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RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.

Lianas are a key growth form in tropical forests. They are believed to be strong competitors for water, thanks to their presumed efficient vascular systems. However, despite being a large polyphyletic group, they are currently often considered as a functionally homogeneous entity. In this study, we challenged this assumption by estimating the variability in hydraulic traits of two common, co-occurring liana species in a water-limited environment, namely, a seasonally dry tropical forest in Costa Rica. We measured vulnerability to embolism at the leaf and branch levels using two different methods (optical and acoustic vulnerability) and found that both species had very different hydraulic properties. Compared to reported P50 values in literature, we found two extreme P50 values: a low value for Bignonia diversifolia (−4.30 ± 0.54 MPa at the leaf level; −7.42 ± 0.54 MPa at the branch level) and a high value for Cissus microcarpa (−1.07 ± 0.14 at the leaf level; −1.20 ± 0.05 MPa at the branch level). Furthermore, B. diversifolia had a higher apparent modulus of elasticity in the radial direction (556.6 ± 401.0 MPa) and a variable midday water potential. On the other hand, C. microcarpa had a low apparent modulus of elasticity in the radial direction (37.8 ± 26.3 MPa) and a high branch water content, which enabled the species to keep its water potential stable during the dehydration experiments and during a drought period in the field. This mechanism may enable this species to coexist with species that are more resistant to drought-induced embolisms such as B. diversifolia. Although only two species were studied, considerable overlap was found between the range of hydraulic properties of trees growing in the same location and trees and lianas growing in two forests in Panama. These findings demonstrate that lianas cannot be considered as a homogeneous group and call for further research into the intra-growth form diversity of liana properties.

Essays are a traditional component of the course requirements in many post-secondary courses. However, the practical and pedagogical disadvantages of essays are significant. These include the increasing ease with which essays can be plagiarized, the lack of peer involvement in the traditional essay submission and feedback process, the usual lack of meaningful instructor-student intellectual discourse in the essay development and feedback process, and the inability to include hyperlinks and non-text media in essays submitted on paper. It is suggested that as instructors make the transition from traditional to blended/online instruction, they consider jettisoning the traditional essay requirement and replace it with some form of "assignment essay/peer review" system such as the one described. Contemporary Learning Management Systems facilitate peer review and peer assessment approaches in ways that were not available in traditional offline education. This paper describes and discusses an online assignment system utilizing peer commentaries that addresses many of the shortcomings of these traditional essay requirement. The system is modeled after peer commentary academic journals such as "Behavioral and Brain Sciences" and "Current Anthropology". This system has successfully been used as a substitute for the traditional essay requirement in a number of third year psychology course sections platformed on both Moodle and Blackboard. The advantages, challenges and practicalities of instituting, managing and grading such peer-reviewed assignments are outlined, and the benefits of the system in terms of student engagement, intellectual modeling, and learning community enhancement are discussed. The peer reviewed assignment system is discussed in the context of recent research indicating some advantages of blended learning approaches compared to traditional approaches. Criticisms of peer feedback approaches are examined, and instructors are encouraged to provide students with detailed instructions and criteria regarding the peer review process. It is hoped that the discussion will be particularly useful to instructors who are in the process of moving from traditional face-to-face course context to the blended/online education environment. (Contains 10 figures.)

Over the past two decades, comparative sequence analysis using codon-substitution models has been honed into a powerful and popular approach for detecting signatures of natural selection from molecular data. A substantial body of work has focused on developing a class of “branch-site” models which permit selective pressures on sequences, quantified by the ω ratio, to vary among both codon sites and individual branches in the phylogeny. We develop and present a method in this class, adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion. By applying models of different complexity to different branches in the phylogeny, aBSREL delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster. Based on simulated data analysis, we offer guidelines for what extent and strength of diversifying positive selection can be detected reliably and suggest that there is a natural limit on the optimal parametric complexity for “branch-site” models. An aBSREL analysis of 8,893 Euteleostomes gene alignments demonstrates that over 80% of branches in typical gene phylogenies can be adequately modeled with a single ω ratio model, that is, current models are unnecessarily complicated. However, there are a relatively small number of key branches, whose identities are derived from the data using a model selection procedure, for which it is essential to accurately model evolutionary complexity.

We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites subject to episodic positive selection on any foreground branches. We compare BUSTED with existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted, with a widget allowing the interactive specification of foreground branches.

Scientific literacy is an important educational and societal goal. Measuring scientific literacy, however, has been problematic because there is no consensus regarding the meaning of scientific literacy. Most definitions focus on the content and processes of major science disciplines, ignoring social factors and citizens’ needs. The authors developed a definition of scientific literacy for the California 4-H Program from the citizen's perspective, concentrating on real-world science-related situations. The definition includes four anchor points: science content; scientific reasoning skills; interest in and attitudes toward science; and contribution through applied participation. The definition provides the California 4-H Science, Engineering, and Technology Initiative with a framework for future science curriculum and program development and implementation, educator professional development, and evaluation.

Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.