Research articles

Platypuses are monotremes and combine aspects of both reptilian and mammalian behaviour. An international consortium reports the genome sequence and analysis of Ornithorhynchus anatinus and as expected, parts of the genome look more like mammals, whereas other parts more like reptiles or even chickens.

A complete three-dimensional branching pattern and lineage of the mouse bronchial tree, reconstructed from an analysis of hundreds of developmental intermediates, is described. The branching process is stereotyped and generated by three simple modes of branching used in three different orders throughout the lung.

Leukocyte migration over two-dimensional surfaces is dependent on the integrin family of adhesion receptors, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In this study, all integrin heterodimers from mouse leukocytes were ablated and it is shown that integrins are not required for migration in 3D environments, in vitro and in vivo. Such non-adhesive migration renders leukocytes autonomous from the tissue environment.

This paper examines eight individual genomes using a clone-based sequencing approach, for structural variants of 8,000 nucleotides or more. One of the first high-quality inversion maps for the human genome is generated, and it is demonstrated that previous estimates of variation of this sort have been too high.

Base lesions can be directly repaired by oxidative dealkylation catalysed by AlkB in bacteria and by ABH2/ABH3 in man. Several structures of AlkB and ABH2 bound to dsDNA are solved. These structures reveal why AlkB prefers ssDNA to dsDNA substrates, and how ABH2 differs structurally, to allow it to repair dsDNA.

Increased volatility of exploited fish stocks is due to amplified nonlinear behaviour caused by fishing. This paper shows how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.

The first large-scale rewiring of a gene regulatory network (that of Escherichia coli) reveals that more than 95% of transcription site swaps are harmless, with many actually beneficial in several culture conditions. The results will help understanding how genomes tolerate pervasive shuffling of DNA segments during evolution.

This paper reports data of shot noise generated by the 5/2 fractional state in an ultraclean two-dimensional electron gas that compellingly points in the direction of the e/4 quasiparticles. It is believed that this observation is a first step towards understanding new fractional charges.

Current debate on the selection of strains for the influenza vaccine highlights the need for epidemiological understanding of human influenza A virus. This paper analyses genomic sequences from global viral isolates, and hypothesizes that the virus follows a 'sink-source' model, where new lineages keep arising from some areas and dying out in other areas.

A map of nucleosome positions across the Drosophila genome reveals a chromatin organization that can be compared with that of budding yeast. The Drosophila nucleosome distribution pattern indicates that RNA polymerase II can access the transcription start site of active genes unimpeded by nucleosomes, but there is a nucleosome positioned at the site where the polymerase pauses.

Epithelial cells sort proteins into apical and basolateral domains. Clathrin plays a key and selective role in the generation of basolateral protein polarity. These results demonstrate an important role of clathrin in sorting of proteins at the trans-Golgi network.

Fungal Pdr1p family proteins bind directly to diverse drugs and xenobiotics, resulting in activation of transcription and induction of multidrug resistance. The mechanism has analogy to regulation of multidrug resistance in vertebrates by nuclear receptors.

A newly discovered mechanism for synaptic plasticity whereby higher-order information can be stored in the forward propagation of local dendritic branch spikes is described. It is reported that coupling between branches and the soma is not static as previously thought, but that an associative form of branch plasticity allows neurons to encode the spatio-temporal correlation of inputs.

The antiangiogenic effect of siRNAs does not depend on the target of the siRNA, or on intraocular administration. Rather, the siRNAs activate TLR3, a cell surface receptor for long viral dsRNAs, and innate immunity.

The aryl hydrocarbon receptor (AHR) is the cellular receptor for a number of environment contaminants. It is shown here to induce regulatory T cells when bound to the ligand TCCD and promote T_H17 differentiation when bound to FICZ.

The beetle Tribolium castaneum is a commonly used laboratory model, combining the ease of systematic RNAi experiments like those in Caenorhabditis elegans, with biology that is more representative of most insects than Drosophila melanogaster. A large consortium has sequenced and analysed the genome of the red flour beetle, creating a resource for biologists everywhere.

Some refractory rocks from the ultra-slow spreading Gakkel ridge (Arctic Ocean) have model ages up to 2 billion years, implying the long-term preservation of refractory domains in the asthenospheric mantle rather than their erasure by mantle convection. It is suggested that the upwelling mantle beneath mid-ocean ridges is highly heterogeneous, which make its composition difficult to be constrained by mid-ocean ridge basalts alone.

This paper examines the changes in gene expression during the first exposure to a long day (such as those found in spring) in Japanese quails and find that two waves of genes are induced as part of the photoperiodic response. This paper also identifies thyrotrophin expression in the pars tuberalis as a critical event in triggering this photoperiodic response.

A computational protein design was used to generate eight enzymes that were able to catalyse the Kemp elimination, a model reaction for proton transfer from carbon. Directed evolution was used to enhance the catalytic activity of the designed enzymes, demonstrating that the combination of computational protein design and directed evolution is a highly effective strategy to create novel enzymes.

A study that combines in vivo systems neuroscience with synaptic physiology and Drosophila genetics identifies a presynaptic form of lateral inhibition in the olfactory system. The mechanism allows for a flexible form of gain control, which promotes coding efficiency when stimuli are strong and unambiguous, but maximizes sensitivity when stimuli are weak and ambiguous.