Host-associated fitness trade-offs do not limit the evolution of diet breadth in the small milkweed bug Lygaeus kalmii (Hemiptera: Lygaeidae)

Theoretical models of evolution in a temporally variable environment predict that genotypes with low variance in fitness across generations will be favored. When host use varies temporally and fitness trade-offs exist among hosts, such that an increase in performance on one host results in a correlated decrease on the other, selection for low variance in fitness across generations will favor genotypes which are generalists. Before predictions such as this can be extended to natural herbivore populations, however, it is necessary to understand the extent to which performance trade-offs limit simultaneous adaptation to multiple hosts. The experiment reported here compares two populations of the common milkweed bug, Lygaeus kalmii (Hemiptera: Lygaeidae) which differ in patterns of host usage. One population is largely restricted to milkweed (Asclepias spp.) when milkweed seeds are available, but becomes a scavenger on a large assortment of available seeds when milkweed seeds are unavailable. The second population is restricted largely to dandelion (Taraxacum officinale), without access to milkweed. We examine these populations to test for host-associated genetic trade-offs between specialization on dandelion (Taraxacum) and two species of milkweed, Asclepias fascicularis, which is low in cardiac glycoside content, and A. speciosa, which is high in cardiac glycoside content. Despite the difference in patterns of host use of the two L. kalmii populations, the populations did not differ in their performance on any of the host plants. Within each population, bugs performed nearly as well on each host, except that bugs had significantly lower survivorship on dandelion than on either milkweed species. Trade-offs in performance among hosts were not present in either population: estimated genetic correlations across hosts were strongly positive. The inability of this study to detect host-associated fitness trade-offs is consistent with most published data on this topic.     

Kinetic analysis of a high-affinity antibody/antigen interaction performed by multiple Biacore users

To explore the reliability of Biacore-based assays, 22 study participants measured the binding of prostate-specific antigen (PSA) to a monoclonal antibody (mAb). Each participant was provided with the same reagents and a detailed experimental protocol. The mAb was immobilized on the sensor chip at three different densities and a two-step assay was used to determine the kinetic and affinity parameters of the PSA/mAb complex. First, PSA was tested over a concentration range of 2.5-600 nM to obtain k(a) information. Second, to define the k(d) of this stable antigen/antibody complex accurately, the highest PSA concentration was retested with the dissociation phase of each binding cycle monitored for 1h. All participants collected data that could be analyzed to obtain kinetic parameters for the interaction. The association and the extended-dissociation data derived from the three antibody surfaces were globally fit using a simple 1:1 interaction model. The average k(a) and k(d) for the PSA/mAb interaction as calculated from the 22 analyses were (4.1+/-0.6) x 10(4) M(-1) s(-1) and (4.5+/-0.6) x 10(-5) s(-1), respectively. Overall, the experimental standard errors in the rate constants were only approximately 14%. Based on the kinetic rate constants, the affinity (K(D)) of the PSA/mAb interaction was 1.1+/-0.2 nM.     

Differential network biology

Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been generated under a single condition, even though biological systems undergo differential change that is dependent on environment, tissue type, disease state, development or speciation. Several recent interaction mapping studies have demonstrated the power of differential analysis for elucidating fundamental biological responses, revealing that the architecture of an interactome can be massively re‐wired during a cellular or adaptive response. Here, we review the technological developments and experimental designs that have enabled differential network mapping at very large scales and highlight biological insight that has been derived from this type of analysis. We argue that differential network mapping, which allows for the interrogation of previously unexplored interaction spaces, will become a standard mode of network analysis in the future, just as differential gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.     

酵母三杂交系统的原理和应用

酵母双杂交系统自出现以来,广泛用于研究蛋白质之间的相互作用,它是一种具有高灵敏度的研究蛋白质之间关系的技术.在酵母双杂交系统基础上发展的酵母三杂交系统将应用范围扩展到蛋白质-蛋白质、蛋白质-RNA、蛋白质-小分子化合物等更广阔的研究领域.本文着重介绍酵母三杂交系统的原理、应用及局限性.     

蛋白质相互作用的生物信息学研究进展

生命过程的分子基础在于生物分子之间的相互作用,其中蛋白质分子之间的相互作用占有极其重要的地位。研究蛋白质相互作用对于理解生命的真谛、探讨致病微生物的致病机理,以及研究新药提高人们的健康水平具有重要的作用。用生物信息学的方法研究蛋白质的相互作用已经取得了许多重要的成果,但也有很多问题还需解决。本文从蛋白质相互作用的数据库、预测方法、可预测蛋白质相互作用的网上服务、蛋白质相互作用网络等几方面,对蛋白质相互作用的生物信息学研究成果及其存在的问题做了概述。     

A statistical analysis of side-chain conformations in proteins: Comparison with ECEPP predictions

A comparison of the statistical distributions of side-chain conformations of 17 amino acids (Gly, Ala, and Pro excluded), observed in 63 nonhomologous globular proteins (covering 10,832 residues), is made with similar distributions calculated from the low-energy conformational states for the same amino acids (blocked with acetyl and N-methylamide groups at the N- and C-termini, respectively) obtained by Vásquezet al. [(1983),Macromolecules 16, 1043–1049 using the ECEPP/2 force field. Those residues (i) with linear side chains (Arg, Lys, Met, Cys, Ser), or those that are unbranched through the-carbon atom (Glu, Gln) show good agreement, whereas (ii) those with side chains that are branched at C or C show poor agreement with ECEPP calculations. A possible explanation for this is shown to be the greater tendency for side-chain atoms in class (ii) to interact with the backbone and/or adjacent side chains. Accordingly, ECEPP/3 calculations, carried out after elongating the backbone chain of the model peptide unit (by adding three Ala residues on each side of the central residue, and then blocking the termini as before), result in distributions that are often closer to the observed side-chain distributions. The implications of these results for the relative importance of short-range versus long-range interactions in determining protein structure are discussed.     

Geographic and taxonomic distribution of a positive interaction: ant-tended homopterans indirectly benefit figs across southern Africa

Although species pairs and assemblages often occur across geographic regions, ecologists know very little about the outcome of their interactions on such large spatial scales. Here, we assess the geographic distribution and taxonomic diversity of a positive interaction involving ant-tended homopterans and fig trees in the genus Ficus. Previous experimental studies at a few locations in South Africa indicated that Ficus sur indirectly benefited from the presence of a homopteran (Hilda patruelis) because it attracted ants (primarily Pheidole megacephala) that reduced the effects of both pre-dispersal ovule gallers and parasitoids of pollinating wasps. Based on this work, we evaluated three conditions that must be met in order to support the hypothesis that this indirect interaction involves many fig species and occurs throughout much of southern Africa and Madagascar. Data on 429 trees distributed among five countries indicated that 20 of 38 Ficus species, and 46% of all trees sampled, had ants on their figs. Members of the Sycomorus subgenus were significantly more likely to attract ants than those in the Urostigma subgenus, and ant-colonization levels on these species were significantly greater than for Urostigma species. On average, each ant-occupied F.sur tree had 37% of its fig crop colonized by ants, whereas the value was 24% for other Ficus species. H. patruelis was the most common source for attracting ants, although figs were also attacked by a range of other ant-tended homopterans. P. megacephala was significantly more common on figs than other ant species, being present on 58% of sampled trees. Ant densities commonly exceeded 4.5 per fig, which a field experiment indicated was sufficient to provide protection from ovule gallers and parasitoids of pollinators. Forty-nine percent of all colonized F. sur trees sampled had ant densities equal to or greater than 4.5 per fig, whereas this value was 23% for other Ficus species. We conclude that there is considerable evidence to suggest that this indirect interaction occurs across four southern African countries and Madagascar, and involves many Ficus species. Received: 11 December 1997 / Accepted: 6 April 1998     

Protein-RNA contacts at crystal packing surfaces

The crystal packing surfaces comprising protein-RNA interactions were analyzed for 50 RNA-protein crystal structures in the Protein Data Bank database. Protein-RNA crystal contacts, which represent nonspecific protein-RNA interfaces, were investigated for their amino acid propensities, hydrogen bond patterns, and backbone and side chain interactions. When compared to biologically relevant interactions, the protein-RNA crystal contacts exhibit similarities as well as differences with respect to the principles of protein-RNA interactions. Similar to what was observed at cognate protein-RNA interfaces, positively charged amino acids have high propensities at noncognate protein-RNA interfaces and preferentially form hydrogen bonds with RNA phosphate groups. In contrast, nonpolar residues are less frequently associated with noncognate interactions. These results highlight the important roles of both electrostatic and hydrogen bonding interactions, facilitated by positively charged amino acids, in mediating both specific and nonspecific protein-RNA interactions.     

Electrodynamics of interactions in electrolyte media. Possible consequences in biological functions

Attention is drawn to the fact that electric charge interactions in aqueous electrolyte solutions, such as physiological media, depend not only on the distance between the interacting charges but also on the frequency at which they move. This fact has important consequences for some biological processes, particularly the kinetic ones. Consideration of charge screening, including the dynamic effects, shows that electrical interactions in quasi-physiological systems are effective even above Debye’s length, provided that charges move at frequencies higher than ～250 MHz. For each electrolyte solution, it is possible to define a threshold frequency, the Maxwell frequency, as the point of crossover between a conducting and a dielectric regime in the solution.     

Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes

The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs), made up of stretches of helix, strand and non-regular (NR) regions. On average 10-11 segments define the protein interface in protein-protein (PP) and protein-DNA (PD) complexes, while the number is higher (14) for protein-RNA (PR) complexes. While the length of helical segments in PP interaction increases with the interface area, this is not the case in PD and PR complexes. The propensities of residues to occur in the three types of secondary structural elements (SSEs) in the interface relative to the corresponding elements in the protein tertiary structures have been calculated. Arg, Lys, Asn, Tyr, His and Gln are preferred residues in PR complexes; in addition, Ser and Thr are also favoured in PD interfaces.     

Genomic survey of NPF and NRT2 transporter gene families in five inbred maize lines and their responses to pathogens infection

Besides manipulating nitrate uptake and allocation, nitrate transporters (NRTs) are also known to play crucial roles in pathogen defense and stress response. By blasting with the model NRT genes of poplar and Arabidopsis, a total of 408 gene members were identified from 5 maize inbred lines in which the number of NRTs ranged from 72 to 88. Phylogenetic analysis showed that the NRT genes of maize were classified into NRT1/PTR (NPF), NRT2 and NRT3 subfamilies, respectively. Marked divergence of the duplication patterns of NRT genes were identified, which may be a new basis for classification and identification of maize varieties. In terms of biotic stress, NRT2.5A showed an enhanced expression during the pathogen infection of Colletotrichum graminicola, while NRT1c4C was down-regulated, suggesting that maize NRT transporters may have both positive and negative roles in the disease resistance response. This work will promote the further studies of NRT gene families in maize, as well as be beneficial for further understanding of their potential roles in plant-pathogen interactions.     

A closer look at the spatial architecture of aphid clones

Nearly 25 years ago, Ellstrand & Roose (1987) reviewed what was known at the time of the genetic structure of clonal plant species. What is the relationship between space and clonal fitness, they asked. What is the best way for a clone to grow within its ecological neighbourhood? The pot had been stirred 10 years previously by Janzen (1977) , who pointed out how little we know about the population biology of clonal organisms like dandelions and aphids. He wondered whether, like good curries, outward appearances masked common ingredients. Because in no small part of the advent of molecular ecology, we know more about clonal life histories today, particularly in plants ( van Dijk 2003 ; Vallejo‐Marín et al. 2010 ). Surprisingly, studies of the spatial architecture of aphid clones have been comparably rare. In this issue of Molecular Ecology, Vantaux et al. characterize the fine‐scale distribution of the black bean aphid (Aphis fabae) and in so doing, help to fill that gap. They describe a moderate degree of intermingling between aphid clones over a growing season—A. fabae clones are ‘sticky’, but only a bit. By mixing, clones directly compete with each other as well. The results of Vantaux et al. (2011) will help to integrate evolutionary patterns in aphids with the appropriate ecological scales out of which those patterns emerge.     

The facilitation of social interactions by domestic dogs

Abstract

Research suggests that dogs can facilitate social interactions, which, in turn, may promote psychological health. This study explored the ability of dogs to facilitate social responses relative to other accompaniments and investigated whether the social catalysis effect is generic or influenced by the appearance of the dog. The behavior of 1800 pedestrians approaching a female experimenter was recorded as a function of the presence of three dogs (Labrador Retriever pup, Labrador adult, Rottweiler adult) and two neutral stimuli (teddy bear, potted plant). The behavior of pedestrians approaching the woman whenever she was alone (control) was also explored. Information was collected on the passers-by’ gender, number of people in the party, type of acknowledgement elicited and length of conversations. More people ignored the experimenter whenever she was alone or with the teddy or plant, than whenever she was walking a dog. The Rottweiler resulted in more nonresponses than the puppy or adult Labrador, who in turn elicited more smiles and verbal responses. Females, and those alone, elicited more smiles and conversations than males, or those in pairs. It is concluded that dogs can facilitate social interactions between adults better than other accompaniments; however, the social catalysis effect is not generic, but dog specific.     

Austrobilharzia terrigalensis: A schistosome dominant in interspecific interactions in the molluscan host

Walker J. C. 1979. Austrobilharzia terrigalensis: a schistosome dominant in interspecific interactions in the molluscan host. International Journal for Parasitology9: 137–140. In the estuarine prosobranch Velacumantus australis the avian schistosome Austrobilharzia terrigalensis is always associated with the germinal sacs of other trematodes. In this association the schistosome retards the development of the other trematode, thereby reducing the intensity of interspecific competition for the limited resource, the host's tissues.     

Comparison of hard-cylinder and screened coulomb interactions in the modeling of supercoiled DNAs

A 1000 base pair (bp) model supercoiled DNA is simulated using spherical screened Coulomb interactions between subunits on one hand and equivalent hard-cylinder interactions on the other. The amplitudes, or effective charges, of the spherical screened Coulomb electrostatic potentials are chosen so that the electrostatic potential surrounding the middle of a linear array of 2001 subunits (31.8 Å diameter) closely matches the solution of the nonlinear Poisson-Boltzmann equation for a cylinder with 12 Å radius and the full linear charge density of DNA at all distances beyond the 24 Å hard-core diameter. This superposition of spherical screened Coulomb potentials is practically identical to the particular solution of the cylindrical linearized Poisson-Boltzmann equation that matches the solution of the nonlinear Poisson-Boltzmann equation at large distances. The interaction energy between subunits is reckoned from the effective charges according to the standard DLVO expression. The equivalent hard-cylinder diameter is chosen following Stigter's protocol for matching second virial coefficients, but for the full linear charge density of DNA. The electrostatic persistence length of the model with screened Coulomb interactions is extremely sensitive to the (arbitrarily) chosen subunit length at the higher salt concentrations. The persistence length of the hard-cylinder model is adjusted to match that of the screened Coulomb model for each ionic condition. Simulations for a superhelix density σ = -0.05 using a spherical screened Coulomb interaction plus a 24 Å hard-cylinder core (SCPHC) potential indicate that the radius of gyration of this 1000 bp DNA actually undergoes a slight increase as the NaCl concentration is raised from 0.01 to 1.0M. Thus, merely softening the potential from hard-cylinder to screened Coulomb form does not produce a large decrease in radius of gyration with increasing NaCl concentration for DNAs of this size. Radii of gyration, static structure factors, and diffusion coefficients obtained using the equivalent hard-cylinder (EHC) potential agree well with those obtained using the SCPHC potential in 1.0M NaCl, but in 0.1M NaCl the agreement is not as good, and in 0.01M NaCl the agreement is definitely unsatisfactory. These conclusions differ in significant respects from those obtained in previous studies. © 1997 John Wiley & Sons, Inc. Biopoly 42: 455–470, 1997     

Associational resistance and shared doom: effects of epibiosis on herbivory

The potential for spatial associations between palatable and unpalatable plant species to reduce herbivore pressure on the palatable species has been described as associational resistance, associational refuge or associational defense for numerous terrestrial and marine communities. One of the closest associations between species-epibiosis-has not been thoroughly investigated in this regard. In this study we evaluated how different associations between host seaweeds and epibiotic plants and animals influenced the movement of an omnivorous sea urchin (Arbacia punctulata) to the host and subsequent feeding on the host. A. punctulata showed clear preferences when given pairwise choices between 12 prey species (3 animals, 9 algae). These preferences were consistent and allowed us to rank the six epibiont species and six host species linearly from least to most preferred by A. punculata. Most host-epibiont associations dramatically changed urchin preference, increasing or decreasing urchin grazing on fouled hosts as compared to clean conspecifics. Herbivory on the host increased when the epibiont was more preferred, and decreased when it was less preferred than the unfouled host alga. Taking the host species as a point of reference, we classified epibiosis-caused decrease in herbivory as associational resistance, while epibiont-caused increases in herbivory were defined as shared doom. These epibiont-host-herbivore interactions could select for hosts that facilitate the growth of certain low preference epibionts on their surfaces in situations where the resulting decreases in herbivory would offset the various negative effects of being fouled. In contrast, in situations where herbivores are common, the negative effects of being fouled by palatable epibionts may be much greater than is generally assumed. In our assays, unpalatable hosts fouled by palatable epibionts became much more attractive to urchins and rose several ranks on the urchins' preference hierarchy.     

Electrostatic interactions in the association of proteins: an analysis of the thrombin-hirudin complex.

The role of electrostatic interactions in stabilization of the thrombin-hirudin complex has been investigated by means of two macroscopic approaches: the modified Tanford-Kirkwood model and the finite-difference method for numerical solution of the Poisson-Boltzmann equations. The electrostatic potentials around the thrombin and hirudin molecules were asymmetric and complementary, and it is suggested that these fields influence the initial orientation in the process of the complex formation. The change of the electrostatic binding energy due to mutation of acidic residues in hirudin has been calculated and compared with experimentally determined changes in binding energy. In general, the change in electrostatic binding energy for a particular mutation calculated by the modified Tanford-Kirkwood approach agreed well with the experimentally observed change. The finite-difference approach tended to overestimate changes in binding energy when the mutated residues were involved in short-range electrostatic interactions. Decreases in binding energy caused by mutations of amino acids that do not make any direct ionic interactions (e.g., Glu 61 and Glu 62 of hirudin) can be explained in terms of the interaction of these charges with the positive electrostatic potential of thrombin. Differences between the calculated and observed changes in binding energy are discussed in terms of the crystal structure of the thrombin-hirudin complex.     

The s-triazine ring, a remarkable unit to generate supramolecular interactions

Supramolecular chemistry is a topical field of contemporary research whose current tremendous progress is aided by the development of crystal structure determination and theoretical studies, both resulting from considerable advances in computer science. Consequently, supramolecular interactions are more easily appraised, and even the weakest ones, such as anion-π contacts, can nowadays be investigated. The present paper gives an account on the different types of interactions encountered by the supramolecular chemist, with an emphasis on the remarkable 1,3,5-triazine ring which can experience all of them, namely coordination bonds, hydrogen bonding, electrostatic and charge-transfer attractions, and aromatic-stacking interactions. Indeed, a thorough search in the Cambridge Structure Database clearly shows that this simple 1,3,5-triazine synthon can be involved in all the categories of supramolecular interactions aforementioned.     

Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth

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Energetics of cell-cell and cell-biopolymer interactions

The energy vs distance balance of cell suspensions (in the presence and in the absence of extracellular biopolymer solutions) is studied, not only in the light of the classical Derjaguin-Landau-Verwey-Over-beek (DLVO) theory (which considered just the electrostatic (EL) and Lifshitz-van der Waals (LW) interactions), but also by taking electron-acceptor/electron-donor, or Lewis acid-base (AB) and osmotic (OS) interactions into account. Since cell surfaces, as well as many biopolymers tend to have strong monopolar electron-donor properties, they are able to engage in a strong mutual AB repulsion when immersed in a polar liquid such as water. The effects of that repulsion have been observed earlier in the guise of hydration pressure. The AB repulsion is, at close range, typically one or two orders of magnitude stronger than the EL repulsion, but its rate of decay is much steeper. In most cases, AB interactions are quantitatively the dominant factor in cell stability (when repulsive) and in “hydrophobic interactions” (when attractive). OS interactions exerted by extracellularly dissolved biopolymers are weak, but their rate of decay is very gradual, so OS repulsions engendered by biopolymer solutions may be of importance in certain long-range interactions. OS interactions exerted by biopolymers attached to cells or particles (e.g., by glycocalix glycoproteins), are very short-ranged and usually are negligibly small in comparison with the other interaction forces, in aqueous media.