Articles in 2013

The authors show that photosynthetically derived glucose drives target-of-rapamycin signalling, resulting in transcriptional reprogramming of genes involved in cell cycle regulation.

Absorption of target molecules into a porous matrix permits single-crystal X-ray diffraction analysis of the ‘guest’ molecules, avoiding the need to obtain them in single-crystal form and making analysis possible using as little as 80 nanograms of sample.

Crystal structures of mammalian CRY2, one of the cryptochrome flavoproteins that have light-independent functions at the core of the circadian clock, show that it binds FAD dynamically and that the F-box protein FBXL3 captures CRY2 by occupying its FAD-binding pocket and burying its PER-binding interface.

Genome sequences of human-infective tapeworm species reveal extreme losses of genes and pathways that are ubiquitous in other animals, species-specific expansions of non-canonical heat shock proteins and families of known antigens, specialized detoxification pathways, and metabolism that relies on host nutrients; this information is used to identify new potential drug targets.

A new approach to magnetic resonance, ‘magnetic resonance fingerprinting', is reported, which combines a data acquisition scheme with a pattern-recognition algorithm that looks for the ‘fingerprints’ of interest within the data.

The authors describe how the eukaryotic replicative helicase is recruited to origins and reveal a novel ATPase-dependent quality control mechanism.

Inactivating the CLP1 RNA kinase in mice leads to a progressive loss of motor neurons, through a mechanism related to the accumulation of a novel set of small RNA fragments derived from aberrant processing of tyrosine pre-transfer RNA.

A population epigenomic analysis of wild Arabidopsis thaliana accessions is presented, obtained by sequencing their whole genomes, methylomes and transcriptomes; thousands of DNA methylation variants are identified, some of which are associated with methylation quantitative trait loci.

A global view of the genetic networks regulating the differentiation of T_H17 cells is presented, based on temporal expression profiling, computational network reconstruction and validation of predicted interactions by nanowire-mediated siRNA perturbation.

The identification of pathogenic mutations within prion-like domains (PrLDs) of the RNA-binding proteins hnRNPA2B1 and hnRNPA1 add to our understanding of how mutations in these proteins lead to degenerative disease, and highlight the potential importance of PrLDs in degenerative diseases of the nervous system, muscle and bone.

A new method to trace the lineage of slow cycling label-retaining cells (LRCs) in vivo identifies a population of LRCs that have features of committed Paneth cells but still express stem-cell markers such as Lgr5; the slow cycling cells differentiate into Paneth cells without cell division, but after injury can also repopulate the stem-cell niche and contribute to the regeneration of all intestinal lineages.

Biochemical, functional and computational analyses are combined to show that circular RNAs are a large class of animal RNAs with regulatory potency.

The auditory response of song premotor HVC neurons in sleeping birds, and HVC activity in singing birds, is synchronized with particular moments of vocal motor movements as defined by a dynamical systems model of song production; this HVC activity could be used as a ‘forward’ model to predict behaviour and evaluate feedback.

Cryo-electron microscopy structures of key intermediates during the sequential assembly of the pre-initiation complex are presented; structures of the closed and open-promoter complexes allow insights into the process of promoter melting.

Multi-electrode cortical recordings during the production of different consonant-vowel syllables reveal distinct speech-articulator representations that are arranged somatotopically, with temporal and spatial patterns of activity across the neural population corresponding to phonetic features and dynamics.

The atomic-resolution structure of the entire respiratory complex I is reported, with the resolution high enough to map out the locations and orientations of nearly all amino-acid side chains—some of which link to human neurodegenerative diseases—and reveals which amino-acid interactions take place at the hydrophilic domain–membrane domain interface.

Intracellular membrane potential changes are measured directly in mouse grid cells during navigation along linear tracks in virtual reality; the recordings reveal that slow ramps of depolarization are the sub-threshold signatures of firing fields, as in attractor network models of grid cells, whereas theta oscillations pace action potential timing.

Autophagy is shown to be an essential mechanism that protects haematopoietic stem cells from metabolic stress; the transcription factor FOXO3A maintains a pro-autophagy gene expression program that poises haematopoietic stem cells to rapidly mount a protective autophagic response upon metabolic stress.

Systematic sampling along the Marion Rise of the Southwest Indian Ridge reveals that its crust is discontinuous and thin, indicating that the rise is supported by low-density depleted mantle beneath it.

The crystal structure of a complete yeast exosome (Exo-10) bound to a region of the Rrp6 nuclease and an RNA substrate is determined, demonstrating that the exosome binds and degrades RNA molecules with a channelling mechanism that is largely conserved in all kingdoms of life and is similar to the mechanism used by the proteasome to degrade polypeptides.