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Sample records for 238u-230th radioactive disequilibrium

  1. Crystallisation ages in coeval silicic magma bodies: 238U-230Th disequilibrium evidence from the Rotoiti and earthquake flat eruption deposits, Taupo volcanic zone, New Zealand

    USGS Publications Warehouse

    Charlier, B.L.A.; Peate, D.W.; Wilson, C.J.N.; Lowenstern, J. B.; Storey, M.; Brown, S.J.A.

    2003-01-01

    The timescales over which moderate to large bodies of silicic magma are generated and stored are addressed here by studies of two geographically adjacent, successive eruption deposits in the Taupo Volcanic Zone, New Zealand. The earlier, caldera-forming Rotoiti eruption (>100 km3 magma) at Okataina volcano was followed, within months at most, by the Earthquake Flat eruption (??? 10 km3 magma) from nearby Kapenga volcano; both generated nonwelded ignimbrite and coeval widespread fall deposits. The Rotoiti and Earthquake Flat deposits are both crystal-rich high-silica rhyolites, with sparse glass-bearing granitoid fragments also occurring in Rotoiti lag breccias generated during caldera collapse. Here we report 238U-230Th disequilibrium data on whole rocks and mineral separates from representative Rotoiti and Earthquake Flat pumices and the co-eruptive Rotoiti granitoid fragments using TIMS and in situ zircon analyses by SIMS. Multiple-grain zircon-controlled crystallisation ages measured by TIMS from the Rotoiti pumice range from 69??3 ka ( 350 ka, with a pronounced peak at 70-90 ka. The weighted mean of isochrons is 83??14 ka, in accord with the TIMS data. One glass-bearing Rotoiti granitoid clast yielded an age of 57??8 ka by TIMS (controlled by Th-rich phases that, however, are not apparently present in the juvenile pumices). Another glass-bearing Rotoiti granitoid yielded SIMS zircon model ages peaking at 60-90 ka, having a similar age distribution to the pumice. Age data from pumices are consistent with a published 64??4 ka eruptive age (now modified to 62??2 ka), but chemical and/or mineralogical data imply that the granitoid lithics are not largely crystalline Rotoiti rhyolite, but instead represent contemporaneous partly molten intrusions reflecting different sources in their chemistries and mineralogies. Similarly, although the Earthquake Flat eruption immediately followed (and probably was triggered by) the Rotoiti event, age data from juvenile material

  2. 238U-230Th dating of chevkinite in high-silica rhyolites from La Primavera and Yellowstone calderas

    USGS Publications Warehouse

    Vazquez, Jorge A.; Velasco, Noel O.; Schmitt, Axel K.; Bleick, Heather A.; Stelten, Mark E.

    2014-01-01

    Application of 238U-230Th disequilibrium dating of accessory minerals with contrasting stabilities and compositions can provide a unique perspective on magmatic evolution by placing the thermochemical evolution of magma within the framework of absolute time. Chevkinite, a Th-rich accessory mineral that occurs in peralkaline and metaluminous rhyolites, may be particularly useful as a chronometer of crystallization and differentiation because its composition may reflect the chemical changes of its host melt. Ion microprobe 128U-230Th dating of single chevkinite microphenocrysts from pre- and post-caldera La Primavera, Mexico, rhyolites yields model crystallization ages that are within 10's of k.y. of their corresponding K-Ar ages of ca. 125 ka to 85 ka, while chevkinite microphenocrysts from a post-caldera Yellowstone, USA, rhyolite yield a range of ages from ca. 110 ka to 250 ka, which is indistinguishable from the age distribution of coexisting zircon. Internal chevkinite-zircon isochrons from La Primavera yield Pleistocene ages with ~5% precision due to the nearly two order difference in Th/U between both minerals. Coupling chevkinite 238U-230Th ages and compositional analyses reveals a secular trend of Th/U and rare earth elements recorded in Yellowstone rhyolite, likely reflecting progressive compositional evolution of host magma. The relatively short timescale between chevkinite-zircon crystallization and eruption suggests that crystal-poor rhyolites at La Primavera were erupted shortly after differentiation and/or reheating. These results indicate that 238U-230Th dating of chevkinite via ion microprobe analysis may be used to date crystallization and chemical evolution of silicic magmas.

  3. 238U-230Th equilibrium in arc magmas and implications for the time scales of mantle metasomatism

    NASA Astrophysics Data System (ADS)

    Reubi, Olivier; Sims, Kenneth W. W.; Bourdon, Bernard

    2014-04-01

    Large excesses of 238U and 226Ra relative to 230Th characterize many arc magmas and are commonly interpreted to represent recent addition of slab-derived fluid to the mantle wedge beneath the arc. A significant proportion of arc magmas are, however, in 238U-230Th radioactive equilibrium. This is generally thought to result from “buffering” of the young slab fluid U-series signal by a sediment component in secular equilibrium. Here we present new 238U-230Th-226Ra and 235U-231Pa measurements for historic andesites from Volcán de Colima, Mexico. In all lavas (230Th/238U) are in equilibrium, whereas (231Pa/235U) and (226Ra/230Th) are significantly greater than one. These data demonstrate that arc magmas with (230Th/238U) equilibrium can have significant 231Pa and 226Ra excesses, precluding ageing of the magmas in the crust as the cause of 230Th/238U equilibrium. Quantitative modeling of metasomatic and melting processes further indicates that addition of sediment melts to a depleted mantle wedge produces significant 230Th excesses and that 238U excesses induced by recent addition of fluids derived from the altered oceanic crust are not sufficient to compensate these 230Th excesses. U-series activity ratios in Colima magmas are best explained by models in which the metasomatised mantle returns to secular equilibrium before melting, implying a time lag ⩾350 kyr, with subsequent production of 231Pa and 226Ra excesses by in-growth during melting rather than by addition of slab fluids. Investigation of a global compilation of U-series data in arc magma indicates that our model proposed for Colima applies to most arc magmas in or near (230Th-238U) equilibrium. The time lag between mantle metasomatism and melting appears to vary between hundreds years to more than 350 kyr in subduction zones. We posit that the absence of U/Th elemental fractionation during melting of arc sources in (230Th/238U) equilibrium reflects a higher fO2 compared to MORB sources that yield

  4. 238U-230Th crystallization ages for the oldest domes of the Mono Craters, eastern California

    NASA Astrophysics Data System (ADS)

    Marcaida, M.; Vazquez, J. A.

    2014-12-01

    The Mono Craters volcanic chain is one of the youngest areas of rhyolitic volcanism in the Mono Lake-Long Valley region of eastern California. Located just south of Mono Lake, the Mono Craters comprise at least 28 individual domes and flows (numbered 3-30, north to south); however, the timing and frequency of eruptions remain poorly resolved. The earliest signs of volcanic activity are preserved as numerous tephra layers (Ashes 1-19, top to bottom) in the late Pleistocene Wilson Creek formation of ancestral Mono Lake, which indicate that rhyolitic volcanism from Mono Craters began by at least ca. 62 ka [1]. Although the current chronology indicates that most of the Mono Craters are younger than ca. 20 ka [2-4], similar compositions of titanomagnetite from both pumice and lava potentially correlate several Wilson Creek tephras to porphyritic biotite-bearing domes 11, 24, and 19 of the Mono Craters [5], suggesting that multiple domes in the Mono Craters chain reflect volcanism older than ca. 20 ka. Ash 3 is correlated to dome 11 based on similar ca. 20 ka ages and titanomagnetite compositions [6]. More recently, we performed ion microprobe 238U-230Th dating of unpolished rims of allanite and zircon from domes 24 and 19, yielding isochron ages of ca. 38 ka and ca. 42 ka, respectively. The age of dome 24 is consistent with the ca. 38 ka age of its potential correlative tephra layers [1, 5], indicating that dome 24 is likely the extrusive equivalent of Ashes 9-10. Dome 19 has titanomagnetite crystals with similar bimodal chemistry to titanomagnetites from Ash 15 [5]. The age of dome 19 is indistinguishable from the 238U-230Th age of Ash 15 [1], which erupted during a prominent geomagnetic excursion, originally designated as the "Mono Lake" excursion. Combining geochronological and titanomagnetite compositional data confirms that Ash 15 and its extrusive equivalent, dome 19, erupted during the Laschamp excursion. [1] Vazquez, J.A. and Lidzbarski, M.I. (2012) EPSL 357

  5. 238U- 230Th- 226Ra disequilibrium in young Mt. Shasta andesites and dacites

    NASA Astrophysics Data System (ADS)

    Volpe, Alan M.

    1992-11-01

    The paper describes 238U-series nuclides and 230Th/ 232Th ratios measured by mass spectrometry in mineral separates of young Mt. Shasta andesites and dacites. The results constrain the timing of recent calc-alkaline magma fractionation at this volcano. Hotlum, Misery Hill and Black Butte rocks show small, < 13% 230Th- 238U and < 6% 226Ra- 230Th, disequilibria. Plagioclase have 7-26% 226Ra excesses, magnetite and groundmass have 4-5% 226Ra deficits, and pyroxenes have equilibrium ( 226Ra/ 230Th) activity ratios. Internal ( 230Th)-( 238U)and Ba-normalized ( 226Ra)-( 230Th) isotope diagrams for Hotlum and Black Butte dacites suggest that closed-system Th-U and Ra-Th fractionation occurred less than 10,000 years ago. Significant 226Ra- 230Th disequilibria in the Black Butte dacite strongly suggests that this rock erupted more recently than 9400 years ago. Results for Hotlum andesites suggest a longer pre-eruption crystal residence time compared to the dacites. There may also have been recent open Ra-Th system changes in the melt composition. Initial Th/U ratios for the rocks are low (2.43-2.57), similar to those in mid-ocean ridge basalts (MORB), and preclude significant assimilation of crust with markedly different Th-U composition.

  6. Resolving the early chronology of Mono Craters volcanism with combined 238U-230Th and 40Ar/39Ar dating

    NASA Astrophysics Data System (ADS)

    Vazquez, J. A.; Calvert, A. T.; Marcaida, M.; Mangan, M.; Lidzbarski, M. I.; Stelten, M. E.

    2013-12-01

    California's largest locus of Pleistocene-Holocene rhyolitic volcanism is the Mono Lake-Long Valley region of eastern California. The Mono Craters chain marks the northern portion of this locus, and is composed of at least 28 individual domes of high-silica rhyolite. The record of Holocene volcanism at Mono Craters is relatively well constrained by tephrostratigraphy and radiocarbon dating. However, the timing and frequency of late Pleistocene dome emplacement is poorly resolved, with most of the chronology based on hydration-rind dating of obsidian. A well-exposed archive of late Pleistocene volcanism from Mono Craters is recorded by tephra beds (ashes numbered 1-19, youngest to oldest) of the informal Wilson Creek formation that accumulated in ancestral Mono Lake. To resolve a precise chronology for late Pleistocene volcanism at Mono Craters and tune the time-series of explosive volcanism preserved by Wilson Creek tephras, we performed ion microprobe 238U-230Th dating of allanite and zircon together with laser-fusion 40Ar/39Ar dating of sanidine from rhyolite domes that yield the oldest hydration rind ages and have relatively subdued morphology. Sanidine from multiple domes, including both hornblende-biotite and fayalite-bearing rhyolite types, yield 40Ar/39Ar ages up to ca. 25 ka. Ion microprobe analyses of unpolished rims on indium-mounted allanite and zircon crystals yield U-Th isochron ages that are indistinguishable from their associated sanidine 40Ar/39Ar ages. However, the interiors of sectioned allanite crystals yield model U-Th ages that may be up to 30 kyr older than their rims. Rims on allanite and zircon from ashes 7-19 in the lower portion of the Wilson Creek stratigraphy yield isochron ages of ca. 27-62 ka [1], which are supported by ages from magnetostratigraphy [2]. Ash 3 contains titanomagnetites that are compositionally distinct from other Wilson Creek tephras, but match those in the hornblende-biotite rhyolite of dome 11. Rims on allanite and

  7. High-resolution tephrochronology of the Wilson Creek Formation (Mono Lake, California) and Laschamp event using 238U-230Th SIMS dating of accessory mineral rims

    NASA Astrophysics Data System (ADS)

    Vazquez, Jorge A.; Lidzbarski, Marsha I.

    2012-12-01

    Sediments of the Wilson Creek Formation surrounding Mono Lake preserve a high-resolution archive of glacial and pluvial responses along the eastern Sierra Nevada due to late Pleistocene climate change. An absolute chronology for the Wilson Creek stratigraphy is critical for correlating the paleoclimate record to other archives in the western U.S. and the North Atlantic region. However, multiple attempts to date the Wilson Creek stratigraphy using carbonates and tephras yield discordant results due to open-system effects and radiocarbon reservoir uncertainties as well as abundant xenocrysts. New ion microprobe 238U-230Th dating of the final increments of crystallization recorded by allanite and zircon autocrysts from juvenile pyroclasts yield ages that effectively date eruption of key tephra beds and delimit the timing of basal Wilson Creek sedimentation to the interval between 26.8±2.1 and 61.7±1.9 ka. Tephra (Ash 15) erupted during the geomagnetic excursion originally designated the Mono Lake excursion yields an age of 40.8±1.9 ka, indicating that the event is instead the Laschamp excursion. The new ages support a depositional chronology from magnetostratigraphy that indicates quasi-synchronous glacial and hydrologic responses in the Sierra Nevada and Mono Basin to regional climate change, with intervals of lake filling and glacial-snowpack melting that are in phase with peaks in spring insolation.

  8. High-resolution tephrochronology of the Wilson Creek Formation (Mono Lake, California) and Laschamp event using 238U-230Th SIMS dating of accessory mineral rims

    USGS Publications Warehouse

    Vazquez, Jorge A.; Lidzbarski, Marsha I.

    2012-01-01

    Sediments of the Wilson Creek Formation surrounding Mono Lake preserve a high-resolution archive of glacial and pluvial responses along the eastern Sierra Nevada due to late Pleistocene climate change. An absolute chronology for the Wilson Creek stratigraphy is critical for correlating the paleoclimate record to other archives in the western U.S. and the North Atlantic region. However, multiple attempts to date the Wilson Creek stratigraphy using carbonates and tephras yield discordant results due to open-system effects and radiocarbon reservoir uncertainties as well as abundant xenocrysts. New ion microprobe 238U-230Th dating of the final increments of crystallization recorded by allanite and zircon autocrysts from juvenile pyroclasts yield ages that effectively date eruption of key tephra beds and delimit the timing of basal Wilson Creek sedimentation to the interval between 26.8±2.1 and 61.7±1.9 ka. Tephra (Ash 15) erupted during the geomagnetic excursion originally designated the Mono Lake excursion yields an age of 40.8±1.9 ka, indicating that the event is instead the Laschamp excursion. The new ages support a depositional chronology from magnetostratigraphy that indicates quasi-synchronous glacial and hydrologic responses in the Sierra Nevada and Mono Basin to regional climate change, with intervals of lake filling and glacial-snowpack melting that are in phase with peaks in spring insolation.

  9. The mechanisms and timescales of rhyolite generation at Yellowstone caldera: New insights from 238U-230Th crystallization ages, trace-elements, and isotope compositions of zircon and sanidine

    NASA Astrophysics Data System (ADS)

    Stelten, M. E.; Cooper, K. M.; Vazquez, J. A.; Calvert, A. T.

    2013-12-01

    The Yellowstone Plateau hosts one of the largest Quaternary magmatic systems on Earth, with caldera forming eruptions at ~2.1 Ma, ~1.3 Ma, and ~0.64 Ma, as well as numerous intracaldera rhyolitic eruptions between caldera-forming events. The most recent post-caldera eruptive episode at Yellowstone produced the Central Plateau Member (CPM) of the Plateau Rhyolite, which erupted intermittently between ca. 170-70 ka with a cumulative volume ≥600 km3. Thus, the CPM rhyolites provide snapshots of a large silicic magmatic system though time. We examine five CPM rhyolites that erupted from ~125 ka to ~70 ka, and constrain the mechanisms and timescales of generating eruptible rhyolites at Yellowstone caldera by comparing (1) 238U-230Th crystallization ages and trace-element compositions of the interiors and surfaces (i.e., unpolished rims) of individual zircons with (2) bulk 238U-230Th crystallization ages and in situ major-element, Ba, and Pb isotope data for sanidines hosted in each rhyolite. The zircon age and trace-element data show that zircons in CPM rhyolites record crystallization from their respective eruption age to >150 ka before eruption, with most zircon surfaces crystallizing close to eruption and many interiors crystallizing 10 kyr to 150 kyr before eruption. At any given age, zircon surfaces have homogeneous trace-element compositions relative to zircon interiors for most elements and element ratios. For example, when considering data from all five CPM rhyolites, the zircon surfaces and interiors show similar broad trends in Eu/Eu* and U/Th over time, but the surfaces display less scatter. These observations suggest that the zircon surfaces grew from a more homogeneous region of the magma reservoir relative to where the zircon interiors grew. Although the zircon surfaces and interiors are similar in some elements and element ratios (e.g., Eu/Eu*, U/Th) at a given age, zircon surfaces and interiors display distinct (Y, MREE, HREE)/(P, U) ratios at a given

  10. Magma mixing and the generation of isotopically juvenile silicic magma at Yellowstone caldera inferred from coupling 238U-230Th ages with trace elements and Hf and O isotopes in zircon and Pb isotopes in sanidine

    NASA Astrophysics Data System (ADS)

    Stelten, Mark E.; Cooper, Kari M.; Vazquez, Jorge A.; Reid, Mary R.; Barfod, Gry H.; Wimpenny, Josh; Yin, Qing-zhu

    2013-08-01

    The nature of compositional heterogeneity within large silicic magma bodies has important implications for how silicic reservoirs are assembled and evolve through time. We examine compositional heterogeneity in the youngest (~170 to 70 ka) post-caldera volcanism at Yellowstone caldera, the Central Plateau Member (CPM) rhyolites, as a case study. We compare 238U-230Th age, trace-element, and Hf isotopic data from zircons, and major-element, Ba, and Pb isotopic data from sanidines hosted in two CPM rhyolites (Hayden Valley and Solfatara Plateau flows) and one extracaldera rhyolite (Gibbon River flow), all of which erupted near the caldera margin ca. 100 ka. The Hayden Valley flow hosts two zircon populations and one sanidine population that are consistent with residence in the CPM reservoir. The Gibbon River flow hosts one zircon population that is compositionally distinct from Hayden Valley flow zircons. The Solfatara Plateau flow contains multiple sanidine populations and all three zircon populations found in the Hayden Valley and Gibbon River flows, demonstrating that the Solfatara Plateau flow formed by mixing extracaldera magma with the margin of the CPM reservoir. This process highlights the dynamic nature of magmatic interactions at the margins of large silicic reservoirs. More generally, Hf isotopic data from the CPM zircons provide the first direct evidence for isotopically juvenile magmas contributing mass to the youngest post-caldera magmatic system and demonstrate that the sources contributing magma to the CPM reservoir were heterogeneous in 176Hf/177Hf at ca. 100 ka. Thus, the limited compositional variability of CPM glasses reflects homogenization occurring within the CPM reservoir, not a homogeneous source.

  11. Cogenetic late Pleistocene rhyolite and cumulate diorites from Augustine Volcano revealed by SIMS 238U-230Th dating of zircon, and implications for silicic magma generation by extraction from mush

    NASA Astrophysics Data System (ADS)

    Coombs, Michelle L.; Vazquez, Jorge A.

    2014-12-01

    Volcano, a frequently active andesitic island stratocone, erupted a late Pleistocene rhyolite pumice fall that is temporally linked through zircon geochronology to cumulate dioritic blocks brought to the surface in Augustine's 2006 eruption. Zircon from the rhyolite yield a 238U-230Th age of ˜25 ka for their unpolished rims, and their interiors yield a bimodal age populations at ˜26 ka and a minority at ˜41 ka. Zircon from dioritic blocks, ripped from Augustine's shallow magmatic plumbing system and ejected during the 2006 eruption, have interiors defining a ˜26 ka age population that is indistinguishable from that for the rhyolite; unpolished rims on the dioritic zircon are dominantly younger (≤12 ka) indicating subsequent crystallization. Zircon from rhyolite and diorite overlap in U, Hf, Ti, and REE concentrations although diorites also contain a second population of high-U, high temperature grains. Andesites that brought dioritic blocks to the surface in 2006 contain zircon with young (≤9 ka) rims and a scattering of older ages, but few zircon that crystallized during the 26 ka interval. Both the Pleistocene-age rhyolite and the 2006 dioritic inclusions plot along a whole-rock compositional trend distinct from mid-Holocene-present andesites and dacites, and the diorites, rhyolite, and two early Holocene dacites define linear unmixing trends often oblique to the main andesite array and consistent with melt (rhyolite) extraction from a mush (dacites), leaving behind a cumulate amphibole-bearing residue (diorites). Rare zircon antecrysts up to ˜300 ka from all rock types indicate that a Quaternary center has been present longer than preserved surficial deposits.

  12. Mid-ocean ridge basalt generation along the slow-spreading, South Mid-Atlantic Ridge (5-11°S): Inferences from 238U-230Th-226Ra disequilibria

    NASA Astrophysics Data System (ADS)

    Turner, Simon; Kokfelt, Thomas; Hauff, Folkmar; Haase, Karsten; Lundstrom, Craig; Hoernle, Kaj; Yeo, Isobel; Devey, Colin

    2015-11-01

    U-series disequilibria have provided important constraints on the physical processes of partial melting that produce basaltic magma beneath mid-ocean ridges. Here we present the first 238U-230Th-226Ra isotope data for a suite of 83 basalts sampled between 5°S and 11°S along the South Mid-Atlantic Ridge. This section of the ridge can be divided into 5 segments (A0-A4) and the depths to the ridge axis span much of the global range, varying from 1429 to 4514 m. Previous work has also demonstrated that strong trace element and radiogenic isotope heterogeneity existed in the source regions of these basalts. Accordingly, this area provides an ideal location in which to investigate the effects of both inferred melt column length and recycled materials. 226Ra-230Th disequilibria indicate that the majority of the basalts are less than a few millennia old such that their 230Th values do not require any age correction. The U-Th isotope data span a significant range from secular equilibrium up to 32% 230Th excess, also similar to the global range, and vary from segment to segment. However, the (230Th/238U) ratios are not negatively correlated with axial depth and the samples with the largest 230Th excesses come from the deepest ridge segment (A1). Two sub-parallel and positively sloped arrays (for segments A0-2 and A3 and A4) between (230Th/238U) and Th/U ratios can be modelled in various ways as mixing between melts from peridotite and recycled mafic lithologies. Despite abundant evidence for source heterogeneity, there is no simple correlation between (230Th/238U) and radiogenic isotope ratios suggesting that at least some of the trace element and radiogenic isotope variability may have been imparted to the source regions >350 kyr prior to partial melting to produce the basalts. In our preferred model, the two (230Th/238U) versus Th/U arrays can be explained by mixing of melts from one or more recycled mafic lithologies with melts derived from chemically heterogeneous

  13. Short-lived radioactivity and magma genesis.

    PubMed

    Gill, J; Condomines, M

    1992-09-01

    Short-lived decay products of uranium and thorium have half-lives and chemistries sensitive to the processes and time scales of magma genesis, including partial melting in the mantle and magmatic differentiation in the crust. Radioactive disequilibrium between (238)U, (230)Th, and (226)Ra is widespread in volcanic rocks. These disequilibria and the isotopic composition of thorium depend especially on the extent and rate of melting as well as the presence and composition of vapor during melting. The duration of mantle melting may be several hundred millennia, whereas ascent times are a few decades to thousands of years. Differentiation of most magmas commonly occurs within a few millennia, but felsic ones can be tens of millennia old upon eruption. PMID:17738278

  14. Uranium-series disequilibrium in tuffs from Yucca Mountain, Nevada, as evidence of pore-fluid flow over the last million years

    USGS Publications Warehouse

    Gascoyne, M.; Miller, N.H.; Neymark, L.A.

    2002-01-01

    Samples of tuff from boreholes drilled into fault zones in the Exploratory Studies Facility (ESF) and relatively unfractured rock of the Cross Drift tunnels, at Yucca Mountain, Nevada, have been analysed by U-series methods. This work is part of a project to verify the finding of fast flow-paths through the tuff to ESF level, indicated by the presence of 'bomb' 36Cl in pore fluids. Secular radioactive equilibrium in the U decay series, (i.e. when the radioactivity ratios 234U/238U, 230Th/234U and 226Ra/230Th all equal 1.00) might be expected if the tuff samples have not experienced radionuclide loss due to rock-water interaction occurring within the last million years. However, most fractured and unfractured samples were found to have a small deficiency of 234U (weighted mean 234U/238U=0.95??0.01) and a small excess of 230Th (weighted mean 230Th/234U 1.10??0.02). The 226Ra/230Th ratios are close to secular equilibrium (weighted mean = 0.94??0.07). These data indicate that 234U has been removed from the rock samples in the last ???350 ka, probably by pore fluids. Within the precision of the measurement, it would appear that 226Ra has not been mobilized and removed from the tuff, although there may be some localised 226Ra redistribution as suggested by a few ratio values that are significantly different from 1.0. Because both fractured and unfractured tuffs show approximately the same deficiency of 234U, this indicates that pore fluids are moving equally through fractured and unfractured rock, More importantly, fractured rock appears not to be a dominant pathway for groundwater flow (otherwise the ratio would be more strongly affected and the Th and Ra isotopic ratios would likely also show disequilibrium). Application of a simple mass-balance model suggests that surface infiltration rate is over an order of magnitude greater than the rate indicated by other infiltration models and that residence time of pore fluids at ESF level is about 400 a. Processes of U

  15. Disequilibrium in naturally occurring radioactive series in some phosphate ores.

    PubMed

    Hamidalddin, Safia H Q; Fakeha, Afaf A; Yeslam, Mai S; Ibraheim, Nagdya M

    2012-01-01

    Eight phosphate ore samples from Egypt and Saudi Arabia were studied by atomic absorption spectrometry for the Bi, Pb, Th and Al concentrations in ppm or ppb or per cent. Also X-ray diffraction spectrometry was applied for determining the mineral and chemical composition of the phosphate ore samples. A gamma spectrometry system, based on HPGe crystal, was applied for determining the concentrations of the radioactive elements in (238)U, (226)Ra and (232)Th series as well as (40)K, in Bq/kg dry weight. Concentrations in ppm were found to be from <10.0 to 20.48, from <7.50 to 27.30 and from <1.0 to 50.0 for Bi, Pb and Th, respectively. Al ranged from <0.05 to 3.13%. Major, minor and trace chemical and mineral compositions were assigned for each sample by XRD spectrometry. Concentrations of the different elements in both radioactive series, (238)U, (226)Ra and (232)Th were compared. Disequilibrium was found in both series. PMID:21982734

  16. Petrogenesis and 230Th-238U disequilibrium at Mt. Shasta, California, and in the Cascades

    NASA Astrophysics Data System (ADS)

    Newman, Sally; MacDougall, J. Douglas; Finkel, Robert C.

    1986-06-01

    Petrogenesis at Mt. Shasta is dominated by mixing of magmas and/or assimilation of wall rock, as is shown by petrographic, major and trace element chemistry, and 238U-230Th disequilibrium data. At least three end- members are involved in these mixing processes. Lavas of very young Cascades lavas, from Mt. Garibaldi in the north to Lassen Peak in the south, are characterized by a large range of thorium isotopic ratios, although series of samples from single volcanoes are characterized by approximately constant (230Th/232Th). There is a monotonic decrease in this ratio from Crater Lake south through Lassen Peak, perhaps reflecting increasing thickness of the underlying crust. Th/U fractionation in Cascades lavas, as evidenced by (230Th/238U)≥ 1, is in the opposite sense to that in most island arc lavas. This trend suggests that fluid transport, which is thought to produce uranium enrichment in island arc, is lacking or somehow modified in the petrogenesis of the Cascades lavas.

  17. Uranium-series disequilibrium in volcanic rocks from the Northeast Japan Arc

    NASA Astrophysics Data System (ADS)

    Yokoyama, T.; Iwamori, H.; Ueki, K.

    2011-12-01

    Subducting slabs are considered to release fluid components as a result of mineralogical reactions during progressive metamorphic dehydration. The fluid released from the slab subsequently induces melting in the mantle wedge as it ascends, resulting in island arc volcanism [1]. To understand the characteristics of slab-derived materials, geochemical tracers such as trace elements, radiogenic isotopes (e.g., Sr, Nd, Pb), and stable isotopes (e.g., B, Li) have been commonly used [2-3]. U-series disequilibria of island arc volcanic rocks have been used to understand melt generation in the source mantle and the timescales of fluid/melt migration in subduction zones. This is possible because of the short half-lives of daughter nuclides of 238U, 235U and 232Th (e.g., 75 kyr for 230Th, and 1.6 kyr for 226Ra). We report our preliminary measurements on 238U-230Th disequilibrium in volcanic rocks from the Northeast Japan Arc. Lava samples of basalts and basaltic andesites were collected from four volcanoes (Iwate, Akita-Komagatake, Yakeyama and Kampu). The eruption ages of these rocks are estimated to be range from 0 to 30 ka. The frontal-arc lavas (Iwate and Akita-Komagatake) are characterized by 238U-230Th disequilibrium with moderate 238U enrichments (5-10%). This is due to the addition to the mantle wedge of slab-derived fluids enriched in fluid-mobile elements (U) relative to less fluid-mobile elements (Th). The extent of 238U enrichment decreases as the slab depth increases, and the rear-arc lavas (Kampu) show 230Th enrichments relative to 238U (~5%). This generally reflects gradual decrease of the amount of slab derived fluid mixed into the wedge mantle. Thus, the 230Th excesses in rear-arc lavas may be predominantly produced by the melting of garnet-bearing upwelling mantle as observed in MORB (dynamic melting). However, our data show 230Th excess with an extremely low (230Th/232Th) ratio (~0.8) that plots outside the MORB data. This strongly argues against a model

  18. Discriminating assimilants and decoupling deep- vs. shallow-level crystal records at Mount Adams using 238U-230Th disequilibria and Os isotopes

    USGS Publications Warehouse

    Jicha, B.R.; Johnson, C.M.; Hildreth, W.; Beard, B.L.; Hart, G.L.; Shirey, S.B.; Singer, B.S.

    2009-01-01

    A suite of 23 basaltic to dacitic lavas erupted over the last 350??kyr from the Mount Adams volcanic field has been analyzed for U-Th isotope compositions to evaluate the roles of mantle versus crustal components during magma genesis. All of the lavas have (230Th/238U) > 1 and span a large range in (230Th/232Th) ratios, and most basalts have higher (230Th/232Th) ratios than andesites and dacites. Several of the lavas contain antecrysts (crystals of pre-existing material), yet internal U-Th mineral isochrons from six of seven lavas are indistinguishable from their eruption ages. This indicates a relatively brief period of time between crystal growth and eruption for most of the phenocrysts (olivine, clinopyroxene, plagioclase, magnetite) prior to eruption. One isochron gave a crystallization age that is ~ 20-25??ka older than its corresponding eruptive age, and is interpreted to reflect mixing of older and juvenile crystals or a protracted period of magma storage in the crust. Much of the eruptive volume since 350??ka consists of lavas that have small to moderate 230Th excesses (2-16%), which are likely inherited from melting of a garnet-bearing intraplate ("OIB-like") mantle source. Following melt generation and subsequent migration through the upper mantle, most Mt. Adams magmas interacted with young, mafic lower crust, as indicated by 187Os/188Os ratios that are substantially more radiogenic than the mantle or those expected via mixing of subducted material and the mantle wedge. Moreover, Os-Th isotope variations suggest that unusually large 230Th excesses (25-48%) and high 187Os/188Os ratios in some peripheral lavas reflect assimilation of small degree partial melts of pre-Quaternary basement that had residual garnet or Al-rich clinopyroxene. Despite the isotopic evidence for lower crustal assimilation, these processes are not generally recorded in the erupted phenocrysts, indicating that the crystal record of the deep-level 'cryptic' processes has been decoupled from shallow-level crystallization. ?? 2008 Elsevier B.V.

  19. Nucleon-Alpha Particle Disequilibrium and Short-Lived r-Process Radioactivities

    NASA Technical Reports Server (NTRS)

    Meyer, B. S.; Clayton, D. D.; Chellapilla, S.; The, L.-S.

    2002-01-01

    r-Process yields can be extremely sensitive to expansion parameters when a persistent disequilibrium between free nucleons and alpha particles is present. This may provide a natural scenario for understanding the variation of heavy and light r-process isotopes in different r-process events. Additional information is contained in the original extended abstract.

  20. 226Ra/238U disequilibrium in an upland organic soil exhibiting elevated natural radioactivity.

    PubMed

    Dowdall, Mark; O'Dea, John

    2002-01-01

    This paper presents the results of a study into the anomalous 226Ra/238U disequilibrium (226Ra/238U of 0.5-9) exhibited by an upland organic soil in Co. Donegal, Ireland. Radiochemical speciation of 226Ra, 238U and 225Ra indicates that in this organic soil the high 226Ra/238U ratio is due to loss of 235U relative to 226Ra via oxidation and mobilisation of 238U in the upper layers of the soil and subsequent loss in solution. At the lower, more reducing depths of the soil profile, 238U and 226Ra are essentially in equilibrium. Loss of 238U appears to occur primarily from the easily oxidised organic and iron oxide fractions of the soil, samples exhibiting high 226Ra/238U ratios displaying significantly lower 238U levels in these fractions than samples whose ratio is below the average value for the soil of the valley. Selective enrichment of 226Ra by plants or preferential leaching of 226Ra from the underlying rock is not supported by the results of this study. PMID:11848154

  1. Study of natural radioactivity and the state of radioactive disequilibrium in U-series for rock samples, North Eastern Desert, Egypt.

    PubMed

    El-Dine, Nadia Walley

    2008-01-01

    Twenty rock samples collected from North Eastern Desert in Egypt have been investigated. Natural radionuclide contents have been measured by gamma-ray spectrometry employing a shielded HPGe detector. The activities of (238)U, (232)Th and (40)K have been determined in Bq/kg dry weight. The absorbed dose rate of gamma radiation ranged from 100.48 to 22,140.53 nGy/h. The representative external hazard index values (H(ex)) for the corresponding samples were estimated. In the present work, the state of radioactive disequilibrium in the U-series at Wadi Baligh area was studied. The activity ratios between (226)Ra/(214)Pb and (214)Pb/(214)Bi were measured. The thorium-to-uranium concentration ratios (Clark value) were also estimated. PMID:17869529

  2. 238U-230Th-226Ra disequilibria in dacite and plagioclase from the 2004-2005 eruption of Mount St. Helens: Chapter 36 in A volcano rekindled: the renewed eruption of Mount St. Helens, 2004-2006

    USGS Publications Warehouse

    Cooper, Kari M.; Donnelly, Carrie T.

    2008-01-01

    230Th)/(232Th) measured for the 1980s reference suite. However, (230Th)/(232Th) for plagioclase separates for dome samples erupted during October and November 2004 are significantly different from corresponding whole-rock values, which suggests that a large fraction (>30 percent) of crystals in each sample are foreign to the host liquid. Furthermore, plagioclase in the two 2004 samples have U-series characteristics distinct from each other and from plagioclase in dacite erupted in 1982, indicating that (1) the current eruption must include a component of crystals (and potentially associated magma) that were not sampled by the 1980-86 eruption, and (2) dacite magmas erupted only a month apart in 2004 contain different populations of crystals, indicating that this foreign component is highly heterogeneous within the 2004-5 magma reservoir.

  3. Dispersion of U-series natural radionuclides in stream sediments from Edale, UK.

    PubMed

    Siddeeg, Saifeldin M; Bryan, Nicholas D; Livens, Francis R

    2014-05-01

    The spatial distribution of (238)U-series radionuclides, specifically 238U, 234U, 230Th and 226Ra, has been determined in stream sediments from Edale, Derbyshire, United Kingdom, to explore the behaviour of U-series radionuclides during weathering. For uranium and thorium, two different extraction methods were used, total dissolution with HNO3/HF in a microwave and leaching with aqua regia. This was followed by radiochemical separation using extraction chromatography, then alpha spectrometry measurement. The total radium contents in the sediments were measured using gamma spectrometry, while the leached fraction was measured in the same way as for uranium and thorium. The total sediment content of uranium and thorium ranges from ∼10 up to ∼200 Bq kg(-1), while the radium specific activity lies between ∼15 and 180 Bq kg(-1). In the aqua regia extractions, the uranium and thorium contents are in the range of ∼5 to ∼100 Bq kg(-1), while the radium specific activities are similar to those measured by total dissolution. All the radionuclides show no correlation with organic matter content. The activity ratios 234U/238U, 230Th/238U and 226Ra/238U were used to determine the degree of radioactive disequilibrium. The data show disequilibrium in most of the sediments, with activity ratios of 234U/238U, 230Th/238U and 226Ra/238U>1, inconsistent with evolution through straightforward weathering processes. Multivariate cluster analysis based on five variables, the specific activities of 238U, 234U, 230Th, 226Ra and loss on ignition, was employed to group the data and identify five distinct clusters. There seems to be a link between high radionuclide concentrations and proximity to landslips. PMID:24562972

  4. U-Th-Pb and 230Th/ 238U disequilibrium isotope systematics: Precise accessory mineral chronology and melt evolution tracing in the Alpine Bergell intrusion

    NASA Astrophysics Data System (ADS)

    Oberli, Felix; Meier, Martin; Berger, Alfons; Rosenberg, Claudio L.; GierÉ, Reto

    2004-06-01

    In order to investigate the potential of combined Th-U-Pb isotope and 230Th/ 238U disequilibrium systematics for tracing magmatic crystallization and melt evolution, conventional high-resolution single-crystal TIMS techniques have been applied to zircon, titanite and fragments of geochemically characterized growth zones of allanite. These minerals were extracted from a single tonalite specimen collected from the feeder zone of the Tertiary Bergell pluton (Southern Steep Belt, S Switzerland/N Italy). The isotopic results document an extended history of crystallization and melt evolution of at least 5 Ma, with well-resolved zircon ages defining an early interval of 33.0 to 32.0 Ma, followed by crystallization of zoned allanite from 32.0 to 28.0 Ma and formation of magmatic epidote possibly as late as 26 Ma. Trace and major element patterns in zoned allanite closely mirror melt evolution, characterized by increase of U concentration and sharp decrease of Th and LREE, reflecting early crystallization of phases low in U and, in particular, the dominating control by allanite precipitation. Preservation of substantial quantities of excess 206Pb derived from initial excess 230Th in all analyzed allanite grains indicates that their isotopic systems have not been reset by loss of radiogenic Pb during prolonged residence at magmatic conditions and regional-metamorphic cooling, and that the measured sequence of 208Pb/ 232Th dates translates into a real age sequence. Major loss of radiogenic Pb from compositionally zoned allanite by volume diffusion would have resulted in a data pattern grossly different from the observed one, as demonstrated by numerical modeling of 232Th- 208Pb- 238U- 230Th- 206Pb isotopic evolution. The results therefore suggest closure temperatures ≥700°C for magmatic allanite. Quantification of 230Th/ 238U disequilibrium relationships reveals a smooth, initially steep decrease of Th/U in the magma from values of 2.9 at 32.0 Ma to < 0.1 at 28.0 Ma in

  5. U-Th-Ra disequilibria in sediments of the Dora Baltea river (Italia)

    NASA Astrophysics Data System (ADS)

    Chabaux, F.; Deloche, A.; Pelt, E.; Granet, M.; Perrone, Th.; Boutin, R.; Viville, D.; Rihs, S.; Stille, P.

    2012-04-01

    In order to constrain the transfer time of sediments in Alpine rivers, we propose to use the U-series nuclides approach recently developed for Himalayan rivers (e.g., Chabaux et al., 2008; Granet et al., 2010). Therefore, a series of bank sediments has beeen collected along the Dora Baltea river (Italia), one of the Po's tributaries draining the southern slope of the Mont Blanc Massif. In addition to U series nuclides, major and trace element concentrations and Sr and Nd isotope ratios have been analyzed for each sample. The study indicates that the (234U/238U)-, (230Th/234U)- and the (226Ra/230Th)- activity ratios are very similar for all the samples, whereas the 230Th/232Th ratios can differ from one sample to another. Such a variation, consistent with the Sr and Nd isotope data, is certainly the consequence of mineralogical heterogeneities in the samples. This suggests that the use of 238U-230Th-232Th systematics alone is probably insufficient for constraining the transfer time of sediments in the Po rivers alluvial plain, whereas the combination of 238U-230Th disequilibrium with the 230Th-226Ra disequilibrium can help to constrain such time information.

  6. Disequilibrium mapping: Composite likelihood for pairwise disequilibrium

    SciTech Connect

    Devlin, B.; Roeder, K.; Risch, N.

    1996-08-15

    The pattern of linkage disequilibrium between a disease locus and a set of marker loci has been shown to be a useful tool for geneticists searching for disease genes. Several methods have been advanced to utilize the pairwise disequilibrium between the disease locus and each of a set of marker loci. However, none of the methods take into account the information from all pairs simultaneously while also modeling the variability in the disequilibrium values due to the evolutionary dynamics of the population. We propose a Composite Likelihood CL model that has these features when the physical distances between the marker loci are known or can be approximated. In this instance, and assuming that there is a single disease mutation, the CL model depends on only three parameters, the recombination fraction between the disease locus and an arbitrary marker locus, {theta}, the age of the mutation, and a variance parameter. When the CL is maximized over a grid of {theta}, it provides a graph that can direct the search for the disease locus. We also show how the CL model can be generalized to account for multiple disease mutations. Evolutionary simulations demonstrate the power of the analyses, as well as their potential weaknesses. Finally, we analyze the data from two mapped diseases, cystic fibrosis and diastrophic dysplasia, finding that the CL method performs well in both cases. 28 refs., 6 figs., 4 tabs.

  7. Marked disequilibrium between 234Th and 230Th of the 238U natural radioactive decay chain in IAEA reference materials n. 312, 313 and 314.

    PubMed

    Colaianni, A; D'Erasmo, G; Pantaleo, A; Schiavulli, L

    2011-02-01

    A new laboratory for the spectroscopy of natural radioactivity with a good energy resolution is presented. It consists of two distinct parts equipped, respectively, the first one with a HpGe γ-ray detector, whose setup has been already completed, and the second one with large area Silicon α-ray detectors and a radiochemical section for thin α-samples preparation, whose setup is yet in progress and will be the argument of a separate work. The γ-ray spectrometer was calibrated by means of IAEA Reference Materials n. 312, 313, 314 and 375. A large difference from the predictions of secular equilibrium emerged between the activities of (234)Th and (230)Th in Materials n. 312, 313 and 314. PMID:21195514

  8. Backward disequilibrium in elderly subjects

    PubMed Central

    Manckoundia, Patrick; Mourey, France; Pérennou, Dominic; Pfitzenmeyer, Pierre

    2008-01-01

    Backward disequilibrium is observed frequently in daily clinical practice. However, there are no epidemiological data concerning this postural disorder. Defined by a posterior position of the centre of mass with respect to the base of support, backward disequilibrium is abnormal postural behavior, usually characterized by a posterior trunk tilt in standing and sitting positions, which predisposes subjects to backward falls. Many afflictions whether they are somatic (degenerative, ischemic and traumatic brain lesions), psychosomatic (psychomotor disadaptation syndrome, confinement to bed, nonuse situations) or psychological (depression) can cause backward disequilibrium. A vicious circle of falls, and loss of autonomy can arise and this is the main consequence of backward disequilibrium. Thus, in this paper, we review backward disequilibrium in elderly subjects with regard to the causes, consequences, assessment, and management. PMID:19281059

  9. U-series disequilibrium in rear-arc volcanoes from the Northern Volcanic Zone in Ecuador; along-arc variation and implications for petrogenetic processes

    NASA Astrophysics Data System (ADS)

    Garrison, J. M.; Matthews, T. P.; Sims, K. W.; Escobar, R. D.; Yogodzinski, G. M.; Waters, C. L.

    2012-12-01

    melting. The U-series data give conflicting results, the highest (238U/230Th) values are at Sumaco, and range from 0.87 to 1.7. The majority of samples have 238U excesses of up to 70% with the exception of the most evolved samples, which have 230Th excesses of 15%. The Reventador samples, on the other hand have much lower 238U excesses of up to only 10% and (238U/230Th) values that range from 0.87 - 1.1. Higher 238U excesses are typically thought to reflect higher fluid input, however the trace element data are consistent with higher fluid input at Reventador, not Sumaco. One possible explanation for this is that the 238U excesses at Sumaco are primarily due to differentiation of minerals that sequester Th, perhaps apatite. The (238U/230Th) of the Sumaco lavas is highly correlated differentiation indexes like La/Yb, MgO and P2O5, whereas the Reventador samples show a much weaker correlation. We conclude that there is a systematic trend showing decreasing H2O input from north to south in the rear arc of the NVZ, and that the U-series data reveal differences in differentiation processes.

  10. Exploring linkage disequilibrium.

    PubMed

    Baird, Stuart J E

    2015-09-01

    Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton ). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles ). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al. ). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD. PMID:26261040

  11. Uranium-series disequilibria as a means to study recent migration of uranium in a sandstone-hosted uranium deposit, NW China.

    PubMed

    Min, Maozhong; Peng, Xinjian; Wang, Jinping; Osmond, J K

    2005-07-01

    Uranium concentration and alpha specific activities of uranium decay series nuclides (234)U, (238)U, (230)Th, (232)Th and (226)Ra were measured for 16 oxidized host sandstone samples, 36 oxic-anoxic (mineralized) sandstone samples and three unaltered primary sandstone samples collected from the Shihongtan deposit. The results show that most of the ores and host sandstones have close to secular equilibrium alpha activity ratios for (234)U/(238)U, (230)Th/(238)U, (230)Th/(234)U and (226)Ra/(230)Th, indicating that intensive groundwater-rock/ore interaction and uranium migration have not taken place in the deposit during the last 1.0 Ma. However, some of the old uranium ore bodies have locally undergone leaching in the oxidizing environment during the past 300 ka to 1.0 Ma or to the present, and a number of new U ore bodies have grown in the oxic-anoxic transition (mineralized) subzone during the past 1.0 Ma. Locally, uranium leaching has taken place during the past 300 ka to 1.0 Ma, and perhaps is still going on now in some sandstones of the oxidizing subzone. However, uranium accumulation has locally occurred in some sandstones of the oxidizing environment during the past 1 ka to 1.0 Ma, which may be attributed to adsorption of U(VI) by clays contained in oxidized sandstones. A recent accumulation of uranium has locally taken place within the unaltered sandstones of the primary subzone close to the oxic-anoxic transition environment during the past 300 ka to 1.0 Ma. Results from the present study also indicate that uranium-series disequilibrium is an important tool to trace recent migration of uranium occurring in sandstone-hosted U deposits during the past 1.0 Ma and to distinguish the oxidation-reduction boundary. PMID:15866456

  12. River Capture in Disequilibrium Landscapes

    NASA Astrophysics Data System (ADS)

    McCoy, S. W.; Perron, J.; Willett, S.; Goren, L.

    2013-12-01

    The process of river piracy or river capture has long drawn interest as a potential mechanism by which drainage basins large and small evolve towards an equilibrium state. River capture transfers both drainage area and drainage lines from one river basin to another, which can cause large, abrupt shifts in network topology, drainage divide positions, and river incision rates. Despite numerous case studies in which river capture has been proposed to have occurred, there is no general, mechanistic framework for understanding the controls on river capture, nor are there quantitative criteria for determining if capture has occurred. Here we use new metrics of landscape disequilibrium to first identify landscapes in which drainage reorganization is occurring. These metrics are based on a balance between an integral of the contributing drainage area and elevation. In an analysis of rivers in the Eastern United States we find that many rivers are in a state of disequilibrium and are experiencing recent or ongoing area exchange between basins. In these disequilibrium basins we find widespread evidence for network rearrangement via river capture at multiple scales. We then conduct numerical experiments with a 2-D landscape evolution model to explore the conditions in which area exchange among drainage basins is likely to occur as discrete capture events as opposed to continuous divide migration. These experiments indicate that: (1) capture activity increases with the degree of disequilibrium induced by persistent spatial gradients in tectonic forcing or by temporal changes in climate or tectonic forcing; (2) capture activity is strongly controlled by the initial planform drainage network geometry; and (3) capture activity scales with the fluvial incision rate constant in the river power erosion law.

  13. 238U-234U-230Th disequilibrium in hydrogenous oceanic Fe-Mn crusts: Palaeoceanographic record or diagenetic alteration?

    USGS Publications Warehouse

    Chabaux, F.; O'Nions, R. K.; Cohen, A.S.; Hein, J.R.

    1997-01-01

    A detailed TIMS study of (234Uexc/238U), (230Th/232Th), and Th/U ratios have been performed on the outermost margin of ten hydrogenous Fe-Mn crusts from the equatorial Pacific Ocean and west-central Indian Ocean. Th/U concentration ratios generally decrease from the crust's surface down to 0.5-1 mm depth and growth rates estimated by uranium and thorium isotope ratios are significantly different in Fe-Mn crusts from the Peru Basin and the west-central Indian Ocean. Fe-Mn crusts from the same geographical area define a single trend in plots of Ln (234Uexc/238U) vs. Ln(230Th/232Th) and Th/U ratios vs. age of the analysed fractions. Results suggest that (1) hydrogenous Fe-Mn crusts remain closed-systems after formation, and consequently (2) the discrepancy observed between the 230Th and 234U chronometers in Fe-Mn crusts, and the variations of the Th/U ratios through the margin of Fe-Mn crusts, are not due to redistribution of uranium and thorium isotopes after oxyhydroxide precipitation, but rather to temporal variations of both Th/U and initial thorium activity ratios recorded by the Fe-Mn layers. Implications of these observations for determination of Fe-Mn crust growth-rates are discussed. Variations of both Th/U and initial Th activity ratios in Fe-Mn crusts might be related to changes in particle input to seawater and/or changes in ocean circulation during the last 150 ka. Copyright ?? 1997 Elsevier Science Ltd.

  14. Uranium series disequilibrium in the Bargmann property area of Karnes County, Texas

    SciTech Connect

    Davidson, J.R.

    1998-02-01

    Historical evidence is presented for natural uranium series radioactive disequilibrium in uranium bearing soils in the Bargmann property area of karnes County on the Gulf Coastal Plain of south Texas. The early history of uranium exploration in the area is recounted and records of disequilibrium before milling and mining operations began are given. The property contains an open pit uranium mine associated with a larger ore body. In 1995, the US Department of Energy (DOE) directed Oak Ridge National Laboratory (ORNL) to evaluate the Bargmann tract for the presence of uranium mill tailings (ORNL 1996). There was a possibility that mill tailings had washed onto or blown onto the property from the former tailings piles in quantities that would warrant remediation under the Uranium Mill Tailings Remediation Action Project. Activity ratios illustrating disequilibrium between {sup 226}Ra and {sup 238}U in background soils during 1986 are listed and discussed. Derivations of uranium mass-to-activity conversion factors are covered in detail.

  15. Positional Cloning by Linkage Disequilibrium

    PubMed Central

    Maniatis, Nikolas; Collins, Andrew; Gibson, Jane; Zhang, Weihua; Tapper, William; Morton, Newton E.

    2004-01-01

    Recently, metric linkage disequilibrium (LD) maps that assign an LD unit (LDU) location for each marker have been developed (Maniatis et al. 2002). Here we present a multiple pairwise method for positional cloning by LD within a composite likelihood framework and investigate the operating characteristics of maps in physical units (kb) and LDU for two bodies of data (Daly et al. 2001; Jeffreys et al. 2001) on which current ideas of blocks are based. False-negative indications of a disease locus (type II error) were examined by selecting one single-nucleotide polymorphism (SNP) at a time as causal and taking its allelic count (0, 1, or 2, for the three genotypes) as a pseudophenotype, Y. By use of regression and correlation, association between every pseudophenotype and the allelic count of each SNP locus (X) was based on an adaptation of the Malecot model, which includes a parameter for location of the putative gene. By expressing locations in kb or LDU, greater power for localization was observed when the LDU map was fitted. The efficiency of the kb map, relative to the LDU map, to describe LD varied from a maximum of 0.87 to a minimum of 0.36, with a mean of 0.62. False-positive indications of a disease locus (type I error) were examined by simulating an unlinked causal SNP and the allele count was used as a pseudophenotype. The type I error was in good agreement with Wald’s likelihood theorem for both metrics and all models that were tested. Unlike tests that select only the most significant marker, haplotype, or haploset, these methods are robust to large numbers of markers in a candidate region. Contrary to predictions from tagging SNPs that retain haplotype diversity, the sample with smaller size but greater SNP density gave less error. The locations of causal SNPs were estimated with the same precision in blocks and steps, suggesting that block definition may be less useful than anticipated for mapping a causal SNP. These results provide a guide to

  16. Whole genome linkage disequilibrium maps in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides bac...

  17. Linkage Disequilibrium Mapping of Meat Quality QTL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies based on linkage analysis have identified broad areas in the bovine genome associated with meat quality. Linkage disequilibrium (LD) analyses have the potential to identify narrower regions and point towards candidate genes. Tenderness and marbling were chosen to be evaluated in a ...

  18. Linkage disequilibrium in Theobroma cacao L. populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the potential of Linkage Disequilibrium (LD) mapping to associate markers to agronomic and horticultural traits has been already recognized in cacao, its real efficiency depends on the nature and structure of the LD in the genome of the populations under study. LD is dependent on several fa...

  19. Estimation of Particle Flux and Remineralization Rate from Radioactive Disequilibrium

    SciTech Connect

    Michael P. Bacon; Roger Francois

    2004-05-24

    Reactive radionuclides, such as the thorium isotopes, show measurable deficiencies in the oceanic water column because of their removal by chemical scavenging due to the particle flux. Measurement of the deficiency, coupled with measurement of the radionuclide concentration in particles, allows a determination of the effective particle sinking velocity. Results to date suggest that the effective particle sinking velocity is remarkably invariant with depth. This leads to the tentative suggestion that POC concentration profiles may, to a good approximation, be used directly to determine length scales for the remineralization of sinking organic matter. Further measurements are in progress to test this idea and to evaluate its limitations. Knowledge of the remineralization length scale is essential to an evaluation of the efficiency of the biological pump as a means for deep sequestering of carbon in the ocean.

  20. U-series dating of Lake Nyos maar basalts, Cameroon (West Africa): Implications for potential hazards on the Lake Nyos dam

    NASA Astrophysics Data System (ADS)

    Aka, Festus T.; Yokoyama, Tetsuya; Kusakabe, Minoru; Nakamura, Eizo; Tanyileke, Gregory; Ateba, Bekoa; Ngako, Vincent; Nnange, Joseph; Hell, Joseph

    2008-09-01

    From previously published 14C and K-Ar data, the age of formation of Lake Nyos maar in Cameroon is still in dispute. Lake Nyos exploded in 1986, releasing CO 2 that killed 1750 people and over 3000 cattle. Here we report results of the first measurements of major elements, trace elements and U-series disequilibria in ten basanites/trachy-basalts and two olivine tholeiites from Lake Nyos. It is the first time tholeiites are described in Lake Nyos. But for the tholeiites which are in 238U- 230Th equilibrium, all the other samples possess 238U- 230Th disequilibrium with 15 to 28% enrichment of 230Th over 238U. The ( 226Ra/ 230Th) activity ratios of these samples indicate small (2 to 4%) but significant 226Ra excesses. U-Th systematics and evidence from oxygen isotopes of the basalts and Lake Nyos granitic quartz separates show that the U-series disequilibria in these samples are source-based and not due to crustal contamination or post-eruptive alteration. Enrichment of 230Th is strong prima facie evidence that Lake Nyos is younger than 350 ka. The 230Th- 226Ra age of Nyos samples calculated with the ( 226Ra/ 230Th) ratio for zero-age Mt. Cameroon samples is 3.7 ± 0.5 ka, although this is a lower limit as the actual age is estimated to be older than 5 ka, based on the measured mean 230Th/ 238U activity ratio. The general stability of the Lake Nyos pyroclastic dam is a cause for concern, but judging from its 230Th- 226Ra formation age, we do not think that in the absence of a big rock fall or landslide into the lake, a big earthquake or volcanic eruption close to the lake, collapse of the dam from erosion alone is as imminent and alarming as has been suggested.

  1. On Detecting Biospheres from Chemical Thermodynamic Disequilibrium in Planetary Atmospheres.

    PubMed

    Krissansen-Totton, Joshua; Bergsman, David S; Catling, David C

    2016-01-01

    Atmospheric chemical disequilibrium has been proposed as a method for detecting extraterrestrial biospheres from exoplanet observations. Chemical disequilibrium is potentially a generalized biosignature since it makes no assumptions about particular biogenic gases or metabolisms. Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium in Solar System atmospheres, in which we quantify the available Gibbs energy: the Gibbs free energy of an observed atmosphere minus that of atmospheric gases reacted to equilibrium. The purely gas phase disequilibrium in Earth's atmosphere is mostly attributable to O2 and CH4. The available Gibbs energy is not unusual compared to other Solar System atmospheres and smaller than that of Mars. However, Earth's fluid envelope contains an ocean, allowing gases to react with water and requiring a multiphase calculation with aqueous species. The disequilibrium in Earth's atmosphere-ocean system (in joules per mole of atmosphere) ranges from ∼20 to 2 × 10(6) times larger than the disequilibria of other atmospheres in the Solar System, where Mars is second to Earth. Only on Earth is the chemical disequilibrium energy comparable to the thermal energy per mole of atmosphere (excluding comparison to Titan with lakes, where quantification is precluded because the mean lake composition is unknown). Earth's disequilibrium is biogenic, mainly caused by the coexistence of N2, O2, and liquid water instead of more stable nitrate. In comparison, the O2-CH4 disequilibrium is minor, although kinetics requires a large CH4 flux into the atmosphere. We identify abiotic processes that cause disequilibrium in the other atmospheres. Our metric requires minimal assumptions and could potentially be calculated from observations of exoplanet atmospheres. However, further work is needed to establish whether thermodynamic disequilibrium is a practical exoplanet biosignature, requiring an assessment of false positives, noisy

  2. The current disequilibrium of North Cascade glaciers

    NASA Astrophysics Data System (ADS)

    Pelto, Mauri S.

    2006-03-01

    Three lines of evidence indicate that North Cascade (Washington, USA) glaciers are currently in a state of disequilibrium. First, annual balance measured on nine glaciers yields a mean cumulative balance for the 1984-2004 period of -8.58 m water equivalent (w.e.), a net loss of ice thickness exceeding 9.5 m. This is a significant loss for glaciers that average 30-50 m in thickness, representing 18-32% of their entire volume.Second, longitudinal profiles completed in 1984 and 2002 on 12 North Cascade glaciers confirm this volume change indicating a loss of -5.7 to -6.3 m in thickness (5.0-5.6 m w.e.) between 1984 and 2002, agreeing well with the measured cumulative balance of -5.52 m w.e. for the same period. The change in thickness on several glaciers has been equally substantial in the accumulation zone and the ablation zone, indicating that there is no point to which the glacier can retreat to achieve equilibrium. Substantial thinning along the entire length of a glacier is the key indicator that a glacier is in disequilibrium.Third, North Cascade glacier retreat is rapid and ubiquitous. All 47 glaciers monitored are currently undergoing significant retreat or, in the case of four, have disappeared. Two of the glaciers where mass balance observations were begun, Spider Glacier and Lewis Glacier, have disappeared. The retreat since 1984 of eight Mount Baker glaciers that were all advancing in 1975 has averaged 297 m. These observations indicate broad regional continuity in glacial response to climate.

  3. Disequilibrium in planetary atmospheres and the search for habitability

    NASA Astrophysics Data System (ADS)

    Simoncini, E.

    It has long been observed that Earth's atmosphere is uniquely far from its thermochemical equilibrium state in terms of its chemical composition. Studying this state of disequilibrium is important for its potential role in the detection of life on other suitable planets \\citep{Lovelock_1965,Kleidon_2010,Simoncini_2015}. We developed a methodology to calculate the extent of atmospheric chemical disequilibrium\\citep{Simoncini_2015,Kondepudi_1996}. This tool allows us to understand, on a thermodynamic basis, how life affected - and still affects - geochemical processes on Earth, and if other planetary atmospheres are habitable or have a disequilibrium similar to the Earth's one. A new computational framework called KROME has been applied to atmospheric models in order to give a correct computation of reactions´ kinetics \\citep{Grassi_2015}. In this work we present a first computation of the extent of disequilibrium for the present Earth atmosphere, considering the specific contribution of the different atmospheric processes, such as thermochemical reactions, eddy diffusion, photochemistry, deposition, and the effect of the biosphere. We then assess the effect of life on atmospheric disequilibrium of the Earth and provide a useful discussion about how the study of atmospheric disequilibrium can help in finding habitable (exo)planets. We finally compare the chemical disequilibrium of Earth and Mars atmospheres, for present and early conditions.

  4. Radium-thorium disequilibrium and zeolite-water ion exchange in a Yellowstone hydrothermal environment

    NASA Astrophysics Data System (ADS)

    Sturchio, N. C.; Bohlke, J. K.; Binz, C. M.

    1989-05-01

    Whole rock samples of hydrothermally altered Biscuit Basin rhyolite from Yellowstone drill cores Y-7 and Y-8 were analyzed for 226Ra and 230Th to determine the extent of radioactive disequilibrium and its relation to the rates and mechanisms of element transport in the shallow portion of an active hydrothermal system. The ( 226Ra/230Th) activity ratios range from 0.73 to 1.46 and are generally correlated with Th-normalized Ba concentrations (Ba N). Values of ( 226Ra/230Th) and Ba N > 1 were found in samples containing large modal fractions of clinoptilolite; whereas values of ( 226Ra/230Th) and Ba N < 1 were found in samples containing large modal fractions of mordenite. Composition clinoptilolite and mordenite in these samples are consistent with ion exchange equilibrium between zeolites and coexisting thermal waters. Average K d mineral-waterBa values are 1.0·10 5 mL/g for clinoptilolite and 1.4·10 4 mL/g for mordenite. Apparent diffustvities through matrix porosity estimated for Ra and Ba range from ˜10 -12 to ˜10 -10 cm 2s -1 in thoroughly zeolitic rhyolite; these rates of diffusion are too low to account for the observed distance scale of ( 226Ra/230Th) disequilibrium. The correlated values of ( 226Ra /230Th) disequilibrium and Ba N represent zeolite-water ion exchange equilibrium that is caused by porous flow of water through the rock matrix and by the relatively rapid diffusion of cations within the zeolite lattices. A water flux of at least ˜2.5 ( cm water3/cm rock3) yr -1 is required to produce measurable ( 226Ra/230Th) disequilibrium, whereas at least ˜23 ( cm water3/cm rock3) yr -1 is r for the sample exhibiting the most extreme ( 226Ra/230Th) disequilibrium; these fluxes are much higher than those that can be inferred from net mass transfers of stable species. The zeolite-water ion exchange process appears to have been operating for at least 8000 yr in the environment of the Y-7 and Y-8 drill holes.

  5. Radium-thorium disequilibrium and zeolite-water ion exchange in a Yellowstone hydrothermal environment

    SciTech Connect

    Sturchio, N.C.; Bohlke, J.K. ); Binz, C.M. )

    1989-05-01

    Whole rock samples of hydrothermally altered Biscuit Basin rhyolite from Yellowstone drill cores Y-7 and Y-8 were analyzed for {sup 226}Ra and {sup 230}Th to determine the extent of radioactive disequilibrium and its relation to the rates and mechanisms of element transport in the shallow portion of an active hydrothermal system. The ({sup 226}Ra/{sup 230}Th) activity ratios range from 0.73 to 1.46 and are generally correlated with Th-normalized Ba concentrations (Ba{sub N}). Compositions of clinoptilolite and mordenite in these samples are consistent with ion exchange equilibrium between zeolites and coexisting thermal waters. Average K{sup Ba}{sub d mineral-water} values are 1.0 {center dot} 10{sup 5} mL/g for clinoptilolite and 1.4 {center dot} 10{sup 4} mL/g for mordenite. Apparent diffusivities through matrix porosity estimated for R and Ba range from {approximately}10{sup {minus}12} to {approximately}10{sup {minus}10} cm{sup 2} s{sup {minus}1} in thoroughly zeolitic rhyolite; these rates of diffusion are too low to account for the observed distance scale of ({sup 226}Ra/{sup 230}Th) disequilibrium. The correlated values of ({sup 226}Ra/{sup 230}Th) disequilibrium and Ba{sub N} represent zeolite-water ion exchange equilibrium that is caused by porous flow of water through the rock matrix and by the relatively rapid diffusion of cations within the zeolite lattices. A water flux of at least {approximately}2.5 (cm{sup 3}{sub water}/cm{sup 3}{sub rock}) yr{sup {minus}1} is required to produce measurable ({sup 226}Ra/{sup 230}Th) disequilibrium, whereas at least {approximately}23 (cm{sup 3}{sub water}/cm{sup 3}{sub rock}) yr{sup {minus}1} is required for the sample exhibiting the most extreme ({sup 226}Ra/{sup 230}Th) disequilibrium; these fluxes are much higher than those that can be inferred from net mass transfers of stable species.

  6. Constructing Linkage Disequilibrium Map with Iterative Approach

    NASA Astrophysics Data System (ADS)

    Ao, S. I.

    2008-05-01

    With recent advance of the genotyping single nucleotide polymorphisms (SNPs) in mass scale of high density in a candidate region of the human genome, the linkage disequilibrium analysis can offer a much higher resolution of the biological samples than the traditional linkage maps. We have formulated this LD mapping problem as a constrained unidimensional scaling problem. Our method, which is directly based on the measurement of LD among SNPs, is non-parametric. Therefore it is different from LD maps derived from the given Malecot model. We have formulated with the quadratic programming approach for solving this constrained unidimensional scaling problem. Different from the classical metric unidimensional scaling problem, the constrained problem is not an NP-hard combinatorial problem. The optimal solution is determined by using the quadratic programming solver. Nevertheless, because of the large requirement for memory during the running time that may cause the out of memory problems, and the high computational time of the quadratic programming algorithm, the iterative algorithm has been developed for solving this LD constrained unidimensional scaling problem.

  7. How Population Growth Affects Linkage Disequilibrium

    PubMed Central

    Rogers, Alan R.

    2014-01-01

    The “LD curve” relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. This article derives new results about the last of these effects. When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population shrinks, the LD curve rises but remains relatively flat. As LD converges toward a new equilibrium, its time path may not be monotonic. Following an episode of growth, for example, it declines to a low value before rising toward the new equilibrium. These changes happen at different rates for different LD statistics. They are especially slow for estimates of σd2, which therefore allow inferences about ancient population history. For the human population of Europe, these results suggest a history of population growth. PMID:24907258

  8. The Structure of Linkage Disequilibrium Around a Selective Sweep

    PubMed Central

    McVean, Gil

    2007-01-01

    The fixation of advantageous mutations by natural selection has a profound impact on patterns of linked neutral variation. While it has long been appreciated that such selective sweeps influence the frequency spectrum of nearby polymorphism, it has only recently become clear that they also have dramatic effects on local linkage disequilibrium. By extending previous results on the relationship between genealogical structure and linkage disequilibrium, I obtain simple expressions for the influence of a selective sweep on patterns of allelic association. I show that sweeps can increase, decrease, or even eliminate linkage disequilibrium (LD) entirely depending on the relative position of the selected and neutral loci. I also show the importance of the age of the neutral mutations in predicting their degree of association and describe the consequences of such results for the interpretation of empirical data. In particular, I demonstrate that while selective sweeps can eliminate LD, they generate patterns of genetic variation very different from those expected from recombination hotspots. PMID:17194788

  9. THE ROLE OF TEMPERATURE DISEQUILIBRIUM IN MONITORING LOW VOLATILITY CONTAMINANT MIGRATION

    EPA Science Inventory

    Temperature disequilibrium is a common phenomenon within and among envirornnental media at local regional continental and global scales. The significance of temperature disequilibrium on low vapor pressure environmental contaminant migration has only rarely been addressed in the ...

  10. Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Prospects for utilizing whole genome association analysis in autogamous plant populations appear promising due to the reported high levels of linkage disequilibrium (LD). To determine the optimal strategies for implementing association analysis in soybean (Glycine max L. Merr.), we analyzed the str...

  11. Chemical evolution of the Earth: Equilibrium or disequilibrium process?

    NASA Technical Reports Server (NTRS)

    Sato, M.

    1985-01-01

    To explain the apparent chemical incompatibility of the Earth's core and mantle or the disequilibrium process, various core forming mechanisms have been proposed, i.e., rapid disequilibrium sinking of molten iron, an oxidized core or protocore materials, and meteorite contamination of the upper mantle after separation from the core. Adopting concepts used in steady state thermodynamics, a method is devised for evaluating how elements should distribute stable in the Earth's interior for the present gradients of temperature, pressure, and gravitational acceleration. Thermochemical modeling gives useful insights into the nature of chemical evolution of the Earth without overly speculative assumptions. Further work must be done to reconcile siderophile elements, rare gases, and possible light elements in the outer core.

  12. Infinite dimensional variational inequalities and dynamic network disequilibrium modeling

    SciTech Connect

    Friesz, T.; Bernstein, D.

    1994-12-31

    In this paper we explain the importance of modeling disequilibrium flow patterns occurring on networks, with special emphasis on automobile networks and the role of information technology. We show how elementary notions of disequilibrium, whether abstract, physical or economic in nature, give rise to an adjustment process expressible as a dynamical system. We comment that when such a system is autonomous its steady states can be given the traditional finite dimensional variational inequality/fixed point representations common to static network equilibria. Beyond this, and unique to our work, we show that if the disequilibrium dynamical system is nonautonomous it may tend toward moving or dynamic (instead of static) network equilibria expressible as infinite dimensional variational inequalities. Using concepts of fast and slow dynamic systems, we show how day-to-day and within-day aspects of automobile travel decision making can be combined to yield a nonautonomous dynamical system with the mathematical properties reviewed previously. We introduce axioms for a proper predictive model of urban network flows which integrates both day-to-day and within-day considerations and postulate one such model for further study.

  13. Linkage disequilibrium in the neurofibromatosis 1 (NF1) region: implications for gene mapping.

    PubMed Central

    Jorde, L B; Watkins, W S; Viskochil, D; O'Connell, P; Ward, K

    1993-01-01

    To test the usefulness of linkage disequilibrium for gene mapping, we compared physical distances and linkage disequilibrium among eight RFLPs in the neurofibromatosis 1 (NF1) region. Seven of the polymorphisms span most of the NF1 gene, while the remaining polymorphism lies approximately 70 kb 3' to a stop codon in exon 49. By using Centre d'Etude du Polymorphisme Humain (CEPH) kindreds, 91-110 unrelated parents were genotyped. A high degree of disequilibrium is maintained among the seven intragenic polymorphisms (r > .82, P < 10(-7)), even though they are separated by as much as 340 kb. The 3' polymorphism is only 68 kb distal to the next polymorphism, but disequilibrium between the 3' polymorphism and all others is comparatively low (magnitude of 4 < .33, P values .27-.001). This result was replicated in three sets of unrelated kindreds: the Utah CEPH families, the non-Utah CEPH families, and an independent set of NF1 families. Trigenic, quadrigenic, three-locus, and four-locus disequilibrium measures were also estimated. There was little evidence of higher-order linkage disequilibrium. As expected for a disease with multiple mutations, no disequilibrium was observed between the disease gene and any of the RFLPs. The observed pattern of high disequilibrium within the gene and a loss of disequilibrium 3' to the stop codon could have implications for gene mapping studies. These are discussed, and guidelines for linkage disequilibrium studies are suggested. PMID:8105688

  14. Dialysis disequilibrium syndrome occurring during continuous renal replacement therapy

    PubMed Central

    Tuchman, Shamir; Khademian, Zarir P.; Mistry, Kirtida

    2013-01-01

    The dialysis disequilibrium syndrome (DDS) is characterized by progressive neurological symptoms and signs attributable to cerebral edema that occurs due to fluid shifts into the brain following a relatively rapid decrease in serum osmolality during hemodialysis (HD). Since continuous renal replacement therapy (CRRT) is less efficient at solute clearance than intermittent HD, it seems logical that this mode of therapy is less likely to cause DDS. This entity has not been previously reported to occur with this modality. Here, we report two cases of DDS associated with CRRT that provide insights into its pathophysiological mechanisms and suggest strategies for its prevention. PMID:26120445

  15. Linkage disequilibrium patterns vary with chromosomal location: A case study from the von Willebrand factor region

    SciTech Connect

    Watkins, W.S.; Zenger, R.; O'Brien, E.; Jorde, L.B. ); Nyman, D. ); Eriksson, A.W. ); Renlund, M.

    1994-08-01

    Linkage disequilibrium analysis has been used as a tool for analyzing marker order and locating disease genes. Under appropriate circumstances, disequilibrium patterns reflect recombination events that have occurred throughput a population's history. As a result, disequilibrium mapping may be useful in genomic regions of <1 cM where the number of informative meioses needed to detect recombinant individuals within pedigrees is exceptionally high. Its utility for refining target areas for candidate disease genes before initiating chromosomal walks and cloning experiments will be enhanced as the relationship between linkage disequilibrium and physical distance is better understood. To address this issue, the authors have characterized linkage disequilibrium in a 144-kb region of the von Willebrand factor gene on chromosome 12. Sixty CEPH and 12 von Willebrand disease families were genotypes for five PCR-based markers, which include two microsatellite repeats and three single-base-pair substitutions. Linkage disequilibrium and physical distance between polymorphisms are highly correlated (r[sub m] = -.76; P<.05) within this region. None of the five markers showed significant disequilibrium with the von Willebrand disease phenotype. The linkage disequilibrium/physical distance relationship was also analyzed as a function of chromosomal location for this and eight previously characterized regions. This analysis revealed a general trend in which linkage disequilibrium dissipates more rapidly with physical distance in telomeric regions than in centromeric regions. This trend is consistent with higher recombination rates near telomeres. 52 refs., 3 figs., 4 tabs.

  16. IXth millenium B.C. ceramics from Niger: detection of a U-series disequilibrium and TL dating

    NASA Astrophysics Data System (ADS)

    Guibert, P.; Schvoerer, M.; Etcheverry, M. P.; Szepertyski, B.; Ney, C.

    A set of pottery sherds collected from two ancient neolithic sites in Niger (Tagalagal and Adrar Bous 10) has been dated by thermoluminescence. The natural radioactivity of these ceramics and of their surrounding sediments was measured using low background gamma spectrometry and atomic emission plasma spectrometry. With gamma spectrometry, the comparison between the activity of 238U (deduced from the 235U and 234Th gamma emissions) and that of 226Ra (deduced from 214Pb and 214Bi γ emissions in equilibrium with 222Rn) shows a significant disequilibrium of the U-series. The activity ratio {38U}/{226Ra}, which is greater than unity in this case, is interpreted as a result of either uranium enrichment ( 234U, 235U, 238U) or radium impoverishment that has been occurring since the burying of the archaeological artefacts. The effects of the changes in radiochemical composition on the annual dose are discussed and various determinations of the annual dose are analysed according to different hypotheses of disequilibrium (either permanent state or recent occurrence). The TL results: Tagalagal — 9820±780-10, 180±780 years/1993, Adrar Bous 10 — 9530±750-10,500±730 years/1993, are consistent with the radiocarbon dates obtained from charcoals collected at the same locations (the uncalibrated 14C dates belong to the 9100-9370 BP range). These results are of fundamental interest for the chronology of early neolithic cultures.

  17. Local thermodynamic equilibrium for globally disequilibrium open systems under stress

    NASA Astrophysics Data System (ADS)

    Podladchikov, Yury

    2016-04-01

    Predictive modeling of far and near equilibrium processes is essential for understanding of patterns formation and for quantifying of natural processes that are never in global equilibrium. Methods of both equilibrium and non-equilibrium thermodynamics are needed and have to be combined. For example, predicting temperature evolution due to heat conduction requires simultaneous use of equilibrium relationship between internal energy and temperature via heat capacity (the caloric equation of state) and disequilibrium relationship between heat flux and temperature gradient. Similarly, modeling of rocks deforming under stress, reactions in system open for the porous fluid flow, or kinetic overstepping of the equilibrium reaction boundary necessarily needs both equilibrium and disequilibrium material properties measured under fundamentally different laboratory conditions. Classical irreversible thermodynamics (CIT) is the well-developed discipline providing the working recipes for the combined application of mutually exclusive experimental data such as density and chemical potential at rest under constant pressure and temperature and viscosity of the flow under stress. Several examples will be presented.

  18. Linkage disequilibrium predicts physical distance in the adenomatous polyposis coli region

    SciTech Connect

    Jorde, L.B.; Watkins, W.S.; Carlson, M.; Albertsen, H.; Thliveris, A.; Leppert, M. )

    1994-05-01

    To test the reliability of linkage-disequilibrium analysis for gene mapping, the authors compared physical distance and linkage disequilibrium among seven polymorphisms in the adenomatous polyposis coli (APC) region on chromosome 5. Three of them lie within the APC gene, and two lie within the nearby MCC (mutated in colon cancer) gene. One polymorphism lies between the two genes, and one is likely to be 5' of MCC. Five of these polymorphisms are newly reported. All polymorphisms were typed in the CEPH kindreds, yielding 179-205 unrelated two-locus haplotypes. Linkage disequilibrium between each pair of polymorphisms is highly correlated with physical distance in this 550-kb region (correlation coefficient [minus].80, P < .006). This result is replicated in both the Utah and non-Utah CEPH kindreds. There is a tendency for greater disequilibrium among pairs of polymorphisms located within the same gene than among other pairs of polymorphisms. Trigenic, quadrigenic, three-locus, and four-locus disequilibrium measures were also estimated, but these measures revealed much less disequilibrium than did the two-locus disequilibrium measures. A review of 19 published disequilibrium studies, including this one, shows that linkage disequilibrium nearly always correlates significantly with physical distance in genomic regions >50-60 kb but that it does not do so in smaller genomic regions. The authors show that this agrees with theoretical predictions. This finding helps to resolve controversies regarding the use of disequilibrium for inferring gene order. Disequilibrium mapping is unlikely to predict gene order correctly in regions <50-60 kb in size but can often be applied successfully in regions of 50-500 kb or so in size. It is convenient that this is the range in which other mapping techniques, including chromosome walking and linkage mapping, become difficult. 81 refs., 3 figs., 5 tabs.

  19. Uranium series disequilibrium and high thorium and radium enrichments in Karst formations

    SciTech Connect

    Gunten, H.R. von; Roessler, E.; Surbeck, H.

    1996-04-01

    We found, in limestone Karst soils of the Jura Mountains and of the mountains in the central part of Switzerland, an enrichment up to a factor 20 of {sup 230}Th and {sup 226}Ra with respect to the activities of their progenitors, {sup 234}U and {sup 238}U. Thus, a significant radioactive disequilibrium exists between {sup 238/234}U and {sup 230}Th and {sup 226}Ra. The enrichment of {sup 226}Ra leads to locally high concentrations of its decay product, the noble gas {sup 222}Rn. We propose continuous chemical weathering of limestone (calcite) fragments within the soil column as a plausible cause for the high {sup 230}Th, {sup 226}Ra, and {sup 222}Rn activities. Uranium, contained within calcite, is released during weathering and migrates as stable uranyl carbonate complexes through the soil column. In contrast, its decay products ({sup 230}Th and {sup 226}Ra) hydrolyze, are strongly sorbed to soil particles, and/or form insoluble compounds that become more and more enriched in the soil as this process continues in time. 39 refs., 3 figs., 5 tabs.

  20. Equilibrium and Disequilibrium Chemistry in Evolved Exoplanet Atmospheres

    NASA Astrophysics Data System (ADS)

    Hu, Renyu

    2015-11-01

    It has been found that sub-Neptune-sized planets, although not existing in our Solar System, are ubiquitous in our interstellar neighborhood. This revelation is profound because, due to their special sizes and proximity to their host stars, Neptune- and sub-Neptune-sized exoplanets may have highly evolved atmospheres. I will discuss helium-dominated atmospheres as one of the outcomes of extensive atmospheric evolution on warm Neptune- and sub-Neptune-sized exoplanets. Due to depleted hydrogen abundance, the dominant carbon and oxygen species may not be methane or water on these evolved planets. Equilibrium and disequilibrium chemistry models are used to compute the molecular compositions of the atmospheres and their spectral features. Applications to GJ 436 b and other Neptune- and sub-Neptune-sized exoplanets will be discussed. As the observations to obtain the spectra of these planets continue to flourish, we will have the opportunity to study unconventional atmospheric chemical processes and test atmosphere evolution theories

  1. Equilibrium and Disequilibrium Chemistry in Evolved Exoplanet Atmospheres

    NASA Astrophysics Data System (ADS)

    Hu, Renyu

    2015-12-01

    It has been found that sub-Neptune-sized planets, although not existing in our Solar System, are ubiquitous in our interstellar neighborhood. This revelation is profound because, due to their special sizes and proximity to their host stars, Neptune- and sub-Neptune-sized exoplanets may have highly evolved atmospheres. I will discuss helium-dominated atmospheres as one of the outcomes of extensive atmospheric evolution on warm Neptune- and sub-Neptune-sized exoplanets. Due to depleted hydrogen abundance, the dominant carbon and oxygen species may not be methane or water on these evolved planets. Equilibrium and disequilibrium chemistry models are used to compute the molecular compositions of the atmospheres and their spectral features. Applications to GJ 436 b and other Neptune- and sub-Neptune-sized exoplanets will be discussed. As the observations to obtain the spectra of these planets continue to flourish, we will have the opportunity to study unconventional atmospheric chemical processes and test atmosphere evolution theories

  2. Neuroendocrine–immune disequilibrium and endometriosis: an interdisciplinary approach

    PubMed Central

    Tariverdian, Nadja; Theoharides, Theoharis C.; Siedentopf, Friederike; Gutiérrez, Gabriela; Jeschke, Udo; Rabinovich, Gabriel A.; Blois, Sandra M.

    2007-01-01

    Endometriosis, a chronic disease characterized by endometrial tissue located outside the uterine cavity, affects one fourth of young women and is associated with chronic pelvic pain and infertility. However, an in-depth understanding of the pathophysiology and effective treatment strategies of endometriosis is still largely elusive. Inadequate immune and neuroendocrine responses are significantly involved in the pathophysiology of endometriosis, and key findings are summarized in the present review. We discuss here the role of different immune mechanisms particularly adhesion molecules, protein–glycan interactions, and pro-angiogenic mediators in the development and progression of the disease. Finally, we introduce the concept of endometrial dissemination as result of a neuroendocrine-immune disequilibrium in response to high levels of perceived stress caused by cardinal clinical symptoms of endometriosis. PMID:17621704

  3. Disequilibrium of uranium isotopes in some Syrian groundwater.

    PubMed

    Abdul-Hadi, A; Alhassanieh, O; Ghafar, M

    2001-07-01

    Uranium concentration in groundwater samples from three areas of Syria was determined using alpha-spectrometry and INAA. It was in the range of 0-6.13 microg/l in the phosphate areas, and lower than 1 ppb in the volcanic areas. The activity ratio of 234U/238U was investigated, and disequilibrium of uranium isotopes was found to occur (234U/238U = 0.52-2.02). The excess of 234U was calculated. This excess can be interpreted by higher mobility of 234U, which more readily forms the soluble (UO2)2+ ion in comparison with 238U, most of which remains in the insoluble 4+ state. This excess increases with increase in uranium concentration. Thorium concentration was measured using INAA, it was found to be in the rang 0-1.15 microg/l. PMID:11339524

  4. Using U-series and beryllium isotopes to reveal the occurrence and relative timing of crustal and mantle processes in the Southern Volcanic Zone of Chile

    NASA Astrophysics Data System (ADS)

    Cooper, L. B.; Reubi, O.; Dungan, M. A.; Bourdon, B.; Langmuir, C. H.; Turner, S. J.; Schaefer, J. M.

    2012-12-01

    the main edifice have been mixed with magma compositions similar to those at surrounding minor eruptive centers (Hickey-Vargas et al., 2002). The latter appear to be decompression melts of enriched mantle which manifest moderate U-Th-Ra disequilibrium and substantial 231Pa-excesses, whereas melts from Villarrica have substantial U- and Ra-excesses. Magmas from Osorno reflect a greater influence of sediments originating from the incoming slab. After discounting assimilated samples, all primary melts have uniformly high Pa-excesses (1.7-2.2) coincident with large variations in 238U-230Th disequilibria. Fluid addition-aging-melting successions at Antuco and Chillán may have led to compositions near U-Th equilibrium or with Th-excesses, respectively. Primary Ra-deficits at Chillán, Lonquimay, and Osorno are under investigation and potentially reflect melting of a cumulate body. Forthcoming 10Be data for select U-series samples will enable further clarification of the regional trend. Preliminary analyses of nine Llaima samples erupted between 1850 and 2009 confirm the successful elimination of a meteoric 10Be component and produce a data array consistent with assimilation. The invocation of radioactive decay to produce U-Th equilibrium (duration of at least 380 ky) could also explain the low 10Be/9Be compositions (half-life of 10Be=1,390 ky). Our comprehensive dataset may shed new light on melting processes in subduction zone systems.

  5. Can calcretes be used to date pedogenic processes in soil profiles under semi arid climate ? An example from U-Th isochrons in calcretes from South India.

    NASA Astrophysics Data System (ADS)

    Durand, Nicolas; Hamelin, Bruno; Deschamps, Deschamps; Gunnel, Yanni; Curmi, Pierre

    2015-04-01

    Pedogenic carbonates, such as calcretes, have often been questioned as possible markers of the pedogenetic evolution of soil profiles under semi-arid climate. However, providing precise chronological constraints on their formation is a perequisite to determine the climatic and paleo-environmental conditions prevailing during and after their formation, and to improve our understanding of the physical and chemical conditions that promoted their development and preservation. On the other hand, these authigenic calcium carbonate precipitates provide us with an interesting test of the U-Th radioactive disequilibrium dating method, the reliability of which has been demonstrated extensively in aragonitic marine formations, and calcitic continental speleothems, but remain much more questionable in highly porous and chemically complex media such as soil profiles. In this study, we combined U-Th systematics with detailed micromorphologic observations of calcretes from South India, investigated at different spatial scales, from the landscape to the soil profile, down to the micro-fabrics of the samples. The U-Th analyses were performed by Thermo-Ionization Mass Spectrometry. Since calcretes are impure carbonates, mixed with various amounts of parent rock and weathered minerals, all ages had to be computed using the isochron technique to correct for the detrital component. This method involves the extraction of several coeval subsamples from a single soil horizon and their U-Th analyses after total dissolution (TDS method). The isochron age is derived from the slope of the mixing line between the pure authigenic carbonate and the detrital phase, and the precision established statistically using the probability of fit and weighted mean deviations (MSWD). Our results show that each set of samples taken from decimetric blocks is characterized by a well defined isochron line, clearly distinct from each other in the 3D Osmond diagram (232Th/238U; 230Th/238U ; 234U/238U). The

  6. Evaluation of Pleistocene groundwater flow through fractured tuffs using a U-series disequilibrium approach, Pahute Mesa, Nevada, USA

    USGS Publications Warehouse

    Paces, James B.; Nichols, Paul J.; Neymark, Leonid A.; Rajaram, Harihar

    2013-01-01

    Groundwater flow through fractured felsic tuffs and lavas at the Nevada National Security Site represents the most likely mechanism for transport of radionuclides away from underground nuclear tests at Pahute Mesa. To help evaluate fracture flow and matrix–water exchange, we have determined U-series isotopic compositions on more than 40 drill core samples from 5 boreholes that represent discrete fracture surfaces, breccia zones, and interiors of unfractured core. The U-series approach relies on the disruption of radioactive secular equilibrium between isotopes in the uranium-series decay chain due to preferential mobilization of 234U relative to 238U, and U relative to Th. Samples from discrete fractures were obtained by milling fracture surfaces containing thin secondary mineral coatings of clays, silica, Fe–Mn oxyhydroxides, and zeolite. Intact core interiors and breccia fragments were sampled in bulk. In addition, profiles of rock matrix extending 15 to 44 mm away from several fractures that show evidence of recent flow were analyzed to investigate the extent of fracture/matrix water exchange. Samples of rock matrix have 234U/238U and 230Th/238U activity ratios (AR) closest to radioactive secular equilibrium indicating only small amounts of groundwater penetrated unfractured matrix. Greater U mobility was observed in welded-tuff matrix with elevated porosity and in zeolitized bedded tuff. Samples of brecciated core were also in secular equilibrium implying a lack of long-range hydraulic connectivity in these cases. Samples of discrete fracture surfaces typically, but not always, were in radioactive disequilibrium. Many fractures had isotopic compositions plotting near the 230Th-234U 1:1 line indicating a steady-state balance between U input and removal along with radioactive decay. Numerical simulations of U-series isotope evolution indicate that 0.5 to 1 million years are required to reach steady-state compositions. Once attained, disequilibrium 234U/238U

  7. Linkage Disequilibrium Under Skewed Offspring Distribution Among Individuals in a Population

    PubMed Central

    Eldon, Bjarki; Wakeley, John

    2008-01-01

    Correlations in coalescence times between two loci are derived under selectively neutral population models in which the offspring of an individual can number on the order of the population size. The correlations depend on the rates of recombination and random drift and are shown to be functions of the parameters controlling the size and frequency of these large reproduction events. Since a prediction of linkage disequilibrium can be written in terms of correlations in coalescence times, it follows that the prediction of linkage disequilibrium is a function not only of the rate of recombination but also of the reproduction parameters. Low linkage disequilibrium is predicted if the offspring of a single individual frequently replace almost the entire population. However, high linkage disequilibrium can be predicted if the offspring of a single individual replace an intermediate fraction of the population. In some cases the model reproduces the standard Wright–Fisher predictions. Contrary to common intuition, high linkage disequilibrium can be predicted despite frequent recombination, and low linkage disequilibrium under infrequent recombination. Simulations support the analytical results but show that the variance of linkage disequilibrium is very large. PMID:18245371

  8. MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

    PubMed Central

    Gaunt, Tom R; Rodriguez, Santiago; Zapata, Carlos; Day, Ian NM

    2006-01-01

    Background Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form. Results We have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. Conclusion MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers. Availability Available from and PMID:16643648

  9. Disequilibrium Textures vs Equilibrium Modelling: Geochronology at the Crossroads

    NASA Astrophysics Data System (ADS)

    Villa, I. M.

    2007-12-01

    Observations made by electron microscopy show the processes affecting minerals at the atomic scale. The majority of reported analyses demonstrate chemical disequilibrium. A classic example are overgrowths of one mineral generation by a secondary one, which may be recognized on textural grounds. Disequilibrium recrystallization is promoted by water, which is everywhere on this planet (granites, contact aureoles, regional metamorphism, faults). It is mostly easier and energetically less costly to recrystallize a mineral at any temperature than to induce genuine volume diffusion in it. However, these observations are only relevant to geochronologists if chemical disequilibria are also accompanied by isotopic disequilibria. If a mineral mixture gives a mixed isotope record, then the interpretation of ages does not come cheap. If, on the contrary, diffusive reequilibration of the isotopic record is faster than that of chemical heterogeneities, then the petrology and microchemistry of a mineral could be ignored and its apparent age termed a "cooling age". First principle arguments and experimental data of the last decade concordantly show that the diffusivity of radiogenic isotopes is never higher than that of major elements forming the mineral structure. And indeed, end- member ages of mineral mixtures can be unravelled if the petrogenesis is understood. This was first shown by CL images of zircon grains (Gebauer et al, Schweiz Min Pet Mitt 68 (1988) 485-490). Similar progress was reported on monazite (Williams et al, Ann Rev Earth Planet Sci 35 (2007) 137-175), amphibole (Belluso et al, Eur J Mineral 12 (2000) 45-62), K-feldspar (Nyfeler et al, Schweiz Min Pet Mitt 78 (1998) 11-21), biotite (Villa et al, Water Rock Interaction 10 (2001) 1589-92). The mechanism for resetting the isotope record in nature thus seems more dependent on the availability of water to enhance disequilibrium recrystallization than on reaching a preset temperature. Intercomparison of laboratory

  10. Peach genetic resources: diversity, population structure and linkage disequilibrium

    PubMed Central

    2013-01-01

    Background Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. Results In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: ‘Yu Lu’ and ‘Hakuho’. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the ‘Yu Lu’ subpopulation there

  11. /sup 230/Th - /sup 238/U disequilibrium systematics in young volcanic rocks

    SciTech Connect

    Newman, S.

    1983-01-01

    Radioactive disequilibrium between /sup 230/Th (t/sub .5/ = 75,200 years) and its parent, /sup 238/U, has two major applications to the study of young volcanic rocks: 1) geochronology and 2) geochemical tracer studies. Geochronological investigations include both the dating of young (< approx.250,000 year-old) lavas by the internal isochron method and the study of the temporal evolution of magma systems feeding volcanoes. Older, K-Ar-dated lavas from Mauna Kea, Hawaii and Marion Island (Prince Edward hot spot) exhibit constant initial (/sup 230/Th//sup 232/Th) (activity) ratios for the past 100,000-275,000 years. At Mt. Shasta, California, a general decrease in (/sup 230/Th//sup 232/Th)/sub 0/ through time, with evidence of possible mixing corroborated by other geochemical data, is observed. Geochemical tracer studies depend on the observations that Th/U and (/sup 230/Th//sup 238/U) can be changed by such processes as partial melting, mixing, or fluid transport, whereas (/sup 230/Th//sup 232/Th) can only be modified by mixing or the passage of time. The (/sup 230/Th//sup 238/U) ratio can be used to identify possible petrogenetic processes. All lavas exhibit (/sup 230/Th//sup 238/U) greater than or equal to 1 except for some from the Aleutians and Marianas. These observations suggest that subduction-related volcanism is the only type in which U may behave as a more incompatible element than Th, although it need not (Cascades). Recent vapor transport of U or retention of Th may explain the U-enrichment in island arc lavas.

  12. Rapid alpha spectroscopy of evaporated liquid residues for emergency response.

    PubMed

    Semkow, T M; Khan, A J; Haines, D K; Bari, A

    2009-04-01

    A new method for alpha spectroscopy of evaporated water residues was developed, consisting of evaporation of drinking water, flaming of the planchets, and alpha-spectroscopic measurements using a grid ionization chamber. The method can identify and quantify radioactivity concentrations > or =3 mBq L-1 in a matter of several hours, whereas determination of sub-mBq L-1 levels is achievable in 1 day. Detailed investigations of flaming of the planchets, the humidity effect, and alpha spectroscopy of thick sources are described. A three-dimensional calibration of the method was performed using standards containing 238U, 230Th, 239Pu, 241Am, and 244Cm radionuclides. In addition to its application to evaporated drinking water, this calibration is common for any environmental sample that can be prepared as a uniform layer, such as the residues from surface water, acidic washing or leaching from materials, as well as biological fluids such as urine. The developed method serves as a fast identifying or screening technique for emergency response involving alpha radioactivity. PMID:19276703

  13. Linkage disequilibrium interval mapping of quantitative trait loci

    PubMed Central

    Boitard, Simon; Abdallah, Jihad; de Rochambeau, Hubert; Cierco-Ayrolles, Christine; Mangin, Brigitte

    2006-01-01

    Background For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods. Results Under a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations. Conclusion Our method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates. PMID:16542433

  14. Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes

    PubMed Central

    Lam, Tze Hau; Tay, Matthew Zirui; Wang, Bei; Xiao, Ziwei; Ren, Ee Chee

    2015-01-01

    Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases. PMID:26593880

  15. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

    PubMed Central

    Vilhjálmsson, Bjarni J.; Yang, Jian; Finucane, Hilary K.; Gusev, Alexander; Lindström, Sara; Ripke, Stephan; Genovese, Giulio; Loh, Po-Ru; Bhatia, Gaurav; Do, Ron; Hayeck, Tristan; Won, Hong-Hee; Ripke, Stephan; Neale, Benjamin M.; Corvin, Aiden; Walters, James T.R.; Farh, Kai-How; Holmans, Peter A.; Lee, Phil; Bulik-Sullivan, Brendan; Collier, David A.; Huang, Hailiang; Pers, Tune H.; Agartz, Ingrid; Agerbo, Esben; Albus, Margot; Alexander, Madeline; Amin, Farooq; Bacanu, Silviu A.; Begemann, Martin; Belliveau, Richard A.; Bene, Judit; Bergen, Sarah E.; Bevilacqua, Elizabeth; Bigdeli, Tim B.; Black, Donald W.; Bruggeman, Richard; Buccola, Nancy G.; Buckner, Randy L.; Byerley, William; Cahn, Wiepke; Cai, Guiqing; Campion, Dominique; Cantor, Rita M.; Carr, Vaughan J.; Carrera, Noa; Catts, Stanley V.; Chambert, Kimberly D.; Chan, Raymond C.K.; Chen, Ronald Y.L.; Chen, Eric Y.H.; Cheng, Wei; Cheung, Eric F.C.; Chong, Siow Ann; Cloninger, C. Robert; Cohen, David; Cohen, Nadine; Cormican, Paul; Craddock, Nick; Crowley, James J.; Curtis, David; Davidson, Michael; Davis, Kenneth L.; Degenhardt, Franziska; Del Favero, Jurgen; DeLisi, Lynn E.; Demontis, Ditte; Dikeos, Dimitris; Dinan, Timothy; Djurovic, Srdjan; Donohoe, Gary; Drapeau, Elodie; Duan, Jubao; Dudbridge, Frank; Durmishi, Naser; Eichhammer, Peter; Eriksson, Johan; Escott-Price, Valentina; Essioux, Laurent; Fanous, Ayman H.; Farrell, Martilias S.; Frank, Josef; Franke, Lude; Freedman, Robert; Freimer, Nelson B.; Friedl, Marion; Friedman, Joseph I.; Fromer, Menachem; Genovese, Giulio; Georgieva, Lyudmila; Gershon, Elliot S.; Giegling, Ina; Giusti-Rodrguez, Paola; Godard, Stephanie; Goldstein, Jacqueline I.; Golimbet, Vera; Gopal, Srihari; Gratten, Jacob; Grove, Jakob; de Haan, Lieuwe; Hammer, Christian; Hamshere, Marian L.; Hansen, Mark; Hansen, Thomas; Haroutunian, Vahram; Hartmann, Annette M.; Henskens, Frans A.; Herms, Stefan; Hirschhorn, Joel N.; Hoffmann, Per; Hofman, Andrea; Hollegaard, Mads V.; Hougaard, David M.; Ikeda, Masashi; Joa, Inge; Julia, Antonio; Kahn, Rene S.; Kalaydjieva, Luba; Karachanak-Yankova, Sena; Karjalainen, Juha; Kavanagh, David; Keller, Matthew C.; Kelly, Brian J.; Kennedy, James L.; Khrunin, Andrey; Kim, Yunjung; Klovins, Janis; Knowles, James A.; Konte, Bettina; Kucinskas, Vaidutis; Kucinskiene, Zita Ausrele; Kuzelova-Ptackova, Hana; Kahler, Anna K.; Laurent, Claudine; Keong, Jimmy Lee Chee; Lee, S. Hong; Legge, Sophie E.; Lerer, Bernard; Li, Miaoxin; Li, Tao; Liang, Kung-Yee; Lieberman, Jeffrey; Limborska, Svetlana; Loughland, Carmel M.; Lubinski, Jan; Lnnqvist, Jouko; Macek, Milan; Magnusson, Patrik K.E.; Maher, Brion S.; Maier, Wolfgang; Mallet, Jacques; Marsal, Sara; Mattheisen, Manuel; Mattingsdal, Morten; McCarley, Robert W.; McDonald, Colm; McIntosh, Andrew M.; Meier, Sandra; Meijer, Carin J.; Melegh, Bela; Melle, Ingrid; Mesholam-Gately, Raquelle I.; Metspalu, Andres; Michie, Patricia T.; Milani, Lili; Milanova, Vihra; Mokrab, Younes; Morris, Derek W.; Mors, Ole; Mortensen, Preben B.; Murphy, Kieran C.; Murray, Robin M.; Myin-Germeys, Inez; Mller-Myhsok, Bertram; Nelis, Mari; Nenadic, Igor; Nertney, Deborah A.; Nestadt, Gerald; Nicodemus, Kristin K.; Nikitina-Zake, Liene; Nisenbaum, Laura; Nordin, Annelie; O’Callaghan, Eadbhard; O’Dushlaine, Colm; O’Neill, F. Anthony; Oh, Sang-Yun; Olincy, Ann; Olsen, Line; Van Os, Jim; Pantelis, Christos; Papadimitriou, George N.; Papiol, Sergi; Parkhomenko, Elena; Pato, Michele T.; Paunio, Tiina; Pejovic-Milovancevic, Milica; Perkins, Diana O.; Pietilinen, Olli; Pimm, Jonathan; Pocklington, Andrew J.; Powell, John; Price, Alkes; Pulver, Ann E.; Purcell, Shaun M.; Quested, Digby; Rasmussen, Henrik B.; Reichenberg, Abraham; Reimers, Mark A.; Richards, Alexander L.; Roffman, Joshua L.; Roussos, Panos; Ruderfer, Douglas M.; Salomaa, Veikko; Sanders, Alan R.; Schall, Ulrich; Schubert, Christian R.; Schulze, Thomas G.; Schwab, Sibylle G.; Scolnick, Edward M.; Scott, Rodney J.; Seidman, Larry J.; Shi, Jianxin; Sigurdsson, Engilbert; Silagadze, Teimuraz; Silverman, Jeremy M.; Sim, Kang; Slominsky, Petr; Smoller, Jordan W.; So, Hon-Cheong; Spencer, Chris C.A.; Stahl, Eli A.; Stefansson, Hreinn; Steinberg, Stacy; Stogmann, Elisabeth; Straub, Richard E.; Strengman, Eric; Strohmaier, Jana; Stroup, T. Scott; Subramaniam, Mythily; Suvisaari, Jaana; Svrakic, Dragan M.; Szatkiewicz, Jin P.; Sderman, Erik; Thirumalai, Srinivas; Toncheva, Draga; Tooney, Paul A.; Tosato, Sarah; Veijola, Juha; Waddington, John; Walsh, Dermot; Wang, Dai; Wang, Qiang; Webb, Bradley T.; Weiser, Mark; Wildenauer, Dieter B.; Williams, Nigel M.; Williams, Stephanie; Witt, Stephanie H.; Wolen, Aaron R.; Wong, Emily H.M.; Wormley, Brandon K.; Wu, Jing Qin; Xi, Hualin Simon; Zai, Clement C.; Zheng, Xuebin; Zimprich, Fritz; Wray, Naomi R.; Stefansson, Kari; Visscher, Peter M.; Adolfsson, Rolf; Andreassen, Ole A.; Blackwood, Douglas H.R.; Bramon, Elvira; Buxbaum, Joseph D.; Børglum, Anders D.; Cichon, Sven; Darvasi, Ariel; Domenici, Enrico; Ehrenreich, Hannelore; Esko, Tonu; Gejman, Pablo V.; Gill, Michael; Gurling, Hugh; Hultman, Christina M.; Iwata, Nakao; Jablensky, Assen V.; Jonsson, Erik G.; Kendler, Kenneth S.; Kirov, George; Knight, Jo; Lencz, Todd; Levinson, Douglas F.; Li, Qingqin S.; Liu, Jianjun; Malhotra, Anil K.; McCarroll, Steven A.; McQuillin, Andrew; Moran, Jennifer L.; Mortensen, Preben B.; Mowry, Bryan J.; Nthen, Markus M.; Ophoff, Roel A.; Owen, Michael J.; Palotie, Aarno; Pato, Carlos N.; Petryshen, Tracey L.; Posthuma, Danielle; Rietschel, Marcella; Riley, Brien P.; Rujescu, Dan; Sham, Pak C.; Sklar, Pamela; St. Clair, David; Weinberger, Daniel R.; Wendland, Jens R.; Werge, Thomas; Daly, Mark J.; Sullivan, Patrick F.; O’Donovan, Michael C.; Kraft, Peter; Hunter, David J.; Adank, Muriel; Ahsan, Habibul; Aittomäki, Kristiina; Baglietto, Laura; Berndt, Sonja; Blomquist, Carl; Canzian, Federico; Chang-Claude, Jenny; Chanock, Stephen J.; Crisponi, Laura; Czene, Kamila; Dahmen, Norbert; Silva, Isabel dos Santos; Easton, Douglas; Eliassen, A. Heather; Figueroa, Jonine; Fletcher, Olivia; Garcia-Closas, Montserrat; Gaudet, Mia M.; Gibson, Lorna; Haiman, Christopher A.; Hall, Per; Hazra, Aditi; Hein, Rebecca; Henderson, Brian E.; Hofman, Albert; Hopper, John L.; Irwanto, Astrid; Johansson, Mattias; Kaaks, Rudolf; Kibriya, Muhammad G.; Lichtner, Peter; Lindström, Sara; Liu, Jianjun; Lund, Eiliv; Makalic, Enes; Meindl, Alfons; Meijers-Heijboer, Hanne; Müller-Myhsok, Bertram; Muranen, Taru A.; Nevanlinna, Heli; Peeters, Petra H.; Peto, Julian; Prentice, Ross L.; Rahman, Nazneen; Sánchez, María José; Schmidt, Daniel F.; Schmutzler, Rita K.; Southey, Melissa C.; Tamimi, Rulla; Travis, Ruth; Turnbull, Clare; Uitterlinden, Andre G.; van der Luijt, Rob B.; Waisfisz, Quinten; Wang, Zhaoming; Whittemore, Alice S.; Yang, Rose; Zheng, Wei; Kathiresan, Sekar; Pato, Michele; Pato, Carlos; Tamimi, Rulla; Stahl, Eli; Zaitlen, Noah; Pasaniuc, Bogdan; Belbin, Gillian; Kenny, Eimear E.; Schierup, Mikkel H.; De Jager, Philip; Patsopoulos, Nikolaos A.; McCarroll, Steve; Daly, Mark; Purcell, Shaun; Chasman, Daniel; Neale, Benjamin; Goddard, Michael; Visscher, Peter M.; Kraft, Peter; Patterson, Nick; Price, Alkes L.

    2015-01-01

    Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R2 increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase. PMID:26430803

  16. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

    PubMed

    Wall, Jeffrey D; Stevison, Laurie S

    2016-01-01

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. PMID:27226166

  17. Equilibrium and Disequilibrium Chemistry in Evolved Exoplanet Atmospheres

    NASA Astrophysics Data System (ADS)

    Hu, Renyu

    2015-08-01

    It has been found that sub-Neptune-sized planets, although not existing in our Solar System, are ubiquitous in our interstellar neighborhood. This revelation is profound because, due to their special sizes and proximity to their host stars, Neptune- and sub-Neptune-sized exoplanets may have highly evolved atmospheres. I will discuss helium-dominated atmospheres as one of the outcomes of extensive atmospheric evolution on warm Neptune- and sub-Neptune-sized exoplanets. Due to depleted hydrogen abundance, the dominant carbon and oxygen species may not be methane or water on these evolved planets. Equilibrium and disequilibrium chemistry models are used to compute the molecular compositions of the atmospheres and their spectral features. Applications to GJ 436 b, HD 97658 b, and other Neptune- and sub-Neptune-sized exoplanets will be discussed. As the observations to obtain the spectra of these planets continue to flourish, we will have the opportunity to study unconventional atmospheric chemical processes and test atmosphere evolution theories.

  18. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium

    PubMed Central

    Wall, Jeffrey D.; Stevison, Laurie S.

    2016-01-01

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. PMID:27226166

  19. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores.

    PubMed

    Vilhjálmsson, Bjarni J; Yang, Jian; Finucane, Hilary K; Gusev, Alexander; Lindström, Sara; Ripke, Stephan; Genovese, Giulio; Loh, Po-Ru; Bhatia, Gaurav; Do, Ron; Hayeck, Tristan; Won, Hong-Hee; Kathiresan, Sekar; Pato, Michele; Pato, Carlos; Tamimi, Rulla; Stahl, Eli; Zaitlen, Noah; Pasaniuc, Bogdan; Belbin, Gillian; Kenny, Eimear E; Schierup, Mikkel H; De Jager, Philip; Patsopoulos, Nikolaos A; McCarroll, Steve; Daly, Mark; Purcell, Shaun; Chasman, Daniel; Neale, Benjamin; Goddard, Michael; Visscher, Peter M; Kraft, Peter; Patterson, Nick; Price, Alkes L

    2015-10-01

    Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R(2) increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase. PMID:26430803

  20. Inferring admixture histories of human populations using linkage disequilibrium.

    PubMed

    Loh, Po-Ru; Lipson, Mark; Patterson, Nick; Moorjani, Priya; Pickrell, Joseph K; Reich, David; Berger, Bonnie

    2013-04-01

    Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese. PMID:23410830

  1. Dialysis disequilibrium syndrome: A preventable fatal acute complication.

    PubMed

    Mah, D Y; Yia, H J; Cheong, W S

    2016-04-01

    Dialysis disequilibrium syndrome (DDS) is a neurological disorder with varying severity that is postulated to be associated with cerebral oedema. We described a case of DDS resulting in irreversible brain injury and death following acute haemodialysis. A 13-year-old male with no past medical history and weighing 30kg, presented to hospital with severe urosepsis complicated by acute kidney injury (Creatinine 1422mmol/L; Urea 74.2mmol/L, Potassium 6.3mmol/L, Sodium 137mmol/L) and severe metabolic acidosis (pH 6.99, HC03 1.7mmol/L). Chest radiograph was normal. Elective intubation was done for respiratory distress. Acute haemodialysis performed due to refractory metabolic acidosis. Following haemodialysis, he became hypotensive which required inotropes. His Riker's score was low with absence of brainstem reflexes after withholding sedation. CT Brain showed generalised cerebral oedema consistent with global hypoxic changes involving the brainstem. The symptoms of DDS are caused by water movement into the brain causing cerebral oedema. Two theories have been proposed: reverse osmotic shift induced by urea removal and a fall in cerebral intracellular pH. Prevention is the key to the management of DDS. It is important to identify high risk patients and haemodialysis with reduced dialysis efficacy and gradual urea reduction is recommended. Patients who are vulnerable to DDS should be monitored closely. Low efficiency haemodialysis is recommended. Acute peritoneal dialysis might be an alternative option, but further studies are needed. PMID:27326954

  2. Genome-wide linkage-disequilibrium profiles from single individuals.

    PubMed

    Lynch, Michael; Xu, Sen; Maruki, Takahiro; Jiang, Xiaoqian; Pfaffelhuber, Peter; Haubold, Bernhard

    2014-09-01

    Although the analysis of linkage disequilibrium (LD) plays a central role in many areas of population genetics, the sampling variance of LD is known to be very large with high sensitivity to numbers of nucleotide sites and individuals sampled. Here we show that a genome-wide analysis of the distribution of heterozygous sites within a single diploid genome can yield highly informative patterns of LD as a function of physical distance. The proposed statistic, the correlation of zygosity, is closely related to the conventional population-level measure of LD, but is agnostic with respect to allele frequencies and hence likely less prone to outlier artifacts. Application of the method to several vertebrate species leads to the conclusion that >80% of recombination events are typically resolved by gene-conversion-like processes unaccompanied by crossovers, with the average lengths of conversion patches being on the order of one to several kilobases in length. Thus, contrary to common assumptions, the recombination rate between sites does not scale linearly with distance, often even up to distances of 100 kb. In addition, the amount of LD between sites separated by <200 bp is uniformly much greater than can be explained by the conventional neutral model, possibly because of the nonindependent origin of mutations within this spatial scale. These results raise questions about the application of conventional population-genetic interpretations to LD on short spatial scales and also about the use of spatial patterns of LD to infer demographic histories. PMID:24948778

  3. Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatell...

  4. A systematic retrieval analysis of secondary eclipse spectra. III. Diagnosing chemical disequilibrium in planetary atmospheres

    SciTech Connect

    Line, Michael R.; Yung, Yuk L.

    2013-12-10

    Chemical disequilibrium has recently become a relevant topic in the study of the atmospheres of transiting extrasolar planets, brown dwarfs, and directly imaged exoplanets. We present a new way of assessing whether or not a Jovian-like atmosphere is in chemical disequilibrium from observations of detectable or inferred gases such as H{sub 2}O, CH{sub 4}, CO, and H{sub 2}. Our hypothesis, based on previous kinetic modeling studies, is that cooler atmospheres will show stronger signs of disequilibrium than hotter atmospheres. We verify this with chemistry-transport models and show that planets with temperatures less than ∼1200 K are likely to show the strongest signs of disequilibrium due to the vertical quenching of CO, and that our new approach is able to capture this process. We also find that in certain instances a planetary composition may appear in equilibrium when it actually is not due to the degeneracy in the shape of the vertical mixing ratio profiles. We determine the state of disequilibrium in eight exoplanets using the results from secondary eclipse temperature and abundance retrievals. We find that all of the planets in our sample are consistent with thermochemical equilibrium to within 3σ. Future observations are needed to further constrain the abundances in order to definitively identify disequilibrium in exoplanet atmospheres.

  5. Linkage-Disequilibrium-Based Binning Affects the Interpretation of GWASs

    PubMed Central

    Christoforou, Andrea; Dondrup, Michael; Mattingsdal, Morten; Mattheisen, Manuel; Giddaluru, Sudheer; Nöthen, Markus M.; Rietschel, Marcella; Cichon, Sven; Djurovic, Srdjan; Andreassen, Ole A.; Jonassen, Inge; Steen, Vidar M.; Puntervoll, Pål; Le Hellard, Stéphanie

    2012-01-01

    Genome-wide association studies (GWASs) are critically dependent on detailed knowledge of the pattern of linkage disequilibrium (LD) in the human genome. GWASs generate lists of variants, usually SNPs, ranked according to the significance of their association to a trait. Downstream analyses generally focus on the gene or genes that are physically closest to these SNPs and ignore their LD profile with other SNPs. We have developed a flexible R package (LDsnpR) that efficiently assigns SNPs to genes on the basis of both their physical position and their pairwise LD with other SNPs. We used the positional-binning and LD-based-binning approaches to investigate whether including these “LD-based” SNPs would affect the interpretation of three published GWASs on bipolar affective disorder (BP) and of the imputed versions of two of these GWASs. We show how including LD can be important for interpreting and comparing GWASs. In the published, unimputed GWASs, LD-based binning effectively “recovered” 6.1%–8.3% of Ensembl-defined genes. It altered the ranks of the genes and resulted in nonnegligible differences between the lists of the top 2,000 genes emerging from the two binning approaches. It also improved the overall gene-based concordance between independent BP studies. In the imputed datasets, although the increases in coverage (>0.4%) and rank changes were more modest, even greater concordance between the studies was observed, attesting to the potential of LD-based binning on imputed data as well. Thus, ignoring LD can result in the misinterpretation of the GWAS findings and have an impact on subsequent genetic and functional studies. PMID:22444669

  6. Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

    PubMed Central

    Lu, Duc; Sargolzaei, Mehdi; Kelly, Matthew; Li, Changxi; Vander Voort, Gordon; Wang, Zhiquan; Plastow, Graham; Moore, Stephen; Miller, Stephen P.

    2012-01-01

    Linkage disequilibrium (LD) and the persistence of its phase across populations are important for genomic selection as well as fine scale mapping of quantitative trait loci (QTL). However, knowledge of LD in beef cattle, as well as the persistence of LD phase between crossbreds (C) and purebreds, is limited. The objective of this study was to understand the patterns of LD in Angus (AN), Charolais (CH), and C beef cattle based on 31,073, 32,088, and 33,286 SNP in each population, respectively. Amount of LD decreased rapidly from 0.29 to 0.23 to 0.19 in AN, 0.22 to 0.16 to 0.12 in CH, 0.21 to 0.15 to 0.11 in C, when the distance range between markers changed from 0–30 kb to 30–70 kb and then to 70–100 kb, respectively. Breeds and chromosomes had significant effects (P < 0.001) on LD decay. There was significant interaction between breeds and chromosomes (P < 0.001). Correlations of LD phase were high between C and AN (0.84), C and CH (0.81), as well as between AN and CH (0.77) for distances less than or equal to 70 kb. These dropped when the distance increased. Estimated effective population sizes for AN and CH were 207 and 285, respectively, for 10 generations ago. Given a useful LD of at least 0.3 between pairs of SNPs, the LD phase between any pair of the three breed groups was highly persistent. The current SNP density would allow the capture of approximately 49% of useful LD between SNP and marker QTL in AN, and 38% in CH. A higher density SNP panel or redesign of the current panel is needed to achieve more of useful LD for the purpose of genomic selection beef cattle. PMID:22912646

  7. Extreme isotopologue disequilibrium in molecular SIMS species during SHRIMP geochronology

    NASA Astrophysics Data System (ADS)

    Magee, Charles W., Jr.; Danišík, Martin; Mernagh, Terry

    2016-04-01

    Isotopologue deficits of up to 200 ‰ below ideal mixing are observed in UO2+ species during SIMS gechronological analyses using the SHRIMP IIe instrument. These are identified by bombarding natural U-bearing minerals with an 18O2-primary beam. The large anomalies are associated with repeat analyses down a single SIMS sputtering crater (Compston et al., 1984), analysis of high-uranium, radiation damaged zircon, and analysis of baddeleyite. Analysis of zircon under routine conditions yield UO2+ isotopologue anomalies generally within a few percent of equilibrium. The conditions under which the isotopologue anomalies are observed are also conditions in which the UOx-based corrections, or calibration, for relative U vs. Pb ionization efficiencies fail. The existence of these isotopologue anomalies suggest that failure of the various UOx species to equilibrate with each other is the reason that none of them will successfully correct the U / Pb ratio. No simple isotopologue-based correction is apparent. However, isotopologue disequilibrium appears to be a more sensitive tool for detecting hi U calibration breakdowns than Raman spectroscopy, which showed sharper peaks for ~ 37 Ma high uranium 20 zircons than for reference zircons OG1 and Temora. U-Th-Sm/He ages were determined for aliquots of reference zircons OG1 (755 ± 71 Ma) and Temora (323 ± 43 Ma), suggesting that the broader Raman lines for the Temora reference zircons may be due to something other than accumulated radiation damage. Isotopologue abundances for UO+ and ThO+ and their energy spectra are consistent with most or all molecular species being 25 the product of atomic recombination when the primary beam impact energy is greater than 5.7 kV. This, in addition with the large UO2+ instrumentally generated isotopologue disequilibria, suggest any attempts to use SIMS to detect naturally occurring isotopologue deviations could be tricky.

  8. Uranium-thorium disequilibrium in north-east Atlantic waters.

    PubMed

    Smith, K J; León Vintró, L; Mitchell, P I; Bally de Bois, P; Boust, D

    2004-01-01

    In this paper we report and compare the concentrations of 234Th and 238U measured in surface and subsurface waters collected in the course of a sampling campaign in the north east Atlantic in June-July 1998. Dissolved 234Th concentrations in surface waters ranged from 5 to 20 Bq m(-3), showing a large deficiency relative to 238U concentrations (typically 42 Bq m-3). This disequilibrium is indicative of active 234Th scavenging from surface waters. Observed 234Th/238U activity ratios, together with corresponding 234Th particulate concentrations, were used to calculate mean residence times for 234Th with respect to scavenging onto particles (tau(diss)) and subsequent removal from surface waters (tau(part)). Residence times in the range 5-30 days were determined for tau(diss) and 4-18 days for tau(part) (n=14). In addition, ultrafiltration experiments at six stations in the course of the same expedition revealed that in north-east Atlantic surface waters a significant fraction (46+/-17%; n=6) of the thorium in the (operationally-defined) dissolved phase (<0.45 microm) is in colloidal form. These observations are consistent with the 'colloidal pumping' model in which it is assumed that 234Th is rapidly absorbed by colloidal particles, which then aggregate, albeit at a slower rate, into larger filterable particles. In essence, colloids act as intermediaries in the transition from the fully dissolved to the filter-retained (>0.45 microm) phase. Thus, the time (tau(c)) for fully dissolved 234Th to appear in the filter-retained fraction is dependent on the rate of colloidal aggregation. Here, we determined tau(c) values in the range 3-17 days. PMID:15063548

  9. URANIUM-SERIES DISEQUILIBRIUM IN TUFF AND GRANITE:HYDROGEOLOGICAL IMPLICATIONS

    SciTech Connect

    M. Gasscoyne; N.H. Miller

    2000-10-27

    Uranium occurs naturally at trace levels in the major rock-forming minerals (quartz, feldspars, micas) in volcanic and plutonic rocks and is concentrated in accessory minerals (zircon, sphene, apatite). It may attain concentrations as high as 1000 ppm in the accessory minerals. Radiometric age determinations on zircon and sphene have shown that uranium migration from these minerals is generally negligible over prolonged periods of geologic time. Zircon grains separated from highly weathered igneous rocks have been found to retain most of their uranium. In contrast, the uranium fixed onto mineral grain boundaries or present in less-resistant minerals such as biotite or hornblende can be readily leached by groundwater. The ubiquitous presence of uranium in a rock makes it an ideal ''natural analogue'' for understanding the mobility of uranium at a potential site for nuclear fuel waste disposal and one that is easily overlooked in the search for suitable analogues for a disposal site. Several of the intermediate radionuclides in the decay series of the two long-lived isotopes of uranium ({sup 238}U and {sup 235}U) have half-lives greater than one year and are, therefore, of geological interest. In a sealed rock mass with no water-rock interactions, all intermediate radionuclides attain radioactive equilibrium with one another within a maximum 1-2 million years. Because rocks of the Yucca Mountain area and the Canadian Shield (both potential sites for nuclear waste disposal in the United States and Canadian programs, respectively) are considerably older, this condition (known as secular equilibrium) should exist in these rocks, and all daughter/parent radionuclide activity ratios should equal unity (1.000). If the ratios are found not to equal unity, then the rock has been disturbed, probably by groundwater transport of more soluble radionuclides into or away from the rock. How recently this migration has occurred can be determined from the half-life of the

  10. Observations of 231Pa/ 235U disequilibrium in volcanic rocks

    NASA Astrophysics Data System (ADS)

    Pickett, David A.; Murrell, Michael T.

    1997-04-01

    We present here the first survey of ( 231Pa/ 235U) ratios in volcanic rocks; such measurements are made possible by new mass spectrometric techniques. The data place new constraints on the timing and extent of magma source and evolutionary processes, particularly due to the sensitivity of the 231Pa- 235U pair and its intermediate time scale ( 231Pat 1/2 = 33 ky). ( 231Pa/ 235U) is found to vary widely, from 0.2 in carbonatites to 1.1-2.9 in basalts and 0.9-2.2 in arcs. Substantial Pa enrichment is nearly ubiquitous, suggestive of the relative incompatibility of Pa, qualitatively consistent with available partitioning data. The level of 231Pa- 235U disequilibrium typically far exceeds that of 230Th- 238U and is comparable to 226Ra- 230Th. The high ( 231Pa/ 235U) ratios in MORB and other basalts reflect a large degree of discrimination between two incompatible elements, posing challenges for modelling of melt generation and migration. Fundamental differences in ( 231Pa/ 235U) among different basaltic environments are likely related to contrasts in melting zone conditions (e.g., melting rate). Strong ( 231Pa/ 235U) disequilibria in continental basalts, for which ( 230Th/ 238U) disequilibria are small or absent, demonstrate that Pa-U fractionation is possible in both garnet and spinel mantle stability fields. In arcs, correlation of ( 231Pa/ 235U) and ( 230Th/ 238U) is consistent with U enrichment via slab-derived fluids, a process which is additional to the still dominant Pa enrichment. An important new constraint is provided by the observation that the near-equilibrium ( 230Th/ 238U) common to arcs and continental basalts is not typically accompanied by near-equilibrium ( 231Pa/ 235U), arguing against the influence of long magma history, crustal material, or equilibrium mantle sources in affecting decay-series ratios. Small sample sets from two silicic centers illustrate: (1) recent, rapid U enrichment in the magma chamber (El Chichón); and (2) the failure of

  11. Performance of random forest when SNPs are in linkage disequilibrium

    PubMed Central

    Meng, Yan A; Yu, Yi; Cupples, L Adrienne; Farrer, Lindsay A; Lunetta, Kathryn L

    2009-01-01

    Background Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change the tree-building algorithm by building each tree in an RF only with SNPs in LE, modify the importance measure (IM), and use haplotypes instead of SNPs to build a RF. Results We evaluated the performance of our alternative methods by simulation of a spectrum of complex genetics models. When a haplotype rather than an individual SNP is the risk factor, we find that the original Random Forest method performed on SNPs provides good performance. When individual, genotyped SNPs are the risk factors, we find that the stronger the genetic effect, the stronger the effect LD has on the performance of the original RF. A revised importance measure used with the original RF is relatively robust to LD among SNPs; this revised importance measure used with the revised RF is sometimes inflated. Overall, we find that the revised importance measure used with the original RF is the best choice when the genetic model and the number of SNPs in LD with risk SNPs are unknown. For the haplotype-based method, under a multiplicative heterogeneity model, we observed a decrease in the performance of RF with increasing LD among the SNPs in the haplotype. Conclusion Our results suggest that by strategically revising the Random Forest method tree-building or importance measure calculation, power can increase when LD exists between SNPs. We conclude that the revised Random Forest method performed on SNPs offers an advantage of not requiring genotype phase, making it a viable tool for use in the

  12. Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

    PubMed Central

    Abdallah, Jihad M; Goffinet, Bruno; Cierco-Ayrolles, Christine; Pérez-Enciso, Miguel

    2003-01-01

    Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance. PMID:12939203

  13. Dialysis disequilibrium syndrome induced by neoplastic meningitis in a patient receiving maintenance hemodialysis

    PubMed Central

    2013-01-01

    Background Dialysis disequilibrium syndrome is characterized by neurological symptoms resulting from cerebral edema, which occurs as a consequence of hemodialysis. Dialysis disequilibrium syndrome most often occurs in patients who have just started hemodialysis, during hemodialysis, or soon after hemodialysis; although it may also occur in patients who are under maintenance hemodialysis with pre-existing neurological disease. Case presentation A 70-year-old woman, who had been receiving maintenance hemodialysis for one year, was diagnosed with ovarian cancer by ascites cytological examination. Two years later, she reported severe headache and nausea during hemodialysis and was diagnosed with dialysis disequilibrium syndrome. Although brain images revealed mild hydrocephalus without any mass lesions, poorly differentiated adenocarcinoma cells were detected in her cerebrospinal fluid. These findings indicated that DDS was induced by neoplastic meningitis due to ovarian cancer metastasis. Conclusion Neoplastic meningitis should be considered and excluded in hemodialysis patients with dialysis disequilibrium syndrome and malignancy by cytological examination of the cerebrospinal fluid even if cerebral imaging shows no obvious lesions. This is the first reported case of dialysis disequilibrium syndrome induced by neoplastic meningitis in a patient receiving maintenance hemodialysis. PMID:24238645

  14. Uranium series disequilibrium studies in Chenchu colony area, Guntur district, Andhra Pradesh, India.

    PubMed

    Shrivastava, H B; Koteswara Rao, V; Singh, R V; Rahman, M; Rout, G B; Banerjee, Rahul; Pandey, B K; Verma, M B

    2015-11-01

    An attempt is made to understand uranium series disequilibrium in unconformity proximal related uranium mineralisation in Chenchu colony area, Guntur district, Andhra Pradesh, India. The uranium mineralization in Chenchu colony is the western continuity of the Koppunuru uranium deposit and predominantly hosted by gritty quartzite/conglomerate, which occasionally transgresses to underlying basement granite/basic rock. Disequilibrium studies are based on borehole core samples (35 boreholes, No. of samples=634) broadly divided in two groups of cover rocks of Banganapalle formation (above unconformity) and basement granites (below unconformity). Linear regression coefficient between uranium and radium is 0.95, which reflects excellent correlation and significant enrichment of parent uranium. Disequilibrium studies have indicated predominant disequilibrium in favour of parent uranium (35%), which is probably due to the weathering process causing migration of some of the radionuclides while dissolution of minerals due to groundwater action might have also played a significant role. Further, escape of radon might have accentuated the disequilibrium factor resulting in an increase in the grade of the mineralization. This is well corroborated by the presence of fractures and faults in the study area providing channels for radon migration/escape. PMID:26313623

  15. Uranium and thorium series disequilibrium in quaternary carbonate deposits from the Serra da Bodoquena and Pantanal do Miranda, Mato Grosso do Sul State, central Brazil.

    PubMed

    Ribeiro, F B; Roque, A; Boggiani, P C; Flexor, J M

    2001-01-01

    Activities of gamma-ray emitting members of the uranium (238U) and thorium (232Th) series were measured in a quaternary limestone deposit that outcrops in the southeastern Pantanal Matogrossense Basin and in quaternary tufas deposited at the drainage of the Serra da Bodoquena. It is a first step in a study of the mobilization of uranium and thorium series and its relation to surface hydrology, in a region where carbonate deposits are being continuously dissolved and reprecipitated. The obtained results show that all these deposits are characterized by very low concentrations of uranium and thorium. The 238U/226Ra and 228Th/228Ra activity ratios are significantly different than 1.0, indicating that both series are in radioactive disequilibrium. Although the Serra da Bodoquena deposits seem to be very recent, their very fine granulation and high porosity suggest that they behave as open systems for geochemical exchanges of uranium and thorium series members. The Pantanal do Miranda limestone has a radiocarbon age of 3900 yr BP. Since the thorium series is in disequilibrium it is also concluded that this deposit behaves as an open system for geochemical exchanges. PMID:11144246

  16. The 87Sr/86Sr and 143Nd/144Nd disequilibrium between Polynesian hot spot lavas and the clinopyroxenes they host: Evidence complementing isotopic disequilibrium in melt inclusions

    NASA Astrophysics Data System (ADS)

    Jackson, Matthew G.; Hart, Stanley R.; Shimizu, Nobumichi; Blusztajn, Jerzy S.

    2009-03-01

    We report 87Sr/86Sr and 143Nd/144Nd data on clinopyroxenes recovered from 10 ocean island lavas from three different hot spots (Samoa, Society, and Cook-Austral island chains). The clinopyroxenes recovered from eight of the 10 lavas analyzed in this study exhibit 87Sr/86Sr disequilibrium with respect to the host lava. The 87Sr/86Sr ratios in clinopyroxene separates are 95-3146 ppm (0.0095-0.31%) different from their respective host whole rocks. Clinopyroxenes in three lavas have 143Nd/144Nd ratios that are 70-160 ppm (0.007-0.016%) different from the host lavas. The 87Sr/86Sr and 143Nd/144Nd disequilibrium in one lava (the oldest lava considered in this study, Mangaia sample MGA-B-47) can be attributed to posteruptive radiogenic ingrowth, but the isotope disequilibrium in the other, younger lavas cannot be explained by this mechanism. In five of the lava samples, two populations of clinopyroxene were isolated (black and green, separated by color). In four out of five of these samples, the 87Sr/86Sr ratios of the two clinopyroxene populations are isotopically different from each other. In addition to 87Sr/86Sr disequilibrium, the two clinopyroxene populations in one of the lavas (Tahaa sample TAA-B-26) have 143Nd/144Nd ratios that are ˜100 ppm different from each other. Given the resilience of clinopyroxene to seawater alteration and the likelihood that the Sr and Nd isotope composition of fresh clinopyroxene separates provides a faithful record of primary magmatic compositions, the clinopyroxene-clinopyroxene isotope disequilibrium in these four lavas provides strong evidence that a mechanism other than seawater alteration has generated the observed isotopic disequilibrium. This study confirms the isotopic diversity in ocean island lavas previously observed in olivine-hosted melt inclusions. For example, the Sr isotopic variability previously observed in olivine-hosted melt inclusions is mirrored by the isotopic diversity in clinopyroxenes isolated from many of

  17. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    SciTech Connect

    Urbanek, M.; Goldman, D.; Long, J.C.

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  18. The genetic structure of natural populations of Drosophila melanogaster XIII. Further studies on linkage disequilibrium.

    PubMed

    Mukai, T; Voelker, R A

    1977-05-01

    The Raleigh, North Carolina, population of Drosophila melanogaster was examined for linkage disequilibrium in 1974, several years after previous analyses in 1968, 1969, and 1970. alphaglycerol-3-phosphate dehydrogenase-1 (alphaGpdh-1), malate dehydrogenase-1 (Mdh-1), alcohol dehydrogenase (Adh), and hexokinase-C (Hex-C, tentative name, F. M. Johnson, unpublished; position determined by the present authors to be 2-74.5) were assayed for 617 second chromosomes, and esterase-C (Est-C) and octanol dehydrogenase (Odh) were assayed for 526 third chromosomes. In addition, two polymorphic inversions in the second chromosomes [In(2L)t and In(2R)NS] were examined, and the following findings were obtained: (1) No linkage disequilibrium between isozyme genes was detected. Significant linkage disequilibria were found only between the polymorphic inversions and isozyme genes [In(2L)t vs. Adh, and In(2R)NS vs. Hex-C]. Significant disequilibrium was not detected between In(2L)t and alphaGpdh-1, which is included in the inversion, but a tendency toward disequilibrium was consistently found from 1968 to 1974. The frequency of two-strand double crossovers within inversion In(2L)t involving a single crossover on each side of alphaGpdh-1 was estimated to be 0.00022. Thus, the consistent but not significant linkage disequilibrium between the two factors can be explained by recombination after the inversion occurred. (2) Previously existing linkage disequilibrium between Adh and In(2R)NS (the distance is about 30 cM, but the effective recombination value is about 1.75%) was found to have disappeared. (3) No higher-order linkage disequilibrium was detected. (4) Linkage disequilibrium between Odh and Est-C (the distance of which was estimated to be 0.0058 +/- 0.002) could not be detected (chi(2) (df=1) = 0.9).-From the above results, it was concluded that linkage disequilibria among isozyme genes are very rare in D. melanogaster, so that the Franklin-Lewontin model (Franklin and Lewontin

  19. Radioactive Wastes.

    PubMed

    Choudri, B S; Baawain, Mahad

    2015-10-01

    Papers reviewed herein present a general overview of radioactive waste activities around the world in 2014. These include safety assessments, decommission and decontamination of nuclear facilities, fusion facilities, transportation and management solutions for the final disposal of low and high level radioactive wastes (LLW and HLW), interim storage and final disposal options for spent fuel (SF), and tritiated wastes, with a focus on environmental impacts due to the mobility of radionuclides in water, soil and ecosystem alongwith other progress made in the management of radioactive wastes. PMID:26420096

  20. Radioactive Wastes.

    PubMed

    Choudri, B S; Baawain, Mahad

    2016-10-01

    Papers reviewed herein present a general overview of radioactive waste activities around the world in 2015. These include safety assessments, decommission and decontamination of nuclear facilities, fusion facilities, transportation and management solutions for the final disposal of low and high level radioactive wastes (LLW and HLW), interim storage and final disposal options for spent fuel (SF), and tritiated wastes, with a focus on environmental impacts due to the mobility of radionuclides in water, soil and ecosystem alongwith other progress made in the management of radioactive wastes. PMID:27620100

  1. Radioactivity Calculations

    ERIC Educational Resources Information Center

    Onega, Ronald J.

    1969-01-01

    Three problems in radioactive buildup and decay are presented and solved. Matrix algebra is used to solve the second problem. The third problem deals with flux depression and is solved by the use of differential equations. (LC)

  2. Simulated Radioactivity

    ERIC Educational Resources Information Center

    Boettler, James L.

    1972-01-01

    Describes the errors in the sugar-cube experiment related to radioactivity as described in Project Physics course. The discussion considers some of the steps overlooked in the experiment and generalizes the theory beyond the sugar-cube stage. (PS)

  3. Concentrating Radioactivity

    ERIC Educational Resources Information Center

    Herrmann, Richard A.

    1974-01-01

    By concentrating radioactivity contained on luminous dials, a teacher can make a high reading source for classroom experiments on radiation. The preparation of the source and its uses are described. (DT)

  4. Disequilibrium of the 238U series in basalt

    USGS Publications Warehouse

    Somayajulu, B.L.K.; Tatsumoto, M.; Rosholt, J.N.; Knight, R.J.

    1966-01-01

    Radioisotope analyses of basalt samples from Hawaii, Japan, and Iwo Jima show that: (1) 234U and 238U are virtually in radioactive equilibrium, (2) 230Th exceeds equilibrium values in all these samples, (3) 210Pb concentrations range from 10-200% of the equilibrium values and average 30% deficient, and (4) 226Ra is probably not in equilibrium with 234U. The source regions of the basalts or magma forming processes are open systems, chemically. The enrichment of some of the uranium-daughter nuclides is insufficient to account for the excess 206Pb in volcanic rocks. The isotopic composition of lead and specific activity of 210Pb in sublimates from Showa-shinzan, Japan are also reported. ?? 1966.

  5. An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD) is the "non-random association of alleles" and can be utilized through association analysis to discover quantitative trait loci (QTLs). The largest resource of soybean germplasm is the Asian landraces that are the most immediate result of domestication. Previously it ha...

  6. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. Linkage disequilibrium (LD)-mapping using nonrandom associations of loci in haplotypes is a powerful high-r...

  7. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in ...

  8. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Signatures of selection are regions in the genome that have been preferentially maintained because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium patterns. The varLD methodol...

  9. Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at COMT locus between populations sampled within the Germplasm Enhance...

  10. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

  11. Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and po...

  12. Germany's Persistent Balance-of-Payments Disequilibrium Revisited. German Studies Notes.

    ERIC Educational Resources Information Center

    Kindleberger, Charles P.

    This essay compares Germany's persistent financial disequilibrium with the balance of payments situation in the United States. Delivered at a Symposium on German Economic Growth and Stability, the author concentrates on Germany's balance of payments surplus and presents U.S. figures mainly as a point of comparison. The material on Germany has been…

  13. Genetic diversity and linkage disequilibrium in Drosophila melanogaster with different rates of development

    SciTech Connect

    Marinkovic, D.; Tucic, N.; Moya, A.; Ayala, F.J.

    1987-11-01

    The authors examined eight enzyme polymorphisms in groups of Drosophila melanogaster flies with fast, intermediate and slow development. The allelic frequencies are similar in all three developmental classes, but the distribution of the genotypes among the class is significantly heterogeneous for the three loci on the second chromosome. When the total sample of 300 individuals is examined, significant gametic disequilibrium appears in 3 out of 13 pairs of genes located on the same chromosome and in 4 out of 15 pairs of genes located on different chromosomes. This 25% incidence of disequilibrium between pairs of genes is larger than previously observed in other natural populations (but similar to the incidence observed in laboratory populations). The greater frequency of significant gametic disequilibrium in our study is probably due to the large number of genomes sampled. Some models specifically predict that individuals with faster rates of development (i.e., greater fitness) should be more heterozygous (and exhibit more linkage disequilibrium) than individuals with slower development. This hypothesis is not supported by our results.

  14. Disequilibrium and Questioning in the Primary Classroom: Establishing Routines that Help Students Learn

    ERIC Educational Resources Information Center

    Carter, Susan

    2008-01-01

    Jean Piaget (1970) defined "disequilibrium" as a conflict between new ideas and current conceptions. In this article, the author describes how introducing this concept to her first graders improved formative assessment results and the overall classroom climate during mathematics class. Students feel success in mathematics even without mastering a…

  15. A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collectio...

  16. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effecti...

  17. Observations of Jupiter at 5 micron from IRTF/TEXES : latitudinal variability of disequilibrium species

    NASA Astrophysics Data System (ADS)

    Drossart, P.; Encrenaz, T.; Greathouse, T. K.; DeWitt, C.; Fouchet, T.; Janssen, M.; Gulkis, S.; Orton, G. S.; Fletcher, L.; Giles, R.; Atreya, S. K.; Boudon, V.

    2015-10-01

    Observations of Jupiter in the 5 μm spectral window,obtained in March/April 2015 at IRTF are presented, in preparation of the arrival of the NASA/JUNO mission in 2016. Sounding of the troposphere of Jupiter below 2 bars is obtained from the observations, to search for the variability of disequilibrium species, related to deep atmospheric circulation.

  18. Extent of linkage disequilibrium in large breed dogs: chromosomal and breed variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purpose: Understanding extent of linkage disequilibrium (LD) is a crucial component for successful utilization of genome-wide association studies (GWAS). The extent of LD in the dog has been described based upon small marker sets in multiple breeds and studies. Understanding variation in LD on a per...

  19. Comparing atmospheric chemical disequilibrium of Earth and Mars to detect the traces of Life

    NASA Astrophysics Data System (ADS)

    Simoncini, Eugenio; Brucato, John Robert; Grassi, Tommaso

    Thanks to rover explorations, satellite mapping and in loco measurements, there are many evidence nowadays that early Mars could have hold extended oceans of liquid water. This makes early Mars similar to early Earth, and a deeper understanding of the conditions which led to the emergence of Life on Earth is needed. It has long been observed that Earth's atmosphere is uniquely far from its thermochemical equilibrium state in terms of its chemical composition. Studying this state of disequilibrium is important for its potential role in the detection of life on other suitable planets [1][2][3]. We developed a methodology to calculate the extent of atmospheric chemical disequilibrium [3][4]. This tool allows us to understand, on a thermodynamic basis, how life affected - and still affects - geochemical processes on Earth, and if other planetary atmospheres are habitable or have a disequilibrium similar to the Earth's one. A new computational framework called KROME has been applied to atmospheric models in order to give a correct computation of reactionś kinetics [5]. In this work we present a first computation of the extent of disequilibrium for the present and early Earth and Mars atmospheres, considering the specific contribution of the different atmospheric processes, such as thermochemical reactions, eddy diffusion, photochemistry, deposition, and the effect of the biosphere. We then assess the effect of life on atmospheric disequilibrium of the Earth and provide a comparison between “alive” and “dead” Earth, present and (plausible) early Mars. Our results provide a comprehensive analysis of atmospheric disequilibrium for rocky and habitable planets, which can be also used for the detection of habitable conditions on farther planetary bodies. [1] Lovelock, J. E.: A physical basis for life detection experiments, Nature, 207, 568 (1965) [2] Kleidon, A., Physics of Life Reviews, 7, 424 (2010) [3] Simoncini E., Grassi T., Disequilibrium in planetary

  20. A rapid method of haplotyping HFE mutations and linkage disequilibrium in a Caucasoid population

    PubMed Central

    Mullighan, C; Bunce, M; Fanning, G; Marshall, S; Welsh, K

    1998-01-01

    Background—HFE mutations are associated with hereditary haemochromatosis. However, a simple method capable of demonstrating the cis/trans arrangement of alleles is lacking, and linkage disequilibrium between HFE alleles and classic HLA loci is unknown. These are important issues as the pathogenic role of the mutations is not known. 
Aims—To develop a simple method of genotyping HFE mutations suitable for clinical use in addition to large disease studies. 
Patients—A total of 330 Caucasoid cadaveric organ donor controls were examined. Ten individuals previously HLA-H genotyped by polymerase chain reaction using restriction fragment length polymorphism (PCR-RFLP) were also examined to validate the method. 
Methods—A simple polymerase chain reaction using sequence specific primers (PCR-SSP) capable of haplotyping the mutations was developed. HFE allele and haplotype frequencies and linkage disequilibrium with eight HLA class I and II loci were examined in the control population. 
Results—27% and 19.7% of patients were positive for the 63D and 282Y alleles, respectively. No chromosome carried both 63D and 282Y. Linkage disequilibrium between 282Y and HLA-A*03 was confirmed, but was not straightforward: some A*03-associated alleles (DRB1*15, DQB1*06), but not all (B*07, Cw*0702), were associated with 282Y. 
Conclusions—Linkage disequilibrium data suggest that an HLA-B*07 containing haplotype contains an element affording protection from haemochromatosis and may suggest the timing of the founder 282Y mutation. 

 Keywords: HFE; haemochromatosis; PCR-SSP; linkage disequilibrium PMID:9616322

  1. RADIOACTIVE BATTERY

    DOEpatents

    Birden, J.H.; Jordan, K.C.

    1959-11-17

    A radioactive battery which includes a capsule containing the active material and a thermopile associated therewith is presented. The capsule is both a shield to stop the radiations and thereby make the battery safe to use, and an energy conventer. The intense radioactive decay taking place inside is converted to useful heat at the capsule surface. The heat is conducted to the hot thermojunctions of a thermopile. The cold junctions of the thermopile are thermally insulated from the heat source, so that a temperature difference occurs between the hot and cold junctions, causing an electrical current of a constant magnitude to flow.

  2. Radioactive Waste.

    ERIC Educational Resources Information Center

    Blaylock, B. G.

    1978-01-01

    Presents a literature review of radioactive waste disposal, covering publications of 1976-77. Some of the studies included are: (1) high-level and long-lived wastes, and (2) release and burial of low-level wastes. A list of 42 references is also presented. (HM)

  3. Radioactive wastes

    SciTech Connect

    Devarakonda, M.S.; Hickox, J.A.

    1996-11-01

    This paper provides a review of literature published in 1995 on the subject of radioactive wastes. Topics covered include: national programs; waste repositories; mixed wastes; decontamination and decommissioning; remedial actions and treatment; and environmental occurrence and transport of radionuclides. 155 refs.

  4. Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?

    PubMed Central

    2010-01-01

    Background Since 2001, the use of more and more dense maps has made researchers aware that combining linkage and linkage disequilibrium enhances the feasibility of fine-mapping genes of interest. So, various method types have been derived to include concepts of population genetics in the analyses. One major drawback of many of these methods is their computational cost, which is very significant when many markers are considered. Recent advances in technology, such as SNP genotyping, have made it possible to deal with huge amount of data. Thus the challenge that remains is to find accurate and efficient methods that are not too time consuming. The study reported here specifically focuses on the half-sib family animal design. Our objective was to determine whether modelling of linkage disequilibrium evolution improved the mapping accuracy of a quantitative trait locus of agricultural interest in these populations. We compared two methods of fine-mapping. The first one was an association analysis. In this method, we did not model linkage disequilibrium evolution. Therefore, the modelling of the evolution of linkage disequilibrium was a deterministic process; it was complete at time 0 and remained complete during the following generations. In the second method, the modelling of the evolution of population allele frequencies was derived from a Wright-Fisher model. We simulated a wide range of scenarios adapted to animal populations and compared these two methods for each scenario. Results Our results indicated that the improvement produced by probabilistic modelling of linkage disequilibrium evolution was not significant. Both methods led to similar results concerning the location accuracy of quantitative trait loci which appeared to be mainly improved by using four flanking markers instead of two. Conclusions Therefore, in animal half-sib designs, modelling linkage disequilibrium evolution using a Wright-Fisher model does not significantly improve the accuracy of the

  5. Linkage disequilibrium between an allele at the dopamine D4 receptor locus and Tourette syndrome, by the transmission-disequilibrium test

    SciTech Connect

    Grice, D.E.; Gelernter, J.; Leckman, J.F.; Pauls, D.L.

    1996-09-01

    Dopaminergic abnormalities are implicated in the pathogenesis of Tourette syndrome (TS) and chronic multiple tics. We used the transmission-disequilibrium test (TDT) method to test for linkage disequilibrium between a specific allele (the seven-repeat allele (DRD4*7R) of the exon 3 VNTR polymorphic site) at the D4 dopamine receptor locus (DRD4) and expression of chronic multiple tics and TS. This particular allele had been shown in functional studies to have different binding properties compared with the other common alleles in this DRD4 polymorphic system. We studied 64 family trios (consisting of an affected person and two parents, at least one heterozygous for DRD4*7R), including 12 nuclear family trios and 52 trios from four large TS kindreds. The DRD4*7R allele was transmitted significantly more frequently than expected ({chi}{sup 2}{sub TDT} ranging from 8.47 [P < .004] to 10.80 [P = .001], depending on breadth of disease definition and inclusion or exclusion of inferred genotypes). Confirmation of this finding will depend on either replication in other samples or the identification of a transmitted functional mutation within this sample. 56 refs., 2 figs., 3 tabs.

  6. Geochemistry of speleothem records from southern Illinois: Development of (234U)/(238U) as a proxy for paleoprecipitation

    USGS Publications Warehouse

    Zhou, Juanzuo; Lundstrom, C.C.; Fouke, B.; Panno, S.; Hackley, K.; Curry, B.

    2005-01-01

    Natural waters universally show fractionation of uranium series (U-series) parent-daughter pairs, with the disequilibrium between 234U and 238U (234U)/(238U) commonly used as a tracer of groundwater flow. Because speleothems provide a temporal record of geochemical variations in groundwater precipitating calcite, (234U)/(238U) variations in speleothems provide a unique method of investigating water-rock interaction processes over millennium time scales. We present high precision Thermal Ionization Mass Spectrometric (TIMS) U-series analyses of speleothems and drip waters from Fogelpole Cave in southern Illinois. Data from all speleothems from the cave show an inverse correlation between (234U)/(238U) and U concentration, following the pattern observed in groundwaters globally. Within a 65-cm-long stalagmite, concordant 234U-238 U-230Th and 235U-231Pa ages for 5 samples indicate accurate chronology from 78.5 ka to 30 ka. Notably, (234U)/(238U)o which differs from most speleothems by having (234U)/(238U)o <1, positively correlates with speleothem growth rate. We generalize this to the observation that speleothems globally show (234U)/ (238U)o deviating farther from secular equilibrium at lower growth rates and approaching secular equilibrium at higher grow rates. Based on the Fogelpole observations, we suggest that groundwater (234U)/(238U) is controlled by the U oxidation state, the U concentration of the water and the fluid velocity. A transport model whereby U-series nuclides react and exchange with mineral surfaces can reproduce the observed trend between growth rate and (234U)/(238U)o. Based on this result, we suggest that (234U)/(238U)o in speleothems may record changes in hydrologic flux with time and thus could provide a useful proxy for long term records of paleoprecipitation. ?? 2005 Elsevier B.V. All rights reserved.

  7. Linkage and Linkage Disequilibrium Scan for Autism Loci in an Extended Pedigree from Finland

    PubMed Central

    Kilpinen, Helena; Ylisaukko-oja, Tero; Rehnström, Karola; Gaál, Emilia; Turunen, Joni A.; Kempas, Elli; von Wendt, Lennart; Varilo, Teppo; Peltonen, Leena

    2009-01-01

    Population isolates, such as Finland, have proved beneficial in mapping rare causative genetic variants due to a limited number of founders resulting in reduced genetic heterogeneity and extensive linkage disequilibrium. We have here used this special opportunity to identify rare alleles in autism by genealogically tracing 20 autism families into one extended pedigree with verified genealogical links reaching back to the 17th century. In this unique pedigree we performed a dense microsatellite marker genome-wide scan of linkage and linkage disequilibrium, and followed initial findings with extensive fine-mapping. We identified a putative autism susceptibility locus at 19p13.3, and obtained further evidence for previously identified loci at 1q23 and 15q11-13. Most promising candidate genes were TLE2 and TLE6 genes clustered at 19p13 and ATP1A2 at 1q23. PMID:19454485

  8. Alpha-recoil damage: Relation to isotopic disequilibrium and leaching of radionuclides

    SciTech Connect

    Fleischer, R.L. )

    1988-06-01

    The observation by Raabe et al. (1973) of large differences between the solubilities of isotopically different plutonium dioxides, has led to the recognition of preferential etching of recoil damage as a widespread phenomenon for alpha-active radionuclides. The associated preferential solubility of the products of alpha decay, along with direct recoil ejection, are the two specific microscopic mechanisms that are documented as causes of isotopic disequilibrium in the U and Th decay series. Similarly, leaching plays a significant role in releasing {sup 222}Rn from natural substances, {sup 222}Rn being the alpha-decay product of {sup 226}Ra. The average annealing time in nature of the damage sites can be inferred from the extent of isotopic disequilibrium for different isotopic pairs in the Th and U decay chains.

  9. Influence of random daughter exposure rate, unattachment fraction, and disequilibrium on occurrence of lung tumors

    SciTech Connect

    Cross, F.T.; Palmer, R.F.; Dagle, G.E.; Busch, R.H.; Buschbom, R.L.

    1983-10-01

    Groups of male, specific-pathogen-free (SPF), Wistar rats were exposed to several concentrations of radon daughters and uranium ore dust to clarify the roles of exposure rate, unattached RaA daughters, and the degree of radon daughter disequilibrium, in the development of respiratory system disease. Modeled, human-dosimetric data indicate that the dose to sensitive tissues of the respiratory tract increases with increasing radon-daughter unattachment fraction and degree of disequilibrium. Experimental verification of these dose-effect relationships is needed to protect the health of workers and of the public exposed to radon-daughter environments. Data bearing on these relationships as well as updated results of experiments designed to test the role of radon-daughter exposure rate on lung-tumor incidence are reported. 13 references, 3 tables.

  10. Th-230 - U-238 series disequilibrium of the Olkaria rhyolites Gregory Rift Valley, Kenya: Residence times

    NASA Technical Reports Server (NTRS)

    Black, S.; Macdonald, R.; Kelly, M.

    1993-01-01

    U-series disequilibrium analyses have been conducted on samples from Olkaria rhyolite centers with ages being available for all but one center using both internal and whole rock isochrons. 67 percent of the rhyolites analyzed show U-Th disequilibrium, ranging from 27 percent excess thorium to 36 percent excess uranium. Internal and whole rock isochrons give crystallization/formation ages between 65 ka and 9 ka, in every case these are substantially older than the eruptive dates. The residence times of the rhyolites (U-Th age minus the eruption date) have decreased almost linearly with time, from 45 ka to 7 Ka suggesting a possible increase of activity within the system related to increased basaltic input. The long residence times are mirrored by large Rn-222 fluxes from the centers which cannot be explained by larger U contents.

  11. A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis.

    PubMed Central

    Lou, Xiang-Yang; Casella, George; Littell, Ramon C; Yang, Mark C K; Johnson, Julie A; Wu, Rongling

    2003-01-01

    For tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium and exhibits two significant advantages over current disequilibrium mapping methods. First, we have derived closed-form solutions for estimating the marker-QTL haplotype frequencies within the maximum-likelihood framework implemented by the EM algorithm. The allele frequencies of putative QTL and their linkage disequilibria with the markers are estimated by solving a system of regular equations. This procedure has significantly improved the computational efficiency and the precision of parameter estimation. Second, our method can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis. This can not only enhance the precision of parameter estimation, but also make it possible to perform whole-genome association studies. We carried out extensive simulation studies to examine the robustness and statistical performance of our method. The application of the new method was validated using a case study from humans, in which we successfully detected significant QTL affecting human body heights. Finally, we discuss the implications of our method for genome projects and its extension to a broader circumstance. The computer program for the method proposed in this article is available at the webpage http://www.ifasstat.ufl.edu/genome/~LD. PMID:12702696

  12. Uranium disequilibrium in groundwater: An isotope dilution approach in hydrologic investigations

    USGS Publications Warehouse

    Osmond, J.K.; Rydell, H.S.; Kaufman, M.I.

    1968-01-01

    The distribution and environmental disequilibrium patterns of naturally occurring uranium isotopes (U234 and U238) in waters of the Floridan aquifer suggest that variations in the ratios of isotopic activity and concentrations can be used quantitatively to evaluate mixing proportions of waters from differing sources. Uranium is probably unique in its potential for this approach, which seems to have general usefulness in hydrologic investigations.

  13. Uranium disequilibrium in groundwater: an isotope dilution approach in hydrologic investigations.

    PubMed

    Osmond, J K; Rydell, H S; Kaufman, M I

    1968-11-29

    The distribution and environmental disequilibrium patterns of naturally occurring uranium isotopes (U(234) and U(238)) in waters of the Floridan aquifer suggest that variations in the ratios of isotopic activity and concentrations can be used quantitatively to evaluate mixing proportions of waters from differing sources. Uranium is probably unique in its potential for this approach, which seems to have general usefulness in hydrologic investigations. PMID:4880720

  14. Selection, Hitchhiking and Disequilibrium Analysis at Three Linked Loci with Application to Hla Data

    PubMed Central

    Robinson, W. P.; Cambon-Thomsen, A.; Borot, N.; Klitz, W.; Thomson, G.

    1991-01-01

    The HLA system has been extensively studied from an evolutionary perspective. Although it is clear that selection has acted on the genes in the HLA complex, the nature of this selection has yet to be fully clarified. A study of constrained disequilibrium values is presented that is applicable to HLA and other less polymorphic systems with three or more linked loci, with the purpose of identifying selection events. The method uses the fact that three locus systems impose additional constraints on the range of possible disequilibrium values for any pair of loci. We have thus examined the behavior of the normalized pairwise disequilibrium measures using two locus (D'), and also three locus (D''), constraints on pairwise disequilibria in a three locus system when one of the three loci is under positive selection. The difference between these measures, δ = |D'| - |D''|, has a distribution for the two unselected loci differing from that for the selected locus with either of the unselected loci (the hallmark is a high positive value of δ for the two unselected loci). An examination of genetic drift indicates that positive δ values are unlikely to be found in human populations in the absence of selection when recombination is greater than about 0.1%. This measure can thus provide insight into which allele of several linked loci might have been subject to selection. Application of this method to HLA haplotypes from a large French population study (Provinces Francaise) identifies selected alleles on particular haplotypes. Application of a complementary method, disequilibrium pattern analysis also confirms the action of selection on these haplotypes. PMID:1752429

  15. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

    PubMed Central

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-01-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r2 measure. In the present study, we tackled the problem of the bias of r2 estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r2 measure. The first one, rS2, uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, rV2, includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes. We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r2 measures, which actually captured ‘true' linkage disequilibrium unlike the usual r2 measure. PMID:21878986

  16. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

    PubMed

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-03-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure. PMID:21878986

  17. Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations

    PubMed Central

    Smith, Michael W.; Lautenberger, James A.; Shin, Hyoung Doo; Chretien, Jean-Paul; Shrestha, Sadeep; Gilbert, Dennis A.; O’Brien, Stephen J.

    2001-01-01

    Population linkage disequilibrium occurs as a consequence of mutation, selection, genetic drift, and population substructure produced by admixture of genetically distinct ethnic populations. African American and Hispanic ethnic groups have a history of significant gene flow among parent groups, which can be of value in affecting genome scans for disease-gene discovery in the case-control and transmission/disequilibrium test designs. Disease-gene discovery using mapping by admixture linkage disequilibrium (MALD) requires a map of polymorphic markers that differentiate between the founding populations, along with differences in disease-gene allele frequencies. We describe markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats (STRs) in African Americans, Hispanics, European Americans, and Asians, by choosing STR markers that have large differences in composite δ, log-likelihood ratios, and/or I*(2) for MALD. Additional markers can be added to this MALD map by utilization of the rapidly growing single-nucleotide–polymorphism databases and the literature, to achieve a 3–10-cM scanning scale. The map will be useful for studies of diseases, including prostate and breast cancer, diabetes, hypertension, and end-stage renal disease, that have large differences in incidence between the founding populations of either Hispanics or African Americans. PMID:11590548

  18. Disequilibrium macro model and catastrophe theory: the case of an oil shock

    SciTech Connect

    German, I.

    1983-01-01

    This study builds a simple disequilibrium macromodel of a small open economy that imports oil from an exogenous unit. The model is motivated by very slow adjustment of prices and wages to disequilibrium. Output on the other hand adjusts to its final level instantaneously. A rationing scheme is specified that explicitly takes into account the spillover effects and differentiates between notional, effective, and actual quantities. In a Solow-Stiglitz (1968) setting, a dynamic model is developed in which the dynamic forces depend on the economic environment specified by the Malinvandian regimes: Classical Unemployment, Keynesian Unemployment, Repressed Inflation, and the Walrasian Equilibrium. Given that dynamic system, the author seeks to identify the stationary points of the system (quasi-equilibria) and to find their stability properties. To the disequilibrium model an oil shock is introduced and its effects on employment, real output, real wage, and the stationary points of the system are investigated. A one-time increase (decrease) in the real price of oil and a continuous increase (decrease) in the real price of oil are considered. The path the economy takes and, in particular, the continuous and discontinuous behavior of the quasi-equilibria are investigated. Finally, the model government policy is incorporated and different policy alternatives are studied.

  19. Thorium-uranium disequilibrium in a geothermal discharge zone at yellowstone

    NASA Astrophysics Data System (ADS)

    Sturchio, Neil C.; Binz, Carl M.; Lewis, Carter H., III

    1987-07-01

    Whole rock samples of hydrothermally-altered Biscuit Basin rhyolite from Yellowstone drill cores Y-7 and Y-8 were analyzed for 230Th, 234U, 238U, and 232Th. Extreme disequilibrium was found, with ( 230Th/ 234U) ranging from 0.30 to 1.27. Values of ( 230Th/ 232Th) and ( 234U/ 232Th) define a linear correlation with a slope of 0.16 ± 0.01, which corresponds to a ( 230Th/ 234U) age of approximately 19 ka. The ( 230Th/ 234U) disequilibrium was apparently caused by U redistribution which occurred mostly at about 19 ka, and is not related simply to the relative degree of hydrothermal alteration and self-sealing of the rhyolite. Mass balance of U requires a large flux of U-bearing groundwater through the rhyolite at the time of U redistribution; rough estimates of minimum water/rock ratio range from 10 2 to 10 4, for a range of possible groundwater U concentrations. Conservative hydraulic calculations indicate that the required groundwater flux could have occurred within a period of hundreds of years prior to self-sealing. The disequilibrium data are consistent with a model involving U redistribution during the initial stages of development of a geothermal discharge zone that formed in response to the hydrogeologic effects of glacial melting and unloading during the decline of the Pinedale Glaciation.

  20. Modeling the disequilibrium species for Jupiter and Saturn: Implications for Juno and Saturn entry probe

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Lunine, Jonathan I.; Mousis, Olivier

    2016-09-01

    Disequilibrium species have been used previously to probe the deep water abundances and the eddy diffusion coefficient for giant planets. In this paper, we present a diffusion-kinetics code that predicts the abundances of disequilibrium species in the tropospheres of Jupiter and Saturn with updated thermodynamic and kinetic data. The dependence on the deep water abundance and the eddy diffusion coefficient is investigated. We quantified the disagreements in CO kinetics that comes from using different reaction networks and identified C2H6 as a useful tracer for the eddy diffusion coefficient. We first apply an H/P/O reaction network to Jupiter and Saturn's atmospheres and suggest a new PH3 destruction pathway. New chemical pathways for SiH4 and GeH4 destruction are also suggested, and another AsH3 destruction pathway is investigated thanks to new thermodynamic and kinetic data. These new models should enhance the interpretation of the measurement of disequilibrium species by JIRAM on board Juno and allow disentangling between methods for constraining the Saturn's deep water abundance with the Saturn entry probes envisaged by NASA or ESA.

  1. High-resolution linkage-disequilibrium mapping of the cartilage-hair hypoplasia gene

    SciTech Connect

    Sulisalo, T.; Klockars, J.; Chapelle, A. de la; Kaitila, I. |; Maekitie, O.; Sistonen, P.; Francomano, C.A.

    1994-11-01

    We recently assigned the gene for an autosomal recessive skeletal dysplasia, cartilage-hair hypoplasia (CHH), to 9p21-p13 in Finnish and Amish families. An association was observed between CHH and alleles at D9S163 in both family series, suggesting that these loci are in linkage disequilibrium and close to each other. Here we extended these studies by exploiting the linkage-disequilibrium information that can be obtained from families with a single affected child, and we studied 66 Finnish CHH families with seven microsatellite markers. The analysis based on the Luria and Delbrueck (1943) method and adapted to the study of human founder populations suggests that the distance between CHH and D9S163 is {approximately}0.3 cM. An eight-point linkage analysis modified to take advantage of all possible information in 15 Finnish and 17 Amish families was capable of narrowing the likely location of CHH to within an interval of 1.7 cM on a male map. The peak lod score of 54.92 was attained 0.03 and 0.1 cM proximal to D9S163 on the male and female maps, respectively. These results confirm the power of genetic resolution, that lies in the study of linkage disequilibrium in well-defined founder populations with one major ancestral disease mutation. 21 refs., 4 figs., 3 tabs.

  2. Mapping by admixture linkage disequilibrium in human populations: limits and guidelines.

    PubMed Central

    Stephens, J. C.; Briscoe, D.; O'Brien, S. J.

    1994-01-01

    Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient's relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racial groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of > or = .3 between admixed parent populations) to produce an efficient approach (> 95% ascertainment) for locating genes not easily tracked in human pedigrees. PMID:7942858

  3. Simple models for disequilibrium fractional melting and batch melting with application to REE fractionation in abyssal peridotites

    NASA Astrophysics Data System (ADS)

    Liang, Yan; Liu, Boda

    2016-01-01

    Disequilibrium melting arises when the kinetics of chemical exchange between a residual mineral and partial melt is sluggish compare to the rate of melting. To better understand the role of a finite crystal-melt exchange rate on trace element fractionation during mantle melting, we have developed a disequilibrium melting model for partial melting in an upwelling steady-state column. We use linear kinetics to approximate crystal-melt mass exchange rate and obtain simple analytical solutions for cases of perfect fractional melting and batch melting. A key parameter determining the extent of chemical disequilibrium during partial melting is an element specific dimensionless ratio (ε) defined as the melting rate relative to the solid-melt chemical exchange rate for the trace element of interest. In the case of diffusion in mineral limited chemical exchange, ε is inversely proportional to diffusivity of the element of interest. Disequilibrium melting is important for the trace element when ε is comparable to or greater than the bulk solid-melt partition coefficient for the trace element (k). The disequilibrium fractional melting model is reduced to the equilibrium perfect fractional melting model when ε is much smaller than k. Hence highly incompatible trace elements with smaller mobilities in minerals are more susceptible to disequilibrium melting than moderately incompatible and compatible trace elements. Effect of chemical disequilibrium is to hinder the extent of fractionation between residual solid and partial melt, making the residual solid less depleted and the accumulated melt more depleted in incompatible trace element abundances relative the case of equilibrium melting. Application of the disequilibrium fractional melting model to REE and Y abundances in clinopyroxene in abyssal peridotites from the Central Indian Ridge and the Vema Lithospheric Section, Mid-Atlantic Ridge revealed a positive correlation between the disequilibrium parameter ε and the

  4. Heterogeneous Crystal Populations: Signatures, Genesis and Chronologies

    NASA Astrophysics Data System (ADS)

    Reid, M. R.; Vazquez, J. A.

    2005-12-01

    The ongoing development of accessory phase-based techniques helps to illuminate possible scenarios for the physical state of magmatic systems between eruptions. These, in turn, may aid in the detection of magmas in the crust. At Long Valley caldera, eastern California, ion microprobe analyses of 238U-230Th in zircon from the youthful Inyo Dome rhyolites show that even though their ages are mainly younger than the 760 k.y. old caldera-forming Bishop Tuff, they are significantly older than eruption (up to 200 k.y. and more). Do these ages date the timing of magma emplacement and show that liquid was present in the system for at least 200 k.y.? Or do the ages represent sampling by the ion beam of bimodal age domains, meaning that they could have been rapidly mobilized from voluminous crystal mushes residual after the Bishop Tuff (e.g., Hildreth, 2004)? Additionally or alternatively, could the "old" zircons be derived via assimilation of young, hydrothermally altered intrusive rocks (Schmitt and Simon, 2004)? The majority of 238U-206Pb analyses of zircons from Deer Mountain (13 of 20) are consistent with a single crystallization age that is somewhat older than previously obtained by 238U-230Th disequilibrium dating; the remaining zircon ages are younger and range to within error of the eruption age. The absence of Bishop Tuff-aged zircons indicates that if crystal mush contributes to the Inyo Dome rhyolites, its remobilization must have involved reheating to temperatures in excess of zircon saturation conditions (T>~800°C). Ion microprobe U-Th ages of allanites from South Deadman Dome range from 150 to <10 ka, in contrast to virtually all of the zircon ages which are >100 ka. The ca. 2-fold ranges in MnO/MgO and La/Nd in the same allanites overlap and extend the range of compositions we obtained for rhyolites from Toba caldera (Vazquez and Reid, 2005). The South Deadman Dome allanites could, by analogy to experimental results for a Toba rhyolite, have crystallized

  5. Use of U-Series Isotopic Disequilibrium to Investigate the Nature and Distribution of Actively Flowing Fractures

    NASA Astrophysics Data System (ADS)

    Nichols, P. J.; Paces, J. B.; Neymark, L. A.; Rajaram, H.

    2011-12-01

    Groundwater transport of radioisotopes from underground nuclear tests at the Nevada National Security Site (NNSS) is of concern to the U.S. Department of Energy. Extensive testing was conducted near or below the regional water table (saturated zone; SZ) at Pahute Mesa and within the unsaturated (or partially saturated) zone at Rainier Mesa. Groundwater flow in these rocks is believed to occur mainly through a connected network of fractures. To better understand flow in these fractured rocks, we analyzed U-series isotopes (238U-234U-230Th) from drill core samples. In rock isolated from flow over the last million years, isotopes in the 238U decay chain reach a state of radioactive secular equilibrium, where 234U/238U and 230Th/238U activity ratios (AR) = 1.0. More recent water-rock interaction results in mobilization of 234U relative to 238U, and U relative to Th in migrating waters. Rock surfaces that incorporate this U or are leached of 234U and U will show U-series disequilibrium. Isotope data can thus provide time-sensitive information on hydrologic conditions in host rocks without directly observing or measuring flowing water. To investigate NNSS fracture networks, core was selected from confining units (bedded and zeolitized felsic tuffs) and aquifers (felsic welded tuffs and lavas) in five boreholes on Pahute Mesa and two boreholes on Rainier Mesa. Samples include interiors of intact core as well as natural fracture surfaces and brecciated core. Intact core and brecciated samples were crushed and powdered. Fracture surfaces were sampled using dental burs to remove the outer 0.1 to 0.5 mm of fracture surfaces, which may have thin mineral coatings of zeolites, clays, and Mn oxides. Samples were totally digested, spiked with a 236U-229Th tracer, and analyzed by a solid-source TRITON° mass spectrometer equipped with an energy filter and single ion counter. Results show that 8 of 9 intact core samples have 234U/238U AR within ±5% of 1.0, suggesting little or no

  6. Radioactivity distribution in some Permian sediments from the Iratí and Corumbataí Formations of the Paraná Basin, Southeastern Brazil.

    PubMed

    Carlos, Dionísio Uendro; Ribeiro, Fernando Brenha; Saad, Antonio Roberto; Nicolai, Silvia Helena de Araújo

    2004-01-01

    In the city of Limeira, southeastern Brazil, an important exposure of Permian sediments of the Paraná basin was revealed by an open pit mine that exploits limestone for production of soil correction compounds and raw materials for the ceramic industry. The radioactivity of these sediments was investigated in some detail and the results provided a general view of the vertical distributions of uranium, thorium and potassium concentrations and of the element ratios U/K, U/Th and Th/K. In general, the concentrations of the main natural radioactive elements are low, with uranium being enriched in some limestone and shale levels. In addition the results showed that the 238U series is in radioactive disequilibrium in many of the analyzed samples. Although the origin of the observed disequilibrium has not been investigated, the results suggest that it is due to weathering processes and water interaction with the rock matrix. PMID:14687638

  7. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo).

    PubMed

    Li, Yi; Kim, Jong-Joo

    2015-07-01

    The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions. PMID:26104396

  8. Thorium-uranium disequilibrium in a geothermal discharge zone at Yellowstone

    SciTech Connect

    Sturchio, N.C.; Binz, C.M.; Lewis C.H. III

    1987-07-01

    Whole rock samples of hydrothermally-altered Biscuit Basin rhyolite from Yellowstone drill cores Y-7 and Y-8 were analyzed for /sup 230/Th, /sup 234/U, /sup 238/U, and /sup 232/Th. Extreme disequilibrium was found, with (/sup 230/Th//sup 234/U) ranging from 0.30 to 1.27. Values of (/sup 230/Th//sup 232/Th) and (/sup 234/U//sup 232/Th) define a linear correlation with a slope of 0.16 +/- 0.01, which corresponds to a (/sup 230/Th//sup 234/) age of approximately 19 ka. The (/sup 230/Th//sup 234/U) disequilibrium was apparently caused by U redistribution which occurred mostly at about 19 ka, and is not related simply to the relative degree of hydrothermal alteration and self-sealing of the rhyolite. Mass balance of U requires a large flux of U-bearing ground water through the rhyolite at the time of U redistribution; rough estimates of minimum water/rock ratio range from 10/sup 2/ to 10/sup 4/, for a range of possible ground water U concentrations. Conservative hydraulic calculations indicate that the required ground water flux could have occurred within a period of hundreds of years prior to self-sealing. The disequilibrium data are consistent with a model involving U redistribution during the initial stages of development of a geothermal discharge zone that formed in response to the hydrogeologic effects of glacial melting and unloading during the decline of the Pinedale Glaciation.

  9. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo)

    PubMed Central

    Li, Yi; Kim, Jong-Joo

    2015-01-01

    The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions. PMID:26104396

  10. Linkage disequilibrium analysis of G-olf{sub {alpha}} (GNAL) in bipolar affective disorder

    SciTech Connect

    Tsiouris, S.J.; Breschel, T.S.; Xu, J.

    1996-09-20

    This study examines G-olf{sub {alpha}} as a possible candidate gene for susceptibility to bipolar affective disorder (BPAD) using the Transmission Disequilibrium Test (TDT). G-olf{sub {alpha}}, which encodes a subunit of a G-protein involved in intracellular signaling, maps within a region of chromosome 18 that has been implicated by two different linkage studies as a potential site of BPAD susceptibility loci. The expression pattern of G-olf{sub {alpha}} in the brain, its coupling to dopamine receptors, and the effects of lithium salts on G-proteins all support G-olf{sub {alpha}} as a candidate gene for BPAD. Our study population consisted of 106 probands and sibs with bipolar I disorder, with a median age-at-onset of 21.5 years ascertained from the United States. There was no evidence of linkage disequilibrium between BPAD and any of the observed G-olf{sub {alpha}} alleles in our sample. Division of families based on sex of the transmitting parent did not significantly change the results. This sample had good power (78%) to detect linkage disequilibrium with alleles conferring a relative risk equal to that estimated for the putative 18p locus (2.58). Our results do not support a major role for G-olf{sub {alpha}} as a susceptibility locus for BPAD in a substantial portion of our sample. Other genes lying near G-olf{sub {alpha}} within the linked region on chromosome 18 cannot be excluded by our data. This study illustrates the use of the TDT in evaluating candidate genes within linked chromosome regions. 24 refs., 1 tab.

  11. Polymorphism, recombination, and linkage disequilibrium within the HLA class II region

    SciTech Connect

    Begovich, A.B.; McClure, G.R.; Suraj, V.C.; Helmuth, R.C.; Fildes, N.; Bugawan, T.L.; Erlich, H.A. ); Klitz, W. )

    1992-01-01

    Thirty-nine CEPH families, comprised of 502 individuals, have been typed for the HLA class II genes DRB1, DQA1, DQB1, and DPB1 using nonradioactive sequence-specific oligonucleotide probes to analyze polymerase chain reaction amplified DNA. This population, which consists of 266 independent chromosomes, contains 27 DRB1, 7 DQA1, 12 DQB1, and 17 DPB1 alleles. Analysis of the distribution of allele frequencies using the homozygosity statistic, which gives an indication of past selection pressures, suggests that balancing selection has acted on the DRB1, DQA1, and DQB1 loci. The distribution of DPB1 alleles, however, suggests a different evolutionary past. Family data permits the estimation of recombination rates and the unambiguous assignment of haplotypes. No recombinants were found between DRB1, DQA1, and DQB1; however, recombinants were detected between DQB1 and DPB1, resulting in an estimated recombination fraction of [ge]0.008 [+-] 0.004. Only 33 distinct DRB1-DQA1-DQB1 haplotypes were found in this population which illustrates the extreme nonrandom haplotypic association of alleles at these loci. A few of these haplotypes are unusual (previously unreported) for a Caucasian population and most likely result from past recombination events between the DR and DQ subregions. Examination of disequilibrium across the HLA region using these data and the available serologic HLA-A and HLA-B types of these samples shows that global disequilibrium between these loci declines with the recombination fraction, approaching statistic nonsignificance at the most distant interval, HLA-A and HLA-DP. DR-DQ haplotypes in linkage disequilibrium with DPB1 and B are noted and, finally, the evolutionary origin of certain class II haplotypes is addressed. 63 refs., 3 figs., 8 tabs.

  12. Linkage disequilibrium between the beta frequency of the human EEG and a GABAA receptor gene locus

    PubMed Central

    Porjesz, Bernice; Almasy, Laura; Edenberg, Howard J.; Wang, Kongming; Chorlian, David B.; Foroud, Tatiana; Goate, Alison; Rice, John P.; O'Connor, Sean J.; Rohrbaugh, John; Kuperman, Samuel; Bauer, Lance O.; Crowe, Raymond R.; Schuckit, Marc A.; Hesselbrock, Victor; Conneally, P. Michael; Tischfield, Jay A.; Li, Ting-Kai; Reich, Theodore; Begleiter, Henri

    2002-01-01

    Human brain oscillations represent important features of information processing and are highly heritable. A common feature of beta oscillations (13–28 Hz) is the critical involvement of networks of inhibitory interneurons as pacemakers, gated by γ-aminobutyric acid type A (GABAA) action. Advances in molecular and statistical genetics permit examination of quantitative traits such as the beta frequency of the human electroencephalogram in conjunction with DNA markers. We report a significant linkage and linkage disequilibrium between beta frequency and a set of GABAA receptor genes. Uncovering the genes influencing brain oscillations provides a better understanding of the neural function involved in information processing. PMID:11891318

  13. Assay for uranium and determination of disequilibrium by means of in situ high resolution gamma-ray spectrometry

    USGS Publications Warehouse

    Tanner, Allan B.; Moxham, Robert M.; Senftle, F.E.

    1977-01-01

    Two sealed sondes, using germanium gamma-ray detectors cooled by melting propane, have been field tested to depths of 79 m in water-filled boreholes at the Pawnee Uranium Mine in Bee Co., Texas. When, used as total-count devices, the sondes are comparable in logging speed and counting rate with conventional scintillation detectors for locating zones of high radioactivity. When used with a multichannel analyzer, the sondes are detectors with such high resolution that individual lines from the complex spectra of the uranium and thorium series can be distinguished. Gamma rays from each group of the uranium series can be measured in ore zones permitting determination of the state of equilibrium at each measurement point. Series of 10-minute spectra taken at 0.3- to 0.5-m intervals in several holes showed zones where maxima from the uranium group and from the 222Rn group were displaced relative to each other. Apparent excesses of 230Th at some locations suggest that uranium-group concentrations at those locations were severalfold greater some tens of kiloyears, ago. At the current state of development a 10-minute count yields a sensitivity of about 80 ppm U308. Data reduction could in practice be accomplished in about 5 minutes. The result is practically unaffected by disequilibrium or radon contamination. In comparison with core assay, high-resolution spectrometry samples a larger volume; avoids problems due to incomplete core recovery, loss of friable material to drilling fluids, and errors in depth and marking; and permits use of less expensive drilling methods. Because gamma rays from the radionuclides are accumulated simultaneously, it also avoids the problems inherent in trying to correlate logs made in separate runs with different equipment. Continuous-motion delayed-gamma activation by a 163-?g 252Cf neutron source attached to the sonde yielded poor sensitivity. A better neutron-activation method, in which the sonde is moved in steps so as to place the detector

  14. Accounting for linkage disequilibrium in genome-wide association studies: A penalized regression method.

    PubMed

    Liu, Jin; Wang, Kai; Ma, Shuangge; Huang, Jian

    2013-01-01

    Penalized regression methods are becoming increasingly popular in genome-wide association studies (GWAS) for identifying genetic markers associated with disease. However, standard penalized methods such as LASSO do not take into account the possible linkage disequilibrium between adjacent markers. We propose a novel penalized approach for GWAS using a dense set of single nucleotide polymorphisms (SNPs). The proposed method uses the minimax concave penalty (MCP) for marker selection and incorporates linkage disequilibrium (LD) information by penalizing the difference of the genetic effects at adjacent SNPs with high correlation. A coordinate descent algorithm is derived to implement the proposed method. This algorithm is efficient in dealing with a large number of SNPs. A multi-split method is used to calculate the p-values of the selected SNPs for assessing their significance. We refer to the proposed penalty function as the smoothed MCP and the proposed approach as the SMCP method. Performance of the proposed SMCP method and its comparison with LASSO and MCP approaches are evaluated through simulation studies, which demonstrate that the proposed method is more accurate in selecting associated SNPs. Its applicability to real data is illustrated using heterogeneous stock mice data and a rheumatoid arthritis. PMID:25258655

  15. Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef.

    PubMed

    Smith, Shavannor M; Yuan, Yinan; Doust, Andrew N; Bennetzen, Jeffrey L

    2012-03-01

    Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the "Green Revolution." All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral divergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous/paralogous relationships. The genetic diversity in the 31 studied accessions was organized into a relatively small number of haplotypes (2-4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide diversity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2-4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin. PMID:22413094

  16. Refining the position of Wilson disease by linkage disequilibrium with polymorphic microsatellites

    SciTech Connect

    Bowcock, A.M.; Tomfohrde, J. ); Weissenbach, J. ); Bonne-Tamir, B.; George-Hyslop, P.; Giagheddu, M.; Cavalli-Sforza, L.L.; Farrer, L.A.

    1994-01-01

    Wilson disease (WND) is an autosomal recessive disorder that is due to an inability to the liver to eliminate copper. Copper buildup in the liver, brain, kidney, and other tissues can result in liver cirrhosis, neurologic and psychiatric defects, and other problems. The authors have localized the disease-containing region to between D13S31 and D13S59, with >70 multiply affected families, and have constructed a YAC contig of >4.5 Mb that spans these loci and orders nine highly polymorphic microsatellites. Here, the authors present an analysis of disequilibrium with markers in this interval and provide evidence for strong allelic associations between AFM084[times]c5 alleles and WND allels in European, Middle Eastern, and East Asian populations. Significant but weaker allelic associations were also observed between WND alleles and alleles at D13S137 and D13S169. The strength of the association between AFM084[times]c5 and WND in all non-Sardinian populations combined (linkage-disequilibrium coefficient [[theta

  17. The importance of temporal stress variation and dynamic disequilibrium for the initiation of plate tectonics

    NASA Astrophysics Data System (ADS)

    Stamenković, V.; Höink, T.; Lenardic, A.

    2016-06-01

    We use 1-D thermal history models and 3-D numerical experiments to study the impact of dynamic thermal disequilibrium and large temporal variations of normal and shear stresses on the initiation of plate tectonics. Previous models that explored plate tectonics initiation from a steady state, single plate mode of convection concluded that normal stresses govern the initiation of plate tectonics, which based on our 1-D model leads to plate yielding being more likely with increasing interior heat and planet mass for a depth-dependent Byerlee yield stress. Using 3-D spherical shell mantle convection models in an episodic regime allows us to explore larger temporal stress variations than can be addressed by considering plate failure from a steady state stagnant lid configuration. The episodic models show that an increase in convective mantle shear stress at the lithospheric base initiates plate failure, which leads with our 1-D model to plate yielding being less likely with increasing interior heat and planet mass. In this out-of-equilibrium and strongly time-dependent stress scenario, the onset of lithospheric overturn events cannot be explained by boundary layer thickening and normal stresses alone. Our results indicate that in order to understand the initiation of plate tectonics, one should consider the temporal variation of stresses and dynamic disequilibrium.

  18. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information

    PubMed Central

    Gholami, Mahmood; Reimer, Christian; Erbe, Malena; Preisinger, Rudolf; Weigend, Annett; Weigend, Steffen; Servin, Bertrand; Simianer, Henner

    2015-01-01

    An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate. PMID:26151449

  19. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

    PubMed Central

    2014-01-01

    Background Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. Methods By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. Results For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. Conclusions The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. PMID:24592996

  20. Evidence of linkage disequilibrium in the Spanish polycystic kidney disease 1 population

    SciTech Connect

    Peral, B.; Ward, C.J.; Thomas, S.; Harris, P.C. ); Stallings, R.L. ); San Millan, J.L.; Moreno, F.

    1994-05-01

    Forty-one Spanish families with polycystic kidney disease 1 (PKD1) were studied for evidence of linkage disequilibrium between the disease locus and six closely linked markers. Four of these loci - three highly polymorphic microsatellites (SM6, CW3, and CW2) and a RFLP marker (BLu24) - are described for the first time in this report. Overall the results reveal many different haplotypes on the disease-carrying chromosome, suggesting a variety of independent PKD1 mutations. However, linkage disequilibrium was found between BLu24 and PKD1, and this was corroborated by haplotype analysis including the microsatellite polymorphisms. From this analysis a group of closely related haplotypes, consisting of four markers, was found on 40% of PKD1 chromosomes, although markers flanking this homogeneous region showed greater variability. This study has highlighted an interesting subpopulation of Spanish PKD1 chromosomes, many of which have a common origin, that may be useful for localizing the PKD1 locus more precisely. 37 refs., 1 fig., 4 tabs.

  1. Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

    PubMed Central

    Carmichael, Gordon A.

    2011-01-01

    Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demographic transition theory postulates initially high birth and death rates, this equilibrium eventually being broken by falling mortality. In Thailand, however, there is likely to have been both significant mortality decline and appreciable fertility increase after 1850, as the virtual elimination of indigenous warfare, rapid growth of the export rice economy and the demise of slavery and corvée labour created a new domestic environment. Characterized by more dispersed, often frontier, settlement, this environment was unprecedentedly sedate and settled, afforded ordinary households a previously unknown level of control over their resources of labour, and generated optimism about prospects for the next generation. PMID:21966299

  2. Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.).

    PubMed

    Tascioglu, Tulin; Metin, Ozge Karakas; Aydin, Yildiz; Sakiroglu, Muhammet; Akan, Kadir; Uncuoglu, Ahu Altinkut

    2016-08-01

    Bread wheat (Triticum aestivum L.) gene pool was analyzed with 117 microsatellite markers scattered throughout A, B, and D genomes. Ninety microsatellite markers were giving 1620 polymorphic alleles in 55 different bread wheat genotypes. These genotypes were found to be divided into three subgroups based on Bayesian model and Principal component analysis. The highest polymorphism information content value for the markers resides on A genome was estimated for wmc262 marker located on 4A chromosome with the polymorphism information content value of 0.960. The highest polymorphism information content value (0.954) among the markers known to be located on B genome was realized for wmc44 marker located on 1B chromosome. The highest polymorphism information content value for the markers specific to D genome was found in gwm174 marker located on 5D chromosome with the polymorphism information content value of 0.948. The presence of linkage disequilibrium between 81 pairwise SSR markers reside on the same chromosome was tested and very limited linkage disequilibrium was observed. The results confirmed that the most distant genotype pairs were as follows Ceyhan-99-Behoth 6, Gerek 79-Douma 40989, and Karahan-99-Douma 48114. PMID:27048293

  3. Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability

    PubMed Central

    Fields, P D; McCauley, D E; McAssey, E V; Taylor, D R

    2014-01-01

    Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D′) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005–0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system. PMID:24002238

  4. Analysis of spontaneous MEG activity in mild cognitive impairment using spectral entropies and disequilibrium measures.

    PubMed

    Bruña, Ricardo; Poza, Jesús; Gómez, Carlos; Fernández, Alberto; Hornero, Roberto

    2010-01-01

    The aim of this study was to explore the ability of several spectral entropies and disequilibrium measures to discriminate between spontaneous magnetoencephalographic (MEG) oscillations from 18 mild cognitive impairment (MCI) patients and 24 controls. The Shannon spectral entropy (SSE), Tsallis spectral entropy (TSE), and Rényi spectral entropy (RSE) were calculated from the normalized power spectral density to evaluate the irregularity patterns. In addition, the Euclidean (ED) and Wootters (WD) distances were computed as disequilibrium measures. Results revealed statistically significant lower SSE and TSE(2) values for MCI patients than for controls (p < 0.05) in the right lateral region of the brain. ED also obtained statistically significant lower values for MCI patients than for controls using the (p < 0.05) in the right lateral region of the brain. These findings suggest that MCI is associated with a significant decrease in irregularity of MEG activity. In addition, the highest accuracy of 64.3% was achieved by the SSE. We conclude that measures from information theory can be useful to both characterize abnormal brain dynamics and help in MCI detection. PMID:21097360

  5. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

  6. HLA class II linkage disequilibrium and haplotype evolution in the Cayapa Indians of Ecuador

    SciTech Connect

    Trachtenberg, E.A.; Erlich, H.A.; Klitz, W.

    1995-08-01

    DNA-based typing of the HLA class II loci in a sample of the Cayapa Indians of Ecuador reveals several lines of evidence that selection has operated to maintain and to diversify the existing level of polymorphism in the class II region. As has been noticed for other Native American groups, the overall level of polymorphism at the DRB1, DQA1, DQB1, and DPB1 loci is reduced relative to that found in other human populations. Nonetheless, the relative eveness in the distribution of allele frequencies at each of the four loci points to the role of balancing selection in the maintenance of the polymorphism. The DQA1 and DQB1 loci, in particular, have near-maximum departures from the neutrality model, which suggests that balancing selection has been especially strong in these cases. Several novel DQA1-DQB1 haplotypes and the discovery of a new DRB1 allele demonstrate an evolutionary tendency favoring the diversification of class II alleles and haplotypes. The recombination interval between the centromeric DPB1 locus and the other class II loci will, in the absence of other forces such as selection, reduce disequilibrium across this region. However, nearly all common alleles were found to be part of DR-DP haplotypes in strong disequilibrium, consistent with the recent action of selection acting on these haplotypes in the Cayapa. 50 refs., 3 figs., 3 tabs.

  7. Linkage Disequilibrium on the Bovine X Chromosome: Characterization and Use in Quantitative Trait Locus Mapping

    PubMed Central

    Sandor, Cynthia; Farnir, Frédéric; Hansoul, Sarah; Coppieters, Wouter; Meuwissen, Théo; Georges, Michel

    2006-01-01

    We herein demonstrate that in the Holstein–Friesian dairy cattle population, microsatellites are as polymorphic on the X chromosome as on the autosomes but that the level of linkage disequilibrium between these markers is higher on the X chromosome than on the autosomes. The latter observation is not compatible with the small male-to-female ratio that prevails in this population and results in a higher gonosomal than autosomal effective population size. It suggests that the X chromosome undergoes distinct selective or mutational forces. We describe and characterize a novel Markovian approach to exploit this linkage disequilibrium to compute the probability that two chromosomes are identical-by-descent conditional on flanking marker data. We use the ensuing probabilities in a restricted maximum-likelihood approach to search for quantitative trait loci (QTL) affecting 48 traits of importance to the dairy industry and provide evidence for the presence of QTL affecting 5 of these traits on the bovine X chromosome. PMID:16648641

  8. Refining the position of Wilson disease by linkage disequilibrium with polymorphic microsatellites.

    PubMed Central

    Bowcock, A. M.; Tomfohrde, J.; Weissenbach, J.; Bonne-Tamir, B.; St George-Hyslop, P.; Giagheddu, M.; Cavalli-Sforza, L. L.; Farrer, L. A.

    1994-01-01

    Wilson disease (WND) is an autosomal recessive disorder that is due to an inability of the liver to eliminate copper. Copper buildup in the liver, brain, kidney, and other tissues can result in liver cirrhosis, neurologic and psychiatric defects, and other problems. We have localized the disease-containing region to between D13S31 and D13S59, with > 70 multiply affected families, and have constructed a YAC contig of > 4.5 Mb that spans these loci and orders nine highly polymorphic microsatellites. Here we present an analysis of disequilibrium with markers in this interval and provide evidence for strong allelic associations between AFM084xc5 alleles and WND alleles in European, Middle Eastern, and East Asian populations. Significant but weaker allelic associations were also observed between WND alleles and alleles at D13S137 and D13S169. The strength of the association between AFM084xc5 and WND in all non-Sardinian populations combined (linkage-disequilibrium coefficient [phi] = .61) suggests that the number of mutations accounting for WND is less than expected on the basis of the variety of clinical symptoms that are observed. PMID:8279473

  9. Linkage disequilibrium mapping of the cornea plana congenita gene CNA2

    SciTech Connect

    Tahvanainen, E.; Karila, E.; Kolehmainen, J.

    1995-12-10

    We recently assigned a gene for autosomal recessive cornea plana congenita (CNA2; MIM No. 217300) by linkage analysis to the approximately 3-cM interval between markers D12S82 and D12S327. Here, we extended these studies by exploiting the haplotype and linkage disequilibrium information that can be derived from the genetically isolated Finnish population and its subpopulations. By testing 32 independent families with 10 polymorphic markers in the CNA2 interval, strong allelic association between CNA2 and a set of markers with a peak at marker D12S351 was detected. Based on linkage disequilibrium analysis, the critical region for CNA2 could be narrowed to only 0.04-0.3 cM from marker D12S351, thus defining a critical interval 0.08-0.60 cM in length. These results provide a basis for highly focused positional cloning of CNA2. 18 refs., 5 figs., 1 tab.

  10. Linkage disequilibrium in wild and cultured populations of Pacific oyster ( Crassostrea gigas)

    NASA Astrophysics Data System (ADS)

    Guo, Xiang; Li, Qi; Kong, Lingfeng; Yu, Hong

    2016-04-01

    Linkage disequilibrium (LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping. The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population, as well as the experimental design for an association analysis. In this study, we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster ( Crassostrea gigas). A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites, respectively. For syntenic marker pairs, no significant association was observed in the wild population; however, three significant associations occurred in the cultured population, and the significant LD extended up to 12.7 cM, indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population. The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population. Furthermore, the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster. The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.

  11. Linkage disequilibrium on the bovine X chromosome: characterization and use in quantitative trait locus mapping.

    PubMed

    Sandor, Cynthia; Farnir, Frédéric; Hansoul, Sarah; Coppieters, Wouter; Meuwissen, Théo; Georges, Michel

    2006-07-01

    We herein demonstrate that in the Holstein-Friesian dairy cattle population, microsatellites are as polymorphic on the X chromosome as on the autosomes but that the level of linkage disequilibrium between these markers is higher on the X chromosome than on the autosomes. The latter observation is not compatible with the small male-to-female ratio that prevails in this population and results in a higher gonosomal than autosomal effective population size. It suggests that the X chromosome undergoes distinct selective or mutational forces. We describe and characterize a novel Markovian approach to exploit this linkage disequilibrium to compute the probability that two chromosomes are identical-by-descent conditional on flanking marker data. We use the ensuing probabilities in a restricted maximum-likelihood approach to search for quantitative trait loci (QTL) affecting 48 traits of importance to the dairy industry and provide evidence for the presence of QTL affecting 5 of these traits on the bovine X chromosome. PMID:16648641

  12. Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

    NASA Astrophysics Data System (ADS)

    Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

    2008-02-01

    The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

  13. Fine mapping of the congenital chloride diarrhea gene by linkage disequilibrium

    SciTech Connect

    Hoeglund, P.; de la Chapelle, A.; Kere, J.

    1995-07-01

    Congenital chloride diarrhea is a recessively inherited intestinal disorder affecting electrolyte transportation. The clinical presentation is a life-threatening watery diarrhea with a high chloride content. Recently, the congenital chloride diarrhea gene (CLD) was assigned to chromosome 7 by linkage in eight Finnish families. In the present study, refined mapping of CLD was performed by studying linkage and linkage disequilibrium in 24 Finnish and 4 Swedish families. Recombination mapping assigned CLD to an {approximately}10-cM region flanked by D7S515 and D7S799. Linkage disequilibrium was detected over this large genetic region, with the strongest allelic association at D7S496. Application of the Luria and Delbrueck-derived analysis allowed for a further narrowing of the CLD region to {approximately}.37 cM from the marker D7S496. Haplotype analysis placed CLD unequivocally between D7S501 and D7S692, very close to D7S496 and most likely on the distal side of D7S496. This combined analytical approach allowed highly accurate mapping of CLD, each component adding complementary and consistent mapping information. 32 refs., 4 figs., 4 tabs.

  14. Anti-Citrullinated Protein Antibodies Induce Macrophage Subset Disequilibrium in RA Patients.

    PubMed

    Zhu, Wei; Li, Xiu; Fang, Shaohong; Zhang, Xiaoli; Wang, Ying; Zhang, Tongshuai; Li, Zhaoying; Xu, Yanwen; Qu, Siying; Liu, Chuanliang; Gao, Fei; Pan, Haile; Wang, Guangyou; Li, Hulun; Sun, Bo

    2015-12-01

    We used samples from rheumatoid arthritis (RA) patients to examine whether Anti-citrullinated protein antibodies (ACPAs) alter macrophage subset distribution and promote RA development. Macrophage subset distributions and interferon regulatory factor 4 (IRF4) and IRF5 expressions were analyzed. ACPAs were purified by affinity column. After RA and osteoarthritis (OA) patients' macrophages were cocultured with ACPAs, macrophage subsets and IRF4 and IRF5 expressions were measured. Small interfering RNAs (siRNAs) were transfected into ACPA-activated cells to suppress IRF4 or IRF5. Fluorescence-activated cell sorting (FACS), Western blot, and immunohistochemistry were performed. Macrophage subset disequilibrium occurred in RA patient synovial fluids. IRF4 and IRF5 were all expressed in the synovial fluid and synovium. ACPAs (40 IU/ml) could induce macrophages to polarize to M1 subsets, and the percentage of increased M1/M2 ratio of RA patients was higher than that of the OA patients. ACPAs also induce IRF4 and IRF5 protein expressions. IRF5 siRNA transfection impaired ACPA activity significantly. We demonstrated that macrophage subset disequilibrium occurred in RA patients. ACPAs induced IRF5 activity and led to M1 macrophage polarization. PMID:26063186

  15. Determination of scatter factor parameters and electron disequilibrium for monoenergetic photon beams.

    PubMed

    McDonough, J; Bloch, P; Bjärngard, B E

    1999-02-01

    The tissue-phantom-ratio (TPR) is expressed as the product of the phantom scatter factor (SF), an electron disequilibrium factor, and an attenuation factor, equal to the zero-area TPR. The scatter factor, as a function of depth d and field size s, has been described by two parameters a and w, SF(d,s) = 1 + asd/(ws + d). We have determined the parameters a and w for 20 monoenergetic photon beams between 1 and 20 MeV. Pencil-beam energy-deposition kernels were obtained using Monte Carlo simulations. The kernels were used to calculate broad-beam depth-dose data, which were converted to TPR and fitted to the equation above using an iterative search over a-w space. The parameter a is nearly equal to the attenuation coefficient for all energies while the parameter w increases with energy. The resulting a and w compare favorably to values determined for clinical photon beams, as a function of the measured attenuation coefficient. With the scatter factor determined, we isolated the electron disequilibrium factor for each monoenergetic beam. It can be characterized as a quadratic function of the depth. The coefficients of the quadratic function can be related to the range of the most energetic secondary electron produced. PMID:10076974

  16. Isotopic disequilibrium and lower crustal contamination in slowly ascending magmas: Insights from Proterozoic anorthosites

    NASA Astrophysics Data System (ADS)

    Bybee, G. M.; Ashwal, L. D.

    2015-10-01

    Many Proterozoic anorthosite massifs show crustal isotopic signatures that have, for decades, fuelled debate regarding the source of these temporally-restricted magmas. Are these signatures indicative of lower crustal melting or of significant assimilation of crustal material into mantle-derived magmas? Traditional whole rock isotopic tracers (Sr, Nd, Pb and Os), like other geochemical, petrological and experimental tools, have failed to identify unambiguously the origins of the crust-like signature and resolve the source controversies for these feldspathic, cumulate intrusives. We make use of high precision Sr, Nd and Pb isotopic compositions of mineral phases (plag, opx, mag) and comagmatic, high-pressure orthopyroxene megacrysts as well as whole rock anorthosites/leuconorites from the Mealy Mountains Intrusive Suite (MMIS) and the Nain Plutonic Suite (NPS) to probe the origin of the crustal isotopic signatures and assess the importance of differentiation at lower crustal depths. This selection of samples represents fragments from various stages of the polybaric ascent of the magmas, while the study of the Mealy Mountains Intrusive Suite and the Nain Plutonic Suite is instructive as each is intruded into crust of significantly different age and isotopic composition. We observe marked differences in the whole-rock isotopic composition of Proterozoic anorthosites and high-pressure megacrysts (e.g. εNd;T = +2 to -10) intruded into crustal terranes of different ages and isotopic compositions. Evidence for varying degrees of internal isotopic disequilibrium (ΔNd, ΔSr, ΔPb) in anorthosites from these different terranes reinforces the notion that crustal contamination, and more importantly, the nature of the crustal assimilant, has a profound influence on the chemical signature of Proterozoic anorthosites. While most samples from the MMIS and NPS show significant and measurable ΔNd and ΔPb disequilibrium, ΔSr compositions cluster around zero. This decoupling in

  17. A Disequilibrium Melting Spectrum: Partially Melted Crustal Xenoliths from the Wudalianchi Volcanic Field, NE China.

    NASA Astrophysics Data System (ADS)

    McLeod, C. L.; McGee, L. E.

    2015-12-01

    Disequilibrium melting has been established as a common process occurring during crustal anatexis and thus demonstrates that crustal assimilation by ascending mantle-derived magmas is likley not a closed system. Observations of extreme compositional heterogeneity within partial melts derived from crustal xenoliths have been documented in several recent examples, however, the retention or transfer of elements to and from residues and glasses, and their relative contributions to potential crustal contaminants warrants further investigation. Sampled lavas from the Huoshaoshan volcano in the Holocene Wudalianchi volcanic field of Northeast China contain crustal xenoliths which preserve a spectrum of partial melting both petrographically and geochemically, thus providing an excellent, natural example of crustal anatexis. Correlations exist between the volume of silicic glass preserved within the xenoliths and bulk rock SiO2 (70-83 wt%), Al2O3 (16-8 wt%), glass 87Sr/86Sr (0.715-0.908), abundances of elements common in feldspars and micas (Sr, Ba, Rb) and elements common in accessory minerals (Y, Zr, Nb). These correlations are likely associated with the consumption of feldspars and micas and the varying retention of accessory phases during partial melting. The xenoliths which contain the greater volumes of silicic glass and residual quartz (interpreted as being the most melted) were found within pahoehoe lava, whilst the least melted xenoliths were found within scoria of the summit cone of Huoshaoshan; thus it is interpreted that the extent of melting is linked to the immersion time in the lava. Small-scale (mm) mingling and transfer of material from the enclosing lava to the xenolith is observed, however, modelling of potential contaminant compositions is inconsistent with crustal contamination during lava petrogenesis. It is inferred that crustal contamination in sampled lavas is localized within the open magmatic system and most likely occurs at the contact zone

  18. Plagioclase-melt (dis)equilibrium due to cooling dynamics: Implications for thermometry, barometry and hygrometry

    NASA Astrophysics Data System (ADS)

    Mollo, Silvio; Putirka, Keith; Iezzi, Gianluca; Del Gaudio, Pierdomenico; Scarlato, Piergiorgio

    2011-07-01

    The compositional variation of plagioclase and the partitioning of major elements between plagioclase and melt have been experimentally measured as a function of the cooling rate. Crystals were grown from a basaltic melt at a pressure of 500 MPa under (i) variable cooling rates of 0.5, 2.1, 3, 9.4, and 15 °C/min from 1250 °C down to 1000 °C, (ii) quenching temperatures of 1025, 1050, 1075, 1090, and 1100 °C at the fixed cooling rate of 0.5 °C/min, and (iii) isothermal temperatures of 1000, 1025, 1050, 1075, 1090, and 1100 °C. Our results show that euhedral, faceted plagioclases form during isothermal and slower cooling experiments exhibiting idiomorphic tabular shapes. In contrast, dendritic shapes are observed from faster cooled charges. As the cooling rate is increased, concentrations of Al + Ca + Fe + Mg increase and Si + Na + K decrease in plagioclase favoring higher An and lower Ab + Or contents. Significant variations of pl-liqKd are also observed by the comparison between isothermal and cooled charges; notably, pl-liqKdAb-An, pl-liqKdCa-Na and pl-liqKdFe-Mg progressively change with increasing cooling rate. Therefore, crystal-melt exchange reactions have the potential to reveal the departure from equilibrium for plagioclase-bearing cooling magmas. Finally, thermometers, barometers, and hygrometers derived through the plagioclase-liquid equilibria have been tested at these non-equilibrium experimental conditions. Since such models are based on assumption of equilibrium, any form of disequilibrium will yield errors. Results show that errors on estimates of temperature, pressure, and melt-water content increase systematically with increasing cooling rate (i.e. disequilibrium condition) depicting monotonic trends towards drastic overestimates. These trends are perfectly correlated with those of pl-liqKdCa-Na, pl-liqKdAb-An, and pl-liqKdFe-Mg, thus demonstrating their ability to test (dis)equilibrium conditions.

  19. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

    PubMed Central

    Garris, Amanda J; McCouch, Susan R; Kresovich, Stephen

    2003-01-01

    To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice. PMID:14573486

  20. Natural uranium and thorium isotopes in sediment cores off Malaysian ports

    NASA Astrophysics Data System (ADS)

    Yusoff, Abdul Hafidz; Sabuti, Asnor Azrin; Mohamed, Che Abd Rahim

    2015-06-01

    Sediment cores collected from three Malaysian marine ports, namely, Kota Kinabalu, Labuan and Klang were analyzed to determine the radioactivities of 234U, 238U, 230Th, 232Th and total organic carbon (TOC) content. The objectives of this study were to determine the factors that control the activity of uranium isotopes and identify the possible origin of uranium and thorium in these areas. The activities of 234U and 238U show high positive correlation with TOC at the middle of sediment core from Kota Kinabalu port. This result suggests that activity of uranium at Kota Kinabalu port was influenced by organic carbon. The 234U/238U value at the upper layer of Kota Kinabalu port was ≥1.14 while the ratio value at Labuan and Klang port was ≤ 1.14. These results suggest a reduction process occurred at Kota Kinabalu port where mobile U(VI) was converted to immobile U(IV) by organic carbon. Therefore, it can be concluded that the major input of uranium at Kota Kinabalu port is by sorptive uptake of authigenic uranium from the water column whereas the major inputs of uranium to Labuan and Klang port are of detrital origin. The ratio of 230Th/232Th was used to estimate the origin of thorium. Low ratio value (lt; 1.5) at Labuan and Klang ports support the suggestion that thorium from both areas were come from detrital input while the high ratio (> 1.5) of 230Th/232Th at Kota Kinabalu port suggest the anthropogenic input of 230Th to this area. The source of 230Th is probably from phosphate fertilizers used in the oil-palm cultivation in Kota Kinabalu that is adjacent to the Kota Kinabalu port.

  1. Small-scale disequilibrium in a magmatic inclusion and its more silicic host

    NASA Technical Reports Server (NTRS)

    Davidson, Jon P.; Holden, Peter; Halliday, Alex N.; De Silva, Shanaka L.

    1990-01-01

    An investigation of small-scale isotopic, compositional, and mineralogical variation across the interface of a basaltic-andesite inclusion and its dacitic host from Cerro-Chascon, a Holocene dome in northern Chile, is discussed. Serial sectioning across the interface of the inclusion and its host dacite, complemented by microdrill sampling and detailed microprobe work, has enabled an examination of the scale of mixing and chemical disequilibrium. The composition of the inclusion is found to be relatively homogeneous; the dacite host is heterogeneous on a small scale; the isotopic composition in the marginal zone shows the highest Sr-87/Sr-86 and lowest Nd-143/Nd-144; the large plagioclase crystals in the inclusions and host are xenocrystic. These differences are reconciled with a model of magma evolution in a crustal magma chamber.

  2. Genomewide linkage disequilibrium mapping of severe bipolar disorder in a population isolate.

    PubMed

    Ophoff, Roel A; Escamilla, Michael A; Service, Susan K; Spesny, Mitzi; Meshi, Dar B; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C; Dong, Penny; Leon, Pedro E; Reus, Victor I; Sandkuijl, Lodewijk A; Freimer, Nelson B

    2002-09-01

    Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

  3. Soiled-based uranium disequilibrium and mixed uranium-thorium series radionuclide reference materials

    SciTech Connect

    Donivan, S.; Chessmore, R.

    1988-12-01

    The US Department of Energy (DOE) Office of Remedial Action and Waste Technology has assigned the Technical Measurements Center (TMC), located at the DOE Grand Junction Colorado, Projects Office and operated by UNC Geotech (UNC), the task of supporting ongoing remedial action programs by providing both technical guidance and assistance in making the various measurements required in all phases of remedial action work. Pursuant to this task, the Technical Measurements Center prepared two sets of radionuclide reference materials for use by remedial action contractors and cognizant federal and state agencies. A total of six reference materials, two sets comprising three reference materials each, were prepared with varying concentrations of radionuclides using mill tailings materials, ores, and a river-bottom soil diluent. One set (disequilibrium set) contains varying amounts of uranium with nominal amounts of radium-226. The other set (mixed-nuclide set) contains varying amounts of uranium-238 and thorium-232 decay series nuclides. 14 refs., 10 tabs.

  4. AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.

    PubMed

    Hiekkalinna, Tero; Terwilliger, Joseph D; Sammalisto, Sampo; Peltonen, Leena; Perola, Markus

    2005-02-01

    Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense. PMID:15836805

  5. Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

    SciTech Connect

    Escamilla, M.A.; Reus, V.I.; Smith, L.B.; Freimer, N.B.

    1996-05-31

    Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP). As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, should be suitable for LD mapping; this assertion is supported by reconstruction of extended haplotypes shared by distantly related individuals in this population suffering low-frequency hearing loss (LFHL1), which has previously been mapped by linkage analysis. A sampling strategy is described for applying LD methods to map genes for BP, and clinical and demographic characteristics of an initially collected sample are discussed. This sample will provide a complement to a previously collected set of Costa Rican BP families which is under investigation using standard linkage analysis. 42 refs., 4 figs., 2 tabs.

  6. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica)

    PubMed Central

    He, Shui-lian; Yang, Yang; Morrell, Peter L.; Yi, Ting-shuang

    2015-01-01

    Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less. PMID:26325578

  7. Disequilibrium in the 238uranium series in samples from yeelirrie, Western Australia

    USGS Publications Warehouse

    Lively, R.S.; Harmon, R.S.; Levinson, A.A.; Bland, C.J.

    1979-01-01

    Uranium-series disequilibrium studies carried out on samples from the Yeelirrie uranium deposit, Western Australia, indicate that uranium and radium have been migrating within the deposit during recent times, and are actually being removed from the deposit. Samples collected for 230Th/234U age dating were found to be substantially out of equilibrium, with 230Th/234U activity ratios ranging from 0.750 to 1.345. This can be explained by a dynamic hydrologic system in which there has been, and continues to be, uranium migration caused by leaching in this arid, oxidizing environment, and a fluctuating water table. Recent, extensive 226Ra migration (226Ra/230Th activity ratios range from 0.53 to 1.30), and a very low emanation factor (E) of 222Rn limit the quantitative application of radon exploration techniques in this environment. ?? 1979.

  8. DECAY-SERIES DISEQUILIBRIUM STUDY OF IN-SITU, LONG-TERM RADIONUCLIDE TRANSPORT IN WATER-ROCK SYSTEMS

    EPA Science Inventory

    Uranium and thorium-series disequilibrium in nature permits the determination of many in-situphysico-chemical, geologic and hydrologic variables that control the long-term migration ofradionuclides in geologic systems. It also provides site-specific, natural analog information...

  9. A First Insight into Population Structure and Linkage Disequilibrium in the US Peanut Mini-core Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the U.S. peanut mini-core colle...

  10. Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The level of population structure and the extent of linkage disequilibrium (LD) can have large impacts on the power, resolution, and design of genome-wide association studies (GWAS) in plants. Until recently, the topics of LD and population structure have not been explored in oat due to the lack of...

  11. Novel microsatellite repeats (MSRs) and linkage disequilibrium analysis in the SMA region of 5q13.1

    SciTech Connect

    Yaraghi, Z.; Roy, N.; MacKenzie, A.E.

    1994-09-01

    The spinal muscular atrophies (SMA) are characterized by degeneration of the anterior horn cells of the spinal cord, leading to muscular atrophy associated with progressive paralysis. The gene involved in SMA has been mapped by linkage analysis to a region of 5q13.1 flanked centromerically by D5S435 and telomerically by D5S557. We are in the process of identifying new microsatellite repeats to further define the genetic map of the SMA region. A contiguous array of YAC clones covering the SMA containing D5S435-D56S112 interval of 5q13.1 was established. From this contig, a 700 kb clone 76C1, which contains the 200 kb CMS-1/CATT-1 critical region, was used to generate a partial Sau3A1 phage library. We have previously shown that 2 CATT-1 subloci are in linkage disequilibrium with type I SMA. The 76C1 subloci are in linkage disequilibrium with type I SMA. The 76C1 phage library has been screened for human MSRs. To date we have identified two novel polymorphic microsatellites and four further candidates are being characterized. Results of linkage disequilibrium studies currently underway will be presented. The identification of a linkage disequilibrium maximum will be helpful in the further narrowing of the SMA region.

  12. Extensive genetic diversity and low linkage disequilibrium within the COMT locus in Germplasm Enhancement of Maize populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at COMT locus between populations sampled within the Germplasm Enhance...

  13. Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To facilitate the mapping of genes in sorghum [Sorghum bicolor (L.) Moench] underlying economically important traits, we analyzed the genetic structure and linkage disequilibrium in a sorghum mini core collection of 242 landraces with 14,739 SNPs. The SNPs were produced using a highly multiplexed g...

  14. Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-gro...

  15. The Effect of Educational Disequilibrium in Field Work on Graduate Social Work Students' Self-Concept and Mental Health

    ERIC Educational Resources Information Center

    Ying, Yu-Wen

    2011-01-01

    The author used a mixed methods design to assess field work-related educational disequilibrium and its effect on the self-concept and mental health of MSW students. Twenty-eight advanced, fourth-semester MSW students were compared with 37 entering, first-semester MSW students in practice-related sense of accomplishment. Compared with first-year…

  16. Assessing Natural Radionuclide Migration in the Legacy Tailings of Uranium Production

    NASA Astrophysics Data System (ADS)

    Bondarenko, G.; Koliabina, I.; Marinich, O.

    2011-12-01

    The former Prydniprovsky Chemical Plant in Dniprodzerzhynsk, Ukraine, processed uranium ore from 1949 until 1991. Multiple tailing ponds containing solid residual waste products from the uranium leaching and processing of uranium were accumulated along the Dnieper River, including the largest, adjacent to the Dnieper Reservoir, containing over 12 million tons of tailings. Samples for this study were selected from a core recovered from the Dnieper tailing pit in 2009, and used to assess radionuclide migration from tailing ponds. Samples were selected from different depths of the tailing pit core, analyzed for total radionuclide concentrations [Marinich et al., 2009], and successively leached using distilled water, followed by 1N ammonium acetate solution, and finally by 1N HCl solution. Leaching times were ~24 h at 15.17 °C. 238U, 230Th and 226Ra leachate activities were measured by γ-spectrometry with a Ge(Li) detector. 210Pb activity was measured using a SEB-01 scintillation β-spectrometer. Errors depended on measuring method, radionuclide, activity and exposure time: 238U, 11.9%; 230Th, 10.9%; 226Ra, 9.3%; 210Pb ~30%. The average total 238U activity in the tailing profile was 4 Bq/g. The concentration of 238U in the water leachates increased with depth from 14.5% (7-7.5 m), to 43% (11-11.5 m). The concentration of 238U in the acid leachates behaved similarly, increasing from 5.5 % to 15.5% with depth. While the total 230Th activity in increased from 30 Bq/g (7-7.5 m) to 540 Bq/g (11-11.5 m), the 230Th concentration in ammonium acetate leachates decreased from ˜15% to ˜1%. The concentration of 226Ra in all leachates was <1%, indicating that, under conditions of the Dnieper tailing pit, 226Ra is essentially immobile. The concentration of 210Pb in the leachates was as high as 10%. In general, the magnitude of mobile activity from the Dnieper tailing pit core samples decreases in the order 238U>230Th≥210Pb> 226Ra. Secular radioactive equilibrium in the 238U

  17. U-series disequilibrium constraints on magma generation at the Jan Mayen hotspot

    NASA Astrophysics Data System (ADS)

    Rivers, E. R.; Chernow, R.; Elkins, L. J.; Sims, K. W.; Blichert-Toft, J.; Devey, C. W.

    2013-12-01

    The incompatible element-enriched magma source beneath the Jan Mayen Island hotspot influences melt generation on the adjacent northern Mid-Atlantic Ridge system and likely derives from either a small, local mantle plume, ancient Icelandic plume material emplaced in the mantle source, and/or sub-continental lithospheric mantle remnants emplaced locally by rifting of Greenland. The slow spreading Northern Kolbeinsey and Southern Mohns Ridges are immediately adjacent to Jan Mayen Island. Both have relatively shallow ridge axes, particularly the extremely shallow Eggvin Bank region of the Northern Kolbeinsey Ridge, which host anomalously large central volcanic edifices. We are currently collecting U-series disequilibrium and long-lived radiogenic isotope data for fresh, glassy mid-ocean ridge basalts from the Northern Kolbeinsey and Southern Mohns Ridge segments to better constrain source composition, depth of melting in the garnet peridotite stability field, solid mantle upwelling rates, and the nature of melt extraction beneath those segments. In particular, we are measuring isotopic data for geographically well-located samples collected from hummocky pillow basalt flows within the axial valley of the Northern Kolbeinsey Ridge segment as well as from the large volcanoes on both ridge segments, to further determine the role of the Jan Mayen hotspot in crustal construction on the Mid-Atlantic Ridge. Recently collected data show particularly high strontium isotope ratios consistent with trace element patterns that suggest a distinct local plume located beneath the Jan Mayen hotspot. A plume model for Jan Mayen is supported by new bathymetric imaging of adjacent ridge segments that reveals excess volcanism beneath the large axial volcanoes and a radial distribution of enrichment surrounding Jan Mayen Island. We predict that age-constrained U-series disequilibrium measurements will support active mantle upwelling focused beneath both Jan Mayen Island and the large axial

  18. An assessment of linkage disequilibrium in Holstein cattle using a Bayesian network.

    PubMed

    Morota, G; Valente, B D; Rosa, G J M; Weigel, K A; Gianola, D

    2012-12-01

    Linkage disequilibrium (LD) is defined as a non-random association of the distributions of alleles at different loci within a population. This association between loci is valuable in prediction of quantitative traits in animals and plants and in genome-wide association studies. A question that arises is whether standard metrics such as D' and r(2) reflect complex associations in a genetic system properly. It seems reasonable to take the view that loci associate and interact together as a system or network, as opposed to in a simple pairwise manner. We used a Bayesian network (BN) as a representation of choice for an LD network. A BN is a graphical depiction of a probability distribution and can represent sets of conditional independencies. Moreover, it provides a visual display of the joint distribution of the set of random variables in question. The usefulness of BN for linkage disequilibrium was explored and illustrated using genetic marker loci found to have the strongest effects on milk protein in Holstein cattle based on three strategies for ranking marker effect estimates: posterior means, standardized posterior means and additive genetic variance. Two different algorithms, Tabu search (a local score-based algorithm) and incremental association Markov blanket (a constraint-based algorithm), coupled with the chi-square test, were used for learning the structure of the BN and were compared with the reference r(2) metric represented as an LD heat map. The BN captured several genetic markers associated as clusters, implying that markers are inter-related in a complicated manner. Further, the BN detected conditionally dependent markers. The results confirm that LD relationships are of a multivariate nature and that r(2) gives an incomplete description and understanding of LD. Use of an LD Bayesian network enables inferring associations between loci in a systems framework and provides a more accurate picture of LD than that resulting from the use of pairwise

  19. The decay of linkage disequilibrium under random union of gametes: how to calculate Bennett's principal components.

    PubMed

    Dawson, K J

    2000-08-01

    How rapidly does an arbitrary pattern of statistical association among a set of loci decay under meiosis and random union of gametes? This problem is non-trivial, even in the case of an infinitely large population where selection and other forces are absent. J. H. Bennett (1954, Ann. Hum. Genet. 18, 311-317) found that, for an arbitrary number of loci with an arbitrary linkage map, it is possible to define measures of linkage disequilibrium that decay geometrically with time. He found a recursive method for deriving expressions for these variables in terms of "allelic moments" (the factorial moments about the origin of the "allelic indicators"), and expressions for the allelic moments in terms of his new variables. However, Bennett no where stated his recursive algorithm explicitly, nor did he give a general formula for his measures of linkage disequilibrium, for an arbitrary number of loci. Recursive definitions of Bennett's variables were obtained by Lyubich. However, the expressions generated by these recursions are not the same as those found by Bennett. (They do not express Bennett's variables as functions of the allelic moments.) Lyubich's derivations employ genetic algebras. Here, I present a method for obtaining explicit expressions for Bennett's variables in terms of the allelic moments. I show that the transformation from the allelic moments to Bennett's variables and the inverse transformation always have the form that Bennett claimed. (This transformation and its inverse have essentially the same form.) I present general recursions for calculating the coefficients in the forward transformation and the coefficients in the inverse transformation. My derivations involve combinatorial arguments and ordinary algebra only. The special case of unlinked loci is briefly discussed. PMID:10944472

  20. Investigating disequilibrium effects in magma ascent dynamics with a new multiphase flow model

    NASA Astrophysics Data System (ADS)

    de'Michieli Vitturi, Mattia; Clarke, Amanda B.; Neri, Augusto; Voight, Barry; La Spina, Giuseppe

    2013-04-01

    Numerical and physical models have greatly enhanced our understanding of eruption dynamics. The multiphase non-equilibrium nature of magma inside a conduit, the development of gas overpressure, and the possibilities for open-system degassing are all recognized as controlling factors affecting changes in eruptive rate and style, yet models of magma ascent considering both distinct velocities and pressures for the different phases have not been deeply studied. The numerical model we present here considers a set of multiphase compressible equations governing magma movement through a subsurface pathway (e.g., from chamber to surface). This model represents a significant advance in its quantitative description of the magma system in that it: 1) is capable of treating both dilute and dense flow regimes; 2) describes flow above and below the fragmentation level in a coupled and consistent way; 3) quantifies the interaction between two phases forming the magmatic mixture with two distinct pressures and two velocities; 4) accounts for disequilibrium crystallization and degassing; and 5) allows for open-system degassing. Here we investigate, through a sensitivity analysis, the role of different disequilibrium processes, in particular those controlling overpressure increase and the retention of gas, in controlling vent conditions and transitions in eruptive style. We develop a reference case using conditions appropriate for the ongoing eruption of Soufrière Hills volcano. As an example, if an andesitic magma with a 5 wt% total water content (about 1.5 vol% of exsolved gas) decompresses to atmospheric pressure from 5km depth as a homogeneous mixture (single pressure and single velocity), the gas volume fraction at the vent should exceed 95 vol% if no further gas exsolution is considered, and 99 vol% with equilibrium exsolution. These values changes significantly when development of gas overpressure and open-system degassing are allowed and considered in the model, and thus

  1. The changing distribution of a major surgical procedure across hospitals: were supply shifts and disequilibrium important?

    PubMed

    Friedman, B; Elixhauser, A

    1995-01-01

    This paper describes and analyzes the changing distribution across hospitals in the U.S. of total hip replacement surgery (THR) for the period 1980-1987. THR is one of the most costly single procedures contributing to health care expenses. Also, the use of THR exhibits a particularly high degree of geographic variation. Recent research pointed to shifts in demand as one plausible economic explanation for increasing use of THR. This paper questions whether shifts in supply may have been large enough to explain changes in patient mix and the relationship of patient mix to the number of procedures performed at a particular hospital. In addition, the relationship between total use of THR and the local availability of orthopaedic surgeons as well as the average allowable Medicare fee for standardized physician services is analyzed. These relationships might yield evidence to support a scenario of induced demand beyond the optimum for patients' welfare, or evidence of supply increase within a disequilibrium scenario. This study, using data for all THR patients in a large sample of hospitals, tends to reject the formulation of a market with independent supply and demand shifts where the supply shifts were the dominant forces. Hospitals with a larger number of THRs performed did not see a higher percentage of older, sicker, and lower income patients. It was more likely that demand shifts generated increases in capacity for surgical services. Moreover, there was little evidence for a persistent disequilibrium and only weak evidence for inducement. Also, we found little evidence that hospitals responded to financial incentives inherent in the Medicare payment system after 1983 to select among THR candidates in favour of those with below average expected cost. We did observe increased concentration over time of THR procedures in facilities with high volume--suggesting plausible demand shifts towards hospitals with a priori quality and cost advantages or who obtained those

  2. Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.

    PubMed Central

    Andolfatto, Peter; Wall, Jeffrey D

    2003-01-01

    Previous multilocus surveys of nucleotide polymorphism have documented a genome-wide excess of intralocus linkage disequilibrium (LD) in Drosophila melanogaster and D. simulans relative to expectations based on estimated mutation and recombination rates and observed levels of diversity. These studies examined patterns of variation from predominantly non-African populations that are thought to have recently expanded their ranges from central Africa. Here, we analyze polymorphism data from a Zimbabwean population of D. melanogaster, which is likely to be closer to the standard population model assumptions of a large population with constant size. Unlike previous studies, we find that levels of LD are roughly compatible with expectations based on estimated rates of crossing over. Further, a detailed examination of genes in different recombination environments suggests that markers near the telomere of the X chromosome show considerably less linkage disequilibrium than predicted by rates of crossing over, suggesting appreciable levels of exchange due to gene conversion. Assuming that these populations are near mutation-drift equilibrium, our results are most consistent with a model that posits heterogeneity in levels of exchange due to gene conversion across the X chromosome, with gene conversion being a minor determinant of LD levels in regions of high crossing over. Alternatively, if levels of exchange due to gene conversion are not negligible in regions of high crossing over, our results suggest a marked departure from mutation-drift equilibrium (i.e., toward an excess of LD) in this Zimbabwean population. Our results also have implications for the dynamics of weakly selected mutations in regions of reduced crossing over. PMID:14668383

  3. Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM)

    SciTech Connect

    Spielman, R.S.; McGinnis, R.E. ); Ewens, W.J. )

    1993-03-01

    A population association has consistently been observed between insulin-dependent diabetes mellitus (IDDM) and the class 1 alleles of the region of tandem-repeat DNA (5[prime] flanking polymorphism [5[prime]FP])adjacent to the insulin gene on chromosome 11p. This finding suggests that the insulin gene region contains a gene or genes contributing to IDDM susceptibility. However, several studies that have sought to show linkage with IDDM by testing for cosegregation in affected sib pairs have failed to find evidence for linkage. As means for identifying genes for complex diseases, both the association and the affected-sib-pairs approaches have limitations. It is well known that population association between a disease and a genetic marker can arise as an artifact of population structure, even in the absence of linkage. On the other hand, linkage studies with modest numbers of affected sib pairs may fail to detect linkage, especially if there is linkage heterogeneity. The authors consider an alternative method to test for linkage with a genetic marker when population association has been found. Using data from families with at least one affected child, they evaluate the transmission of the associated marker allele from a heterozygous parent to an affected offspring. This approach has been used by several investigators, but the statistical properties of the method as a test for linkage have not been investigated. In the present paper they describe the statistical basis for this transmission test for linkage disequilibrium (transmission/disequilibrium test [TDT]). They then show the relationship of this test to tests of cosegregation that are based on the proportion of haplotypes or genes identical by descent in affected sibs. The TDT provides strong evidence for linkage between the 5[prime]FP and susceptibility to IDDM. 27 refs., 6 tabs.

  4. Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm

    PubMed Central

    2011-01-01

    Background Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm. Results A total of 264 and 238 inbred lines from the yield type and sugar type inbreds of the pollen parent heterotic gene pools, respectively, which had been genotyped with 328 SNP markers, were used in this study. Two distinct subgroups were detected based on different statistical methods within the elite sugar beet germplasm set, which was in accordance with its breeding history. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis. Gene diversity and modified Roger's distance between the examined germplasm types varied considerably across the genome, which might be due to artificial selection. This observation indicates that population genetic approaches could be used to identify candidate genes for the traits under selection. Due to the fact that r2 >0.8 is required to detect marker-phenotype association explaining less than 1% of the phenotypic variance, our observation of a low proportion of SNP loci pairs showing such levels of LD suggests that the number of markers has to be dramatically increased for powerful genome-wide association mapping. Conclusions We provided a genome-wide distribution map of genetic diversity and linkage disequilibrium for the elite sugar beet germplasm, which is useful for the application of genome-wide association

  5. RADIO-ACTIVE TRANSDUCER

    DOEpatents

    Wanetick, S.

    1962-03-01

    ABS>ure the change in velocity of a moving object. The transducer includes a radioactive source having a collimated beam of radioactive particles, a shield which can block the passage of the radioactive beam, and a scintillation detector to measure the number of radioactive particles in the beam which are not blocked by the shield. The shield is operatively placed across the radioactive beam so that any motion normal to the beam will cause the shield to move in the opposite direction thereby allowing more radioactive particles to reach the detector. The number of particles detected indicates the acceleration. (AEC)

  6. Abscess scan - radioactive

    MedlinePlus

    Radioactive abscess scan; Abscess scan; Indium Scan; Indium-labelled white blood cell scan ... the white blood cells are tagged with a radioactive substance called indium. The cells are then injected ...

  7. Radioactive iodine uptake

    MedlinePlus

    ... the testing center so that the amount of radioactivity in the thyroid gland can be measured. This ... The amount of radioactivity is very small, and there have been no documented side effects. The amount of iodine used is less than ...

  8. Radioactive diagnostic agent

    SciTech Connect

    Shigematsu, A.; Aihara, M.; Matsuda, M.; Suzuki, A.; Tsuya, A.

    1984-02-07

    A radioactive diagnostic agent for renal cortex, adrenal cortex, myocardium, brain stem, spinal nerve, etc., which comprises as an essential component monoiodoacetic acid wherein the iodine atom is radioactive.

  9. Temperature and precipitation records from stalagmites grown under disequilibrium conditions: A model approach.

    NASA Astrophysics Data System (ADS)

    Mühlinghaus, C.; Scholz, D.; Mangini, A.

    2009-04-01

    To reconstruct past variations in Earth's climate, a variety of climate archives are studied. During the last decades stalagmites came into focus due to their long, continuous growth and absolute dating techniques. In this study a numerical model was developed, which calculates variations in temperature and precipitation during the growth period of stalagmites grown under isotopic disequilibrium conditions using the isotope profiles both along the growth axis and individual growth layers as well as the growth depth relation. The model is based on the inversion and combination of existing models (Dreybrodt 1999, Kaufmann et al. 2004, Mühlinghaus et al. 2007, Scholz et al. 2008, Mühlinghaus et al. 2008b) and incorporates important parameters describing the cave and the overlying soil. Beside the dependence on temperature and water supply it depends on the isotopic composition of the drip water, the pCO2 pressure of the soil and the cave atmosphere as well as on the mixing coefficient, which describes mixing between the impinging drop and the existing solution layer. To determine the characteristics of temperature and precipitation, in a first step all other parameters are assumed to remain constant over the whole growth period to simplify calculations. This allows to run the model with only two input variables: the isotopic composition ^13C of the drip water and a temperature information at any point of time during the growth period of the stalagmite (e.g. the recent cave temperature). All other parameters are determined by the model. The CSM (Combined Stalagmite Model, Mühlinghaus et al. 2008a) was applied to three stalagmites from the Marcelo Arévalo cave in Southern Patagonia, Chile (Schimpf 2005, Kilian et al. 2006, Schimpf et al. in prep). These stalagmites grew in a small cave next to each other during the last 4500 years. However, their isotopic profiles along the growth axis show different kinetic influences. Despite these conditions, the temperature

  10. Delayed, disequilibrium degassing in rhyolite magma: Decompression experiments and implications for explosive volcanism

    USGS Publications Warehouse

    Mangan, M.; Sisson, T.

    2000-01-01

    Recent numerical models and analog shock tube experiments show that disequilibrium degassing during magma ascent may lead to violent vesiculation very near the surface. In this study a series of decompression experiments using crystal-free, rhyolite melt were conducted to examine the development of large supersaturations due to delayed, homogenous (spontaneous) bubble nucleation. Melts were saturated at 900??C and 200 MPa with either 5.2 wt% dissolved H2O, or with 4.2 wt% H2O and 640 ppm CO2, and isothermally decompressed at linear rates of either 0.003, 0.025, or 8.5 MPa/s to final pressures between 25 and 175 MPa. Additional isobaric saturation experiments (900??C, 200-25 MPa) using pure H2O or mixed H2O-CO2 fluids establish reference equilibrium solubility curves/values. Homogenous nucleation is triggered in both H2O-only and H2O-CO2 experiments once the supersaturation pressure (??Pss) reaches ?? 120-150 MPa and the melt contains ?? two times its equilibrium water contents. Bubble number density and nucleation rate depend on the supersaturation pressure, with values on the order of 102/cm3 and < 1/cm3/s for ??Pss~120 MPa; 106/cm3 and 103-105/cm3/s for ??Pss??~130-150 MPa; and 107/cm3 and 106/cm3/s for ??Pss??160-175 MPa. Nucleation rates are consistent with classical nucleation theory, and infer an activation energy for nucleation of 1.5 x 10-18 J/nucleus, a critical bubble radius of 2 x 10-9 m, and an effective surface tension for rhyolite at 5.2 wt% H2O and 900??C of 0.10-0.11 N/m. The long nucleation delay limits the time available for subsequent diffusion such that disequilibrium dissolved H2O and CO2 contents persist to the end of our runs. The disequilibrium degassing paths inferred from our experiments contrast markedly with the equilibrium or quasi-equilibrium paths found in other studies where bubble nucleation occurs heterogenously on crystals or other discontinuities in the melt at low ??Pss. Homogenous and heterogenous nucleation rates are

  11. Isotopic Disequilibrium and High-Crystallinity Magma Ascent: Clues to the Temporal Restriction of Proterozoic Anorthosites

    NASA Astrophysics Data System (ADS)

    Bybee, G. M.

    2014-12-01

    Many Proterozoic anorthosite massifs show crustal isotopic signatures that have fuelled debate regarding the source (mantle vs. lower crust) of these temporally restricted magmas. The models advocating a mantle derivation for these rocks suggest that lower crustal assimilation plays an important role in developing the isotopic signature of the massifs, but no evidence exists to support this. We make use of Sr, Nd and Pb isotopic compositions of anorthosites from the Mealy Mountains Intrusive Suite (MMIS), the Nain Plutonic Suite (NPS) and the Rogaland Anorthosite Province (RAP), their internal mineral phases and comagmatic, high-pressure pyroxene megacrysts, which represent samples from various stages of the polybaric ascent of the magmas, to probe the origin of the crustal isotopic signatures and assess the importance of differentiation at lower crustal depths. Study of the MMIS and NPS is instructive as each is intruded into crust of significantly different age and isotopic composition. We observe varying degrees of internal isotopic disequilibrium, enforcing the notion that the nature of the crustal assimilant has a profound influence on the chemical signature of the magmas (Fig. 1). We also find unexpected patterns of internal isotopic disequilibrium, such as isotopically depleted orthopyroxene relative to plagioclase (Fig. 1), which suggests that anorthosite petrogenesis is not a "simple" case of progressive crustal contamination during polybaric magma ascent, but is more likely to involve significant differentiation and solidification at lower crust depths. The 100 m.y. magmatic timescales observed in these anorthosite systems may be caused by significant magmatic differentiation at Moho/lower crustal levels, as well as formation in long-lived arc environments. These long-lived magmatic timescales contrast with recent observations suggesting that the duration of magma ascent from the Moho to surface in arc environments is on the order of months to years. Such

  12. Precise geochronology of phoscorites and carbonatites: - The critical role of U-series disequilibrium in age interpretations

    NASA Astrophysics Data System (ADS)

    Amelin, Yuri; Zaitsev, Anatoly N.

    2002-07-01

    We present the results of a comparative study of several geochronometer minerals (baddeleyite, zircon, apatite, phlogopite and tetraferriphlogopite) and isotopic systems (U-Pb, Th-Pb and Rb-Sr) from phoscorites (magnetite-forsterite-apatite-calcite rocks) and carbonatites of the Kovdor ultramafic-alkaline-carbonatite massif, Kola Peninsula, Russia. Uranium, thorium and their decay products are extremely fractionated by minerals that crystallise from carbonatite and phoscorite magma. We obtain high-precision ages from different chronometers, compare their accuracy, and evaluate the role of geochronological pitfalls of initial radioactive disequilibrium, differential migration of radiogenic isotopes, and inaccurate decay constants. Apatite yielded concordant U-Th-Pb ages between 376 and 380 Ma. The accuracy of the apatite 238U- 206Pb ages is, however, compromised by uncertainty in the amount of radiogenic 206Pb produced from initial excess 230Th. The 235U- 207Pb ages are relatively imprecise due to large common Pb correction and the uncertainty in the initial Pb isotopic composition. The Th-Pb system yields a more precise age of 376.4 ± 0.6 Ma. Zircon from two carbonatite samples is characterised by moderate to low U contents, high Th contents, and very high Th/U ratios up to 9000. The 206Pb*/ 238U systems in the zircon are strongly affected by the presence of excess 206Pb*, produced by decay of initial 230Th. The 208Pb*/ 232Th ages of zircon from both carbonatite samples are uniform and yield a weighted average of 377.52 ± 0.94 Ma. Baddeleyite U-Pb analyses are 3 to 6% normally discordant and have variable 207Pb*/ 206Pb* apparent ages. Eleven alteration-free baddeleyite fractions from three samples with no evidence for Pb loss yield uniform 206Pb*/ 238U ages with a weighted average of 378.54±0.23 Ma (378.64 Ma after correction for initial 230Th deficiency), which we consider the best estimate for age of the phoscorite-carbonatite body of the Kovdor massif. The

  13. Porosity and pressure: Role of compaction disequilibrium in the development of geopressures in a Gulf Coast Pleistocene basin

    SciTech Connect

    Hart, B.S.; Flemings, P.B.; Deshpande, A. )

    1995-01-01

    Measured pressures in Pleistocene strata of the Eugene Island block 330 area of offshore Louisiana reach approx. nine-tenths of the lithostatic pressures below 2 km depth; three-fourths of these geopressures are due to compaction disequilibrium. We show the relation between effective stress and porosity for compacting sediments to be exponential in shallow, normally pressured strata, then use the relation to calculate fluid pressure at depth in geopressured strata. Measured pressures below 2 km exceed our predicted values. A plot of effective stress vs. porosity demonstrates that compaction disequilibrium accounts for about three-quarters of the overpressures. We infer that the remainder must be due to pore-pressure generation at depth that occurred after the rocks reached their present porosity. 22 refs., 5 figs.

  14. Potential linkage disequilibrium between schizophrenia and locus D22S278 on the long arm of chromosome 22

    SciTech Connect

    Moises, H.W.; Yang, L.; Havsteen, B.

    1995-10-09

    Locus D22S278 at 22q12 has been implicated in schizophrenia by sib-pair analysis. In order to replicate these results, we performed the transmission test for linkage disequilibrium (TDT) in 113 unrelated schizophrenic patients and their 226 parents. Evidence for potential linkage disequilibrium was obtained between schizophrenia and allele 243 of the marker AFM 182xd12 at the locus D22S278 (P = 0.02). The results of our study suggest a detectable oligogenic gene in a multigene system for schizophrenia closely linked to D22S278 on the long arm of chromosome 22. If confirmed by others, this finding could lead to the identification of a schizophrenia susceptibility gene. 12 refs., 1 tab.

  15. Heritability and Familiality of Temperament and Character Dimensions in Korean Families with Schizophrenic Linkage Disequilibrium

    PubMed Central

    Lee, Byung Dae; Park, Je Min; Lee, Young Min; Moon, Eunsoo; Jeong, Hee Jeong; Chung, Young In; Yi, Young Mi

    2016-01-01

    Objective Categorical syndromes such as schizophrenia may represent complexes of many continuous psychological structural phenotypes along several dimensions of personality development/degeneration. The present study investigated the heritability and familiality of personality dimensions in Korean families with schizophrenic linkage disequilibrium (LD). Methods We recruited 179 probands (with schizophrenia) as well as, whenever possible, their parents and siblings. We used the Temperament and Character Inventory (TCI) to measure personality and symptomatic dimensions. The heritability of personality dimensions in a total of 472 family members was estimated using Sequential Oligogenic Linkage Analysis Routines (SOLAR). To measure familiality, we compared the personality dimensions of family members with those of 336 healthy unrelated controls using analysis of variance (ANOVA) analysis. Results Three of the seven TCI variables were significantly heritable and were included in subsequent analyses. The three groups (control, unaffected first-degree relative, case) were found to significantly differ from one another, with the expected order of average group scores, for all heritable dimensions. Conclusion Despite several study limitations with respect to family recruitment and phenotyping, our results show that aberrations in several personality dimensions related to genetic-environment coactions or interactions may underlie the complexity of the schizophrenic syndrome. PMID:27121432

  16. A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

    PubMed Central

    Goicoechea, P G; Herrán, A; Durand, J; Bodénès, C; Plomion, C; Kremer, A

    2015-01-01

    We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the ‘species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory. PMID:25515016

  17. Mineral disequilibrium in lavas explained by convective self-mixing in open magma chambers.

    PubMed

    Couch, S; Sparks, R S; Carroll, M R

    2001-06-28

    Characteristic features of many porphyritic andesite and dacite lavas are that they are rich in crystals and display a range of disequilibrium features, including reversely zoned crystals, resorption surfaces, wide ranges of mineral compositions and minerals which are not in equilibrium with the surrounding rock matrix. These features are often interpreted as evidence of the mixing of magmas of contrasting composition, temperature and origin. Here, however, we propose that such features can also be caused by convection within a magma body with a single composition, that is heated from below and cooled from above. We describe petrological observations of andesite lava erupted at the Soufrière Hills volcano, Montserrat, which indicate a heating event and the intermingling of crystals that have very different thermal histories. We present experimental data on a representative groundmass composition of this lava, which indicate that it is difficult to explain the calcic compositions of plagioclase overgrowth rims and microphenocrysts unless parts of the magma were at temperatures much higher than the inferred average temperature. The concept of convective self-mixing allows us to explain the occurrence of compositions of minerals that apparently cannot coexist under equilibrium conditions. PMID:11429601

  18. Transmission disequilibrium suggests a role for the sulfotransferase-4A1 gene in schizophrenia.

    PubMed

    Brennan, Mark D; Condra, Jodi

    2005-11-01

    Previous studies suggest a role for chromosome 22q13 in schizophrenia. This segment of chromosome 22 contains the sulfotransferase-4A1 (Sult4A1) gene, which encodes an enzyme thought to be involved in neurotransmitter metabolism in the central nervous system. To evaluate this candidate, we developed a microsatellite marker targeting a polymorphism in its 5' nontranslated region (D22s1749E). Using samples obtained from the National Institutes of Mental Health Schizophrenia Genetics Initiative, we evaluated 27 families having multiple siblings with schizophrenia and schizophrenia-spectrum disorders for transmission disequilibrium (TDT) of this marker along with three single nucleotide polymorphisms (SNPs) spanning a 37 kb segment containing the Sult4A1 gene. TDT for D22s1749E was significant (P < 0.05), with a tendency for the 213 nt allele to be preferentially transferred to affected children (P = 0.0079). Global chi-square values for haplotypes involving the SNPs (ss146366, ss146407, and ss146420) and D22s1749E, also showed significant TDT values (P = 0.0006-0.0016). Consequently, we proposed that Sult4A merited more careful scrutiny as a candidate gene for schizophrenia susceptibility. PMID:16152568

  19. Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese

    PubMed Central

    2009-01-01

    Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD in the São Miguel population. Data regarding the distribution of DXS1225-DXS8082 haplotypes indicate that there are no significant differences among all the populations studied, (Azorean geographical groups, the Azores archipelago and mainland Portugal). Moreover, in these as well as in other European populations, the most frequent DXS1225-DXS8082 haplotype is 210-219. Even though São Miguel islanders and Azoreans do not constitute isolated populations and show LD for only very short physical distances, certain characteristics, such as the absence of genetic structure, the same environment and the possibility of constructing extensive pedigrees through church and civil records, offer an opportunity for dissecting the genetic background of complex diseases in these populations. PMID:21637671

  20. Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach.

    PubMed

    Carlsen, Michelle; Fu, Guifang; Bushman, Shaun; Corcoran, Christopher

    2016-02-01

    Genome-wide data with millions of single-nucleotide polymorphisms (SNPs) can be highly correlated due to linkage disequilibrium (LD). The ultrahigh dimensionality of big data brings unprecedented challenges to statistical modeling such as noise accumulation, the curse of dimensionality, computational burden, spurious correlations, and a processing and storing bottleneck. The traditional statistical approaches lose their power due to [Formula: see text] (n is the number of observations and p is the number of SNPs) and the complex correlation structure among SNPs. In this article, we propose an integrated distance correlation ridge regression (DCRR) approach to accommodate the ultrahigh dimensionality, joint polygenic effects of multiple loci, and the complex LD structures. Initially, a distance correlation (DC) screening approach is used to extensively remove noise, after which LD structure is addressed using a ridge penalized multiple logistic regression (LRR) model. The false discovery rate, true positive discovery rate, and computational cost were simultaneously assessed through a large number of simulations. A binary trait of Arabidopsis thaliana, the hypersensitive response to the bacterial elicitor AvrRpm1, was analyzed in 84 inbred lines (28 susceptibilities and 56 resistances) with 216,130 SNPs. Compared to previous SNP discovery methods implemented on the same data set, the DCRR approach successfully detected the causative SNP while dramatically reducing spurious associations and computational time. PMID:26661113

  1. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium.

    PubMed

    Ramstein, Guillaume P; Evans, Joseph; Kaeppler, Shawn M; Mitchell, Robert B; Vogel, Kenneth P; Buell, C Robin; Casler, Michael D

    2016-01-01

    Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families' parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs. PMID:26869619

  2. Detection of linkage disequilibrium between the myotonic dystrophy locus and a new polymorphic DNA marker.

    PubMed Central

    Harley, H G; Brook, J D; Floyd, J; Rundle, S A; Crow, S; Walsh, K V; Thibault, M C; Harper, P S; Shaw, D J

    1991-01-01

    We have examined the linkage of two new polymorphic DNA markers (D19S62 and D19S63) and a previously unreported polymorphism with an existing DNA marker (ERCC1) to the myotonic dystrophy (DM) locus. In addition, we have used pulsed-field gel electrophoresis to obtain a fine-structure map of this region. The detection of linkage disequilibrium between DM and one of these markers (D19S63) is the first demonstration of this phenomenon in a heterogeneous DM population. The results suggest that at least 58% of DM patients in the British population, as well as those in a French-Canadian subpopulation, are descended from the same ancestral DM mutation. We discuss the implications of this finding in terms of strategies for cloning the DM gene, for a possible role in modification of risk for prenatal and presymptomatic testing, and we speculate on the origin and number of existing mutations which may result in a DM phenotype. PMID:2063878

  3. Linkage Disequilibrium Decay and Past Population History in the Human Genome

    PubMed Central

    Park, Leeyoung

    2012-01-01

    The fluctuation of population size has not been well studied in the previous studies of theoretical linkage disequilibrium (LD) expectation. In this study, an improved theoretical prediction of LD decay was derived to account for the effects of changes in effective population sizes. The equation was used to estimate effective population size (Ne) assuming a constant Ne and LD at equilibrium, and these Ne estimates implied the past changes of Ne for a certain number of generations until equilibrium, which differed based on recombination rate. As the influence of recent population history on the Ne estimates is larger than old population history, recent changes in population size can be inferred more accurately than old changes. The theoretical predictions based on this improved expression showed accurate agreement with the simulated values. When applied to human genome data, the detailed recent history of human populations was obtained. The inferred past population history of each population showed good correspondence with historical studies. Specifically, four populations (three African ancestries and one Mexican ancestry) showed population growth that was significantly less than that of other populations, and two populations originated from China showed prominent exponential growth. During the examination of overall LD decay in the human genome, a selection pressure on chromosome 14, the gephyrin gene, was observed in all populations. PMID:23056365

  4. Fine-scale genetic mapping based on linkage disequilibrium: theory and applications.

    PubMed

    Xiong, M; Guo, S W

    1997-06-01

    Linkage-disequilibrium mapping (LDM) recently has been hailed as a powerful statistical method for fine-scale mapping of disease genes. After reviewing its historical background and methodological development, we present a general, mathematical, and conceptually coherent framework for LDM that incorporates multilocus and multiallelic markers and mutational processes at the marker and disease loci. With this framework, we address several issues relevant to fine-scale mapping and propose some efficient computational methods for LDM. We implement various LDM methods that incorporate population growth, recurrent mutation, and marker mutations, on the basis of a general framework. We demonstrate these methods by applying them to published data on cystic fibrosis, Huntington disease, Friedreich ataxia, and progressive myoclonus epilepsy. Since the genes responsible for these diseases all have been cloned, we can evaluate the performance of our methods and can compare ours with that of other methods. Using the proposed methods, we successfully and accurately predicted the locations of genes responsible for these diseases, on the basis of published data only. PMID:9199574

  5. Linkage Disequilibrium and Genome-Wide Association Mapping in Tetraploid Wheat (Triticum turgidum L.)

    PubMed Central

    Laidò, Giovanni; Marone, Daniela; Russo, Maria A.; Colecchia, Salvatore A.; Mastrangelo, Anna M.; De Vita, Pasquale; Papa, Roberto

    2014-01-01

    Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker–trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker–trait associations. PMID:24759998

  6. Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.

    PubMed Central

    Rossi, Monica; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Rau, Domenico; Attene, Giovanna; Papa, Roberto

    2009-01-01

    Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes. PMID:25567895

  7. Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium

    PubMed Central

    Carlson, Christopher S.; Eberle, Michael A.; Rieder, Mark J.; Yi, Qian; Kruglyak, Leonid; Nickerson, Deborah A.

    2004-01-01

    Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing common polymorphism is inefficient, because genotypes at many of these sites are strongly correlated. Thus, it is not necessary to assay all common variants if the patterns of allelic association between common variants can be described. We have developed an algorithm to select the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies, such that all known common polymorphisms either are directly assayed or exceed a threshold level of association with a tagSNP. The algorithm is based on the r2 linkage disequilibrium (LD) statistic, because r2 is directly related to statistical power to detect disease associations with unassayed sites. We show that, at a relatively stringent r2 threshold (r2>0.8), the LD-selected tagSNPs resolve >80% of all haplotypes across a set of 100 candidate genes, regardless of recombination, and tag specific haplotypes and clades of related haplotypes in nonrecombinant regions. Thus, if the patterns of common variation are described for a candidate gene, analysis of the tagSNP set can comprehensively interrogate for main effects from common functional variation. We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries. PMID:14681826

  8. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium

    PubMed Central

    Ramstein, Guillaume P.; Evans, Joseph; Kaeppler, Shawn M.; Mitchell, Robert B.; Vogel, Kenneth P.; Buell, C. Robin; Casler, Michael D.

    2016-01-01

    Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs. PMID:26869619

  9. Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus.

    PubMed

    Subrahmanyan, L; Eberle, M A; Clark, A G; Kruglyak, L; Nickerson, D A

    2001-08-01

    The T-cell receptor (TCR) plays a central role in the immune system, and > 90% of human T cells present a receptor that consists of the alpha TCR subunit (TCRA) and the beta subunit (TCRB). Here we report an analysis of 63 variable genes (BV), spanning 553 kb of TCRB that yielded 279 single-nucleotide polymorphisms (SNPs). Samples were drawn from 10 individuals and represent four populations-African American, Chinese, Mexican, and Northern European. We found nine variants that produce nonfunctional BV segments, removing those genes from the TCRB genomic repertoire. There was significant heterogeneity among population samples in SNP frequency (including the BV-inactivating sites), indicating the need for multiple-population samples for adequate variant discovery. In addition, we observed considerable linkage disequilibrium (LD) (r(2) > 0.1) over distances of approximately 30 kb in TCRB, and, in general, the distribution of r(2) as a function of physical distance was in close agreement with neutral coalescent simulations. LD in TCRB showed considerable spatial variation across the locus, being concentrated in "blocks" of LD; however, coalescent simulations of the locus illustrated that the heterogeneity of LD we observed in TCRB did not differ markedly from that expected from neutral processes. Finally, examination of the extended genotypes for each subject demonstrated homozygous stretches of >100 kb in the locus of several individuals. These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association. PMID:11438886

  10. Sequence Variation and Linkage Disequilibrium in the Human T-Cell Receptor β (TCRB) Locus

    PubMed Central

    Subrahmanyan, Lakshman; Eberle, Michael A.; Clark, Andrew G.; Kruglyak, Leonid; Nickerson, Deborah A.

    2001-01-01

    The T-cell receptor (TCR) plays a central role in the immune system, and >90% of human T cells present a receptor that consists of the α TCR subunit (TCRA) and the β subunit (TCRB). Here we report an analysis of 63 variable genes (BV), spanning 553 kb of TCRB that yielded 279 single-nucleotide polymorphisms (SNPs). Samples were drawn from 10 individuals and represent four populations—African American, Chinese, Mexican, and Northern European. We found nine variants that produce nonfunctional BV segments, removing those genes from the TCRB genomic repertoire. There was significant heterogeneity among population samples in SNP frequency (including the BV-inactivating sites), indicating the need for multiple-population samples for adequate variant discovery. In addition, we observed considerable linkage disequilibrium (LD) (r2>0.1) over distances of ∼30 kb in TCRB, and, in general, the distribution of r2 as a function of physical distance was in close agreement with neutral coalescent simulations. LD in TCRB showed considerable spatial variation across the locus, being concentrated in “blocks” of LD; however, coalescent simulations of the locus illustrated that the heterogeneity of LD we observed in TCRB did not differ markedly from that expected from neutral processes. Finally, examination of the extended genotypes for each subject demonstrated homozygous stretches of >100 kb in the locus of several individuals. These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association. PMID:11438886

  11. Constructing a linkage–linkage disequilibrium map using dominant-segregating markers

    PubMed Central

    Zhu, Xuli; Dong, Leiming; Jiang, Libo; Li, Huan; Sun, Lidan; Zhang, Hui; Yu, Weiwu; Liu, Haokai; Dai, Wensheng; Zeng, Yanru; Wu, Rongling

    2016-01-01

    The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage–LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage–LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution. PMID:26622063

  12. Shades of gray: A comparison of linkage disequilibrium between Hutterites and Europeans

    PubMed Central

    Thompson, Emma E; Sun, Ying; Nicolae, Dan; Ober, Carole

    2014-01-01

    Founder or isolated populations have advantages for genetic studies due to decreased genetic and environmental heterogeneity. However, whereas longer range linkage disequilibrium (LD) in these populations is expected to facilitate gene localization, extensive LD may actually limit the ability for gene discovery. The North American Hutterite population is one of the best characterized young founder populations and members of this isolate have been the subjects of our studies of complex traits, including fertility, asthma and cardiovascular disease, for >20 years. Here, we directly assess the patterns and extent of global LD using single nucleotide polymorphism (SNP) genotypes with minor allele frequencies (MAFs) ≥5% from the Affymetrix GeneChip® Mapping 500K array in 60 relatively unrelated Hutterites and 60 unrelated Europeans (HapMap CEU). Although LD among some marker pairs extends further in the Hutterites than in Europeans, the pattern of LD and minor allele frequencies are surprisingly similar. These results indicate that 1) identifying disease genes should be no more difficult in the Hutterites than in outbred European populations, 2) the same common susceptibility alleles for complex diseases should be present in the Hutterites and outbred European populations, and 3) imputation algorithms based on HapMap CEU should be applicable to the Hutterites. PMID:19697328

  13. Experimental Designs for Reliable Detection of Linkage Disequilibrium in Unstructured Random Population Association Studies

    PubMed Central

    Ball, Roderick D.

    2005-01-01

    A method is given for design of experiments to detect associations (linkage disequilibrium) in a random population between a marker and a quantitative trait locus (QTL), or gene, with a given strength of evidence, as defined by the Bayes factor. Using a version of the Bayes factor that can be linked to the value of an F-statistic with an existing deterministic power calculation makes it possible to rapidly evaluate a comprehensive range of scenarios, demonstrating the feasibility, or otherwise, of detecting genes of small effect. The Bayes factor is advocated for use in determining optimal strategies for selecting candidate genes for further testing or applications. The prospects for fine-scale mapping of QTL are reevaluated in this framework. We show that large sample sizes are needed to detect small-effect genes with a respectable-sized Bayes factor, and to have good power to detect a QTL allele at low frequency it is necessary to have a marker with similar allele frequency near the gene. PMID:15781715

  14. Contemporaneous Disequilibrium, a New Hypothesis to Explain the „Paradox of the Plankton”*

    PubMed Central

    Richerson, Peter; Armstrong, Richard; Goldman, Charles R.

    1970-01-01

    The diversity of lake phytoplankton is unexpectedly high, since the epilimnion of a lake is continuously mixing and might be expected to have only one or at most a few niches for primary producers. However, a carefully replicated series of samples from Castle Lake, Calif., showed a high degree of patchiness for many phytoplankton species, indicating that the rate of mixing is slow enough relative to the reproductive rate of the algae for many different niches to exist simultaneously. Productivity per unit biomass ratios, measured at Lake Tahoe, California-Nevada, shows that the turnover times for carbon in even this ultraoligotrophic lake are often less than 1 day. High diversity is associated with high productivity per unit biomass and high zooplankton populations in this lake. A contemporaneous disequilibrium model to explain the diversity of the lake phytoplankton is therefore highly plausible. At any one time, many patches of water exist in which one species is at a competitive advantage relative to the others. These water masses are stable enough to permit a considerable degree of patchiness to occur in phytoplankton, but are obliterated frequently enough to prevent the exclusive occupation of each niche by a single species. PMID:5275371

  15. Linkage Disequilibrium Estimation of Chinese Beef Simmental Cattle Using High-density SNP Panels

    PubMed Central

    Zhu, M.; Zhu, B.; Wang, Y. H.; Wu, Y.; Xu, L.; Guo, L. P.; Yuan, Z. R.; Zhang, L. P.; Gao, X.; Gao, H. J.; Xu, S. Z.; Li, J. Y.

    2013-01-01

    Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size (Ne) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of r2 were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and Ne was 73 at five generations ago. PMID:25049849

  16. Constructing a linkage-linkage disequilibrium map using dominant-segregating markers.

    PubMed

    Zhu, Xuli; Dong, Leiming; Jiang, Libo; Li, Huan; Sun, Lidan; Zhang, Hui; Yu, Weiwu; Liu, Haokai; Dai, Wensheng; Zeng, Yanru; Wu, Rongling

    2016-02-01

    The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage-LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage-LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution. PMID:26622063

  17. Species Discrimination, Population Structure and Linkage Disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis Using SSR Markers

    PubMed Central

    Arumugasundaram, Shanmugapriya; Ghosh, Modhumita; Veerasamy, Sivakumar; Ramasamy, Yasodha

    2011-01-01

    Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD) existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR) loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC) ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims. PMID:22163287

  18. Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

    PubMed Central

    Yan, Jianbing; Shah, Trushar; Warburton, Marilyn L.; Buckler, Edward S.; McMullen, Michael D.; Crouch, Jonathan

    2009-01-01

    A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets. PMID:20041112

  19. sup 13 C and sup 18 O isotopic disequilibrium in biological carbonates: I. Patterns

    SciTech Connect

    McConnaughey, T. )

    1989-01-01

    Biological carbonates frequently precipitate out of {sup 18}O and {sup 13}C equilibrium with ambient waters. Two patterns of isotopic disequilibrium are particularly common. Kinetic disequilibria, so designated because they apparently result from kinetic isotope effects during CO{sub 2} hydration and hydroxylation, involve simultaneous depletions of {sup 18}O and {sup 13}C as large as 4{per thousand} and 10 to 15{per thousand}, respectively. Rapid skeletogenesis favors strong kinetic effects, and approximately linear correlations between skeletal {delta}{sup 18}O and {delta}{sup 13}C are common in carbonates showing mainly the kinetic pattern. Metabolic effects involve additional positive or negative modulation of skeletal {delta}{sup 13}C, reflecting changes in the {delta}{sup 13}C of dissolved inorganic carbon, caused mainly by photosynthesis and respiration. Kinetic isotope disequilibria tend to be fairly consistent in rapidly growing parts of photosynthetic corals, and time dependent isotopic variations therefore reflect changes in environmental conditions. {delta}{sup 18}O variations from Galapagos corals yields meaningful clues regarding seawater temperature, while {delta}{sup 13}C variations reflect changes in photosynthesis, modulated by cloudiness.

  20. Extensive Long-Range and Nonsyntenic Linkage Disequilibrium in Livestock Populations: Deconstruction of a Conundrum

    PubMed Central

    Lipkin, E.; Straus, K.; Stein, R. Tal; Bagnato, A.; Schiavini, F.; Fontanesi, L.; Russo, V.; Medugorac, I.; Foerster, M.; Sölkner, J.; Dolezal, M.; Medrano, J. F.; Friedmann, A.; Soller, M.

    2009-01-01

    Great interest was aroused by reports, based on microsatellite markers, of high levels of statistically significant long-range and nonsyntenic linkage disequilibrium (LD) in livestock. Simulation studies showed that this could result from population family structure. In contrast, recent SNP-based studies of livestock populations report much lower levels of LD. In this study we show, on the basis of microsatellite data from four cattle populations, that high levels of long-range LD are indeed obtained when using the multi-allelic D′ measure of LD. Long-range and nonsyntenic LD are exceedingly low, however, when evaluated by the standardized chi-square measure of LD, which stands in relation to the predictive ability of LD. Furthermore, specially constructed study populations provided no evidence for appreciable LD resulting from family structure at the grandparent level. We propose that the high statistical significance and family structure effects observed in the earlier studies are due to the use of large sample sizes, which accord high statistical significance to even slight deviations from asymptotic expectations under the null hypothesis. Nevertheless, even after taking sample size into account, our results indicate that microsatellites testify to the presence of usable LD at considerably wider separation distances than SNPs, suggesting that use of SNP haplotypes may considerably increase the usefulness of a given fixed SNP array. PMID:19087960

  1. An empiric comparison of linkage disequilibrium parameters in disease gene localizations; the myotonic dystrophy experience

    SciTech Connect

    Podolsky, L.; Baird, S.; Korneluk, R.G.

    1994-09-01

    Analyses of linkage disequilibrium (LD) between markers of known location and disease phenotypes often provide valuable information in efforts to clone the causative genes. However, there exist a number of factors which may attenuate a consistent inverse relationship between physical distance and LD for a given pairing of a genetic marker and a human disease gene. Chief among these is the effect of the general population frequency of an allele which demonstrates LD with a disease gene. Possibly as a result of this, a number of methods of calculating LD has been proposed. We have calculated seven such LD parameters for twelve physically mapped RFLP`s from a 1.3 Mb DM gene containing region of 19q13.3 using 107 DM and 213 non-DM chromosomes. Correlation of the DM-marker physical distance with LD for the 12 loci reveals the Yule coefficient and Dij{prime} parameter to give the most consistent relationship. The D{prime} parameter shown to have a relative allele frequency independence gave only a weak correlation. A similar analysis is being carried out on published cystic fibrosis genetic and physical mapping data. The parameters identified in this study may be the most appropriate for future LD based localizations of disease genes.

  2. Linkage disequilibrium analysis of case-control data: an application to generalized aggressive periodontitis.

    PubMed

    Scapoli, C; Trombelli, L; Mamolini, E; Collins, A

    2005-02-01

    Several studies have shown a role for the involvement of interleukin (IL)-1 gene cluster polymorphisms in the risk of periodontal diseases. In the present study, we tested polymorphisms, derived from genes of the IL-1 cluster, for association with generalized aggressive periodontitis (GAP) through both allelic association and by constructing a linkage disequilibrium (LD) map of the 2q13-14 disease candidate region. The IL-1RN (VNTR) genotype distribution observed was significantly different in GAP and control subjects (P=0.019). We also observed some evidence for an association between GAP and the IL-1B(+3953) polymorphism (P=0.039). The pattern of association in the region, represented as an LD map, identifies a recombination hot area between the IL-1B(+3953) and IL-1B(-511) polymorphisms. Multilocus modelling of association with disease gives a location for the peak association at the IL-1B(+3953) marker, although support for the peak is not significant. Haplotype analysis identifies a IL-1B(+3953)-IL-1B(-511) haplotype as having the lowest P-value in the region. Recognition of the presence of a recombination hot area between the IL-1B(+3953) and IL-1B(-511) polymorphisms will have an important bearing on future efforts to develop higher resolution SNP analysis in this region for both this and other diseases for which this cluster is implicated. PMID:15602586

  3. Possible thermochemical disequilibrium in the atmosphere of the exoplanet GJ 436b.

    PubMed

    Stevenson, Kevin B; Harrington, Joseph; Nymeyer, Sarah; Madhusudhan, Nikku; Seager, Sara; Bowman, William C; Hardy, Ryan A; Deming, Drake; Rauscher, Emily; Lust, Nate B

    2010-04-22

    The nearby extrasolar planet GJ 436b-which has been labelled as a 'hot Neptune'-reveals itself by the dimming of light as it crosses in front of and behind its parent star as seen from Earth. Respectively known as the primary transit and secondary eclipse, the former constrains the planet's radius and mass, and the latter constrains the planet's temperature and, with measurements at multiple wavelengths, its atmospheric composition. Previous work using transmission spectroscopy failed to detect the 1.4-mum water vapour band, leaving the planet's atmospheric composition poorly constrained. Here we report the detection of planetary thermal emission from the dayside of GJ 436b at multiple infrared wavelengths during the secondary eclipse. The best-fit compositional models contain a high CO abundance and a substantial methane (CH(4)) deficiency relative to thermochemical equilibrium models for the predicted hydrogen-dominated atmosphere. Moreover, we report the presence of some H(2)O and traces of CO(2). Because CH(4) is expected to be the dominant carbon-bearing species, disequilibrium processes such as vertical mixing and polymerization of methane into substances such as ethylene may be required to explain the hot Neptune's small CH(4)-to-CO ratio, which is at least 10(5) times smaller than predicted. PMID:20414304

  4. An investigation of genetic heterogeneity and linkage disequilibrium in 161 families with spinal muscular atrophy

    SciTech Connect

    Merette, C.; Gilliam, T.C.; Brzustowicz, L.M. ); Daniels, R.J.; Davies, K.E. ); Melki, J.; Munnich, A. ); Pericak-Vance, M.A. ); Siddique, T. ); Voosen, B. )

    1994-05-01

    The authors performed linkage analysis of 161 families with spinal muscular atrophy (SMA) in which affected individuals suffer from the intermediate or mild form of the disease (Types II or III). Markers for six loci encompassing the chromosome 5q11.2-q13.3 region were typed. The best map location for the disease locus was found to be between D5S6 and MAP1B. The corresponding 1 lod unit support interval is confined to this interval and spans 0.5 cM. The data strongly support the hypothesis of linkage heterogeneity (likelihood ratio, 1.14 [times] 10[sup 4]), with 5% of the families unlinked. Four families have a probability of less than 50% of segregating the SMA gene linked to the region 5q11.2-q13.3. A likelihood approach to test for linkage disequilibrium revealed no significant departure from Hardy-Weinberg equilibrium with any marker under study. 28 refs., 4 figs., 3 tabs.

  5. Linkage disequilibrium and haplotype analysis among Polish families with spinal muscular atrophy

    SciTech Connect

    Brzustowicz, L.M.; Wang, C.H.; Matseoane, D.; Kleyn, P.W.; Vitale, E.; Das, K.; Penchaszadeh, G.K.; Gilliam, T.C.; Munsat, T.L.; Hausmanowa-Petrusewicz, I.

    1995-01-01

    Spinal muscular atrophy (SMA) is an inherited degenerative disorder of anterior horn cells that results in progressive muscle weakness and atrophy. The autosomal recessive forms of childhood-onset SMA have been mapped to chromosome 5q11.2-13.3, in a number of studies examining different populations. A total of 9 simple sequence repeat markers were genotyped against 32 Polish families with SMA. The markers span an {approximately}0.7 cM region defined by the SMA flanking markers D5S435 and MAP1B. Significant linkage disequilibrium (corrected P<0.5) was detected at four of these markers, with D/D{sub max} values of {le}.89. Extended haplotype analysis revealed a predominant haplotype associated with SMA. The apparently high mutation rate of some of the markers has resulted in a number of haplotypes that vary slightly from this predominant haplotype. The predominant haplotype and these closely related patterns represent 25% of the disease chromosomes and none of the nontransmitted parental chromosomes. This predominant haplotype is present both in patients with acute (type I) and in chronic (types II and III) forms of SMA and occurs twice in a homozygous state, both times in children with chronic SMA. 34 refs., 2 figs., 2 tabs.

  6. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

    PubMed Central

    Miller, Joshua M; Poissant, Jocelyn; Malenfant, René M; Hogg, John T; Coltman, David W

    2015-01-01

    Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D′, and χ′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible. PMID:26380673

  7. Th-230 - U-238 series disequilibrium of the Olkaria basalts Gregory Rift Valley, Kenya

    NASA Technical Reports Server (NTRS)

    Black, S.; Macdonald, R.; Kelly, M.

    1993-01-01

    U-Th disequilibrium analyses of the Naivasha basalts show a very small (U-238/Th-230) ratios which are lower than any previously analyzed basalts. The broadly positive internal isochron trend from one sample indicates that the basalts may have source heterogeneities, this is supported by earlier work. The Naivasha complex comprises a bimodal suite of basalts and rhyolites. The basalts are divided into two stratigraphic groups each of a transitional nature. The early basalt series (EBS) which were erupted prior to the Group 1 comendites and, the late basalt series (LBS) which erupted temporally between the Broad Acres and the Ololbutot centers. The basalts represent a very small percentage of the overall eruptive volume of material at Naivasha (less than 2 percent). The analyzed samples come from four stratigraphic units in close proximity around Ndabibi, Hell's Gate and Akira areas. The earliest units occur as vesicular flows from the Ndabibi plain. These basalts are olivine-plagioclase phyric with the associated hawaiites being sparsely plagioclase phyric. An absolute age of 0.5Ma was estimated for these basalts. The next youngest basalts flows occur as younger tuft cones in the Ndabibi area and are mainly olivine-plagioclase-clinopyroxcene phyric with one purely plagioclase phyric sample. The final phase of activity at Ndabibi resulted in much younger tuft cones consisting of air fall ashes and lapilli tufts. Many of these contain resorbed plagioclase phenocrysts with sample number 120c also being clinopyroxene phyric. The isotopic evidence for the basalt formation is summarized.

  8. [sup 226]Ra-[sup 230]Th disequilibrium in axial and off-axis mid-ocean ridge basalts

    SciTech Connect

    Volpe, A.M.; Goldstein, S.J. Los Alamos National Lab., NM )

    1993-03-01

    The authors describe [sup 226]Ra-[sup 230]Th disequilibrium in mid-ocean ridge basalt (MORB) glasses from the Juan de Fuca, Gorda, and East Pacific ridges. These first mass spectrometric measurements of [sup 226]Ra in MORB glasses at sub-picogram abundance levels confirm the large excesses over [sup 230]Th determined by radon-emanation techniques and alpha spectrometry. All off-axis MORB glasses have [sup 226]Ra-[sup 230]Th and [sup 234]U-[sup 238]U in secular equilibrium. This suggests that magmatic processes, not secondary post-eruption alteration, generate [sup 238]U-series disequilibrium in these MORB. Least evolved, N-MORB from axial valleys have ([sup 226]Ra/[sup 230]Th) between 2.2-2.3. Differentiated and enriched E-type MORB have consistently low ([sup 226]Ra/[sup 230]Th) ratios compared with N-MORB from the same ridge sections. Ra-Th fractionation may be less pronounced, or magma residence-transit periods may be long for differentiated MORB. Also, E-MORB may be generated by different melt extraction volumes and rates. Estimated [sup 226]Ra-[sup 230]Th ages for N-MORB agree with location on and off ridge segments, and with Th-U model ages. These preliminary results show that [sup 226]Ra-[sup 230]Th disequilibrium could be used to quantify volcanic episodicity at ocean ridges. 39 refs., 6 figs., 4 tabs.

  9. A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci

    SciTech Connect

    Terwilliger, J.D.

    1995-03-01

    Historically, most methods for detecting linkage disequilibrium were designed for use with diallelic marker loci, for which the analysis is straightforward. With the advent of polymorphic markers with many alleles, the normal approach to their analysis has been either to extend the methodology for two-allele systems (leading to an increase in df and to a corresponding loss of power) or to select the allele believed to be associated and then collapse the other alleles, reducing, in a biased way, the locus to a diallelic system. I propose a likelihood-based approach to testing for linkage disequilibrium, an approach that becomes more conservative as the number of alleles increases, and as the number of markers considered jointly increases in a multipoint test for linkage disequilibrium, while maintaining high power. Properties of this method for detecting associations and fine mapping the location of disease traits are investigated. It is found to be, in general, more powerful than conventional methods, and it provides a tractable framework for the fine mapping of new disease loci. Application to the cystic fibrosis data of Kerem et al. is included to illustrate the method. 12 refs., 4 figs., 4 tabs.

  10. Radioactivity and food

    SciTech Connect

    Olszyna-Marzys, A.E. )

    1990-03-01

    Two topics relating to radioactivity and food are discussed: food irradiation for preservation purposes, and food contamination from radioactive substances. Food irradiation involves the use of electromagnetic energy (x and gamma rays) emitted by radioactive substances or produced by machine in order to destroy the insects and microorganisms present and prevent germination. The sanitary and economic advantages of treating food in this way are discussed. Numerous studies have confirmed that under strictly controlled conditions no undesirable changes take place in food that has been irradiated nor is radioactivity induced. Reference is made to the accident at the Chernobyl nuclear power station, which aroused public concern about irradiated food. The events surrounding the accident are reviewed, and its consequences with regard to contamination of different foods with radioactive substances, particularly iodine-131 and cesium-137, are described. Also discussed are the steps that have been taken by different international organizations to set limits on acceptable radioactivity in food.15 references.