Test for interaction between two unlinked loci

Despite the growing consensus on the importance of testing gene-gene interactions in genetic studies of complex diseases, the effect of gene-gene interactions has often been defined as a deviance from genetic additive effects, which is essentially treated as a residual term in genetic analysis and leads to low power in detecting the presence of interacting effects. To what extent the definition of gene-gene interaction at population level reflects the genes' biochemical or physiological interaction remains a mystery. In this article, we introduce a novel definition and a new measure of gene-gene interaction between two unlinked loci (or genes). We developed a general theory for studying linkage disequilibrium (LD) patterns in disease population under two-locus disease models. The properties of using the LD measure in a disease population as a function of the measure of gene-gene interaction between two unlinked loci were also investigated. We examined how interaction between two loci creates LD in a disease population and showed that the mathematical formulation of the new definition for gene-gene interaction between two loci was similar to that of the LD between two loci. This finding motived us to develop an LD-based statistic to detect gene-gene interaction between two unlinked loci. The null distribution and type I error rates of the LD-based statistic for testing gene-gene interaction were validated using extensive simulation studies. We found that the new test statistic was more powerful than the traditional logistic regression under three two-locus disease models and demonstrated that the power of the test statistic depends on the measure of gene-gene interaction. We also investigated the impact of using tagging SNPs for testing interaction on the power to detect interaction between two unlinked loci. Finally, to evaluate the performance of our new method, we applied the LD-based statistic to two published data sets. Our results showed that the P values of the LD-based statistic were smaller than those obtained by other approaches, including logistic regression models.     

On the rate of convergence in topology preserving neural networks

A formal analysis of the neighborhood interaction function selection in the topology preserving unsupervised neural network is presented in this paper. The definition of the neighborhood interaction function is motivated by anatomical evidence as opposed to what is currently used, which is a uniform neighborhood interaction set. By selecting a neighborhood interaction function with a neighborhood amplitude of interaction which is decreasing in spatial domain the topological order is always enforced and the rate of self-organization to final equilibrium state is improved. Several simulations are carried out to show the improvement in rate between using a neighborhood interaction function vs. using a neighborhood interaction set. An error measure functional is further defined to compare the two approaches quantitatively.     

Disordered Binding Regions and Linear Motifs—Bridging the Gap between Two Models of Molecular Recognition

Intrinsically disordered proteins (IDPs) exist without the presence of a stable tertiary structure in isolation. These proteins are often involved in molecular recognition processes via their disordered binding regions that can recognize partner molecules by undergoing a coupled folding and binding process. The specific properties of disordered binding regions give way to specific, yet transient interactions that enable IDPs to play central roles in signaling pathways and act as hubs of protein interaction networks. An alternative model of protein-protein interactions with largely overlapping functional properties is offered by the concept of linear interaction motifs. This approach focuses on distilling a short consensus sequence pattern from proteins with a common interaction partner. These motifs often reside in disordered regions and are considered to mediate the interaction roughly independent from the rest of the protein. Although a connection between linear motifs and disordered binding regions has been established through common examples, the complementary nature of the two concepts has yet to be fully explored. In many cases the sequence based definition of linear motifs and the structural context based definition of disordered binding regions describe two aspects of the same phenomenon. To gain insight into the connection between the two models, prediction methods were utilized. We combined the regular expression based prediction of linear motifs with the disordered binding region prediction method ANCHOR, each specialized for either model to get the best of both worlds. The thorough analysis of the overlap of the two methods offers a bioinformatics tool for more efficient binding site prediction that can serve a wide range of practical implications. At the same time it can also shed light on the theoretical connection between the two co-existing interaction models.     

Interactions in Contingency Table Analysis

Proceeding from Lancaster's definition of interactions between random variables, the authors set up a model for contingency tables of any dimension. Three-dimensional contingency tables are used as an example to discuss first and second order interaction effects, and the conventional independence are expressed by hypotheses concerning interaction effects. The opinions of other authors regarding second order interaction effects are discussed.     

<Emphasis Type="Italic">Umwelträume</Emphasis> and Multisensory Integration. Mirror Perspectives on the Subject–Object Dichotomy

This paper concerns epistemic developments in the field of sensory perception. I argue that Uexküll’s concept of the Umwelträume and certain principles of multisensory integration explain and describe in similar terms the manner in which different sensory modalities interact. Indeed, they both concern knowledge, describing in spatial terms how the mind makes itself up, makes up its objects, and how the objects, in turn, make up the mind. My intention is to set side by side these two trends of thought in order to mutually explain them. I suggest that there is some sort of dialectic at work between the Umwelträume and multisensory integration: in the first case interaction between the senses results in the creation of high definition subjects, whereas in the latter the interaction of the senses results in high definition objects.     

Local description of surface tension through thermodynamic and mechanical definitions

For a half century, the calculation of local pressure components and surface tension along the normal to the surface have been carried out using mechanical definitions. This has led to three principal definitions: Irving and Kirkwood, Harasima and Kirkwood–Buff. Recently, thermodynamic definitions based on the energy calculation have been introduced to compute the local properties. We propose here to compare both definitions for Lennard–Jones particles interacting through a truncated and shifted potential. For this, two locations of the pairwise interaction involved in the calculation of the local pressure components and surface tension within the thermodynamic routes are investigated. For the first time, we show that the thermodynamic definition suffers, to one least degree with respect to the mechanical definition, from the same ambiguity. From a numerical standpoint, thermodynamic definition is more simple and less computationally expensive. Therefore, with the complicated potential, the thermodynamic approach appears to be most interesting to compute macroscopic and local pressure and surface tension.     

景观服务研究进展

生态系统服务强调了生态组成要素对人类福祉贡献的服务功能特性,近年来逐渐成为生态学研究的热点。然而,如何从生态组成要素的综合格局——景观的服务角度阐述生态系统服务,仍然是当前研究的巨大挑战。本文详细介绍了景观服务的概念、分类和应用尺度,并从制图方法和评价指标两方面阐述了景观服务的定量化方法,在此基础上探讨了景观服务在规划设计中的应用问题。最后,提出了新的研究展望,即要继续完善景观服务概念及分类体系,探讨景观服务的多尺度相互影响机理,寻求有效的景观服务空间定量化制图方法,评价景观服务未来发展变化,探索多项景观服务间的相互影响机理以及系统的景观服务规划方法,以期为今后景观服务的应用研究提供方向性参考意见。     

Physiological time and time-invariance

An operational definition of physiological time is suggested that involves a non-linear transformation of a physical time-scale such that a certain temperature-dependent process becomes time-invariant. The definition expresses that physiological time has the dimension of time, and can be measured in units such as days or weeks. It is shown that the quantification of a physiological time-scale requires the specification of an arbitrary constant, which equals the rate of change of the process in physiological time. When the process-rate also depends on some internal variable, the interaction of this variable with temperature must be multiplicative, if a single physiological time-scale is to be used. The relationship with conventional uses of physiological time is discussed. The time-scale, as defined here, reduces to degree-day summation or development accumulation if certain multiplicative constants are deleted.     

Can the evolution of plant defense lead to plant-herbivore mutualism?

Moderate rates of herbivory can enhance primary production. This hypothesis has led to a controversy as to whether such positive effects can result in mutualistic interactions between plants and herbivores. We present a model for the ecology and evolution of plant-herbivore systems to address this question. In this model, herbivores have a positive indirect effect on plants through recycling of a limiting nutrient. Plants can evolve but are constrained by a trade-off between growth and antiherbivore defense. Although evolution generally does not lead to optimal plant performance, our evolutionary analysis shows that, under certain conditions, the plant-herbivore interaction can be considered mutualistic. This requires in particular that herbivores efficiently recycle nutrients and that plant reproduction be positively correlated with primary production. We emphasize that two different definitions of mutualism need to be distinguished. A first ecological definition of mutualism is based on the short-term response of plants to herbivore removal, whereas a second evolutionary definition rests on the long-term response of plants to herbivore removal, allowing plants to adapt to the absence of herbivores. The conditions for an evolutionary mutualism are more stringent than those for an ecological mutualism. A particularly counterintuitive result is that higher herbivore recycling efficiency results both in increased plant benefits and in the evolution of increased plant defense. Thus, antagonistic evolution occurs within a mutualistic interaction.     

Pharmacophore model for antiepileptic drugs acting on sodium channels

Fifteen antiepileptic drugs (AED), active against the maximal electroshock seizure test and able to block the neuronal voltage-dependent sodium channel, have been studied by means of a similarity analysis. Structural and electronic, quantum chemically derived characteristics are compared. Rigid analogs are included, because of the flexibility of some structures, in order to discern the conformational requirements associated with these ligands in the moment of the interaction. An inactive compound (ethosuximide) helps in the definition of the structural factors that are important for the activity. We propose a pharmacophore model that, giving an interpretation of the biological activity, allows the design of new AED with a well-defined mechanism of interaction.     

Ser/Arg-rich protein-mediated communication between U1 and U2 small nuclear ribonucleoprotein particles

Previous work demonstrated that U1 small nuclear ribonucleoprotein particle (snRNP), bound to a downstream 5' splice site, can positively influence utilization of an upstream 3' splice site via exon definition in both trans- and cis-splicing systems. Although exon definition results in the enhancement of splicing of an upstream intron, the nature of the factors involved has remained elusive. We assayed the interaction of U1 snRNP as well as the positive effect of a downstream 5' splice site on trans-splicing in nematode extracts containing either inactive (early in development) or active (later in development) serine/arginine-rich splicing factors (SR proteins). We have determined that U1 snRNP interacts with the 5' splice site in the downstream exon even in the absence of active SR proteins. In addition, we determined that U1 snRNP-directed loading of U2 snRNP onto the branch site as well as efficient trans-splicing in these inactive extracts could be rescued upon the addition of active SR proteins. Identical results were obtained when we examined the interaction of U1 snRNP as well as the requirement for SR proteins in communication across a cis-spliced intron. Weakening of the 3' splice site uncovered distinct differences, however, in the ability of U1 snRNP to promote U2 addition, dependent upon its position relative to the branch site. These results demonstrate that SR proteins are required for communication between U1 and U2 snRNPs whether this interaction is across introns or exons.     

Hydrophobic interaction and structural changes in the solvent

The effect of structural changes in the solvent (usually water) on the thermodynamics of the hydrophobic interaction process is examined within the framework of classical statistical mechanics. The concept of the “structure of water” is first defined in a precise way, yet reflecting the conventional definition that has been, implicitly and qualitatively, employed by many authors. Using this concept, we proceed to show that structural changes in the solvent, induced by the hydrophobic interaction process, cannot affect the strength of the hydrophobic interaction. On the other hand, the entropy and enthalpy changes, associated with the same process, may well be affected. Some qualitative arguments are presented showing that large structural changes are expected from a complex solvent such as water.     

Modular organization of protein interaction networks

MOTIVATION: Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization of biological systems. RESULT: In this paper, we present a framework to identify modules within biological networks. In this approach, the concept of degree is extended from the single vertex to the sub-graph, and a formal definition of module in a network is used. A new agglomerative algorithm was developed to identify modules from the network by combining the new module definition with the relative edge order generated by the Girvan-Newman (G-N) algorithm. A JAVA program, MoNet, was developed to implement the algorithm. Applying MoNet to the yeast core protein interaction network from the database of interacting proteins (DIP) identified 86 simple modules with sizes larger than three proteins. The modules obtained are significantly enriched in proteins with related biological process Gene Ontology terms. A comparison between the MoNet modules and modules defined by Radicchi et al. (2004) indicates that MoNet modules show stronger co-clustering of related genes and are more robust to ties in betweenness values. Further, the MoNet output retains the adjacent relationships between modules and allows the construction of an interaction web of modules providing insight regarding the relationships between different functional modules. Thus, MoNet provides an objective approach to understand the organization and interactions of biological processes in cellular systems. AVAILABILITY: MoNet is available upon request from the authors.     

Automated identification of social interaction criteria in Drosophila melanogaster

The study of social behaviour within groups has relied on fixed definitions of an ‘interaction’. Criteria used in these definitions often involve a subjectively defined cut-off value for proximity, orientation and time (e.g. courtship, aggression and social interaction networks) and the same numerical values for these criteria are applied to all of the treatment groups within an experiment. One universal definition of an interaction could misidentify interactions within groups that differ in life histories, study treatments and/or genetic mutations. Here, we present an automated method for determining the values of interaction criteria using a pre-defined rule set rather than pre-defined values. We use this approach and show changing social behaviours in different manipulations of Drosophila melanogaster. We also show that chemosensory cues are an important modality of social spacing and interaction. This method will allow a more robust analysis of the properties of interacting groups, while helping us understand how specific groups regulate their social interaction space.     

Additivity in both thermodynamic stability and thermal transition temperature for rubredoxin chimeras via hybrid native partitioning

Given any operational definition of pairwise interaction, the set of residues that differ between two structurally homologous proteins can be uniquely partitioned into subsets of clusters for which no such interactions occur between clusters. Although hybrid protein sequences that preserve such clustering are consistent with tertiary structures composed of only parental native-like interactions, the stability of such predicted structures will depend upon the physical robustness of the assumed interaction potential. A simple distance cutoff criterion was applied to the most thermostable protein known to predict such a seven-residue cluster in the metal binding site region of Pyrococcus furiosus rubredoxin and a mesophile homolog. Both conformational stability and thermal transition temperature measurements demonstrate that 39% of the differential stability arises from these seven residues.     

Chromosomal replication and the cell membrane

The importance of the cell membrane in bacterial chromosomal replication continues to emerge. Recent advances include better definition of the biochemical interaction between membrane acidic phospholipids and the replication initiator, DnaA protein, the physiological impact that an altered membrane lipid composition has on chromosomal replication and the identification and characterization of recently identified membrane-associated proteins that regulate replication and participate in chromosomal segregation.     

Exploiting gene-environment interaction to detect genetic associations

Complex disease by definition results from the interplay of genetic and environmental factors. However, it is currently unclear how gene-environment interaction can best be used to locate complex disease susceptibility loci, particularly in the context of studies where between 1,000 and 1,000,000 markers are scanned for association with disease. We present a joint test of marginal association and gene-environment interaction for case-control data. We compare the power and sample size requirements of this joint test to other analyses: the marginal test of genetic association, the standard test for gene-environment interaction based on logistic regression, and the case-only test for interaction that exploits gene-environment independence. Although for many penetrance models the joint test of genetic marginal effect and interaction is not the most powerful, it is nearly optimal across all penetrance models we considered. In particular, it generally has better power than the marginal test when the genetic effect is restricted to exposed subjects and much better power than the tests of gene-environment interaction when the genetic effect is not restricted to a particular exposure level. This makes the joint test an attractive tool for large-scale association scans where the true gene-environment interaction model is unknown.     

International Workshop at the Nobel Forum,Karolinska Institutet on G protein-coupled receptors: finding the words to describe monomers,oligomers, and their molecular mechanisms and defining their meaning. Can a consensus be reached?

A meeting was held May 19, 2010 at the Karolinski Institute on Nomenclature in Pharmacology. This meeting occurred in conjunction with the Symposium The Changing World of G Protein Coupled Receptors: From Monomers to Dimers and Receptor Mosaics (Higher-order Oligomers) held the previous day at the Royal Swedish Academy of Science. Two broad topics of nomenclature were discussed; ligand nomenclature and the definition of ‘receptor–receptor’ interactions. This paper summarizes discussions on these topics along with a consensus definition of the term ‘receptor–receptor’ interaction.     

A graphical notation for biochemical networks

A solid definition and comprehensive graphical representation of biological networks is essential for efficient and accurate dissemination of information on biological models. Several proposals have already been made toward this aim. The most well known representation of this kind is a molecular interaction map, or ‘Kohn Map’. However, although the molecular interaction map is a well-defined and compact notation, there are several drawbacks, such as difficulties in intuitive understanding of temporal changes of reactions and additional complexities arising from particular graphical representations. This article proposes several improvements to the molecular interaction map, as well as the use of the ‘process diagram’ to help understand temporal sequences of reactions.     

Stability of ecosystems with complex food webs.

In a complex food web, various interaction pathways may connect pairs of species. A high carnivore might prey upon both a lesser carnivore and the prey of the lesser carnivore, forming a “loop” in the food web. This report contains one technical definition for stability of an ecosystem. Sufficient conditions for stability are presented. The conditions require that loops in food webs be in a sense “balanced.”