Fingerprint-based structure retrieval using electron density

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy.     

Altitudinal variation in the morphometric characteristics of Aedes vexans Meigen from northeastern Turkey

Body size is one of the most significant features of organisms and is correlated with a large number of ecological and physiological variables. Similar to size, biological shape is one of the most conspicuous aspects of an organism's phenotype and provides a link between the genotype and the environment. Body size may change with altitude and also habitat differences associated with altitude may affect the biological shape and some morphological characteristics. Four populations of Aedes vexans Meigen occurring in different ecological subregions at altitudes between 808–1,620 m in the Aras Valley from northeastern Turkey were compared using traditional and geometric morphometrics. When the wing shape differences of populations were analyzed by UPGM, the cluster analyses recognized two main groups of populations. Gödekli (808 m) comprised the first group while Zülfikar (848 m), Sürmeli (944 m), and Cilehane (1,620 m) populations comprised the second group. In the second group, Zülfikar and Cilehane populations showed a similar grouping pattern while Sürmeli appeared as a different group. Centroid sizes were used as measures of overall wing size differences among different regions. Aedes vexans from the Sürmeli region had relatively larger wings.     

Spatial patterns of variation in color and spine shape in the sea urchin Heliocidaris erythrogramma

Abstract. Here we report on the first quantitative survey of morphological variation in the sea urchin Heliocidaris erythrogramma within Western Australia and distinguish between two subspecies found to co‐occur in this region. We surveyed urchins at multiple spatial scales along the Western Australian coastline to assess variation in dermis and spine color and, using landmark‐based geometric morphometrics, spine morphology. Both color and morphology proved to be useful for separating subspecies within Western Australia. There were four major color morphs: red dermis/violet spines (56%), red/violet‐green (23%), red/green (7%), and white/green (10%). Members of the first two color morphs had bulbous spines with wide, flattened tips, a morphology that is unique to Western Australia and characteristic of H. e. armigera, and members of the latter two consistently exhibited the narrow, pointed spines typical of specimens of H. e. erythrogramma, which has a broader distribution. In Western Australia, H. e. armigera was relatively abundant both within and among sites, but H. e. erythrogramma was found only in a few localized patches. Shifts in the relative abundance of these two subspecies occurred at fine spatial scales (<5 km), although environmental correlates of these transitions were unclear. Contrary to expectations, neither dermis color nor spine morphology varied with relative wave exposure: individuals with a red dermis or thickened spine morphology occurred at most sites regardless of exposure, and while white dermis and thinner spines only occurred at high‐exposure sites, these features were not common across the majority of exposed sites. Both color morph frequencies and spine morphology remained stable within sites over the 3‐year duration of this study. While the ecological significance of this morphological variation remains unclear, the consistency of the association between color and spine morphology, occurring across fine spatial scales, suggests that strong environmental or genetic factors are involved in maintaining morphological differentiation between these two subspecies.     

Optimal foraging for multiple nutrients in an unpredictable environment

Foraging theory has typically been concerned with the acquisition of a single resource even though organisms from mammals to protozoa are capable of balancing their requirements for multiple resources. Existing theory concerning multiple nutrients from multiple foods does not predict the sequence of food selection. We constructed an optimisation model of the simplest case of two foods containing differing amounts of two nutrients. We begin with the well-supported assumption that reproductive value declines with the distance from target nutrient intake. We show that nutrient space divides into two distinct areas where the animal should exclusively consume one food or the other. The organism thus initially concentrates on one food type until the border between the areas is reached and then moves as closely as possible along the border to approach the target. This strategy is commonly observed in a range of organisms, suggesting that the assumed fitness function is common.     

Re-orienting in space: do animals use global or local geometry strategies?

Here we compare whether birds encode surface geometry using principal axes, medial axes or local geometry. Birds were trained to locate hidden food in two geometrically identical corners of a rectangular arena and subsequently tested in an L-shaped arena. The chicks showed a primary local geometry strategy, and a secondary medial axes strategy, whereas the pigeons showed a medial axes strategy. Neither species showed behaviour supportive of the use of principal axes. This is, to our knowledge, the first study to directly examine these three current theories of geometric encoding.     

Geometric morphometrics reveals body shape differences between sympatric redfish Sebastes mentella, Sebastes fasdatus and their hybrids in the Gulf of St Lawrence

Significant body shape differences were observed between two commercially important redfish species Sebastes fasdatus and Sebastes mentella , in the Gulf of St Lawrence, first classified according to the variability at the MDH-A* locus, a diagnostic criterion for the two species in allopatry. The observed sexual dimorphism was probably related to the presence of gravid females in the sample. Sebastes mentella appeared to be more fusiform than S. fasdatus , a characteristic that may reflect the more pelagic behaviour of S. mentella . The body shape of their hybrids was closer to that of S. mentella . Similarities between hybrids and S. mentella were also observed for meristic characteristics and depth distribution. The implications of these similarities for introgression are discussed. Body shape variability of specimens of hybrid origin was greater than that of either parental species, with features ranging from S. mentella-like to S. fasciatus -like. The role of introgression in generating morphological variability is emphasized.     

A geometric morphometric analysis of the shape of the first upper molar in mice of the genus Mus (Muridae, Rodentia)

Phenotypic variation in the shape of the first upper molar among 595 mice, representing nine extant and three extinct taxa of the genus Mus , was studied with thin-plate spline analysis. The reliability of classification of individual specimens into known groups based on their molars varied from 75 to 100%, depending on group and method used. Including 13 sliding semilandmarks to the analysis improved the detection of different kinds of size and shape variation as well as visualization of shape differences between studied groups. Correlation between phylogenetic and morphometric distances suggested about 80% contribution of phylogenetic inertia to the molar shape variation; moreover, the importance of localized versus global shape changes was similar in the detection of phylogenetic signals. Finally, shape changes along individual evolutionary lineages were revealed, suggesting a few cases of reversals, convergence and/or retention of ancestral shape. The evolution of mouse molars has thus been driven by random effects of drift together with stabilizing selection and convergence.     

Chemical constraints on the evolution of olfactory communication channels of moths

It is estimated there are over 100,000 moth species (Lepidoptera) that produce sex pheromones comprising communication channels used in specific-mate-recognition systems (SMRS) involved in pre-zygotic mating isolation and speciation. About 1572 moth species have been found to use 377 pheromone components, the majority being alcohols, aldehydes or acetate esters of olefinic chains of 10-22 carbons. Since there are limited numbers of possible unsaturated (double bonded) E- and Z-configured isomers of these chains, there may be constraints on incipient species evolving new pheromone components, especially if they are utilized by existing species. Here I develop algorithms that count and name all possible structures of chains with or without a functional group. The results show that for acetate esters there are only seven or nine monounsaturated isomers of six or seven carbon chains, respectively, suggesting use of these compounds could limit the number of communication channels available for radiation of new species (no moths use these short chains). For commonly used 14-carbon chains with an acetate ester functional group, and 1-3 unsaturations, there are 1039 isomers. A total of 2,096,883 isomers were counted from all multiply unsaturated 10-22-carbon chain acetate esters. The number of possible signals quickly extends into millions when considering pheromone blends of 2-4 components used by most species. There should be little chemical constraint on evolution of new communication channels based on compounds of 10 or more carbons, even for closely related species (e.g. ermine moths, Yponomeuta).     

Synthesis of fagopyritols A1 and B1 from D-chiro-inositol

Fagopyritol A1 (3-O-alpha-d-galactopyranosyl-d-chiro-inositol) and fagopyritol B1 (2-O-alpha-d-galactopyranosyl-d-chiro-inositol) have been synthesized by glycosylation of the diequatorial diol 1,4,5,6-tetra-O-benzoyl-d-chiro-inositol, readily obtained from d-chiro-inositol, with 2,3,4,6-tetra-O-benzyl-d-galactopyranosyl trichloroacetimidate.     

Variation in scale shape among alternative sympatric phenotypes of Arctic charr Salvelinus alpinus from two lakes in Scotland

Landmark‐based geometric morphometric analysis was used to detect differences in scale shape between ecologically distinct phenotypes of Arctic charr Salvelinus alpinus coexisting in the same lake. Relative warp analysis and standard multivariate analyses of the partial warps, obtained after a Procrustes superimposition, showed that scale landmarks were efficient in discriminating among two closely related alternative phenotypes within each of the two lakes. In Loch Tay, S. alpinus exhibited a bimodal body size‐frequency distribution among sexually mature fish, whereas in Loch Awe, S. alpinus are unimodal in body size but segregated into two distinct spawning phenotypes. In both lakes, alternative phenotypes showed significant differences in foraging ecology, habitat use and life history. It is probable that differences in scale shape reflect differences in ecology of these forms.