Structural plasticity in RNA and its role in the regulation of protein translation in coliphage Q beta

We have analyzed both conformational and functional changes caused by two large cis-acting deletions (delta 159 and delta 549) located within the read-through domain, a 850 nucleotide hairpin, in coliphage Q beta genomic RNA. Studies in vivo show that co-translational regulation of the viral coat and replicase genes has been uncoupled in viral genomes carrying deletion delta 159. Translational regulation is restored in deletion delta 549, a naturally evolved pseudorevertant. Structural analysis by computer modeling shows that structural features within the read-through domain of delta 159 RNA are less well determined than they are in the read-through domain of wild-type RNA, whereas predicted structure in the read-through domain of evolved pseudorevertant delta 549 is unusually well determined. Structural analysis by electron microscopy of the genomic RNAs shows that several long range helices at the base of the read-through domain, that suppress translational initiation of the viral replicase gene in the wild-type genome, have been destabilized in delta 159 RNA. In addition, the structure of local hairpins within the read-through region is more variable in delta 159 RNA than in wild-type RNA. Stable RNA secondary structure is restored in the read-through domain of delta 549 RNA. Our analyses suggest that structure throughout the read-through domain affects the regulation of viral replicase expression by altering the likelihood that long-range interactions at the base of the domain will form. We discuss possible kinetic and equilibrium models that can explain this effect, and argue that observed changes in structural plasticity within the read-through domain of the mutant genomes are key in understanding the process. During the course of these studies, we became aware of the importance of the information contained in the energy dot plot produced by the RNA secondary structure prediction program mfold. As a result, we have improved the graphical representation of this information through the use of color annotation in the predicted optimal folding. The method is presented here for the first time.     

p-aminohippurate uptake by syncytial microvillous membrane vesicles of human term placenta

The mechanism of uptake of p-aminohippurate (PAH) by syncytial microvillous membrane vesicles of human term placenta was investigated. Initial PAH uptake and efflux were increased in the presence of a pH-gradient and a Cl(-)-gradient, respectively. Forced negative and positive membrane potentials did not influence the uptake, which indicated that the transport is not electrogenic. The pH-dependent increase is probably the result of a higher rate of diffusion due to a lower degree of dissociation of PAH. Because several organic anions failed to transstimulate PAH uptake and FCCP did not decrease the uptake in the presence of an inwardly directed H(+)-gradient, ruling out a PAH/OH- antiport, an anion exchange system does not appear to be present in these membranes. Since electrogenicity and anion exchange seem not to be involved in the Cl(-)-dependent increase, an allosteric effect of Cl- on the transporter might be possible. Various organic anions were able to inhibit pH-stimulated PAH uptake significantly. Kinetic analysis of the probenecid sensitive part of uptake provided further evidence for mediated transport of PAH (Km = 7.4 +/- 2.6 mM and Vmax = 2.0 +/- 0.4 nmol/mg/15 s). Non-inhibitable diffusion accounted for the main part of total transport. Concentration dependent inhibition of PAH transport by probenecid showed a Ki of 2.5 +/- 0.9 mM. It is concluded that human placental syncytial microvillous membrane vesicles possess a low affinity transport mechanism for PAH with low specificity. The importance of this system, for placental excretion of anionic drugs, will depend on the intrasyncytial concentration of these drugs, caused by the transport across the basal membrane.     

Editorial: Special Issue on “Texture Analysis and Synthesi”

International Journal of Computer Vision -     

An overview of ultra-wideband microwave imaging via space-time beamforming for early-stage breast-cancer detection

Ultra-wideband (UWB) microwave imaging has recently been proposed for detecting small malignant breast tumors. In this article, we review the current research status of this approach. First, we introduce the concept of microwave imaging via space-time (MIST) beamforming and related signal-processing algorithms. The objective of these signal-processing techniques is to form a spatial image of scattered microwave energy, and to identify the presence and location of malignant lesions from their scattering signatures. Next, we present numerical studies based on finite-difference time-domain simulations to demonstrate the efficacy of MIST beamforming for detecting small malignant breast lesions in both prone and supine configurations. Finally, the experimental feasibility of UWB microwave imaging is demonstrated using an initial imaging prototype and multilayered breast phantoms.     

Passive-Based Walking Robot

In this article, we presented our passive-based biped Denise. Using only two foot contact switches as sensors and simple on/off pneumatic muscle action, it walks at 0.4 m/s and can handle floor disturbances up to 6 mm (leg length is 0.7 m). Its simplicity, efficiency, and die natural look of its motions make it a promising lead for the development of commercially viable humanoid robots. The aim of this article is to provide other researchers enough details so that they can reproduce the work or use it as a basis for future research.     

Axisymmetric extrusion through adaptable dies—Part 1: Flexible velocity fields and power terms

An adaptable die is one that not only produces the correct geometrical shape, but also is designed through an adaptable method to impart other desirable properties to the product or process. In this first part of a series of papers, six kinematically admissible velocity fields are developed for use in upper bound models for axisymmetric extrusion through various dies, including extrusion through adaptable dies. Three base velocity fields are presented:

(1) assuming proportional angles in the deformation zone,

(2) assuming proportional areas in the deformation zone, or

(3) assuming proportional distances from the centerline in the deformation zone.

The base velocity is modified by an additional term comprised of two functions. One function allows extra flexibility in the radial direction, and the second function allows extra flexibility in the angular direction. There are two forms of the second function, which meet the required boundary conditions. The flexibility function in the radial direction is represented by a series of Legendre polynomials, which are orthogonal over the deformation region. The power terms derived for these velocity fields for use in upper bound models are also presented.Part 2 of this series compares the results obtained in upper bound models for the six velocity fields for a spherical extrusion die. In Part 3, the use of the best velocity field for extrusion through streamlined dies is developed to determine the adaptable die shape, which minimizes the required extrusion pressure. Additionally, the adaptable die shape is compared with results from Yang and Han for arbitrarily curved and streamlined dies.     

On-body propagation velocity estimation using ultra-wideband frequency-domain spatial correlation analyses

On-body communications around the human torso are considered, using ultra-wideband transmissions. The velocity of the diffracted wave propagating around the body is extracted from frequency- domain spatial correlation analyses.     

High modulus of isotactic polypropylene attained by coextrusion with atactic polystyrene

Orientation-induced crystallization of crystallizable polymer melts can occur, under certain conditions, during flow through converging channels. Attempts have been made to achieve this phenomenon in a two-phase system, i.e., during simultaneous extrusion of a continuous concentric core of polypropylene within a polystyrene matrix through a conical duct. On one occasion, using Carlona P SY6100 (MFI = 11.0) with Hostyren N2000-V-01 (MFI = 25.0), a highly oriented polypropylene thread with a modulus of 14.6 GPa and a melting point of 178°C was extruded at a die temperature of approximately 170°C and a pressure lower than 40 MPa. It is, in principle, possible to form highly oriented, fiber-like structures as reinforcing elements in a polymer matrix.     

The Construction of Minimal DNA Expressions

We describe a formal language/notation for DNA molecules that may contain nicks and gaps. The elements of the language, DNA expressions, denote formal DNA molecules. Different DNA expressions may denote the same formal DNA molecule. We analyse the shortest DNA expressions denoting a given formal DNA molecule. We determine lower bounds on their lengths and explain how we construct these minimal DNA expressions.