Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS

OxyS and RprA are two small noncoding RNAs (sRNAs) that modulate the expression of rpoS, encoding an alternative sigma factor that activates transcription of multiple Escherichia coli stress-response genes. While RprA activates rpoS for translation, OxyS down-regulates the transcript. Crucially, the RNA binding protein Hfq is required for both sRNAs to function, although the specific role played by Hfq remains unclear. We have investigated RprA and OxyS interactions with Hfq using biochemical and biophysical approaches. In particular, we have obtained the molecular envelopes of the Hfq–sRNA complexes using small-angle scattering methods, which reveal key molecular details. These data indicate that Hfq does not substantially change shape upon complex formation, whereas the sRNAs do. We link the impact of Hfq binding, and the sRNA structural changes induced, to transcript stability with respect to RNase E degradation. In light of these findings, we discuss the role of Hfq in the opposing regulatory functions played by RprA and OxyS in rpoS regulation

Vortex tubes in velocity fields of laboratory isotropic turbulence: dependence on the Reynolds number

The streamwise and transverse velocities are measured simultaneously in isotropic grid turbulence at relatively high Reynolds numbers, Re(lambda) = 110-330. Using a conditional averaging technique, we extract typical intermittency patterns, which are consistent with velocity profiles of a model for a vortex tube, i.e., Burgers vortex. The radii of the vortex tubes are several of the Kolmogorov length regardless of the Reynolds number. Using the distribution of an interval between successive enhancements of a small-scale velocity increment, we study the spatial distribution of vortex tubes. The vortex tubes tend to cluster together. This tendency is increasingly significant with the Reynolds number. Using statistics of velocity increments, we also study the energetical importance of vortex tubes as a function of the scale. The vortex tubes are important over the background flow at small scales especially below the Taylor microscale. At a fixed scale, the importance is increasingly significant with the Reynolds number.Comment: 8 pages, 3 PS files for 8 figures, to appear in Physical Review

Multi-year Observations of Mid-latitude Middle Atmospheric Winds, Waves, and Temperature associated with SSW Events over Northern Utah

We investigate the behavior of 14 years of wind, wave, and temperature observations in the middle atmosphere over northeastern Utah, USA during periods of sudden stratospheric warming events. This systematic review of the impacts of sudden stratospheric warming events on the middle atmosphere at a northern mid-latitude site is conducted using ground based measurements from imaging Doppler interferometry and meteor wind radar and Na and Raleigh lidar and space based measurements made by the Sounding of the Atmosphere Using Broadband Emission Radiometry sensor onboard the NASA sponsored Thermosphere Ionosphere mesosphere Energetics Dynamics Mission

Biological measurement beyond the quantum limit

Quantum noise places a fundamental limit on the per photon sensitivity attainable in optical measurements. This limit is of particular importance in biological measurements, where the optical power must be constrained to avoid damage to the specimen. By using non-classically correlated light, we demonstrated that the quantum limit can be surpassed in biological measurements. Quantum enhanced microrheology was performed within yeast cells by tracking naturally occurring lipid granules with sensitivity 2.4 dB beyond the quantum noise limit. The viscoelastic properties of the cytoplasm could thereby be determined with a 64% improved measurement rate. This demonstration paves the way to apply quantum resources broadly in a biological context

Mechanical model of the ultra-fast underwater trap of Utricularia

The underwater traps of the carnivorous plants of the Utricularia species catch their preys through the repetition of an "active slow deflation / passive fast suction" sequence. In this paper, we propose a mechanical model that describes both phases and strongly supports the hypothesis that the trap door acts as a flexible valve that buckles under the combined effects of pressure forces and the mechanical stimulation of trigger hairs, and not as a panel articulated on hinges. This model combines two different approaches, namely (i) the description of thin membranes as triangle meshes with strain and curvature energy, and (ii) the molecular dynamics approach, which consists in computing the time evolution of the position of each vertex of the mesh according to Langevin equations. The only free parameter in the expression of the elastic energy is the Young's modulus E of the membranes. The values for this parameter are unequivocally obtained by requiring that the trap model fires, like real traps, when the pressure difference between the outside and the inside of the trap reaches about 15 kPa. Among other results, our simulations show that, for a pressure difference slightly larger than the critical one, the door buckles, slides on the threshold and finally swings wide open, in excellent agreement with the sequence observed in high-speed videos.Comment: Accepted for publication in Physical Review

Epidemics on contact networks: a general stochastic approach

Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our systematic framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible (SIS) and susceptible-infectious-removed (SIR) dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.Comment: Main document: 16 pages, 7 figures. Electronic Supplementary Material (included): 6 pages, 1 tabl