Dynamics of evolutionary patterns of clades in a food web system model

The evolutionary patterns of animal species clades in an evolving food web system were examined by computer simulation. In this system, each animal species fed on other species according to feeding preference. The food web system evolved via the appearance and extinction of species. The model succeeded in reproducing evolutionary patterns of diversity similar to those seen in the fossil record. This result indicates that the model reproduced the temporal changes of the rates of colonization and extinction of species in the system, which have been decided a priori in the previous stochastic models. In the food web system, the numbers of both predatory and prey species influenced the temporal diversity patterns in each clade in the system. The number of prey species fluctuated strongly, whereas the number of predatory species gradually increased with time. Therefore, temporal diversity patterns were influenced mainly by the number of predatory species. As a result of the gradual increase of the number of predatory species, it was difficult for each clade to maintain its species diversity for a long time. Slight changes of interspecific interaction can sometimes decide the destiny of a clade. When a clade is faced with extinction, if one predatory species of the clade becomes extinct and one or two prey species of the clade appear, the species diversity in the clade increases again. This result indicates that slight changes of interspecific interaction sometimes decide the destiny of a clade.     

Competition between <Emphasis Type="Italic">Eucalyptus victrix</Emphasis> seedlings and grass species

Competition in a natural system may be interspecific or intraspecific. In semiarid ecosystems, competition for resources between established neighboring grass species and newly recruited seedlings is very high. To examine the effects of grass species density, growing space and time of establishment on Eucalyptus victrix seedlings (interspecific competition), and the effect of density and growing space within E.victrix (intraspecific competition) we conducted an experiment under controlled conditions. We tested four hypotheses (i) E.victrix seedling growth is not affected by grass density; (ii) there is no difference in E.victrix survival and growth between early and later grass establishment; (iii) interspecific competition is not more intense than intraspecific competition in E.victrix; and (iv) growth of E.victrix seedlings is not dependent on available growing space. In a monoculture of E.victrix, seedling mortality was higher (10%) in large pots. In mixed culture pots, where E.victrix seedlings and grass seedlings were planted on the same day, E.victrix seedlings survived for up to 4weeks, but started to die after week five in the smallest pots. However, mortalities occurred in pots of all sizes when grass was established before E.victrix seedlings. Results also indicated that the resources necessary for the growth of individual E.victrix seedlings were more limiting under conditions of increased density of neighboring grass species rather than intraspecific competition. In particular, photosynthetic area of E.victrix seedlings was drastically reduced in mixed cultures. Although density, pot size and time of planting had impacts on E.victrix seedlings, the patterns of these impacts were variable.     

An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues

The antibody-binding site is formed as a result of the association between VH and VL domains. Several studies have shown that this association plays an important role in the mechanism of antigen-antibody interaction (Stanfield et al. Structure 1: 83-93, 1993). Considering this, we propose that variations in the VH-VL association are part of the diversification strategy of the antibody repertoires. Previously, a model of association for VH-VL domains based on geometrical characteristics of the packing at the interface was developed by Chothia et al. (J. Mol. Biol. 186: 61-663, 1985). This model includes a common association form for antibodies and a three-layer structure for the interface. In the present work, a complementary model is introduced to account for the general geometrical restrictions of the VH-VL interface, and particular arrangements related to the chemical properties or the side-chain orientations of participating residues. Groups of residues assume common side-chain orientations, which are apparently related to particular functions of different interface zones. Analyses of amino acid usage and network are in agreement with the side-chain orientation patterns. Based on these observations, a three-zone model has evolved to illuminate geometrical and functional restrictions acting over the VH-VL interface. Additionally, this study has revealed the asymmetrical relationships between VH and VL residues important for the association of the two domains.     

Species association among predaceous and phytophagous apple mites (Acari: Eriophyidae, Phytoseiidae, Stigmaeidae, Tetranychidae)

Predator–predator, predator–prey, and prey–prey associations among nine species of mites were studied in a plot of 100 Red Delicious apple (Malus pumila Miller) trees from 1990 to 1997. In 1990, seven-year-old trees were inoculated with Panonychus ulmi (Koch), Tetranychus urticae Koch (Acari: Tetranychidae) or both, and sprayed with azinphosmethyl (alone or plus endosulfan), or nothing. The species Zetzellia mali (Ewing) (Acari: Stigmaeidae), Amblyseius andersoni Chant (Acari: Phytoseiidae), Eotetranychus sp., Bryobia rubrioculus (Scheuten) (Acari: Tetranychidae), and Aculus schlechtendali Nalepa (Acari: Eriophyidae) were already present or immigrated into plots, and Galendromus occidentalis (Nesbitt) and Typhlodromus pyri Scheuten (Acari: Phytoseiidae) were introduced. Yule's V association index was used to measure positive, neutral, or negative interspecific associations for each species pair, because of its robustness with spatially autocorrelated data. We found that pesticide and release treatments did not greatly affect the association results, but there were strong seasonal differences. Predator–predator associations were the strongest and most consistent, showing negative associations in the early and mid seasons, and neutral ones in late season. Negative associations of T. pyri with other predators were the strongest, which is consistent with evidence that this mite can detect other predators on a leaf. Predator–prey seasonal associations were mixed, with some positive and others negative, with most significant associations occurring in the mid season. One prey–prey interaction was positive, again in mid season, most likely because of similar habitat preferences.     

Carboxyl-terminal modification alters the subunit interactions and assembly pathways of normal and sickle hemoglobins

Parallel isofocusing studies established that carboxypeptidase A removal of the His-146 (HC3) and Tyr-145 (HC2) residues of heme subunits affected the assembly properties of both Des (A) and Des (S) with heme chains, albeit to differing degrees. Indeed, the rate of Des (A) oligomer dissociation (k ₁), as determined by visible spectroscopy, was 4.3-fold faster than that of its native (A) counterpart. Furthermore, Soret spectral studies have affirmed distinct rates of normal (HbA), sickle (HbS), and Des HbA hemoglobin assembly (k₂) from their and [Des (A)] heme-containing monomers. Matching kinetic analysis of Des (A) and Des (S) chain assembly (with an identical chain) revealed 4.6- and 7.8-fold faster combination rates than those seen for (A) and (S) chains, respectively. This 3-fold disparity in rates strongly supports the critical role of the -6 (A3) residue, and its amino-terminal region, in chain partner recognition and subsequent human hemoglobin assembly.     

Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB

Turkey ovomucoid third domain (OMTKY3) is a canonical inhibitor of serine proteinases. Upon complex formation, the inhibitors fully exposed P1 residue becomes fully buried in the preformed cavity of the enzyme. All 20 P1 variants of OMTKY3 have been obtained by recombinant DNA technology and their equilibrium association constants have been measured with six serine proteinases. To rationalize the trends observed in this data set, high resolution crystal structures have been determined for OMTKY3 P1 variants in complex with the bacterial serine proteinase, Streptomyces griseus proteinase B (SGPB). Four high resolution complex structures are being reported in this paper; the three beta-branched variants, Ile18I, Val18I, and Thr18I, determined to 2.1, 1.6, and 1.7 A resolution, respectively, and the structure of the Ser18I variant complex, determined to 1.9 A resolution. Models of the Cys18I, Hse18I, and Ape18I variant complexes are also discussed. The beta-branched side chains are not complementary to the shape of the S1 binding pocket in SGPB, in contrast to that of the wild-type gamma-branched P1 residue for OMTKY3, Leu18I. Chi1 angles of approximately 40 degrees are imposed on the side chains of Ile18I, Val18I, and Thr18I within the S1 pocket. Dihedral angles of +60 degrees, -60 degrees, or 180 degrees are more commonly observed but 40 degrees is not unfavorable for the beta-branched side chains. Thr18I Ogamma1 also forms a hydrogen bond with Ser195 Ogamma in this orientation. The Ser18I side chain adopts two alternate conformations within the S1 pocket of SGPB, suggesting that the side chain is not stable in either conformation.     

Molecular evidence of natural hybridization between abies veitchii and A. homolepis (Pinaceae) revealed by chloroplast, mitochondrial and nuclear DNA markers

Sub-alpine Abies veitchii and A. homolepis are distributed in the central part of Honshu Island, Japan, and their habitats are segregated vertically. These species sometimes form a mixed forest in the overlapping area of the two species, that is, in the upper limit of the A. homolepis habitat and the lower limit of A. veitchii. These species have been considered to be distantly related because they were classified into different sections by most conventional classifications. No natural hybridization has been reported between the two species. The aim of this study was to demonstrate, through the use of molecular markers, whether natural hybridization takes place between these two species at two experimental sites on Mt. Fuji, where the species occur naturally. DNA markers from paternally inherited chloroplast DNA (cpDNA), maternally inherited mitochondrial DNA (mtDNA) and biparentally inherited nuclear DNA (nDNA), were used for this study. As organelle DNA markers, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) markers were developed to determine the maternal and paternal species for each individual. Two of 334 individuals possessed a cpDNA haplotype derived from A. homolepis and a mtDNA haplotype from A. veitchii. Furthermore, the nDNA of these two individuals was analysed using the random amplified polymorphic DNA (RAPD) assay to investigate their genomic composition. RAPD analysis indicated that the nuclear genomes of the two individuals were derived from both species. We conclude that A. veitchii and A. homolepis produce natural hybrids, and that their systematic relationship should be re-evaluated.     

Competitive ability and the coexistence of anuran larvae in freshwater rock‐pools

• 1 I examined the competitive ability of larval common frogs (Rana temporaria) and common toads (Bufo bufo) in a laboratory experiment by manipulating the number and size of Rana and the number of Bufo.
• 2 Bufo was the most active tadpole type, whereas small Rana was more active than large Rana.
• 3 Especially at high food availability, the growth rate of large Rana at metamorphosis was reduced in the presence of small Rana, whereas that of small Rana was not affected by larger conspecifics.
• 4 Both size classes of Rana were negatively affected by the presence of Bufo. Size at metamorphosis of Bufo was greater when large Rana was present. These results suggest that activity level is important in determining competitive ability.
• 5 To study competition in the field, tadpoles of Bufo were introduced to small rock‐pools that did not support Bufo naturally, but were with or without Rana.
• 6 In the experimental pools, there were no interspecific effects on the growth rate of either species. However, the growth rate of Bufo was lower in the experimental pools than in pools inhabited naturally. Futher, survival of Bufo was low in small pools. Lower food availability or physical factors associated with small pools, rather than interspecific competition, may be the reason why Bufo avoids breeding in small rock‐pools.

     

Cannibalism and Intraguild Predation Among Phytoseiid Mites: Are Aggressiveness and Prey Preference Related to Diet Specialization?

We tested whether specialist and generalist phytoseiid mites differ in aggressiveness and prey choice in cannibalism and intraguild predation. Specialists tested were Galendromus occidentalis, Neoseiulus longispinosus, Phytoseiulus persimilis, and P. macropilis; tested were Amblyseius andersoni, Euseius finlandicus, E. hibisci, Kampimodromus aberrans, Neoseiulus barkeri, N. californicus, N. cucumeris, N. fallacis, and Typhlodromus pyri. Aggressiveness of cannibalistic females against larvae was not related to diet specialization except that highly aggressive species were exclusively generalists. Seldom to moderately cannibalizing species occurred in both generalist and specialist phytoseiids. In contrast to aggressiveness in cannibalism, generalists and specialists differed in aggressiveness in intraguild predation. Adult females of specialists were only slightly aggressive against heterospecific larvae, whereas adult females of all generalists except T. pyri were highly aggressive. Adult females of generalists were able to discriminate between con- and heterospecific larvae and preferentially consumed the latter when given a choice. Adult females of specialists except G. occidentalis showed no preference when given a choice between con- and heterospecific larvae. We conclude that aggressiveness in intraguild predation, species recognition and subsequent preferential consumption of heterospecifics when given a choice is common in generalist but not specialist phytoseiids. We discuss the evolutionary pathways that might have led to the difference between specialists and generalists in species discrimination.     

A Theoretical Model for the Association Probabilities of Saturated Phospholipids from Two-Component Bilayer Lipid Membranes

The non-random mixing of biomembrane components, especially saturated phospholipids, exhibits important consequences in molecular biology. Particularly, the distribution of lipids within natural and model membranes is strongly determined by the selective association processes. These processes of phospholipids take place due to the cooperative modes in multiparticle systems as well as the specific lipid-lipid interactions both in the hydrophobic core and in the region of the polar headgroups. We demonstrated that the investigation of the selective association processes of saturated phospholipids might contribute to the insight of the lipid domains appearance inside the bilayer membranes. The association probabilities of like-pairs and cross-pairs from a binary mixture of saturated phospholipids were tested for both parallel and anti-parallel alignments of the polar headgroups. The present model confirms the experimental evidence for saturated phospholipids to have a high tendency for association in parallel configuration of the electric dipole moments of the polar headgroups whether the cross-sectional area of the polar headgroup is in an usual range of 25-55 2. There are three major lipid domains in a binary mixture of saturated phospholipids: (i) lipid domains in non-mixed phase of the first mixture component, in parallel alignment of the polar headgroups; (ii) lipid domains in non-mixed phase of the second mixture component, in anti-parallel alignment of the polar headgroups; (iii) lipid domains in mixed phase. We think that the selective association processes of phospholipids are neither exclusively, nor only involved in promoting the lipid domains appearance through bilayer phospholipid membranes.