Monte carlo simulations of protein folding. II. Application to protein A,ROP, and crambin

The hierarchy of lattice Monte Carlo models described in the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338–352, 1994) is applied to the simulation of protein folding and the prediction of 3-dimensional structure. Using sequence information alone, three proteins have been successfully folded: the B domain of staphylococcal protein A, a 120 residue, monomeric version of ROP dimer, and crambin. Starting from a random expanded conformation, the model proteins fold along relatively well-defined folding pathways. These involve a collection of early intermediates, which are followed by the final (and rate-determining) transition from compact intermediates closely resembling the molten globule state to the native-like state. The predicted structures are rather unique, with native-like packing of the side chains. The accuracy of the predicted native conformations is better than those obtained in previous folding simulations. The best (but by no means atypical) folds of protein A have a coordinate rms of 2.25 Å from the native Cα trace, and the best coordinate rms from crambin is 3.18 Å. For ROP monomer, the lowest coordinate rms from equivalent Cαs of ROP dimer is 3.65 Å. Thus, for two simple helical proteins and a small α/β protein, the ability to predict protein structure from sequence has been demonstrated. © 1994 John Wiley & Sons, Inc.     

Photosynthetic gas exchange response of poplars to steady-state and dynamic light environments

The steady-state and dynamic photosynthetic response of two poplar species (Populus tremuloides and P. fremontii) to variations in photon flux density (PFD) were observed with a field portable gas exchange system. These poplars were shown to be very shade intolerant with high light saturation (800 to 1300 mol photons m^–2 s^–1) and light compensation (70 to 100 mol m^–2 s^–1) points. Understory poplar leaves showed no physiological acclimation to understory light environments. These plants become photosynthetically induced quickly (10 min). Activation of Rubisco was the primary limitation for induction, with stomatal opening playing only a minor role. Leaves maintained high stomatal conductances and stomata were unresponsive to variations in PFD. Leaves were very efficient at utilizing rapidly fluctuating light environments similar to those naturally occurring in canopies. Post-illumination CO₂ fixation contributed proportionally more to the carbon gain of leaves during short frequent lightflecks than longer less frequent ones. The benefits of a more dynamic understory light environment for the carbon economy of these species are discussed.     

NaN_3对叶绿体Mg~（2＋）－ATPase的抑制作用再探

ＮａＮ３能抑制新鲜菠菜叶片叶绿体经ＤＴＴ和光激活的Ｍｇ２＋－ＡＴＰａｓｅ活力。这种抑制属非竞争性抑制。ＮａＮ３还能降低新鲜菠菜叶片叶绿体的反映光合磷酸化高能态的毫秒延迟发光和减少反映类爱体膜质子吸收变化的叶绿体的９－氨基吖啶的荧光猝灭。菠菜叶片经低温贮存几天后其叶绿体的超微结构发生变化,ＮａＮ３对叶绿体的上述影响就消失或基本消失。本实验指出ＮａＮ３是新鲜叶片叶绿体Ｈ＋－ＡＴＰａｓｅ的一个强有力的抑制剂。其影响受叶绿体制剂的内源无机磷酸盐含量调节。     

An ecosystems approach to base-rich freshwater wetlands,with special reference to fenlands

A survey of base-rich wetlands in The Netherlands is presented. The main area of their occurrence is the low-lying Holocene part of the country, until some thousand years ago a large and coherent wetland landscape: the Holland wetland. The development of various parts of the Holland wetland into marshes, fens and bogs can be understood from hydrological relations in mire basins, as recognized in the distinction of primary, secondary and tertiary mire basin stages. Presently, the remnants of the Holland wetland are separate base-rich wetlands. The succession of their vegetation reflects various abiotic conditions and human influences. Three main developmental periods are distinguished as regards these factors. The first, geological period of mire development is seen as a post-glacial relaxation, with the inertia due to the considerable mass of wetland as a stabilizing factor. Biological “grazing” influences, as an aspect of utilization by humans, converted base-rich wetlands to whole new types in the second, historical period. Presently, mass and harvesting have decreased in importance, and actual successions in terrestrializing turbaries seem to reflect rapidly changing environmental conditions. Human control could well become the most important factor in the future development of wetland nature. The present value of open fen vegetation strongly depends on the continuation of the historical harvesting. The development of wooded fen may help to increase the mass of wetland in the future. Best results in terms of biodiversity are expected when their base state is maintained through water management. The vegetation and hydrology of floating fens in terrestrializing turbaries is treated in some more detail. Various lines and phases in the succession are distinguished. Open fen vegetation at base-rich, yet nutrient-poor sites is very rich in species threatened elsewhere. The fast acidification of certain such fens is attributed to hydrological and management factors. This acidification is illustrated in the profile of a floating raft sample. At the scale of these small fens, the elemental structure comprising base-rich fen, transitional fen and bog vegetation, is not as stable as it was in the large Holland wetland. A critical role seems to be played by the supply of bases with the water influx. The changing base state is supposed to change the nutrient cycling to such an extent that it would be correct to call this trophic excitation of the ecosystem, rather than just eutrophication. Eutrophication indicates a quantitative reaction to an increased nutrient supply, the internal system being unaltered. The drainage of fens, resulting in an increased productivity of the vegetation, provides another example of excitation, to the effect that the functional system is dramatically changed internally.     

Environmental and physiological factors influencing phototactic flight of Bemisia tabaci

Abstract. Experiments were conducted in a glasshouse and in the laboratory to determine the environmental and physiological parameters that affect flight behaviour of Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae). The number of whiteflies taking off and exhibiting a positive response to sky light in the glasshouse was greatest from 08.30 to 10.00 hours. During peak flight activity less than 5% of the population engaged in phototactic orientation. Temperature was the best single predictor for the phototactic response, accounting for 75% of the variability in whitefly ascent. Sex ratios were determined for individuals remaining on poinsettia, Euphorbia pulcherrima (Willd.), and for individuals that exhibited phototactic orientation; both groups deviated from an expected 1:1 ratio. Males were more prevalent on the plants (1:0.76), whereas females were much more prevalent (1:3.02) among the whiteflies responding to sky light. A higher percentage of the females displaying a phototactic response contained eggs when compared to females remaining on poinsettia (87 v 65%). The two groups of females did not differ significantly in their weights, but males that remained on the plants were heavier than males that responded to sky light. Mark–recapture studies and experiments where phototactic individuals were removed from the population established that the response was short-lived. Whiteflies exhibiting a phototactic response in the glasshouse were more likely to exhibit long-duration, phototactic flights in a vertical flight chamber when compared to individuals that remained on poinsettia (80.7 ± 6.7 v 36.0 ± 5.8% phototactic response; 7.0 ±3.2 v 0.7±0.2min flights). There was also less deviation in flight across the horizontal plane among the individuals that exhibited a positive response to sky light in the glasshouse in comparison to individuals that remained on their host. However, initial rates of climb were not significantly different between the two groups of whiteflies.     

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

Temperature dependence of thermal inactivation rate constants of bacterial spores in a glassy state

Summary Differential scanning calorimetry data obtained from corn embryos is consistent with the hypothesis of their glassy state. This work extends that hypothesis to explain the speculation about the high heat resistance of bacterial spores. By considering the protoplast to be in a glassy solid-state, it can be assumed that the configurational rearrangements of the key life dependent polymer chain backbones (DNA, etc.) are extremely slow, thereby ceasing thermal motions. It is assumed that at the glass transition temperature, the spore protoplast undergoes a discontinuity in the thermal expansion coefficient, and above this critical temperature, the rate of thermal inactivation of spores is free volume dependent and can be described adequately by the William, Landel and Ferry (WLF) equation. Glass transition temperatures forBacillus stearothermophilus andClostridium botulinum spores, obtained by fitting the inactivation rate data to the WLF equation, indicate a decrease in the inactivation rates with increasing glass-transition temperatures.     

Joyful by nature: approaches to investigate the evolution and function of joy in non-human animals

The nature and evolution of positive emotion is a major question remaining unanswered in science and philosophy. The study of feelings and emotions in humans and animals is dominated by discussion of affective states that have negative valence. Given the clinical and social significance of negative affect, such as depression, it is unsurprising that these emotions have received more attention from scientists. Compared to negative emotions, such as fear that leads to fleeing or avoidance, positive emotions are less likely to result in specific, identifiable, behaviours being expressed by an animal. This makes it particularly challenging to quantify and study positive affect. However, bursts of intense positive emotion (joy) are more likely to be accompanied by externally visible markers, like vocalisations or movement patterns, which make it more amenable to scientific study and more resilient to concerns about anthropomorphism. We define joy as intense, brief, and event-driven (i.e. a response to something), which permits investigation into how animals react to a variety of situations that would provoke joy in humans. This means that behavioural correlates of joy are measurable, either through newly discovered ‘laughter’ vocalisations, increases in play behaviour, or reactions to cognitive bias tests that can be used across species. There are a range of potential situations that cause joy in humans that have not been studied in other animals, such as whether animals feel joy on sunny days, when they accomplish a difficult feat, or when they are reunited with a familiar companion after a prolonged absence. Observations of species-specific calls and play behaviour can be combined with biometric markers and reactions to ambiguous stimuli in order to enable comparisons of affect between phylogenetically distant taxonomic groups. Identifying positive affect is also important for animal welfare because knowledge of positive emotional states would allow us to monitor animal well-being better. Additionally, measuring if phylogenetically and ecologically distant animals play more, laugh more, or act more optimistically after certain kinds of experiences will also provide insight into the mechanisms underlying the evolution of joy and other positive emotions, and potentially even into the evolution of consciousness.     

Structural analysis based on state-space modeling.

A new method has been developed to compute the probability that each amino acid in a protein sequence is in a particular secondary structural element. Each of these probabilities is computed using the entire sequence and a set of predefined structural class models. This set of structural classes is patterned after Jane Richardson''s taxonomy for the domains of globular proteins. For each structural class considered, a mathematical model is constructed to represent constraints on the pattern of secondary structural elements characteristic of that class. These are stochastic models having discrete state spaces (referred to as hidden Markov models by researchers in signal processing and automatic speech recognition). Each model is a mathematical generator of amino acid sequences; the sequence under consideration is modeled as having been generated by one model in the set of candidates. The probability that each model generated the given sequence is computed using a filtering algorithm. The protein is then classified as belonging to the structural class having the most probable model. The secondary structure of the sequence is then analyzed using a "smoothing" algorithm that is optimal for that structural class model. For each residue position in the sequence, the smoother computes the probability that the residue is contained within each of the defined secondary structural elements of the model. This method has two important advantages: (1) the probability of each residue being in each of the modeled secondary structural elements is computed using the totality of the amino acid sequence, and (2) these probabilities are consistent with prior knowledge of realizable domain folds as encoded in each model. As an example of the method''s utility, we present its application to flavodoxin, a prototypical alpha/beta protein having a central beta-sheet, and to thioredoxin, which belongs to a similar structural class but shares no significant sequence similarity.