sequences also exhibit lower translation efficiency. We propose that inefficient translation initiation allows these stall-containing endogenous mRNAs to escape collision-stimulated reduction in gene expression

Noise underlies switching behavior of the bacterial flagellum

We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions