Distributed phenomics with the unPAK project reveals the effects of mutations

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.

Undergraduates Phenotyping Arabidopsis Knockouts in a Course-Based Undergraduate Research Experience: Exploring Plant Fitness and Vigor Using Quantitative Phenotyping Methods

We present a curriculum description, an initial student outcome investigation, and sample scientific results for a representative Course-Based Undergraduate Research Experience (CURE) that is part of the "Undergraduates Phenotyping Arabidopsis Knockouts" (unPAK) network. CUREs in the unPAK network characterize quantitative phenotypes of the model plant Arabidopsis from across environments to uncover connections between genotype and phenotype. Students in unPAK CUREs grow plants in a replicated block design and make quantitative measurements throughout the semester. This CURE enables students to answer plant science questions that draw from fields such as environmental science, genetics, ecology, and evolution. Findings indicate that this experience provides students with opportunities to make relevant scientific discoveries. Eighty percent of student datasets produced from the CURE met criteria for inclusion in the project database, indicative of student learning in data collection and analysis of quantitative plant traits. Student datasets uncovered novel effects of mutation on plant form. In addition, students' science self-efficacy increased as a result of course participation, and faculty feedback on course implementation was positive. We present unPAK as a new network that supports CUREs and research experiences focused on collecting biological data made publicly available to the scientific community. The unPAK CUREs can be tailored to address instructor interests or pedagogical needs while involving students in research investigating quantitative plant phenotypes.

MEASURING NATURAL SELECTION ON PHENOTYPIC PLASTICITY

To understand natural selection we need to integrate its measure across environments. We present a method for measuring phenotypic selection that combines the potential for both environmental variation and phenotypic plasticity. The method uses path analysis and a measure of selection that is analogous to selection on breeding values. For individuals growing in alternative environments, paths are created that represent potential changes in the environment. The probabilities for these changes are then multiplied by the path coefficients to calculate selection coefficients. Selection on plasticity is measured as the difference in selection within each environment. We illustrate these methods using data on selection in an experimental population of Arabidopsis thaliana. Individuals from 36 families were grown in one of four environments, a factorial combination of shaded/open and early/late shading. For final height of the inflorescence, there was positive selection in both the open and shaded environments and negative selection on plasticity of height. For bolting time, there was also positive selection in both environments, but no selection on plasticity. We show how to use this information to examine how selection would change with changes in environmental frequencies and their transition probabilities. These methods can be expanded to encompass continuous traits and continuous environments as well as other complexities of natural selection.

Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies

Root traits vary enormously among plant species but we have little understanding of how this variation affects their functioning. Of central interest is how root traits are related to plant resource acquisition strategies from soil. We examined root traits of 33 woody species from northeastern US forests that form two of the most common types of mutualisms with fungi, arbuscular mycorrhizas (AM) and ectomycorrhizas (EM). We examined root trait distribution with respect to plant phylogeny, quantifying the phylogenetic signal (K statistic) in fine root morphology and architecture, and used phylogenetically independent contrasts (PICs) to test whether taxa forming different mycorrhizal associations had different root traits. We found a pattern of species forming roots with thinner diameters as species diversified across time. Given moderate phylogenetic signals (K = 0.44-0.68), we used PICs to examine traits variation among taxa forming AM or EM, revealing that hosts of AM were associated with lower branching intensity (r PIC = -0.77) and thicker root diameter (r PIC = -0.41). Because EM evolved relatively more recently and intermittently across plant phylogenies, significant differences in root traits and colonization between plants forming AM and EM imply linkages between the evolution of these biotic interactions and root traits and suggest a history of selection pressures, with trade-offs for supporting different types of associations. Finally, across plant hosts of both EM and AM, species with thinner root diameters and longer specific root length (SRL) had less colonization (r PIC = 0.85, -0.87), suggesting constraints on colonization linked to the evolution of root morphology.

Experimentally reduced root-microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

BACKGROUND AND AIMS

Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous.

METHODS

To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations.

KEY RESULTS

Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10-20 %) and increased specific root length (approx. 10-30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples.

CONCLUSIONS

The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root trait variation, interactions with symbionts and recent progress in standardization of methods for quantifying root traits.

Circulating TNF alpha receptor levels identify older adults who fail to regain weight after acute weight loss

OBJECTIVE

Some healthy older adults have difficulty regaining weight after acute weight loss, and the reason for this failure to regain weight is unknown. The objective of this study was to determine if elevated leptin or pro-inflammatory cytokine levels are associated with failure to regain weight over two years after an acute weight loss intervention.

DESIGN

Two year prospective study after an acute weight loss intervention.

SETTING

University of Washington Medical Center from 2001-2006.

PARTICIPANTS

Nineteen older (≥ 70 years old) men and women.

MEASUREMENTS

Body weights, health status questionnaire, body composition data, serum leptin, glucose, insulin, C- reactive protein and pro-inflammatory cytokine levels were measured every six months for two years.

RESULTS

Five subjects out of 19 failed to regain weight after two years. The subjects who failed to regain weight after 2 years had higher circulating levels of tumor necrosis factor receptor particle 55 (TNFRp55) at baseline and at 6, 12, 18 and 24 months of follow up compared to subjects who regained weight after 2 years (P = 0.02 ).

CONCLUSION

Five out of 19 older subjects had difficulty regaining weight for up to 2 years following an acute weight loss intervention, and their TNFRp55 levels were persistently higher than in subjects who regained weight. Greater TNF α action, as reflected by higher circulating levels of TNFRp55, could be contributing towards inability of some older persons to regain weight after acute weight loss.

Leptin levels recover normally in healthy older adults after acute diet-induced weight loss

OBJECTIVES

Involuntary weight loss affects 20% of community dwelling older adults. The underlying mechanism for this disorder is unknown. Objective is to determine if failure of older persons to regain weight is associated with elevated pro-inflammatory cytokine and leptin levels.

DESIGN

Prospective diet intervention study.

SETTING

University of Washington Medical Center from 2001-2005.

PARTICIPANTS

Twenty-one younger (18-35 years old) and nineteen older (>or= 70 years old) men and women.

INTERVENTION

Each subject was placed for two weeks on a weight-maintaining diet, followed in sequence by 2 weeks of 30% caloric restriction, then 4 weeks of ad libitum food intake.

MEASUREMENTS

Plasma leptin levels, fasting serum pro-inflammatory cytokine levels, and peripheral blood mononuclear cell cytokine levels were measured.

RESULTS

Leptin levels in the two cohorts decreased after caloric restriction and increased after ad-libitum food consumption resumed. Plasma TNF alpha levels were higher in older subjects compared to younger adults. However, there was no association between changes in TNF alpha levels and changes in AUC leptin.

CONCLUSION

Leptin levels in healthy older individuals responded appropriately in a compensatory manner to changes in body weight. These data do not support a cytokine dependent elevation in leptin levels as being responsible for the failure of older adults to regain weight.

Phenotypic plasticity, costs of phenotypes, and costs of plasticity: toward an integrative view

Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic basis of plasticity. In this vein, microbial work is especially illuminating and has three additional strengths. First, information about the machinery underlying plasticity--such as structural and regulatory genes, sensory proteins, and biochemical pathways--helps link population-level studies with underlying physiological and genetic mechanisms. Second, microbial studies involve many generations, large populations, and replication. Finally, empirical estimation of key parameters (e.g., mutation rates) is tractable. Together, these allow for rigorous investigation of gene interactions, drift, mutation, and selection--all potential factors influencing the maintenance or loss of inducible traits along with phenotypic and plasticity costs. Messages emerging from microbial work can guide future efforts to understand the evolution of plastic traits in diverse organisms.

Indirect consequences of artificial selection on plasticity to light quality in Arabidopsis thaliana

Covariation between light quality- and photoperiod-mediated phenotypic plasticity was investigated using Arabidopsis thaliana. Three episodes of artificial selection were imposed on an index that quantified the plastic response to reduced red to far-red ratios (R:FR), with higher index values indicating greater plasticity. Relative to control lines, two high plasticity (HP) lines showed 1.6- and 2.4-fold increases in the index; low plasticity (LP) lines showed 1.4- and 1.1-fold decreases. A factorial experiment combining high and low R:FR conditions with long and short photoperiods assessed indirect consequences of selection on plasticity. Despite divergent R:FR-mediated plasticities in HP vs. LP lines, all four lines showed increases in photoperiod-mediated responses and decreases in mean leaf number. Complex relationships among trait means, plasticities and underlying mechanisms caution against generalizing about the genetic architecture of plastic traits. Partially independent developmental and evolutionary responses to R:FR and photoperiod are somewhat unsurprising, given this species' cosmopolitan nature.

Plasticity genes and plasticity costs: a new approach using an Arabidopsis recombinant inbred population

Earlier flowering is triggered by vernalization in some but not all Arabidopsis ecotypes, often reflecting allelic variation at the FRIGIDA (FRI) locus. Using a recombinant inbred (RI) population polymorphic at FRI, we examined fitness consequences of variation for plasticity. Flowering and fitness were scored for 68 RI genotypes following full and partial vernalization treatments. Within-environment and mixed-model anovas estimated variance components for a genotype effect and a G x E term, respectively. Selection analyses examined whether delayed bolting increases fitness; a plasticity costs analysis asked whether increased plasticity lowers fitness. We also explored whether trait QTL had environment-specific effects, colocated in the immediate vicinity of FRI, or overlapped with fitness QTL. Selection may favor fri alleles and constitutive early flowering, especially in conditions that only partially vernalize plants. Plasticity costs, detected only after partial vernalization and only marginally significant, were nonetheless consistent with FRI-FLC function. We discuss how information about QTL with environment-specific effects, fitness QTL, and knowledge about plasticity genes can improve interpretation of selection or plasticity cost analyses.

Phenotypic Integration and the Plasticity of Integration in an Amphicarpic Annual

In annual plants, including amphicarpic annuals, variation in light availability can evoke phenotypic plasticity in multiple traits. We examined plasticity to light availability of vegetative and reproductive performance traits in Amphicarpaea bracteata (Fabaceae) by developing and evaluating three path-analysis models using data from a greenhouse study. To assess whether light availability altered the phenotypic integration of these performance traits, we examined the models' fit to data collected within a high- or a low-light treatment. We also examined whether a single model or alternate models were required to fit data from the two contrasting light treatments. Using our path-analysis approach, we also made comparisons among three population types: shade- and sun-native populations of the widespread variety A. bracteata var. bracteata and sun-native populations of the variety A. bracteata var. comosa. Although each type of population was somewhat distinctive in patterns of integration and in the plasticity of integration, patterns did not correspond to contrasting ecological affinity, i.e., shade- and sun-native population types or to genetic relatedness of the two varieties. Counter to the prediction that selection regimes involving variation in one or more environmental factor favor intermediate levels of integration, phenotypic integration in A. bracteata was very flexible, with plasticity occurring in a trait-by-trait manner. In particular, there was an inverse relationship between aerial and subterranean reproductive modes in low but not high light. Previous studies of amphicarpic annuals have not observed this type of environment-specific life history trade-off.

Developmental phenotypic plasticity: where ecology and evolution meet molecular biology

The plastic response of phenotypic traits to environmental change is a common research focus in several disciplines-from ecology and evolutionary biology to physiology and molecular genetics. The use of model systems such as the flowering plant Arabidopsis thaliana has facilitated a dialogue between developmental biologists asking how plasticity is controlled (proximate causes) and organismal biologists asking why plasticity exists (ultimate causes). Researchers studying ultimate causes and consequences are increasingly compelled to reject simplistic, 'black box' models, while those studying proximate causes and mechanisms are increasingly obliged to subject their interpretations to ecological 'reality checks.' We review the successful multidisciplinary efforts to understand the phytochrome-mediated shade-avoidance and light-seeking responses of flowering plants as a pertinent example of convergence between evolutionary and molecular biology. In this example, the two-way exchange between reductionist and holist camps has been essential to rapid and sustained progress. This should serve as a model for future collaborative efforts towards understanding the responses of organisms to their constantly changing environments.