Research articles

TDG is a member of the uracil DNA glycosylase family of DNA repair enzymes. It has been implicated in gene regulation but its biological functions have been unclear. Here, a knockout of the Tdg gene in mice reveals functions in embryonic development and in the maintenance of chromatin states.

Here, the full two-year Hubble Ultra Deep Field (HUDF09) data are used to conduct an ultra-deep search for z≈10 galaxies in the heart of the reionization epoch, only 500 million years after the Big Bang. One possible z≈10 galaxy candidate is found. It is also shown that regardless of source detections, the star formation rate density is much smaller (∼10%) at this time than it is just ∼200 million years later at z≈8. The 100–200 million years prior to z≈10 is clearly a crucial phase in the assembly of the earliest galaxies.

Circadian clocks are critical timing regulators of physiology and behaviour that are ubiquitous in eukaryotes. Most mechanistic models of the this clock are based on transcription cycles, but some evidence for post-translational regulation has recently surfaced in plants and cyanobacteria. This is one of two groups demonstrating a role for the oxidation of peroxiredoxin proteins in maintaining an entrainable oscillation in human red blood cells and a unicellular alga. These data indicate a role for non-transcriptional mechanisms in clock models and open the door to future work exploring the connections between the transcriptional and non transcriptional circadian machinery.

The Berezinskii–Kosterlitz–Thouless (BKT) phase transition, occurring in two-dimensional Bose gases, is expected to show an extended range of universal scaling behaviour in thermodynamic quantities; however, a clear demonstration of this 'critical' behaviour has remained elusive. Its existence is now confirmed through in situ density and density-fluctuation measurements of two-dimensional caesium Bose gases at different temperatures and interaction strengths.

A complex of RNA and protein known as the box C/D RNP catalyses the site-specific modification of RNAs with a 2′-O-methylation group. The structure of the full complex has now been solved, including the guide RNA and either of two substrate RNAs. This structure reveals how the guide and target RNAs are aligned, and how the methyltransferase subunit, fibrillarin, facilitates placement of the target ribose into the active site.

Basal lubrication — the input of melt water to the interface between glaciers or ice sheets and bedrock — is often thought to increase ice velocity. However, recent theoretical work illustrated how the development of efficient subglacial drainage associated with high melt-water input can lead to reductions in ice velocity. Now, satellite observations of ice velocity in Greenland are used to provide empirical support: although initial ice speed-up is similar in all years, warm years with high melt-water input experience a dramatic late summer slowdown, relative to warm years. The findings show that expectations of speed-up from basal lubrication alone cannot be assumed to cause net ice speed-up.

Bifidobacteria are natural inhabitants of the human gut and are known to provide protection from infection. It is now shown that certain features of bifidobacterial metabolism that ultimately lead to the production of acetate are involved in this effect.

The genome of the southeast Asian orang-utan has been sequenced. The draft assembly of a Sumatran individual alongside sequence data from five Sumatran and five Bornean orang-utan genomes is presented. The resources and analyses described offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Scanning probe techniques such as atomic force microscopy can be readily harnessed to prepare nanoscale structures with exquisite resolution, but are not in general suited for high-throughput patterning. Techniques based on contact printing, on the other hand, offer high throughput over large areas, but can't compete on resolution. Now, an approach is described that offers the best of both worlds: by attaching an array of hard, scanning-probe-like silicon tips to a flexible elastomeric substrate (similar to those used in contact printing), it is possible to rapidly create arbitrary patterns with sub-50-nm resolution over centimetre-scale areas.

Circadian clocks are critical timing regulators of physiology and behaviour that are ubiquitous in eukaryotes. Most mechanistic models of the this clock are based on transcription cycles, but some evidence for post-translational regulation has recently surfaced in plants and cyanobacteria. This is one of two groups demonstrating a role for the oxidation of peroxiredoxin proteins in maintaining an entrainable oscillation in human red blood cells and a unicellular alga. These data indicate a role for non-transcriptional mechanisms in clock models and open the door to future work exploring the connections between the transcriptional and non-transcriptional circadian machinery.

Genetic imprinting, or the preferential expression of a single parental allele, has typically been implicated as an influential factor during development, but whether unequal representation of one allele can influence social behaviour has not been studied. Here, it is demonstrated that the adaptor protein Grb10 is predominantly expressed from the paternal allele in brain and that ablating this allelic bias induces behavioural modifications of a social nature. At this time, Grb10 is unique in the sense that tissue-specific actions of each parental allele can influence distinct physiological or behavioural processes.

The standard view of the genome is that the two DNA strands are linked by Watson–Crick base pairing. Some deviations from this canonical pairing have been observed when DNA is bound to a ligand. This paper now shows that naked DNA itself can transiently adopt a Hoogsteen base-pairing arrangement. This excited state base pairing provides a means to expand the chemistry and structure of DNA, and has implications for the binding of proteins to and repair of DNA.

After learning, memories are strengthened through a process called 'consolidation', which requires new gene and protein expression, rendering new information less vulnerable to disruption. Several transcription factor families are involved in this process, but many of the relevant downstream targets are unknown. Here, IGF-II, a protein typically implicated in somatic tissue growth and repair, is identified as an essential factor in memory retention. IGF-II initiates its own network of signalling cascades that can lead to synaptic potentiation and are most effective within a short time frame immediately after learning. Thus, IGF-II represents an endogenous target for potentially modulating cognitive enhancement.

Fish can regenerate nephrons (the functional units of the kidney) de novo after kidney injury, whereas adult mammals lack this ability. This study identifies a pool of self renewing nephron stem/progenitor cells that are responsible for nephrogenesis during kidney growth and regeneration in zebrafish. The findings might provide an insight into how mammalian renal regeneration may be therapeutically activated.

Some chromosomal locations, known as common fragile sites, are predisposed to breakage. These sites have pathogenic relevance as they are frequently associated with chromosomal translocations. Here, it is found that rather than breakage being due to replication stalling, the fragility of site FRA3B results from an unusually low density of replication origins in this region. Unexpectedly, fragility is found to be cell-type-specific, which may have implications for current models of translocations.

This paper demonstrates a simple route for encoding a predetermined superstructure into the surface properties of colloidal spheres, enabling them to self-assemble into an intricate open crystalline lattice that is quite distinct from the close-packed periodic arrangements commonly encountered in colloidal crystals.

Supermassive black holes have been detected in all galaxies that contain bulge components. Bigger black holes are found in bigger bulges, implying that black-hole growth and bulge formation regulate each other. Reports of a similar correlation between black holes and the dark matter haloes suggest that unknown, exotic physics controls black-hole growth. Here it is shown that there is almost no correlation between dark matter and parameters that measure black holes unless the galaxy also contains a bulge. It is concluded that black holes do not correlate directly with dark matter, and that black holes coevolve only with bulges.

Using large-scale exome sequencing, this study identifies a second (after VHL) frequently mutated gene in clear cell renal cell carcinomas, the most frequent type of kidney cancer. PBRM1, a member of the SWI/SNF complex involved in transcriptional regulation, is mutated in about 40% of cases and shown to function as tumour suppressor gene. PBRM1 was independently found as a putative cancer gene involved in pancreatic cancer in a mouse transposon screen.

The masses of supermassive black holes are known to correlate with the properties of the bulge components of their host galaxies. In contrast, they appear not to correlate with galaxy disks. Disk-grown pseudobulges are intermediate in properties between bulges and disks. This paper reports pseudobulge classifications for a sample of nearby galaxies, and combines them with recent measurements of velocity dispersions in the biggest bulgeless galaxies to confirm that black holes do not correlate with disks, and that they correlate little or not at all with pseudobulges.

Spin ensembles, such as those used in liquid-state nuclear magnetic resonance, have been important for the development of quantum control methods. However, these demonstrations contained no entanglement, which is essential for a quantum information processor. This study reports the on-demand generation of entanglement between an ensemble of electron and nuclear spins in phosphorus-doped silicon, simultaneously creating 10¹⁰ spin pairs.