Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings

The structure of the ¹³C,¹⁵N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond ¹H-¹³C, ¹H-¹⁵N, ¹³C-¹³C and ¹³C-¹⁵N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.     

Program MULDER -- a tool for extracting torsion angles from NMR data

MULDER (Mostly UniversaL Dihedral angle ExtractoR) is a program for extraction of torsion angle information from NMR data. Currently, it can analyze two types of input data: The torsion angle data, where several ³J-coupling constants and/or interatomic distances are combined in order to reduce the torsion angle ambiguity arising from solving the isolated Karplus (or distance) equation, and the sugar pucker data, where the dynamics of five-membered sugar rings is evaluated by postprocessing the results calculated from ³J_(HH) coupling constants by program PSEUROT. Program MULDER can be used either as an alternative to r-MD programs in situations where only specific structural features are studied, or as a preparatory tool in connection with full r-MD structure calculation for extraction of unambiguous torsion angle restraints.     

Improved gas chromatographic-mass spectrometric determination of the N-methylcarbamoyl adduct at the N-terminal valine of globin,a metabolic product of the solvent N,N-dimethylformamide

A sensitive method for determination of the N-methylcarbamoyl adduct at the N-terminal valine of globin, a new metabolic product of the industrial solvent N,N-dimethylformamide (DMF), has been developed and validated. The method includes conversion of the adduct by the Edman degradation to 3-methyl-5-isopropylhydantoin (MVH), which is followed by optimized gas chromatographic analysis with mass spectrometric detection at m/z 114. The recovery of MVH from terminal N-methylcarbamoylvaline was determined using a model dipeptide to be 90%. Calibration of the method is done with MVH, employing 3-methyl-5-isobutylhydantoin as the internal standard. The limit of detection is 0.2 nmol MVH/g globin when a 100-mg sample is used. Within- and between-day precision is 4-10%. The method has been used to determine the background levels of MVH in unexposed subjects. Further, toxicokinetic studies in volunteers laid the grounds for setting the reference value for biological monitoring of occupational exposure to DMF.     

The spectral analysis of syllables in patients using dentures

Changes in the oral cavity resulting from the loss of teeth and the ensuing reconstruction of a set of teeth by dentures (partial or complete) may cause changes in the speech and voice of the patient. The aim of the present investigation was to study the changes in speech and voice in patients suffering from teeth loss and the degree of speech improvement using dentures. Voice and speech parameters of a set of tested syllables were analysed in 10 patients at the 2nd Clinic of Stomatology. The analysis was carried out by means of an FFT, SoundForge 5.0 programme. Differently expressed acoustic changes in both consonants and vowels were ascertained in a percentage of the patients under examination. These concerned especially the sibilant ("s", "(see text)"), labiodental ("f", "v") and vibrating ("r", "(see text)") consonants. Changes in the FFT spectrum and air leakage in constrictive consonants were also found. In some patients the vowels, especially the closed ones ("i", "u"), may change their fundamental frequency and show noise admixture manifested as a blurred delimitation of the formants. A denture should, inter alia, render it possible for the patient to produce the same articulation to which he/she had been accustomed before the loss of teeth. For the construction of dentures the most important factors from a phonetic point of view appear to be the following: overbite, overjet, the height of the plate, the thickness of the palatal material, the incisor position, and the modelling of the ruga palatina on the hard palate. In case of wrong denture construction the acoustic changes may continue, resulting in the patient's stress load dependent upon sex, age, psychic condition and seriousness of the problem.     

Venous hypertension following average arterious-venous fistula for haemodialysis

The authors emphasize the need for the investigation of the central venous system prior to the insertion of an avfistula, this they consider to be of utmost importance in patients with anamnesis of central vessel access. After the av-fistula is inserted, an unrecognized obstacle (stenosis or thrombosis) may result in the occurrence of venous hypertension and hypofunction, this may lead to av-fistula malfunction.     

Serodiagnostics of chlamydial infections--significance of positivity in IgA and/or IgM antibody classes only

There was followed the development of serological findings in patients with proved positivity only in classes IgA and/or IgM of chlamydial antibodies (without IgG), which can be suspected of showing "false" positivity. 184 patients were repeatedly examined for chlamydial antibodies in their sera (interval between collections up to three months) using a genus specific rELISA. Sera were also tested for the evidence of IgM antibodies against capside antigen of Epstein-Barr virus (EBV) and against cytomegalovirus (CMV) using ELISA methods. In 75 (40.8%) of patients, IgA/IgM individual positivities were demonstrated even during the following sample test(s). In 28 (15.2%) of them, IgG evidence preceded and in 29 (15.7%) other patients positive seroconversion followed in this class. In 13 (7.1%) patients, IgG antibodies disappeared and subsequently reappeared. Only in 39 (21.2%) of these probands, antibodies IgA/IgM were not demonstrated at another examination. Active EBV, resp. CMV infection was proved in 24 (13.0%), resp. in 18 (9.8%) of patients. It is concluded that the evidence of positivities only in classes IgA and/or IgM mostly signal the onset of a primary infection (reinfection) or an active infection in patients with IgG production failures respectively. In these cases, a "false" positivity can be supposed to occur only in a minor extent.     

Coding of periodic pulse stimulation in chemoreceptors

In natural conditions odorants released continuously by animals and plants are broken in discontinuous clumps and filaments. In the case of flying insects these discontinuities are perceived as periodic variations in the concentration of the stimulus. This periodicity has been shown to be essential to orientation and location of mate and food. We study analytically and numerically a model of the receptor-ligand interaction that takes place in the receptor neurons. We show that this model can account quantitatively for the range of optimum stimulus frequencies measured experimentally in the sex-pheromone system of moths. The results obtained suggest that the rate constants characterising the pheromone-receptor interaction are optimally adapted to the temporal characteristics of the signal it perceives.     

Analysis of the role of RecQ helicases in RNAi in mammals

The identity of mammalian genes involved in RNA interference (RNAi), the targeted sequence-specific mRNA degradation by double-stranded RNA (dsRNA), is poorly defined. Here we report the analysis of mice with null mutations of Wrn, Blm, and RecQ1 genes that are related to Mut-7 and Qde3, two genes essential for RNAi in Caenorhabditis elegans and quelling in Neurospora, respectively. Our results suggest that Wrn, Blm, and RecQ1 are not involved in sequence-specific mRNA degradation in mammals in response to dsRNA, suggesting potential differences in the mammalian RNAi pathway.     

Vibrational circular dichroism spectroscopy study of paroxetine and femoxetine precursors

The solution structures of (3R,4S)- and (3S,4R)- 4-(4-fluorophenyl)-3-hydroxylmethyl- 1-methylpiperidine, which are intermediates in the synthesis of the two pharmaceuticals paroxetine and femoxetine, were studied by vibrational circular dichroism (VCD) spectroscopy. In addition, six derivatives with different substituents attached to the C3 atom were prepared and their VCD and absorption spectra discussed with the aid of ab initio simulations. The VCD spectra were found to be sensitive to the geometry changes. In addition, a subtle variation caused by intermolecular aggregation was apparent in the spectra. The VCD technique can be applied for structural analysis of chiral pharmaceuticals in solutions.     

Structural features of two distinct molecular complexes of copper(II) cationic porphyrin and deoxyribonucleotides

The associations of the water-soluble cationic copper(II)-5,10,15,20-meso-tetrakis(4-N-methylpyridyl) porphyrin (CuP) with d(pT)9 oligothymidylate and its building blocks deoxythymidine (dT) and deoxythymidine 5'-monophosphate (dTMP) were investigated by spectrophotometric titration [absorption, nanosecond transient resonance Raman (ns-RR) and picosecond time-resolved resonance Raman (ps-TR3) spectroscopies] to elucidate the structural requirements for the CuP exciplex formation in molecular complexes with unchained mononucleotides. In the d(pT)9 a factor analysis and global fit of the CuP absorption spectra revealed the formation of a single spectral species attributable to a 1 : 1 CuP. d(pT)9 complex throughout a wide range of d(pT)9/CuP ratios (0-10). Using ps-TR3 spectroscopy, the CuP. d(pT)9 complex was shown to be fully responsible for exciplex formation. In contrast, CuP mixed with dTMP ([dTMP]/[CuP] < 3000) yielded two spectroscopically distinct types of molecular complexes with 1 : 1 (CuP. dTMP) and 1 : 2 (CuP. (dTMP)2) (or even higher for [dTMP]/[CuP] > 3000) stoichiometry, the latter being spectroscopically identical to the CuP. d(pT)9 and providing a microenvironment favorable for exciplex formation to the same extent as the oligothymidylate. On the other hand, the 1 : 1 CuP. dTMP complex (prevailing for [dTMP]/[CuP] < 100) yielded no exciplex features. Similar behavior was observed for the CuP complexed with dT. To explain the difference in the ability of the CuP. dTMP and CuP. (dTMP)2 species to form the exciplex, two types of molecular complexes were suggested and discussed, differing in the orientation of the thymine planes with respect to the porphyrin macrocycle.