The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.     

The Role of Cytokinins in Plant Under Salt Stress

The plant hormone cytokinins (CKs) were generally considered associated with plant development. More recently, functions of CKs in plant stress defense including salt have been increasingly characterized. Under saline conditions, not only CKs homeostasis but also its signal transduction pathway is disturbed in a plant species-dependent manner. In turn, through manipulating exogenous CKs application or endogenous CKs metabolism or signaling, plant behavior can also be diverse across species. In this review, we systematically summarized this mutual regulation between CKs and salt stress. Considering the senescence-delaying effect of CKs, its roles in mitigating salt-induced senescence and maintaining crop yields are specifically highlighted. We also discussed here how CKs crosstalk with other phytohormones, including ABA and ethylene, to mediate salt response. In sum, this review provides a comprehensive integration of current knowledge on the regulatory role of CKs upon salt stress and puts forward research directions for future studies.

     

Towards model-driven characterization and manipulation of plant lipid metabolism

Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.     

Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales

Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties.     

Negative plant–soil feedback and species coexistence

Different mechanisms, including equilibrium and non-equilibrium processes, have been taken into account as possible theoretical explanations of species coexistence. Despite the ample evidence on the existence of negative plant–soil feedback in both agriculture and natural vegetation, the role of these processes in the organization and dynamics of plant communities has so far been neglected. In this study, simulations by an individual-based competition model show how the intensity of negative feedback on individual plant performance can produce faster successional dynamics and allow species coexistence in two- and multi-species systems. The results show that even low levels of negative plant–soil feedback can enable species coexistence and often produce cyclic population dynamics. Moreover, the model highlights how negative feedback can generate positive reciprocal interspecific interactions at the population level, despite the fact that only competitive interactions is present between individual plants. In fact, competitive effects occur on a short-term scale, but positive reciprocal species interactions emerge only if negative feedback affects all species and if longer periods of simulation, more than the species life span, are considered. An important outcome of the model is the evidence that the effects at population level are timescale-dependent, thus showing the limitation of short-term species removal experiments used in traditional competition studies.     

Peptides in lipid bilayers: the power of simple models

Interactions between proteins and lipids lie at the heart of virtually all membrane processes, but on a molecular level they are still poorly understood. Nowadays, simple model systems comprising designed transmembrane peptides in synthetic lipid bilayers are increasingly being recognized as powerful tools to uncover basic principles of protein-lipid interactions. Such model systems enable detailed analysis of how the properties of lipids influence the structure and dynamics of transmembrane helices, how these helices are anchored at the lipid-water interface, and how the length and composition of transmembrane segments influence the organization and dynamics of membrane lipids. In addition, well-characterized model systems have proven useful to refine computational approaches and to develop new techniques for studies of protein-lipid interactions.     

Clonal plants and facilitation research: bridging the gap

Over the last twenty years there has been increasing interest in facilitative plant-plant interactions. Research has examined the relationships between the role of plant interactions and gradients of environmental severity, the consequences of facilitation for biodiversity at a range of scales and the integration of facilitation into mainstream ecological theories. However, there appears to be a lack of research that explicitly links facilitation and the study of plant clonality. This is surprising given the common co-occurrence of high levels of facilitation and clonality in some systems, for example arctic and alpine environments, and the possibility for clonality to play a role in regulating facilitation processes. I propose a number of areas where there is considerable potential for bringing these two topics together, including the re-analysis of large-scale databases and multi-site experiments, the development of modelling approaches combining both facilitation and clonality and the testing of these approaches through field experimentation. I also discuss some of the studies that are starting to address this research gap, and that indicate how we might in future bring these research topics closer together.     

Ecological consequences of phenotypic plasticity

Phenotypic plasticity is widespread in nature, and often involves ecologically relevant behavioral, physiological, morphological and life-historical traits. As a result, plasticity alters numerous interactions between organisms and their abiotic and biotic environments. Although much work on plasticity has focused on its patterns of expression and evolution, researchers are increasingly interested in understanding how plasticity can affect ecological patterns and processes at various levels. Here, we highlight an expanding body of work that examines how plasticity can affect all levels of ecological organization through effects on demographic parameters, direct and indirect species interactions, such as competition, predation, and coexistence, and ultimately carbon and nutrient cycles.     

Environmental conditions influence the plant functional diversity effect on potential denitrification

Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD)) and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP). We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning.     

Evolution and applications of plant pathway resources and databases

Plants are important sources of food and plant products are essential for modern human life. Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. Considering these applications, database infrastructure for plant model systems deserves much more attention. Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology. In this article we review plant pathway databases and the resources that are currently available. We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration. We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems. We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.     

Three-dimensional chromatin organization in brain function and dysfunction

The three-dimensional (3D) organization of chromatin within the nucleus is now recognized as a bona fide epigenetic property influencing genome function, replication, and maintenance. In the recent years, several studies have revealed how 3D chromatin organization is associated with brain function and its emerging role in disorders of the brain. 3D chromatin organization plays a crucial role in the development of different cell types of the nervous system and some neuronal cell types have adapted unique modifications to this organization that deviates from all other cell types. In post-mitotic neurons, dynamic changes in chromatin interactions in response to neuronal activity underlie learning and memory formation. Finally, new evidence directly links 3D chromatin organization to several disorders of the brain. These recent findings position 3D chromatin organization as a fundamental regulatory mechanism poised to reveal the etiology of brain function and dysfunctions.     

Host-plant leaps versus host-plant shuffle: a global survey reveals contrasting patterns in an oligophagous insect group (Hemiptera,Psylloidea)

Global analyses of interspecific interactions are rapidly increasing our understanding of patterns and processes at large scales. Understanding how biodiversity assembles and functions on a global scale will increasingly require analyses of complex interactions at different ecological and phylogenetic levels. We present an analysis of host-plant associations in the sap-sucking Psylloidea (～3,800 species) using the most comprehensive assemblage of host data for this group compiled from 66?% of published records. Psyllids are known for high levels of host specificity and host switching between related plants at local scales, but a global survey implicates historical processes that are not entirely consistent with those at local scales. In particular, saltationary host switching events appear to have been a key factor explaining the wide but patchy distribution of psyllid host-plants throughout the angiosperm phylogeny. Alternative explanations involving co-diversification with subsequent extinction seem implausible. At the seed plant family level, we compare associations for psyllids with those of their relatives the aphids, but, despite notable differences in biogeographic distributions, find few plant families (2%) that host only psyllids but not aphids, while a much larger percentage (31%) host aphids but not psyllids, and 43% of plant families distributed throughout the plant phylogeny host neither group.