Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

Total root length as estimated from small sub-samples

A method is proposed for estimating the total length of a root system from sub-samples. This method is based on the measurement of the length and diameter of small pieces of roots, and on the measurements of the bulk density of root sub-samples. It is assumed that roots are cylinders with a given bulk density. The length and diameter of small root pieces are measured by image analysis. A weighted quadratic mean (W.Q.M.) root diameter is then calculated and used in estimating the root length. This W.Q.M. diameter is defined as the real mean diameter of an equivalent single root with the same length and volume as the tested root system. The accuracy of prediction is demonstrated for one theoretical root system. The standard deviation of estimation can be calculated using sampling simulations.     

Guild structure in solitary spider-hunting wasps (Hymenoptera: Pompilidae) compared with null model predictions

Abstract.

• 1 Three aspects of prey utilization are documented in a guild of spider-hunting pompilid wasps at a Breckland heath site: female phenology, size, and microhabitat utilization.
• 2 Twenty-four species were present at the site, 59% of the British fauna. Ten species individually represented more than 1% of the guild.
• 3 Pompilid abundance peaked in early July and mid-late August. Anoplius viaticus had a different life-history from other common guild members, making its inclusion in the guild questionable.
• 4 Most species represented by large samples occurred in all microhabitats and time intervals, and all species overlapped in size with all other species except A. viaticus. Arachnospila anceps was numerically dominant in all microhabitats and most time intervals.
• 5 Mean pair-wise overlaps in phenology and microhabitat utilization were significantly lower than predicted by null models, consistent with the idea that interspecific competition has been important in determining guild structure.
• 6 Female size is highly correlated with prey size, but the distribution of mean female sizes did not generally differ from null expectations.
• 7 Interpretation of comparisons with null models is problematic, particularly because it is difficult to quantify evolutionary ‘favourability’ of different resource states. Null models are currently of limited use because the patterns expected to result from key processes such as competition are uncertain in multi-dimensional systems.

     

Confidence Intervals on Ratios of Variance Components for the Unbalanced Two Factor Nested Model

The model considered in this article is the two-factor nested unbalanced variance component model: for p = 1, 2, …, P; q = 1, 2, …, Q_p; and r = 1, 2, …, R_pq. The random variables Y_pqr are observable. The constant μ is an unknown parameter, and A_p, B_pq and C_pqr are (unobservable) normal and independently distributed random variables with zero means and finite variances σ²_A, σ²_B, and σ²_C, respectively. Approximate confidence intervals on ?_A and ?_B using unweighted means are derived, where The performance of these approximate confidence intervals are evaluated using computer simulation. The simulated results indicate that these proposed confidence intervals perform satisfactorily and can be used in applied problems.     

Effect of Zeitgeber Intensity Reduction on a Simulated Dual-Oscillator Human Circadian System: Classical and Dynamic Analysis

The two-oscillator model of human circadian rhythmicity was analyzed when a zeitgeber relative intensity of 1, 0.5, or 0.1 was introduced into the equations. Fourier analysis was compared with dynamic analysis such as attractor reconstruction or Liapunov exponent calculation. After a 50 or 90% reduction in zeitgeber intensity, the dynamics of the system became equivalent and differed significantly from those of a system with maximal zeitgeber intensity. When 10% aleatory noise was added to the data, the analysis was still applicable, and the results obtained were essentially the same as in the absence of noise. Dynamic analysis could thus provide a distinct classification for periodic data, based on the type of analysis.     

Stochastic simulation of clonal growth in the tall goldenrod,Solidago altissima

Summary As clonal plants grow they move through space. The movement patterns that result can be complex and difficult to interpret without the aid of models. We developed a stochastic simulation model of clonal growth in the tall goldenrod, Solidago altissima. Our model was calibrated with field data on the clonal expansion of both seedlings and established clones, and model assumptions were verified by statistical analyses.When simulations were based on empirical distributions with long rhizome lengths, there was greater dispersal, less leaf overlap, and less spatial aggregation than when simulations were based on distributions with comparatively short rhizome lengths. For the field data that we utilized, variation in rhizome lengths had a greater effect than variation for either branching angles or rhizome initiation points (see text). We also found that observed patterns of clonal growth in S. altissima did not cause the formation of fairy rings. However, simulations with an artificial distribution of branching angles demonstrate that fairy rings can result solely from a plant's clonal morphology.Stochastic simulation models that incorporated variation in rhizome lengths, branching angles, and rhizome initiation points produced greater dispersal and less leaf overlap than deterministic models. Thus, variation for clonal growth parameters may increase the efficiency of substrate exploration by increasing the area covered and by decreasing the potential for intraclonal competition. We also demonstrated that ramet displacements were slightly, but consistently lower in stochastic simulation models than in random-walk models. This difference was due to the incorporation of details on rhizome bud initiation into stochastic simulation models, but not random-walk models. We discuss the advantages and disadvantages of deterministic, stochastic simulation, and random-walk models of clonal growth.     

神农架金丝猴的生态学观察

金丝猴(Rhinopithecus roxellanae)仅产于我国,属国家Ⅰ级保护动物,自然分布于四川、陕西、甘肃的部分地区和湖北省神农架自然保护区。1983年以来,笔者对神农架金丝猴生存环境生态习性等作了长期观察研究,结果报道如下。     

Reduced orthostatic tolerance following 4 h head-down tilt

The cardiovascular responses to a 10-min 1.22 rad (70 degrees) head-up tilt orthostatic tolerance test (OST) was observed in eight healthy men following each of a 5-min supine baseline (control), 4 h of 0.1 rad (6 degrees) head-down tilt (HDT), or 4 h 0.52 rad (30 degrees) head-up tilt (HUT). An important clinical observation was presyncopal symptoms in six of eight subjects following 4 h HDT, but in no subjects following 4 h HUT. Immediately prior to the OST, there were no differences in heart rate, stroke volume, cardiac output, mean arterial pressure and total peripheral resistance for HDT and HUT. However, stroke volume and cardiac output were greater for the control group. Mean arterial pressure for the control group was less than HDT but not HUT. Over the full 10-min period of OST, the mean arterial pressure was not different between groups. Heart rate increased to the same level for all three treatments. Stroke volume decreased across the full time period for control and HDT, but only at 3 and 9 min for HUT. There was a higher total peripheral resistance in the HDT group than control or HUT. The pre-ejection period to left ventricular ejection time ratio was less in HDT than for control or HUT groups. These data indicate a rapid adaptation of the cardiovascular system to 4 h HDT that appears to be inappropriate on reapplication of a head to foot gravity vector. We speculate that the cause of the impaired orthostatic tolerance is decreased tone in venous capacitance vessels so that venous return is inadequate.     

Aedes aegypti: model for blood finding strategy and prediction of parasite manipulation

Aedes aegypti mosquitoes salivate during intradermal probing of vertebrate prey before ingesting blood (Griffiths and Gordon 1952). Nonsalivating mosquitoes locate blood more slowly; this difference was ascribed to an anti-platelet activity found in the mosquito's saliva (Ribeiro et al. 1984). Mosquitoes infected with Plasmodium gallinaceum suffer pathology that specifically impairs saliva anti-hemostatic activity but without reducing volume of output (Rossignol et al. 1984). The complexity of the feeding apparatus of mosquitoes provides opportunity for a variety of strategies in which pathogens may produce specific lesions that enhance their transmission, but the variables that affect the duration of probing by mosquitoes have not been defined. We sought to resolve this complexity by identifying and quantifying relevant parameters of probing behavior. Mosquitoes thrust their mouthparts repeatedly through their host's skin while searching for blood. Female A. aegypti thrust at 7-sec intervals. If this search results in success, feeding ensues. Alternatively, the mosquito "desists," the mouthparts stylets are withdrawn, and the mosquito attempts to feed at another site. Even after previous desistance, the probability of finding blood remains undiminished. Functions for the probability of feeding success and desistance over time were derived using data from observations on 300 mosquitoes. The probability of feeding success was interpreted as being a function of the density of vessels in the skin, their geometric distribution, and the conditions locally affecting hemostasis. During each probe, the probability of desisting increased linearly with time, and after desisting once, mosquitoes tended to desist more rapidly. A model was developed incorporating Monte Carlo simulation which closely fit observed data. By changing values for the several parameters of the probability functions, we predicted modes in which parasites may manipulate their hosts to enhance transmission, both to and from the vector. In particular, parasite strategies in the vector would include induced salivary pathology; increased duration of probing thrusts; decreased desistance time; and inhibited phagoreception. Predicted parasite strategies in the reservoir host would include increased skin vascular volume and impaired host hemostasis. Our model supports the hypothesis of a mutualistic interaction of malaria and mosquitoes.