Responses of Escherichia coli Bacteria to Two Opposing Chemoattractant Gradients Depend on the Chemoreceptor Ratio

Escherichia coli chemotaxis has long served as a simple model of environmental signal processing, and bacterial responses to single chemical gradients are relatively well understood. Less is known about the chemotactic behavior of E. coli in multiple chemical gradients. In their native environment, cells are often exposed to multiple chemical stimuli. Using a recently developed microfluidic chemotaxis device, we exposed E. coli cells to two opposing but equally potent gradients of major attractants, methyl-aspartate and serine. The responses of E. coli cells demonstrated that chemotactic decisions depended on the ratio of the respective receptor number of Tar/Tsr. In addition, the ratio of Tar to Tsr was found to vary with cells’ growth conditions, whereby it depended on the culture density but not on the growth duration. These results provide biological insights into the decision-making processes of chemotactic bacteria that are subjected to multiple chemical stimuli and demonstrate the importance of the cellular microenvironment in determining phenotypic behavior.In their natural environment, both prokaryotic and eukaryotic cells are exposed to multiple chemical stimuli. It is thus important to learn how cells make a decision when confronted with complex chemical stimuli. Escherichia coli bacteria have long served as a model system for chemotaxis studies due to their known and simple genetic makeup. Signaling in bacterial chemotaxis is comparatively well understood (3, 18, 19). To summarize it briefly, there are five types of chemoreceptors in E. coli, of which Tar and Tsr are the most abundant. The basic functional chemosensing unit is a ternary complex that consists of transmembrane chemoreceptors, a linker molecule, CheW, and a histidine kinase, CheA. Within each functional receptor complex, the receptors are known to function in a cooperative manner (9, 12, 16). Upon the binding of attractant molecules, this sensory complex undergoes a conformational change that suppresses the autophosphorylation activity of CheA. This response is then transmitted to the flagellar motor via a regulator protein, CheY. As a result, the run time of an E. coli bacterium is lengthened when swimming toward a high-chemoattractant-concentration region (4).While the molecular mechanisms governing bacterial chemotaxis in a single gradient have been investigated extensively both in experiments and in theory (see reference 8 and references therein), very little is known about how bacteria behave in the presence of dual chemical gradients (1, 17). Early work by Adler and Tso explored the chemotactic responses of E. coli cells in the presence of both attractant and repellent gradients by using a microcapillary chemotaxis assay (1). Twenty years later, Strauss et al. (17) revisited the problem by using a stop-flow chamber. Both investigations concluded that bacteria sum the chemical signals to provide a coordinated output to control flagellar rotation. However, the molecular mechanisms responsible for this calculation have not yet been explored.In this paper, we investigated the molecular mechanism that underlies the bacterial decision-making processes in two opposing attractant gradients that are sensed by the two most abundant E. coli receptors, Tar and Tsr, respectively. By varying the relative expression levels of Tar and Tsr, we demonstrated that the receptor ratio defines the attractant preference in dual gradients of their ligands. The Tar-to-Tsr ratio itself depends on the cell culture density but not on the duration of growth.     

Self-Generated Chemoattractant Gradients: Attractant Depletion Extends the Range and Robustness of Chemotaxis

Chemotaxis is fundamentally important, but the sources of gradients in vivo are rarely well understood. Here, we analyse self-generated chemotaxis, in which cells respond to gradients they have made themselves by breaking down globally available attractants, using both computational simulations and experiments. We show that chemoattractant degradation creates steep local gradients. This leads to surprising results, in particular the existence of a leading population of cells that moves highly directionally, while cells behind this group are undirected. This leading cell population is denser than those following, especially at high attractant concentrations. The local gradient moves with the leading cells as they interact with their surroundings, giving directed movement that is unusually robust and can operate over long distances. Even when gradients are applied from external sources, attractant breakdown greatly changes cells'' responses and increases robustness. We also consider alternative mechanisms for directional decision-making and show that they do not predict the features of population migration we observe experimentally. Our findings provide useful diagnostics to allow identification of self-generated gradients and suggest that self-generated chemotaxis is unexpectedly universal in biology and medicine.     

Robustness of Oscillatory Behavior in Correlated Networks

Understanding network robustness against failures of network units is useful for preventing large-scale breakdowns and damages in real-world networked systems. The tolerance of networked systems whose functions are maintained by collective dynamical behavior of the network units has recently been analyzed in the framework called dynamical robustness of complex networks. The effect of network structure on the dynamical robustness has been examined with various types of network topology, but the role of network assortativity, or degree–degree correlations, is still unclear. Here we study the dynamical robustness of correlated (assortative and disassortative) networks consisting of diffusively coupled oscillators. Numerical analyses for the correlated networks with Poisson and power-law degree distributions show that network assortativity enhances the dynamical robustness of the oscillator networks but the impact of network disassortativity depends on the detailed network connectivity. Furthermore, we theoretically analyze the dynamical robustness of correlated bimodal networks with two-peak degree distributions and show the positive impact of the network assortativity.     

Non-Newtonian Behavior of Blood in Oscillatory Flow

Sinusoidal oscillatory flow of blood and of aqueous glycerol solutions was produced in rigid cylindrical tubes. For aqueous glycerol, the amplitude of the measured pressure gradient wave form conformed closely to that predicted by Womersley's theory of oscillatory flow, up to Reynolds numbers approaching 2000. Blood differed significantly from aqueous glycerol solutions of comparable viscosity, especially at low frequencies and high hematocrits. As frequency increased, the hydraulic impedance of blood decreased to a minimum at a frequency of about 1-2 CPS, increasing monotonically at higher frequencies. The dynamic apparent viscosity of blood, calculated from Womersley's theory, decreased with increasing flow amplitude. The reactive component of the hydraulic impedance increased with frequency as predicted by theory; the resistive component decreased with increasing frequency, differing from the resistance of a Newtonian fluid which increased with frequency.     

Simulation and Analysis of Tethering Behavior of Neutrophils with Pseudopods

P-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) play important roles in mediating the inflammatory cascade. Selectin kinetics, together with neutrophil hydrodynamics, regulate the fundamental adhesion cascade of cell tethering and rolling on the endothelium. The current study uses the Multiscale Adhesive Dynamics computational model to simulate, for the first time, the tethering and rolling behavior of pseudopod-containing neutrophils as mediated by P-selectin/PSGL-1 bonds. This paper looks at the effect of including P-selectin/PSGL-1 adhesion kinetics. The parameters examined included the shear rate, adhesion on-rate, initial neutrophil position, and receptor number sensitivity. The outcomes analyzed included types of adhesive behavior observed, tether rolling distance and time, number of bonds formed during an adhesive event, contact area, and contact time. In contrast to the hydrodynamic model, P-selectin/PSGL-1 binding slows the neutrophil’s translation in the direction of flow and causes the neutrophil to swing around perpendicular to flow. Several behaviors were observed during the simulations, including tethering without firm adhesion, tethering with downstream firm adhesion, and firm adhesion upon first contact with the endothelium. These behaviors were qualitatively consistent with in vivo data of murine neutrophils with pseudopods. In the simulations, increasing shear rate, receptor count, and bond formation rate increased the incidence of firm adhesion upon first contact with the endothelium. Tethering was conserved across a range of physiological shear rates and was resistant to fluctuations in the number of surface PSGL-1 molecules. In simulations where bonding occurred, interaction with the side of the pseudopod, rather than the tip, afforded more surface area and greater contact time with the endothelial wall.     

Oscillatory behaviour control in a continuous culture under double-substrate limitation

The paper discusses the possibility of using a mixture of two growth limiting substrates to induce or eliminate self-sustained oscillations in a continuous culture process. The proportion of both substrates in the mixture is treated as a new control variable. The presented approach is based on the assumption that the oscillatory behaviour occurs for selected substrates in some range of dilution rates. Because a double-substrate limitation may occur, the analysis is performed for two fundamental substrate utilization patterns: simultaneous consumption and diauxic growth. By using model simulations and bifurcation analysis, we show that an appropriate proportion of two substrates in the mixture allows for the control of the oscillatory behaviour.     

The Mechanism of Bactericidal Activity in Phagosomes of Neutrophils

Myeloperoxidase plays the key role in antimicrobial of phagocytes. This enzyme uses hydrogen peroxide and chloride to catalyze hypochlorous acid formation. HOCl is the most probable agent in the oxygen-dependent bactericidal activity in the phagocyte phagosome. Chlorination markers indicate HOCl generation in the quantities lethal for bacteria. Enzymatic assay for myeloperoxidase indicates proceeding of other reactions involved in bactericidal activity. Superoxide integrates many activities of this kind and is important for physiological function of myeloperoxidase. Elucidation of phagosomes biochemistry can help us to understand why certain pathogens survive in such unfavorable environment.     

Sulphate-controlled Diversity of Subterranean Microbial Communities over Depth in Deep Groundwater with Opposing Gradients of Sulphate and Methane

The groundwater system in Olkiluoto, Finland, is stratified with a mixing layer at a depth of approximately 300 m between sulphate-rich, methane-poor and sulphate-poor, methane-rich groundwaters. New sequence library data obtained by 454 pyrotag sequencing of the v4v6 16S rDNA region indicated that sulphate-reducing bacteria (SRB) dominated the mixing layer while SRB could not be detected in the deep sulphate-poor groundwater samples. With the indispensable support of the sequence data, it could be demonstrated that sulphate was the only component needed to trigger a very large community transition in deep sulphate-poor, methane-rich groundwater from a non-sulphate-reducing community comprising Hydrogenophaga, Pseudomonas, Thiobacillus, Fusibacter, and Lutibacter to a sulphate-reducing community with Desulfobacula, Desulfovibrio, Desufobulbaceae, Desulfobacterium, Desulfosporosinus, and Desulfotignum. Experiments with biofilms and planktonic microorganisms in flow cells under in situ conditions confirmed that adding sulphate to the sulphate-poor groundwater generated growth of cultivable SRB and detectable SRB-related sequences. It was also found that the 16S rDNA diversity of the biofilms was conserved over 103 d and that there was great similarity in diversity between the microorganisms in the biofilms and in the flowing groundwater. This work demonstrates that the presence/absence of only one geochemical parameter, i.e., sulphate, in the groundwater significantly influenced the diversity of the investigated subterranean microbial community.     

含阻尼项二阶泛函差分方程的振动性质

从解的渐近状态入手,应用分类讨论方法和Raccati技巧,讨论了一类广泛的二阶泛函差分方程解的振动性与非振动性,建立了四个新的振动性定理,推广并改进了已有文献中的相关结果.     

高阶线性泛函方程解的振动性

考虑一类高阶线性泛函方程解的振动性,我们获得一些新的振动准则.这些振动准则,推广或改进了一些文献中的某些结果.     

酒精酵母在连续发酵中的振荡行为研究

初步分析酒精酵母在连续发酵中的振荡行为的产生条件及产生机理。通过改变稀释率、pH值、溶氧和进料葡萄糖浓度等条件 ,观察不同操作条件对酒精酵母菌生长和代谢行为的影响。在 10～ 15 g/L的较低葡萄糖浓度 ,0 .10～ 0 .2 0h-1的较低稀释率 ,以及 70 %左右的适度的溶氧浓度等发酵条件下 ,酒精酵母会出现同步的代谢振荡现象。一定条件下 ,菌体浓度处于振荡状态 ,残余葡萄糖浓度不可测或在很低水平振荡 ,这些发现预示着控制机制的新发展。     

The Mechanism of Spontaneous Oscillatory Contractions in Skeletal Muscle

Most striated muscles generate steady contractile tension when activated, but some preparations, notably cardiac myocytes and slow-twitch fibers, may show spontaneous oscillatory contractions (SPOC) at low levels of activation. We have provided what we believe is new evidence that SPOC is a property of the contractile system at low actin-myosin affinity, whether caused by a thin-filament regulatory system or by other means. We present a quantitative single-sarcomere model for isotonic SPOC in skeletal muscle with three basic ingredients: i), actin and myosin filaments initially in partial overlap, ii), stretch activation by length-dependent changes in the lattice spacing, and iii), viscoelastic passive tension. Modeling examples are given for slow-twitch and fast-twitch fibers, with periods of 10 s and 4 s respectively. Isotonic SPOC occurs in a narrow domain of parameter values, with small minimum and maximum values for actin-myosin affinity, a minimum amount of passive tension, and a maximum transient response rate that explains why SPOC is favored in slow-twitch fibers. The model also predicts the contractile, relaxed and SPOC phases as a function of phosphate and ADP levels. The single-sarcomere model can also be applied to a whole fiber under auxotonic and fixed-end conditions if the remaining sarcomeres are treated as a viscoelastic load. Here the model predicts an upper limit for the load stiffness that leads to SPOC; this limit lies above the equivalent loads expected from the rest of the fiber.     

Bilateral Regulation as a Behavior Mechanism

1. With the appearance of cybernetics there has been a considerable increase in interest in problems of the regulation of processes in various complex systems, including the biological. In psychology and physiology, experience has been accumulated in the investigation of certain nerve and mental phenomena as regulatory. This has included study of the emotions in the total cycle of neurohumoral regulation, and of voluntary attention in the regulation of activity.     

Oscillatory NAD(P)H Waves and Calcium Oscillations in Neutrophils? A Modeling Study of Feasibility

The group of Howard Petty has claimed exotic metabolic wave phenomena together with mutually phase-coupled NAD(P)H- and calcium-oscillations in human neutrophils. At least parts of these phenomena are highly doubtful due to extensive failure of reproducibility by several other groups and hints that unreliable data from the Petty lab are involved in publications concerning circular calcium waves. The aim of our theoretical spatiotemporal modeling approach is to propose a possible and plausible biochemical mechanism which would, in principle, be able to explain metabolic oscillations and wave phenomena in neutrophils. Our modeling suggests the possibility of a calcium-controlled glucose influx as a driving force of metabolic oscillations and a potential role of polarized cell geometry and differential enzyme distribution for various NAD(P)H wave phenomena. The modeling results are supposed to stimulate further controversial discussions of such phenomena and potential mechanisms and experimental efforts to finally clarify the existence and biochemical basis of any kind of temporal and spatiotemporal patterns of calcium signals and metabolic dynamics in human neutrophils. Independent of Petty's observations, they present a general feasibility study of such phenomena in cells.     

Pannexin 1 Channels Link Chemoattractant Receptor Signaling to Local Excitation and Global Inhibition Responses at the Front and Back of Polarized Neutrophils

Neutrophil chemotaxis requires excitatory signals at the front and inhibitory signals at the back of cells, which regulate cell migration in a chemotactic gradient field. We have previously shown that ATP release via pannexin 1 (PANX1) channels and autocrine stimulation of P2Y₂ receptors contribute to the excitatory signals at the front. Here we show that PANX1 also contributes to the inhibitory signals at the back, namely by providing the ligand for A_2A adenosine receptors. In resting neutrophils, we found that A_2A receptors are uniformly distributed across the cell surface. In polarized cells, A_2A receptors redistributed to the back where their stimulation triggered intracellular cAMP accumulation and protein kinase A (PKA) activation, which blocked chemoattractant receptor signaling. Inhibition of PANX1 blocked A_2A receptor stimulation and cAMP accumulation in response to formyl peptide receptor stimulation. Treatments that blocked endogenous A_2A receptor signaling impaired the polarization and migration of neutrophils in a chemotactic gradient field and resulted in enhanced ERK and p38 MAPK signaling in response to formyl peptide receptor stimulation. These findings suggest that chemoattractant receptors require PANX1 to trigger excitatory and inhibitory signals that synergize to fine-tune chemotactic responses at the front and back of neutrophils. PANX1 channels thus link local excitatory signals to the global inhibitory signals that orchestrate chemotaxis of neutrophils in gradient fields.     

Suboxic Deposition of Ferric Iron by Bacteria in Opposing Gradients of Fe(II) and Oxygen at Circumneutral pH

The influence of lithotrophic Fe(II)-oxidizing bacteria on patterns of ferric oxide deposition in opposing gradients of Fe(II) and O₂ was examined at submillimeter resolution by use of an O₂ microelectrode and diffusion microprobes for iron. In cultures inoculated with lithotrophic Fe(II)-oxidizing bacteria, the majority of Fe(III) deposition occurred below the depth of O₂ penetration. In contrast, Fe(III) deposition in abiotic control cultures occurred entirely within the aerobic zone. The diffusion microprobes revealed the formation of soluble or colloidal Fe(III) compounds during biological Fe(II) oxidation. The presence of mobile Fe(III) in diffusion probes from live cultures was verified by washing the probes in anoxic water, which removed ca. 70% of the Fe(III) content of probes from live cultures but did not alter the Fe(III) content of probes from abiotic controls. Measurements of the amount of Fe(III) oxide deposited in the medium versus the probes indicated that ca. 90% of the Fe(III) deposited in live cultures was formed biologically. Our findings show that bacterial Fe(II) oxidation is likely to generate reactive Fe(III) compounds that can be immediately available for use as electron acceptors for anaerobic respiration and that biological Fe(II) oxidation may thereby promote rapid microscale Fe redox cycling at aerobic-anaerobic interfaces.     

On the Plasma Quasineutrality under Oscillatory Confinement Based on a Nanosecond Vacuum Discharge

Plasma Physics Reports - One of the main problems for inertial electrostatic confinement devices with electron injection is the space charge neutralization. This work is devoted to the analysis of...     

Asc1 Supports Cell-Wall Integrity Near Bud Sites by a Pkc1 Independent Mechanism

Background

The yeast ribosomal protein Asc1 is a WD-protein family member. Its mammalian ortholog, RACK1 was initially discovered as a receptor for activated protein C kinase (PKC) that functions to maintain the active conformation of PKC and to support its movement to target sites. In the budding yeast though, a connection between Asc1p and the PKC signaling pathway has never been reported.

Methodology/Principal Findings

In the present study we found that asc1-deletion mutant (asc1Δ) presents some of the hallmarks of PKC signaling mutants. These include an increased sensitivity to staurosporine, a specific Pkc1p inhibitor, and susceptibility to cell-wall perturbing treatments such as hypotonic- and heat shock conditions and zymolase treatment. Microscopic analysis of asc1Δ cells revealed cell-wall invaginations near bud sites after exposure to hypotonic conditions, and the dynamic of cells'' survival after this stress further supports the involvement of Asc1p in maintaining the cell-wall integrity during the mid-to late stages of bud formation. Genetic interactions between asc1 and pkc1 reveal synergistic sensitivities of a double-knock out mutant (asc1Δ/pkc1Δ) to cell-wall stress conditions, and high basal level of PKC signaling in asc1Δ. Furthermore, Asc1p has no effect on the cellular distribution or redistribution of Pkc1p at optimal or at cell-wall stress conditions.

Conclusions/Significance

Taken together, our data support the idea that unlike its mammalian orthologs, Asc1p acts remotely from Pkc1p, to regulate the integrity of the cell-wall. We speculate that its role is exerted through translation regulation of bud-site related mRNAs during cells'' growth.     

猴免疫缺陷病毒引起多形核嗜中性白细胞凋亡的可能机理

本实验目的是研究猴免疫缺陷病毒（SIV）引起多形核嗜中性白细胞（PMNs）凋亡的机理。实验用PCR技术扩增gag基因,用Western blot法测定p53和bcl-2基因的表达。结果显示PMNs在被SIV感染后随着保温时间的延长存活率下降,在感染后24h可以从PMNs中扩增出gag基因。PMNs中p53基因的表达在感染后24h增加。同时bcl-2基因的表达在对照组和SIV感染组都增加,但在SIV感染组bcl-2蛋白的表达明显低于对照组。结果揭示SIV能够感染PMNs,p53和bcl-2基因表达的改变可能是SIV感染PMNs引起细胞凋亡的机理。