Letters in 2013

Here it is proposed that RNA viruses can adapt to use the antiviral properties of microRNAs to limit viral replication and suppress innate immunity in particular cell types, and this restriction can lead to exacerbation of disease severity.

A pulse of C/EBPα followed by overexpression of the transcription factors Oct4, Sox2, Klf4 and Myc leads to fast and very efficient reprogramming of B cell precursors to induced pluripotent stem cells; C/EBPα facilitates transient chromatin accessibility and accelerates expression of pluripotency genes through a mechanism that involves activation of the Tet2 enzyme.

The crystal structure of a ternary complex of the lentiviral accessory protein Vpx with the E3 ligase substrate adaptor DCAF1 and the HIV-1 restriction factor SAMHD1 shows how Vpx recruits SAMHD1 to the cell’s ubiquitination machinery.

The regularly spaced arrangement of plant organs around the stem known as phyllotaxis depends on auxin-based inhibitory fields; this study identifies another hormone-based inhibitory field downstream of auxin which is generated by movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 and regulates the periodicity of organ production.

Here a genome-wide RNAi library screen is used to identify components of the signalling pathway that allow transformation of Trypanosoma brucei spp., the protozoan parasite responsible for important human and livestock diseases in sub-Saharan Africa, from proliferative slender forms to arrested stumpy forms which are transmitted to the tsetse fly vector.

Global carbon budgets reveal that inland waters emit substantial amounts of carbon, which is believed to originate from the terrestrial biosphere; however, here the carbon emitted from the Amazon River system is shown to originate from temporary wetlands in the flooded area itself, such as flooded forests.

The bacteria responsible for causing tuberculosis in mammals and zebrafish are shown to preferentially recruit and infect permissive macrophages while evading microbicidal ones.

Here, the atomic structure of a virally encoded, cell-wall-spanning, DNA-translocating conduit from bacteriophage ΦX174 is described.

Despite a reduction in nutrient supply to the North Pacific subtropical gyre, it has undergone a recent increase in nitrogen fixation, and here records of nitrogen isotopes preserved in Hawaiian corals show that this is a trend that could be linked to climate change since the end of the Little Ice Age.

Understanding how RNA structure influences its function has been hampered by a lack of approaches that can accurately quantify RNA structure in vivo; here, RNA structure is revealed on a global scale and with nucleotide-level resolution, showing that there is less structure within cells than expected from in vitro and in silico analyses.

Primary cilia are known as specialized calcium signalling compartments on the cell surface, but the ionic permeability and other physiological properties of these protrusions are unknown—this is one of two studies identifying the ion channels that densely populate primary cilia, with direct measurements revealing cilia as a unique, functionally independent calcium signalling compartment that modulates hedgehog signalling pathways.

Unlike the tidal (in and out) breathing of mammals, bird lungs have unidirectional airflow patterns; here the savannah monitor lizard is shown to have unidirectional airflow too, with profound implications for the evolution of unidirectional airflow in reptiles, predating the origin of birds.

High-quality graphene is grown on copper and then transferred to the underlying substrate, typically silicon oxide or quartz, by simply etching away the copper; the graphene is held in place during etching by capillary bridges.

Fibroblasts constitute the major mesenchymal cell type in the connective tissue and their functions are remarkably diverse: here, by characterising lineages of mouse skin fibroblasts, it is shown that distinct subpopulations contribute to skin development and repair during injury.

Whole-exome sequencing reveals that a rare variant of phospholipase D3 (PLD3(V232M)) segregates with Alzheimer’s disease status in two independent families and doubles risk for the disease in case–control series, and that several other PLD3 variants increase risk for Alzheimer’s disease in African Americans and people of European descent.

A three-dimensional global climate model shows that the loss of a planet’s oceans through complete vaporization or evaporative escape to space will occur at considerably higher insolation than previously thought, owing to stabilizing atmospheric effects.

In adult mouse hippocampus, a learning-associated plasticity mechanism may exist that depends on the configuration of parvalbumin(PV)-expressing basket cell networks; trial and error learning initially promotes a higher fraction of cells with low PV expression, whereas learning completion promotes a higher fraction of cells with high PV expression, and these opposite configurations modulate learning and the underlying structural plasticity.

Primary cilia are known as specialized calcium signalling compartments on the cell surface, but the ionic permeability and other physiological properties of these protrusions are unknown—this is one of two studies identifying the ion channels that densely populate primary cilia, with direct measurements revealing cilia as a unique, functionally independent calcium signalling compartment that modulates hedgehog signalling pathways.

Strong, rapid adhesion between two hydrogels and even slices of animal tissue can be achieved at room temperature by using a silica nanoparticle solution as a ‘glue’.

Peptidoglycan is an essential structural component of the cell wall in the majority of bacteria, but the obligate intracellular human pathogen Chlamydia trachomatis was thought to be one of the few exceptions; here a click chemistry approach is used to label peptidoglycan in replicating C. trachomatis with novel d-amino acid dipeptide probes.