Long timestep dynamics of peptides by the dynamics driver approach

Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full α_R-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix–coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.     

An Australian trial of ThinPrep: a new cytopreparatory technique

To evaluate the sensitivity and suitability of ThinPrep, a new slide preparation technique, 2026 paired cervical cytology slides were examined. After conventional Papanicolaou smears were prepared, the sampling instruments were rinsed in a fluid fixative. ThinPrep slides were then prepared in the laboratory from the surplus cells in the fixative. Compared with the Pap smears, ThinPrep slides were easier and quicker to screen, were inconclusive less often, and had similar rates for detecting abnormalities and infection. There were more unsatisfactory ThinPrep slides and more ThinPrep slides lacked endocervical cells. Both of these shortcomings were found to be linked to the choice of sampling implements. This study, in which a variety of sampling instruments was used, fails to confirm some of the previous claims made for the new technique.     

Evaluation of sticky light traps for sampling mosquito larvae

Very simply constructed aquatic sticky light traps employing a chemical solution emitting a bright light attracted large numbers of all larval instars, but few pupae of Aedes cantans in trials in England. During April numbers of larvae per trap ranged from 73±14.2 to 163±19.9, whereas dipping with a ladle yielded only 6.9±5.5 to 11.8±7.7 larvae/dip. The traps were also effective in sampling larvae of Culiseta morsitans and in Sierra Leone larvae of Aedes aegypti. It was concluded that sticky light traps could be valuable in sampling relative numbers of mosquito larvae and merited further evaluation.

---

Résumé Des pièges adhésifs lumineux faciles à réaliser sont construits pour les captures des larves de moustiques. Ils sont formés de paires de boîtes de Pétri en plastique contenant une solution émettrice de lumière provenant de bâtons lumineux chimiques Cyalume^®. Chaque piège est recouvert d'une feuille de plastique de 16×16 cm enduite d'une substance qui reste adhésive sous l'eau. Les larves de moustiques attirées vers la source lumineuse viennent se coller à la feuille adhésive.Ces pièges ont été utilisés avec succès en Angleterre pour l'échantillonnage de tous les stades larvaires d'Aedes cantans, mais pas avec le même efficacité pour les nymphes. Des tests plus restreints ont montré que la technique était également utilisable pour les larves de Culiseta morsitans. Les nombres moyens d'A. cantans capturés pendant une piode de 12 h (73±14,2–163±19,9) étaient supérieux à ceux obtenus en plongeant une louche (6,9±5,5–11,8±7,7). En utilisant les pièges adhésifs lumineux, les captures moyennes de C. morsitans étaient également supérieures (12,6±4,7–35,8±8,9) contre (5,7±6,1–8,9±7,8) avec la méthode de la louche.En Sierra Leone, des stades larvaires immatures d'A. aegypti se développant dans des containers de stockage d'eau ont également pu être capturés à l'aide de ces pièges.Bien qu'une évaluation plus poussée soit encore nécessaire, il ne fait aucun doute que ces pièges adhésifs lumineux aient un intérêt considérable pour l'échantillonnage larvaire dans les sites inaccessibles, tels que les trous d'arbres ou les trous de crabes, où les méthodes d'échantillonage classiques sont souvent d'un emploi difficile.

     

Fast sampling,rapid filtration apparatus: Principal characteristics and validation from studies ofd-glucose transport in human jejunal brush-border membrane vesicles

Summary Kinetic data in (brush-border) membrane vesicles which rely on the validity of the initial rate assumption for their interpretation and depend on tracer flux studies using the rapid filtration technique for their experimental measurement have been limited to some extent by the absence of techniques that would allow for real-time data analysis. In this paper, we report on our successful design of a fast sampling, rapid filtration apparatus (FSRFA) which seems to fill up this technical gap since showing the following characteristics: (i) rapid injection (5 msec) and mixing (less than 100 msec) of small amounts of vesicles (10–40 l) with an incubation medium (0.2–1.0 ml); (ii) fast (20 to 80 msec depending on the sample volume) and multiple (up to 18 samples at a maximal rate of 4/sec) sampling of the uptake mixture followed by rapid quenching in the stop solution (approximately 5 msec) according to a predetermined time schedule (any time combination from 0.25 to 9999 sec); and (iii) fast, automated, and sampling-synchronized filtration and washings of the quenched uptake medium (only 15–20 sec are necessary for the first filtration followed by two washings and extra filtrations). As demonstrated using adult human jejunal brush-border membrane vesicles and Na⁺-d-glucose cotransport as models, the FSRFA accurately reproduces the manual aspects of the rapid filtration technique while allowing for very precise initial rate determinations. Moreover, the FSRFA has also been designed to provide as much versatility as possible and, in its present version, allows for a very precise control of the incubation temperature and also permits a few efflux protocols to be performed. Finally, its modular design, which separates the fast sampling unit from the rapid filtration device, should help in extending its use to fields other than transport measurement.     

Binomial sequential sampling of adult Saccharicoccus sacchari on sugarcane

The between-stalk dispersion characteristics of adults of the pink sugarcane mealybug Saccharicoccus sacchari (Cockerell) were determined in southern Queensland. Iwao's patchiness regression was inappropriate to describe the relationship between mean and variance. Taylor's power law indicated that adults were aggregated, especially at the beginning and end of the ratoon growth period. Binomial data were modelled by the Nachman model; the model of Grout and two models of Wilson & Room were inappropriate to describe the relationship between proportion of stalks infested and mean numbers of adults per stalk. Relationships to determine sample sizes for fixed levels of precision and binomial fixed-precision-level stop lines are developed for different sampling times using Taylor's power law and Nachman's equation.     

广西地区脑血管病城乡抽样对比分析

本文着重分析了广西城市和农村脑血管病发病情况的差异。我们发现城市CVD发病率、患病率明显高于农村,但是农村CVD的死亡率高于城市,其中我们对其原因作了初步的探讨。     

Automatic whole broth multi-fermentor sampling

Summary An efficient, aseptic method of obtaining whole broth fermentation samples was developed based on a piston-valve, a local sample loop, and an ability to drive the entire sample volume with sterile air through a sample line and into a remote tube. The configuration delivers 10-ml samples 10 m away with about 4 ml of broth wasted in the sampling process. An autosampler was enhanced and programmed to control acquisition into chilled tubes. The autosampler-based system represents a convenient way to provide frequent samples to profile intracellular and extracellular components for yeast and bacterial fermentations. A configuration to provide sampling from six fermentors with a multi-rack autosampler will be presented.     

Spatial distribution and sequential sampling of adults ofGonocephalum macleayi andPterohelaeus darlingensis in different cropping regimes

Counts of adults of the false wirewormsGonocephalum macleayi (Blackburn) andPterohelaeus darlingensis Carter in pitfall traps in burnt, mulched and sorghum treatments conformed to Taylor's power law. Within a species there were no significant differences in distributions of counts of either sex in any habitat butG. macleayi were more aggregated thanP. darlingensis (Taylor'sb 1.35 and 1.26, respectively). Relationships to determine sample sizes for fixed levels of precision and fixed-precision-level stop lines for sequential sampling are developed for each species using Taylor's parameters for combined data over all habitats.     

Spatial patterns and sampling plans for cereal aphids [Hom.: Aphididae] killed by entomophthoralean fungi and hymenopterous parasitoids in spring wheat

Cereal aphids infesting spring wheat in southwestern Idaho were surveyed during 1988 and 1989 for the presence of entomophthoralean fungi and hymenopterous parasitoids. Cereal aphids killed by the fungi (cadavers) and parasitoids (mummies) includedDiuraphis noxia (Mordvilko),Metopolophium dirhodum (Walker),Sitobion avenae (F.), andSchizaphis graminum (Rondani). Taylor's power law was used to describe the relationships between mean densities of cadavers or mummies (number per tiller) and associated variances. Except forS. graminum mummies, which were at low levels throughout the growing seasons and tended to be randomly distributed, Taylor's slopes exceeded 1.0 for all the aphid cadavers and mummies, indicating varying degrees of clumping in spatial pattern. The spatial patterns ofD. noxia andM. dirhodum cadavers were similar, simply reflecting those of their own populations, but more aggregated than were their respective mummies resulting from parasitoid attack. The intercepts and slopes from the power law analysis were used to generate functional relationships between the proportion of wheat tillers bearing cadavers or mummies of each aphid species and the mean density, and develop optimal numerical (direct counting) and binomial (presence or absence) sample size curves for both cadavers and mummies of each aphid species.