Hyperforin: more than an antidepressant bioactive compound?

Hyperforin is a lipophilic compound that is present in great amounts in St. John's wort and that has been described as the main responsible for the antidepressant effects of this medicinal plant. In the last few years, evidence has accumulated pointing to other different effects of hyperforin with potential pharmacological interest. They include other neurological effects, effects on inflammation, as well as antibacterial, antitumoral and antiangiogenic effects.     

Functional mixed effects models

In this article, a new class of functional models in which smoothing splines are used to model fixed effects as well as random effects is introduced. The linear mixed effects models are extended to nonparametric mixed effects models by introducing functional random effects, which are modeled as realizations of zero-mean stochastic processes. The fixed functional effects and the random functional effects are modeled in the same functional space, which guarantee the population-average and subject-specific curves have the same smoothness property. These models inherit the flexibility of the linear mixed effects models in handling complex designs and correlation structures, can include continuous covariates as well as dummy factors in both the fixed or random design matrices, and include the nested curves models as special cases. Two estimation procedures are proposed. The first estimation procedure exploits the connection between linear mixed effects models and smoothing splines and can be fitted using existing software. The second procedure is a sequential estimation procedure using Kalman filtering. This algorithm avoids inversion of large dimensional matrices and therefore can be applied to large data sets. A generalized maximum likelihood (GML) ratio test is proposed for inference and model selection. An application to comparison of cortisol profiles is used as an illustration.     

边缘效应与生物多样性

自从边缘效应提出以来,许多生态学家对它与生物多样性之间的关系进行了研究。大量的事实显示出边缘效应会表现出正效应或负效应,其结果并不完全一致。边缘效应的利用、管理和生物多样性保护是一项有意义而紧迫的工作。     

Dangerously few liaisons: a review of mate-finding Allee effects

In this paper, we review mate-finding Allee effects from ecological and evolutionary points of view. We define ‘mate-finding’ as mate searching in mobile animals, and also as the meeting of gametes for sessile animals and plants (pollination). We consider related issues such as mate quality and choice, sperm limitation and physiological stimulation of reproduction by conspecifics, as well as discussing the role of demographic stochasticity in generating mate-finding Allee effects. We consider the role of component Allee effects due to mate-finding in generating demographic Allee effects (at the population level). Compelling evidence for demographic Allee effects due to mate-finding (as well as via other mechanisms) is still limited, due to difficulties in censusing rare populations or a failure to identify underlying mechanisms, but also because of fitness trade-offs, population spatial structure and metapopulation dynamics, and because the strength of component Allee effects may vary in time and space. Mate-finding Allee effects act on individual fitness and are thus susceptible to change via natural selection. We believe it is useful to distinguish two routes by which evolution can act to mitigate mate-finding Allee effects. The first is evolution of characteristics such as calls, pheromones, hermaphroditism, etc. which make mate-finding more efficient at low density, thus eliminating the Allee effect. Such adaptations are very abundant in the natural world, and may have arisen to avoid Allee effects, although other hypotheses are also possible. The second route is to avoid low density via adaptations such as permanent or periodic aggregation. In this case, the Allee effect is still present, but its effects are avoided. These two strategies may have different consequences in a world where many populations are being artificially reduced to low density: in the first case, population growth rate can be maintained, while in the second case, the mechanism to avoid Allee effects has been destroyed. It is therefore in these latter populations that we predict the greatest evidence for mate-finding Allee effects and associated demographic consequences. This idea is supported by the existing empirical evidence for demographic Allee effects. Given a strong effect that mate-finding appears to have on individual fitness, we support the continuing quest to find connections between component mate-finding Allee effects (individual reproductive fitness) and the demographic consequences. There are many reasons why such studies are difficult, but it is important, particularly given the increasing number of populations and species of conservation concern, that the ecological community understands more about how widespread demographic Allee effects really are, and why.     

Physiology and toxicology of hormone-disrupting chemicals in higher plants

Higher plants are exposed to natural environmental organic chemicals, associated with plant–environment interactions, and xenobiotic environmental organic chemicals, associated with anthropogenic activities. The effects of these chemicals result not only from interaction with metabolic targets, but also from interaction with the complex regulatory networks of hormone signaling. Purpose-designed plant hormone analogues thus show extensive signaling effects on gene regulation and are as such important for understanding plant hormone mechanisms and for manipulating plant growth and development. Some natural environmental chemicals also act on plants through interference with the perception and transduction of endogenous hormone signals. In a number of cases, bioactive xenobiotics, including herbicides that have been designed to affect specific metabolic targets, show extensive gene regulation effects, which are more in accordance with signaling effects than with consequences of metabolic effects. Some of these effects could be due to structural analogies with plant hormones or to interference with hormone metabolism, thus resulting in situations of hormone disruption similar to animal cell endocrine disruption by xenobiotics. These hormone-disrupting effects can be superimposed on parallel metabolic effects, thus indicating that toxicological characterisation of xenobiotics must take into consideration the whole range of signaling and metabolic effects. Hormone-disruptive signaling effects probably predominate when xenobiotic concentrations are low, as occurs in situations of residual low-level pollutions. These hormone-disruptive effects in plants may thus be of importance for understanding cryptic effects of low-dosage xenobiotics, as well as the interactive effects of mixtures of xenobiotic pollutants.     

Effects of Multi-Generational Stress Exposure and Offspring Environment on the Expression and Persistence of Transgenerational Effects in Arabidopsis thaliana

Plant phenotypes can be affected by environments experienced by their parents. Parental environmental effects are reported for the first offspring generation and some studies showed persisting environmental effects in second and further offspring generations. However, the expression of these transgenerational effects proved context-dependent and their reproducibility can be low. Here we study the context-dependency of transgenerational effects by evaluating parental and transgenerational effects under a range of parental induction and offspring evaluation conditions. We systematically evaluated two factors that can influence the expression of transgenerational effects: single- versus multiple-generation exposure and offspring environment. For this purpose, we exposed a single homozygous Arabidopsis thaliana Col-0 line to salt stress for up to three generations and evaluated offspring performance under control and salt conditions in a climate chamber and in a natural environment. Parental as well as transgenerational effects were observed in almost all traits and all environments and traced back as far as great-grandparental environments. The length of exposure exerted strong effects; multiple-generation exposure often reduced the expression of the parental effect compared to single-generation exposure. Furthermore, the expression of transgenerational effects strongly depended on offspring environment for rosette diameter and flowering time, with opposite effects observed in field and greenhouse evaluation environments. Our results provide important new insights into the occurrence of transgenerational effects and contribute to a better understanding of the context-dependency of these effects.     

Generalized semiparametrically structured ordinal models

Semiparametrically structured models are defined as a class of models for which the predictors may contain parametric parts, additive parts of covariates with an unspecified functional form, and interactions which are described as varying coefficients. In the case of an ordinal response the complexity of the predictor is determined by different sorts of effects. Global effects and category-specific effects are distinguished; the latter allow the effect to vary across response categories. A general framework is developed in which global as well as category-specific effects may have unspecified functional form. The framework extends various existing methods of modeling ordinal responses. The Wilkinson-Rogers notation is extended to incorporate smooth model parts and varying coefficient terms, the latter being important for the smooth specification of category-specific effects.     

Indirect genetic effects from ecological interactions in Arabidopsis thaliana

Indirect genetic effects arise when genes expressed in one individual affect the expression of traits in other individuals. The importance of indirect genetic effects has been recognized for a diversity of evolutionary processes including kin selection, sexual selection, community structure and multilevel selection, but data regarding their genetic architecture and prevalence throughout the genome remain scarce, especially for interactions between unrelated individuals. Using a set of 411 Bay-0 x Shahdara Arabidopsis recombinant inbred lines grown with Landsberg neighbours, we examined quantitative trait loci (QTL) having direct and indirect effects on size, developmental, and fitness related traits. Using an interval mapping approach, we identified 15 QTL with direct effects and found that 13 of these QTL had significant indirect effects on trait expression in neighbouring plants. These results suggest widespread pleiotropy, as nearly all direct effect QTL have associated pleiotropic indirect effects. Paradoxically, most indirect effects were of the same sign as direct effects, creating a pattern of nearly universal positive pleiotropy that makes most covariances between direct and indirect effects positive. These results are consistent with a complex genetic basis for intraspecific interactions, but suggest that interactions between neighbouring plants are largely positive, rather than negative as would be expected for competition. In addition to their evolutionary and ecological importance, these pleiotropic relationships between DGE and IGE loci have implications for quantitative genetic studies of natural populations as well as experimental design considerations. Additionally, studies that ignore IGEs may over- or underestimate quantitative genetic parameters, as well as the effect of and variance contributed by QTL.     

In vitro and in vivo genotoxicity of radiofrequency fields

There has been growing concern about the possibility of adverse health effects resulting from exposure to radiofrequency radiations (RFR), such as those emitted by wireless communication devices. Since the introduction of mobile phones many studies have been conducted regarding alleged health effects but there is still some uncertainty and no definitive conclusions have been reached so far. Although thermal effects are well understood they are not of great concern as they are unlikely to result from the typical low-level RFR exposures. Concern rests essentially with the possibility that RFR-exposure may induce non-thermal and/or long-term health effects such as an increased cancer risk. Consequently, possible genetic effects have often been studied but with mixed results. In this paper we review the data on alleged RFR-induced genetic effects from in vitro and in vivo investigations as well as from human cytogenetic biomonitoring surveys. Attention is also paid to combined exposures of RFR with chemical or physical agents. Again, however, no entirely consistent picture emerges. Many of the positive studies may well be due to thermal exposures, but a few studies suggest that biological effects can be seen at low levels of exposure. Overall, however, the evidence for low-level genotoxic effects is very weak.     

The effects of fire on wetland structure and functioning

Fire is an extensively used wetland management tool in both tropical and temperate areas, but its effects on wetlands are not well understood. The purpose of this paper is to review the effects of fire on wetland hydrology, biogeochemical cycling and vegetation composition, including primary effects that take place during the fire such as combustion of plant material, loss of volatile substances to the atmosphere and deposition of ash on the soil surface, and secondary effects such as alteration of soil pH as a result of ash deposition, exposure of the soil surface to solar radiation, and increased availability of nutrients. Several of the secondary effects are most dramatic immediately after a fire, but become progressively modulated by newly stimulated vegetation growth. The findings suggest that the effects of fire depend upon a wetland's characteristics, including its climatic and hydrological context, as well as upon interactions with other disturbances such as grazing. Thus, similar fire regimes may have dramatically different outcomes. Where knowledge gaps were identified, some general predictions are offered, drawing from comparable ecosystems such as mesic grasslands. These predictions provide potential hypotheses for further research.     

A mixed-model approach to mapping quantitative trait loci in barley on the basis of multiple environment data

In this article, I propose a mixed-model method to detect QTL with significant mean effect across environments and to characterize the stability of effects across multiple environments. I demonstrate the method using the barley dataset by the North American Barley Genome Mapping Project. The analysis raises the need for mixed modeling in two different ways. First, it is reasonable to regard environments as a random sample from a population of target environments. Thus, environmental main effects and QTL-by-environment interaction effects are regarded as random. Second, I expect a genetic correlation among pairs of environments caused by undetected QTL. I show how random QTL-by-environment effects as well as genetic correlations are straightforwardly handled in a mixed-model framework. The main advantage of this method is the ability to assess the stability of QTL effects. Moreover, the method allows valid statistical inferences regarding average QTL effects.     

A mother’s legacy: the strength of maternal effects in animal populations

Although mothers influence the traits of their offspring in many ways beyond the transmission of genes, it remains unclear how important such ‘maternal effects’ are to phenotypic differences among individuals. Synthesizing estimates derived from detailed pedigrees, we evaluated the amount of phenotypic variation determined by maternal effects in animal populations. Maternal effects account for half as much phenotypic variation within populations as do additive genetic effects. Maternal effects most greatly affect morphology and phenology but, surprisingly, are not stronger in species with prolonged maternal care than in species without. While maternal effects influence juvenile traits more than adult traits on average, they do not decline across ontogeny for behaviour or physiology, and they do not weaken across the life cycle in species without maternal care. These findings underscore maternal effects as an important source of phenotypic variation and emphasise their potential to affect many ecological and evolutionary processes.     

Use of isotope effects to elucidate enzyme mechanisms

The chemical bond breaking steps are normally not rate limiting for enzymatic reactions. However, comparison of deuterium and tritium isotope effects on the same reaction, especially when coupled with 13C isotope effects for the same step measured with deuterated as well as unlabeled substrates, allows calculation of the intrinsic isotope effects on the bond breaking steps and thus a determination of the commitments to catalysis for the reactants. The variation in observed isotope effects as a function of reactant concentration can be used to determine kinetic mechanisms, while the pH variation of isotope effects can determine the stickiness of the reactants and which portions of the reactant mechanism are pH dependent. Finally the size of primary and secondary intrinsic isotope effects can be used to determine transition state structure.     

Maternal effects as the cause of parent-of-origin effects that mimic genomic imprinting

Epigenetic effects are increasingly recognized as an important source of variation in complex traits and have emerged as the focus of a rapidly expanding area of research. Principle among these effects is genomic imprinting, which has generally been examined in analyses of complex traits by testing for parent-of-origin-dependent effects of alleles. However, in most of these analyses maternal effects are confounded with genomic imprinting because they can produce the same patterns of phenotypic variation expected for various forms of imprinting. Distinguishing between the two is critical for genetic and evolutionary studies because they have entirely different patterns of gene expression and evolutionary dynamics. Using a simple single-locus model, we show that maternal genetic effects can result in patterns that mimic those expected under genomic imprinting. We further demonstrate how maternal effects and imprinting effects can be distinguished using genomic data from parents and offspring. The model results are applied to a genome scan for quantitative trait loci (QTL) affecting growth- and weight-related traits in mice to illustrate how maternal effects can mimic imprinting. This genome scan revealed five separate maternal-effect loci that caused a diversity of patterns mimicking those expected under various modes of genomic imprinting. These results demonstrate that the appearance of parent-of-origin-dependent effects (POEs) of alleles at a locus cannot be taken as direct evidence that the locus is imprinted. Moreover, they show that, in gene mapping studies, genetic data from both parents and offspring are required to successfully differentiate between imprinting and maternal effects as the cause of apparent parent-of-origin effects of alleles.     

污染物在根-土界面的化学行为与生态效应

根-土界面是污染物进入植物体内的主要通道和导致一系列生态安全问题的特殊微生态区,本文提出污染物在根-土界面上的化学行为和生态效应包括根际化学行为与生态效应,根系化学行为与生态效应两个方面的具体内容,并从理论上根据最新的研究进展对这两方面内容进行了探讨,指出根际化学行为与生态效应包括根际pH环境与吸附行为、根际氧化-还原行为、根际化学致毒效应、根际微生物效应及根际生物酶反应等;根系化学行为与生态效应包括根系分泌物、根系酶系统的影响、干扰正常生理过程、改变细胞结构与功能、干扰生物大分子的结构和功能等,并阐述根-土界面上的化学行为和生态效应在污染生态学中的重要性以及研究中存在的问题。     

Bigger mothers are better mothers: disentangling size-related prenatal and postnatal maternal effects

Despite a vast literature on the factors controlling adult size, few studies have investigated how maternal size affects offspring size independent of direct genetic effects, thereby separating prenatal from postnatal influences. I used a novel experimental design that combined a cross-fostering approach with phenotypic manipulation of maternal body size that allowed me to disentangle prenatal and postnatal maternal effects. Using the burying beetle Nicrophorus vespilloides as model organism, I found that a mother''s body size affected egg size as well as the quality of postnatal maternal care, with larger mothers producing larger eggs and raising larger offspring than smaller females. However, with respect to the relative importance of prenatal and postnatal maternal effects on offspring growth, only the postnatal effects were important in determining offspring body size. Thus, prenatal effects can be offset by the quality of postnatal maternal care. This finding has implications for the coevolution of prenatal and postnatal maternal effects as they arise as a consequence of maternal body size. In general, my study provides evidence that there can be transgenerational phenotypic plasticity, with maternal size determining offspring size leading to a resemblance between mothers and their offspring above and beyond any direct genetic effects.     

An analysis of pre- and post-hatching maternal effects mediated by carotenoids in the blue tit

Maternal effects increase phenotypic plasticity in offspring traits and may therefore facilitate adaptation to environmental variability. Carotenoids have been hypothesized to mediate costs of reproduction in females as well as maternal effects. However, assessing potential transgenerational and population consequences of environmental availability of carotenoids requires a better understanding of mechanisms of maternal effects mediated by these antioxidant pigments. Manipulating dietary availability of carotenoids to egg-laying female blue tits and subsequently cross-fostering nestlings between female treatments allowed us to specifically investigate the relative importance of maternal effects through egg carotenoids and through post-hatching care mediated by antioxidants in females. Nestling body size and mass and plasma antioxidants were not significantly affected by pre- or post-hatching maternal effects mediated by antioxidants, although both types of maternal effects in interaction explained the variation in growth, as measured by wing length. Development of the ability to mount a cell-mediated immune response as well as its temporal dynamics was influenced by both pre- and post-hatching maternal effects, with an advantage to nestlings originating from, or reared by, carotenoid-supplemented females. In addition, nestlings reared by carotenoid-fed females had a lower blood sedimentation rate, indicating that they may have been less infected than nestlings from controls. Finally, prehatching maternal effects in interaction with nestling plasma carotenoid levels affected the development of carotenoid-based plumage. Maternal effects mediated by carotenoids may thus act as a proximate factor in development and phenotypic plasticity in traits associated with nestling fitness, such as immune response and ability to metabolize and use antioxidants, and ultimately participate in the evolution of phenotypic traits.     

Legacy of past exposure to hypoxia and warming regulates an ecosystem service provided by oysters

Climate change is having substantial impacts on organism fitness and ability to deliver critical ecosystem services, but these effects are often examined only in response to current environments. Past exposure to stress can also affect individuals via carryover effects, and whether these effects scale from individuals to influence ecosystem function and services is unknown. We explored within-generation carryover effects of two coastal climate change stressors—hypoxia and warming—on oyster (Crassostrea virginica) growth and nitrogen bioassimilation, an important ecosystem service. Oysters were exposed to a factorial combination of two temperature and two diel-cycling dissolved oxygen treatments at 3-months-old and again 1 year later. Carryover effects of hypoxia and warming influenced oyster growth and nitrogen storage in complex and context-dependent ways. When operating, carryover effects of single stressors generally reduced oyster nitrogen bioassimilation and relative investment in tissue versus shell growth, particularly in warm environments, while early life exposure to multiple stressors generally allowed oysters to perform as well as control oysters. When extrapolated to the reef scale, carryover effects decreased nitrogen stored by modeled oyster reefs in most conditions, with reductions as large as 41%, a substantial decline in a critical ecosystem service. In some scenarios, however, carryover effects increased nitrogen storage by modeled oyster reefs, again highlighting the complexity of these effects. Hence, even brief exposure to climate change stressors early in life may have persistent effects on an ecosystem service 1 year later. Our results show for the first time that within-generation carryover effects on individual phenotypes can impact processes at the ecosystem scale and may therefore be an overlooked factor determining ecosystem service delivery in response to anthropogenic change.     

All Effects of Psychophysical Variables on Color Attributes: A Classification System

This paper reports the research and structuring of a classification system for the effects of psychophysical variables on the color attributes. A basic role of color science is to psychophysically specify color appearance. An early stage is to specify the effects of the psychophysical variables (as singles, pairs, etc) on the color attributes (as singles, pairs, etc), for example to model color appearance. Current data on effects are often scarce or conflicting. Few effects are well understood, and the practice of naming effects after their discoverer(s) is inadequate and can be confusing. The number and types of possible effects have never been systematically analyzed and categorized. We propose a simple and rigorous system of classification including nomenclature. The total range of effects is computed from the possible combinations of three psychophysical variables (luminance, dominant wavelength, purity) and six color attributes (lightness, brightness, hue, chroma, colorfulness, saturation) in all modes of appearance. Omitting those effects that are normally impossible to perceive at any one time (such as four- or five-dimensional colors), the total number perceivable is 161 types of effects for all modes of appearance. The type of effect is named after the psychophysical stimulus (or stimuli) and the relevant color attribute(s), e.g., Luminance-on-hue effect (traditionally known as Bezold-Brucke effect). Each type of effect may include slightly different effects with infinite variations depending on experimental parameters.