Some insights into protein structural class prediction

It has been quite clear that the success rate for predicting protein structural class can be improved significantly by using the algorithms that incorporate the coupling effect among different amino acid components of a protein. However, there is still a lot of confusion in understanding the relationship of these advanced algorithms, such as the least Mahalanobis distance algorithm, the component-coupled algorithm, and the Bayes decision rule. In this communication, a simple, rigorous derivation is provided to prove that the Bayes decision rule introduced recently for protein structural class prediction is completely the same as the earlier component-coupled algorithm. Meanwhile, it is also very clear from the derivative equations that the least Mahalanobis distance algorithm is an approximation of the component-coupled algorithm, also named as the covariant-discriminant algorithm introduced by Chou and Elrod in protein subcellular location prediction (Protein Engineering, 1999; 12:107-118). Clarification of the confusion will help use these powerful algorithms effectively and correctly interpret the results obtained by them, so as to conduce to the further development not only in the structural prediction area, but in some other relevant areas in protein science as well.     

The P1' specificity of tobacco etch virus protease

Affinity tags have become indispensable tools for protein expression and purification. Yet, because they have the potential to interfere with structural and functional studies, it is usually desirable to remove them from the target protein. The stringent sequence specificity of the tobacco etch virus (TEV) protease has made it a useful reagent for this purpose. However, a potential limitation of TEV protease is that it is believed to require a Gly or Ser residue in the P1' position of its substrates to process them with reasonable efficiency. Consequently, after an N-terminal affinity tag is removed by TEV protease, the target protein will usually retain a non-native Ser or Gly residue on its N-terminus, and in some cases this may affect its biological activity. To investigate the stringency of the requirement for Gly or Ser in the P1' position of a TEV protease recognition site, we constructed 20 variants of a fusion protein substrate with an otherwise optimal recognition site, each containing a different amino acid in the P1' position. The efficiency with which these fusion proteins were processed by TEV protease was compared both in vivo and in vitro. Additionally, the kinetic parameters K(M) and k(cat) were determined for a representative set of peptide substrates with amino acid substitutions in the P1' position. The results indicate that many side-chains can be accommodated in the P1' position of a TEV protease recognition site with little impact on the efficiency of processing.     

Patterns in species associations in plant communities: the importance of scale

Abstract. Present discussions on competitive interactions and the occurrence of predictable patterns in species composition – including assembly rules – are likely to benefit from appropriate analyses of the spatial structure in plant communities. We suggest such an analysis when we specifically want to detect scale regions where fine-scale local processes may affect the spatial pattern of species composition. We combine indirect ordination in the form of Detrended Correspondence Analysis (DCA) and geostatistics in the form of variography. The species abundance data in the sampled quadrats are summarized as positions on the axes in the ordination. Each axis is used as a regionalized variable in the variography to obtain the spatial dependence of the quadrats. The spatial pattern found will suggest the relevant scale region in which to perform an analysis of species associations. A significant spatial dependence (the ‘range’ in geostatistical jargon) will define the size of a sampling plot that will minimize both the problem of being too small and thus having the risk of oversampling of e.g. clonal individuals and of being too large which will risk including individuals that do not interact. We also suggest that plots are spaced at least a ‘range’ apart to insure spatial and statistical independence. Comparisons of species compositions in such plots will reveal any positive or negative associations between species on a scale where these should reflect species-species interactions. To illustrate the method it is applied to three different data sets from two different plant communities.     

Determinants of local abundance in a major radiation of Australian passerines (Aves: Meliphagoidea)

Aim  To identify the factors that contribute to variation in abundance (population density), and to investigate whether habitat breadth and diet breadth predict macroecological patterns in a suborder of passerine birds (Meliphagoidea).
Location  Australia (including Tasmania).
Methods  Mean abundance data were collated from site surveys of bird abundance (the Australian Bird Count); range size and latitudinal position data from published distribution maps; and body mass and diet breadth information from published accounts. A diversity index of habitats used (habitat breadth) was calculated from the bird census data. We used bivariate correlation and multiple regression techniques, employing two phylogenetic comparative methods: phylogenetic generalized least squares and independent contrasts.
Results  Body mass and latitude were the only strong predictors of abundance, with larger-bodied and lower-latitude species existing at lower densities. Together, however, body mass and latitude explained only 11.1% of the variation in mean abundance. Range size and habitat breadth were positively correlated, as were diet breadth and body mass. However, neither range size, nor habitat breadth and diet breadth, explained patterns in abundance either directly or indirectly.
Main conclusions  Levels of abundance (population density) in meliphagoid birds are most closely linked to body mass and latitudinal position, but not range size. As with many other macroecological analyses, we find little evidence for aspects of niche breadth having an effect on patterns of abundance. We hypothesize that evolutionary age may also have a determining effect on why species tend to be rarer (less abundant) in the tropics.     

The effect of island area on body size in a primate species from the Sunda Shelf Islands

Aim  We examine the effect of island area on body dimensions in a single species of primate endemic to Southeast Asia, the long-tailed macaque ( Macaca fascicularis ). In addition, we test Allen's rule and a within-species or intraspecific equivalent of Bergmann's rule (i.e. Rensch's rule) to evaluate body size and shape evolution in this sample of insular macaques.
Location  The Sunda Shelf islands of Southeast Asia.
Methods  Body size measurements of insular macaques gathered from the literature were analysed relative to island area, latitude, maximum altitude, isolation from the mainland and other islands, and various climatic variables using linear regression.
Results  We found no statistically significant relationship between island area and body length or head length in our sample of insular long-tailed macaques. Tail length correlated negatively with island area. Head length and body length exhibited increases corresponding to increasing latitude, a finding seemingly consistent with the expression of Bergmann's rule within a single species. These variables, however, were not correlated with temperature, indicating that Bergmann's rule is not in effect. Tail length was not correlated with either temperature or increasing latitude, contrary to that predicted by Allen's rule.
Main conclusions  The island rule dictating that body size will covary with island area does not apply to this particular species of primate. Our study is consistent with results presented in the literature by demonstrating that skull and body length in insular long-tailed macaques do not, strictly speaking, conform to Rensch's rule. Unlike previous studies, however, our findings suggest that tail-length variation in insular macaques does not support Allen's rule.     

Subterranean rodents of the genus Ctenomys (Caviomorpha, Ctenomyidae) follow the converse to Bergmann's rule

Aim We analysed body‐size variation in relation to latitude, longitude, elevation and environmental variables in Ctenomys (tuco‐tucos), subterranean rodents in the Ctenomyidae (Caviomorpha). We tested the existence of inter‐ and intraspecific size clines to determine if these rodents follow Bergmann's rule, to compare intra‐ and interspecific size trends and to assess the relevance of the subterranean lifestyle on these trends. Location South America, south of 15° latitude. Methods This paper is based on 719 specimens of tuco‐tucos from 133 localities of Argentina, Bolivia, Chile, Paraguay, Peru and Uruguay, representing 47 named species and 32 undescribed forms. Intraspecific analyses were performed for Ctenomys talarum Thomas, 1898 and the Ctenomys perrensi Thomas, 1896 species complex. Head and body length and weight were used for estimating body size. Geographical independent variables included latitude, longitude and altitude. Environmental independent variables were mean minimal and maximal monthly temperature, mean annual temperature, mean minimal and maximal precipitation, and total annual precipitation. To estimate seasonality, the annual variability of the climatic factors was calculated as their coefficients of variation and the difference between maximum and minimum values. Mean annual actual evapotranspiration (AET), and mean annual, January (summer) and July (winter) potential evapotranspiration (PET) values were also calculated for each locality, as well as annual, summer and winter water balance (WB). Statistical analyses consisted of simple and multiple regression and nonparametric correlation. Results Body size of Ctenomys decreases interspecifically from 15°00′ S to 48°15′ S and from 56°33′ W to 71°46′ W, and is positively correlated with ambient temperature and precipitation. The best predictors of body size according to multiple regression analyses were mean annual temperature, the difference between mean maximum and minimum annual temperatures, annual PET, the difference between summer and winter PET, and annual and winter water balance. These patterns are repeated, but not identically, at a smaller geographical scale within the species C. talarum and the superspecies C. perrensi. Main conclusions Tuco‐tucos follow the converse to Bergmann's rule at the interspecific level. At the intraspecific level some parallel trends were observed, but the smaller scale of these analyses, involving a very reduced variation of environmental factors, necessitates caution in interpreting results. The subterranean lifestyle probably insulates these rodents from the external temperature. The observed latitudinal body‐size gradients are more probably related to seasonality, ambient energy, primary productivity and/or intensity of predation.     

Comparison of dwarf bamboos (Indocalamus sp.) leaf parameters to determine relationship between spatial density of plants and total leaf area per plant

The relationship between spatial density and size of plants is an important topic in plant ecology. The self‐thinning rule suggests a ?3/2 power between average biomass and density or a ?1/2 power between stand yield and density. However, the self‐thinning rule based on total leaf area per plant and density of plants has been neglected presumably because of the lack of a method that can accurately estimate the total leaf area per plant. We aimed to find the relationship between spatial density of plants and total leaf area per plant. We also attempted to provide a novel model for accurately describing the leaf shape of bamboos. We proposed a simplified Gielis equation with only two parameters to describe the leaf shape of bamboos one model parameter represented the overall ratio of leaf width to leaf length. Using this method, we compared some leaf parameters (leaf shape, number of leaves per plant, ratio of total leaf weight to aboveground weight per plant, and total leaf area per plant) of four bamboo species of genus Indocalamus Nakai (I. pedalis (Keng) P.C. Keng, I. pumilus Q.H. Dai and C.F. Keng, I. barbatus McClure, and I. victorialis P.C. Keng). We also explored the possible correlation between spatial density and total leaf area per plant using log‐linear regression. We found that the simplified Gielis equation fit the leaf shape of four bamboo species very well. Although all these four species belonged to the same genus, there were still significant differences in leaf shape. Significant differences also existed in leaf area per plant, ratio of leaf weight to aboveground weight per plant, and leaf length. In addition, we found that the total leaf area per plant decreased with increased spatial density. Therefore, we directly demonstrated the self‐thinning rule to improve light interception.     

Clinal variation in the morph ratio of Black Sparrowhawks Accipiter melanoleucus in South Africa and its correlation with environmental variables

The morph ratio distribution in polymorphic species often varies clinally, with a gradual change in morph ratios across the distributional range of the species. In polymorphic bird populations, clinal variation is rarely quantified. We describe a cline in the morph ratios of Black Sparrowhawks across South Africa, which is principally driven by a higher ratio of dark morph birds in the newly colonized southwest of the country. Across the 1400 km of our cline, the probability of a bird being a dark morph declined from over 80% close to the Cape Peninsula to under 20% in the northeast. Higher frequencies of dark morphs were associated with a higher proportion of rainfall falling during the winter breeding months. Further investigation revealed relationships between the proportion of dark morphs and altitude, amount of rainfall during the breeding months, and an interaction between this variable and temperature. These results provide some support for the suggestion that the higher frequency of dark morphs in the southwest is an adaptive response, rather than the result of a founder effect or genetic drift. These findings also suggest that, in theory, polymorphic species may be better adapted to cope with the challenges of climate change or may be able to expand their ranges more quickly into novel climatic areas, since selection pressure can act on a pre‐existing trait that may be beneficial in new conditions.     

Structure–activity relationship of dihydroxy-4-methylcoumarins as powerful antioxidants: Correlation between experimental & theoretical data and synergistic effect

The chain-breaking antioxidant activities of eight coumarins [7-hydroxy-4-methylcoumarin (1), 5,7-dihydroxy-4-methylcoumarin (2), 6,7-dihydroxy-4-methylcoumarin (3), 6,7-dihydroxycoumarin (4), 7,8-dihydroxy-4-methylcoumarin (5), ethyl 2-(7,8-dihydroxy-4-methylcoumar-3-yl)-acetate (6), 7,8-diacetoxy-4-methylcoumarin (7) and ethyl 2-(7,8-diacetoxy-4-methylcoumar-3-yl)-acetate (8)] during bulk lipid autoxidation at 37 °C and 80 °C in concentrations of 0.01–1.0 mM and their radical scavenging activities at 25 °C using TLC–DPPH test have been studied and compared. It has been found that the o-dihydroxycoumarins 3–6 demonstrated excellent activity as antioxidants and radical scavengers, much better than the m-dihydroxy analogue 2 and the monohydroxycoumarin 1. The substitution at the C-3 position did not have any effect either on the chain-breaking antioxidant activity or on the radical scavenging activity of the 7,8-dihydroxy- and 7,8-diacetoxy-4-methylcoumarins 6 and 8. The comparison with DL-α-tocopherol (TOH), caffeic acid (CA) and p-coumaric acid (p-CumA) showed that antioxidant efficiency decreases in the following sequence: