The landscape of Arabidopsis tRNA aminoacylation.

The function of transfer RNAs (tRNAs) depends on enzymes that cleave primary transcript ends, add a 3' CCA tail, introduce post-transcriptional base modifications, and charge (aminoacylate) mature tRNAs with the correct amino acid. Maintaining an available pool of the resulting aminoacylated tRNAs is essential for protein synthesis. High-throughput sequencing techniques have recently been developed to provide a comprehensive view of aminoacylation state in a tRNA-specific fashion.

Deep, hot, ancient melting recorded by ultralow oxygen fugacity in peridotites.

The oxygen fugacity (f) of convecting upper mantle recorded by ridge peridotites varies by more than four orders of magnitude. Although much attention has been given to mechanisms that drive variations in mantle f between tectonic settings and to comparisons of f between modern rocks and ancient-mantle-derived rocks, comparatively little has been done to understand the origins of the high variability in f recorded by peridotites from modern mid-ocean ridge settings. Here we report the petrography and geochemistry of peridotites from the Gakkel Ridge and East Pacific Rise (EPR), including 16 new high-precision determinations of f.

How do bacterial endosymbionts work with so few genes?

The move from a free-living environment to a long-term residence inside a host eukaryotic cell has profound effects on bacterial function. While endosymbioses are found in many eukaryotes, from protists to plants to animals, the bacteria that form these host-beneficial relationships are even more diverse. Endosymbiont genomes can become radically smaller than their free-living relatives, and their few remaining genes show extreme compositional biases.

Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss.

The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs.

Aminoacyl-tRNA Synthetase Evolution within the Dynamic Tripartite Translation System of Plant Cells.

Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria.

Incompatibility and Interchangeability in Molecular Evolution.

There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities.

Outcomes of Parent-Child Interaction Therapy (PCIT) for families presenting with child maltreatment: A systematic review.

Background: The developmental consequences of childhood trauma for young children are extensive and impact a diverse range of areas. Young children require treatments that consider their developmental stage and are inclusive of caregiver involvement. Parent-Child Interaction Therapy (PCIT), with its dyadic focus and developmental sensitivity, is uniquely positioned to offer therapeutic support to young children and their families.

Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss.

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs.

Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs.

Although tRNA structure is one of the most conserved and recognizable shapes in molecular biology, aberrant tRNAs are frequently found in the mitochondrial genomes of metazoans. The extremely degenerate structures of several mitochondrial tRNAs (mt-tRNAs) have led to doubts about their expression and function. Mites from the arachnid superorder Acariformes are predicted to have some of the shortest mt-tRNAs, with a complete loss of cloverleaf-like shape.

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification.

Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies.

Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria.

Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol.

CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis.

The function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins.

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts.

Genomic datasets sometimes support conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (=concatenation) approach, several methods that measure the distribution of support and conflict among loci were introduced over 15 years ago.

Cytonuclear integration and co-evolution.

The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes.

Size effects resolve discrepancies in 40 years of work on low-temperature plasticity in olivine.

The strength of olivine at low temperatures and high stresses in Earth's lithospheric mantle exerts a critical control on many geodynamic processes, including lithospheric flexure and the formation of plate boundaries. Unfortunately, laboratory-derived values of the strength of olivine at lithospheric conditions are highly variable and significantly disagree with those inferred from geophysical observations. We demonstrate via nanoindentation that the strength of olivine depends on the length scale of deformation, with experiments on smaller volumes of material exhibiting larger yield stresses.

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes.

Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation.

Olivine anisotropy suggests Gutenberg discontinuity is not the base of the lithosphere.

Tectonic plates are a key feature of Earth's structure, and their behavior and dynamics are fundamental drivers in a wide range of large-scale processes. The operation of plate tectonics, in general, depends intimately on the manner in which lithospheric plates couple to the convecting interior. Current debate centers on whether the transition from rigid lithosphere to flowing asthenosphere relates to increases in temperature or to changes in composition such as the presence of a small amount of melt or an increase in water content below a specified depth.

Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions.