3D visualization of HIV virions by cryoelectron tomography.

The structure of the human immunodeficiency virus (HIV) and some of its components have been difficult to study in three-dimensions (3D) primarily because of their intrinsic structural variability. Recent advances in cryoelectron tomography (cryo-ET) have provided a new approach for determining the 3D structures of the intact virus, the HIV capsid, and the envelope glycoproteins located on the viral surface. A number of cryo-ET procedures related to specimen preservation, data collection, and image processing are presented in this chapter. The techniques described herein are well suited for determining the ultrastructure of bacterial and viral pathogens and their associated molecular machines in situ at nanometer resolution.

Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography.

Genetic and biochemical studies have suggested the existence of a bacteriophage-like, DNA-packaging/ejecting portal complex in herpesviruses capsids, but its arrangement remained unknown. Here, we report the first visualization of a unique vertex in the Kaposi's sarcoma-associated herpesvirus (KSHV) capsid by cryoelectron tomography, thus providing direct structural evidence for the existence of a portal complex in a gammaherpesvirus. This putative KSHV portal is an internally localized, umbilicated structure and lacks all of the external machineries characteristic of portals in DNA bacteriophages.

A COMPARISON OF TWO METHODS FOR THE DETECTION OF FECAL POLLUTION IN DRINKING WATER (HYDROGEN SULFIDE, INDICATOR, MODIFICATION)

A new technique for the detection of microbiological fecal pollution in drinking and in raw surface water has been modified and tested against the standard multiple-tube fermentation technique (most-probable-number, MPN). The performance of the new test in detecting fecal pollution in drinking water has been tested at different incubation temperatures. The basis for the new test was the detection of hydrogen sulfide produced by the hydrogen sulfide producing bacteria which are usually associated with the coliform group. The positive results are indicated by the appearance of a brown to black color in the contents of the fermentation tube within 18 to 24 hours of incubation at 35 (+OR-) .5(DEGREES)C. For this study 158 water samples of different sources have been used. The results were analyzed statistically with the paired t-test and the one-way analysis of variance. No statistically significant difference was noticed between the two methods, when tested 35 (+OR-) .5(DEGREES)C, in detecting fecal pollution in drinking water. The new test showed more positive results with raw surface water, which could be due to the presence of hydrogen sulfide producing bacteria of non-fecal origin like Desulfovibrio and Desulfomaculum. The survival of the hydrogen sulfide producing bacteria and the coliforms was also tested over a 7-day period, and the results showed no significant difference. The two methods showed no significant difference when used to detect fecal pollution at a very low coliform density. The results showed that the new test is mostly effective, in detecting fecal pollution in drinking water, when used at 35 (+OR-) .5(DEGREES)C. The new test is effective, simple, and less expensive when used to detect fecal pollution in drinking water and raw surface water at 35 (+OR-) .5(DEGREES)C. The method can be used for qualitative and/or quantitative analysis of water in the field and in the laboratory. ^

Therapeutic drug monitoring of once daily aminoglycoside dosing: comparison of two methods and investigation of the optimal blood sampling strategy.

PURPOSE Therapeutic drug monitoring of patients receiving once daily aminoglycoside therapy can be performed using pharmacokinetic (PK) formulas or Bayesian calculations. While these methods produced comparable results, their performance has never been checked against full PK profiles. We performed a PK study in order to compare both methods and to determine the best time-points to estimate AUC0-24 and peak concentrations (C max). METHODS We obtained full PK profiles in 14 patients receiving a once daily aminoglycoside therapy. PK parameters were calculated with PKSolver using non-compartmental methods. The calculated PK parameters were then compared with parameters estimated using an algorithm based on two serum concentrations (two-point method) or the software TCIWorks (Bayesian method). RESULTS For tobramycin and gentamicin, AUC0-24 and C max could be reliably estimated using a first serum concentration obtained at 1 h and a second one between 8 and 10 h after start of the infusion. The two-point and the Bayesian method produced similar results. For amikacin, AUC0-24 could reliably be estimated by both methods. C max was underestimated by 10-20% by the two-point method and by up to 30% with a large variation by the Bayesian method. CONCLUSIONS The ideal time-points for therapeutic drug monitoring of once daily administered aminoglycosides are 1 h after start of a 30-min infusion for the first time-point and 8-10 h after start of the infusion for the second time-point. Duration of the infusion and accurate registration of the time-points of blood drawing are essential for obtaining precise predictions.

Speech outcome in complete unilateral cleft lip and palate - a comparison of three methods of the hard palate closure.

The aim of this study was to compare the speech in subjects with cleft lip and palate, in whom three methods of the hard palate closure were used. One hundred and thirty-seven children (96 boys, 41 girls; mean age = 12 years, SD = 1·2) with complete unilateral cleft lip and palate (CUCLP) operated by a single surgeon with a one-stage method were evaluated. The management of the cleft lip and soft palate was comparable in all subjects; for hard palate repair, three different methods were used: bilateral von Langenbeck closure (b-vL group, n = 39), unilateral von Langenbeck closure (u-vL group, n = 56) and vomerplasty (v-p group, n = 42). Speech was assessed: (i) perceptually for the presence of a) hypernasality, b) compensatory articulations (CAs), c) audible nasal air emissions (ANE) and d) speech intelligibility; (ii) for the presence of compensatory facial grimacing, (iii) with clinical intra-oral evaluation and (iv) with videonasendoscopy. A total rate of hypernasality requiring pharyngoplasty was 5·1%; total incidence post-oral compensatory articulations (CAs) was 2·2%. The overall speech intelligibility was good in 84·7% of cases. Oronasal fistulas (ONFs) occurred in 15·7% b-vL subjects, 7·1% u-vL subjects and 50% v-p subjects (P < 0·001). No statistically significant intergroup differences for hypernasality, CAs and intelligibility were found (P > 0·1). In conclusion, the speech after early one-stage repair of CUCLP was satisfactory. The method of hard palate repair affected the incidence of ONFs, which, however, caused relatively mild and inconsistent speech errors.

The effects of type of interval, sensory modality, base duration, and psychophysical task on the discrimination of brief time intervals

The present study was designed to investigate the influences of type of psychophysical task (two-alternative forced-choice [2AFC] and reminder tasks), type of interval (filled vs. empty), sensory modality (auditory vs. visual), and base duration (ranging from 100 through 1,000 ms) on performance on duration discrimination. All of these factors were systematically varied in an experiment comprising 192 participants. This approach allowed for obtaining information not only on the general (main) effect of each factor alone, but also on the functional interplay and mutual interactions of some or all of these factors combined. Temporal sensitivity was markedly higher for auditory than for visual intervals, as well as for the reminder relative to the 2AFC task. With regard to base duration, discrimination performance deteriorated with decreasing base durations for intervals below 400 ms, whereas longer intervals were not affected. No indication emerged that overall performance on duration discrimination was influenced by the type of interval, and only two significant interactions were apparent: Base Duration × Type of Interval and Base Duration × Sensory Modality. With filled intervals, the deteriorating effect of base duration was limited to very brief base durations, not exceeding 100 ms, whereas with empty intervals, temporal discriminability was also affected for the 200-ms base duration. Similarly, the performance decrement observed with visual relative to auditory intervals increased with decreasing base durations. These findings suggest that type of task, sensory modality, and base duration represent largely independent sources of variance for performance on duration discrimination that can be accounted for by distinct nontemporal mechanisms.

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called “similarity mapplets” allowing interactive content browsing and linked to a “Multifingerprint Browser for ChEMBL” (also accessible directly at www.gdb.unibe.ch) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30 300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.