A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.     

A RhoGDP dissociation inhibitor spatially regulates growth in root hair cells

Root hairs are cellular protuberances extending from the root surface into the soil; there they provide access to immobile inorganic ions such as phosphate, which are essential for growth. Their cylindrical shape results from a polarized mechanism of cell expansion called tip growth in which elongation is restricted to a small area at the surface of the hair-forming cell (trichoblast) tip. Here we identify proteins that spatially control the sites at which cell growth occurs by isolating Arabidopsis mutants (scn1) that develop ectopic sites of growth on trichoblasts. We cloned SCN1 and showed that SCN1 is a RhoGTPase GDP dissociation inhibitor (RhoGDI) that spatially restricts the sites of growth to a single point on the trichoblast. We showed previously that localized production of reactive oxygen species by RHD2/AtrbohC NADPH oxidase is required for hair growth; here we show that SCN1/AtrhoGDI1 is a component of the mechanism that focuses RHD2/AtrbohC-catalysed production of reactive oxygen species to hair tips during wild-type development. We propose that the spatial organization of growth in plant cells requires the local RhoGDI-regulated activation of the RHD2/AtrbohC NADPH oxidase.     

Antibody neutralization and escape by HIV-1

Neutralizing antibodies (Nab) are a principal component of an effective human immune response to many pathogens, yet their role in HIV-1 infection is unclear. To gain a better understanding of this role, we examined plasma from patients with acute HIV infection. Here we report the detection of autologous Nab as early as 52 days after detection of HIV-specific antibodies. The viral inhibitory activity of Nab resulted in complete replacement of neutralization-sensitive virus by successive populations of resistant virus. Escape virus contained mutations in the env gene that were unexpectedly sparse, did not map generally to known neutralization epitopes, and involved primarily changes in N-linked glycosylation. This pattern of escape, and the exceptional density of HIV-1 envelope glycosylation generally, led us to postulate an evolving 'glycan shield' mechanism of neutralization escape whereby selected changes in glycan packing prevent Nab binding but not receptor binding. Direct support for this model was obtained by mutational substitution showing that Nab-selected alterations in glycosylation conferred escape from both autologous antibody and epitope-specific monoclonal antibodies. The evolving glycan shield thus represents a new mechanism contributing to HIV-1 persistence in the face of an evolving antibody repertoire.     

Protease-activated-receptor-2 affects protease-activated-receptor-1-driven breast cancer

Mammalian protease-activated-receptor-1 and -2 (PAR₁ and PAR₂) are activated by proteases found in the flexible microenvironment of a tumor and play a central role in breast cancer. We propose in the present study that PAR₁ and PAR₂ act together as a functional unit during malignant and physiological invasion processes. This notion is supported by assessing pro-tumor functions in the presence of short hairpin; shRNA knocked-down hPar2 or by the use of a truncated PAR₂ devoid of the entire cytoplasmic tail. Silencing of hPar2 by shRNA-attenuated thrombin induced PAR₁ signaling as recapitulated by inhibiting the assembly of Etk/Bmx or Akt onto PAR₁-C-tail, by thrombin-instigated colony formation and invasion. Strikingly, shRNA-hPar2 also inhibited the TFLLRN selective PAR₁ pro-tumor functions. In addition, while evaluating the physiological invasion process of placenta extravillous trophoblast (EVT) organ culture, we observed inhibition of both thrombin or the selective PAR₁ ligand; TFLLRNPNDK induced EVT invasion by shRNA-hPar2 but not by scrambled shRNA-hPar2. In parallel, when a truncated PAR₂ was utilized in a xenograft mouse model, it inhibited PAR₁–PAR₂-driven tumor growth in vivo. Similarly, it also attenuated the interaction of Etk/Bmx with the PAR₁-C-tail in vitro and decreased markedly selective PAR₁-induced Matrigel invasion. Confocal images demonstrated co-localization of PAR₁ and PAR₂ in HEK293T cells over-expressing YFP-hPar2 and HA-hPar1. Co-immuno-precipitation analyses revealed PAR₁-PAR₂ complex formation but no PAR₁-CXCR4 complex was formed. Taken together, our observations show that PAR₁ and PAR₂ act as a functional unit in tumor development and placenta-uterus interactions. This conclusion may have significant consequences on future breast cancer therapeutic modalities and improved late pregnancy outcome.     

Differential responses to nitrogen form and concentration for Oryzopsis hymenoides and Elymus lanceolatus

In a greenhouse experiment, effects of nitrogen form and concentration on productivity and dry matter allocation differed between two species native to semiarid ecosystems of the Great Basin. Aboveground production of green surface area and of dry matter were consistently enhanced by increased nitrogen for the rhizomatous grass Elymus lanceolatus , but not for the bunchgrass Oryzopsis hymenoides . These differences were likely due to inherently low growth rates of O. hymenoides . Aboveground dry matter allocation also differed between the two species. O. hymenoides had more leaves per tiller with increased nitrogen, whereas leaf size but not number increased for E. lanceolatus . Furthermore, increases in tiller density with increased nitrogen for E. lanceolatus were almost three times greater than those for O. hymenoides . E. lanceolatus , but not O. hymenoides , was sensitive to the form of nitrogen supplied to the plants. When NH 4 -N was the only form of nitrogen supplied, high concentrations of NH 4 -N inhibited aboveground production of E. lanceolatus .     

High levels of gene flow in the California vole ( Microtus californicus ) are consistent across spatial scales

Gene flow links the genetic and demographic structures of species. Despite the fact that similar genetic and demographic patterns shape both local population structure and regional phylogeography, the 2 levels of population connectivity are rarely studied simultaneously. Here, we studied gene flow in the California vole ( Microtus californicus ), a small-bodied rodent with limited vagility but high local abundance. Within a 4.86-km 2 preserve in central California, genetic diversity in 6 microsatellites was high, and Bayesian methods indicated a single genetic cluster. However, individual-based genetic analysis detected a clear signal for isolation-by-distance (IBD) and fine-scale population structure. Mitochondrial cytochrome b sequencing revealed 11 unique haplotypes from the one local area where we sequenced 62 individuals. Phylogeographic analysis of these individuals combined with those sampled from the northern geographic range of the species (the range of the species spans western North America from southern Oregon to northern Mexico and is centered geographically within the state of California) again indicated a lack of structure but a signal for IBD. Patterns of gene flow thus are consistent across spatial scales: while dispersal of the California vole is limited across geographic distance, there is nonetheless considerable movement across the landscape. We conclude that in this species, high local population abundances overcome the potential genetic and demographic effects of limited dispersal.     

The permeability of tumour vessels

Summary Experimental proof that tumour vessels are permeable to humoral agents but impermeable to cellular elements viz. leucocytes. The cause of this impermeability is believed to be the deposition of immunosuppressive alpha globulin on the walls of tumour vessels. This concept is of relevance in organ transplantation and cancer immunotherapy.     

On the lymphatic spread of cancer

Summary Experimental demonstration that agents promoting cellular motility and/or vascular permeability enhance the spread of tumour to regional or distant lymph nodes. Tumour emboli appear to reach the regional glands via the lymphatic channels and the distant nodes by haematogenous route.