Research articles

The analysis of multiple SIV vaccine regimens in macaques leads to the identification of a key two-amino-acid signature that confers resistance to neutralizing antibodies; a similar mechanism of immune escape is shown to operate in HIV and may explain the limited efficacy seen in HIV vaccine trials.

A full genome sequence is presented of sugar beet Beta vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions.

A description of a new histone modification, methylation of glutamine, on histone H2A in yeast and human cells.

A molecular marker is required to monitor artemisinin-resistant Plasmodium falciparum parasites in southeast Asia; here mutations in K13-propeller are associated with artemisinin resistance in vitro and in vivo and also cluster in Cambodian provinces where resistance is prevalent.

Basal-plane dislocations, identified as fundamental defects in bilayer graphene by transmission electron microscopy and atomistic simulations, reveal striking size effects, most notably a pronounced buckling of the graphene membrane, which drastically alters the strain state and is of key importance for the material’s mechanical and electronic properties.

A complete genome sequence is presented of a female Neanderthal from Siberia, providing information about interbreeding between close relatives and uncovering gene flow events among Neanderthals, Denisovans and early modern humans, as well as establishing substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

Rare copy-number variants (CNVs) conferring risk of schizophrenia or autism affect fecundity of carriers in Iceland, and carriers of these CNVs who do not suffer disease or have not been diagnosed with intellectual disability show phenotypes in brain structure and cognitive abilities between those of non-carrier controls and patients with schizophrenia.

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.