Space Partitioning within Populations of Sea Anemones (Genus: Anthopleura) in the California Rocky Intertidal Zone

The spatial patterns of sea anemones (genus: Anthopleura) were analyzed off the rocky intertidal of California. A. elegantissima partitions space in a regular or even pattern and interferes with conspecifics. Its associate A. xanthogrammica shows no signs of interference with conspecifics or congenerics and displays a clumped spatial distribution.     

Drivers of host plant shifts in the leaf beetle Chrysomela lapponica: natural enemies or competition?

1. The leaf beetle, Chrysomela lapponica, originally uses the salicyl glucosides (SGs) of its host plants to sequester salicylaldehyde, which serves as a defence against generalist enemies but attracts specialist enemies. However, some populations of C. lapponica have shifted to SG‐poor hosts, and their secretions do not contain salicylaldehyde. 2. In was suggested that beetles shift to SG‐poor hosts to escape from specialist enemies. To test this hypothesis, we compared field mortality between two populations of C. lapponica that were associated with SG‐rich willow, Salix myrsinifolia (Kola Peninsula and Finland) and two populations that fed on SG‐poor willows, S. glauca (Ural) and S. caprea (Belarus). 3. Mortality from generalist enemies was significantly higher in Belarus than in three other populations, whereas mortality from specialists did not differ among populations. A specialist predator (syrphid fly larvae, Parasyrphus nigritarsis) and specialist parasitoids (phorid flies, Megaselia spp.) were attracted to the secretions of larvae reared on both SG‐rich and SG‐poor hosts. 4. Feeding on leaves of S. caprea and S. myrsinifolia both previously damaged by leaf puncturing and by the larvae of potentially competing species Chrysomela vigintipunctata, decreased the weight and prolonged the development of C. lapponica. 5. Thus, populations of C. lapponica that have shifted to SG‐poor willow species did not obtain enemy‐free space because specialist enemies have developed adaptations to herbivores that switched to a novel host plant. We suggest that in some populations host plant shift was favoured by interspecific competition with the early season SG‐using specialist, C. vigintipunctata.     

Dynamical systems analysis of arterial blood pressure signals in relation to heart rate fluctuations in chick embryos

We attempted a new approach based on a modern dynamical system theory to reconstruct the arterial blood pressure signals in relation to heart rate fluctuations of developing chick embryos. The dynamical systems approach in general is to model a phenomenon that is presented by a single time series record and approximate the dynamical property (e.g. heart rate fluctuations) of a system based only on information contained in a single-variable (arterial blood pressure) of the system. The time-series data of the arterial blood pressure was reconstructed in 3-dimensional space to draw characteristic orbits. Since the reconstructed orbits of the blood pressure should retain information contained in the pressure signals, we attempted to derive instantaneous heart rate (IHR) from the reconstructed orbits. The derived IHR presenting HR fluctuations coincided well with the IHR obtained conventionally from the peak-to-peak time intervals of the maximum blood pressure. Movements of the reconstructed orbits of the arterial blood pressure in 3-dimensional space reflected HR fluctuations (i.e. transient decelerations and accelerations).     

Functional design space of single-veined leaves: role of tissue hydraulic properties in constraining leaf size and shape

BACKGROUND AND AIMS: Morphological diversity of leaves is usually quantified with geometrical characters, while in many cases a simple set of biophysical parameters are involved in constraining size and shape. One of the main physiological functions of the leaf is transpiration and thus one can expect that leaf hydraulic parameters can be used to predict potential morphologies, although with the caveat that morphology in turn influences physiological parameters including light interception and boundary layer thickness and thereby heat transfer and net photosynthesis. METHODS: An iterative model was used to determine the relative sizes and shapes that are functionally possible for single-veined leaves as defined by their ability to supply the entire leaf lamina with sufficient water to prevent stomatal closure. The model variables include the hydraulic resistances associated with vein axial and radial transport, as well as with water movement through the mesophyll and the leaf surface. KEY RESULTS: The four parameters included in the model are sufficient to define a hydraulic functional design space that includes all single-veined leaf shapes found in nature, including scale-, awl- and needle-like morphologies. This exercise demonstrates that hydraulic parameters have dissimilar effects: surface resistance primarily affects leaf size, while radial and mesophyll resistances primarily affect leaf shape. CONCLUSIONS: These distinctions between hydraulic parameters, as well as the differential accessibility of different morphologies, might relate to the convergent evolutionary patterns seen in a variety of fossil lineages concerning overall morphology and anatomical detail that frequently have evolved in linear and simple multi-veined leaves.     

Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins

Mitochondria import nuclear-encoded precursor proteins to four different subcompartments. Specific import machineries have been identified that direct the precursor proteins to the mitochondrial outer membrane, inner membrane or matrix, respectively. However, a machinery dedicated to the import of mitochondrial intermembrane space (IMS) proteins has not been found so far. We have identified the essential IMS protein Mia40 (encoded by the Saccharomyces cerevisiae open reading frame YKL195w). Mitochondria with a mutant form of Mia40 are selectively inhibited in the import of several small IMS proteins, including the essential proteins Tim9 and Tim10. The import of proteins to the other mitochondrial subcompartments does not depend on functional Mia40. The binding of small Tim proteins to Mia40 is crucial for their transport across the outer membrane and represents an initial step in their assembly into IMS complexes. We conclude that Mia40 is a central component of the protein import and assembly machinery of the mitochondrial IMS.     

A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology

Based on the recent development in the gene ontology and functional domain databases, a new hybridization approach is developed for predicting protein subcellular location by combining the gene product, functional domain, and quasi-sequence-order effects. As a showcase, the same prokaryotic and eukaryotic datasets, which were studied by many previous investigators, are used for demonstration. The overall success rate by the jackknife test for the prokaryotic set is 94.7% and that for the eukaryotic set 92.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross-validation test procedure, suggesting that such a hybrid approach may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. The very high success rates also reflect the fact that the subcellular localization of a protein is closely correlated with: (1). the biological objective to which the gene or gene product contributes, (2). the biochemical activity of a gene product, and (3). the place in the cell where a gene product is active.     

Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC

A revised version of the Conformational Space Annealing (CSA) global optimization method is developed, with three separate measures of structural similarity, in order to overcome the inability of a single distance measure to evaluate multiple-chain protein structures adequately. A second search method, Conformational Family Monte Carlo (CFMC), involving genetic-type moves, Monte Carlo-with-minimization perturbations, and explicit clustering of the population into conformational families, is adapted to treat multiple-chain proteins. These two methods are applied to two oligomeric proteins, the retro-GCN4 leucine zipper and the synthetic domain-swapped dimer. CFMC proves superior to CSA in its search for low-energy representatives of its conformational families, but both methods encounter difficulty in finding the native packing arrangements in the absence of native-like symmetry constraints, even when native monomers are present in the population.     

Exocytosis of a 60 kDa protein (calreticulin) from activated hamster oocytes

The sp50 protein localized at the acrosomal region of guinea pig sperm was suggested to participate in acrosome exocytosis, the acrosome reaction (AR). On the other hand, the cortical reaction (CR), also an exocytotic event, occurs during egg activation. The aim of the present work was to identify sp50 and also to define if sp50 is present in hamster eggs, as well as its location before and after CR. Sp50 was identified as calreticulin (CRT), based on: (a) its NH(2)-terminal amino acid (25 aa) sequence, (b) a cross-recognition of pure sp50 and pure CRT with anti-CRT (from Santa Cruz, anti-CRTsc), and anti-sp50 (anti-sp50/CRT) antibodies, respectively, and (c) that both antibodies revealed a 50 kDa protein in a Brij sperm extract. On the other hand, CRT presence in eggs was positively determined by Western blotting (Wb) using anti-sp50/CRT antibody which recognized a 60 kDa protein in the egg extract, and by indirect immunofluorescence (IIF), CRT was located in the cortical granules (CG). It was defined by a granular pattern and co-localization with mannose, a specific carbohydrate of the CG. Additionally, a decrease in CRT concentration occurred in eggs after their activation and, in parallel, the protein was revealed in the egg's incubation medium. In activated eggs with zona pellucida (ZP), CRT remains as a halo in the perivitelline space and around the polar body. From these results we suggest that: (1) CRT is present in the CG of non-activated hamster eggs, (2) CRT is exocytosed during the CR, in response to egg activation, and (3) CRT might participate in the block to polyspermy, together with other CG components.     

Behavioral adaptations increase the value of enemy-free space for Heliothis subflexa,a specialist herbivore

We investigated the importance of specialized behaviors in the use of enemy-free space by comparing the host-use behavior of two closely related moths, Heliothis subflexa Guenee and H. virescens Fabricius. Heliothis subflexa is a specialist on plants in the genus Physalis, whereas H. virescens is an extreme generalist, feeding on plants in at least 14 families. Heliothis subflexa uses the inflated calyx surrounding Physalis fruits as enemy-free space, and field rates of parasitism for H. subflexa on Physalis are much lower than for H. virescens on tobacco and cotton, common hosts found in the same habitat as Physalis. If Physalis, architecture were solely responsible for H. subflexa's low rates of parasitism on Physalis, we predicted that H. virescens larvae experimentally induced to feed on Physalis would experience parasitism rates similar to those of H. subflexa. We found, however, that specialized host-use and host-acceptance behaviors are integral to the use of enemy-free space on Physalis and strongly augment the effects of the structural refuge. In laboratory assays, we found considerable differences between the larval behavior of the specialist. H. subflexa, and the generalist, H. virescens, and these contributed to H. subflexa's superior use of enemy-free space on Physalis. We tested the importance of these behavioral differences in the field by comparing parasitism of H. virescens on Physalis, H. virescens on tobacco, and H. subflexa on Physalis by Cardiochiles nigriceps Vierick, a specialist braconid parasitoid. For H. virescens, a threefold decrease in parasitism occurred when feeding on Physalis (mean parasitism +/- SEM = 13 +/- 4%) rather than tobacco (43 +/- 4%), a difference we attribute to the structural refuge provided by Physalis. However, parasitism of H. virescens on Physalis was more than ten times as great as that of H. subflexa on Pliv.salis (1 +/- 4%), supporting the hypothesis that specialized behaviors have a substantial impact on use of Physalis as enemy-free space. Behavioral adaptations may be central to the use of enemy-free space by phytophagous insects and may act as an important selective force in the evolution of dietary specialization.     

Quantifying the similarities within fold space

We have used GRATH, a graph-based structure comparison algorithm, to map the similarities between the different folds observed in the CATH domain structure database. Statistical analysis of the distributions of the fold similarities has allowed us to assess the significance for any similarity. Therefore we have examined whether it is best to represent folds as discrete entities or whether, in fact, a more accurate model would be a continuum wherein folds overlap via common motifs. To do this we have introduced a new statistical measure of fold similarity, termed gregariousness. For a particular fold, gregariousness measures how many other folds have a significant structural overlap with that fold, typically comprising 40% or more of the larger structure. Gregarious folds often contain commonly occurring super-secondary structural motifs, such as beta-meanders, greek keys, alpha-beta plait motifs or alpha-hairpins, which are matching similar motifs in other folds. Apart from one example, all the most gregarious folds matching 20% or more of the other folds in the database, are alpha-beta proteins. They also occur in highly populated architectural regions of fold space, adopting sandwich-like arrangements containing two or more layers of alpha-helices and beta-strands.Domains that exhibit a low gregariousness, are those that have very distinctive folds, with few common motifs or motifs that are packed in unusual arrangements. Most of the superhelices exhibit low gregariousness despite containing some commonly occurring super-secondary structural motifs. In these folds, these common motifs are combined in an unusual way and represent a small proportion of the fold (<10%). Our results suggest that fold space may be considered as continuous for some architectural arrangements (e.g. alpha-beta sandwiches), in that super-secondary motifs can be used to link neighbouring fold groups. However, in other regions of fold space much more discrete topologies are observed with little similarity between folds.