scholarly journals Modelling and analysis of bacterial tracks suggest an active reorientation mechanism inRhodobacter sphaeroides

2014 ◽  
Author(s):  
Gabriel Rosser ◽  
Ruth E. Baker ◽  
Judith P. Armitage ◽  
Alexander George Fletcher
Keyword(s):  
Computational Algorithm ◽  
Rotational Diffusion ◽  
Particle Model ◽  
Summary Statistics ◽  
Cell Geometry ◽  
Brownian Rotation ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
Open Question ◽  
Straight Lines

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechanism in the monoflagellate speciesRhodobacter sphaeroides. The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. A further two models also include stochastic reorientations, describing 'run-and-tumble' motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events inR. sphaeroides. This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.

scholarly journals Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter sphaeroides

2014 ◽  
Vol 11 (97) ◽  
pp. 20140320 ◽  
Author(s):  
Gabriel Rosser ◽  
Ruth E. Baker ◽  
Judith P. Armitage ◽  
Alexander G. Fletcher
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Computational Algorithm ◽  
Rotational Diffusion ◽  
Particle Model ◽  
Cell Geometry ◽  
Brownian Rotation ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
Open Question ◽  
Straight Lines

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides . The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. Two further models incorporate stochastic reorientations, describing ‘run-and-tumble’ motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events in R. sphaeroides . This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.

scholarly journals Stochastic Model for Direction Changes of Swimming Bacteria

2016 ◽  
Author(s):  
G. Fier ◽  
D. Hansmann ◽  
R. C. Buceta
Keyword(s):  
Stochastic Model ◽  
Control Parameter ◽  
Rotational Diffusion ◽  
Steady State Solution ◽  
E Coli ◽  
Isotropic Media ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
The Green Function ◽  
Centers Of Mass

AbstractIn this work we introduce a stochastic model to describe directional changes in the movement of swimming bacteria. We use the probability density function (PDF) of turn angles, measured on tumbling E. coli wild-type, to build a Langevin equation for the deflection of the bacterial body swimming in isotropic media. We solved analytically this equation by means of the Green function method and show that three parameters are sufficient to describe the movement: a characteristic time, the steady-state solution and a control parameter. We conclude that the tumble motion, which is manifested as abrupt turns, is primarily caused by the rotational boost generated by the flagellar motor and complementarily by the rotational diffusion introduced by noise. We show that, in the tumble motion, the deflection is a non-stationary stochastic processes during times where the tumble occurs. By tuning the control parameter our model is able to explain small turns of the bacteria around their centers of mass along the run. We show that the deflection during the run is an Ornstein-Uhlenbeck process, which for typical run times is stationary. We conclude that, along the run, the rotational boosts do not exist or are neglectable and that only the rotational diffusion remains. Thus we have a single model to explain the turns of the bacterium during the run or tumble movements, through a control parameter that can be tuned through a critical value that can explain the transition between the two turn behaviours. This model is also able to explain very satisfactory all available statistical experimental data, such as PDFs and average values of turning angles and times, of both run and tumble motions.

scholarly journals New Insights into the Dynamics of Swarming Bacteria: A Theoretical Study

2016 ◽  
Author(s):  
David Hansmann ◽  
Guido Fier ◽  
Rubén C. Buceta
Keyword(s):  
Inelastic Collision ◽  
Theoretical Study ◽  
Rotational Diffusion ◽  
Agar Plate ◽  
Soft Agar ◽  
E Coli ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
K 12 ◽  
Swarming Behaviour

In the present work we simulate the basic two-dimensional dynamics of swarmingE. colibacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with each other only through inelastic collision and with the highly viscous environment through damping forces. The motion of single agents is modelled closely corresponding to the behaviour of swimming bacteria. The dynamics of the model were adjusted to reproduce the experimental measurements of swimmingE. coliK-12. Accordingly, simulations with loosely packed agents (ρ≈0) show typical run-and-tumble statistics. In contrast, simulations with densely packed agents (ρ≈0.3-0.7) are dominated by interactions (collisions) between agents which lead to the emergence of swarming behaviour. In addition, we model the motion of single agents on the base of modified run-and-tumble dynamics, where the bacteria do not turn actively during the tumble. We show that simulations with densely packed modified agents lead as well the emergence of swarming behaviour, if rotational diffusion is considered.

scholarly journals Langevin equations for the run-and-tumble of swimming bacteria

Soft Matter ◽  
2018 ◽  
Vol 14 (19) ◽  
pp. 3945-3954 ◽  
Author(s):  
G. Fier ◽  
D. Hansmann ◽  
R. C. Buceta
Keyword(s):  
Langevin Equations ◽  
Turning Angle ◽  
Change Of Direction ◽  
Swimming Bacteria ◽  
Run And Tumble

The run and tumble motions of a swimming bacterium are well characterized by two stochastic variables: the speed v(t) and the change of direction or deflection x(t) = cos φ(t), where φ(t) is the turning angle at time t.

scholarly journals Evidence of polygenic adaptation at height-associated loci in mainland Europeans and Sardinians

2019 ◽  
Author(s):  
Minhui Chen ◽  
Carlo Sidore ◽  
Masato Akiyama ◽  
Kazuyoshi Ishigaki ◽  
Yoichiro Kamatani ◽  
...  
Keyword(s):  
Large Scale ◽  
Adult Height ◽  
Genetic Difference ◽  
Asian Population ◽  
Effect Sizes ◽  
Summary Statistics ◽  
Polygenic Adaptation ◽  
Robust Adaptive ◽  
Open Question ◽  
European Populations

AbstractAdult height was one of the earliest putative examples of polygenic adaptation in human. By constructing polygenic height scores using effect sizes and frequencies from hundreds of genomic loci robustly associated with height, it was reported that Northern Europeans were genetically taller than Southern Europeans beyond neutral expectation. However, this inference was recently challenged. Sohail et al. and Berg et al. showed that the polygenic signature disappeared if summary statistics from UK Biobank (UKB) were used in the analysis, suggesting that residual uncorrected stratification from large-scale consortium studies was responsible for the previously noted genetic difference. It thus remains an open question whether height loci exhibit signals of polygenic adaptation in any human population. In the present study, we re-examined this question, focusing on one of the shortest European populations, the Sardinians, as well as on the mainland European populations in general. We found that summary statistics from UKB significantly correlate with population structure in Europe. To further alleviate concerns of biased ascertainment of GWAS loci, we examined height-associated loci from the Biobank of Japan (BBJ). Applying frequency-based inference over these height-associated loci, we showed that the Sardinians remain significantly shorter than expected (~ 0.35 standard deviation shorter than CEU based on polygenic height scores, P = 1.95e-6). We also found the trajectory of polygenic height scores decreased over at least the last 10,000 years when compared to the British population (P = 0.0123), consistent with a signature of polygenic adaptation at height-associated loci. Although the same approach showed a much subtler signature in mainland European populations, we found a clear and robust adaptive signature in UK population using a haplotype-based statistic, tSDS, driven by the height-increasing alleles (P = 4.8e-4). In summary, by examining frequencies at height loci ascertained in a distant East Asian population, we further supported the evidence of polygenic adaptation at height-associated loci among the Sardinians. In mainland Europeans, we also found an adaptive signature, although becoming more pronounced only in haplotype-based analysis.

scholarly journals Critical behavior in active lattice models of motility-induced phase separation

2021 ◽  
Vol 44 (4) ◽  
Author(s):  
Florian Dittrich ◽  
Thomas Speck ◽  
Peter Virnau
Keyword(s):  
Phase Separation ◽  
Critical Behavior ◽  
Rotational Diffusion ◽  
Lattice Models ◽  
Universality Class ◽  
Computationally Efficient ◽  
Lattice Systems ◽  
Active Particles ◽  
Open Question

Abstract Lattice models allow for a computationally efficient investigation of motility-induced phase separation (MIPS) compared to off-lattice systems. Simulations are less demanding, and thus, bigger systems can be accessed with higher accuracy and better statistics. In equilibrium, lattice and off-lattice models with comparable interactions belong to the same universality class. Whether concepts of universality also hold for active particles is still a controversial and open question. Here, we examine two recently proposed active lattice systems that undergo MIPS and investigate numerically their critical behavior. In particular, we examine the claim that these systems and MIPS in general belong to the Ising universality class. We also take a more detailed look on the influence and role of rotational diffusion and active velocity in these systems. Graphic Abstract

Mars: was There an Ancient Eden?

1997 ◽  
Vol 161 ◽  
pp. 203-218 ◽  
Author(s):  
Tobias C. Owen
Keyword(s):  
Positive Answer ◽  
Biogenic Elements ◽  
Habitable Zones ◽  
The Face ◽  
The Origin Of Life ◽  
Early Mars ◽  
Favorable Conditions ◽  
Open Question ◽  
Rocky Planets ◽  
Impact Erosion

AbstractThe clear evidence of water erosion on the surface of Mars suggests an early climate much more clement than the present one. Using a model for the origin of inner planet atmospheres by icy planetesimal impact, it is possible to reconstruct the original volatile inventory on Mars, starting from the thin atmosphere we observe today. Evidence for cometary impact can be found in the present abundances and isotope ratios of gases in the atmosphere and in SNC meteorites. If we invoke impact erosion to account for the present excess of129Xe, we predict an early inventory equivalent to at least 7.5 bars of CO2. This reservoir of volatiles is adequate to produce a substantial greenhouse effect, provided there is some small addition of SO2(volcanoes) or reduced gases (cometary impact). Thus it seems likely that conditions on early Mars were suitable for the origin of life – biogenic elements and liquid water were present at favorable conditions of pressure and temperature. Whether life began on Mars remains an open question, receiving hints of a positive answer from recent work on one of the Martian meteorites. The implications for habitable zones around other stars include the need to have rocky planets with sufficient mass to preserve atmospheres in the face of intensive early bombardment.

Domain Formation in Synthetic Quartz

1971 ◽  
Vol 29 ◽  
pp. 156-157
Author(s):  
Joseph J. Comer
Keyword(s):  
Electron Beam ◽  
Room Temperature ◽  
Domain Formation ◽  
Synthetic Quartz ◽  
Transmission Electron ◽  
Black Spots ◽  
Diffraction Mode ◽  
Domain Boundaries ◽  
Kikuchi Lines ◽  
Straight Lines

Domains visible by transmission electron microscopy, believed to be Dauphiné inversion twins, were found in some specimens of synthetic quartz heated to 680°C and cooled to room temperature. With the electron beam close to parallel to the [0001] direction the domain boundaries appeared as straight lines normal to <100> and <410> or <510> directions. In the selected area diffraction mode, a shift of the Kikuchi lines was observed when the electron beam was made to traverse the specimen across a boundary. This shift indicates a change in orientation which accounts for the visibility of the domain by diffraction contrast when the specimen is tilted. Upon exposure to a 100 KV electron beam with a flux of 5x 1018 electrons/cm2sec the boundaries are rapidly decorated by radiation damage centers appearing as black spots. Similar crystallographio boundaries were sometimes found in unannealed (0001) quartz damaged by electrons.

On the Semantic Content of Grammatical Gender and Its Impact on the Representation of Human Referents

2010 ◽  
Vol 57 (5) ◽  
pp. 367-375 ◽  
Author(s):  
Lisa Irmen ◽  
Julia Kurovskaja
Keyword(s):  
Semantic Content ◽  
Grammatical Gender ◽  
Differential Effects ◽  
Gender Information ◽  
Masculine Role ◽  
Feminine Role ◽  
And Gender ◽  
Gender Categories ◽  
Open Question

Grammatical gender has been shown to provide natural gender information about human referents. However, due to formal and conceptual differences between masculine and feminine forms, it remains an open question whether these gender categories influence the processing of person information to the same degree. Experiment 1 compared the semantic content of masculine and feminine grammatical gender by combining masculine and feminine role names with either gender congruent or incongruent referents (e.g., Dieser Lehrer [masc.]/Diese Lehrerin [fem.] ist mein Mann/meine Frau; This teacher is my husband/my wife). Participants rated sentences in terms of correctness and customariness. In Experiment 2, in addition to ratings reading times were recorded to assess processing more directly. Both experiments were run in German. Sentences with grammatically feminine role names and gender incongruent referents were rated as less correct and less customary than those with masculine forms and incongruent referents. Combining a masculine role name with an incongruent referent slowed down reading to a greater extent than combining a feminine role name with an incongruent referent. Results thus specify the differential effects of masculine and feminine grammatical gender in denoting human referents.

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