The enigma of frequency-dependent selection

Frequency-dependent selection is so fundamental to modern evolutionary thinking that everyone `knows' the concept. Yet the term is used to refer to different types of selection. The concept is well defined in the original context of population genetics theory, which focuses on short-term evolutionary change. The original concept becomes ambiguous, however, when used in the context of long-term evolution, where density dependence becomes essential. Weak and strong frequency dependence, as distinguished in this article, refer to two very different forms of selection.     

The shape of the spatial kernel and its implications for biological invasions in patchy environments

Ecological and epidemiological invasions occur in a spatial context. We investigated how these processes correlate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or epidemiological units. Distance dependence is described by a spatial kernel, characterized by its shape (kurtosis) and width (variance). We also developed a novel method to analyse and generate point-pattern landscapes based on spectral representation. This involves two measures: continuity, which is related to autocorrelation and contrast, which refers to variation in patch density. We also analysed some empirical data where our results are expected to have implications, namely distributions of trees (Quercus and Ulmus) and farms in Sweden. Through a simulation study, we found that kernel shape was not important for predicting the invasion speed in randomly distributed patches. However, the shape may be essential when the distribution of patches deviates from randomness, particularly when the contrast is high. We conclude that the speed of invasions depends on the spatial context and the effect of the spatial kernel is intertwined with the spatial structure. This implies substantial demands on the empirical data, because it requires knowledge of shape and width of the spatial kernel, and spatial structure.     

TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites

In mammalian genomes, cytosine methylation occurs predominantly at CG (or CpG) dinucleotide contexts. As part of dynamic epigenetic regulation, 5-methylcytosine (mC) can be erased by active DNA demethylation, whereby ten-eleven translocation (TET) enzymes catalyze the stepwise oxidation of mC to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), thymine DNA glycosylase (TDG) excises fC or caC, and base excision repair yields unmodified cytosine. In certain cell types, mC is also enriched at some non-CG (or CH) dinucleotides, however hmC is not. To provide biochemical context for the distribution of modified cytosines observed in biological systems, we systematically analyzed the activity of human TET2 and TDG for substrates in CG and CH contexts. We find that while TET2 oxidizes mC more efficiently in CG versus CH sites, this context preference can be diminished for hmC oxidation. Remarkably, TDG excision of fC and caC is only modestly dependent on CG context, contrasting its strong context dependence for thymine excision. We show that collaborative TET-TDG oxidation-excision activity is only marginally reduced for CA versus CG contexts. Our findings demonstrate that the TET-TDG-mediated demethylation pathway is not limited to CG sites and suggest a rationale for the depletion of hmCH in genomes rich in mCH.     

Scale-dependent linkages between nitrate isotopes and denitrification in surface soils: implications for isotope measurements and models

Oecologia - Natural abundance nitrate (NO3 −) isotopes represent a powerful tool for assessing denitrification, yet the scale and context dependence of relationships between isotopes and...     

Outer surface modification of synthetic multifunctional pores

The characteristics of pores formed by p-octiphenyl beta-barrels with LWV triads at the outer surface are reported in comparison with the conventional rigid-rod beta-barrels with all-L outer surface. Maintained multifunctionality of tetrameric pores with external LWV triads (inversion of ion selectivity, molecular recognition and transformation) is implicative for intact barrel interior. Increased pore activity supports dominance of high bilayer affinity for W over low affinity for V. Transmembrane p-octiphenyl orientation (from fluorescence depth quenching) supports barrel-stave (rather than toroidal) pores and dominance of transmembrane preference of rigid rods over interfacial preference of W. Destabilization of beta-barrel pores in membranes (from short single-channel lifetimes) and in the media (from 4th-power dependence on monomer concentration) by LWV triads supports dominance of low beta-propensity for W over high beta-propensity for V. The relation between the stability of supramolecular (pre)pores and dependence of activity on monomer concentration is discussed in a more general context.     

Genetik der Nikotinabhängigkeit

Nicotine dependence is a heritable disorder predictive of difficulty with smoking cessation and carries most of the morbidity associated with smoking. Several independent studies have shown an allelic association between nicotine dependence and DNA variants in the region of the α5-α3-β4 nicotinic receptor gene cluster on chromosome 15. Interestingly, the same region has been associated with lung cancer and chronic obstructive pulmonary disease. This highlights the importance of understanding the genetics of nicotine dependence in the context of smoking-related illness.     

Natural selection and context-dependent values

A simple model in which an animal makes a choice between two simultaneously available foraging options is used to show that we cannot expect natural selection to assign an absolute value (based on fitness) to each option. The example shows that the value of an option depends on its context; in particular, it depends on the option with which it is paired. This dependence results in a pattern of choice that violates a stochastic form of transitivity.     

Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis

Guanine:adenine (G:A) mismatches and in particular tandem G:A (tG:A) mismatches are frequently observed in biological RNA molecules and can serve as sites for tertiary interaction, metal binding and protein recognition. Depending on the surrounding sequence tG:A mismatches can adopt different basepairing topologies. In the sequence context (5'-) GGAC (tandem G:A in bold) a face-to-face (imino or Watson-Crick-like) pairing is preferred whereas in the CGAG context, G and A adopt a sheared arrangement. Systematic conformational searches with a generalized Born continuum model and molecular dynamics simulations including explicit water molecules and ions have been used to generate face-to-face and sheared tG:A mismatches in both CGAG and GGAC sequence contexts. Conformations from both approaches were evaluated using the same force field and a Poisson-Boltzmann continuum solvent model. Although the substate analysis predicted the sheared arrangement to be energetically preferred in both sequence contexts, a significantly greater preference of the sheared form was found for the CGAG context. In agreement with the experimental observation, the analysis of molecular dynamics trajectories indicated a preference of the sheared form in the case of the CGAG-context and a favorization of the face-to-face form in the case of the GGAC context. The computational studies allowed to identify energetic contributions that stabilize or destabilize the face-to-face and sheared tandem mismatch topologies. The calculated nonpolar solvation and Lennard-Jones packing interaction were found to stabilize the sheared topology independent of the sequence context. Electrostatic contributions are predicted to make the most significant contribution to the sequence context dependence on the structural preference of tG:A mismatches.     

Coevolutionary Patterns in Cytochrome c Oxidase Subunit I Depend on Structural and Functional Context

The strength and pattern of coevolution between amino acid residues vary depending on their structural and functional environment. This context dependence, along with differences in analytical technique, is responsible for the different results among coevolutionary analyses of different proteins. It is thus important to perform detailed study of individual proteins to gain better insight into how context dependence can affect coevolutionary patterns even within individual proteins, and to unravel the details of context dependence with respect to structure and function. Here we extend our previous study by presenting further analysis of residue coevolution in cytochrome c oxidase subunit I sequences from 231 vertebrates using a statistically robust phylogeny-based maximum likelihood ratio method. As in previous studies, a strong overall coevolutionary signal was detected, and coevolution within structural regions was significantly related to the C_α distances between residues. While the strong selection for adjacent residues among predicted coevolving pairs in the surface region indicates that the statistical method is highly selective for biologically relevant interactions, the coevolutionary signal was strongest in the transmembrane region, although the distances between coevolving residues were greater. This indicates that coevolution may act to maintain more global structural and functional constraints in the transmembrane region. In the transmembrane region, sites that coevolved according to polarity and hydrophobicity rather than volume had a greater tendency to colocalize with just one of the predicted proton channels (channel H). Thus, the details of coevolution in cytochrome c oxidase subunit I depend greatly on domain structure and residue physicochemical characteristics, but proximity to function appears to play a critical role. We hypothesize that coevolution is indicative of a more important functional role for this channel. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The Two Faces of Social Interaction Reward in Animal Models of Drug Dependence

Drug dependence is a serious health and social problem. Social factors can modify vulnerability to developing drug dependence, acting as risk factors or protective factors. Whereas stress and peer environment that encourage substance use may increase drug taking, strong attachments between family members and peer environment that do not experience drug use may protect against drug taking and, ultimately, drug dependence. The rewarding effects of drug abuse and social interaction can be evaluated using animal models. In this review we focus on evaluating social interaction reward in the conditioned place preference paradigm. We give an overview of how social interaction, if made available within the drug context, may facilitate, promote and interact with the drug’s effects. However, social interaction, if offered alternatively outside the drug context, may have pronounced protective effects against drug abuse and relapse. We also address the importance of the weight difference parameter between the social partners in determining the positive or “agonistic” versus the hostile or “antagonistic” social interaction. We conclude that understanding social interaction reward and its subsequent effects on drug reward is sorely needed for therapeutic interventions against drug dependence.     

Modelling the pH-dependent properties of Kv1 potassium channels

It is known that the pH dependence of conductance for the rat potassium channel Kv1.4 is susbstantially reduced upon mutation of either H508 or K532. These residues lie in the extracellular mouth of the channel pore. We have used continuum electrostatics to investigate their interactions with K(+) sites in the pore. The predicted scale of interactions between H508/K532 and potassium sites is sufficient to significantly alter potassium occupancy and thus channel function. We interpret the effect of K532 mutation as indicating that the pH-dependent effect requires not only an ionisable group with a suitable pK(a) value (i.e. histidine), but also that other charged groups set the potential profile at a threshold level. This hypothesis is examined in the context of pH dependence for other members of the Kv1 family, and may represent a general tool with which to study potassium channels.     

Temperature dependence of electron transfer between bacteriopheophytin and ubiquinone in protonated and deuterated reaction centers of Rhodopseudomonas sphaeroides.

The rate of the electron-transfer reaction between bacteriopheophytin and the first quinone in isolated reaction centers of Rhodopseudomonas sphaeroides has an unusual temperature dependence. The rate increases about threefold with decreasing temperature between 300 and 25 K, and decreases abruptly at temperatures below 25 K. Partial deuteration of the reaction centers alters the temperature dependence of the rate constant. Qualitative features of the temperature dependence can be understood in the context of a theory of nonadiabatic electron transfer (Sarai, 1980. Biochim. Biophys. Acta 589:71-83). We conclude that very low-energy (10-50 cm-1) processes, perhaps skeletal vibrations of the protein, are important to electron transfer. Higher-energy vibrations, possibly involving the pyrrolic N--H bonds of bacteriopheophytin, also are important in this process.     

Einfluss von Alkohol auf Homocystein-Metabolismus und Epigenetik

Alcohol dependence and alcohol-associated diseases play an important role in nowadays society. Providing adequate therapy and prevention demands a broad understanding of moleculare mechanisms of alcohol-associated diseases. In this context ?Epigenetic“ plays a significant role. Chronic alcohol-consumption in patients with alcohol dependence is associated with elevated homocysteine levels. The amino acid homocysteine acts as an agonist at the NMDA-receptor. Excitotoxcity, induced by hyperhomocysteineaemia, offers an explanation for alcohol-withdrawal seizures and alcoholism-associated brain atrophy. Furthermore elevated levels effect epigenetic regulation-mechanisms. Global DNA-methylation is affected as well as promoterspecific methylation-status. Recent studies of genes (i.e. HERP, Alpha-Synnuclein), involved in addictive disorders, showed a global DNA-hypermethylation and a hypermethylation of their promoters. These findings offer a first moleculargenetic explanation for homocysteine-induced dysfunctions in patients with alcohol dependence.     

A model of contextual effect on reproduced extents in recall tasks: the issue of the imputed motion hypothesis

In this article the fundamental question of space and time dependencies in the reproduction of spatial or temporal extents is studied. The functional dependence of spatial responses on the temporal context and the corresponding dependence of temporal responses on spatial context are reported as the tau and kappa effects, respectively. A common explanation suggested that the participant imputes motion to discontinuous displays. Using a mathematical model we explore the imputed velocity hypothesis and provide a globally fit model that addresses the question of sequences modelling. Our model accounts for observed data in the tau experiment. The accuracy of the model is improved introducing a new hypothesis based on small velocity variations. On the other hand, results show that the imputed velocity hypothesis fails to reproduce the kappa effect. This result definitively shows that both effects are not symmetric.     

Innate plasticity of a predatory behavior: nonlearned context dependence of avian flush-displays

If a foraging adaptation comprises a signal for sensory exploitationof prey, does the behavior and its use develop through learning,like many foraging behaviors or does it depend on nonlearnedstereotypical motor actions, like many signals for sensory exploitation?We asked whether the visually conspicuous motor pattern of bodypivoting with spread tail and wings used by the painted redstart(Myioborus pictus) to flush insect prey is a nonlearned phenotypictrait. The motion pattern and the increase in these displaysunder branches (context dependence based on physical propertiesof the habitat) help the wild birds in foraging because preythat rest on substrates is visually stimulated, flushed intothe air, and consequently chased in aerial pursuits. In unrewardedconditions in the aviary, both the foraging-experienced adultsand the foraging-naive hand-raised fledglings increased thefrequency of flush-displays at locations with substrates abovebirds, recreating the pattern of foraging observed in adultsin their natural habitats. The results imply that parent–offspringcultural transmission or learning during foraging is not requiredfor the development of both the display motion pattern and theadaptive context-dependent increase in display frequency. Sucha nonlearned context dependence based on physical propertiesof the habitat is remarkable considering that avian foragingcontext-dependent plasticity is often based on learning. Wehypothesize that this innate character of the signals may bea result of evolution to exploit universal properties of visuallytriggered escape behaviors of various insects that are predictablyflushed from their resting sites in the habitat.     

All thumbs?

In this otherwise insightful line of investigation, some aspects of rules of thumb (RoT) remain underspecified: their evolution and function, how they are selected for a task, how they are learned, and the dependence of their apparent simplicity on their embodiment and context. Theories of operant and respondent conditioning may serve as the theoretical framework required to flesh out those details.     

Environmentally coupled hydrogen tunneling. Linking catalysis to dynamics.

Many biological C-H activation reactions exhibit nonclassical kinetic isotope effects (KIEs). These nonclassical KIEs are too large (kH/kD > 7) and/or exhibit unusual temperature dependence such that the Arrhenius prefactor KIEs (AH/AD) fall outside of the semiclassical range near unity. The focus of this minireview is to discuss such KIEs within the context of the environmentally coupled hydrogen tunneling model. Full tunneling models of hydrogen transfer assume that protein or solvent fluctuations generate a reactive configuration along the classical, heavy-atom coordinate, from which the hydrogen transfers via nuclear tunneling. Environmentally coupled tunneling also invokes an environmental vibration (gating) that modulates the tunneling barrier, leading to a temperature-dependent KIE. These properties directly link enzyme fluctuations to the reaction coordinate for hydrogen transfer, making a quantum view of hydrogen transfer necessarily a dynamic view of catalysis. The environmentally coupled hydrogen tunneling model leads to a range of magnitudes of KIEs, which reflect the tunneling barrier, and a range of AH/AD values, which reflect the extent to which gating modulates hydrogen transfer. Gating is the primary determinant of the temperature dependence of the KIE within this model, providing insight into the importance of this motion in modulating the reaction coordinate. The potential use of variable temperature KIEs as a direct probe of coupling between environmental dynamics and the reaction coordinate is described. The evolution from application of a tunneling correction to a full tunneling model in enzymatic H transfer reactions is discussed in the context of a thermophilic alcohol dehydrogenase and soybean lipoxygenase-1.     

Abstraction and context in concept representation

This paper develops the notion of abstraction in the context of the psychology of concepts, and discusses its relation to context dependence in knowledge representation. Three general approaches to modelling conceptual knowledge from the domain of cognitive psychology are discussed, which serve to illustrate a theoretical dimension of increasing levels of abstraction.     

Variation in the strength of inbreeding depression across environments: Effects of stress and density dependence

In what types of environments should we expect to find strong inbreeding depression? Previous studies indicate that inbreeding depression, δ, is positively correlated with the stressfulness of the environment in which it is measured. However, it remains unclear why stress, per se, should increase δ. To our knowledge, only “competitive stress” has a logical connection to δ. Through competition for resources, better quality (outbred) individuals make the environment worse for lower quality (inbred) individuals, accentuating the differences between them. For this reason, we expect inbreeding depression to be stronger in environments where the fitness of individuals is more sensitive to the presence of conspecifics (i.e., where fitness is more density dependent). Indeed, some studies suggest a role for competition within environments, but this idea has not been tested in the context of understanding variation in δ across environments. Using Drosophila melanogaster, we estimated δ for viability in 22 different environments. These environments were simultaneously characterized for (1) stressfulness and (2) density dependence. Although stress and density dependence are moderately correlated with each other, inbreeding depression is much more strongly correlated with density dependence. These results suggest that mean selection across the genome is stronger in environments where competition is intense, rather than in environments that are stressful for other reasons.     

Netrin-1 in the developing enteric nervous system and colorectal cancer

Netrin-1 is a well-characterised chemoattractant involved in neuronal guidance in the developing enteric nervous system (ENS), but it is also a regulator of tumorigenesis. Two of its well-characterised receptors, deleted in colorectal cancer (DCC) and uncoordinated-5 homolog (UNC-5H), belong to a family of dependence receptors that transmit either pro- or anti-apoptosis signals depending on the availability of ligand, in this case netrin-1. This review summarises these two effects of netrin-1 and highlights the additional research needed information about to allow better utilisation of netrin-1 as a therapeutic target for axonal regeneration in the context of colorectal cancer.