Structural parameters affecting the kinetics of RNA hairpin formation.

There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program 'Kinfold'. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem-loop structures.

Comparison of quantitative shear wave MR-elastography with mechanical compression tests.

The mechanical properties of in vivo soft tissue are generally determined by palpation, ultrasound measurements (US), and magnetic resonance elastography (MRE). While it has been shown that US and MRE are capable of quantitatively measuring soft tissue elasticity, there is still some uncertainty about the reliability of quantitative MRE measurements. For this reason it was decided to determine in vitro how MRE measurements correspond with other quantitative methods of measuring characteristic elasticity values. This article presents the results of experiments with tissue-like agar-agar gel phantoms in which the wavelength of strain waves was measured by shear wave MR elastography and the resultant shear modulus was compared with results from mechanical compression tests with small gel specimens. The shear moduli of nine homogeneous gels with various agar-agar concentrations were investigated. The elasticity range of the gels covered the elasticity range of typical soft tissues. The systematic comparison between shear wave MRE and compression tests showed good agreement between the two measurement techniques.

A pH-jump approach for investigating secondary structure refolding kinetics in RNA.

It has been shown that premature translation of the plasmid-mediated toxin in hok/sok of plasmid R1 and pnd/pndB of plasmid R483 is prevented during transcription of the hok and pnd mRNAs by the formation of metastable hairpins at the 5'-end of the mRNA. Here, an experimental approach is presented, which allows the accurate measurement of the refolding kinetics of the 5'-end RNA fragments in vitro without chemically modifying the RNA. The method is based on acid denaturation followed by a pH-jump to neutral pH as a novel way to trap kinetically favoured RNA secondary structures, allowing the measurement of a wide range of biologically relevant refolding rates, with or without the use of standard stopped-flow equipment. The refolding rates from the metastable to the stable conformation in both the hok74 and pnd58 5'-end RNA fragments were determined by using UV absorbance changes corresponding to the structural rearrangements. The measured energy barriers showed that the refolding path does not need complete unfolding of the metastable structures before the formation of the final structures. Two alternative models of such a pathway are discussed.

Effects of gender and age on the cardiac baroreceptor reflex in hypertension.

The present study examined whether alterations in the cardiac baroreceptor reflex in hypertension may be a function of constitutional differences associated with gender and age. These hypotheses were tested using a cross-sectional design that compared 20 normotensive and 21 hypertensive men and women of varying age for differences in baroreceptor reflex sensitivity and response latency for heart rate, obtained using a modified bolus phenylephrine (Oxford) method. Relative to their respective normotensive controls, baroreceptor reflex sensitivity was reduced in hypertensive men, but not in hypertensive women. Among normotensive subjects, men had greater baroreceptor reflex sensitivity than women. Independent from the effects associated with differences in blood pressure, age was not a significant predictor of reduction in baroreceptor reflex sensitivity. However, a combination of high blood pressure and older age was associated with a significant increase in baroreceptor reflex response time. In summary, gender and aging interacted with hypertension to alter two different aspects of the baroreceptor reflex. These results provide a preliminary indication that a decline in arterial baroreflex sensitivity may be more specific to hypertension in men than in women. Prolongation in baroreflex response latency in older hypertensive subjects also suggested that aging and hypertension may have a synergistic effect on cardiac parasympathetic function.

Metastable structures and refolding kinetics in hok mRNA of plasmid R1.

Programmed cell death by hok/sok of plasmid R1 and pnd/pndB of R483 mediates plasmid maintenance by killing of plasmid-free cells. It has been previously suggested that premature translation of the plasmid-mediated toxin is prevented during transcription of the hok and pnd mRNAs by the formation of metastable hairpins in the mRNA at the 5' end. Here, experimental evidence is presented for the existence of metastable structures in the 5' leader of the hok and pnd mRNAs in vitro. The kinetics of refolding from the metastable to the stable structure in the isolated fragments of the 5' ends of both the hok and pnd mRNAs could be estimated, in agreement with the structural rearrangement in this region, as predicted to occur during transcription and mRNA activation. The refolding rates of hok and pnd structures are slow enough to allow for the formation of downstream hairpin structures during elongation of the mRNAs, which thereby helps to stabilize the metastable structures. Thus, the kinetic refolding parameters of the hok and pnd mRNAs are consistent with the proposal that the metastable structures prevent premature translation and/or antisense RNA binding during transcription.

Signal fidelity requirements for deriving impedance cardiographic measures of cardiac function over a broad heart rate range.

Our findings indicate that the impedance cardiogram spectrum extends from DC to 50 Hz. Any amplifier with an upper band limit less than 50 Hz can be expected to produce attenuation and distortion of the impedance cardiogram. This signal attenuation may be systematically enhanced under conditions of high heart rate when a greater proportion of signal energy will be in the upper frequency range of the impedance cardiogram spectrum. Therefore, the present study was designed to assess the influence of amplifier bandwidth on dZ/dtmax, stroke volume, and systolic time intervals (LVET, PEP, QZ, QX). Simultaneously measured delta Z and dZ/dt signals from two impedance cardiographs, with corner frequencies of 120 and 60 Hz for the delta Z and 50 and 15 Hz for dZ/dt channels, were contrasted over a broad range of heart rate (70-150 bpm). In addition to the analog dZ/dt signals obtained from the instruments, the delta Z signals were digitally converted to dZ/dt by off-line digital differentiation with a 50 Hz corner frequency. The results demonstrated that the measurements with the 15 Hz corner frequency, when compared with the 50 Hz corner frequency measurements, systematically attenuated the dZ/dtmax amplitude and stroke volume measurements as heart rate increased. The attenuation of dZ/dtmax and stroke volume ranged from about 13% to 26% as heart rate increased from 70 to 150 bpm. When the upper bandlimit was 50 Hz, the dZ/dt signal had greater resolution of waveform events and produced less prolonged systolic time intervals. The 15 Hz amplifier differentially influenced the B point, Z-peak and X minimum, having no apparent effect on the temporal location of the B point, but delaying the Z-peak about 21.7 ms and the X minimum about 7.4 ms. These findings indicate that impedance cardiographs with insufficient upper bandlimits will differentially influence ICG-derived measurements as heart rate varies.

Differential patterns of dynamic cardiovascular regulation as a function of task.

In cardiovascular reactivity studies, interpretations of the processes supporting the blood pressure response may become problematic when systolic blood pressure, diastolic blood pressure, and heart rate all increase in response to a behavioral challenge. Therefore, in addition to evaluating these cardiovascular responses, this study examined cardiac output, total peripheral resistance and systolic time intervals derived from impedance cardiogram, electrocardiogram and phonocardiogram recordings during a speech stressor, a mirror tracing task, and a foot cold pressor test. All of the behavioral stressors elicited increases in blood pressure and heart rate, with the largest changes occurring during the overt speech. Based on the examination of the response patterns of the underlying hemodynamic variables it would appear that, in both men and women, the blood pressure increase during the speech preparation period was supported by increased cardiac output; the speech itself resulted in a mixed pattern of increased cardiac output and total peripheral resistance; whereas, the mirror tracing and cold pressor tasks produced increased total peripheral resistance. Although men and women produced similar response patterns to the behavioral challenges, sex differences in the estimates of myocardial contractility were observed during rest. These results provide evidence that different behavioral stressors can produce a distinct yet integrated pattern of responses, whose differences may be revealed, when impedance cardiography is used, to derive sufficient response measures for assessing dynamic cardiovascular processes.

New signal processing techniques for improved precision of noninvasive impedance cardiography.

Impedance cardiographic determination of clinically important cardiac parameters such as systolic time intervals, stroke volume, and related cardiovascular parameters has not yet found adequate application in clinical practice, since its theoretical basis remains controversial, and the precision of beat-to-beat parameter estimation has until recently suffered under severe shortcomings of available signal processing techniques. High levels of noise and motion artifacts deteriorate signal quality and result in poor event detection. To improve the precision of impedance cardiography, new techniques for event detection and parameter estimation have been developed. Specifically, matched filtering and various signal segmentation and decomposition techniques have been tested on impedance signals with various levels of artificially superimposed noise and on actual recordings from subjects in a laboratory study of cardiovascular response to a cognitive challenge. Substantial improvement in the precision of impedance cardiography was obtained using the newly developed signal processing techniques. In addition, some preliminary evidence from comparisons of the impedance cardiogram with invasive aortic electromagnetic flow measurement in anesthetized rabbits is presented to address questions relating to the origin of the impedance signal.