Determining cell shape: adaptive regulation of cyanobacterial cellular differentiation and morphology

Similar to other bacteria, cyanobacteria exist in a wide-ranging diversity of shapes and sizes. However, three general shapes are observed most frequently: spherical, rod and spiral. Bacteria can also grow as filaments of cells. Some filamentous cyanobacteria have differentiated cell types that exhibit distinct morphologies: motile hormogonia, nitrogen-fixing heterocysts, and spore-like akinetes. Cyanobacterial cell shapes, which are largely controlled by the cell wall, can be regulated by developmental and/or environmental cues, although the mechanisms of regulation and the selective advantage(s) of regulating cellular shape are still being elucidated. In this review, recent insights into developmental and environmental regulation of cell shape in cyanobacteria and the relationship(s) of cell shape and differentiation to organismal fitness are discussed.     

翻译延伸因子EF-P的结构和功能及其研究进展

EF-P(Elongation factor P)是普遍存在于细菌中的蛋白质翻译延伸因子,因其L型结构与t RNA类似,可挽救聚脯氨酸导致的翻译延宕,减缓核糖体的失速效应。EF-P虽然不是细菌生存的必需蛋白,但是对细菌自身的环境适应性以及一些致病菌的毒性维持至关重要。本文综述了细菌EF-P的结构、功能及其相关研究进展。     

Molecular dynamics simulation for shape change of water-in-oil droplets

We performed molecular dynamics (MD) simulations of water-in-oil droplet shape transformations induced by the addition of polymer chains. In a prior experiment, transformations of spherical droplets to rod-like, worm-like and network-like droplets were observed. In our previous study, we reproduced rod-like droplets via coarse-grained MD simulations, and the mechanism for the droplet shape change was elucidated by considering the contact area between the chains and the surfactant head groups. However, in that simulation model, we could not reproduce the worm-like and network-like droplets. In this study, we improved the simulation model. For a small number of chains, several spherical droplets were obtained. As the number of chains increased, the spherical droplets were transformed to rod-like, worm-like and network-like shapes by coalescence of the droplets. The calculated and experimental results agreed well, and we verified that the mechanism for the droplet shape transformations observed in the present simulations could be explained by the mechanism suggested in the previous study.     

Mechanical Control of Bacterial Cell Shape

In bacteria, cytoskeletal filament bundles such as MreB control the cell morphology and determine whether the cell takes on a spherical or a rod-like shape. Here we use a theoretical model to describe the interplay of cell wall growth, mechanics, and cytoskeletal filaments in shaping the bacterial cell. We predict that growing cells without MreB exhibit an instability that favors rounded cells. MreB can mechanically reinforce the cell wall and prevent the onset of instability. We propose that the overall bacterial shape is determined by a dynamic turnover of cell wall material that is controlled by mechanical stresses in the wall. The model affirms that morphological transformations with and without MreB are reversible, and quantitatively describes the growth of irregular shapes and cells undergoing division. The theory also suggests a unique coupling between mechanics and chemistry that can control organismal shapes in general.     

Dielectric characterization of bacterial cells using dielectrophoresis

Measurements of dielectrophoretic collection spectra of Escherichia coli and Staphylococcus aureus suspensions are used for obtaining dielectric characteristics of both types of bacteria. The experiments are interpreted using a numerical method that models the cells as compartmented spherical or rod-like particles. We show the usefulness of this simple method to extract significant information about the electrical properties of Gram-negative and -positive bacteria.     

A practical method for assessment of dose conversion coefficients for aquatic biota

Radiological impact assessment for flora and fauna requires adequate dosimetric data. Due to the variability of habitats, shapes, and masses of the non-human biota, assessment of doses is a challenging task. External and internal dose conversion coefficients for photons and electrons have been systematically calculated by Monte Carlo methods for spherical and ellipsoidal shapes in water medium. An interpolation method has been developed to approximate absorbed fractions for elliptical shape organisms from absorbed fractions for spherical shapes with reasonable accuracy. The method allows an evaluation of dose conversion coefficients for arbitrary ellipsoids for photon and electron sources with energies from 10 keV to 5 MeV, and for organism masses in the range from 10(-6) to 10(3) kg. As an example of the application of the method, a set of dose coefficients for aquatic organisms discussed as reference animals and plants in a draft of an up-coming publication of the International Commission on Radiological Protection has been determined.     

A tactile response in Staphylococcus aureus

It is well established that bacteria are able to respond to temporal gradients (e.g., by chemotaxis). However, it is widely held that prokaryotes are too small to sense spatial gradients. This contradicts the common observation that the vast majority of bacteria live on the surface of a solid substrate (e.g., as a biofilm). Herein we report direct experimental evidence that the nonmotile bacterium Staphylococcus aureus possesses a tactile response, or primitive sense of touch, that allows it to respond to spatial gradients. Attached cells recognize their substrate interface and localize adhesins toward that region. Braille-like avidity maps reflect a cell's biochemical sensory response and reveal ultrastructural regions defined by the actual binding activity of specific proteins.     

Getting into shape: How do rod-like bacteria control their geometry?

Rod-like bacteria maintain their cylindrical shapes with remarkable precision during growth. However, they are also capable to adapt their shapes to external forces and constraints, for example by growing into narrow or curved confinements. Despite being one of the simplest morphologies, we are still far from a full understanding of how shape is robustly regulated, and how bacteria obtain their near-perfect cylindrical shapes with excellent precision. However, recent experimental and theoretical findings suggest that cell-wall geometry and mechanical stress play important roles in regulating cell shape in rod-like bacteria. We review our current understanding of the cell wall architecture and the growth dynamics, and discuss possible candidates for regulatory cues of shape regulation in the absence or presence of external constraints. Finally, we suggest further future experimental and theoretical directions which may help to shed light on this fundamental problem.     

Distribution of bacteria in the velocity gradient centrifuge.

Cells in different parts of the cell cycle can be separated by brief centrifugation in a density stabilized gradient: the Mitchison-Vincent technique. The position of a cell in the tube depends upon its size, shape, and density, upon the gradients of density, viscosity, and centrifugal force through which it sediments, and upon time. A program to compute the velocities and integrate the velocity profile for particles of a particular size class is presented. Because enteric bacteria are a form intermediate between right cylinders and prolate ellipsoids of revolution, the program uses values for the frictional coefficient intermediate between those calculated for ellipsoids and for cylinders. The formula f=6pietab(a/b)1/2 possesses this property and because of its simplicity greatly speeds the calculations. A second program computes the distribution of masses and then of sedimentation constants for a bacterial population, expressed either as a frequency distribution or as total mass per s-class. The effect of the known variation in cell size at division is included in these calculations, which apply to organisms undergoing balanced, asynchronous growth in which mass increase is proportional to cell size. The two programs in conjunction compute the mass or cell-number profile in an arbitrary gradient. The programs have been used to design gradients to maximize the resolution of the technique.     

Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits.

A procedure is devised for the calculation of hydrodynamic properties of rigid macromolecules composed subunits that are modeled as ellipsoids of revolution and cylinders. Owing to the axial symmetry of these shapes, smooth shell models can be constructured for the subunit structure. The bead shell model so constructed is employed for the calculation of the properties. A computer program, HYDROSUB, has been written implementing both the model building and the hydrodynamic calculation. A detailed example of the use of this methodology is presented for the case of the solution properties of the human antibody molecule immunoglobulin G3 (IgG3). Finally, hints are given on other uses and applications of the procedure.     

Optical Extinction Spectroscopy of Oblate, Prolate and Ellipsoid Shaped Gold Nanoparticles: Experiments and Theory

Localized Surface Plasmons (LSP) on metallic nanoparticles of different shapes are investigated by extinction spectroscopy. Experimental results are compared to simulations by a Finite-Difference Time-Domain (FDTD) method. Three different shapes of nanoparticles are compared, oblates, prolates and ellipsoids, in terms of spectral tunability of the LSP resonance (LSPR). It is found that the complete geometry of the nanoparticle must be given to truly define the LSP resonance and that ellipsoids offer the widest spectral tunability.     

Effect of UV Radiation on the Bacterivory of a Heterotrophic Nanoflagellate

The effects of UV-B radiation on the heterotrophic nanoflagellate Bodo saltans (Kinetoplastida) were examined under controlled conditions with artificial UV sources and also under natural solar radiation in an oligotrophic lake. In both types of experiments, the characteristic elongated cell morphology of this flagellate changed into a spherical one. This effect was due to UV-B but also to UV-A radiation, and after 4 h of exposure at 0.5 m of depth, 99% (UV-B plus UV-A plus photosynthetically active radiation) and 69% of the cells (UV-A plus photosynthetically active radiation) were spherical. At 6 m of depth where only 10% of the UV-B (305 nm) at the surface was measured, no significant effect was observed. The spherical cells were nonmotile, but before the morphological change took place, the swimming speed was ca. 3.5 times lower in the plus-UV-B treatment. The negative relation between the abundance of spherical cells and the average ingestion of fluorescently labeled bacteria per cell indicates that these cells are not able to feed upon bacteria. In bacterivory experiments lasting for 6 h, the total number of grazed bacteria was up to 70% lower in the plus-UV-B treatment than in the control without UV-B. This resulted in a positive feedback between UV-B and bacterial growth. The high sensitivity of B. saltans to solar UV-B and UV-A radiation strongly reduces its ability to live near the surface at times of high UV radiation.     

Utilisation of controlled pore topology for the separation of bioparticles in a mixed-glass beads column

To study the flow of shaped particles in porous media, elution of spherical and rod-like micro-organisms was performed through beds of spherical glass beads. A 0.04 cm/s constant flow rate was used with 5 microm yeast suspensions, 1 microm latex micro-spheres and rod-like bacilli Lactobacillus bulgaricus 6 microm long and 0.5 microm in diameter. Yeast cells' diameter is close to the bacilli length and micro-spheres have the same diameter as bacilli. All particle types have similar density. To make the different packing beds, 1.125 mm coarse beads and 0.1115 mm fine beads were used. Experiments were carried out using a column loaded with the binary packing (volume fraction of coarse particles in the mixture 0.7) or a monosize packing with the same amount of coarse or fine particles as used in the binary packing. Analysis of experimental results was based on two models: pure exclusion effect and hydrodynamic separation model [hydrodynamic chromatography (HDC)]. Results for spheres show that the classic HDC model fits to the experimental data whenever the ratio of particle size to the pathway bend scale is high ( approximately 1/100, micro-spheres). However, if this ratio increases and becomes approximately 1/20, the HDC model needs to be corrected due to the effect of channel wall curvature on exclusion. This led to a modified HDC equation of the form R=B/(1+2lambda-2.8lambda(2)), where R is the retention, lambda is the aspect ratio and constant B>or=1. Bacillus separation follows an exclusion mechanism, since pore topology is important in the separation of shaped particles when the aspect ratio approaches lambda=0.1. In the case of a binary packing bed, rod-like particles display a different behaviour than the one exhibited by the spherical particles of the same scale as bacilli, either in length or in diameter. This may be explained by the interaction between rod-like bacilli and the bed's pore topology. A generalised exclusion model for particles was proposed to be R=A/(1-lambda)(z), where A is the coefficient proportional to the tortuosity and the parameter z=1, 2 or 3 depends mainly on pore shape. Controlled pore topology opens interesting applications for bio-separation (in porous micro-fluidic devices, deep bed filtration) and might be especially important for macromolecules and micro-organisms separation with different shapes.     

N-thiolated beta-lactams: a new family of anti-Bacillus agents

This report describes the evaluation of N-thiolated beta-lactam antibiotics as potential anti-Bacillus agents. N-Thiolated beta-lactams are a new family of antibacterials that previously have been found to selectively inhibit the growth of Staphylococcus bacteria over many other genera of microbes. From the data presented herein, these lactams similarly inhibit a variety of Bacillus species, including Bacillus anthracis. The preliminary structure-activity studies suggest that there is a need to balance the lipophilic character of the C3/C4 groups in order to obtain optimal anti-Bacillus activity. Elongation or extensive branching of the organothio substituent diminishes antibacterial effects, with the sec-butylthio derivative providing the strongest activity.     

Characterizing the adhesion of motile and nonmotile Escherichia coli to a glass surface using a parallel-plate flow chamber

A parallel-plate flow chamber was used to measure the attachment and detachment rates of Escherichia coli to a glass surface at various fluid velocities. The effect of flagella on adhesion was investigated by performing experiments with several E. coli strains: AW405 (motile); HCB136 (nonmotile mutant with paralyzed flagella); and HCB137 (nonmotile mutant without flagella). We compared the total attachment rates and the fraction of bacteria retained on the surface to determine how the presence and movement of the flagella influence transport to the surface and adhesion strength in this dynamic system. At the lower fluid velocities, there was no significant difference in the total attachment rates for the three bacterial strains; nonmotile strains settled at a rate that was of the same order of magnitude as the diffusion rate of the motile strain. At the highest fluid velocity, the effect of settling was minimized to better illustrate the importance of motility, and the attachment rates of both nonmotile strains were approximately five times slower than that of the motile bacteria. Thus, different processes controlled the attachment rate depending on the parameter regime in which the experiment was performed. The fractions of motile bacteria retained on the glass surface increased with increasing velocity, whereas the opposite trend was found for the nonmotile strains. This suggests that the rotation of the flagella enables cells to detach from the surface (at the lower fluid velocities) and strengthens adhesion (at higher fluid velocities), whereas nonmotile cells detach as a result of shear. There was no significant difference in the initial attachment rates of the two nonmotile species, which suggests that merely the presence of flagella was not important in this stage of biofilm development.     

Microorganisms that break down alkyl sulfates

The following bacteria assimilating alkyl sulphates as a sole source of carbon and energy were isolated from various substrates: Pseudomonas, Achromobacter, Flavobacterium, Citrobacter, Enterobacter. The bacteria decomposed sodium dodecyl sulphate at a high rate, and some of them, industrial preparations of alkyl sulphates. The ability to assimilate alkyl sulphates was tested in 257 collection cultures belonging to different taxonomic groups. Alkyl sulphates were found to be decomposed by heterotrophous gram-negative rod-like bacteria belonging to different families and genera. The frequency of bacteria destroying alkyl sulphates at a high rate was found most often in the Pseudomonas genus.     

Spatial sensing of stimulus gradients can be superior to temporal sensing for free-swimming bacteria.

Predictions of the minimal size an organism must have to swim along stimulus gradients were used to compare the relative advantages of sensory systems employing spatial (simultaneous) and temporal (sequential) gradient detection mechanisms for small free-swimming bacteria, leading to the following conclusions: 1) there are environmental conditions where spatial detection mechanisms can function for smaller organisms than can temporal mechanisms, 2) temporal mechanisms are superior (have a smaller size limit) for the difficult conditions of low concentration and shallow gradients, but 3) observed bacterial chemotaxis occurs mostly under conditions where spatial mechanisms have a smaller size limit, and 4) relevant conditions in the natural environment favor temporal mechanisms in some cases and spatial mechanisms in others. Thus, sensory ecology considerations do not preclude free-swimming bacteria from employing spatial detection mechanisms, as has been thought, and microbiologists should be on the lookout for them. If spatial mechanisms do not occur, the explanation should be sought elsewhere.     

SELECTION AND EVOLUTION OF CAUSALLY COVARYING TRAITS

When traits cause variation in fitness, the distribution of phenotype, weighted by fitness, necessarily changes. The degree to which traits cause fitness variation is therefore of central importance to evolutionary biology. Multivariate selection gradients are the main quantity used to describe components of trait‐fitness covariation, but they quantify the direct effects of traits on (relative) fitness, which are not necessarily the total effects of traits on fitness. Despite considerable use in evolutionary ecology, path analytic characterizations of the total effects of traits on fitness have not been formally incorporated into quantitative genetic theory. By formally defining “extended” selection gradients, which are the total effects of traits on fitness, as opposed to the existing definition of selection gradients, a more intuitive scheme for characterizing selection is obtained. Extended selection gradients are distinct quantities, differing from the standard definition of selection gradients not only in the statistical means by which they may be assessed and the assumptions required for their estimation from observational data, but also in their fundamental biological meaning. Like direct selection gradients, extended selection gradients can be combined with genetic inference of multivariate phenotypic variation to provide quantitative prediction of microevolutionary trajectories.     

Preferred Temperature of Meloidogyne incognita

In laboratory thermal gradients, newly hatched infective juveniles of the plant-parasitic root-knot nematode Meloidogyne incognita migrated toward a preferred temperature that was several degrees above the temperature to which they were acclimated. After shifting egg masses to a new temperature, the preferred temperature was reset in less than a day. Possible functions of this type of thermotaxis are discussed, including the use of thermal gradients around plant roots to locate hosts and to maintain a relatively straight path while ranging in the absence of other cues (a collimating stimulus).     

Flagellar Motility Confers Epiphytic Fitness Advantages upon Pseudomonas syringae

The role of flagellar motility in determining the epiphytic fitness of an ice-nucleation-active strain of Pseudomonas syringae was examined. The loss of flagellar motility reduced the epiphytic fitness of a normally motile P. syringae strain as measured by its growth, survival, and competitive ability on bean leaf surfaces. Equal population sizes of motile parental or nonmotile mutant P. syringae strains were maintained on bean plants for at least 5 days following the inoculation of fully expanded primary leaves. However, when bean seedlings were inoculated before the primary leaves had expanded and bacterial populations on these leaves were quantified at full expansion, the population size of the nonmotile derivative strain reached only 0.9% that of either the motile parental or revertant strain. When fully expanded bean primary leaves were coinoculated with equal numbers of motile and nonmotile cells, the population size of a nonmotile derivative strain was one-third of that of the motile parental or revertant strain after 8 days. Motile and nonmotile cells were exposed in vitro and on plants to UV radiation and desiccating conditions. The motile and nonmotile strains exhibited equal resistance to both stresses in vitro. However, the population size of a nonmotile strain on leaves was less than 20% that of a motile revertant strain when sampled immediately after UV irradiation. Epiphytic populations of both motile and nonmotile P. syringae declined under desiccating conditions on plants, and after 8 days, the population size of a nonmotile strain was less than one-third that of the motile parental or revertant strain.