Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

The 5'-cap-structures of higher eukaryote mRNAs are ribose 2'-O-methylated. Likewise, a number of viruses replicating in the cytoplasm of eukayotes have evolved 2'-O-methyltransferases to modify autonomously their mRNAs. However, a defined biological role of mRNA 2'-O-methylation remains elusive. Here we show that viral mRNA 2'-O-methylation is critically involved in subversion of type-I-interferon (IFN-I) induction. We demonstrate that human and murine coronavirus 2'-O-methyltransferase mutants induce increased IFN-I expression, and are highly IFN-I sensitive. Importantly, IFN-I induction by 2'-O-methyltransferase-deficient viruses is dependent on the cytoplasmic RNA sensor melanoma differentiation-associated gene 5 (MDA5). This link between MDA5-mediated sensing of viral RNA and mRNA 2'-O-methylation suggests that RNA modifications, such as 2'-O-methylation, provide a molecular signature for the discrimination of self and non-self mRNA.

Finite- N effects for ideal polymer chains near a flat impenetrable wall

This paper addresses the statistical mechanics of ideal polymer chains next to a hard wall. The principal quantity of interest, from which all monomer densities can be calculated, is the partition function, G N(z) , for a chain of N discrete monomers with one end fixed a distance z from the wall. It is well accepted that in the limit of infinite N , G N(z) satisfies the diffusion equation with the Dirichlet boundary condition, G N(0) = 0 , unless the wall possesses a sufficient attraction, in which case the Robin boundary condition, G N(0) = - x G N ′(0) , applies with a positive coefficient, x . Here we investigate the leading N -1/2 correction, D G N(z) . Prior to the adsorption threshold, D G N(z) is found to involve two distinct parts: a Gaussian correction (for z <~Unknown control sequence '\lesssim' aN 1/2 with a model-dependent amplitude, A , and a proximal-layer correction (for z <~Unknown control sequence '\lesssim' a described by a model-dependent function, B(z).

Differential recognition of Staphylococcus aureus quorum-sensing signals depends on both extracellular loops 1 and 2 of the transmembrane sensor AgrC.

Virulence in Staphylococcus aureus is regulated via agr-dependent quorum sensing in which an autoinducing peptide (AIP) activates AgrC, a histidine protein kinase. AIPs are usually thiolactones containing seven to nine amino acid residues in which the thiol of the central cysteine is linked to the alpha-carboxyl of the C-terminal amino acid residue. The staphylococcal agr locus has diverged such that the AIPs of the four different S. aureus agr groups self-activate but cross-inhibit. Consequently, although the agr system is conserved among the staphylococci, it has undergone significant evolutionary divergence whereby to retain functionality, any changes in the AIP-encoding gene (agrD) that modifies AIP structure must be accompanied by corresponding changes in the AgrC receptor. Since AIP-1 and AIP-4 only differ by a single amino acid, we compared the transmembrane topology of AgrC1 and AgrC4 to identify amino acid residues involved in AIP recognition. As only two of the three predicted extracellular loops exhibited amino acid differences, site-specific mutagenesis was used to exchange the key AgrC1 and AgrC4 amino acid residues in each loop either singly or in combination. A novel lux-based agrP3 reporter gene fusion was constructed to evaluate the response of the mutated AgrC receptors. The data obtained revealed that while differential recognition of AIP-1 and AIP-4 depends primarily on three amino acid residues in loop 2, loop 1 is essential for receptor activation by the cognate AIP. Furthermore, a single mutation in the AgrC1 loop 2 resulted in conversion of (Ala5)AIP-1 from a potent antagonist to an activator, essentially resulting in the forced evolution of a new AIP group. Taken together, our data indicate that loop 2 constitutes the predicted hydrophobic pocket that binds the AIP thiolactone ring while the exocyclic amino acid tail interacts with loop 1 to facilitate receptor activation.

The occipital lateral plate mesoderm - a novel source for vertebrate neck musculature

In vertebrates, body musculature originates from somites, whereas head muscles originate from the cranial mesoderm. Neck muscles are located in the transition between these regions. We show that the chick occipital lateral plate mesoderm has myogenic capacity and gives rise to large muscles located in the neck and thorax. We present molecular and genetic evidence to show that these muscles not only have a unique origin, but additionally display a distinct temporal development, forming later than any other muscle group described to date. We further report that these muscles, found in the body of the animal, develop like head musculature rather than deploying the programme used by the trunk muscles. Using mouse genetics we reveal that these muscles are formed in trunk muscle mutants but are absent in head muscle mutants. In concordance with this conclusion, their connective tissue is neural crest in origin. Finally, we provide evidence that the mechanism by which these neck muscles develop is conserved in vertebrates.

Feedback dew-point sensor utilising optimally cut plastic optical fibres

A plastic optical fibre reflectance sensor that makes full use of the critical angle of the fibres is implemented to monitor dew formation on a Peltier-cooled reflector surface. The optical configuration permits isolation of optoelectronic components from the sensing head and better light coupling between the reflector and the detecting fibre, giving a better signal of the onset of dew formation on the reflector. Continuous monitoring of the rate of change in reflectance as well as the absolute reflectance signals, the use of a novel polymethyl-methacrylate-coated hydrophobic film reflector on the Peltier element and the application of feedback around the point of dew formation, further reduces the possibility of contamination of the sensor head. Under closed-loop operation, the sensor is capable of cycling around the point of dew formation at a frequency of 2.5 Hz.

Charge measurements in stratiform cloud from a balloon based sensor

Abstract. The electrification of stratiform clouds has is little investigated in comparison with thunderstorms and fair weather atmospheric electricity. Theory indicates that, at the upper and lower horizontal boundaries of layer clouds, charging will arise from vertical flow of cosmogenic ions in the global atmospheric electric circuit. Charge is transferred to droplets and particles, affecting cloud microphysical processes such as collision and droplet activation. Due to the lack of in-situ measurements, the magnitude and distribution of charge in stratiform clouds is not well known. A sensitive, inexpensive, balloon borne charge sensor has been developed to make in-situ measurements of edge charging in stratiform cloud using a standard meteorological radiosonde system. The charge sensor has now been flown through over 20 stratiform clouds and frequently detected charge up to 200 pC m-3 near cloud edges. These results are compared with measurements from the same sensor used to investigate charge in particle layers, such as volcanic ash from the Eyjafjallajökull eruption, and Saharan dust in the Cape Verde Isles. 1.

A wind-tunnel study of flow distortion at a meteorological sensor on top of the BT Tower, London, UK

High quality wind measurements in cities are needed for numerous applications including wind engineering. Such data-sets are rare and measurement platforms may not be optimal for meteorological observations. Two years' wind data were collected on the BT Tower, London, UK, showing an upward deflection on average for all wind directions. Wind tunnel simulations were performed to investigate flow distortion around two scale models of the Tower. Using a 1:160 scale model it was shown that the Tower causes a small deflection (ca. 0.5°) compared to the lattice on top on which the instruments were placed (ca. 0–4°). These deflections may have been underestimated due to wind tunnel blockage. Using a 1:40 model, the observed flow pattern was consistent with streamwise vortex pairs shed from the upstream lattice edge. Correction factors were derived for different wind directions and reduced deflection in the full-scale data-set by <3°. Instrumental tilt caused a sinusoidal variation in deflection of ca. 2°. The residual deflection (ca. 3°) was attributed to the Tower itself. Correction of the wind-speeds was small (average 1%) therefore it was deduced that flow distortion does not significantly affect the measured wind-speeds and the wind climate statistics are reliable.

The occipital lateral plate mesoderm is a novel source for vertebrate neck musculature

In vertebrates, body musculature originates from somites, whereas head muscles originate from the cranial mesoderm. Neck muscles are located in the transition between these regions. We show that the chick occipital lateral plate mesoderm has myogenic capacity and gives rise to large muscles located in the neck and thorax. We present molecular and genetic evidence to show that these muscles not only have a unique origin, but additionally display a distinct temporal development, forming later than any other muscle group described to date. We further report that these muscles, found in the body of the animal, develop like head musculature rather than deploying the programme used by the trunk muscles. Using mouse genetics we reveal that these muscles are formed in trunk muscle mutants but are absent in head muscle mutants. In concordance with this conclusion, their connective tissue is neural crest in origin. Finally, we provide evidence that the mechanism by which these neck muscles develop is conserved in vertebrates.

Visible-near infrared spectroscopy sensor for predicting curd and whey composition during cheese processing

The potential of visible-near infrared spectra, obtained using a light backscatter sensor, in conjunction with chemometrics, to predict curd moisture and whey fat content in a cheese vat was examined. A three-factor (renneting temperature, calcium chloride, cutting time), central composite design was carried out in triplicate. Spectra (300–1,100 nm) of the product in the cheese vat were captured during syneresis using a prototype light backscatter sensor. Stirring followed upon cutting the gel, and samples of curd and whey were removed at 10 min intervals and analyzed for curd moisture and whey fat content. Spectral data were used to develop models for predicting curd moisture and whey fat contents using partial least squares regression. Subjecting the spectral data set to Jack-knifing improved the accuracy of the models. The whey fat models (R = 0.91, 0.95) and curd moisture model (R = 0.86, 0.89) provided good and approximate predictions, respectively. Visible-near infrared spectroscopy was found to have potential for the prediction of important syneresis indices in stirred cheese vats.

Novel on-line sensor technology for continuous monitoring of milk coagulation and whey separation in cheese making

The cheese industry has continually sought a robust method to monitor milk coagulation. Measurement of whey separation is also critical to control cheese moisture content, which affects quality. The objective of this study was to demonstrate that an online optical sensor detecting light backscatter in a vat could be applied to monitor both coagulation and syneresis during cheesemaking. A prototype sensor having a large field of view (LFV) relative to curd particle size was constructed. Temperature, cutting time, and calcium chloride addition were varied to evaluate the response of the sensor over a wide range of coagulation and syneresis rates. The LFV sensor response was related to casein micelle aggregation and curd firming during coagulation and to changes in curd moisture and whey fat contents during syneresis. The LFV sensor has potential as an online, continuous sensor technology for monitoring both coagulation and syneresis during cheesemaking.

Development of a light scatter sensor technology for on-line monitoring of milk coagulation and whey separation

The objective of this study was to investigate a novel light backscatter sensor, with a large field of view relative to curd size, for continuous on-line monitoring of coagulation and syneresis to improve curd moisture content control. A three-level, central composite design was employed to study the effects of temperature, cutting time, and CaCl2 addition on cheese making parameters. The sensor signal was recorded and analyzed. The light backscatter ratio followed a sigmoid increase during coagulation and decreased asymptotically after gel cutting. Curd yield and curd moisture content were predicted from the time to the maximum slope of the first derivative of the light backscatter ratio during coagulation and the decrease in the sensor response during syneresis. Whey fat was affected by coagulation kinetics and cutting time, suggesting curd rheological properties at cutting are dominant factors determining fat losses. The proposed technology shows potential for on-line monitoring of coagulation and syneresis. 2007 Elsevier Ltd. All rights reserved..

Viscous coupling of shear-free turbulence across nearly flat fluid interfaces

The interactions between shear-free turbulence in two regions (denoted as + and − on either side of a nearly flat horizontal interface are shown here to be controlled by several mechanisms, which depend on the magnitudes of the ratios of the densities, ρ+/ρ−, and kinematic viscosities of the fluids, μ+/μ−, and the root mean square (r.m.s.) velocities of the turbulence, u0+/u0−, above and below the interface. This study focuses on gas–liquid interfaces so that ρ+/ρ− ≪ 1 and also on where turbulence is generated either above or below the interface so that u0+/u0− is either very large or very small. It is assumed that vertical buoyancy forces across the interface are much larger than internal forces so that the interface is nearly flat, and coupling between turbulence on either side of the interface is determined by viscous stresses. A formal linearized rapid-distortion analysis with viscous effects is developed by extending the previous study by Hunt & Graham (J. Fluid Mech., vol. 84, 1978, pp. 209–235) of shear-free turbulence near rigid plane boundaries. The physical processes accounted for in our model include both the blocking effect of the interface on normal components of the turbulence and the viscous coupling of the horizontal field across thin interfacial viscous boundary layers. The horizontal divergence in the perturbation velocity field in the viscous layer drives weak inviscid irrotational velocity fluctuations outside the viscous boundary layers in a mechanism analogous to Ekman pumping. The analysis shows the following. (i) The blocking effects are similar to those near rigid boundaries on each side of the interface, but through the action of the thin viscous layers above and below the interface, the horizontal and vertical velocity components differ from those near a rigid surface and are correlated or anti-correlated respectively. (ii) Because of the growth of the viscous layers on either side of the interface, the ratio uI/u0, where uI is the r.m.s. of the interfacial velocity fluctuations and u0 the r.m.s. of the homogeneous turbulence far from the interface, does not vary with time. If the turbulence is driven in the lower layer with ρ+/ρ− ≪ 1 and u0+/u0− ≪ 1, then uI/u0− ~ 1 when Re (=u0−L−/ν−) ≫ 1 and R = (ρ−/ρ+)(v−/v+)1/2 ≫ 1. If the turbulence is driven in the upper layer with ρ+/ρ− ≪ 1 and u0+/u0− ≫ 1, then uI/u0+ ~ 1/(1 + R). (iii) Nonlinear effects become significant over periods greater than Lagrangian time scales. When turbulence is generated in the lower layer, and the Reynolds number is high enough, motions in the upper viscous layer are turbulent. The horizontal vorticity tends to decrease, and the vertical vorticity of the eddies dominates their asymptotic structure. When turbulence is generated in the upper layer, and the Reynolds number is less than about 106–107, the fluctuations in the viscous layer do not become turbulent. Nonlinear processes at the interface increase the ratio uI/u0+ for sheared or shear-free turbulence in the gas above its linear value of uI/u0+ ~ 1/(1 + R) to (ρ+/ρ−)1/2 ~ 1/30 for air–water interfaces. This estimate agrees with the direct numerical simulation results from Lombardi, De Angelis & Bannerjee (Phys. Fluids, vol. 8, no. 6, 1996, pp. 1643–1665). Because the linear viscous–inertial coupling mechanism is still significant, the eddy motions on either side of the interface have a similar horizontal structure, although their vertical structure differs.

A 96-well plate fluorescence assay for assessment of cellular permeability and active efflux in Salmonella enterica serovar Typhimurium and Escherichia coli

Multiply antibiotic-resistant (MAR) mutants of Escherichia coli and Salmonella enterica are characterized by reduced susceptibility to several unrelated antibiotics, biocides and other xenobiotics. Porin loss and/or active efflux have been identified as a key mechanisms of MAR. A single rapid test was developed for MAR. The intracellular accumulation of the fluorescent probe Hoechst (H) 33342 (bisbenzimide) by MAR mutants and those with defined disruptions in efflux pump and porin genes was determined in 96-well plate format. The accumulation of H33342 was significantly (P < 0.0001) reduced in MAR mutants of S. enterica serovar Typhimurium (n = 4) and E. coli (n = 3) by 41 +/- 8% and 17.3 +/- 7.2%, respectively, compared with their parental strains, which was reversed by the transmembrane proton gradient-collapsing agent carbonyl cyanide-m-chlorophenyl hydrazone (CCCP) and the efflux pump inhibitor phenylalanine-arginine-beta-naphthylamide (PA beta N). The accumulation of H33342 was significantly reduced in mutants of Salmonella Typhimurium with defined disruptions in genes encoding the porins OmpC, OmpF, OmpX and OmpW, but increased in those with disruptions in efflux pump components TolC, AcrB and AcrF. Reduced accumulation of H33342 in three other MAR mutants of Salmonella Typhimurium correlated with the expression of porin and efflux pump proteins. The intracellular accumulation of H33342 provided a sensitive and specific test for MAR that is cheap and relatively rapid. Differential sensitivity to CCCP and PA beta N provided a further means to phenotypically identify MAR mutants and the role of active efflux in each strain.