Volume 499 Issue 7457, 11 July 2013

Germany’s main funding agency must specify how it will deal with false charges of misconduct.

Science communication is changing, but investigative reporting is still important.

The United Kingdom’s decision to trial the technique of mitochondrial replacement is premature and ill-conceived, says Marcy Darnovsky.

The week in science: Ancient pyramid destroyed in Peru, stem-cell patents challenged, and solar plane crosses the United States.

The Large Binocular Telescope gets off to a sluggish start.

Global copyright agreement will increase availability of scientific texts in accessible formats.

Physical limits mean that electron microscopy may be nearing highest possible resolution.

Researchers fear reforms will bring cuts to basic science.

Commercialization rules threaten to curtail SBIR grants.

Efforts to predict the near-term climate are taking off, but their record so far has been patchy.

Fiona Fox and her Science Media Centre are determined to improve Britain's press. Now the model is spreading around the world.

Massoud Amin outlines how the United States should make its electricity infrastructure self-healing to avoid massive power failures.

Four insiders explain how they would make the savings in US science required by the budget sequester.

With the yearly exodus from labs and lecture theatres imminent, Nature's regular reviewers and editors share some tempting holiday reads.

Research shows how the malaria parasite Plasmodium falciparum manipulates the expression of its var genes to avoid recognition by the host immune system. Four experts comment on the implications of these results for our understanding of gene regulation in general and the development of antimalaria vaccines. See Letter p.223

Rifting of continents is usually explained by one of two mechanisms based on effects that originate far from the zone of rifting. Laboratory experiments show that this geodynamic process can also be caused by local effects.

Using a material called a photonic crystal, researchers have designed a mirror that is, in a certain sense, perfect — there is in principle no light transmitted through it nor absorbed by it. See Letter p.188

An assessment of allowable carbon emissions that factors in multiple climate targets finds smaller permissible emission budgets than those inferred from studies that focus on temperature change alone. See Letter p.197

Transport vesicles that bud from one cell membrane must change identity before fusing with another. During the process of clathrin-mediated endocytosis, various lipid phosphates mediate this identity change. See Letter p.233

Building a device capable of factoring large numbers is a major goal of quantum computing; an algorithm for quantum factoring (Shor’s algorithm) exists, and a simple coin-tossing exercise is used to illustrate the dangers of oversimplification when implementing this algorithm experimentally.

The Shc1 scaffold mediates a switch in the signaling output of the epidermal growth factor receptor tyrosine kinase over time through recruitment of successive waves of proteins with distinct biological functions.

This study reports a global analysis of binding sites for over 200 RNA-binding proteins (RBPs) from 24 species; conserved RNA-binding motifs are identified, and their analysis allows prediction of interaction sites based on the sequence of the RNA-binding domain alone.

Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.

The narrow rings seen in some debris disks, thought to be evidence for hidden exoplanets, might instead be caused by gas–dust interaction and a recently identified photoelectric instability.

Theoretical and experimental studies reveal that light can be confined within a planar dielectric photonic crystal slab even though the frequency of this optical bound state is inside the continuous spectrum of extended states from the same symmetry group.

Phthaloyl peroxide functions as a selective oxidant of C–H bonds in the transformation of arenes to phenols under mild conditions, in a reaction that is compatible with a wide array of functional groups.

The amount of greenhouse gas emissions that will limit the risks from such emissions has been set by the goal of keeping global warming below two degrees Celsius above preindustrial, but this study sets thresholds for sea level rise, ocean acidification and agricultural productivity as well as warming and shows that emissions need to be lowered even further.

Variations in Earth's rotation show clear signals of a 5.9-year oscillation and jumps in Earth’s moment of inertia; correlation with the geomagnetic field suggests an origin in Earth’s core and constrains the conductivity and thus the composition and mineralogy of the deep mantle.

Gene expression of microbes in anaerobic sediment from the Peru Margin at depths up to 159 metres below the sea floor is analysed: anaerobic metabolism of amino acids, carbohydrates and lipids are seen to be the dominant metabolic processes, and genes associated with cell division are found to be correlated with microbial cell concentration, suggesting that ongoing cell division contributes to biomass turnover.

A reference genome from the coccolithophore Emiliania huxleyi is presented, along with sequences from 13 additional isolates, revealing a pan genome comprising core genes and genes variably distributed between strains: E. huxleyi is found to harbour extensive genetic variability under different metabolic repertoires, explaining its ability to thrive under a diverse range of environmental conditions.

As the sample size in cancer genome studies increases, the list of genes identified as significantly mutated is likely to include more false positives; here, this problem is identified as stemming largely from mutation heterogeneity, and a new analytical methodology designed to overcome this problem is described.

By exploring the phageome in mice, antibiotic treatment is shown to lead to enrichment of phage-encoded genes that are related to antibiotic resistance.

The malaria parasite Plasmodium falciparum escapes immune detection by expressing one of 60 antigenically distinct var genes at any one time during the course of infection: here it is shown that the P. falciparum protein PfSETvs has a key role in var gene silencing through the trimethylation of histone H3K36.

Nail stem cells (NSCs) reside in the proximal nail matrix, and early nail progenitors undergo Wnt-dependent differentiation into the nail; after amputation, Wnt activation is required for nail and digit regeneration, and amputations proximal to the Wnt-active nail progenitors fail to regenerate, but β-catenin stabilization in the NSC region induces regeneration.

Phosphoinositides are important regulators of intracellular membrane traffic, and although the role of PI(4,5)P₂ has been well characterised, the function of PI(3,4)P₂ remains unclear; here the formation of PI(3,4)P₂ by the class II phosphatidylinositol-3-kinase C2α enzyme is shown to control clathrin-mediated endocytosis.

A genome-wide RNA interference analysis identifies the septin family of cytoskeletal filaments as important regulators of store-operated Ca²⁺ entry into the cell; septins are shown to organize plasma membrane microdomains important in STIM1 and ORAI1 signalling, and may also be relevant in membrane microdomains underlying other signalling processes.

Meeting up in person is still the best way to make contacts and ease career moves.

Successful musical composition and scientific research share important traits, argues Stephane Detournay.

A holiday to remember.