Volume 456 Issue 7224, 18 December 2008

Europe needs a better way to plan, prioritize and fund the next generation of research infrastructure.

Could the United States topple Europe as the driver of international climate-change regulations?

Nature's manuscript editors made a selection of 'favourites' from the papers we published in 2008.

The year in which …

Minor progress in Poland on adaptation and deforestation sets the stage for Copenhagen in 2009.

Heavy industry wins key concessions in last-minute negotiations.

Obama appointments likely to focus on renewable energy and implementing cap and trade.

Microscopy tracks living cells as they move through the body.

Outcry as stem-cell agency puts chairman on the payroll.

This gallery showcases some of the year's most eye-catching science, from a close encounter with squid suckers that look like a carnivorous cartoon choir to mathematical forms given shape in purple yarn. It also recalls some of the biggest science news stories: the staggering devastation wrought by Hurricane Ike; a Nobel prize for putting a glowing protein to work; and the ongoing robotic exploration of Mars.

Medals, cash and fame rained down on the heads of prominent scientists in 2008. Ashley Yeager rounds up some of them.

He did more than anyone to build the Large Hadron Collider. This year he saw it finished -- and then break down. Geoff Brumfiel profiles the LHC's project leader, Nature's newsmaker of the year.

Not all problems will yield to technology. Deciding which will and which won't should be central to setting innovation policy, say Daniel Sarewitz and Richard Nelson.

Stephen Jay Gould's idea of evolution by bursts was controversial. But it gave the field of palaeontology a long-overdue boost, explains Steve Jones.

A sixteenth-century Dutch master's carefully orchestrated winter landscape may have benefited from his knowledge of geographers' techniques of the time, explains Martin Kemp.

The movement of people into societies that offer a better way of life is a more powerful driver of cultural evolution than conflict and conquest, say Peter J. Richerson and Robert Boyd.

The spliceosome is best known for shepherding primary messenger RNA transcripts to maturity. This enzyme complex also contributes to the synthesis of an enzyme that maintains chromosome ends.

Before picking up the phone and calling a technician to fix a faulty microwave oven, there are always a few simple things one should check. So far, “stop looking at it” has not been part of the checklist.

Daily remodelling of histone proteins underlies interactions between circadian clock genes and metabolic genes. This regulatory mechanism could be widespread, affecting other physiological processes.

Some transition-metal catalysts control organic reactions so that, given a choice of two mirror-image products, only one forms. The metal atom in these catalysts has been ignored as a source of control — until now.

Everyone carries some baggage they would like to lose. For the histone protein H3, that baggage is a chunk of its tail, which when clipped off affects the expression of genes with which the histone is associated.

The frustration that atomic interactions can undergo is not unlike that occurring when human aims are thwarted. An elegant study offers a way of visualizing the hitherto mysterious dynamics of 'frustrated' systems.

An analysis of neuronal proteins reveals that many are regulated through covalent attachment of the lipid palmitate. This reversible modification seems to affect the form and function of synaptic junctions.

In drought conditions, forest soils can serve as a small but surprisingly persistent sink for the greenhouse gas nitrous oxide. The effect highlights a research avenue necessary for predicting Earth's climate.

Geometric frustration arises when lattice structure prevents energetic interactions between neighbouring particles to be minimized, leading to complex phases of matter. This paper reports a simple geometrically frustrated system composed of closely packed colloidal spheres confined between parallel walls. Because the diameter of the spheres is tunable, the system provides a unique means to directly visualize the dynamics of frustration, thermal excitations and defects.

A proteomics study unveils a large collection of proteins that get reversibly palmitoylated in response to neuronal activity — the neuronal palmitoyl-proteome. In particular, this study focuses on the discovery of a brain-specific isoform of the small GTPase Cdc42, whose unexpected palmitoylation specifically affects dendritic spine morphogenesis in response to neuronal activity. These findings identify palmitoylation as a key modifiable signal on many synapse-enriched proteins that contribute to activity-driven changes in synapse morphology and function.

This work identifies the spliceosome, which normally excises introns from mRNAs, as being responsible for generating the 3′ end of TER. It does so by performing a site-specific cleavage reaction that previously had not been observed for the spliceosome.

When damaged DNA is replicated, gaps can be left behind in the replicated DNA. Two processes, recombinational repair or post-replication repair (PRR), were thought to act independently in gap filling. This study defines how the error-free branch of PRR is involved in lesion bypass and finds that when the replicative clamp PCNA is SUMO modified, Rad18 and Rad5 are able to promote polyubiquitination of PCNA.

The structure of a thermophilic Ago protein bound to a duplex nucleic acid that mimics the interaction of the single-strand of the small RNA and the target mRNA has been solved. This structure reveals the conformational changes that are necessary to accommodate the target, and the changes that occur in the vicinity of the site of cleavage.

This paper reports the discovery of a water maser at redshift 2.64 in the dust- and gas-rich gravitationally lensed type-1 quasar MG J0414+0534. Using the locally determined luminosity function, the probability of finding a maser this luminous associated with any single active galaxy is 10⁻⁶, leading to the conclusion that the volume densities and luminosities of masers are higher at that epoch.

A new family of superconductors containing layers of iron arsenide has attracted considerable interest because of their high transition temperatures and similarities with the high-T_c copper oxide superconductors. This paper reports inelastic neutron scattering observations of a magnetic resonance below T_c in Ba_0.6K_0.4Fe₂As₂, demonstrating that the superconducting energy gap has unconventional symmetry.

This paper discloses a new class of chiral catalysts that initiate olefin metathesis with exceptional efficiency and enantioselectivity. These new catalysts bear a stereogenic metal centre and carry only monodentate ligands; the molybdenum-based complexes are rendered non-racemic by a stereoselective ligand exchange process involving an enantiomerically pure aryloxide, a class of ligands rarely used in asymmetric catalysis.

This study presents a global analysis of seafloor roughness derived from marine gravity data and finds that residual roughness anomalies remain over large swaths of ocean floor. The Atlantic ocean floor that formed over mantle previously overlain by the Pangaea supercontinent displays anomalously low roughness, and attribute this observation to a sub-Pangaean supercontinental mantle temperature anomaly leading to slightly thicker than normal Atlantic crust. In contrast, ocean crust formed above Pacific superswells is not associated with basement roughness anomalies.

Phylogeny-driven reconstructions of ancestral protein sequences have predicted that the last universal common ancestor (LUCA) was a thermophile, but analyses of ribosomal RNA sequences suggested that LUCA preferred a cooler environment. rRNA and protein sequences are used to show that thermotolerance initially increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and Archaea–Eukaryota, and then subsequently decreased.

Several species are observed to expand their habitat range towards cooler, higher latitude environments as a result of climate warming. It is shown that plant migrations can lead to successful invasions due to their relatively low susceptibility to native soil pathogens and herbivores.

In Drosophila more than 95% of the genes have remained on the same chromosome arm in 12 species that diverged 63 Myr ago.

This study finds that only a quarter of D. melanogaster Y linked genes are also Y-linked in these 12 species. Gene losses are known to play a major role in the evolution of Y chromosomes, but this study shows that in contrast with the mammalian Y, gene gains play an important role in the evolution of the Drosophila Y chromosome.

Neural circuits in the visual cortex are immature at birth, and require exposure to visual stimuli to form the connections and selectivity of the mature visual system. It has been unclear how stimulus-driven neural activity guides the emergence of properties such as direction selectivity. This paper tracks this process with a combination of intrinsic and two-photon calcium imaging in visually naive ferrets. After exposing the animals to stimuli moving along one single axis of motion, it is found that selectivity for those directions emerges rapidly as well as the local organization of direction preference between neighbouring cells.

This paper studies a phenomenon called contact inhibition of locomotion, whereby fibroblast cells grown in cell culture retract their protrusions and change their direction on contact. It is shown that this occurs in vivo, and the molecular basis is revealed. Neural crest cells, highly migratory cells of embryonic origin, exhibit contact inhibition of locomotion both in vivo and in vitro, which accounts for their directional migration. However, when a neural crest cell meets another cell type, it fails to display contact inhibition of locomotion, allowing it to invade the tissue.

The polar transport of the plant hormone auxin is dependent on the localization of its efflux carriers called PINs, but the mechanism mediating polarity of PIN proteins within cells remains unclear. This study suggests a two-step mechanism generating PIN polarity. PINs are first targeted to the plasma membrane in a non-polar manner, and polarity is established in subsequent step involving internalization and recycling. Interference with endocytosis results in the loss of PIN polarity leading to a perturbation in auxin gradients.

Whether G proteins have a role in hedgehog (Hh) signal transduction has been controversial. In this study, Smoothened (Smo) is shown to activate a G protein, Gα_i, to modulate intracellular cyclic AMP levels in response to Hh.

This study shows that Myc-driven tumourigenesis is dependent on its ability to increase protein synthesis, as haploinsufficiency in ribosomal proteins decreases Myc-induced tumour formation. However, tumours caused by the loss of p53, were not affected. Myc stimulates cap-dependent protein translation at the expense of IRES-dependent translation, leading to the synthesis of a different set of proteins, and this effect is reversed by ribosomal protein haploinsufficiency.

During clathrin-mediated endocytosis, cargo proteins are recognized by clathrin adaptors. The clathrin adaptor AP2 recognizes two major classes of endocytic motifs, including an acidic dileucine motif. This study presents the crystal structure of AP2 in complex with the diceucine motif of a cargo protein, thereby revealing the mechanism of cargo–adaptor recognition.

MicroRNAs are expressed in a type of heart cell known as cardiomyocytes and their aberrant regulation was correlated with heart disease. This study looks at how miRNAs in other heart cells may contribute to disease. It is found that in cardiac fibroblasts, miR-21 is upregulated in diseased heart. This activates a signalling pathway that exacerbates cardiac disease. By using an RNA molecule directed against miR-21, it was possible to reverse these effects, demonstrating that therapeutic treatment to downregulate a microRNA can be effective in vivo.

The NS1 protein of the influenza virus is a critical virulence factor that antagonizes the host antiviral response by multiple mechanisms, including the binding and sequestration of double-stranded RNA. This paper describes the structure of full-length NS1 protein and shows that individual domains interact in such a way as to form tubules, which may sequester dsRNA, allowing the virus to evade the innate immune response.

The classical pentraxins, serum amyloid P component (SAP) and C-reactive protein (CRP), are major acute phase reactants in mouse and man. It is shown that pentraxins recognize various FcγRs and SAP opsonization activates FcγR-mediated phagocytosis and cytokine secretion. The receptor binding sites for SAP and IgG overlap, resulting in competition of IgG binding to FcγR as well as inhibition of immune complex-mediated phagocytosis by soluble pentraxins.

The exosome is a multisubunit exonuclease complex that degrades many types of RNAs, in many different contexts, in a 3′ to 5′ manner. The catalytic component of the exosome is the Dis3 subunit. Dis3 contains a PIN domain, which is sometimes associated with nuclease activity. This work shows that the Dis3 PIN domain also possesses endonuclease activity (that is, it can cleave RNA internally, rather than from an end). Mutations in either this domain or in the exonuclease domain exhibit a growth phenotype, suggesting that both activities are physiologically important.

This paper shows that specific genetic disruption of the Ncor–HdaC3 interaction in mice causes aberrant regulation of clock genes and results in abnormal circadian behaviour. These mice are also leaner and more insulin sensitive due to increased energy expenditure. Loss of a functional Ncor–HdaC3 complex in vivo changes the oscillatory patterns of several metabolic genes, demonstrating that circadian regulation of metabolism is critical for normal energy balance.

The chlorophyll biosynthetic enzyme NADPH:protochlorophyllide oxidoreductase, which catalyses a light-driven reaction involving hydride and proton transfers is examined. It is determined that prior excitation of the enzyme–substrate complex with a laser pulse induces a more favourable conformation of the active site and increases the catalytic efficiency of the coupled hydride and proton transfer reactions. Spectral changes in the mid-infrared after the absorption of one photon reveal significant conformational changes in the enzyme.

It's a constant worry.

Genomic clues settle debate about ancestor of all life forms.