Variation in reaction norms: Statistical considerations and biological interpretation

Analysis of reaction norms, the functions by which the phenotype produced by a given genotype depends on the environment, is critical to studying many aspects of phenotypic evolution. Different techniques are available for quantifying different aspects of reaction norm variation. We examine what biological inferences can be drawn from some of the more readily applicable analyses for studying reaction norms. We adopt a strongly biologically motivated view, but draw on statistical theory to highlight strengths and drawbacks of different techniques. In particular, consideration of some formal statistical theory leads to revision of some recently, and forcefully, advocated opinions on reaction norm analysis. We clarify what simple analysis of the slope between mean phenotype in two environments can tell us about reaction norms, explore the conditions under which polynomial regression can provide robust inferences about reaction norm shape, and explore how different existing approaches may be used to draw inferences about variation in reaction norm shape. We show how mixed model‐based approaches can provide more robust inferences than more commonly used multistep statistical approaches, and derive new metrics of the relative importance of variation in reaction norm intercepts, slopes, and curvatures.     

Introducing biological realism into the study of developmental plasticity in behaviour

There is increasing attention for integrating mechanistic and functional approaches to the study of (behavioural) development. As environments are mostly unstable, it is now often assumed that genetic parental information is in many cases not sufficient for offspring to become optimally adapted to the environment and that early environmental cues, either indirectly via the parents or from direct experience, are necessary to prepare them for a specific environment later in life. To study whether these early developmental processes are adaptive and through which mechanism, not only the early environmental cues but also how they impinge on the later-life environmental context has therefore to be taken into account when measuring the animal's performance. We first discuss at the conceptual level six ways in which interactions between influences of different time windows during development may act (consolidation, cumulative information gathering and priming, compensation, buffering, matching and mismatching, context dependent trait expression). In addition we discuss how different environmental factors during the same time window may interact in shaping the phenotype during development. Next we discuss the pros and cons of several experimental designs for testing these interaction effects, highlighting the necessity for full, reciprocal designs and the importance of adjusting the nature and time of manipulation to the animal's adaptive capacity. We then review support for the interaction effects from both theoretical models and animal experiments in different taxa. This demonstrates indeed the existence of interactions at multiple levels, including different environmental factors, different time windows and between generations. As a consequence, development is a life-long, environment-dependent process and therefore manipulating only the early environment without taking interaction effects with other and later environmental influences into account may lead to wrong conclusions and may also explain inconsistent results in the literature.     

Mechanistic models for radiation carcinogenesis and the atomic bomb survivor data

Recently, Heidenreich et al. (Radiat. Res., 158, 607-617, 2002) suggested that the Radiation Effects Research Foundation (RERF) A-bomb survivor cohort study is not large enough to discriminate between various possible carcinogenic mechanisms. At least with the current follow-up, this is true to some extent, but I think the specific issues are rather different than they suggest. In particular, I do not think it is true-as they further indicate-that various models fit the data about equally well while estimating very different patterns of excess risk, which would imply that these patterns cannot be reasonably well characterized. I will point to specific criticisms of their approach to the data and offer some more general comments on mechanistic modeling approaches. Although there are important distinctions, I suggest on a very optimistic note that the two major approaches may be converging, and soon the main differences may not be in the assumptions made but in the aims of the modeling.     

Timing Mechanisms in Early Embryonic Development

Embryological development takes place in four dimensions and requires the existence of time measuring processes within the embryo. Evidence is accumulating that suggests that the emergence of many events during early embryonic development is controlled by timing mechanisms or developmental clocks. The purpose of this work is to review recent studies on developmental timing with speculations about underlying possible mechanisms. It is an attractive idea that the development of an embryo is timed by a single clock set in motion at fertilization, but this seems infeasible. The clock mechanism which determines the time of initiation of cellular differentiation may be independent of that for the timing of morphogenesis. The clock mechanism for cellular differentiation may be closely associated with the cycles of DNA replication, while the clock which counts the time to onset of early morphogenetic events is found in the cytoplasm. These ideas can provide a framework which may help to organize existing observations and to stimulate new experimental approaches to the problem.     

Early warning signals for critical transitions: a generalized modeling approach

Critical transitions are sudden, often irreversible, changes that can occur in a large variety of complex systems; signals that warn of critical transitions are therefore highly desirable. We propose a new method for early warning signals that integrates multiple sources of information and data about the system through the framework of a generalized model. We demonstrate our proposed approach through several examples, including a previously published fisheries model. We regard our method as complementary to existing early warning signals, taking an approach of intermediate complexity between model-free approaches and fully parameterized simulations. One potential advantage of our approach is that, under appropriate conditions, it may reduce the amount of time series data required for a robust early warning signal.     

Estimates of the number of clonogenic cells in crypts of murine small intestine

There is a proliferative cell hierarchy in the mouse intestinal crypt with ancestral stem cells which can regenerate all components of the lineage after injury (clonogenic cells). The number of these clonogenic or regenerative cells per crypt can be estimated from radiobiological experiments where doses of radiation are used to kill cells and ablate crypts. Various approaches can be adopted which provide different estimates of this number of cells. One of the conventional approaches used in the past provided estimates of about 70-80 clonogenic cells per crypt (i.e. about 50% of the proliferative or 30% of all crypt cells). A technically simpler approach has recently been suggested. This has been used here to provide many independent estimates of the number of crypt clonogenic cells. These suggest about 32 clonogenic cells exist per crypt i.e. about half the previous estimate and about twice the number of putative "functional" stem cells (those which operate as stem cells in the normal steady-state crypt). The reasons for the differences are discussed. The new estimates are compatible with the hypothesis that the crypt contains a ring of about 16 functional stem cells which are expected to be clonogenic, besides which there is a second ring of 16 clonogenic cells which represent early transit cells (the immediate daughters of the stem cells) which can act as clonogenic cells if required after radiation injury.     

Integrating the statistical analysis of spatial data in ecology

In many areas of ecology there is an increasing emphasis on spatial relationships. Often ecologists are interested in new ways of analyzing data with the objective of quantifying spatial patterns, and in designing surveys and experiments in light of the recognition that there may be underlying spatial pattern in biotic responses. In doing so, ecologists have adopted a number of widely different techniques and approaches derived from different schools of thought, and from other scientific disciplines. While the adaptation of a diverse array of statistical approaches and methodologies for the analysis of spatial data has yielded considerable insight into various ecological problems, this diversity of approaches has sometimes impeded communication and retarded more rapid progress in this emergent area. Many of these different statistical methods provide similar information about spatial characteristics, but the differences among these methods make it difficult to compare the results of studies that employ contrasting approaches. The papers in this mini-series explore possible areas of agreement and synthesis between a diversity of approaches to spatial analysis in ecology.     

A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard

Modeling diagnostic error without a gold standard has been an active area of biostatistical research. In a majority of the approaches, model-based estimates of sensitivity, specificity, and prevalence are derived from a latent class model in which the latent variable represents an individual's true unobserved disease status. For simplicity, initial approaches assumed that the diagnostic test results on the same subject were independent given the true disease status (i.e., the conditional independence assumption). More recently, various authors have proposed approaches for modeling the dependence structure between test results given true disease status. This note discusses a potential problem with these approaches. Namely, we show that when the conditional dependence between tests is misspecified, estimators of sensitivity, specificity, and prevalence can be biased. Importantly, we demonstrate that with small numbers of tests, likelihood comparisons and other model diagnostics may not be able to distinguish between models with different dependence structures. We present asymptotic results that show the generality of the problem. Further, data analysis and simulations demonstrate the practical implications of model misspecification. Finally, we present some guidelines about the use of these models for practitioners.     

The two faces of protein misfolding: gain- and loss-of-function in neurodegenerative diseases

The etiologies of neurodegenerative diseases may be diverse; however, a common pathological denominator is the formation of aberrant protein conformers and the occurrence of pathognomonic proteinaceous deposits. Different approaches coming from neuropathology, genetics, animal modeling and biophysics have established a crucial role of protein misfolding in the pathogenic process. However, there is an ongoing debate about the nature of the harmful proteinaceous species and how toxic conformers selectively damage neuronal populations. Increasing evidence indicates that soluble oligomers are associated with early pathological alterations, and strikingly, oligomeric assemblies of different disease-associated proteins may share common structural features. A major step towards the understanding of mechanisms implicated in neuronal degeneration is the identification of genes, which are responsible for familial variants of neurodegenerative diseases. Studies based on these disease-associated genes illuminated the two faces of protein misfolding in neurodegeneration: a gain of toxic function and a loss of physiological function, which can even occur in combination. Here, we summarize how these two faces of protein misfolding contribute to the pathomechanisms of Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease and prion diseases.     

Anxiété et personnalité: études catégorielle et dimensionnelle de leur association et facteurs de vulnérabilité

Anxiety disorders often appear in patients with particular personality traits, and in some cases with actual personality disorders. This clinical observation may question the respective interactions between personality and anxiety disorders: Is it possible to evaluate the personality of patients with severe anxiety disorders reliably? What is the real co-morbidity between personality disorders and anxiety disorders? Are there psychopathological and etiological links between these two disorders? Studies relying on categorical approaches of personality suggest that about 40-60% of anxious patients fulfill the diagnostic criteria of at least one personality disorder. The most frequent diagnoses belong to the cluster C of the DSM-IV axis II classification, with a majority having avoidant and dependent personalities, but without any real specificity according to the types of anxiety disorders. On the other hand, dimensional studies have shown that anxiety disorders are often associated with avoidant personality traits, with very deviant scores in some cases, even after treatment of the anxiety disorder. These works support the existence of some temperament traits, underlined by psychobiological, stable, and inheritable dimensions, which may constitute early vulnerability factors for anxiety disorders in both children and adults.     

Stabilizing cumulative incidence estimation of pregnancy outcome with delayed entries

A pregnancy may end up with (at least) three possible events: live birth, spontaneous abortion, or elective termination, yielding a competing risks issue when studying an association between a risk factor and a pregnancy outcome. Cumulative incidences (probabilities to end up with the different outcomes depending on gestational age) can be estimated via the Aalen–Johansen estimate. Another issue is that women are usually not entering such an observational study from the first day of pregnancy, resulting in delayed entries. As in traditional survival analysis, this can be solved by considering “at risk” at a given gestational age only for those women who entered the study before that age. However, the number of women at risk at an early gestational age might be extremely low, such that the estimates of cumulative incidence may increase exaggeratedly at that age because of a single event. One solution to reduce the problem has been recently proposed in the literature, which is to ignore simply those early events, creating a small mean bias but enhancing stability of estimates. In the present paper, we propose an alternative computationally simple approach to tackle this problem that consists to postpone to later gestational ages (rather than to ignore) those early events. The two approaches are compared with respect to bias, stability, and sensitivity on the smoothing parameter via simulations reproducing realistic pregnancy scenarios, and are illustrated with data from a study on the effects of statins on pregnancy outcomes. We also outline that all three approaches are asymptotically equivalent.     

Sympatric Speciation: When Is It Possible in Bacteria?

According to theory, sympatric speciation in sexual eukaryotes is favored when relatively few loci in the genome are sufficient for reproductive isolation and adaptation to different niches. Here we show a similar result for clonally reproducing bacteria, but which comes about for different reasons. In simulated microbial populations, there is an evolutionary tradeoff between early and late stages of niche adaptation, which is resolved when relatively few loci are required for adaptation. At early stages, recombination accelerates adaptation to new niches (ecological speciation) by combining multiple adaptive alleles into a single genome. Later on, without assortative mating or other barriers to gene flow, recombination generates unfit intermediate genotypes and homogenizes incipient species. The solution to this tradeoff may be simply to reduce the number of loci required for speciation, or to reduce recombination between species over time. Both solutions appear to be relevant in natural microbial populations, allowing them to diverge into ecological species under similar constraints as sexual eukaryotes, despite differences in their life histories.     

Philosophical background of attitudes toward and treatment of invertebrates

People who interact with or make decisions about invertebrate animals have an attitude toward them, although they may not have consciously worked it out. Three philosophical approaches underlie this attitude. The first is the contractarian, which basically contends that animals are only automata and that we humans need not concern ourselves with their welfare except for our own good, because cruelty and neglect demean us. A second approach is the utilitarian, which focuses on gains versus losses in interactions between animals, including humans. Given the sheer numbers of invertebrates-they constitute 99% of the animals on the planet- this attitude implicitly requires concern for them and consideration in particular of whether they can feel pain. Third is the rights-based approach, which focuses on humans-treatment of animals by calling for an assessment of their quality of life in each human-animal interaction. Here scholars debate to what extent different animals have self-awareness or even consciousness, which may dictate our treatment of them. Regardless of the philosophical approach to invertebrates, information and education about their lives are critical to an understanding of how humans ought to treat them.     

Experimental observation, theoretical models, and biomechanical inference in the study of mandibular form

Experimental studies and mathematical models are disparate approaches for inferring the stress and strain environment in mammalian jaws. Experimental designs offer accurate, although limited, characterization of biomechanical behavior, while mathematical approaches (finite element modeling in particular) offer unparalleled precision in depiction of strain magnitudes, directions, and gradients throughout the mandible. Because the empirical (experimental) and theoretical (mathematical) perspectives differ in their initial assumptions and their proximate goals, the two methods can yield divergent conclusions about how masticatory stresses are distributed in the dentary. These different sources of inference may, therefore, tangibly influence subsequent biological interpretation. In vitro observation of bone strain in primate mandibles under controlled loading conditions offers a test of finite element model predictions. Two issues which have been addressed by both finite element models and experimental approaches are: (1) the distribution of torsional shear strains in anthropoid jaws and (2) the dissipation of bite forces in the human alveolar process. Not surprisingly, the experimental data and mathematical models agree on some issues, but on others exhibit discordance. Achieving congruence between these methods is critical if the nature of the relationship of masticatory stress to mandibular form is to be intelligently assessed. A case study of functional/mechanical significance of gnathic morphology in the hominid genus Paranthropus offers insight into the potential benefit of combining theoretical and experimental approaches. Certain finite element analyses claim to have identified a biomechanical problem unrecognized in previous comparative work, which, in essence, is that the enlarged transverse dimensions of the postcanine corpus may have a less important role in resisting torsional stresses than previously thought. Experimental data have identified subperiosteal cortical thinning as a culprit in diminishing the role of cross-sectional geometry in conditioning the strain environment. These observations raise questions concerning the biomechanical significance of mandibular form in early hominids, fueling persistent arguments over whether gnathic morphology can be related to dietary specialization in the "robust" australopithecines. Nonmechanical explanations (e.g., tooth size or body size) for Paranthropus mandibular dimensions, however, are not compelling as competing hypotheses. Both theoretical and experimental models are in need of refinement before it is possible to conclude that the jaws of the "robust" australopithecines are not functionally linked to elevated masticatory loads.     

Structure and function of the homeotic gene complex (HOM-C) in the beetle, Tribolium castaneum

The powerful combination of genetic, developmental and molecular approaches possible with the fruit fly, Drosophila melanogaster, has led to a profound understanding of the genetic control of early developmental events. However, Drosophila is a highly specialized long germ insect, and the mechanisms controlling its early development may not be typical of insects or Arthropods in general. The beetle, Tribolium castaneum, offers a similar opportunity to integrate high resolution genetic analysis with the developmental/molecular approaches currently used in other organisms. Early results document significant differences between insect orders in the functions of genes responsible for establishing developmental commitments.     

A cautionary note on the correct structure assignment of phytoprostanes and the emergence of a new prostane ring system

Considerable confusion exists about the correct structural representation of phytoprostanes (PhytoP). Improper use of the different nomenclature systems leads to incorrect structure assignment of PhytoP, which results in wrong synthetic approaches to these molecules and may lead to wrong rationalization of biological activity. A new prostane ring system was found, which is proposed to be termed L₁-PhytoP or L₂-IsoP, respectively.     

Modeling feature-based attention as an active top-down inference process

Vision is a crucial sensor. It provides a very rich collection of information about our environment. The difficulty in vision arises, since this information is not obvious in the image, it has to be constructed. Wheres earlier approaches have favored a bottom-up approach, which maps the image onto an internal representation of the world, more recent approaches search for alternatives and develop frameworks which make use of top-down connections. In these approaches vision is inherently a constructive process which makes use of a priory information. Following this line of research, a model of primate object perception is presented and used to simulate an object detection task in natural scenes. The model predicts that early responses in extrastriate visual areas are modulated by the visual goal.     

Probing the druggability of membrane-bound Rab5 by molecular dynamics simulations

Rab5 is a small GTPase and a key regulator in early endosomal trafficking. Rab5 and its effectors are involved in a large number of infectious diseases and certain types of cancer. We performed µs atomistic molecular dynamics simulations of inactive and active full-length Rab5 anchored to a complex model bilayer with composition of the early endosome membrane. Direct interactions between the Rab5?G domain and the bilayer were observed. We found two dominant nucleotide-dependent orientations characterised by a different accessibility of the switch regions. The “buried switch” orientation was mainly associated with inactive Rab5 accompanied with a rather extended structure of the hypervariable C-terminal region. Active Rab5 preferred an orientation in which the switch regions are accessible to effector proteins. These structural differences may provide an opportunity to selectively target one Rab5 state and lead to new approaches in the development of Rab5-specific therapies.     

Modeling feature-based attention as an active top-down inference process

Vision is a crucial sensor. It provides a very rich collection of information about our environment. The difficulty in vision arises, since this information is not obvious in the image, it has to be constructed. Wheres earlier approaches have favored a bottom-up approach, which maps the image onto an internal representation of the world, more recent approaches search for alternatives and develop frameworks which make use of top-down connections. In these approaches vision is inherently a constructive process which makes use of a priory information. Following this line of research, a model of primate object perception is presented and used to simulate an object detection task in natural scenes. The model predicts that early responses in extrastriate visual areas are modulated by the visual goal.     

Molecular and chemical genetic approaches to developmental origins of aging and disease in zebrafish

The incidence of diseases increases rapidly with age, accompanied by progressive deteriorations of physiological functions in organisms. Aging-associated diseases are sporadic but mostly inevitable complications arising from senescence. Senescence is often considered the antithesis of early development, but yet there may be factors and mechanisms in common between these two phenomena over the dynamic process of aging. The association between early development and late-onset disease with advancing age is thought to come from a consequence of developmental plasticity, the phenomenon by which one genotype can give rise to a range of physiologically and/or morphologically adaptive states in response to different environmental or genetic perturbations. On the one hand, we hypothesized that the future aging process can be predictive based on adaptivity during the early developmental period. Modulating the thresholds of adaptive plasticity by chemical genetic approaches, we have been investigating whether any relationship exists between the regulatory mechanisms that function in early development and in senescence using the zebrafish (Danio rerio), a small freshwater fish and a useful model animal for genetic studies. We have successfully conducted experiments to isolate zebrafish mutants expressing apparently altered senescence phenotypes during embryogenesis (“embryonic senescence”), subsequently showing shortened lifespan in adulthoods. We anticipate that previously uncharacterized developmental genes may mediate the aging process and play a pivotal role in senescence. On the other hand, unexpected senescence-related genes might also be involved in the early developmental process and regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes and small molecular compounds that can be linked to the senescence phenotype, and thereby facilitates searching for the evolutionary and developmental origins of aging in vertebrates. This article is part of a Special Issue entitled: Animal Models of Disease.