Geophysics: a moving fluid pulse in a fault zone

In the Gulf of Mexico, fault zones are linked with a complex and dynamic system of plumbing in the Earth's subsurface. Here we use time-lapse seismic-reflection imaging to reveal a pulse of fluid ascending rapidly inside one of these fault zones. Such intermittent fault 'burping' is likely to be an important factor in the migration of subsurface hydrocarbons.     

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution

Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.     

Determinants of woody cover in African savannas

Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties. The availability of resources (water, nutrients) and disturbance regimes (fire, herbivory) are thought to be important in regulating woody cover, but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than approximately 650 mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered 'stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP-controlled upper bound. Above a MAP of approximately 650 mm, savannas are 'unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances (fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation may considerably affect their distribution and dynamics.     

Doping semiconductor nanocrystals

Doping--the intentional introduction of impurities into a material--is fundamental to controlling the properties of bulk semiconductors. This has stimulated similar efforts to dope semiconductor nanocrystals. Despite some successes, many of these efforts have failed, for reasons that remain unclear. For example, Mn can be incorporated into nanocrystals of CdS and ZnSe (refs 7-9), but not into CdSe (ref. 12)--despite comparable bulk solubilities of near 50 per cent. These difficulties, which have hindered development of new nanocrystalline materials, are often attributed to 'self-purification', an allegedly intrinsic mechanism whereby impurities are expelled. Here we show instead that the underlying mechanism that controls doping is the initial adsorption of impurities on the nanocrystal surface during growth. We find that adsorption--and therefore doping efficiency--is determined by three main factors: surface morphology, nanocrystal shape, and surfactants in the growth solution. Calculated Mn adsorption energies and equilibrium shapes for several nanocrystals lead to specific doping predictions. These are confirmed by measuring how the Mn concentration in ZnSe varies with nanocrystal size and shape. Finally, we use our predictions to incorporate Mn into previously undopable CdSe nanocrystals. This success establishes that earlier difficulties with doping are not intrinsic, and suggests that a variety of doped nanocrystals--for applications from solar cells to spintronics--can be anticipated.     

Licensing of natural killer cells by host major histocompatibility complex class I molecules

Self versus non-self discrimination is a central theme in biology from plants to vertebrates, and is particularly relevant for lymphocytes that express receptors capable of recognizing self-tissues and foreign invaders. Comprising the third largest lymphocyte population, natural killer (NK) cells recognize and kill cellular targets and produce pro-inflammatory cytokines. These potentially self-destructive effector functions can be controlled by inhibitory receptors for the polymorphic major histocompatibility complex (MHC) class I molecules that are ubiquitously expressed on target cells. However, inhibitory receptors are not uniformly expressed on NK cells, and are germline-encoded by a set of polymorphic genes that segregate independently from MHC genes. Therefore, how NK-cell self-tolerance arises in vivo is poorly understood. Here we demonstrate that NK cells acquire functional competence through 'licensing' by self-MHC molecules. Licensing involves a positive role for MHC-specific inhibitory receptors and requires the cytoplasmic inhibitory motif originally identified in effector responses. This process results in two types of self-tolerant NK cells--licensed or unlicensed--and may provide new insights for exploiting NK cells in immunotherapy. This self-tolerance mechanism may be more broadly applicable within the vertebrate immune system because related germline-encoded inhibitory receptors are widely expressed on other immune cells.     

Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations

Mutations involving gains of glycosylation have been considered rare, and the pathogenic role of the new carbohydrate chains has never been formally established. We identified three children with mendelian susceptibility to mycobacterial disease who were homozygous with respect to a missense mutation in IFNGR2 creating a new N-glycosylation site in the IFNgammaR2 chain. The resulting additional carbohydrate moiety was both necessary and sufficient to abolish the cellular response to IFNgamma. We then searched the Human Gene Mutation Database for potential gain-of-N-glycosylation missense mutations; of 10,047 mutations in 577 genes encoding proteins trafficked through the secretory pathway, we identified 142 candidate mutations ( approximately 1.4%) in 77 genes ( approximately 13.3%). Six mutant proteins bore new N-linked carbohydrate moieties. Thus, an unexpectedly high proportion of mutations that cause human genetic disease might lead to the creation of new N-glycosylation sites. Their pathogenic effects may be a direct consequence of the addition of N-linked carbohydrate.     

The Collaborative Cross, a community resource for the genetic analysis of complex traits

The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.     

Millennial and orbital variations of El Niño/Southern Oscillation and high-latitude climate in the last glacial period

The El Ni?o/Southern Oscillation (ENSO) phenomenon is believed to have operated continuously over the last glacial-interglacial cycle. ENSO variability has been suggested to be linked to millennial-scale oscillations in North Atlantic climate during that time, but the proposals disagree on whether increased frequency of El Ni?o events, the warm phase of ENSO, was linked to North Atlantic warm or cold periods. Here we present a high-resolution record of surface moisture, based on the degree of peat humification and the ratio of sedges to grass, from northern Queensland, Australia, covering the past 45,000 yr. We observe millennial-scale dry periods, indicating periods of frequent El Ni?o events (summer precipitation declines in El Ni?o years in northeastern Australia). We find that these dry periods are correlated to the Dansgaard-Oeschger events--millennial-scale warm events in the North Atlantic climate record--although no direct atmospheric connection from the North Atlantic to our site can be invoked. Additionally, we find climatic cycles at a semiprecessional timescale (approximately 11,900 yr). We suggest that climate variations in the tropical Pacific Ocean on millennial as well as orbital timescales, which determined precipitation in northeastern Australia, also exerted an influence on North Atlantic climate through atmospheric and oceanic teleconnections.