Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping

INTRODUCTION: Mitochondrial genetics are an important but largely neglected area of research in Alzheimer's disease. A major impediment is the lack of data sets. METHODS: We used an innovative, rigorous approach, combining several existing tools with our own, to accurately assemble and call variants in 809 whole mitochondrial genomes. RESULTS: To help address this impediment, we prepared a data set that consists of 809 complete and annotated mitochondrial genomes with samples from the Alzheimer's Disease Neuroimaging Initiative. These whole mitochondrial genomes include rich phenotyping, such as clinical, fluid biomarker, and imaging data, all of which is available through the Alzheimer's Disease Neuroimaging Initiative website. Genomes are cleaned, annotated, and prepared for analysis. DISCUSSION: These data provide an important resource for investigating the impact of mitochondrial genetic variation on risk for Alzheimer's disease and other phenotypes that have been measured in the Alzheimer's Disease Neuroimaging Initiative samples

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway

Apoptotic cell clearance (efferocytosis) elicits an anti-inflammatory response by phagocytes, but the mechanisms that underlie this response are still being defined. Here, we uncover a chloride-sensing signalling pathway that controls both the phagocyte 'appetite' and its anti-inflammatory response. Efferocytosis transcriptionally altered the genes that encode the solute carrier (SLC) proteins SLC12A2 and SLC12A4. Interfering with SLC12A2 expression or function resulted in a significant increase in apoptotic corpse uptake per phagocyte, whereas the loss of SLC12A4 inhibited corpse uptake. In SLC12A2-deficient phagocytes, the canonical anti-inflammatory program was replaced by pro-inflammatory and oxidative-stress-associated gene programs. This 'switch' to pro-inflammatory sensing of apoptotic cells resulted from the disruption of the chloride-sensing pathway (and not due to corpse overload or poor degradation), including the chloride-sensing kinases WNK1, OSR1 and SPAK-which function upstream of SLC12A2-had a similar effect on efferocytosis. Collectively, the WNK1-OSR1-SPAK-SLC12A2/SLC12A4 chloride-sensing pathway and chloride flux in phagocytes are key modifiers of the manner in which phagocytes interpret the engulfed apoptotic corpse

KELT-1b: A Strongly Irradiated, Highly Inflated, Short Period, 27 Jupiter-mass Companion Transiting a mid-F Star

We present the discovery of KELT-1b, the first transiting low-mass companion from the wide-field Kilodegree Extremely Little Telescope-North (KELT-North) survey. The V=10.7 primary is a mildly evolved, solar-metallicity, mid-F star. The companion is a low-mass brown dwarf or super-massive planet with mass of 27.23+/-0.50 MJ and radius of 1.110+0.037-0.024 RJ, on a very short period (P=1.21750007) circular orbit. KELT-1b receives a large amount of stellar insolation, with an equilibrium temperature assuming zero albedo and perfect redistribution of 2422 K. Upper limits on the secondary eclipse depth indicate that either the companion must have a non-zero albedo, or it must experience some energy redistribution. Comparison with standard evolutionary models for brown dwarfs suggests that the radius of KELT-1b is significantly inflated. Adaptive optics imaging reveals a candidate stellar companion to KELT-1, which is consistent with an M dwarf if bound. The projected spin-orbit alignment angle is consistent with zero stellar obliquity, and the vsini of the primary is consistent with tidal synchronization. Given the extreme parameters of the KELT-1 system, we expect it to provide an important testbed for theories of the emplacement and evolution of short-period companions, and theories of tidal dissipation and irradiated brown dwarf atmospheres.Comment: 30 pages, 19 figures. Submitted to Ap

KELT-3b: A Hot Jupiter Transiting a V=9.8 Late-F Star

We report the discovery of KELT-3b, a moderately inflated transiting hot Jupiter with a mass of 1.477 (-0.067, +0.066) M_J, and radius of 1.345 +/- 0.072 R_J, with an orbital period of 2.7033904 +/- 0.000010 days. The host star, KELT-3, is a V=9.8 late F star with M_* = 1.278 (-0.061, +0.063) M_sun, R_* = 1.472 (-0.067, +0.065) R_sun, T_eff = 6306 (-49, +50) K, log(g) = 4.209 (-0.031, +0.033), and [Fe/H] = 0.044 (-0.082, +0.080), and has a likely proper motion companion. KELT-3b is the third transiting exoplanet discovered by the KELT survey, and is orbiting one of the 20 brightest known transiting planet host stars, making it a promising candidate for detailed characterization studies. Although we infer that KELT-3 is significantly evolved, a preliminary analysis of the stellar and orbital evolution of the system suggests that the planet has likely always received a level of incident flux above the empirically-identified threshold for radius inflation suggested by Demory & Seager (2011).Comment: 12 pages, 12 figures, accepted to Ap

KELT-6b: A P~7.9 d Hot Saturn Transiting a Metal-Poor Star with a Long-Period Companion

We report the discovery of KELT-6b, a mildly-inflated Saturn-mass planet transiting a metal-poor host. The initial transit signal was identified in KELT-North survey data, and the planetary nature of the occulter was established using a combination of follow-up photometry, high-resolution imaging, high-resolution spectroscopy, and precise radial velocity measurements. The fiducial model from a global analysis including constraints from isochrones indicates that the V=10.38 host star (BD+31 2447) is a mildly evolved, late-F star with T_eff=6102 \pm 43 K, log(g_*)=4.07_{-0.07}^{+0.04} and [Fe/H]=-0.28 \pm 0.04, with an inferred mass M_*=1.09 \pm 0.04 M_sun and radius R_star=1.58_{-0.09}^{+0.16} R_sun. The planetary companion has mass M_P=0.43 \pm 0.05 M_J, radius R_P=1.19_{-0.08}^{+0.13} R_J, surface gravity log(g_P)=2.86_{-0.08}^{+0.06}, and density rho_P=0.31_{-0.08}^{+0.07} g~cm^{-3}. The planet is on an orbit with semimajor axis a=0.079 \pm 0.001 AU and eccentricity e=0.22_{-0.10}^{+0.12}, which is roughly consistent with circular, and has ephemeris of T_c(BJD_TDB)=2456347.79679 \pm 0.00036 and P=7.845631 \pm 0.000046 d. Equally plausible fits that employ empirical constraints on the host star parameters rather than isochrones yield a larger planet mass and radius by ~4-7%. KELT-6b has surface gravity and incident flux similar to HD209458b, but orbits a host that is more metal poor than HD209458 by ~0.3 dex. Thus, the KELT-6 system offers an opportunity to perform a comparative measurement of two similar planets in similar environments around stars of very different metallicities. The precise radial velocity data also reveal an acceleration indicative of a longer-period third body in the system, although the companion is not detected in Keck adaptive optics images.Comment: Published in AJ, 17 pages, 15 figures, 6 table

Feasibility Study of Short Takeoff and Landing Urban Air Mobility Vehicles Using Geometric Programming

Electric Short Takeoff and Landing (eSTOL) vehicles are proposed as a path towards implementing an Urban Air Mobility (UAM) network that reduces critical vehicle certification risks and offers advantages in vehicle performance compared to the widely proposed Electric Vertical Takeoff and Landing (eVTOL) aircraft. An overview is given of the system constraints and key enabling technologies that must be incorporated into the design of the vehicle. The tradeoffs between vehicle performance and runway length are investigated using geometric programming, a robust optimization framework. Runway lengths as short as 100-300 ft are shown to be feasible, depending on the level of technology and the desired cruise speed. The tradeoffs between runway length and the potential to build new infrastructure in urban centers are investigated using Boston as a representative case study. The placement of some runways up to 600ft is shown to be possible in the urban center, with a significant increase in the number of potential locations for runways shorter than 300ft. Key challenges and risks to implementation are discussed

Fostering relations: first sex and marital timings for children raised by kin and non-kin carers

Kinship fostering is generally preferred to non-kin fostering by policy makers in the U.S. and elsewhere. Researchers and policy makers alike tend to provide several proximate reasons for why this may be, generally neglecting an ultimate evolutionary framework. However, kin selection theory predicts that in the absence of genetically related parents, care from kin will result in the most similar life history outcomes. In low-fertility settings, parents typically favour increased investment in embodied capital and thus delayed reproductive life history strategy. Using archival data from the original Kinsey survey, collected in the U.S. from 1938 to 1963, we used survival analyses to compare the effects of living with kin and non-kin fosterers in childhood on timings of first sex and marriage. Our results support a kin selection hypothesis showing that while fostered children have accelerated life histories compared to children from "intact families", kin fosterers buffer children from early sexual and reproductive behaviors, compared to children cared for by non-kin. © 2014 The Authors