4,025 research outputs found
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
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
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
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
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