Information‐theoretic analysis of the reference state in contact potentials used for protein structure prediction

Using information‐theoretic concepts, we examine the role of the reference state, a crucial component of empirical potential functions, in protein fold recognition. We derive an information‐based connection between the probability distribution functions of the reference state and those that characterize the decoy set used in threading. In examining commonly used contact reference states, we find that the quasi‐chemical approximation is informatically superior to other variant models designed to include characteristics of real protein chains, such as finite length and variable amino acid composition from protein to protein. We observe that in these variant models, the total divergence, the operative function that quantifies discrimination, decreases along with threading performance. We find that any amount of nativeness encoded in the reference state model does not significantly improve threading performance. A promising avenue for the development of better potentials is suggested by our information‐theoretic analysis of the action of contact potentials on individual protein sequences. Our results show that contact potentials perform better when the compositional properties of the data set used to derive the score function probabilities are similar to the properties of the sequence of interest. Results also suggest to use only sequences of similar composition in deriving contact potentials, to tailor the contact potential specifically for a test sequence. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Genetic networks regulated by ASYMMETRIC LEAVES1 (AS1) and AS2 in leaf development in Arabidopsis thaliana: KNOX genes control five morphological events

The asymmetric leaves 1 ( as1 ) and as2 mutants of Arabidopsis thaliana exhibit pleiotropic phenotypes. Expression of a number of genes, including three class-1 KNOTTED -like homeobox ( KNOX ) genes ( BP , KNAT2 and KNAT6 ) and ETTIN / ARF3 , is enhanced in these mutants. In the present study, we attempted to identify the phenotypic features of as1 and as2 mutants that were generated by ectopic expression of KNOX genes, using multiple loss-of-function mutations of KNOX genes as well as as1 and as2 . Our results revealed that the ectopic expression of class-1 KNOX genes resulted in reductions in the sizes of leaves, reductions in the size of sepals and petals, the formation of a less prominent midvein, the repression of adventitious root formation and late flowering. Our results also revealed that the reduction in leaf size and late flowering were caused by the repression, by KNOX genes, of a gibberellin (GA) pathway in as1 and as2 plants. The formation of a less prominent midvein and the repression of adventitious root formation were not, however, related to the GA pathway. The asymmetric formation of leaf lobes, the lower complexity of higher-ordered veins, and the elevated frequency of adventitious shoot formation on leaves of as1 and as2 plants were not rescued by multiple mutations in KNOX genes. These features must, therefore, be controlled by other genes in which expression is enhanced in the as1 and as2 mutants.     

A plasma global metabolic profiling approach applied to an exercise study monitoring the effects of glucose, galactose and fructose drinks during post-exercise recovery

A global metabolic profiling methodology based on gas chromatography coupled to time-of-flight mass spectrometry (GC-TOFMS) for human plasma was applied to a human exercise study focused on the effects of beverages containing glucose, galactose, or fructose taken after exercise and throughout a recovery period of 6 h and 45 min. One group of 10 well trained male cyclists performed 3 experimental sessions on separate days (randomized, single center). After performing a standardized depletion protocol on a bicycle, subjects consumed one of three different beverages: maltodextrin (MD)+glucose (2:1 ratio), MD+galactose (2:1), and MD+fructose (2:1), consumed at an average of ～1.25 g of carbohydrate (CHO) ingested per minute. Blood was taken straight after exercise and every 45 min within the recovery phase. With the resulting blood plasma, insulin, free fatty acid (FFA) profile, glucose, and GC-TOFMS global metabolic profiling measurements were performed. The resulting profiling data was able to match the results obtained from the other clinical measurements with the addition of being able to follow many different metabolites throughout the recovery period. The data quality was assessed, with all the labelled internal standards yielding values of <15% CV for all samples (n=335), apart from the labelled sucrose which gave a value of 15.19%. Differences between recovery treatments including the appearance of galactonic acid from the galactose based beverage were also highlighted.     

Interaction of Allium sativum leaf agglutinin with midgut brush border membrane vesicles proteins and its stability in Helicoverpa armigera

Allium sativum leaf agglutinin (ASAL) binds to several proteins in the midgut of Helicoverpa armigera and causes toxicity. Most of these were glycosylated. Six ASAL-binding proteins were selected for identification. PMF and MS/MS data showed their similarity with midgut aminopeptidase APN2, polycalins and alkaline phosphatase of H. armigera, cadherin-N protein (partial AGAP009726-PA) of Acyrthosiphon pisum, cytochrome P450 (CYP315A1) of Manduca sexta and alkaline phosphatase of Heliothis virescens. Some of the ASAL-binding midgut proteins were similar to the larval receptors responsible for the binding of δ-endotoxin proteins of Bacillus thuringiensis. Galanthus nivalis agglutinin also interacted with most of the ASAL-binding proteins. The ASAL showed resistance to midgut proteases and was detected in the larval hemolymph and excreta. Immunohistochemical staining revealed the presence of ASAL in the body tissue also.     

Context‐specific influence of water temperature on brook trout growth rates in the field

1. Modelling the effects of climate change on freshwater fishes requires robust field‐based estimates accounting for interactions among multiple factors. 2. We used data from an 8‐year individual‐based study of a wild brook trout (Salvelinus fontinalis) population to test the influence of water temperature on season‐specific growth in the context of variation in other environmental (i.e. season, stream flow) or biotic factors (local brook trout biomass density and fish age and size) in West Brook, a third‐order stream in western Massachusetts, U.S.A. 3. Changes in ambient temperature influenced individual growth rates. In general, higher temperatures were associated with higher growth rates in winter and spring and lower growth rates in summer and autumn. However, the effect of temperature on growth was strongly context‐dependent, differing in both magnitude and direction as a function of season, stream flow and fish biomass density. 4. We found that stream flow and temperature had strong and complex interactive effects on trout growth. At the coldest temperatures (in winter), high stream flows were associated with reduced trout growth rates. During spring and autumn and in typical summers (when water temperatures were close to growth optima), higher flows were associated with increased growth rates. In addition, the effect of flow at a given temperature (the flow‐temperature interaction) differed among seasons. 5. Trout density negatively affected growth rate and had strong interactions with temperature in two of four seasons (i.e. spring and summer) with greater negative effects at high temperatures. 6. Our study provided robust, integrative field‐based estimates of the effects of temperature on growth rates for a species which serves as a model organism for cold‐water adapted ectotherms facing the consequences of environmental change. Results of the study strongly suggest that failure to derive season‐specific estimates, or to explicitly consider interactions with flow regime and fish density, will seriously compromise our ability to predict the effects of climate change on stream fish growth rates. Further, the concordance we found between empirical observations and likely energetic mechanisms suggests that our general results should be relevant at broader spatial and temporal scales.     

Spatio‐temporal scaling of biodiversity and the species–time relationship in a stream fish assemblage

1. The increase of species richness with the area of the habitat sampled, that is the species–area relationship, and its temporal analogue, the species–time relationship (STR), are among the few general laws in ecology with strong conservation implications. However, these two scale‐dependent phenomena have rarely been considered together in biodiversity assessment, especially in freshwater systems. 2. We examined how the spatial scale of sampling influences STRs for a Central‐European stream fish assemblage (second‐order Bernecei stream, Hungary) using field survey data in two simulation‐based experiments. 3. In experiment one, we examined how increasing the number of channel units, such as riffles and pools (13 altogether), and the number of field surveys involved in the analyses (12 sampling occasions during 3 years), influence species richness. Complete nested curves were constructed to quantify how many species one observes in the community on average for a given number of sampling occasions at a given spatial scale. 4. In experiment two, we examined STRs for the Bernecei fish assemblage from a landscape perspective. Here, we evaluated a 10‐year reach level data set (2000–09) for the Bernecei stream and its recipient watercourse (third‐order Kemence stream) to complement results on experiment one and to explore the mechanisms behind the observed patterns in more detail. 5. Experiment one indicated the strong influence of the spatial scale of sampling on the accumulation of species richness, although time clearly had an additional effect. The simulation methodology advocated here helped to estimate the number of species in a diverse combination of spatial and temporal scale and, therefore, to determine how different scale combinations influence sampling sufficiency. 6. Experiment two revealed differences in STRs between the upstream (Bernecei) and downstream (Kemence) sites, with steeper curves for the downstream site. Equations of STR curves were within the range observed in other studies, predominantly from terrestrial systems. Assemblage composition data suggested that extinction–colonisation dynamics of rare, non‐resident (i.e. satellite) species influenced patterns in STRs. 7. Our results highlight that the determination of species richness can benefit from the joint consideration of spatial and temporal scales in biodiversity inventory surveys. Additionally, we reveal how our randomisation‐based methodology may help to quantify the scale dependency of diversity components (α, β, γ) in both space and time, which have critical importance in the applied context.     

A comparative analysis of vibrissa count and infraorbital foramen area in primates and other mammals

Vibrissae are specialized sensory “hairs” that respond to mechanical stimuli. Sensory information from vibrissae is transmitted to the brain via the infraorbital nerve, which passes through the infraorbital foramen (IOF). Several analyses have documented that primates have smaller IOFs than non-primate mammals, and that haplorhines have smaller IOFs than strepsirrhines. These grade shifts in IOF area were attributed to differences in “vibrissa development.” Following earlier analyses, IOF area has been used to derive a general estimate of “whiskeredness” in extinct primates, and consequently, IOF area has been used in phylogenetic and paleoecological interpretations. Yet, the relationship between IOF area and vibrissa count has not been tested, and little is known about how IOF area and vibrissa counts vary among mammals. This study explores how relative IOF area and vibrissa count differ among 25 mammalian orders, and tests for a correlation between IOF area and vibrissa count. Results indicate that primates and dermopterans (Primatomorpha) have smaller IOFs than most non-primate mammals, but they do not have fewer vibrissae. In addition, strepsirrhines and haplorhines do not differ from one another in relative IOF area or vibrissa counts. Despite different patterns documented for IOF area and vibrissa count variation across mammals, results from this study do confirm that vibrissa count and IOF area are significantly and positively correlated (p < 0.0001). However, there is considerable scatter in the data, suggesting that vibrissa counts cannot be predicted from IOF area. There are three implications of these finding. First, IOF area reflects all mechanoreceptors in the maxillary region, not just vibrissae. Second, IOF area may be an informative feature in interpretations of the fossil record. Third, paleoecological interpretations based on vibrissae are not recommended.