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M Zacharias

Publications and source records attributed to M Zacharias.

At least 37 records · Page 2Linked to original sources
PubMed2000

Conformational deformability of RNA: a harmonic mode analysis.

The harmonic mode analysis method was used to characterize the conformational deformability of regular Watson-Crick paired, mismatch- and bulge-containing RNA. Good agreement between atomic Debye-Waller factors derived from x-ray crystallography of a regular RNA oligonucleotide and calculated atomic fluctuations was obtained. Calculated helical coordinate fluctuations showed a small sequence dependence of up to approximately 30-50%. A negative correlation between motions at a given base pair step and neighboring steps was found for most helical coordinates. Only very few calculated modes contribute significantly to global motions such as bending, twisting, and stretching of the RNA molecules. With respect to a local helical description of the RNA helix our calculations suggest that RNA bending is mostly due to a periodic change in the base pair step descriptors slide and roll. The presence of single guanine:uridine or guanine:adenine mismatches had little influence on the calculated RNA flexibility. In contrast, for tandem guanine:adenine base pairs the harmonic mode approach predicts a significantly reduced conformational flexibility in the case of a sheared arrangement and slightly enhanced flexibility for a face-to-face (imino proton) pairing relative to regular RNA. The presence of a single extra adenine bulge nucleotide stacked between flanking sequences resulted in an increased local atomic mobility around the bulge site (approximately 40%) and a slightly enhanced global bending flexibility. For an adenine bulge nucleotide in a looped-out conformation a strongly enhanced bulge nucleotide mobility but no increased bending flexibility compared to regular RNA was found.

Adenine↗
PubMed2000

Simulation of the structure and dynamics of nonhelical RNA motifs.

Computer simulation methods are increasingly being used to study possible conformations and dynamics of structural motifs in RNA. Recent results of molecular dynamics simulations and continum solvent studies of RNA structures and RNA-ligand complexes show promising agreement with experimental data. Combined with the ongoing progress in the experimental characterization of RNA structure and thermodynamics, these computational approaches can help to better understand the mechanism of RNA structure formation and the binding of ligands.

Animals↗
PubMed1999

Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.

The analysis and prediction of non-canonical structural motifs in RNA is of great importance for an understanding of the function and design of RNA structures. A hierarchical method has been employed to generate a large variety of sterically possible conformations for a single-base adenine bulge structure in A -form DNA and RNA. A systematic conformational search was performed on the isolated bulge motif and neighboring nucleotides under the constraint to fit into a continuous helical structure. These substructures were recombined with double-stranded DNA or RNA. Energy minimization resulted in more than 300 distinct bulge conformations. Energetic evaluation using a solvation model based on the finite-difference Poisson-Boltzmann method identified three basic classes of low-energy structures. The three classes correspond to conformations with the bulge base stacked between flanking nucleotides (I), location of the bulge base in the minor groove (II) and conformations with a continuous stacking of the flanking helices and a looped out bulge base (III). For the looped out class, two subtypes (IIIa and IIIb) with different backbone geometries at the bulge site could be distinguished. The conformation of lowest calculated energy was a class I structure with backbone torsion angles close to those in standard A -form RNA. Conformations very close to the extra-helical looped out bulge structure determined by X-ray crystallography were also among the low-energy structures. In addition, topologies observed in other experimentally determined bulge structures have been found among low-energy conformers. The implicit solvent model was further tested by comparing an uridine and adenine bulge flanked by guanine:cytosine base-pairs, respectively. In agreement with the experimental observation, a looped out form was found as the energetically most favorable form for the uridine bulge and a stacked conformation in case of the adenine bulge. The inclusion of solvation effects especially electrostatic reaction field contributions turned out to be critically important in order to select realistic low-energy bulge structures from a large number of sterically possible conformations. The results indicate that the approach might be useful to model the three-dimensional structure of non-canonical motifs embedded in double-stranded RNA, in particular, to restrict the number of possible conformations to a manageable number of conformers with energies below a certain threshold.

DNA↗
PubMed1999

Stereoselective urinary excretion of bupivacaine and its metabolites during epidural infusion.

A sensitive and efficient chiral assay for bupivacaine and its three principal metabolites desbutylbupivacaine, 4'-hydroxybupivacaine, and 3'-hydroxybupivacaine has been applied to urine from five male patients receiving postoperative epidural infusions of rac-bupivacaine fentanyl over 60-120 hr. The fraction of the dose of bupivacaine (total dose 840-2093 mg) accounted for in urine was 75 +/- 6%. The rate of excretion of bupivacaine enantiomers' approximated a steady state after approximately 30 hr with values of 1.27 +/- 0.26 and 0.76 +/- 0.13 mg hr-1 for (R)- and (S)-enantiomers, respectively. The fraction of the dose of bupivacaine enantiomer excreted unchanged in the urine (fe) varied from 14.3% to 39.1% for (+)-(R)-bupivacaine and 9.2% to 14.0% for (-)-(S)-bupivacaine in the five patients. The rate of excretion of all metabolites also reached a steady state after approximately 30 hr and the relative amounts of metabolites excreted into urine (fm) suggest bupivacaine is subject to regioselective and stereoselective clearance, which may vary from patient to patient.

Aged↗
PubMed1998

[Equipment-independent ultrasound tissue characterization of testis and prostate].

The result of a B-scan ultrasound examination is strongly dependent on the type of the used B-system, the chosen system parameters and the experience and critical analysis of the clinical investigator. The estimation of quantitative acoustic parameters, independent of the type of the used B-system, is one way to overcome the subjective nature and the problems of the interpretation of B-scan images. A procedure was developed to determine acoustical tissue specific parameters (ultrasound attenuation, relative backscatter coefficient) in terms of the ultrasound spectroscopy and to correct the system effects. A requirement for the calculation of acoustical parameters is the availability of primary rf echo signals without any preprocessing. Up to now measurements of phantom materials and in-vivo investigations on human testis and prostate have been carried out. The effects of pathological changes in the tissue state on the acoustical parameters are demonstrated in some examples.

Artifacts↗
PubMed1998

Two methods of administration of propofol for dental sedation.

Propofol was used for intravenous sedation in a group of 19 healthy fit young patients undergoing third molar extractions. We compared two ways of giving the drug, patient-controlled and operator-controlled, in a crossover trial. There were no differences between the two methods. The psychomotor functions returned to normal by 60 min, there was a high incidence of partial or complete amnesia and both methods were acceptable to 18/19 patients. There were only minimal changes in the respiratory function, and oxygen saturation remained normal. The only problem noted was mild pain on injection in 4 patients.

Adolescent↗
PubMed1998

Tenoxicam does not alter renal function during anaesthesia in normal individuals.

BACKGROUND: Anaesthesia and surgery alter renal function. Inhibition of prostaglandin synthesis by non-steroidal anti-inflammatory drugs (NSAIDs) administered with anaesthesia may further compromise renal function. AIM: To study the effects of tenoxicam (NSAID) administered immediately prior to anaesthesia on renal function in normal individuals undergoing routine surgery. METHODS: A randomised single blind placebo controlled study comparing tenoxicam (40 mg intravenously) with placebo was carried out in 20 healthy (ASA I) patients undergoing lower spinal surgery. Glomerular filtration rate (GFR) was determined by creatinine clearance and renal tubular function measured as osmolar and free water clearance. RESULTS: GFR fell by 60% at the end of surgery but returned to pre-operative values by six hours post-operatively. There was no difference between placebo or tenoxicam with regard to changes in GFR. Tubular function was not altered by tenoxicam. CONCLUSIONS: Current clinical practice of using NSAIDs for post-operative analgesia in low risk individuals appears to have no adverse effects on renal function.

Adult↗
PubMed1998

Comparison of oral and intravenous routes of giving tenoxicam.

Twenty-five fit patients undergoing third molar surgery received the non-steroidal anti-inflammatory drug tenoxicam 40 mg given orally the night before surgery or intravenously at the time of surgery in a randomised, double-blind, cross-over trial. Propofol was used for intravenous sedation. Pain on injection was noted with propofol in 32-56 percent of subjects, but was mostly of minor nature. There was high (100 percent) acceptance of the method of sedation, with 60-84 percent rate of amnesia. Experience of post-operative pain, intake of medication, and trismus were similar with both methods of administration of tenoxicam. We conclude that both oral and intravenous administration of 40 mg tenoxicam are equally effective in healthy young patients undergoing third molar surgery.

Administration, Oral↗
PubMed1997

Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations.

Bends in nucleic acid helices can be quantified in a transient electric birefringence (TEB) experiment from the ratio of the terminal decay times of the bent molecule and its fully duplex counterpart (tau-ratio method). The apparent bend angles can be extracted from the experimental tau-ratios through the application of static (equilibrium-ensemble) hydrodynamic models; however, such models do not properly address the faster component(s) of the birefringence decay profile, which can represent up to 80% of the total birefringence signal for large band angles. To address this latter issue, the relative amplitudes of the components in the birefringence decay profile have been analyzed through a series of Brownian dynamics (BD) simulations. Decay profiles have been simulated for three-, five-, and nine-bead models representing RNA molecules with central bends of 30 degrees, 60 degrees, and 90 degrees, and with various degrees of associated angle dispersion. The BD simulations are in close agreement with experimental results for the fractional amplitudes, suggesting that both amplitudes and terminal tau-ratios can be used as a measure of the magnitudes of bends in the helix axis. Although the current results indicate that it is generally not possible to distinguish between relatively fixed and highly flexible bends from single tau-ratio measurements, because they can lead to similar reductions in terminal decay time and amplitude, measurements of the dependence of the fractional amplitudes on helix length may afford such a distinction.

Algorithms↗
PubMed1997

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.

A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form.

Adenine↗
PubMed1996

The influence of symmetric internal loops on the flexibility of RNA.

Internal loops are structural elements, often highly conserved, that are found in many RNA molecules of biological importance. They consist of short stretches of sequence in which the bases in one strand are not able to form canonical pairs with bases in the other strand, and are bounded on either side by helical RNA. In an effort to examine the influence of internal loops on the relative angular orientations of the flanking helices, we have quantified the apparent bend angles for symmetric internal loops of the form A(n)-A(n) and U(n)-U(n) (n=2, 4, and 6), located at the center of 150 to 154 bp RNA molecules, using the method of transient electric birefringence. This hydrodynamic method exploits the extreme sensitivity of the rate of rotational reorientation of the RNA molecules to the presence and magnitude of internal bends and/or points of increased flexibility. The birefringence decay behavior of the loop-containing RNA molecules was found to be much less strongly influenced by the presence of symmetric internal loops than by bulges of the same sequence and size. This general observation is mirrored by the electrophoretic behavior of the loop-containing molecules, which are much less strongly retarded on polyacrylamide gels than are corresponding, bulge-containing RNA molecules. The apparent bend angles for the symmetric loops range from approximately 20 degrees to 40 degrees as n is increased 2 to 6 with a marginal shift to smaller angles in the presence of Mg2+. The apparent angles were similar when represented either as fixed bends of the specified angles (static representation), or as points of increased flexibility of specified root-mean-square angle (dynamic representation). For the. For the latter representation, the corresponding angular dispersion would correspond to a loop persistence length of approximately 60 to 150 A, compared to 700 A for duplex RNA and depending slightly on sequence and buffer conditions.

Base Sequence↗
PubMed1996

The absence of any pre-emptive analgesic effect for non-steroidal anti-inflammatory drugs.

Pre-emptive analgesic efficacy of the non-steroidal anti-inflammatory drug, diclofenac sodium, was tested in 21 young, fit, patients undergoing third molar extractions in a double-blind, randomised, cross-over, trial. Pain scores and mouth opening were observed for 1 week after the operation and these did not show any differences following pre- and postoperative oral administration of diclofenac sodium 100 mg (P > 0.05). There were no differences in the patients' preference for the two methods of treatment (P > 0.05). The study suggests that the non-steroidal anti-inflammatory drug diclofenac sodium does not cause any significant pre-emptive analgesic effects in the dose administered.

Adult↗
PubMed1996

Nitrous oxide and the rate of gas uptake from an unventilated lung in dogs.

We have studied the effect of FIO2 of a nitrous oxide-oxygen mixture on the rate of gas uptake from an unventilated lung. Nine anaesthetized dogs were studied, each breathing four nitrous oxide-oxygen mixtures (FIO2 0.3, 0.5, 0.75 and 1.0) in random order. A double-lumen endobronchial tube separated lung ventilation. Both lungs were given the nitrous oxide-oxygen mixture for an equilibration period. Then the right lung was connected to a spirometer containing the same gas, and gas uptake measured. In every dog, gas uptake was faster with an FIO2 of 0.5 or 0.75 than with an FIO2 of 1.0. When breathing a nitrous oxide-oxygen mixture with FIO2 > 0.3, the rate of gas uptake from the unventilated lung was faster than with 100% oxygen.

Anesthetics, Inhalation↗
PubMed1996

Effectiveness of preoperative analgesics on postoperative dental pain: a study.

Patients undergoing extractions of third molar teeth under general anesthesia were given a placebo, diclofenac (a nonsteroidal anti-inflammatory drug) 100 mg, or methadone (an opiate) 10 mg 60 to 90 min prior to surgery, and their pain scores and postoperative medication requirements were measured for 3 days. All patients received local anesthetic blocks and analgesic drugs during the perioperative period. There were no significant differences between the three groups in the pain scores and medication requirements during the period of study. It was concluded that preoperative use of nonsteroidal anti-inflammatory drugs and opiates may not offer a preemptive analgesic effect in patients who have had adequate analgesia during the surgery. Continued use of analgesic drugs during the postoperative period is perhaps more useful for this purpose. There appears to be a higher incidence of vomiting following opiates (methadone), precluding its clinical use in day-care patients.

Adult↗
PubMed1996

Respiratory effects of intravenous midazolam.

Thirty-four healthy, young-adult patients receiving intravenous midazolam for third-molar surgery had their respiratory parameters measured by respiratory inductive plethysmography. Tidal volume and minute volume showed significant changes during the initial 5-10 minutes of sedation, the changes being maximal during the first 5 minutes from the completion of injection of midazolam. The measurement of phase angle, an indicator of respiratory asynchrony, showed no significant change from normal, although a few patients showed some asynchrony of breathing, suggesting some amount of respiratory obstruction. A few patients showed a short period of apnoea and a small fall in the oxygen saturation. None of these changes caused any clinical concerns. It is suggested that the absence of stimulation after injection of midazolam, particularly in the initial few minutes, may contribute to the potential onset of respiratory problems.

Adolescent↗