Hetero-alpha-helical, two-chain, coiled coils: alpha beta hybrid tropomyosin

The nature of the interhelix interaction in two-chain, α-helical, coiled coils is studied by experiments on the formation of hydrid molecules in which one helical chain is an α-tropomyosin and the other a β-tropomoysin. By means of a recently developed assay, the population of heterohelical (i.e., αβ hybrid) molecules relative to their homohelical (αα and ββ) parent species is determined under a variety of conditions, both equilibrium and nonequilibrium. It is found that mixed intact αα and ββ molecules do not form hybrid species in detectible amounts even after incubation at room temperature (or below) for periods of over one week. That the lack of αβ species in this “native-exchange” system is a result of a kinetic barrier is evident from experiments involving a thermal denaturation–renaturation cycle in which the largely dissociated, unfolded chains at higher temperature are annealed to benign temperatures over a period of 6 h, thus assuring an equilibrium population of two-chain species. In the resulting equilibrium state, the αβ population is one-half the total, indicating that recombination is random. Furthermore, this same (equilibrium) state is reached if the separated, mostly unfolded chains are renatured by a rapid (～ 40 s) quench to benign temperatures. Some implications of these results for the thermodynamics of interhelix interation, for kinetics of chain dissociation and recombination, and for in vivo genesis of two-chain coiled coils are discussed.     

Isolation and characterization of polymorphic nuclear microsatellite loci in Pinus cembra L

We developed eight polymorphic nuclear microsatellite markers for the Swiss stone pine (Pinus cembra L.), of which seven may be amplified in a multiplex polymerase chain reaction. Allelic polymorphism across all loci and 40 individuals representing two populations in the Swiss Alps was high (mean = 7.6 alleles). No significant linkage disequlibrium was displayed between pairs of loci. Significant deviation from Hardy–Weinberg equilibrium was revealed at three loci in one population. Cross–amplification was achieved in two related species within the genus (P. sibirica and P. pumila). Thus, the markers may be useful for population genetic studies in these three pine species. They will be applied in ongoing projects on genetic diversity and patterns of gene flow in P. cembra.     

Specific Optical Rotations and the Horeau Effect

The observation of nonequivalence of optical and enantiomeric purities, referred to as the Horeau effect, is thought to arise from molecular aggregation in liquid solutions. Although this effect was first observed in 1969, the conditions under which this effect may, or may not, be observable are not established. Considering the formation of dimers as the simplest form of aggregation, the expressions for specific optical rotations in the presence of homochiral and heterochiral monomer–dimer equilibria are presented. Analysis of these equations indicates that the Horeau effect will not be observable even in the presence of aggregation under either of the following two situations: 1) The specific optical rotation of the monomeric species is equal to that of the dimeric species; 2) The heterochiral equilibrium constant is twice that of the homochiral equilibrium constant. Chirality 28:181–185, 2016. © 2015 Wiley Periodicals, Inc.     

Eight polymorphic microsatellite markers for kelp bass,Paralabax clathratus,amplified in three multiplex polymerase chain reaction sets

Kelp bass, Paralabrax clathratus, is an important sport fishery of California, USA and Baja, Mexico. Here we describe eight microsatellite loci developed for this species. Two loci were derived from known primers for other species in the family, Serranidae and six were developed anew using a clone enrichment protocol. Loci were arranged into three multiplex PCR (polymerase chain reaction) sets for fast throughput; 564 individuals from nine populations across the species’ range were genotyped. Polymorphism ranged from four to 47 alleles and all populations at all loci displayed Hardy–Weinberg and linkage equilibrium.     

Modifications des écosystèmes des vasières cotières du sud-Bretagne

Summary The northern part of the Bay of Biscaye consists of muddy areas which were the subject of many surveys conducted from the early sixties revealing important modifications. Communities living in these muddy areas are very rich in quality as well as quantity and with high interactions between the different species. With their trophic ethology, their biogenic actions, these species modify largely the sediment quality, its compactness for example is related to the tubicolous species presence. The disappearance of certain dominant species is due to some climatic anomalies causing an important disturbance of the ecosystem. In the infralittoral muddy areas, Zostera beds had been replaced momently by the abundant populations of Melinna. In the coastal muddy sites the recent disappearance of the Maldane cause a momentary imbalance, and for many long years, an equilibrium based on a new dominant species may appear. The intervention of an allogenic factor may in this case, opposite autogenic succession of the community or call the equilibrium which seems established in question again.

     

榕树–榕小蜂协同进化中的非对称性相互作用及其集合种群效应

在协同进化研究中,传统观点认为物种之间的相互作用是对称性的,在进化过程中将形成一个稳定的均衡状态或进化稳定策略。然而,近来的观测和实验数据表明,物种间的协同进化可能存在非对称性相互作用,而且这种非对称性可能造成集合种群效应(metapopulation effect)或形成非均衡状态(例如混沌,chaos)。本文利用"榕树–榕小蜂"这一经典的协同进化模式系统来介绍协同进化过程中的非对称性相互作用,以及这种非对称性如何产生集合种群效应。在榕–蜂共生系统中,栖身于榕果中的榕小蜂除了传粉小蜂之外,还有一些"投机"的非传粉小蜂。非传粉小蜂比传粉小蜂具有更强的竞争力,而榕树则可惩罚不合作的非传粉蜂,同时奖励合作的传粉小蜂,从而形成了复杂的非对称性种间相互作用。在某个斑块生境中,非传粉小蜂通过竞争作用排斥传粉小蜂,然而随着非传粉小蜂在蜂群中的比例不断升高,榕树惩罚作用(如落果等)常常会导致整个非传粉蜂群的数量急剧下降,甚至局域性灭绝。随后,其他斑块的传粉小蜂则迁移过来填补空白。然而,随着传粉小蜂种群的数量增长,该斑块又会集聚更多的投机性非传粉小蜂,进而诱发榕树再次进行惩罚。这样的非对称性相互作用导致了非传粉小蜂、传粉小蜂以及榕树种群的集合效应,其种群大小呈现周期性的"此消彼长"式的循环。     

Isolation and characterization of microsatellites in lane snapper (Lutjanus synagris), mutton snapper (Lutjanus analis), and yellowtail snapper (Ocyurus chrysurus)

Polymerase chain reaction primer pairs for a total of 25 nuclear‐encoded microsatellites (loci) were developed from genomic DNA libraries of lane snapper (Lutjanus synagris), mutton snapper (Lutjanus analis), and yellowtail snapper (Ocyurus chrysurus). The microsatellites include 24 perfect (21 dinucleotide and three trinucleotide) and one imperfect (combination tetranucleotide/tetranucleotide) repeat motifs. A total of 32 individuals of each species were assayed for allelic variation at all 25 microsatellites; reliable amplification products were generated for lane snapper (25 loci), mutton snapper (21 loci), and yellowtail snapper (24 loci). Significant deviations from Hardy–Weinberg expectations, following Bonferroni corrections, were found for one microsatellite in lane and yellowtail snappers, and for three microsatellites in mutton snapper. All pairwise comparisons of microsatellites (all three species) did not deviate significantly from genotypic equilibrium.     

Testing for context-dependence in a processing chain interaction among detritus-feeding aquatic insects

Abstract 1. Scirtid beetles may benefit mosquitoes Ochlerotatus triseriatus (Say) by consuming whole leaves and leaving behind fine particles required by mosquito larvae. Such interactions based on the sequential use of a resource that occurs in multiple forms are known as processing chains.
2. Models of processing chains predict that interactions can vary from commensal (0, +) to amensal (0, –), depending on how quickly resource is processed in the absence of consumers.
3. The scirtid– O. triseriatus system was used to test the prediction derived from processing chain models that, as consumer-independent processing increases, scirtids benefit mosquitoes less. Consumer-independent processing rate was manipulated by using different leaf species that vary in decay rate, or by physically crushing a single leaf type to different degrees.
4. Although scirtids increased the production of fine particles, the effects of scirtids on mosquitoes were weak and were not dependent on consumer-independent processing rate.
5. In the leaf manipulation experiment, a correlation between scirtid feeding and consumer-independent processing was detected. Numerical simulations suggest that such a correlation may eliminate shifts from commensal to amensal at equilibrium; because mosquito populations are typically not at equilibrium, however, this correlation may not be important.
6. There was evidence that mosquitoes affected scirtids negatively, which is inconsistent with the structure of processing chain interactions in models. Processing chain models need to incorporate more detail on the biology of scirtids and O. triseriatus , especially alternative mechanisms of interaction, if they are to describe scirtid– O. triseriatus dynamics accurately.     

Impermeant potential-sensitive oxonol dyes: II. The dependence of the absorption signal on the length of alkyl substituents attached to the dye

Summary We have measured the potential-dependent light absorption changes of 43 impermeant oxonol dyes with an oxidized cholesterol bilayer lipid membrane system. The size of the signal is strongly dependent on the chain length of alkyl groups attached to the chromophore. Dye molecules with intermediate chain lengths give the largest signals. To better understand the dependence of the absorbance signal on alkyl chain length, a simple equilibrium thermodynamic analysis has been derived. The analysis uses the free energy of dye binding to the membrane and the on-off model (E.B. George et al.,J. Membrane Biol.,103:245–253, 1988a) for the potential-sensing mechanism. In this model, a population of dye molecules in nonpolar membrane binding sites is in a potential-dependent equilibrium with a second population of dye that resides in an unstirred layer adjacent to the membrane. Dye in the unstirred layer is in a separate equilibrium with dye in the bulk bathing solution. The equilibrium binding theory predicts a sigmoidally shaped increase in signal with increasing alkyl chain length, even for very nonpolar dyes. We suggest that aggregation of the more hydrophobic dyes in the membrane bathing solution may be responsible for their low signals, which are not predicted by the theory.     

Isolation and characterization of 27 polymorphic microsatellite loci for the common snook,Centropomus undecimalis

Here we describe 32 di‐, tri‐ and tetranucleotide microsatellite loci isolated by PIMA, a polymerase chain reaction (PCR)‐based procedure, for the common snook (Centropomus undecimalis). Five loci were monomorphic, and the remaining loci averaged 6.7 alleles per locus in a sample of 45 common snook. For polymorphic loci, expected heterozygosities ranged from 0.02 to 0.91 (mean = 0.538). Significant departures from Hardy–Weinberg equilibrium expectations occurred in two loci. Exact tests for genotype disequilibrium gave evidence for linkage at one pair of loci. Many cross‐species primer assays yielded PCR fragments of the expected size for 11 species of Centropomus and two species of the confamilial genus Lates.     

In comparison with nitrate nutrition,ammonium nutrition increases growth of the frostbite1 Arabidopsis mutant

Ammonium nutrition inhibits the growth of many plant species, including Arabidopsis thaliana. The toxicity of ammonium is associated with changes in the cellular redox state. The cellular oxidant/antioxidant balance is controlled by mitochondrial electron transport chain. In this study, we analysed the redox metabolism of frostbite1 (fro1) plants, which lack mitochondrial respiratory chain complex I. Surprisingly, the growth of fro1 plants increased under ammonium nutrition. Ammonium nutrition increased the reduction level of pyridine nucleotides in the leaves of wild‐type plants, but not in the leaves of fro1 mutant plants. The observed higher activities of type II NADH dehydrogenases and cytochrome c oxidase in the mitochondrial electron transport chain may improve the energy metabolism of fro1 plants grown on ammonium. Additionally, the observed changes in reactive oxygen species (ROS) metabolism in the apoplast may be important for determining the growth of fro1 under ammonium nutrition. Moreover, bioinformatic analyses showed that the gene expression changes in fro1 plants significantly overlap with the changes previously observed in plants with a modified apoplastic pH. Overall, the results suggest a pronounced connection between the mitochondrial redox system and the apoplastic pH and ROS levels, which may modify cell wall plasticity and influence growth.     

Return time and vulnerability for a food chain model

Simulation studies have shown that the time it takes for a system of interacting species in a food chain to return to equilibrium after a disturbance increases as the number of trophic levels increase. It has been argued that this effect is important in limiting the length of food chains subject to perturbations of the real world. We show that for an asymptotically stable system a lower bound on the return time is directly proportional to the number of trophic levels in agreement with simulation studies. In addition, the lower bound on the return time is shown to be inversely proportional to the sum of products of the intraspecific competition coefficient and equilibrium population of the species. A new method for directly computing the vulnerability of a system to external perturbations is presented. Using this method we demonstrate that for a food chain where the number of species is equal to the number of trophic levels, the return time alone is not a proper measure of system vulnerability. Indeed, adding an additional trophic level may make the system less vulnerable to disturbances. Interspecific coupling between the trophic levels is shown to be an important factor in determining system vulnerability.     

Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium

The olive shells of the genus Amalda comprises readily recognized species of marine neogastropod mollusks found around the world. The New Zealand Amalda fauna has particular notoriety as providing one of the best demonstrations of evolutionary morphological stasis, a prerequisite for punctuated equilibrium theory. An excellent fossil record includes representation of three extant endemic Amalda species used to explore patterns of form change. However, the phylogenetic relationship of the New Zealand Amalda species and the timing of their lineage splitting have not been studied, even though these would provide valuable evidence to test predictions of punctuated equilibrium. Here, we use entire mitogenome and long nuclear rRNA gene cassette data from 11 Amalda species, selected from New Zealand and around the world in light of high rates of endemicity among extant and fossil Amalda. Our inferred phylogenies do not refute the hypothesis that New Zealand Amalda are a natural monophyletic group and therefore an appropriate example of morphological stasis. Furthermore, estimates of the timing of cladogenesis from the molecular data for the New Zealand group are compatible with the fossil record for extant species and consistent with expectations of punctuated equilibrium.     

Arid vegetation in disequilibrium with livestock grazing: Evidence from long‐term exclosures

In recent decades, the conventional equilibrium paradigm for explaining rangeland vegetation dynamics has been challenged. Proponents of an alternative non‐equilibrium paradigm argue that in variable rangeland environments, external climatic events are critical to vegetation dynamics and there is little opportunity for plant–herbivore interactions to reach equilibrium. Understanding which paradigm more effectively describes an ecosystem has important consequences for management. In particular, some authors have argued that a focus on reducing stocking rates in non‐equilibrium systems may be futile, and management should be opportunistic in response to unpredictable rainfall events. We measured herbaceous biomass and plant species richness and abundance at five 14‐year exclosures on Innamincka Regional Reserve. Four were situated in the dunefields land system, and one on the Cooper Creek floodplain. We did not detect any significant differences between grazed and ungrazed treatments in total species richness or abundance, life form richness or abundance, or herbaceous biomass. Only one species, Portulaca oleracea, showed differences in abundance between treatments at more than one site, but the direction of these differences was not consistent. These results suggest that the non‐equilibrium paradigm more accurately describes vegetation dynamics in the dunefields and floodplains of north‐eastern South Australia. It is possible that some species had been lost from the study area prior to the establishment of the exclosures, thereby precluding recovery with protection from grazing; however, a regional analysis of the flora reveals little evidence of this. We argue that the dominance of ephemeral species confers resilience by limiting the development of strong feedbacks between grazing intensity and vegetation dynamics. Current grazing practices seem consistent with the conservation of plant species diversity across the dunefields and floodplains. Future studies should focus on the impacts of cattle grazing on areas of the landscape dominated by palatable perennials, as well as the small number of rare and potentially grazing‐sensitive species identified.     

A new primer set for sex identification in the genus Sorex (Soricidae,Insectivora)

In order to develop a new accurate method for sexing in Sorex species (Soricidae, Insectivora), we synthesized a polymerase chain reaction (PCR) primer set to amplify a part of Sry HMG box in the long‐clawed shrew, Sorex unguiculatus. When the primers were applied to the samples of known sex, PCR products were successfully obtained for males as a clear, single band on 3% agarose gels after electrophoresis in Sorex unguiculatus and five other Sorex species, but not for females of these six species. Thus, PCR amplification using the primer set may be applicable to discern sex in the six Sorex species.     

中立型Logistic方程组的振动性

本文讨论中立型 Ｌｏｇｉｓｔｉｃ方程组的所有关于它的正平衡点振动的正解的充分条件。     

Cellular automaton models for competition in patchy environments: Facilitation, inhibition, and tolerance

We have developed cellular automaton models for two species competing in a patchy environment. We have modeled three common types of competition: facilitation (in which the winning species can colonize only after the losing species has arrived) inhibition (in which either species is able to prevent the other from colonizing) and tolerance (in which the species most tolerant of reduced resource levels wins). The state of a patch is defined by the presence or absence of each species. State transition probabilities are determined by rates of disturbance, competitive exclusion, and colonization. Colonization is restricted to neighboring patches. In all three models, disturbance permits regional persistence of species that are excluded by competition locally. Persistence, and hence diversity, is maximized at intermediate disturbance frequencies. If disturbance and dispersal rates are sufficiently high, the inferior competitor need not have a dispersal advantage to persist. Using a new method for measuring the spatial patterns of nominal data, we show that none of these competition models generates patchiness at equilibrium. In the inhibition model, however, transient patchiness decays very slowly. We compare the cellular automaton models to the corresponding mean-field patch-occupancy models, in which colonization is not restricted to neighboring patches and depends on spatially averaged species frequencies. The patch-occupancy model does an excellent job of predicting the equilibrium frequencies of the species and the conditions required for coexistence, but not of predicting transient behavior.     

The Life History of Chactas reticulatus Kraepelin, 1912 (Scorpiones, Chactidae), with a Comparative Analysis of the Reproductive Traits of Three Scorpion Lineages in Relation to Habitat

An account is given of the life history, growth, population densities, habitat, reproductive systems, courtship and mating, litter size and sex ratio, iteroparity, molting and development of the scorpion Chactas reticulatus Kraepelin. These same traits are compared in three distinct scorpion lineages, buthid, chactid and ischnurid in relation to habitat characteristics. Correlations are drawn between reproductive and adaptative strategies, and it is suggested that if non-buthid scorpions may present some homogeneity as equilibrium species, buthid scorpions are not necessarily opportunistic species. Many groups can be characterized within the buthids, and these different lineages show variable ecological requirements.     

Gene flow between populations of two invertebrates in springs

1. Using allozymes, we analysed genetic structure of the freshwater gastropod Bythinella dunkeri and the freshwater flatworm Crenobia alpina. The two species are habitat specialists, living almost exclusively in springs. The sampled area in Hesse (Germany) covers a spatial scale of 20 km and includes two river drainages. From the biology of the two species we expected little dispersal along rivers. However, the possibility exists that groundwater provide suitable pathways for dispersal. 2. In B. dunkeri heterozygosity decreased from west to east. For some alleles we found clines in this geographic direction. These clines generated a positive correlation between geographic distance and genetic differentiation. Furthermore patterns of genetic variation within populations suggested that populations may have been faced with bottlenecks and founder effects. If populations are not in population genetic equilibrium, such founder effects would also explain the rather high amount of genetic differentiation between populations (10%). 3. For C. alpina the mean number of alleles decreased with increasing isolation of populations. Genetic differentiation between populations contributed 19% to the total genetic variation. Genetic differentiation was not correlated to geographic distance, but compared with B. dunkeri variability of pairwise differentiation between pairs of populations was higher in C. alpina. 4. Overall B. dunkeri appears to be a fairly good disperser, which may use groundwater as dispersal pathway. Furthermore populations seem to be not in equilibrium. In contrast C. alpina forms rather isolated populations with little dispersal between springs and groundwater seems to play no important role for dispersal.