A Modular Gradient-Sensing Network for Chemotaxis in Escherichia coli Revealed by Responses to Time-Varying Stimuli

The Escherichia coli chemotaxis-signaling pathway computes time derivatives of chemoeffector concentrations. This network features modules for signal reception/amplification and robust adaptation, with sensing of chemoeffector gradients determined by the way in which these modules are coupled in vivo. We characterized these modules and their coupling by using fluorescence resonance energy transfer to measure intracellular responses to time-varying stimuli. Receptor sensitivity was characterized by step stimuli, the gradient sensitivity by exponential ramp stimuli, and the frequency response by exponential sine-wave stimuli. Analysis of these data revealed the structure of the feedback transfer function linking the amplification and adaptation modules. Feedback near steady state was found to be weak, consistent with strong fluctuations and slow recovery from small perturbations. Gradient sensitivity and frequency response both depended strongly on temperature. We found that time derivatives can be computed by the chemotaxis system for input frequencies below 0.006 Hz at 22°C and below 0.018 Hz at 32°C. Our results show how dynamic input–output measurements, time honored in physiology, can serve as powerful tools in deciphering cell-signaling mechanisms.Molecular and Cellular Biolog

Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species

A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajectories of the canonical lab strain $C. elegans$ N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting ``bet-hedging'' strategies for foraging.Comment: 46 pages, 18 figures, 6 table

Pressure-induced unconventional superconductivity in the heavy-fermion antiferromagnet CeIn3: An 115In-NQR study under pressure

We report on the pressure-induced unconventional superconductivity in the heavy-fermion antiferromagnet CeIn3 by means of nuclear-quadrupole-resonance (NQR) studies conducted under a high pressure. The temperature and pressure dependences of the NQR spectra have revealed a first-order quantum-phase transition (QPT) from an AFM to PM at a critical pressure Pc=2.46 GPa. Despite the lack of an AFM quantum critical point in the P-T phase diagram, we highlight the fact that the unconventional SC occurs in both phases of the AFM and PM. The nuclear spin-lattice relaxation rate 1/T1 in the AFM phase have provided evidence for the uniformly coexisting AFM+SC phase. In the HF-PM phase where AFM fluctuations are not developed, 1/T1 decreases without the coherence peak just below Tc, followed by a power-law like T dependence that indicates an unconventional SC with a line-node gap. Remarkably, Tc has a peak around Pc in the HF-PM phase as well as in the AFM phase. In other words, an SC dome exists with a maximum value of Tc = 230 mK around Pc, indicating that the origin of the pressure-induced HF SC in CeIn3 is not relevant to AFM spin fluctuations but to the emergence of the first-order QPT in CeIn3. When the AFM critical temperature is suppressed at the termination point of the first-order QPT, Pc = 2.46 GPa, the diverging AFM spin-density fluctuations emerge at the critical point from the AFM to PM. The results with CeIn3 leading to a new type of quantum criticality deserve further theoretical investigations

Conductance renormalization and conductivity of a multi-subband Tomonaga-Luttinger model

We studied the conductance renormalization and conductivity of multi-subband Tomonaga-Luttinger models with inter-subband interactions. We found that, as in single-band systems, the conductance of a multi-subband system with an arbitrary number of subbands is not renormalized due to interaction between electrons. We derived a formula for the conductivity in multi-subband models. We applied it to a simplified case and found that inter-subband interaction enhances the conductivity, which is contrary to the intra-subband repulsive interaction, and that the conductivity is further enhanced for a larger number of subbands.Comment: 12 pages, no figures. to be published in Physical Review B as a brief repor

Cell boundary confinement sets the size and position of the E. coli chromosome

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome

A quark model analysis of the charge symmetry breaking in nuclear force

In order to investigate the charge symmetry breaking (CSB) in the short range part of the nuclear force, we calculate the difference of the masses of the neutron and the proton, $\Delta {\rm M}$, the difference of the scattering lengths of the p-p and n-n scatterings, $\Delta a$, and the difference of the analyzing power of the proton and the neutron in the n-p scattering, $\Delta A(\theta)$, by a quark model. In the present model the sources of CSB are the mass difference of the up and down quarks and the electromagnetic interaction. We investigate how much each of them contributes to $\Delta {\rm M}$, $\Delta a$ and $\Delta A(\theta)$. It is found that the contribution of CSB of the short range part in the nuclear force is large enough to explain the observed $\Delta A(\theta)$, while $\Delta a$ is rather underestimated.Comment: 26 pages,6 figure

The numerical renormalization group method for quantum impurity systems

In the beginning of the 1970's, Wilson developed the concept of a fully non-perturbative renormalization group transformation. Applied to the Kondo problem, this numerical renormalization group method (NRG) gave for the first time the full crossover from the high-temperature phase of a free spin to the low-temperature phase of a completely screened spin. The NRG has been later generalized to a variety of quantum impurity problems. The purpose of this review is to give a brief introduction to the NRG method including some guidelines of how to calculate physical quantities, and to survey the development of the NRG method and its various applications over the last 30 years. These applications include variants of the original Kondo problem such as the non-Fermi liquid behavior in the two-channel Kondo model, dissipative quantum systems such as the spin-boson model, and lattice systems in the framework of the dynamical mean field theory.Comment: 55 pages, 27 figures, submitted to Rev. Mod. Phy

ACE-ASIA - Regional climatic and atmospheric chemical effects of Asian dust and pollution

Although continental-scale plumes of Asian dust and pollution reduce the amount of solar radiation reaching the earth's surface and perturb the chemistry of the atmosphere, our ability to quantify these effects has been limited by a lack of critical observations, particularly of layers above the surface. Comprehensive surface, airborne, shipboard, and satellite measurements of Asian aerosol chemical composition, size, optical properties, and radiative impacts were performed during the Asian Pacific Regional Aerosol Characterization Experiment (ACE-Asia) study. Measurements within a massive Chinese dust storm at numerous widely spaced sampling locations revealed the highly complex structure of the atmosphere, in which layers of dust, urban pollution, and biomass-burning smoke may be transported long distances as distinct entities or mixed together. The data allow a first-time assessment of the regional climatic and atmospheric chemical effects of a continental-scale mixture of dust and pollution. Our results show that radiative flux reductions during such episodes are sufficient to cause regional climate change