A measure of bending in nucleic acids structures applied to A-tract DNA.

A method is proposed to measure global bending in DNA and RNA structures. It relies on a properly defined averaging of base-fixed coordinate frames, computes mean frames of suitably chosen groups of bases and uses these mean frames to evaluate bending. The method is applied to DNA A-tracts, known to induce considerable bend to the double helix. We performed atomistic molecular dynamics simulations of sequences containing the A(4)T(4) and T(4)A(4) tracts, in a single copy and in two copies phased with the helical repeat. Various temperature and salt conditions were investigated. Our simulations indicate bending by roughly 10 degrees per A(4)T(4) tract into the minor groove, and an essentially straight structure containing T(4)A(4), in agreement with electrophoretic mobility data. In contrast, we show that the published NMR structures of analogous sequences containing A(4)T(4) and T(4)A(4) tracts are significantly bent into the minor groove for both sequences, although bending is less pronounced for the T(4)A(4) containing sequence. The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers.

Deep brain stimulation of the subthalamic nucleus and cognitive functions in Parkinson's disease.

Deep brain stimulation of the subthalamic nucleus (DBS/STN) is an effective treatment for motor symptoms in advanced Parkinson's disease (PD). However, it is less clear how DBS/STN affects cognitive functions. We investigated 19 PD patients (13 male, 6 female, mean age 57 +/- 6, mean PD duration 15 +/- 4 years) who received bilateral DBS/STN. Neuropsychological assessment was done before the surgery and at least 12 months after DBS implantation. The patients were examined in their optimal motor status. Global cognitive performance measured by Mattis Dementia Rating Scale was not significantly changed after DBS STN. The performance in Wechsler Memory Scale III decreased in the subtest Logical Memory, in delayed recall (p < 0.05) and in recognition (p < 0.05). In Stroop Test, the performance worsened in the second (p < 0.05), and third condition (p < 0.01) measuring interference and ability to suppress automatic reactions. In conclusion, patients treated by DBS/STN tend to worsen in executive functions and in logical memory.

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. The most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. To increase sampling of rare events, the native simulation was continued at 400 K. A partial, irreversible unfolding of the molecule was initiated by slippage of C8(N3+) relative to G12 and continued by sudden concerted changes in hydrogen-bonding involving A23, A24, and A25. These events were followed by a gradual loss of stacking interactions in loop 2. Of the Watson-Crick base-pairs, only the 5'-terminal pair of stem 1 dissociated at 400 K, while the trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature simulations were carried out to obtain insights into the structural and dynamic effects of selected mutations. In two of these, C8 was left unprotonated. Considerable local rearrangements occurred that were not observed in the crystal structure, thus confirming N3-protonation of C8 in the native molecule. We also investigated the effect of mutating C8(N3+) to U8, to correlate with experimental and phylogenetic studies, and of changing the G4 x C17 base-pair to A4 x U17 to weaken the trans sugar-edge interaction between positions 4 and 20 and to test models of unfolding. The simulations indicate that the C8 x G12 x C26 base-triple at the junction is the most labile region of the frame-shifting pseudoknot. They provide insights into the roles of the other non-Watson-Crick base-pairs in the early stages of unfolding of the pseudoknot, which must occur to allow readthrough of the message by the ribosome. The simulations revealed several critical, highly ordered hydration sites with close to 100 % occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50 % were also observed.

Spatial memory deficits in patients with lesions to the right hippocampus and to the right parahippocampal cortex.

Spatial memory tasks, performance of which is known to be sensitive to hippocampal lesions in the rat, or to medial temporal lesions in the human, were administered in order to investigate the effects of selective damage to medial temporal lobe structures of the human brain. The patients had undergone thermo-coagulation with a single electrode along the amygdalo-hippocampal axis in an attempt to alleviate their epilepsy. With this surgical technique, lesions to single medial temporal lobe structures can be carried out. The locations of the lesions were assessed by means of digital high-resolution magnetic resonance imaging and software allowing a 3-D reconstruction of the brain. A break in the collateral sulcus, dividing it into the anterior collateral sulcus and the posterior collateral sulcus is reported. This division may correspond to the end of the entorhinal/perirhinal cortex and the start of the parahippocampal cortex. The results confirmed the role of the right hippocampus in visuo-spatial memory tasks (object location, Rey-Osterrieth Figure with and without delay) and the left for verbal memory tasks (Rey Auditory Verbal Learning Task with delay). However, patients with lesions either to the right or to the left hippocampus were unimpaired on several memory tasks, including a spatial one, with a 30 min delay, designed to be analogous to the Morris water maze. Patients with lesions to the right parahippocampal cortex were impaired on this task with a 30 min delay, suggesting that the parahippocampal cortex itself may play an important role in spatial memory.

Increased REM density in narcolepsy-cataplexy and the polysymptomatic form of idiopathic hypersomnia.

The present work is focused on REM sleep density in patients with primary hypersomnia in comparison with non-hypersomnia subjects. 28 unmedicated patients with narcolepsy-cataplexy (NC) and 10 unmedicated patients suffering from the polysymptomatic form of idiopathic hypersomnia (IH) and their age- and sex-matched controls were included in the study. The clinical diagnosis was confirmed by MSLT and nocturnal PSG, HLA typing was performed in a respective group of narcoleptic patients. Polygraphical recordings were visually scored with particular regard to the two most characteristic phasic features of REM sleep: the number of rapid eye movements (REMs) and chin muscle twitches (Tws) per minute. These events were evaluated according to recognized criteria; a closer look was taken at both their frequency and their distribution across all the nocturnal REM periods (REMPs). The following main differences between hypersomniac patients (of both groups examined) and healthy controls were found in terms of phasic activity: (I) REM density (expressed in REMs/min and Tws/min in each REM period) was significantly increased in the hypersomniac patients in comparison with the controls. (p>0.05).(II) The intra-night phasic activity distribution was found rising more conspicuously in the hypersomniacs than in the controls.

[Effect of normalization of an isolated increase in TSH on the neuropsychological profile of patients]. / Vliv normalizace izolovane zvýseného TSH na neuropsychologický profil pacientu.

BACKGROUND: Isolated TSH increase--"subclinical hypothyreosis" (SH) appears to be comparatively common. Its incidence among women over sixty has been estimated up to 17%. Though SH was assumed to be entirely asymptomatic, recent findings revealed various fine subjective and objective symptoms of the disease. METHODS AND RESULTS: Twenty otherwise healthy female patients with SH diagnosis were examined. Using personality questionnaire MMPI/100 eight different clinical scales and two control scales were evaluated, using Wechsler's memory scale WM-R 5 memory quotients were tested. The group was randomised into a subgroup treated for six month with placebo and a subgroup where thyroxin was administrated and thyroidal test normalised. Psychological testing repeated before and after the treatment, results evaluated using paired t-test. Results indicate that: 1. Patients with SH did not differ in personality features, they only had a higher tendency to the depressive mood, which could be positively influenced by thyroxin (significance at 5% level). 2. Thyroxin treatment brought about improvement of some cognitive parameters of the verbal (p < 0.01), visual (p < 0.05), and general memory (p < 0.01). 3. Results of psychological and cognitive tests correlate better with FT4 than TSH level. CONCLUSIONS: Though SH cannot be associated with changes in personality features, TSH normalisation results in statistically significant improvement of cognitive function--verbal, visual and general memory.

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations.

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.

[The nocturnal eating syndrome (2 case reports and polysomnography)]. / Syndrom nocního ujídání (dve kazuistiky a polysomnografie).

The nocturnal eating syndrome (NES) is a nocturnal sleep disorder caused by repeated awakening and the inability to fall a sleep again unless the patient ingests some food or drinks something. In children the NES is frequent, in adults rather rare and may be associated with various pathological conditions. The latter include in particular somnabulism, periodic movements of the lower extremities, narcolepsy, chronic triazolam intoxication, probably anorexia nervosa, and other eating disorders. The authors submit two case-histories of middle aged women (30 and 37 years old) without disturbances of the day-time eating behaviour, without obvious psychopathology where the symptomatology of NES developed slowly from the age of 14 and 25 years resp. Both patients ate at night small amounts of easily consumed foods which they went to fetch in the kitchen as often as five times per night. Their behaviour was calm and aimed. Usually they did not remember the nocturnal eating. Polysomnographic examination in both patients revealed poor sleep with frequent changes of the sleep stages, with frequent awakenings, in both patients incl. even awakening from deep NREM sleep. The authors conclude that in these two patients NES with somnabulism is involved.

Changes of event related potential and cognitive processes in patients with subclinical hypothyroidism after thyroxine treatment.

OBJECTIVE: Recently, it has been repeatedly shown that patients with subclinical hypothyroidism (SH) formerly considered as completely symptom free, may have numerous minimal, often non-specific subjective complaints, and that in those patients it is possible to prove many subtle but objective deviations. We decided to quantify whether there are event related potential (ERP) deviations as electrophysiological markers of cognitive activity in patients with SH and whether ERP could be influenced by thyroxine treatment leading to normalization of TSH level in serum. SUBJECTS AND DESIGN: Event related potential (ERP) was examined in thirty one patients (mean age 52 +/- 12.5 years) with SH and without any other endocrine or metabolic diseases and in 29 subjects of the control group. From 31 patients 20 women (mean age 61.8 +/-6.8 years) were selected and divided into a group of 10 women treated six months with L-thyroxine until the normalization of TSH and remaining 10 women receiving placebo. ERP examination was repeated and all such patients also underwent neuropsychological examination consisting of the Wechsler Memory Scale and the MMPI/100 (Minnesota Multiphasic Personality Inventory). The interval between the diagnosis of SH and final evaluation of treatment was 16 months. RESULTS: In SH thyroxine treated patients the average P3 wave latency was 374 ms (SD 40.6), while in placebo group it was 340 ms (SD 32.3. P<0.01). In addition, the treatment with thyroxine normalized the TSH level resulted in a decrease of P3 wave latency from 374 +/- 36.3 ms to 343 +/- 16.3 ms (P<0.01). However, in the placebo group such changes were not observed, the latency of P3 being 387 +/- 24.3 ms at the beginning and 379 +/- 36.5 ms at the end of observation period. No significant correlations between P3 wave latency and thyroid parameters were found. In thyroxine treated group a significant improvement in verbal memory (P<0.01), visual memory (P<0.01) and total memory scores (P<0.01) was found, while no changes in these parameters were observed in the placebo group. No significant differences were found in the MMPI test evaluation. CONCLUSION: SH patients had significantly longer P3 wave latency in ERP examination as compared to healthy individuals which gives evidence for impaired cognitive functions in SH patients. In these patients the normalization of TSH level by thyroxine treatment resulted also in the normalization of P3 wave latency. In addition, also verbal, visual and total memory scores improved significantly with the TSH normalization.

Apomorphine induced cognitive changes in Parkinson's disease.

Auditory event related potentials (ERPs) and visual evoked potentials (VEPs) were recorded from eight patients with Parkinson's disease, before and after a single dose of apomorphine. To assess the treatment effects, the patients' motor state, Benton visual retention test (BVRT), and digit span tests were also examined. After apomorphine, although motor performance improved, the ERP latencies were delayed and the N2-P3 ERP amplitude was significantly diminished by comparison with pretreatment values. These data suggest that apomorphine induces, besides its motor effects in patients with Parkinson's disease, a slowing down of cognitive processing. Preferential stimulation of dopamine autoreceptors in mesocortical and mesolimbic systems may represent a neural mechanism for these effects. Also, the posttreatment BVRT rotation errors significantly increased, suggesting an apomorphine induced impairment of visuospatial perception.

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.

Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations.

Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.

[Excessive daytime somnolence and its psychosocial sequelae]. / Nadmerná denní spavost a její psychosociální dusledky.

Excessive daytime sleepiness arises frequently as a consequence of insufficient or shortened nocturnal sleep, or as a result of poor sleeps hygiene. One of the most common dyssomnias with imperative sleepiness is narcolepsy. Narcolepsy is a chronic disease that greatly affects quality of life. The present study of 57 patients shows that the negative assessment is partly due to the subjective views exhibited by the narcoleptic personality prone to underestimation, negative self-image and depressive disposition. The personality traits may be due to an adaptation reaction to the disease but also to the biological predisposition. Comparison with population data for our Republic brought no evidence of progress at education or family life being adversely affected by narcolepsy, however, decreased assertion in employment and limitation in self-realization in free time was an explicit consequence of the disease. All 57 patients reported excessive daytime sleepiness as the most discomforting symptom that in 40% of them was responsible for career curtailment in a productive age and for living on partial or full disability.