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Jim Henson's The Storyteller. Fairies
\"Showcases four enchanting tales of fairies and their mystical realms, inspired by the folklore from around the world and told in the spirit of Jim Henson's beloved television series\"--Page four of cover.
Book
Identification of metabolic networks by genetic co-essentiality analysis
In this Tools of the Trade article, Benjamin Jackson (at the Finley lab) describes the use of genetic co-essentiality analysis to interrogate the assembly of metabolic networks, fuelling discovery of new aspects of metabolism.
Journal Article
Bangkok dangerous
\"Original Bangkok Dangerous directors Danny and Oxide Pang return to familiar territory with this remake of their own popular 1999 thriller about a ruthless hitman (Nicolas Cage) who travels to Bangkok in order to carry out four crucial jobs. During the course of his missions, the triggerman falls in love with a pretty local girl while also forming a friendly bond with his young errand boy\"--Allmovie.com, viewed November 21, 2017.
DVD
Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site
It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state—maximum parsimony—is prone to misinference. Estimates of counts of sites that have a certain number of copies of the derived allele in a sample (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species using information from two outgroups while assuming simple models of nucleotide substitution. Here, we extend this approach to allow multiple outgroups (implemented for three outgroups), potentially any phylogenetic tree topology, and more complex models of nucleotide substitution. We find, however, that two outgroups and the Kimura two-parameter model are adequate for uSFS inference in most cases. We show that using parsimony to infer the ancestral state at a specific site seriously breaks down in two situations. The first is where the outgroups provide no information about the ancestral state of variation in the focal species. In this case, nucleotide variation will be underestimated if such sites are excluded. The second is where the minor allele in the focal species agrees with the allelic state of the outgroups. In this situation, parsimony tends to overestimate the probability of the major allele being derived, because it fails to account for the fact that sites with a high frequency of the derived allele tend to be rare. We present a method that corrects this deficiency and is capable of providing nearly unbiased estimates of ancestral state probabilities on a site-by-site basis and the uSFS.
Journal Article
Linking litter decomposition of above- and below-ground organs to plant-soil feedbacks worldwide
1. Conceptual frameworks relating plant traits to ecosystem processes such as organic matter dynamics are progressively moving from a leaf-centred to a whole-plant perspective. Through the use of meta-analysis and global literature data, we quantified the relative roles of litters from above-and below-ground plant organs in ecosystem labile organic matter dynamics. 2. We found that decomposition rates of leaves, fine roots and fine stems were coordinated across species worldwide although less strongly within ecosystems. We also show that fine roots and stems had lower decomposition rates relative to leaves, with large differences between woody and herbaceous species. Further, we estimated that on average below-ground litter represents approximately 33 and 48% of annual litter inputs in grasslands and forests, respectively. 3. These results suggest a major role for below-ground litter as a driver of ecosystem organic matter dynamics. We also suggest that, given that fine stem and fine root litters decompose approximately 1.5 and 2.8 times slower, respectively, than leaf litter derived from the same species, cycling of labile organic matter is likely to be much slower than predicted by data from leaf litter decomposition only. 4. Synthesis. Our results provide evidence that within ecosystems, the relative inputs of above-versus belowground litter strongly control the overall quality of the litter entering the decomposition system. This in turn determines soil labile organic matter dynamics and associated nutrient release in the ecosystem, which potentially feeds back to the mineral nutrition of plants and therefore plant trait values and plant community composition.
Journal Article
Plant secondary metabolites: a key driver of litter decomposition and soil nutrient cycling
1. A broad and diversified group of compounds, secondary metabolites, are known to govern species interactions in ecosystems. Recent studies have shown that secondary metabolites can also play a major role in ecosystem processes, such as plant succession or in the process of litter decomposition, by governing the interplay between plant matter and soil organisms. 2. We reviewed the ecological role of the three main classes of secondary metabolites and the methodological challenges and novel avenues for their study. We highlight emerging general patterns of the impacts of secondary metabolites on decomposer communities and litter decomposition and argue for the consideration of secondary compounds as key drivers of soil functioning and ecosystem functioning. 3. Synthesis. Gaining a greater understanding of plant–soil organisms relationships and underlying mechanisms, including the role of secondary metabolites, could improve our ability to understand ecosystem processes. We outline some promising directions for future research that would stimulate studies aiming to understand the interactions of secondary metabolites across a range of spatio-temporal scales. Detailed mechanistic knowledge could help us to develop models for the process of litter decomposition and nutrient cycling in ecosystems and help us to predict future impacts of global changes on ecosystem functioning.
Journal Article
Detecting positive selection in the genome
Population geneticists have long sought to understand the contribution of natural selection to molecular evolution. A variety of approaches have been proposed that use population genetics theory to quantify the rate and strength of positive selection acting in a species’ genome. In this review we discuss methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data. We also discuss recently proposed methods to detect positive selection from a population’s haplotype structure. The application of these tests has resulted in the detection of pervasive adaptive molecular evolution in multiple species.
Journal Article
A non-canonical tricarboxylic acid cycle underlies cellular identity
The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity
1
,
2
. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.
A non-canonical tricarboxylic acid cycle is required for changes in cell state.
Journal Article
Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits
There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa). The composition of all soil community groups was affected by plant species identity, both in monocultures and in mixed communities. Moreover, plant community composition predicted additional variation in soil community composition beyond what could be predicted from soil abiotic characteristics. In addition, analysis of the field aboveground plant community composition and the composition of plant roots suggests that plant community attributes are better predictors of soil communities than root distributions. However, neither plant phylogeny nor plant traits were strong predictors of soil communities in either experiment. Our results demonstrate that grassland plant species form specific associations with soil community members and that information on plant species distributions can improve predictions of soil community composition. These results indicate that specific associations between plant species and complex soil communities are key determinants of biodiversity patterns in grassland soils.
Journal Article
Global relationship of wood and leaf litter decomposability: the role of functional traits within and across plant organs
AIM: Recent meta‐analyses have revealed that plant traits and their phylogenetic history influence decay rates of dead wood and leaf litter, but it remains unknown if decay rates of wood and litter covary over a wide range of tree species and across ecosystems. We evaluated the relationships between species‐specific wood and leaf litter decomposability, as well as between wood and leaf traits that control their respective decomposability. LOCATION: Global. METHODS: We compiled data on rates of wood and leaf litter decomposition for 324 and 635 tree species, respectively, and data on six functional traits for both organs. We used hierarchical Bayesian meta‐analysis to estimate, for the first time, species‐specific values for wood and leaf litter decomposability standardized to reference conditions (k*wₒₒd and k*ₗₑₐf) across the globe. With these data, we evaluated the relationships: (1) between wood and leaf traits, (2) between each k* and the selected traits within and across organs, and (3) between wood and leaf k*. RESULTS: Across all species k*wₒₒd and k*ₗₑₐf were positively correlated, phylogenetically clustered and correlated with plant functional traits within and across organs. k* of both organs was usually better described as a function of within‐ and cross‐organ traits, than of within‐organ traits alone. When analysed for angiosperms and gymnosperms separately, wood and leaf k* were no longer significantly correlated, but each k* was still significantly correlated to the functional traits. MAIN CONCLUSIONS: We demonstrate important relationships among wood and leaf litter decomposability as after‐life effects of traits from the living plants. These functional traits influence the decomposability of senesced tissue which could potentially lead to alterations in the rates of biogeochemical cycling, depending on the phylogenetic structure of the species pool. These results provide crucial information for a better representation of decomposition rates in dynamic global vegetation models.
Journal Article