Modelling the recent common ancestry of all living humans

If a common ancestor of all living humans is defined as an individual who is a genealogical ancestor of all present-day people, the most recent common ancestor (MRCA) for a randomly mating population would have lived in the very recent past. However, the random mating model ignores essential aspects of population substructure, such as the tendency of individuals to choose mates from the same social group, and the relative isolation of geographically separated groups. Here we show that recent common ancestors also emerge from two models incorporating substantial population substructure. One model, designed for simplicity and theoretical insight, yields explicit mathematical results through a probabilistic analysis. A more elaborate second model, designed to capture historical population dynamics in a more realistic way, is analysed computationally through Monte Carlo simulations. These analyses suggest that the genealogies of all living humans overlap in remarkable ways in the recent past. In particular, the MRCA of all present-day humans lived just a few thousand years ago in these models. Moreover, among all individuals living more than just a few thousand years earlier than the MRCA, each present-day human has exactly the same set of genealogical ancestors.     

Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products

The anti-oxidant naphterpin is a natural product containing a polyketide-based aromatic core with an attached 10-carbon geranyl group derived from isoprenoid (terpene) metabolism. Hybrid natural products such as naphterpin that contain 5-carbon (dimethylallyl), 10-carbon (geranyl) or 15-carbon (farnesyl) isoprenoid chains possess biological activities distinct from their non-prenylated aromatic precursors. These hybrid natural products represent new anti-microbial, anti-oxidant, anti-inflammatory, anti-viral and anti-cancer compounds. A small number of aromatic prenyltransferases (PTases) responsible for prenyl group attachment have only recently been isolated and characterized. Here we report the gene identification, biochemical characterization and high-resolution X-ray crystal structures of an architecturally novel aromatic PTase, Orf2 from Streptomyces sp. strain CL190, with substrates and substrate analogues bound. In vivo, Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis. In vitro, Orf2 catalyses carbon-carbon-based and carbon-oxygen-based prenylation of a diverse collection of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin. These crystal structures, coupled with in vitro assays, provide a basis for understanding and potentially manipulating the regio-specific prenylation of aromatic small molecules using this structurally unique family of aromatic PTases.     

How Prometheus creates structure in Saturn's F ring

Images of Saturn's narrow and contorted F ring returned by the Cassini spacecraft have revealed phenomena not previously detected in any planetary ring system. The perturbing effect of the inner shepherding satellite, Prometheus, seems to introduce channels through the F ring and a 'streamer'--a line of particles that link the ring to the satellite. The detailed mechanism for the formation of these features has been lacking an explanation. Here we show that these phenomena can be understood in terms of a simple gravitational interaction as Prometheus approaches and recedes from the F ring every 14.7 hours. Our numerical models show that as Prometheus recedes from its closest approach to the F ring, it draws out ring material; one orbital period later, this affected region has undergone keplerian shear and is visible as a channel, in excellent agreement with structures seen in the Cassini images. Prometheus' periodic disruption of the F ring will become more pronounced as the two orbits approach their minimum separation in 2009. The model predicts that the appearance of streamers and the associated channels will vary in a regular fashion on a timescale of one orbital period.     

Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection

It has recently been established that both acute human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections are accompanied by a dramatic and selective loss of memory CD4+ T cells predominantly from the mucosal surfaces. The mechanism underlying this depletion of memory CD4+ T cells (that is, T-helper cells specific to previously encountered pathogens) has not been defined. Using highly sensitive, quantitative polymerase chain reaction together with precise sorting of different subsets of CD4+ T cells in various tissues, we show that this loss is explained by a massive infection of memory CD4+ T cells by the virus. Specifically, 30-60% of CD4+ memory T cells throughout the body are infected by SIV at the peak of infection, and most of these infected cells disappear within four days. Furthermore, our data demonstrate that the depletion of memory CD4+ T cells occurs to a similar extent in all tissues. As a consequence, over one-half of all memory CD4+ T cells in SIV-infected macaques are destroyed directly by viral infection during the acute phase-an insult that certainly heralds subsequent immunodeficiency. Our findings point to the importance of reducing the cell-associated viral load during acute infection through therapeutic or vaccination strategies.     

Strong polarization enhancement in asymmetric three-component ferroelectric superlattices

Theoretical predictions--motivated by recent advances in epitaxial engineering--indicate a wealth of complex behaviour arising in superlattices of perovskite-type metal oxides. These include the enhancement of polarization by strain and the possibility of asymmetric properties in three-component superlattices. Here we fabricate superlattices consisting of barium titanate (BaTiO3), strontium titanate (SrTiO3) and calcium titanate (CaTiO3) with atomic-scale control by high-pressure pulsed laser deposition on conducting, atomically flat strontium ruthenate (SrRuO3) layers. The strain in BaTiO3 layers is fully maintained as long as the BaTiO3 thickness does not exceed the combined thicknesses of the CaTiO3 and SrTiO3 layers. By preserving full strain and combining heterointerfacial couplings, we find an overall 50% enhancement of the superlattice global polarization with respect to similarly grown pure BaTiO3, despite the fact that half the layers in the superlattice are nominally non-ferroelectric. We further show that even superlattices containing only single-unit-cell layers of BaTiO3 in a paraelectric matrix remain ferroelectric. Our data reveal that the specific interface structure and local asymmetries play an unexpected role in the polarization enhancement.     

Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak

Genealogy can illuminate the evolutionary path of important human pathogens. In some microbes, strict clonal reproduction predominates, as with the worldwide dissemination of Mycobacterium leprae, the cause of leprosy. In other pathogens, sexual reproduction yields clones with novel attributes, for example, enabling the efficient, oral transmission of the parasite Toxoplasma gondii. However, the roles of clonal or sexual propagation in the origins of many other microbial pathogen outbreaks remain unknown, like the recent fungal meningoencephalitis outbreak on Vancouver Island, Canada, caused by Cryptococcus gattii. Here we show that the C. gattii outbreak isolates comprise two distinct genotypes. The majority of isolates are hypervirulent and have an identical genotype that is unique to the Pacific Northwest. A minority of the isolates are significantly less virulent and share an identical genotype with fertile isolates from an Australian recombining population. Genotypic analysis reveals evidence of sexual reproduction, in which the majority genotype is the predicted offspring. However, instead of the classic a-alpha sexual cycle, the majority outbreak clone appears to have descended from two alpha mating-type parents. Analysis of nuclear content revealed a diploid environmental isolate homozygous for the major genotype, an intermediate produced during same-sex mating. These studies demonstrate how cryptic same-sex reproduction can enable expansion of a human pathogen to a new geographical niche and contribute to the ongoing production of infectious spores. This has implications for the emergence of other microbial pathogens and inbreeding in host range expansion in the fungal and other kingdoms.     

General observation of n-type field-effect behaviour in organic semiconductors

Organic semiconductors have been the subject of active research for over a decade now, with applications emerging in light-emitting displays and printable electronic circuits. One characteristic feature of these materials is the strong trapping of electrons but not holes: organic field-effect transistors (FETs) typically show p-type, but not n-type, conduction even with the appropriate low-work-function electrodes, except for a few special high-electron-affinity or low-bandgap organic semiconductors. Here we demonstrate that the use of an appropriate hydroxyl-free gate dielectric--such as a divinyltetramethylsiloxane-bis(benzocyclobutene) derivative (BCB; ref. 6)--can yield n-channel FET conduction in most conjugated polymers. The FET electron mobilities thus obtained reveal that electrons are considerably more mobile in these materials than previously thought. Electron mobilities of the order of 10(-3) to 10(-2) cm(2) V(-1) s(-1) have been measured in a number of polyfluorene copolymers and in a dialkyl-substituted poly(p-phenylenevinylene), all in the unaligned state. We further show that the reason why n-type behaviour has previously been so elusive is the trapping of electrons at the semiconductor-dielectric interface by hydroxyl groups, present in the form of silanols in the case of the commonly used SiO2 dielectric. These findings should therefore open up new opportunities for organic complementary metal-oxide semiconductor (CMOS) circuits, in which both p-type and n-type behaviours are harnessed.     

Dystrophic heart failure blocked by membrane sealant poloxamer

Dystrophin deficiency causes Duchenne muscular dystrophy (DMD) in humans, an inherited and progressive disease of striated muscle deterioration that frequently involves pronounced cardiomyopathy. Heart failure is the second leading cause of fatalities in DMD. Progress towards defining the molecular basis of disease in DMD has mostly come from studies on skeletal muscle, with comparatively little attention directed to cardiac muscle. The pathophysiological mechanisms involved in cardiac myocytes may differ significantly from skeletal myofibres; this is underscored by the presence of significant cardiac disease in patients with truncated or reduced levels of dystrophin but without skeletal muscle disease. Here we show that intact, isolated dystrophin-deficient cardiac myocytes have reduced compliance and increased susceptibility to stretch-mediated calcium overload, leading to cell contracture and death, and that application of the membrane sealant poloxamer 188 corrects these defects in vitro. In vivo administration of poloxamer 188 to dystrophic mice instantly improved ventricular geometry and blocked the development of acute cardiac failure during a dobutamine-mediated stress protocol. Once issues relating to optimal dosing and long-term effects of poloxamer 188 in humans have been resolved, chemical-based membrane sealants could represent a new therapeutic approach for preventing or reversing the progression of cardiomyopathy and heart failure in muscular dystrophy.     

Sexual reproduction between partners of the same mating type in Cryptococcus neoformans

Cryptococcus neoformans is a globally distributed human fungal pathogen that causes life-threatening meningoencephalitis in immunocompromised patients. It has a defined sexual cycle involving haploid cells of alpha and a mating types, yet the vast majority of environmental and clinical isolates are alpha (ref. 3). Sexual recombination is normally expected to occur between isolates of opposite mating type in organisms with two mating types (or sexes). How sexual reproductive potential can be maintained in an organism with a largely unisexual, nearly clonal population genetic structure is unknown. One clue, however, is that alpha strains undergo fruiting, a process that resembles sexual mating but is thought to be strictly mitotic and asexual. We report here that hallmarks of mating occur during fruiting, including diploidization and meiosis. Pheromone response pathway elements and the key meiotic regulator Dmc1 are required for efficient fruiting. Furthermore, fusion and meiosis can occur between non-isogenic alpha strains, enabling genetic exchange. These studies reveal how sexual reproduction can occur between partners of the same mating type. These findings have implications for the evolution of microbial pathogens, as well as for parthenogenesis, cell fusion events and transitions between self-fertilizing and outcrossing modes of reproduction observed in both fungi and other kingdoms.     

A size of approximately 1 au for the radio source Sgr A* at the centre of the Milky Way

Although it is widely accepted that most galaxies have supermassive black holes at their centres, concrete proof has proved elusive. Sagittarius A* (Sgr A*), an extremely compact radio source at the centre of our Galaxy, is the best candidate for proof, because it is the closest. Previous very-long-baseline interferometry observations (at 7 mm wavelength) reported that Sgr A* is approximately 2 astronomical units (au) in size, but this is still larger than the 'shadow' (a remarkably dim inner region encircled by a bright ring) that should arise from general relativistic effects near the event horizon of the black hole. Moreover, the measured size is wavelength dependent. Here we report a radio image of Sgr A* at a wavelength of 3.5 mm, demonstrating that its size is approximately 1 au. When combined with the lower limit on its mass, the lower limit on the mass density is 6.5 x 10(21)M(o) pc(-3) (where M(o) is the solar mass), which provides strong evidence that Sgr A* is a supermassive black hole. The power-law relationship between wavelength and intrinsic size (size proportional, variantwavelength(1.09)) explicitly rules out explanations other than those emission models with stratified structure, which predict a smaller emitting region observed at a shorter radio wavelength.