From genotype to phenotype: buffering mechanisms and the storage of genetic information

Alcohol Intake and Serum Glucose Levels from the Perspective of a Mendelian Randomization Design: The KCPS-II Biobank

Background

Previous studies have suggested that alcohol intake is associated with increased fasting serum glucose (FSG), but the nature of the relationship remains unknown. We used Mendelian randomization analysis to assess the causal effect of alcohol intake on FSG in a middle-aged Korean population.

Methods

Clinical data including FSG and alcohol intake were collected from 156,386 Koreans aged 20 years or older who took part in the Korean Cancer Prevention Study-II (KCPS-II) Biobank Cohort. The single nucleotide polymorphism rs671 in ALDH2 was genotyped among 2,993 men and 1,374 women in 2016. This was a randomly selected subcohort of KCPS-II Biobank participants.

Results

Alcohol consumption was positively associated with FSG level in men, but not in women. The rs671 major G allele was associated with increased alcohol intake (F-statistic = 302.62) and an increase in FSG in men. Using Mendelian randomization analysis, alcohol intake increased FSG by 1.78 mg/dL per alcohol unit (10 g ethanol) per day (95% CI: 0.97–2.59) in men. The associations became stronger when we excluded heavy drinkers and the elderly. However, in women, no significant association between rs671 and alcohol or serum glucose was found.

Conclusion

Using Mendelian randomization analysis, we suggest a causal relationship between alcohol intake and FSG among Korean men. Moreover, we found that the ALDH2 variant rs671 was not associated with FSG among Korean women.

Genetic structure of phenotypic robustness in the collaborative cross mouse diallel panel

Developmental stability and canalization describe the ability of developmental systems to minimize phenotypic variation in the face of stochastic micro-environmental effects, genetic variation and environmental influences. Canalization is the ability to minimize the effects of genetic or environmental effects, whereas developmental stability is the ability to minimize the effects of micro-environmental effects within individuals. Despite much attention, the mechanisms that underlie these two components of phenotypic robustness remain unknown. We investigated the genetic structure of phenotypic robustness in the collaborative cross (CC) mouse reference population. We analysed the magnitude of fluctuating asymmetry (FA) and among-individual variation of cranial shape in reciprocal crosses among the eight parental strains, using geometric morphometrics and a diallel analysis based on a Bayesian approach. Significant differences among genotypes were found for both measures, although they were poorly correlated at the level of individuals. An overall positive effect of inbreeding was found for both components of variation. The strain CAST/EiJ exerted a positive additive effect on FA and, to a lesser extent, among-individual variance. Sex- and other strain-specific effects were not significant. Neither FA nor among-individual variation was associated with phenotypic extremeness. Our results support the existence of genetic variation for both developmental stability and canalization. This finding is important because robustness is a key feature of developmental systems. Our finding that robustness is not related to phenotypic extremeness is consistent with theoretical work that suggests that its relationship to stabilizing selection is not straightforward.

Regulatory mechanisms link phenotypic plasticity to evolvability

Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

Representing vision and blindness

BACKGROUND

There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a variety of reasons. Blindness has escaped ontological capture at least in part because: blindness or the employment of the term 'blindness' seems to vary from context to context, blindness can present in a myriad of types and degrees, and there is no precedent for representing complex phenomena such as blindness.

METHODS

We explore current attempts to represent vision or blindness, and show how these attempts fail at representing subtypes of blindness (viz., color blindness, flash blindness, and inattentional blindness). We examine the results found through a review of current attempts and identify where they have failed.

RESULTS

By analyzing our test cases of different types of blindness along with the strengths and weaknesses of previous attempts, we have identified the general features of blindness and vision. We propose an ontological solution to represent vision and blindness, which capitalizes on resources afforded to one who utilizes the Basic Formal Ontology as an upper-level ontology.

CONCLUSIONS

The solution we propose here involves specifying the trigger conditions of a disposition as well as the processes that realize that disposition. Once these are specified we can characterize vision as a function that is realized by certain (in this case) biological processes under a range of triggering conditions. When the range of conditions under which the processes can be realized are reduced beyond a certain threshold, we are able to say that blindness is present. We characterize vision as a function that is realized as a seeing process and blindness as a reduction in the conditions under which the sight function is realized. This solution is desirable because it leverages current features of a major upper-level ontology, accurately captures the phenomenon of blindness, and can be implemented in many domain-specific ontologies.

Bringing clinical pharmacogenomics information to pharmacists: A qualitative study of information needs and resource requirements

INTRODUCTION

As key experts in supporting medication-decision making, pharmacists are well-positioned to support the incorporation of pharmacogenomics into clinical care. However, there has been little study to date of pharmacists' information needs regarding pharmacogenomics. Understanding those needs is critical to design information resources that help pharmacists effectively apply pharmacogenomics information.

OBJECTIVES

We sought to understand the pharmacogenomics information needs and resource requirements of pharmacists.

METHODS

We conducted qualitative inquiries with 14 pharmacists representing 6 clinical environments, and used the results of those inquiries to develop a model of pharmacists' pharmacogenomics information needs and resource requirements.

RESULTS

The inquiries identified 36 pharmacogenomics-specific and pharmacogenomics-related information needs that fit into four information needs themes: background information, patient information, medication information, and guidance information. The results of the inquiries informed a model of pharmacists' pharmacogenomics resource requirements, with 3 themes: structure of the resource, perceptions of the resource, and perceptions of the information.

CONCLUSION

Responses suggest that pharmacists anticipate an imminently growing role for pharmacogenomics in their practice. Participants value information from trust-worthy resources like FDA product labels, but struggle to find relevant information quickly in labels. Specific information needs include clinically relevant guidance about genotypes, phenotypes, and how to care for their patients with known genotypes. Information resources supporting the goal of incorporating complicated genetic information into medication decision-making goals should be well-designed and trustworthy.

From the genetic architecture to synaptic plasticity in autism spectrum disorder

Genetics studies of autism spectrum disorder (ASD) have identified several risk genes that are key regulators of synaptic plasticity. Indeed, many of the risk genes that have been linked to these disorders encode synaptic scaffolding proteins, receptors, cell adhesion molecules or proteins that are involved in chromatin remodelling, transcription, protein synthesis or degradation, or actin cytoskeleton dynamics. Changes in any of these proteins can increase or decrease synaptic strength or number and, ultimately, neuronal connectivity in the brain. In addition, when deleterious mutations occur, inefficient genetic buffering and impaired synaptic homeostasis may increase an individual's risk for ASD.

Alcohol Use and Gamma-Glutamyltransferase Using a Mendelian Randomization Design in the Guangzhou Biobank Cohort Study

Background

Observational studies and small intervention studies suggest alcohol raises gamma-glutamyltransferase (GGT). We used Mendelian randomization to assess the causal effect of alcohol use on GGT in older Chinese people.

Methods

An instrumental variable (IV) analysis in 2,321 men and 2,757 women aged 50+ years from phase 3 of the Guangzhou Biobank Cohort Study with ALDH2 (rs671) genotyped, alcohol use and GGT available was used to assess the causal effect of alcohol use on GGT. Rs671 was used as an IV and F-statistics was used to test for weak instrument hypothesis. An F-statistic of ≥10 indicates the IV is not weak.

Results

In men, the F-statistic for rs671 on alcohol use was 70. Using IV analysis alcohol use increased GGT by 10.60 U/L per alcohol unit (10 gram ethanol) per day (95% confidence interval (CI) 6.58 to 14.62). The estimate was lower in observational multivariate regression: 3.48 U/L GGT per alcohol unit per day (95% CI 2.84 to 4.11) adjusted for age, education, physical activity and smoking. In women, rs671 was not associated with alcohol or GGT and the F-statistic was 7 precluding IV analysis.

Conclusion

In Mendelian randomization, we found confirmative evidence that alcohol use increases GGT among Southern Chinese men. Moreover, we found that the ALDH2 variant rs671 was not associated with GGT among Southern Chinese women who generally consume very low levels of alcohol. Taken together our findings strongly suggest that alcohol increases GGT, although we cannot rule out the possibility that other unknown factors may cause a different relation between alcohol and GGT in other populations.

Shifts in subsistence type and its impact on the human skull's morphological integration

OBJECTIVE

Here we evaluate morphological integration patterns and magnitudes in different skull regions to detect if shifts in morphological integration are correlated to the appearance of more processed (softer) diets.

METHODS

To do so, three transitional populations were analyzed, including samples from groups that inhabited the same geographical region and for which the evidence shows that major changes occurred in their subsistence mode. Ninety three-dimensional landmarks were digitized on 357 skulls and used as the raw data to develop geometric morphometric analyses. The landmark coordinates were divided into several different regions of biomechanical interest, following a three-level hierarchically nested scheme: the whole skull, further subdivided into neurocranium (divided into the vault and basicranium), the facial (divided into the lower and upper facial), and the masticatory apparatus (divided into alveolar, temporal, and temporo-mandibular joint).

RESULTS

Our results indicate that the morphological integration and variability patterns significantly vary across skull regions but are maintained across the transitions. The alveolar border and the lower facial are the regions manifesting greater value of morphological integration and variability, while the upper facial, the temporo-mandibular joint, and the basicranium are highly integrated and poorly variable.

CONCLUSIONS

The transition to softer diets increased morphological variation across cranial regions that are more exposed to masticatory strains effects.

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

Recently, great progress has been made in single cell genomics and transcriptomics. Here, we present an integrative method, termed single-cell transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells. This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells. Mouse embryonic fibroblasts were treated with the powerful mutagen ethylnitrosourea (ENU) and subjected to SCTG. Interestingly, while germline variants were found to be transcribed in an allelically balanced fashion, a significantly different pattern of allelic exclusion was observed for ENU-mutant variants. These results suggest that the adverse effects of induced mutations, in contrast to germline variants, may be mitigated by allelically biased transcription. They also illustrate how SCTG can be instrumental in the direct assessment of phenotypic consequences of genomic variants.

DNA Dispose, but Subjects Decide. Learning and the Extended Synthesis

Adaptation by means of natural selection depends on the ability of populations to maintain variation in heritable traits. According to the Modern Synthesis this variation is sustained by mutations and genetic drift. Epigenetics, evodevo, niche construction and cultural factors have more recently been shown to contribute to heritable variation, however, leading an increasing number of biologists to call for an extended view of speciation and evolution. An additional common feature across the animal kingdom is learning, defined as the ability to change behavior according to novel experiences or skills. Learning constitutes an additional source for phenotypic variation, and change in behavior may induce long lasting shifts in fitness, and hence favor evolutionary novelties. Based on published studies, I demonstrate how learning about food, mate choice and habitats has contributed substantially to speciation in the canonical story of Darwin's finches on the Galapagos Islands. Learning cannot be reduced to genetics, because it demands decisions, which requires a subject. Evolutionary novelties may hence emerge both from shifts in allelic frequencies and from shifts in learned, subject driven behavior. The existence of two principally different sources of variation also prevents the Modern Synthesis from self-referring explanations.

toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map

The genotype-phenotype map is an essential object to understand organismal complexity and adaptability. However, its experimental characterisation is a daunting task. Thus, simple models have been proposed and investigated. They have revealed that genotypes differ in their robustness to mutations; phenotypes are represented by a broadly varying number of genotypes, and simple point mutations suffice to navigate the space of genotypes while maintaining a phenotype. Nonetheless, most current models focus only on one level of the map (folded molecules, gene regulatory networks, or networks of metabolic reactions), so that many relevant questions cannot be addressed. Here we introduce toyLIFE, a multi-level model for the genotype-phenotype map based on simple genomes and interaction rules from which a complex behaviour at upper levels emerges -remarkably plastic gene regulatory networks and metabolism. toyLIFE is a tool that permits the investigation of how different levels are coupled, in particular how and where mutations affect phenotype or how the presence of certain metabolites determines the dynamics of toyLIFE gene regulatory networks. The model can easily incorporate evolution through more complex mutations, recombination, or gene duplication and deletion, thus opening an avenue to explore extended genotype-phenotype maps.

Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution

We propose the cooperative model of phenotype-driven evolution, in which natural selection operates on a phenotype caused by both genetic and epigenetic factors. The conventional theory of evolutionary synthesis assumes that a phenotypic value (P) is the sum of genotypic value (G) and environmental deviation (E), P=G+E, where E is the fluctuations of the phenotype among individuals in the absence of environmental changes. In contrast, the cooperative model assumes that an evolution is triggered by an environmental change and individuals respond to the change by phenotypic plasticity (epigenetic changes). The phenotypic plasticity, while essentially qualitative, is denoted by a quantitative value F which is modeled as a normal random variable like E, but with a much larger variance. Thus, the fundamental equation of the cooperative model is given as P=G+F where F includes the effect of E. Computer simulations using a genetic algorithm demonstrated that the cooperative model realized much faster evolution than the evolutionary synthesis. This accelerated evolution was found to be due to the cumulative evolution made possible by a ratchet mechanism due to the epigenetic contribution to the phenotypic value. The cooperative model can well account for the phenomenon of genetic assimilation, which, in turn, suggests the mechanism of cumulative selection. The cooperative model may also serve as a theoretical basis to understand various ideas and phenomena of the phenotype-driven evolution such as genetic assimilation, the theory of facilitated phenotypic variation, and epigenetic inheritance over generations.

Effects of environmental disturbance on phenotypic variation: an integrated assessment of canalization, developmental stability, modularity, and allometry in lizard head shape

When populations experience suboptimal conditions, the mechanisms involved in the regulation of phenotypic variation can be challenged, resulting in increased phenotypic variance. This kind of disturbance can be diagnosed by using morphometric tools to study morphological patterns at different hierarchical levels and evaluate canalization, developmental stability, integration, modularity, and allometry. We assess the effect of urbanization on phenotypic variation in the common wall lizard (Podarcis muralis) by using geometric morphometrics to assess disturbance to head shape development. The head shapes of urban lizards were more variable and less symmetric, suggesting that urban living is more likely to disturb development. Head shape variation was congruent within and across individuals, which indicated that canalization and developmental stability are two related phenomena in these organisms. Furthermore, urban lizards exhibited smaller mean head sizes, divergent size-shape allometries, and increased deviation from within-group allometric lines. This suggests that mechanisms regulating head shape allometry may also be disrupted. The integrated evaluation of several measures of developmental instability at different hierarchical levels, which provided in this case congruent results, can be a powerful methodological guide for future studies, as it enhances the detection of environmental disturbances on phenotypic variation and aids biological interpretation of the results.

Host alkaloids differentially affect developmental stability and wing vein canalization in cactophilic Drosophila buzzatii

Host shifts cause drastic consequences on fitness in cactophilic species of Drosophila. It has been argued that changes in the nutritional values accompanying host shifts may elicit these fitness responses, but they may also reflect the presence of potentially toxic secondary compounds that affect resource quality. Recent studies reported that alkaloids extracted from the columnar cactus Trichocereus terscheckii are toxic for the developing larvae of Drosophila buzzatii. In this study, we tested the effect of artificial diets including increasing doses of host alkaloids on developmental stability and wing morphology in D. buzzatii. We found that alkaloids disrupt normal wing venation patterning and affect viability, wing size and fluctuating asymmetry, suggesting the involvement of stress-response mechanisms. Theoretical implications are discussed in the context of developmental stability, stress, fitness and their relationship with robustness, canalization and phenotypic plasticity.

On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms

Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.

Stress-mediated tuning of developmental robustness and plasticity in flies

Organisms have to be sufficiently robust to environmental and genetic perturbations, yet plastic enough to cope with stressful scenarios to which they are not fully adapted. How this apparent conflict between robustness and plasticity is resolved at the cellular and whole organism levels is not clear. Here we review and discuss evidence in flies suggesting that the environment can modulate the balance between robustness and plasticity. The outcomes of this modulation can vary from mild sensitizations that are hardly noticeable, to overt qualitative changes in phenotype. The effects could be at both the cellular and whole organism levels and can include cellular de-/trans-differentiation ('Cellular reprogramming') and gross disfigurements such as homeotic transformations ('Tissue/whole organism reprogramming'). When the stress is mild enough, plastic changes in some processes may prevent drastic changes in more robust traits such as cell identity and tissue integrity. However, when the stress is sufficiently severe, this buffering may no longer be able to prevent such overt changes, and the resulting phenotypic variability could be subjected to selection and might assist survival at the population level. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.

Cryptic genetic variation: evolution's hidden substrate

Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.

Protein-protein interaction detection: methods and analysis

Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Thus, in silico methods which include sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, phylogenetic tree, phylogenetic profile, and gene expression-based approaches were developed. Elucidation of protein interaction networks also contributes greatly to the analysis of signal transduction pathways. Recent developments have also led to the construction of networks having all the protein-protein interactions using computational methods for signaling pathways and protein complex identification in specific diseases.

Primate transcript and protein expression levels evolve under compensatory selection pressures

Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen

The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant. Instead, the phenotype is a function of the allele, the genetic background in which it occurs and the environment where the mutational effects are expressed. While the influence of genetic background on the expressivity of individual mutations is recognized, its consequences on the interactions between genes, or the genetic network they form, is largely unknown. The description of genetic networks is essential for much of biology; yet if, and how, the topologies of such networks are influenced by background is unknown. Furthermore, a comprehensive examination of the background dependent nature of genetic interactions may lead to identification of novel modifiers of biological processes. Previous work in Drosophila melanogaster demonstrated that wild-type genetic background influences the effects of an allele of scalloped (sd), with respect to both its principal consequence on wing development and its interactions with a mutation in optomotor blind. In this study we address whether the background dependence of mutational interactions is a general property of genetic systems by performing a genome wide dominant modifier screen of the sd(E3) allele in two wild-type genetic backgrounds using molecularly defined deletions. We demonstrate that ~74% of all modifiers of the sd(E3) phenotype are background-dependent due in part to differential sensitivity to genetic perturbation. These background dependent interactions include some with qualitative differences in the phenotypic outcome, as well as instances of sign epistasis. This suggests that genetic interactions are often contingent on genetic background, with flexibility in genetic networks due to segregating variation in populations. Such background dependent effects can substantially alter conclusions about how genes influence biological processes, the potential for genetic screens in alternative wild-type backgrounds identifying new loci that contribute to trait expression, and the inferences of the topology of genetic networks.

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution

The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with traditional genetic analyses and the foundational knowledge they have provided, we argue that the time and tools are ripe to return to the underexplored aspects of gene function and embrace the context-dependent nature of genetic effects. We assert that a broad understanding of genetic effects and the evolutionary dynamics of alleles requires identifying how mutational outcomes depend upon the 'wild type' genetic background. Furthermore, we discuss how best to exploit genetic background effects to broaden genetic research programs.

Degeneracy allows for both apparent homogeneity and diversification in populations

Trait diversity - the substrate for natural selection - is necessary for adaptation through selection, particularly in populations faced with environmental changes that diminish population fitness. In habitats that remain unchanged for many generations, stabilizing selection maximizes exploitation of resources by reducing trait diversity to a narrow optimal range. One might expect that such ostensibly homogeneous populations would have a reduced potential for heritable adaptive responses when faced with fitness-reducing environmental changes. However, field studies have documented populations that, even after long periods of evolutionary stasis, can still rapidly evolve in response to changed environmental conditions. We argue that degeneracy, the ability of diverse population elements to function similarly, can satisfy both the current need to maximize fitness and the future need for diversity. Degenerate ensembles appear functionally redundant in certain environmental contexts and functionally diverse in others. We propose that genetic variation not contributing to the observed range of phenotypes in a current population, also known as cryptic genetic variation (CGV), is a specific case of degeneracy. We argue that CGV, which gradually accumulates in static populations in stable environments, reveals hidden trait differences when environments change. By allowing CGV accumulation, static populations prepare themselves for future rapid adaptations to environmental novelty. A greater appreciation of degeneracy's role in resolving the inherent tension between current stabilizing selection and future directional selection has implications in conservation biology and may be applied in social and technological systems to maximize current performance while strengthening the potential for future changes.

The relationship between phenotypic and environmental variation: do physiological responses reduce interindividual differences?

What is the effect of a variable environment on phenotypic variation? Does the physiological response to a new environment increase or decrease the differences among individuals? We provide a speculative hypothesis suggesting that the induction of a physiological response to environmental change minimizes phenotypic differences among individuals in outbred genetically variable populations. Although this suggestion runs counter to the general idea that environmental variation induces phenotypic variation, we provide evidence that this is not always the case. One explanation for this counterintuitive hypothesis is that in a variable environment, the physiological mechanism that maintains homeostasis changes the concentrations of active transcription factors (TFs). This change in TFs reduces the effectiveness of nucleotide polymorphisms in TF binding sites and thus reduces the variation among individuals in mRNA expression and in the phenotypes affected by these mRNA transcripts. Thus, there are fewer differences among individuals in a variable environment compared with the variation observed in a constant environment. Our conjecture is that the physiological mechanisms that maintain homeostasis in response to environmental variation canalize phenotypic variation. If our hypothesis is correct, then the physiological canalization of gene expression in a variable environment hides genetic variation and thereby reduces the evolutionary costs of polymorphism. This hypothesis provides a new perspective on the mechanisms by which high levels of genetic variation can persist in real-world populations.

Evolution of novel mosaic castes in ants: modularity, phenotypic plasticity, and colonial buffering

Many ants have independently evolved castes with novel morphology as well as function, such as soldiers and permanently wingless (ergatoid) queens. We present a conceptual model, based on modularity in morphology and development, in which evolutionary innovation is facilitated by the ancestral ant polyphenism of winged queens and wingless workers. We suggest that novel castes evolved from rare intercastes, anomalous mosaics of winged queens and workers, erratically produced by colonies through environmental or genetic perturbations. The colonial environment is highly accommodating and buffers viable intercastes from individual selection. Their cost is limited because they are diluted by the large number of nestmates, yet some can bring disproportionate benefits to their colonies in the context of defense or reproduction (e.g., wingless intercastes able to mate). Useful intercastes will increase in frequency as their morphology is stabilized through genetic accommodation. We show that both soldiers and ergatoid queens are mosaics of winged queens and workers, and they are strikingly similar to some intercastes. Modularity and developmental plasticity together with winged/wingless polyphenism thus allow for the production of highly variable mosaic intercastes, and colonies incubate the advantageous mosaics.

Biological robustness: paradigms, mechanisms, and systems principles

Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g., mutational, environmental) are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior.

Possible genetic and epigenetic links between human inner speech, schizophrenia and altruism

Unique mental abilities have been crucial for evolutionary success of Homo sapiens and for the development of his complex social organization. However, these abilities have also become a target for mental disorders which often result in a reduced fitness and in conflicts between the individual and the conventions of society. To account for this evolutionary maladaptation, we advance a new concept: that of "mis-exaptation", derived from SJ Gould and E Vrba's concept of exaptation. Mis-exaptation is a characteristic which, although it may confer positive effects in one field of activity, may reach an inappropriate degree of specialisation to have deleterious effects in that or in another field thereby leading to a decrease in fitness of the individual. This paper considers "inner speech" as an exaptation. Although inner speech is usually a positive aid to learning and reasoning, it may also favour the emergence of mental disturbances, such as the auditory hallucinations which are characteristic of schizophrenia. There is, nevertheless, a possible evolutionary value in mis-exaptational inner speech; two traits associated with the mis-exapted state would be altruistic behaviour and heightened creativity, the latter being over-expressed in relatives of schizophrenic patients. A possible solution for the evolutionary-genetic paradox posed by altruism and schizophrenia arising from mis-exaptation will be suggested in the light of a cryptic genetic repertoire. A selection of illustrative examples of each of these mental states is presented as they appear in the pages of the European literature. This article is part of a Special Issue entitled: Brain Integration.

Parental identity influences progeny responses to incubation thermal stress in sockeye salmon Onchorhynchus nerka

The influence of individual parentage on progeny responses to early developmental temperature stress was examined in a cross-fertilization experiment using sockeye salmon Oncorhynchus nerka. Differences in survival, hatch timing and size were examined among five paternally linked and five maternally linked offspring families (Weaver Creek population, British Columbia, Canada) incubated at 12, 14 and 16° C from just after fertilization to hatch. Mean embryonic survival was significantly lower at 14 and 16° C; however, offspring families had substantially different survival responses across the thermal gradient (crossing reaction norms). Within temperature treatments, substantial variation in embryonic survival, alevin mass, time-to-hatch and hatch duration were attributable to family identity; however, most traits were governed by significant temperature-family interactions. For embryonic survival, large differences between families at 16° C were due to both female and male spawner influence, whereas inter-family differences were obscured at 14° C (high intra-family variation), and minimal at 12° C (only maternal influence detected). Despite post-hatch rearing under a common cool thermal regime, persistent effects of both temperature and parentage were detected in alevin and 3 week-old fry. Collectively, these findings highlight the crucial role that parental influences on offspring may have in shaping future selection within salmonid populations exposed to elevated thermal regimes. An increased understanding of parental and temperature influences and their persistence in early development will be essential to developing a more comprehensive view of population spawning success and determining the adaptive capacity of O. nerka populations in the face of environmental change.

Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae

The integrity of mitosis is dependent upon strict regulation of microtubule stability and dynamics. Although much information has been accumulated on regulators of the microtubule cytoskeleton, our knowledge of the specific pathways involved is still limited. Here we designed genetic screens to identify regulators of microtubule stability that are dispensable in the wild type yet become essential under microtubule-disrupting conditions. We found that the transcriptional cofactor Swi6p and activator Swi4p, as well as the G(2)/M-specific cyclin Clb2p, are required in a microtubule-destabilizing environment. Swi6p and Swi4p can combine as a transcriptional complex, called the SBF complex (SBF for Swi4/6 cell cycle box [SCB]-binding factor) that is functionally homologous to the metazoan DP1/2-E2F complex and that controls the G(1)/S transition through the genes it regulates. We show that Swi6p's contribution to microtubule stability can be either dependent or independent of the SBF complex. The SBF-dependent pathway requires downregulation of SBF complex levels and may thereby reroute the transcriptional program in favor of greater microtubule stability. This pathway can be triggered by overexpression of Fcp1p, a phosphatase in the general transcription machinery, or by expression of an allele of SWI6 that is associated with reduced transcription from SBF-controlled promoters. The SBF-independent pathway is activated by a constitutively nuclear allele of Swi6p. Our results introduce novel roles in microtubule stability for genes whose participation in the process may be masked under normal conditions yet nonetheless acquire a dominant role when microtubule stability is compromised.

Functional interactions among morphologic and tissue quality traits define bone quality

BACKGROUND

Advances in diagnostic and treatment regimens that aim to reduce fracture incidence will benefit from a better understanding of how bone morphology and tissue quality define whole-bone mechanical properties.

QUESTIONS/PURPOSES

The goal of this article was to review what is known about the interactions among morphologic and tissue quality traits and how these interactions contribute to bone quality (ie, whole-bone mechanical function). Several questions were addressed. First, how do interactions among morphology and tissue quality traits relate to functional adaptation? Second, what are the emergent patterns of functionally adapted trait sets in long bones? Third, how effective is phenotypic integration at establishing function across a population? Fourth, what are the emergent patterns of functionally adapted trait sets in corticocancellous structures? Fifth, how do functional interactions change with aging?

METHODS

A literature review was conducted with papers identified primarily through citations listed in reference sections as well as general searches using Google Scholar and PubMed.

RESULTS

The interactions among adult traits or phenotypic integration are an emergent property of the compensatory mechanisms complex systems used to establish function or homeostasis. Traits are not regulated independently but vary simultaneously (ie, covary) in specific ways to establish function. This covariation results in individuals acquiring unique sets of traits to establish bone quality.

CONCLUSIONS AND CLINICAL RELEVANCE

Biologic constraints imposed on the skeletal system result in a population showing a pattern of trait sets that is predictable based on external bone size and that can be used to identify individuals with reduced bone quality relative to their bone size and body size.

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

Cryptic variation is caused by the robustness of phenotypes to mutations. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation. This is possible if the cryptic variation happens to be pre-adapted, or "exapted", to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution.

Overcoming redundancy: an RNAi enhancer screen for morphogenesis genes in Caenorhabditis elegans

Morphogenesis is an important component of animal development. Genetic redundancy has been proposed to be common among morphogenesis genes, posing a challenge to the genetic dissection of morphogenesis mechanisms. Genetic redundancy is more generally a challenge in biology, as large proportions of the genes in diverse organisms have no apparent loss of function phenotypes. Here, we present a screen designed to uncover redundant and partially redundant genes that function in an example of morphogenesis, gastrulation in Caenorhabditis elegans. We performed an RNA interference (RNAi) enhancer screen in a gastrulation-sensitized double-mutant background, targeting genes likely to be expressed in gastrulating cells or their neighbors. Secondary screening identified 16 new genes whose functions contribute to normal gastrulation in a nonsensitized background. We observed that for most new genes found, the closest known homologs were multiple other C. elegans genes, suggesting that some may have derived from rounds of recent gene duplication events. We predict that such genes are more likely than single copy genes to comprise redundant or partially redundant gene families. We explored this prediction for one gene that we identified and confirmed that this gene and five close relatives, which encode predicted substrate recognition subunits (SRSs) for a CUL-2 ubiquitin ligase, do indeed function partially redundantly with each other in gastrulation. Our results implicate new genes in C. elegans gastrulation, and they show that an RNAi-based enhancer screen in C. elegans can be used as an efficient means to identify important but redundant or partially redundant developmental genes.

Use of genetic markers and gene-diet interactions for interrogating population-level causal influences of diet on health

Differences in diet appear to contribute substantially to the burden of disease in populations, and therefore changes in diet could lead to major improvements in public health. This is predicated on the reliable identification of causal effects of nutrition on health, and unfortunately nutritional epidemiology has deficiencies in terms of identifying these. This is reflected in the many cases where observational studies have suggested that a nutritional factor is protective against disease, and randomized controlled trials have failed to verify this. The use of genetic variants as proxy measures of nutritional exposure-an application of the Mendelian randomization principle-can contribute to strengthening causal inference in this field. Genetic variants are not subject to bias due to reverse causation (disease processes influencing exposure, rather than vice versa) or recall bias, and if obvious precautions are applied are not influenced by confounding or attenuation by errors. This is illustrated in the case of epidemiological studies of alcohol intake and various health outcomes, through the use of genetic variants related to alcohol metabolism (in ALDH2 and ADH1B). Examples from other areas of nutritional epidemiology and of the informative nature of gene-environment interactions interpreted within the Mendelian randomization framework are presented, and the potential limitations of the approach addressed.

Adaptation of cells to new environments

The evolutionary success of an organism is a testament to its inherent capacity to keep pace with environmental conditions that change over short and long periods. Mechanisms underlying adaptive processes are being investigated with renewed interest and excitement. This revival is partly fueled by powerful technologies that can probe molecular phenomena at a systems scale. Such studies provide spectacular insight into the mechanisms of adaptation, including rewiring of regulatory networks via natural selection of horizontal gene transfers, gene duplication, deletion, readjustment of kinetic parameters, and myriad other genetic reorganizational events. Here, we discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.

Antagonistic interactions between the cAMP-dependent protein kinase and Tor signaling pathways modulate cell growth in Saccharomyces cerevisiae

Eukaryotic cells integrate information from multiple sources to respond appropriately to changes in the environment. Here, we examined the relationship between two signaling pathways in Saccharomyces cerevisiae that are essential for the coordination of cell growth with nutrient availability. These pathways involve the cAMP-dependent protein kinase (PKA) and Tor proteins, respectively. Although these pathways control a similar set of processes important for growth, it was not clear how their activities were integrated in vivo. The experiments here examined this coordination and, in particular, tested whether the PKA pathway was primarily a downstream effector of the TORC1 signaling complex. Using a number of reporters for the PKA pathway, we found that the inhibition of TORC1 did not result in diminished PKA signaling activity. To the contrary, decreased TORC1 signaling was generally associated with elevated levels of PKA activity. Similarly, TORC1 activity appeared to increase in response to lower levels of PKA signaling. Consistent with these observations, we found that diminished PKA signaling partially suppressed the growth defects associated with decreased TORC1 activity. In all, these data suggested that the PKA and TORC1 pathways were functioning in parallel to promote cell growth and that each pathway might restrain, either directly or indirectly, the activity of the other. The potential significance of this antagonism for the regulation of cell growth and overall fitness is discussed.

Mendelian Randomization for Strengthening Causal Inference in Observational Studies: Application to Gene × Environment Interactions

Identification of environmentally modifiable factors causally influencing disease risk is fundamental to public-health improvement strategies. Unfortunately, observational epidemiological studies are limited in their ability to reliably identify such causal associations, reflected in the many cases in which conventional epidemiological studies have apparently identified associations that randomized controlled trials have failed to verify. The use of genetic variants as proxy measures of exposure -an application of the Mendelian randomization principle-can contribute to strengthening causal inference. Genetic variants are not subject to bias due to reverse causation (disease processes influencing exposure, rather than vice versa) or recall bias, and if simple precautions are applied, they are not influenced by confounding or attenuation by errors. The principles of Mendelian randomization are illustrated with specific reference to studies of the effects of alcohol intake on various health-related outcomes through the utilization of genetic variants related to alcohol metabolism (in ALDH2 and ADH1B). Ways of incorporating Gene × Environment interactions into the Mendelian randomization framework are developed, and the strengths and limitations of the approach discussed.

Epistasis contributes to the genetic buffering of plasma HDL cholesterol in mice

Stressful environmental factors, such as a high-fat diet, can induce responses in the expression of genes that act to maintain physiological homeostasis. We observed variation in plasma concentrations of high-density lipoprotein (HDL) cholesterol across inbred mouse strains in response to high dietary fat intake. Several strains, including C57BL/6J, have stable levels of plasma HDL independent of diet, whereas other strains, including DBA2/J, show marked changes in plasma HDL. To explore this phenomenon further, we used publicly available data from a C57BL/6J × DBA/2J intercross to identify genetic factors that associate with HDL under high-fat diet conditions. Our analysis identified an epistatic interaction that plays a role in the buffering of HDL levels in C57BL/6J mice, and we have identified Arl4d as a candidate gene that mediates this effect. Structural modeling further elucidates the interaction of genetic factors that contribute to the robustness of HDL in response to high-fat diet in the C57BL/6J strain.

Genetically determined phenotype covariation networks control bone strength

To identify genes affecting bone strength, we studied how genetic variants regulate components of a phenotypic covariation network that was previously shown to accurately characterize the compensatory trait interactions involved in functional adaptation during growth. Quantitative trait loci (QTLs) regulating femoral robustness, morphologic compensation, and mineralization (tissue quality) were mapped at three ages during growth using AXB/BXA Recombinant Inbred (RI) mouse strains and adult B6-i(A) Chromosome Substitution Strains (CSS). QTLs for robustness were identified on chromosomes 8, 12, 18, and 19 and confirmed at all three ages, indicating that genetic variants established robustness postnatally without further modification. A QTL for morphologic compensation, which was measured as the relationship between cortical area and body weight, was identified on chromosome 8. This QTL limited the amount of bone formed during growth and thus acted as a setpoint for diaphyseal bone mass. Additional QTLs were identified from the CSS analysis. QTLs for robustness and morphologic compensation regulated bone structure independently (ie, in a nonpleiotropic manner), indicating that each trait may be targeted separately to individualize treatments aiming to improve strength. Multiple regression analyses showed that variation in morphologic compensation and tissue quality, not bone size, determined femoral strength relative to body weight. Thus an individual inheriting slender bones will not necessarily inherit weak bones unless the individual also inherits a gene that impairs compensation. This systems genetic analysis showed that genetically determined phenotype covariation networks control bone strength, suggesting that incorporating functional adaptation into genetic analyses will advance our understanding of the genetic basis of bone strength.