Abstract: High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.

Abstract: As an economic crop, pepper satisfies people’s spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 ( C. annuum L.) and its wild progenitor Chiltepin ( C. annuum var. glabriusculum ). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

Abstract: Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

Abstract: Aspects of the mechanism proposed for ATL are likely to be applicable to other fusion reactions, including ER fusion mediated by the functional orthologs of ATL in yeast and plants, Sey1p, and RHD3, and the fusion of mitochondrial outer membranes by the mitofusins/Fzo1p. As in the case of ATLs, membrane fusion mediated by SNARE proteins during intracellular vesicular transport or by viral proteins often involves lipid-interacting amphipathic helices as well as a specific function for the TMs that goes beyond a role as mere membrane anchors. Our results suggest a refined model for ATL-mediated membrane fusion in which the CT and TMs of ATL cooperate with the N-terminal cytosolic domain. First, several ATL molecules in a membrane associate with each other through their TM segments ( Fig. P1 A ). Second, these complexes interact with similarly assembled ATL molecules in another membrane ( Fig. P1 B ); the interaction of ATL molecules across the two membranes requires GTP binding. It also is conceivable that the first and second steps are coordinated rather than occurring in a strictly consecutive manner. Third, GTP hydrolysis and the release of inorganic phosphate trigger a conformational change that pulls the membranes toward each other for fusion ( Fig. P1 C and D ). The nucleotide-independent oligomerization of ATL molecules might increase the efficiency of fusion by allowing several ATL molecules in each membrane to undergo the conformational changes synchronously. Local perturbation of the membrane bilayer by the CT ( Fig. P1 C ; magenta and yellow circles) also could contribute to the process by lowering the energy barrier for the approach and eventual merging of the membranes. Finally, once fusion is completed and the postfusion conformation is reached, GDP is released ( Fig. P1 D and E ), allowing the nucleotide-dependent ATL dimers to dissociate and to start a new round of fusion. Although wild-type human ATL1 can replace its functional ortholog Sey1p in Saccharomyces cerevisiae to maintain ER morphology, fusion-defective point mutants in the CT or the TMs cannot, indicating that these domains are important for fusion in vivo. The physiological relevance of the CT is supported further by the fact that C-terminal truncation mutants of human ATL1 cause HSP. Our present results show that the CT is required for efficient membrane fusion. The key feature of the CT is a conserved amphipathic helix that immediately follows the TMs. Deletion of the CT or point mutations in the helix greatly reduce the GTP-dependent fusion of ATL-containing vesicles. A synthetic peptide corresponding to the helix (CTH), but not to unrelated amphipathic helices, can act in trans to restore the fusion activity of tailless ATL. This reaction is strictly GTP dependent, as with wild-type ATL, and involves fusion of both leaflets of the bilayer and a concomitant size increase of the ATL-containing vesicles. Using biophysical assays, we demonstrated that the CTH promotes vesicle fusion by interacting directly with and perturbing the lipid bilayer. However, disturbance of the bilayer by the C-terminal helix does not cause significant lysis during fusion, as shown by an assay that measures the mixing of vesicle contents during fusion: No leakage of content was detected in the reaction with wild-type ATL, and only a low level was observed with tailless ATL in the presence of the CTH. The TM segments also play an important role in ATL-mediated membrane fusion. They do not serve as mere membrane anchors for the cytosolic domain, because they cannot be replaced by unrelated TMs. Further, point mutations in the TMs can affect ATL’s ability to catalyze fusion. Using coimmunoprecipitation experiments, we showed that the TMs mediate nucleotide-independent oligomerization of ATL molecules. Two crystal structures of the cytosolic domain of ATL ( 3 , 4 ), which likely represent pre- and postfusion conformations, suggest that ATL molecules undergo a GTP hydrolysis–induced conformational change that pulls the membranes together so that they can fuse ( Fig. P1 ). The differences in interaction surface area in the pre- and postfusion structures indicate that the energy gain from the conformational change is not large, raising the possibility that the TMs and CT, which are not included in the crystal structures, could be important for ATL-mediated fusion. Homotypic fusion, which involves the merging of identical membranes, is required for the remodeling of organelles, including the endoplasmic reticulum (ER) and mitochondria. These organelles contain membrane tubules that are connected into a network by homotypic fusion. The homotypic fusion of ER membranes is catalyzed by the atlastins (ATLs) ( 1 , 2 ), membrane-bound GTPases of the dynamin family. The physiological importance of the ATLs is indicated by the fact that mutations in one of the isoforms are known to cause a dominantly inherited form of hereditary spastic paraplegia (HSP), a neuromuscular disorder. The ATLs contain an N-terminal cytosolic domain comprising a GTPase module and a three-helix bundle, two closely spaced transmembrane (TM) segments, and a C-terminal tail (CT) ( Fig. P1 ). Here, we demonstrate that membrane fusion by ATL is achieved by the cooperation of a conformational change in the cytosolic domain with protein–lipid and protein–protein interactions within the membrane mediated by its CT and TM segments, respectively.

Abstract: How promising are Mn-based compounds as potential superconductors? The schematic phase diagram ( Fig. P1 ) shows that superconductivity is achieved in compounds that are exquisitely balanced between metal and insulator and where magnetic order is on the verge of complete destruction. Achieving higher T c requires something more. Perhaps the cuprates have higher T c than the Fe-pnictides because their correlations are strong enough to make them insulating in the absence of doping. The correlations in the Mn-pnictides may be even stronger. Compounds such as LaMnPO are important because they may expose the upper bound on T c . Our calculations reveal, however, that applied pressure succeeds in delocalizing electrons in LaMnPO. The magnitude of the moments found in neutron diffraction measurements of LaMnPO is in superb agreement with the values predicted by DMFT. Given this success, we took theory as our guide. We calculated the magnetic moments and band gaps of LaMnPO at high pressures by taking as our starting point the exact crystal structures we determined from high-pressure X-ray diffraction measurements. These measurements revealed that the lattice contracts suddenly near 30 GPa (300,000 atmospheres), which corresponds to the vanishing of the ordered magnetic moment as revealed by our calculations. Moreover, we find that the band gap of LaMnPO is driven to zero between 8.5 and 16 GPa, just as we experimentally observed another lattice contraction followed by an orthorhombic distortion. While these seem like large pressures, the volume was reduced by only ∼10%, similar to the values required to induce superconductivity itself in LaFeAsO and BaFe 2 As 2 ( 3 ). Furthermore, similar distortions have been observed in Fe-based superconductors, where they are instrumental in collapsing magnetic moments and producing itinerant carriers, setting the stage for superconductivity. We first attempted to induce metallization by replacing O ions in LaMnPO with F, which has been observed to disrupt the antiferromagnetic state and lead to superconductivity in isostructural LaFeAsO ( 1 ). We observed little change in the insulating gap, magnetic ordering temperature, and ordered moment, suggesting that LaMnPO is too far from metallization to be driven there by chemical doping. We grew high-quality single crystals of one such Mn-based compound, LaMnPO, and subjected it to a number of experimental and theoretical tests to gauge the likelihood of it exhibiting superconductivity. The presence of a band gap—the defining feature of an insulator—was confirmed by optical conductivity, electrical resistivity, and photoemission measurements, and its observed magnitude was in excellent agreement with the theoretical gap obtained from our first principles calculations, establishing an important link between theory and experiment. Our calculations were carried out within dynamical mean field theory (DMFT), one of the few schemes capable of overcoming the difficulties inherent in modeling strongly correlated systems ( 2 ). Formal valence counting, in which electron transfer is estimated by considering a full valence shell for each atom, predicts divalent Mn ions in LaMnPO (La 3+ Mn 2+ P 3- O 2- ). Our DMFT calculations, which were independently confirmed by x-ray absorption measurements, show that this simple picture is not entirely correct, and substantial variations in the Mn electronic state provide the first indication that LaMnPO is close to becoming metallic, and thus nonmagnetic. Superconductivity results from mutual interactions among electrons in a material that cause their relative motions to become correlated, effectively binding them into pairs. In extreme cases, correlations can be so strong that all electrons become localized, resulting in the material becoming an insulator. Delocalized or mobile electrons are required for superconductivity, and they can be obtained from insulators either by introducing extra charges via doping or by weakening the correlations themselves. Experiments on different types of superconductors, including cuprates, indicate that superconductivity occurs just when these delocalized electrons appear. Fig. P1 summarizes the behaviors possible for different strengths of correlations and degrees of charge doping. The highest known T c ’s are found in cuprates, but lower T c ’s are found in the more weakly correlated and metallic Fe-pnictides ( 1 ). Can even higher T c ’s be found in compounds that are isostructural with Fe-pnictides but nevertheless host stronger correlations? The insulating Mn-pnictides provide an ideal testing ground for this proposal, although it is generally believed that prohibitively high pressures or large amounts of doping would be required to metallize these compounds. Fig. P1. Compounds with different strengths of correlations and degrees of charge doping. Compounds with strong correlations, such as the cuprates, are insulating until doping drives them to becoming metallic. Weakly correlated compounds such as the Fe-pnictides are always metallic, although doping destroys magnetic order. Superconductivity is nestled in the confluence of the metal-insulator transition and where magnetic order is destroyed. Mn-pnictides such as LaMnPO may be more strongly correlated than cuprates, potentially leading to larger values of T c . Superconducting materials conduct electricity without dissipating energy, but their applications have been limited by their low critical temperatures ( T c ), above which they conduct electricity as normal metals. Hopes of developing new superconductor-based technologies for energy distribution, communications, and medical imaging rely on the discovery of new materials exhibiting superconductivity above cryogenic temperatures, i.e., temperatures within about 100 degrees of absolute zero. Record high T c ’s in cuprate superconductors are achieved by chemically modifying (doping) the insulating host until it conducts electricity and loses magnetic order. Our calculations reveal that a Mn-based antiferromagnetic insulator, LaMnPO, undergoes a similar transition under the application of modest pressure, raising the possibility of high-temperature superconductivity in a new family of materials.

Abstract: Mutations in leucine-rich repeat kinase 2 ( LRRK2 ) cause inherited Parkinson disease (PD), and common variants around LRRK2 are a risk factor for sporadic PD. Using protein–protein interaction arrays, we identified BCL2-associated athanogene 5, Rab7L1 (RAB7, member RAS oncogene family-like 1), and Cyclin-G–associated kinase as binding partners of LRRK2. The latter two genes are candidate genes for risk for sporadic PD identified by genome-wide association studies. These proteins form a complex that promotes clearance of Golgi-derived vesicles through the autophagy–lysosome system both in vitro and in vivo. We propose that three different genes for PD have a common biological function. More generally, data integration from multiple unbiased screens can provide insight into human disease mechanisms.

Abstract: We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus . The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans ( Apis mellifera and Nasonia vitripennis ) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Abstract: Here we report a human intellectual disability disease locus on chromosome 14q31.3 corresponding to mutation of the ZC3H14 gene that encodes a conserved polyadenosine RNA binding protein. We identify ZC3H14 mRNA transcripts in the human central nervous system, and we find that rodent ZC3H14 protein is expressed in hippocampal neurons and colocalizes with poly(A) RNA in neuronal cell bodies. A Drosophila melanogaster model of this disease created by mutation of the gene encoding the ZC3H14 ortholog dNab2, which also binds polyadenosine RNA, reveals that dNab2 is essential for development and required in neurons for normal locomotion and flight. Biochemical and genetic data indicate that dNab2 restricts bulk poly(A) tail length in vivo, suggesting that this function may underlie its role in development and disease. These studies reveal a conserved requirement for ZC3H14/dNab2 in the metazoan nervous system and identify a poly(A) RNA binding protein associated with a human brain disorder.

Abstract: Epidemiological and preclinical evidence supports that omega-3 dietary fatty acids (fish oil) reduce the risks of macular degeneration and cancers, but the mechanisms by which these omega-3 lipids inhibit angiogenesis and tumorigenesis are poorly understood. Here we show that epoxydocosapentaenoic acids (EDPs), which are lipid mediators produced by cytochrome P450 epoxygenases from omega-3 fatty acid docosahexaenoic acid, inhibit VEGF- and fibroblast growth factor 2-induced angiogenesis in vivo, and suppress endothelial cell migration and protease production in vitro via a VEGF receptor 2-dependent mechanism. When EDPs (0.05 mg⋅kg −1 ⋅d −1 ) are coadministered with a low-dose soluble epoxide hydrolase inhibitor, EDPs are stabilized in circulation, causing ∼70% inhibition of primary tumor growth and metastasis. Contrary to the effects of EDPs, the corresponding metabolites derived from omega-6 arachidonic acid, epoxyeicosatrienoic acids, increase angiogenesis and tumor progression. These results designate epoxyeicosatrienoic acids and EDPs as unique endogenous mediators of an angiogenic switch to regulate tumorigenesis and implicate a unique mechanistic linkage between omega-3 and omega-6 fatty acids and cancers.

Abstract: The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii , the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.