Research articles

One of two papers in this issue that reveal the prevalence of cryptic or hidden transcription in the yeast genome. Cryptic unstable transcripts (CUTs) are a major class of RNA polymerase II transcripts in budding yeast and are degraded immediately after being synthesized. In these papers, high-resolution genome analyses reveal that CUTs arise predominantly from promoter regions and in an antisense direction. There is therefore a widespread occurrence of inherently bidirectional promoters in yeast.

The transcriptomes of eukaryotic cells are unexpectedly complex, with virtually the entire non-repeat portions of many genomes being transcribed. Using deep sequencing, this study reveals that a remarkable breadth of RNA species that come from both within annotated genes and from unannotated intergenic regions in human cells. Many of these small RNAs possess cap structures and seem to be processed from mature mRNAs resulting in populations of long and short RNAs with capped 5' ends that coincide.

One of two papers in this issue that reveal the prevalence of cryptic or hidden transcription in the yeast genome. Cryptic unstable transcripts (CUTs) are a major class of RNA polymerase II transcripts in budding yeast and are degraded immediately after being synthesized. In these papers, high-resolution genome analyses reveal that CUTs arise predominantly from promoter regions and in an antisense direction. There is therefore a widespread occurrence of inherently bidirectional promoters in yeast.

This paper reports the unusual structure of the metabolite-sensing domain of a flavin mononucleotide (FMN)-specific riboswitch bound to FMN, riboflavin and an antibiotic. The relatively open ligand-binding pocket suggests that antimicrobials based on FMN could be devised.

Here it is shown that Hedgehog signalling is important in chronic myeloid leukaemia (CML), where it acts to maintain leukaemia stem cells by regulating the expression of Numb. CML stem cells can be depleted when Hedgehog signalling is inhibited, including cells that are resistant to the drug imatinib that is used to treat CML.

The Antarctic Peninsula is known to be warming rapidly, but the overall pattern of climate change for the full Antarctic continent has been uncertain. This work finds that the entire continent is warming at a rate of 0.12 ± 0.07 °C per decade, with stronger warming in winter and spring and over West Antarctica.

Aspergillus fumigatus is an opportunistic human pathogen in immunocompromised individuals and is associated with severe asthma and sinusitis, and has only been known to reproduce asexually. This paper now shows that it can reproduce sexually, for which isolates of complementary mating type are required.

Actin exists in two forms in cells. Monomeric globular actin (G-actin) polymerizes to form filamentous actin (F-actin), which drives several processes such as cell motility. This paper presents a high resolution structure of F-actin and describes the differences between the conformations of the two forms of actin.

Massive galaxies in the young universe (ten billion years ago) formed stars at surprising intensities. Although this is commonly attributed to violent mergers, the properties of many of these galaxies are incompatible with mergers. This paper reports that they are 'stream-fed galaxies', growing via steady, narrow, cold gas streams. Unlike destructive mergers, the smoother flows are likely to keep the rotating disc configuration intact.

This paper demonstrates a high-Q microcavity for surface plasmons that is fabricated by coating the surface of high-Q silica microresonator with a thin layer of noble metal. This structure enables room-temperature operation with a Q-factor of around 1380 in the near infrared for surface plasmon modes. The work also includes a coupling scheme where a tapered optical fibre is in near-contact with the cavity, which provides a convenient way for selectively exciting and probing confined plasmon modes.

Variations in the seasonal cycle of temperatures at the Earth's surface are spatially mapped on both land and sea, and trends in the recent past (1954–2007) are compared with those occurring earlier (1900–1954). Assuming that the earlier part of the temperature record is dominated by natural variations, the recent trends seem highly anomalous: temperatures on land show a shift to earlier seasons by 1.7 days, and the amplitude of the cycle has decreased in this period.

Functional magnetic resonance imaging (fMRI) of brain activity relies on the assumption that increases in local blood flow in the brain are directly correlated with the neuronal activity in that brain region. Using simultaneous direct recording and fMRI in monkeys, this study demonstrates that this is not the whole story; some of the fMRI signal does correspond to actual brain activity, but there is also increased blood flow in less active regions of the brain in anticipation of their employment in the near future.

The mitotic regulator Cdc14 is shown to mediate transcriptional silencing of yeast ribosomal genes by preventing the nucleolar localization of a subunit of RNA polymerase I. If ribosomal transcription is not shut down, the presence of transcripts prevents the loading of condensin and blocks chromosome condensation and segregation.

This paper shows that the protein AIM2 (absent in melanoma 2) is a receptor of cytoplasmic DNA and the double-stranded DNA vaccinia virus, and is a component of the inflammasome pathway for caspase-1 activation.

Using two-photon calcium imaging these authors map the response of nearly every neuron in a small region of the cat visual cortex, and find that the responses to ocular dominance and binocular disparity exist on defined axes within the brain that are independent and orthogonal to each other.

A range of plastic semiconductors have been developed that have the combination of physical and chemical properties required to enable printable electronic circuitry, but these are almost exclusively 'hole transporting' materials. If an electron-transporting equivalent could be found, it could be combined with the existing classes of materials to produce yet more powerful devices. This paper reports the development of a such a material: the electron-transporting plastic semiconductor exhibits unprecedented device performance, and is compatible with a broad range of printing and processing technologies.

In this paper AIM2 is shown to sense cytoplasmic DNA and to interact with ASC in activation of caspase-1.

This study uses a new fibre-optic method to record dendritic calcium signals in freely moving animals. The strength of a sensory stimulus is gradually encoded in somatosensory cortex neurons' dendrites, under the control of local inhibitory circuitry. The findings illustrate that the representation of sensory stimuli by cortical neurons cannot be fully described by traditional integrate-and-fire models.

Using quadruple whole-cell recordings, this study tested for synaptic connections among heterogeneous populations of cortical excitatory cells (pyramidal neurons), and found highly connected local circuits of neurons, each reflecting the neurons' long-range projections to a different brain region. The findings illustrate a diversity of dense cortical microcircuitry associated with the variety of information streams that produce our repertoire of behaviours and internal states.

Turbulent rotating convection controls many observed features in stars and planets, such as magnetic fields. It has been argued that the influence of rotation on turbulent convection dynamics is governed by the ratio of the relevant global-scale forces: the Coriolis force and the buoyancy force. This paper presents results from laboratory and numerical experiments which exhibit transitions between rotationally dominated and non-rotating behaviour that are not determined by this global force balance. Instead, the transition is controlled by the relative thicknesses of the thermal (non-rotating) and Ekman (rotating) boundary layers.