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Sample records for 238u-230th radioactive disequilibrium

  1. Geochronology and petrogenesis of MORB from the Juan de Fuca and Gorda ridges by 238U230Th disequilibrium

    USGS Publications Warehouse

    Goldstein, S.J.; Murrell, M.T.; Janecky, D.R.; Delaney, J.R.; Clague, D.A.

    1991-01-01

    A highly precise mass spectrometric method of analysis was used to determine 238U234U230Th232Th in axial and off-axis basalt glasses from Juan de Fuca (JDF) and Gorda ridges. Initial 230Th activity excesses in the axial samples range from 3 to 38%, but generally lie within a narrow range of 12 to 15%. Secondary alteration effects were evaluated using ??234U and appear to be negligible; hence the 230Th excesses are magmatic in origin. Direct dating of MORB was accomplished by measuring the decrease in excess 230Th in off-axis samples. 238U230Th ages progressively increase with distance from axis. Uncertainties in age range from 10 to 25 ka for UTh ages of 50 to 200 ka. The full spreading rate based on UTh ages for Endeavour segment of JDF is 5.9 ?? 1/2 cm/yr, with asymmetry in spreading between the Pacific (4.0 ?? 0.6 cm/yr) and JDF (1.9 ?? 0.6 cm/yr) plates. For northern Gorda ridge, the half spreading rate for the JDF plate is found to be 3.0 ?? 0.4 cm/yr. These rates are in agreement with paleomagnetic spreading rates and topographic constraints. This suggests that assumptions used to determine ages, including constancy of initial 230Th 232Th ratio over time, are generally valid for the areas studied. Samples located near the axis of spreading are typically younger than predicted by these spreading rates, which most likely reflects recent volcanism within a 1-3 km wide zone of crustal accretion. Initial 230Th/232Th ratios and 230Th activity were also used to examine the recent Th/U evolution and extent of melting of mantle sources beneath these ridges. A negative anomaly in 230Th 232Th for Axial seamount lavas provides the first geochemical evidence of a mantle plume source for Axial seamount and the Cobb-Eickelberg seamount chain and indicates recent depletion of other JDF segment sources. Large 230Th activity excesses for lavas from northern Gorda ridge and Endeavour segment indicate formation from a lower degree of partial melting than other segments. An

  2. 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

  3. 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.

  4. 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

  5. 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

  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

    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.

  8. 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.

  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. 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.

  11. 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.

  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. 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

  14. 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

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

    NASA Astrophysics Data System (ADS)

    Jicha, Brian R.; Johnson, Clark M.; Hildreth, Wes; Beard, Brian L.; Hart, Garret L.; Shirey, Steven B.; Singer, Brad 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.

  16. 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.

  17. 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.

  18. 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.; Sherrod, David R.; Scott, William E.; Stauffer, Peter H.

    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.

  19. 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

  20. Timescales of magma differentiation from basalt to andesite beneath Hekla Volcano, Iceland: Constraints from U-series disequilibria in lavas from the last quarter-millennium flows

    NASA Astrophysics Data System (ADS)

    Chekol, Takele A.; Kobayashi, Katsura; Yokoyama, Tetsuya; Sakaguchi, Chie; Nakamura, Eizo

    2011-01-01

    Measurements of 238U- 230Th- 226Ra disequilibria, Sr-Nd-Pb-Hf isotopes and major-trace elements have been conducted for lavas erupted in the last quarter-millennium at Hekla volcano, Iceland. The volcanic rocks range from basalt to dacite. Most of the lavas (excluding dacitic samples) display limited compositional variations in radiogenic Sr-Nd-Pb-Hf isotopes ( 87Sr/ 86Sr = 0.70319-0.70322; 143Nd/ 144Nd = 0.51302-0.51305; 206Pb/ 204Pb = 19.04-19.06; 207Pb/ 204Pb = 15.53-15.54; 208Pb/ 204Pb = 38.61-38.65; 176Hf/ 177Hf = 0.28311-0.28312). All the samples possess ( 230Th/ 238U) disequilibrium with 230Th excesses, and they show systematic variations in ( 230Th/ 232Th) and ( 238U/ 232Th) ratios. The highest 226Ra excesses occur in the basalt and most differentiated andesite lavas, while some basaltic-andesite lavas have ( 226Ra/ 230Th) ratio that are close to equilibrium. The 238U- 230Th- 226Ra disequilibria variations cannot be produced by simple closed-system fractional crystallization with radioactive decay of 230Th and 226Ra in a magma chamber. A closed-system fractional crystallization model and assimilation and fractional crystallization (AFC) model indicate that the least differentiated basaltic andesites were derived from basalt by fractional crystallization with a differentiation age of ˜24 ± 11 kyr, whereas the andesites were formed by assimilation of crustal material and fractionation of the basaltic-andesites within 2 kyr. Apatite is inferred to play a key role in fractionating the parent-daughter nuclides in 230Th- 238U and 226Ra- 230Th to make the observed variations. Our proposed model is that several batches of basaltic-andesite magmas that formed by fractional crystallization of a basaltic melt from a deeper reservoir, were periodically injected into the shallow crust to form individual magma pockets, and subsequently modifying the original magma compositions via simultaneous assimilation and fractional crystallization. The assimilant is the dacitic

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Geochemical evolution of historical lavas from Askja Volcano, Iceland: Implications for mechanisms and timescales of magmatic differentiation

    NASA Astrophysics Data System (ADS)

    Kuritani, Takeshi; Yokoyama, Tetsuya; Kitagawa, Hiroshi; Kobayashi, Katsura; Nakamura, Eizo

    2011-01-01

    The mechanisms and the timescales of magmatic evolution were investigated for historical lavas from the Askja central volcano in the Dyngjufjöll volcanic massif, Iceland, using major and trace element and Sr, Nd, and Pb isotopic data, as well as 238U- 230Th- 226Ra systematics. Lavas from the volcano show marked compositional variation from magnesian basalt through ferrobasalt to rhyolite. In the magnesian basalt-ferrobasalt suite (5-10 wt% MgO), consisting of lavas older than 1875 A.D., 87Sr/ 86Sr increases systematically with increasing SiO 2 content; this suite is suggested to have evolved in a magma chamber located at ˜600 MPa through assimilation and fractional crystallization. On the other hand, in the ferrobasalt-rhyolite suite (1-5 wt% MgO), including 1875 A.D. basalt and rhyolite and 20th century lavas, 87Sr/ 86Sr tends to decrease slightly with increasing SiO 2 content. It is suggested that a relatively large magma chamber occupied by ferrobasalt magma was present at ˜100 MPa beneath the Öskjuvatn caldera, and that icelandite and rhyolite magmas were produced by extraction of the less and more evolved interstitial melt, respectively, from the mushy boundary layer along the margin of the ferrobasalt magma chamber, followed by accumulation of the melt to form separate magma bodies. Ferrobasalt and icelandite lavas in the ferrobasalt-rhyolite suite have a significant radioactive disequilibrium in terms of ( 226Ra/ 230Th), and its systematic decrease with magmatic evolution is considered to reflect aging, along with assimilation and fractional crystallization processes. Using a mass-balance model in which simultaneous fractional crystallization, crustal assimilation, and radioactive decay are taken into account, the timescale for the generation of icelandite magma from ferrobasalt was constrained to be <˜3 kyr which is largely dependent on Ra crystal-melt partition coefficients we used.

  7. 210Pb-226Ra disequilibria in Icelandic basalts and implications for melt transport time

    NASA Astrophysics Data System (ADS)

    Sigmarsson, O.

    2003-04-01

    Primitive basalts with radioactive disequilibrium between isotopes of the 238U decay chain may provide constraints on the timescales of mantle melt migration. The disequilibria between 238U, 230Th and 226Ra have been studied in several Recent basalts whereas very few results exist on the 210Pb-226Ra disequilibria. Only basalts significantly younger than 100 years old can be studied for 210Pb-226Ra disequilibria due to the short half-live of 210Pb (22.3 years). Most lavas measured so far show either 210Pb-226Ra equilibria or 210Pb-deficit which have been attributed to the degassing of 222Rn in shallow magma chambers. Icelandic tholeiites from the last century are in radioactive equilibrium with (210Pb/226Ra) equal to unity. These basalts are fed from shallow magma chambers having residence time exceeding 100 years. In contrast, primitive alkaline basalts (MgO =7-12%) from Surtsey island had (210Pb/226Ra) ranging from 0.45±0.04 to 0.82±0.06 at the time of eruption. These large 210Pb deficits are unlikely to result from shallow magma degassing since no magma chamber existed beneath this volcanic island which was born during the 1963-67 eruption. The 210Pb-226Ra disequilibria increase from the beginning towards the end of the eruption when the most primitive basalts were produced, and decreases systematically with increasing Th content. These same basalts show a negative correlation between Pb and Cu abundances which are inconsistent with exsolution of sulfur rich liquid or crystallisation of sulphides as a fractionation mechanism of 210Pb and 226Ra. The large deficit of 210Pb in Surtsey lavas were thus most likely generated during mantle partial melting. In such a case, the time of melt transport from the source region to surface is constrained to be significantly shorter than 100 years.

  8. 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.

  9. 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.

  10. 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.

  11. Linkage Disequilibrium in Wild Mice

    PubMed Central

    Laurie, Cathy C; Nickerson, Deborah A; Anderson, Amy D; Weir, Bruce S; Livingston, Robert J; Dean, Matthew D; Smith, Kimberly L; Schadt, Eric E; Nachman, Michael W

    2007-01-01

    Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD) in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1) Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2) they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3) LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits. PMID:17722986

  12. Linkage disequilibrium in human populations

    PubMed Central

    Lonjou, Christine; Zhang, Weihua; Collins, Andrew; Tapper, William J.; Elahi, Eiram; Maniatis, Nikolas; Morton, Newton E.

    2003-01-01

    Whereas the human linkage map appears on limited evidence to be constant over populations, maps of linkage disequilibrium (LD) vary among populations that differ in gene history. The greatest difference is between populations of sub-Saharan origin and populations remotely derived from Africa after a major bottleneck that reduced their heterozygosity and altered their Malecot parameters, increasing the intercept M that reflects association in founders and decreasing the exponential decline ɛ. Variation among populations within this ethnic dichotomy is much smaller. These observations validate use of a cosmopolitan LD map based on a sizeable sample representing a large population reliably typed for markers at high density. Then an LD map for a region or isolate within an ethnic group may be created by fitting the sample LD to the cosmopolitan map, estimating Malecot parameters simultaneously. The cosmopolitan map scaled by ɛ recovers 95% of the information that a local map at the same density gives and therefore more than the information in a low-resolution local map. Relative to a Eurasian cosmopolitan map the scaling factors are estimated to be 0.82 for isolates of European descent, 1.53 for Yorubans, and 1.74 for African Americans. These observations are consistent with a common bottleneck (perhaps but not necessarily speciation) ≈173,500 years ago, if the bottleneck associated with migration out of Africa was 100,000 years ago. Eurasian populations (especially isolates with numerous cases) are efficient for genome scans, and populations of recent African origin (such as African Americans) are efficient for identification of causal polymorphisms within a candidate sequence. PMID:12721363

  13. 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.

  14. 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

  15. 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 ...

  16. Transmission-disequilibrium tests for quantitative traits

    SciTech Connect

    Allison, D.B.

    1997-03-01

    The transmission-disequilibrium test (TDT) of Spielman et al. is a family-based linkage-disequilibrium test that offers a powerful way to test for linkage between alleles and phenotypes that is either causal (i.e., the marker locus is the disease/trait allele) or due to linkage disequilibrium. The TDT is equivalent to a randomized experiment and, therefore, is resistant to confounding. When the marker is extremely close to the disease locus or is the disease locus itself, tests such as the TDT can be far more powerful than conventional linkage tests. To date, the TDT and most other family-based association tests have been applied only to dichotomous traits. This paper develops five TDT-type tests for use with quantitative traits. These tests accommodate either unselected sampling or sampling based on selection of phenotypically extreme offspring. Power calculations are provided and show that, when a candidate gene is available (1) these TDT-type tests are at least an order of magnitude more efficient than two common sib-pair tests of linkage; (2) extreme sampling results in substantial increases in power; and (3) if the most extreme 20% of the phenotypic distribution is selectively sampled, across a wide variety of plausible genetic models, quantitative-trait loci explaining as little as 5% of the phenotypic variation can be detected at the .0001 a level with <300 observations. 57 refs., 2 figs., 5 tabs.

  17. The disequilibrium between 210Po and 210Pb in raw and drinking waters.

    PubMed

    Idoeta, R; Herranz, M; Legarda, F

    2011-01-01

    Many countries have to monitor and control the radioactivity in drinking waters in order to ensure compliance with the requirements of their respective regulations. Among radionuclides responsible for this radioactivity there are (210)Po and (210)Pb, which are usually not in radioactive equilibrium in waters. This paper deals with the analysis of this disequilibrium and the way that the water treatment plants affect it. To do this, (210)Po and (210)Pb activity concentrations were measured in raw and drinking water. The measurements were performed by alpha-particle spectrometry and gas flow proportional counting and the corresponding formulae for uncertainties and detection limits are presented. The values obtained show that the Po/Pb ratio is lower in surface than in ground waters. Regarding water treatment, this ratio adopts values lower in drinking water than in raw waters. In any case, for the waters analysed in this work the committed effective doses due to these radionuclides, are negligible.

  18. Radiological exposure assessment from soil, underground and surface water in communities along the coast of a shallow water offshore oilfield in Ghana.

    PubMed

    Kpeglo, D O; Mantero, J; Darko, E O; Emi-Reynolds, G; Akaho, E H K; Faanu, A; Garcia-Tenorio, R

    2015-02-01

    Radiometric determinations have been carried out to assess public exposure to radioactivity for communities along the coast of a shallow water offshore oilfield in Ghana (which started their operations recently) in order to establish baseline data using alpha spectrometry after radiochemical separation and non-destructive gamma spectrometry. The average activity concentrations of (234)U, (238)U, (230)Th and (232)Th by alpha-particle spectrometry and of (226)Ra, (228)Ra, (228)Th, (40)K, (210)Pb, (234)Th and (137)Cs by gamma-ray spectrometry were determined in the soil samples. The activity concentrations of (234)U, (238)U, (230)Th and (232)Th were determined in the water samples by alpha-particle spectrometry and of (226)Ra by liquid scintillation counting. The total annual effective dose to the public was estimated from the measured activity concentrations and this was clearly below the International Commission on Radiological Protection (ICRP) reference level of 1 mSv y(-1) for public exposure control. In addition, the estimated values of Raeq, Hex and Hin were all lower than the recommended acceptable values and the mean values of gross alpha and gross beta determinations performed for all the water samples give values that were all below the Ghana Standards Authority and World Health Organization recommended guideline values for drinking water quality. The results obtained show insignificant public exposure to radioactivity. However, this study provides important information for future studies on subsequent evaluations of the possible future environmental contamination due to activities of the oil industry in Ghana.

  19. Neighborhood type, social disequilibrium, and happiness.

    PubMed

    Wenz, F V

    1977-01-01

    This study attempts to relate (a) types of urban neighborhoods with extreme scores on the economic status dimension and rates of social and psychological disequilibrium to happiness of its residents, and (b) both aggregate and individual measures of economic status to happiness. Nonverbal behaviors such as suicide, attempted suicide, homicide, marital separation, and psychiatric disruptions served as indicators of the location of "more or less" happiness in the urban environment. Interviews in two types of neighborhoods revealed that people in the high economic-low misery neighborhood experienced greater happiness than those living in the low economic-high misery neighborhood.

  20. Disequilibrium melt distributions during static recrystallisation

    NASA Astrophysics Data System (ADS)

    Walte, N. P.; Bons, P. D.; Passchier, C. W.; Koehn, D.; Arnold, J.

    2003-04-01

    DISEQUILIBRIUM MELT DISTRIBUTIONS DURING STATIC RECRYSTALLISATION N.P. Walte (1), P.D. Bons (2), C.W. Passchier (1), D. Koehn (1), J. Arnold (1) (1) Institute for Earth Sciences, Johannes Gutenberg-University, Mainz, Germany, (2) Institute for Earth Sciences, Eberhard Karls University, Tübingen, Germany (walte@mail.uni-mainz.de) The geometry of melt-filled pores in a partially molten rock strongly controls the permeability, rheology and initial segregation of melt. Current theory for monomineralic aggregates, using only the wetting angle and melt fraction as parameters, predicts a perfectly regular melt framework or equally shaped melt inclusions on grain boundary junctions. However, published melt-present high-temperature experiments with rock forming minerals such as quartz or olivine show considerable deviations from this predicted regular equilibrium melt geometry. Disequilibrium features, such as fully wetted grain boundaries, melt lenses, and large melt patches have been described, and were attributed to surface energy anisotropy of the minerals. This study used static analogue experiments with norcamphor plus ethanol liquid, that allow continuous in-situ observation of the evolving distribution of melt during static recrystallisation. The liquid-crystal surface energy of norcamphor is effectively isotropic. For the experiments an approximately 0.1 mm thin sample of norcamphor plus ethanole was placed between two glass plates and observed with a miroscope. Ethanol was used as a melt analogue because it allows to run experiments at room temperature, avoiding any temperature gradients. The wetting angle is approximately 15°, which is well below 60° and within the range reported for quartz and olivine plus melt experiments. The experiments show that all described disequilibrium features can form during fluid-enhanced static recrystallisation, especially where surrounding grains consume small, few-sided grains. These features are unstable and transient: a

  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. 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

  3. How population growth affects linkage disequilibrium.

    PubMed

    Rogers, Alan R

    2014-08-01

    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 [Formula: see text], which therefore allow inferences about ancient population history. For the human population of Europe, these results suggest a history of population growth.

  4. 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.

  5. 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.

  6. Mitonuclear linkage disequilibrium in human populations

    PubMed Central

    Sloan, Daniel B.; Fields, Peter D.; Havird, Justin C.

    2015-01-01

    There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy. PMID:26378221

  7. Mitonuclear linkage disequilibrium in human populations.

    PubMed

    Sloan, Daniel B; Fields, Peter D; Havird, Justin C

    2015-09-22

    There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.

  8. A genomic survey of linkage disequilibrium

    SciTech Connect

    Peterson, A.; Freimer, N.; Slakin, M.

    1994-09-01

    Linkage disequilibrium (LD), the association of alleles between two or more loci, is a powerful tool for genetic mapping. LD is governed by recombination, mutation, selection, and population admixture; little is known about their relative importance or the distribution of LD across the genome. We used microsatellite markers to conduct a survey of the genomic distribution of LD on chromosome 4, which was chosen because an available radiation hybrid map enabled assessment of LD distribution based on genetic as well as physical distance. To minimize the effect of admixture, we studied a population from Finland, which has a long history of relative isolation. We compared the informativeness of haplotyped and genotyped samples. 33 markers were typed; 29 significant pairwise associations were observed (p<0.05). Although LD was detected between several loci apparently separated by > 2 cM on linkage maps, it was rarely detected between loci separated by more than 40 centiRays on the radiation hybrid map (about 2 megabases). In several instances, LD was not detected between adjacent markers apparently seperated by < 1 cM. In most of these cases, one locus had low heterozygosity or multiple recombination events were directly observed. Contrary to expectation, there was no evident correlation between the ratio of genetic/physical distance and detection of LD; this is likely partially due to the imprecision of linkage maps over small distances. Detection of LD was roughly equivalent in the haplotyped and genotyped samples, probably reflecting the inadequacy of current methods for detection of LD across multiple loci in a single analysis. Conclusion: LD is widely distributed across large genome regions. Marker heterozygosity and physical distance are correlated with detection of LD, and directly observed recombination events may be more useful than linkage maps in evaluating genetic distance in relation to detection of LD.

  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. Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.).

    PubMed

    Ecke, Wolfgang; Clemens, Rosemarie; Honsdorf, Nora; Becker, Heiko C

    2010-03-01

    Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies >or=0.1 were used for the analysis of linkage disequilibrium in a population of 85 canola quality winter rapeseed genotypes. A low overall level of linkage disequilibrium was found with a mean r (2) of only 0.027 over all 356,590 possible marker pairs. At a significance threshold of P = 2.8 x 10(-7), which was derived by a Bonferroni correction from a global alpha-level of 0.1, only 0.78% of the marker pairs were in significant linkage disequilibrium. Among physically linked marker pairs, the level of linkage disequilibrium was about five times higher with more than 10% of marker pairs in significant linkage disequilibrium. Linkage disequilibrium decayed rapidly with distance between linked markers with high levels of linkage disequilibrium extending only for about 2 cM. Owing to the rapid decay of linkage disequilibrium with distance association analyses in canola quality rapeseed will have a significantly higher resolution than QTL analyses in segregating populations by interval mapping, but much larger number of markers will be necessary to cover the whole genome. A major impact of the recent breeding history of rapeseed on linkage disequilibrium could not be observed.

  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. Maximum-likelihood estimation of gene location by linkage disequilibrium

    SciTech Connect

    Hill, W.G. ); Weir, B.S. )

    1994-04-01

    Linkage disequilibrium, D, between a polymorphic disease and mapped markers can, in principle, be used to help find the map position of the disease gene. Likelihoods are therefore derived for the value of D conditional on the observed number of haplotypes in the sample and on the population parameter Nc, where N is the effective population size and c the recombination fraction between the disease and marker loci. The likelihood is computed explicitly for the case of two loci with heterozygote superiority and, more generally, by computer simulations assuming a steady state of constant population size and selective pressures or neutrality. It is found that the likelihood is, in general, not very dependent on the degree of selection at the loci and is very flat. This suggests that precise information on map position will not be obtained from estimates of linkage disequilibrium. 15 refs., 5 figs., 21 tabs.

  13. [Linkage disequilibrium analysis for microsatellite loci in six cattle breeds].

    PubMed

    Kiseleva, T Iu; Kantanen, J; Vorob'ev, N I; Podoba, B E; Terletskiĭ, V P

    2014-04-01

    Autosomal microsatellites are valuable tools for investigating genetic diversity and population structure and making conservation decisions to preserve valuable breeds of domestic animals. We carried out a linkage disequilibrium analysis using 29 microsatellite markers in six cattle populations: Suksun, Istoben, Yaroslavl, Kholmogory, Grey Ukrainian and Pechora type Kholmogory breeds. We discovered a significant linkage between microsatellites INRA037 and CSRM60 in Grey Ukrainian breed.

  14. Direct and disequilibrium effects on precipitation in transient climates

    NASA Astrophysics Data System (ADS)

    McInerney, D.; Moyer, E.

    2012-08-01

    Climate models are in broad agreement that global precipitation increases with surface temperature as atmospheric CO2 concentrations rise, but recent studies have shown that climates that are not yet in equilibrium exhibit additional "transient precipitation effects". In conditions of rising CO2, for example, precipitation at a given temperature is suppressed relative to its equilibrium value. Some authors argue that the primary driver of these effects is ocean heat uptake, but most recent studies assume that they result from some direct radiative effect. We show here that global precipitation and temperature anomalies are insufficient to resolve mechanisms, since the conventional "fast/slow" representation of transient precipitation effects is degenerate with a "disequilibrium" representation that posits control only by ocean heat uptake. We use regional anomalies instead to show in multiple ways that ocean heat uptake is the dominant driver of transient precipitation effects in CO2-forced climates. Precipitation suppression appears predominantly over the ocean, with response over land of the opposite sign. The coefficients of a disequilibrium representation are uncorrelated, suggesting that they capture physically meaningful processes, while those of a fast/slow representation are highly correlated. Further, the regional patterns of transient precipitation response are highly similar for both CO2 and solar forcing, with a relatively small and homogeneous offset between them. Examination of the surface energy budget allows us to conclude that energy balance in solar-forced climates is achieved by the superposition of both disequilibrium and direct processes. Our results highlight the importance of using regional information rather than global aggregates for understanding the physics of transient climate change and its impacts on societies.

  15. Linkage disequilibrium, haplotype analysis and Werner`s syndrome

    SciTech Connect

    Wijsman, E.M.; Goddard, K.A.B.; Martin, G.M.

    1994-09-01

    Werner`s syndrome (WS) is a rare, autosomal, recessive disorder of premature aging. Although the underlying defect is unknown, the gene for the disorder, WRN, has been mapped to the 8p11.1-21.1 region. We have assembled a sample of 30 Japanese and 24 non-Japanese (primary Caucasian) WS patients, as well as a control sample from each population. 25 of the Japanese patients and 10 of the Caucasian patients are from consanguineous marriages. We recently presented evidence from these families which places WRN in the 10.2 cM interval between D8S87 and D8S137. However, because WS is so rare and because many patients are from consanguineous marriages, fine localization of the gene by traditional meiotic mapping methods is unlikely to succeed. The existence of linkage disequilibrium is now recognized as a key piece of evidence in defining a small region (typically under 1-2 cM) containing a gene of interest. Thus an alternative approach for refining the location of WRN may be to identify linked markers which are in linkage disequilibrium with the disease. We recently suggested that WRN may be close to D8S339 and GSR in the above interval because of the presence of statistically significant evidence of linkage disequilibrium in the Japanese sample. In addition, there was evidence in both populations that a limited number of haplotypes was associated with the disease. Here we report an extension of this study to include a number of additional markers. We present additional evidence that there is linkage disequilibrium between many of these markers and WRN in both the Japanese and Caucasian samples. In addition, the additional markers do not markedly subdivide the disease haplotypes defined by D8S339 and GSR, while at the same time they introduce substantial numbers of new haplotypes into the control populations. These results suggest that the haplotypes associated with WS may be used to further define the limits of WRN.

  16. 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.

  17. 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.

  18. 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.

  19. The Potential of Uranium-Series Disequilibrium in Marine and Lacustrine Diatom Frustules as a Tool for Geochronological and Paleoenvironmental Studies

    NASA Astrophysics Data System (ADS)

    Luo, S.; Tsai, Y.

    2008-12-01

    Accurate age dating of deep-sea sediment records from the polar region remains one of the major challenging issues in paleoceanographic and paleoclimatologic studies. As diatom is ubiquitous in aquatic systems, in particular in cold waters of the polar region, this study seeks to explore the utilities of uranium- series disequilibrium in diatom frustules as a chronometer for absolute age dating and/or as a proxy for paleo-environmental studies. In the uranium series, uranium-238, with a half-life of 4.468 billion year, decays to a stable nuclide lead-206 through a series of shorter-lived radionuclides. Uranium-238 and all of its daughter nuclides will achieve secular equilibrium on a time scale of about one million years in an igneous rock. Disequilibrium between the daughter and parent nuclides would occur in aquatic environments, such as in oceans and lakes, as a result of various naturally-occurring physical/chemical processes. This study shows that diatom acquires its uranium isotope composition from its ambient seawater, creating significant radioactive disequilibrium between uranium and its daughter nuclides in diatom frustules. This salient feature makes diatom frustules very useful for absolute age dating as well as for assessing the past changes of many geophysical and geochemical processes in the ocean and on the continents.

  20. 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.

  1. The transmission/disequilibrium test: History, subdivision, and admixture

    SciTech Connect

    Ewens, W.J.; Spielman, R.S.

    1995-08-01

    Disease association with a genetic marker is often taken as a preliminary indication of linkage with disease susceptibility. However, population subdivision and admixture may lead to diease association even in the absence of linkage. In a previous paper, we described a test for linkage (and linkage disequilibrium) between a genetic marker and disease susceptibility; linkage is detected by this test only if association is also present. This transmission/disequilibrium test (TDT) is carried out with data on transmission of marker alleles from parents heterozygous for the marker alleles to affected offspring. The TDT is a valid test for linkage and association, even when the association is caused by population subdivision and admixture. In the previous paper, we did not explicitly consider the effect of recent history on population structure. Here we extend the previous results by examining in detail the effects of subdivision and admixture, viewed as processes in population history. We describe two models for these processes. For both models, we analyze the properties of (a) the TDT as a test for linkage (and association) between marker and disease and (b) the conventional contingency statistic used with family data to test for population association. We show that the contingency test statistic does not have a {chi}{sup 2} distribution if subdivision or admixture is present. In contrast, the TDT remains a valid {chi}{sub 2} statistic for the linkage hypothesis, regardless of population history. 20 refs., 2 figs., 5 tabs.

  2. Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).

    PubMed

    Olson, Matthew S; Robertson, Amanda L; Takebayashi, Naoki; Silim, Salim; Schroeder, William R; Tiffin, Peter

    2010-04-01

    *Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Steady-state 226Ra/ 230Th disequilibrium in mantle minerals: Implications for melt transport rates in island arcs

    NASA Astrophysics Data System (ADS)

    Feineman, Maureen D.; DePaolo, Donald J.

    2003-10-01

    Measurements of the concentrations of the 238U decay series isotopes ( 234U, 230Th, 226Ra) have been used to estimate the rates at which magma is generated and transported in the mantle. The usual assumption is that solid mantle minerals are in radioactive equilibrium prior to melting. However, if one or more of the nuclides in the chain is strongly concentrated by a minor mineral, and if the diffusivity of that nuclide is large enough, steady-state radioactive disequilibrium can result in the solid phase. It can be inferred from available data that radium is strongly concentrated in minor hydroxyl-bearing mantle minerals (phlogopite and amphibole) relative to Th, and Ra diffusion in clinopyroxene is fast relative to the typical grain diameter at ca. 1100°C. Consequently, we show with simple analytical models that a steady-state Ra deficiency in clinopyroxene (cpx), accompanied by a complementary steady-state Ra excess in neighboring phlogopite (phlog) or amphibole (amph), is likely to be the normal situation in hydrous mantle peridotite with average clinopyroxene grain radii of ca. 1 mm. The steady state ( 226Ra/ 230Th) (parentheses indicating activity ratio) in the hydrous mineral is limited roughly by the mass ratio with clinopyroxene (i.e. cpx/phlog or cpx/amph) and could be as high as 10-100. The exceptionally high ( 226Ra/ 230Th) of some island arc lavas could therefore be a result of preferential contribution of phlogopite or amphibole during partial melting of hydrous mantle. This effect may ease time constraints for source-to-surface melt migration at island arcs. Incipient melting of hydrous minerals from channel walls during melt transport and/or late-stage incorporation of phlogopite or amphibole into arc magmas may also contribute to generating high ( 226Ra/ 230Th). Steady-state ( 226Ra/ 230Th) disequilibrium due to diffusive loss of 226Ra from clinopyroxene is also important for melt/solid and fluid/solid partitioning, and must be incorporated into

  9. 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)

  10. 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)

  11. 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)

  12. 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

  13. Likelihood ratio tests for linkage and linkage disequilibrium: Asymptotic distribution and power

    SciTech Connect

    1996-05-01

    Terwilliger proposes an interesting likelihood ratio test for linkage disequilibrium that appears conservative under the null hypothesis and powerful when one of several alleles is positively associated with the disease. We discuss in detail the aspects of linkage disequilibrium with a simpler asymptotic distribution. 3 refs.

  14. Modeling Linkage Disequilibrium in Natural Populations: The Example of the Soay Sheep Population of St. Kilda, Scotland

    PubMed Central

    McRae, Allan F.; Pemberton, Josephine M.; Visscher, Peter M.

    2005-01-01

    The use of linkage disequilibrium to localize the genes underlying quantitative traits has received considerable attention in the livestock genetics community over the past few years. This has resulted in the investigation of linkage disequilibrium structures of several domestic livestock populations to assess their potential use in fine-mapping efforts. However, the linkage disequilibrium structure of free-living populations has been less well investigated. As the direct evaluation of linkage disequilibrium can be both time consuming and expensive the use of simulations that include as many aspects of population history as possible is advocated as an alternative. A simulation of the linkage disequilibrium structure of the Soay sheep population of St. Kilda, Scotland, is provided as an example. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping of quantitative trait loci. PMID:15965254

  15. Linkage disequilibrium in the neurofibromatosis I (NF1) region: Implications for gene mapping

    SciTech Connect

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

    1993-11-01

    To test the usefulness of linkage disequilibrium for gene mapping, the authors compared physical distances and linkage disequilibrium among eight RFLPs in the neutrofibromatosis 1 (NF1) region. Seven of the polymorphisms span most of the NF1 gene, while the remaining polymorphism lies approximately 70 kb 3[prime] 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[sup [minus]7]), even though they are separated by as much as 340 kb. The 3[prime] polymorphism is only 68 kb distal to the next polymorphism, but disequilibrium between the 3[prime] polymorphism and all others is comparatively low ([vert bar]r[vert bar] < .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[prime] to the stop codon could have implications for gene mapping studies. These are discussed, and guidelines for linkage disequilibrium studies are suggested. 80 refs., 2 figs., 5 tabs.

  16. 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.

  17. Radioactivity method.

    USGS Publications Warehouse

    Duval, J.S.

    1980-01-01

    Radioactivity measurements have played an important role in geophysics since about 1935, and they have increased in importance to the present. The most important areas of application have been in petroleum and uranium exploration. Radioactivity measurements have proved useful in geologic mapping, as well as in specialized applications such as reactor-site monitoring. The technological development of the method has reached a plateau, and the future of the method for some applications will depend upon development of more sophisticated data processing and interpretation. -Author

  18. /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.

  19. 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)

  20. 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.

  1. Design and sample-size considerations in the detection of linkage disequilibrium with a disease locus

    SciTech Connect

    Olson, J.M.; Wijsman, E.M.

    1994-09-01

    The presence of linkage disequilibrium between closely linked loci can aid in the fine mapping of disease loci. The authors investigate the power of several designs for sampling individuals with different disease genotypes. As expected, haplotype data provide the greatest power for detecting disequilibrium, but, in the absence of parental information to resolve the phase of double heterozygotes, the most powerful design samples only individuals homozygous at the trait locus. For rare diseases, such a scheme is generally not feasible, and the authors also provide power and sample-size calculations for designs that sample heterozygotes. The results provide information useful in planning disequilibrium studies. 17 refs., 3 figs., 4 tabs.

  2. 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

  3. Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

    PubMed Central

    Gray, Melissa M.; Granka, Julie M.; Bustamante, Carlos D.; Sutter, Nathan B.; Boyko, Adam R.; Zhu, Lan; Ostrander, Elaine A.; Wayne, Robert K.

    2009-01-01

    Assessing the extent of linkage disequilibrium (LD) in natural populations of a nonmodel species has been difficult due to the lack of available genomic markers. However, with advances in genotyping and genome sequencing, genomic characterization of natural populations has become feasible. Using sequence data and SNP genotypes, we measured LD and modeled the demographic history of wild canid populations and domestic dog breeds. In 11 gray wolf populations and one coyote population, we find that the extent of LD as measured by the distance at which r2 = 0.2 extends <10 kb in outbred populations to >1.7 Mb in populations that have experienced significant founder events and bottlenecks. This large range in the extent of LD parallels that observed in 18 dog breeds where the r2 value varies from ∼20 kb to >5 Mb. Furthermore, in modeling demographic history under a composite-likelihood framework, we find that two of five wild canid populations exhibit evidence of a historical population contraction. Five domestic dog breeds display evidence for a minor population contraction during domestication and a more severe contraction during breed formation. Only a 5% reduction in nucleotide diversity was observed as a result of domestication, whereas the loss of nucleotide diversity with breed formation averaged 35%. PMID:19189949

  4. 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

  5. Structural effects of linkage disequilibrium on the transcriptome

    PubMed Central

    Martin, Joshua S.; Halvorsen, Matthew; Davis-Neulander, Lauren; Ritz, Justin; Gopinath, Chetna; Beauregard, Arthur; Laederach, Alain

    2012-01-01

    A majority of SNPs (single nucleotide polymorphisms) map to noncoding and intergenic regions of the genome. Noncoding SNPs are often identified in genome-wide association studies (GWAS) as strongly associated with human disease. Two such disease-associated SNPs in the 5′ UTR of the human FTL (Ferritin Light Chain) gene are predicted to alter the ensemble of structures adopted by the mRNA. High-accuracy single nucleotide resolution chemical mapping reveals that these SNPs result in substantial changes in the structural ensemble in agreement with the computational prediction. Furthermore six rescue mutations are correctly predicted to restore the mRNA to its wild-type ensemble. Our data confirm that the FTL 5′ UTR is a “RiboSNitch,” an RNA that changes structure if a particular disease-associated SNP is present. The structural change observed is analogous to that of a bacterial Riboswitch in that it likely regulates translation. These data further suggest that specific pairs of SNPs in high linkage disequilibrium (LD) will form RNA structure-stabilizing haplotypes (SSHs). We identified 484 SNP pairs that form SSHs in UTRs of the human genome, and in eight of the 10 SSH-containing transcripts, SNP pairs stabilize RNA protein binding sites. The ubiquitous nature of SSHs in the transcriptome suggests that certain haplotypes are conserved to avoid RiboSNitch formation. PMID:22109839

  6. 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.

  7. 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

  8. Accounting for linkage disequilibrium in association analysis of diverse populations.

    PubMed

    Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

    2014-04-01

    The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases.

  9. Extensive linkage disequilibrium in small human populations in Eurasia.

    PubMed

    Kaessmann, Henrik; Zöllner, Sebastian; Gustafsson, Anna C; Wiebe, Victor; Laan, Maris; Lundeberg, Joakim; Uhlén, Mathias; Pääbo, Svante

    2002-03-01

    The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations-Evenki and Saami-and two larger food-producing populations-Finns and Swedes-in northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.

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

    PubMed

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

    2015-11-23

    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.

  11. 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.

  12. Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites.

    PubMed

    Skelly, Daniel A; Magwene, Paul M; Stone, Eric A

    2016-02-01

    Demographic, genetic, or stochastic factors can lead to perfect linkage disequilibrium (LD) between alleles at two loci without respect to the extent of their physical distance, a phenomenon that Lawrence et al. (2005a) refer to as "genetic indistinguishability." This phenomenon can complicate genotype-phenotype association testing by hindering the ability to localize causal alleles, but has not been thoroughly explored from a theoretical perspective or using large, dense whole-genome polymorphism data sets. We derive a simple theoretical model of the prevalence of genetic indistinguishability between unlinked loci and verify its accuracy via simulation. We show that sample size and minor allele frequency are the major determinants of the prevalence of perfect LD between unlinked loci but that demographic factors, such as deviations from random mating, can produce significant effects as well. Finally, we quantify this phenomenon in three model organisms and find thousands of pairs of moderate-frequency ([Formula: see text]) genetically indistinguishable variants in relatively large data sets. These results clarify a previously underexplored population genetic phenomenon with important implications for association studies and define conditions under which it is likely to manifest.

  13. Asymmetric linkage disequilibrium: Tools for assessing multiallelic LD.

    PubMed

    Single, Richard M; Strayer, Nick; Thomson, Glenys; Paunic, Vanja; Albrecht, Mark; Maiers, Martin

    2016-03-01

    Standard measures of linkage disequilibrium (LD) provide an incomplete description of the correlation between two loci. Recently, Thomson and Single (2014) described a new asymmetric pair of LD measures (ALD) that give a more complete description of LD. The ALD measures are symmetric and equivalent to the correlation coefficient r when both loci are bi-allelic. When the numbers of alleles at the two loci differ, the ALD measures capture this asymmetry and provide additional detail about the LD structure. In disease association studies the ALD measures are useful for identifying additional disease genes in a genetic region, by conditioning on known effects. In evolutionary genetic studies ALD measures provide insight into selection acting on individual amino acids of specific genes, or other loci in high LD (see Thomson and Single (2014) for these examples). Here we describe new software for computing and visualizing ALD. We demonstrate the utility of this software using haplotype frequency data from the National Marrow Donor Program (NMDP). This enhances our understanding of LD patterns in the NMDP data by quantifying the degree to which LD is asymmetric and also quantifies this effect for individual alleles.

  14. 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

  15. 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

  16. Does strong linkage disequilibrium guarantee redundant association results?

    PubMed

    Nielsen, Dahlia M; Suchindran, Sunil; Smith, Christopher P

    2008-09-01

    A substantial amount of effort has been expended recently towards the identification and evaluation of tag single nucleotide polymorphisms; markers that, due to linkage disequilibrium (LD) patterns in the genome, are able to act as "proxies" for other polymorphic sites. As such, these tag markers are assumed to capture, on their own, a large proportion of the genetic variation contributed by a much greater number of polymorphic sites. One important consequence of this is the potential ability to reduce the cost of genotyping in an association study without a corresponding loss of power. This application carries an implicit assumption that strong LD between markers implies high correlation between the accompanying association test results, so that once a tag marker is evaluated for association, its outcome will be representative of all the other markers for which it serves as proxy. We examined this assumption directly. We find that in the null hypothesis situation, where there is no association between the markers and the phenotype, the relationship between LD and the correlation between association test outcomes is clear, though it is not always ideal. In the alternative case, when genetic association does exist in the region, the relationship becomes much more complex. Here, reasonably high LD between markers does not necessarily imply that the association test result of one marker is a direct substitute for that of the other. In these cases, eliminating one of these markers from the set to be genotyped in an association study will lead to a reduction in overall power. PMID:18393391

  17. Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

    PubMed Central

    Kolkman, Judith M.; Berry, Simon T.; Leon, Alberto J.; Slabaugh, Mary B.; Tang, Shunxue; Gao, Wenxiang; Shintani, David K.; Burke, John M.; Knapp, Steven J.

    2007-01-01

    Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression−the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (θ = 0.0094) than wild populations (θ = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome (∼3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping. PMID:17660563

  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. 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

  20. Patterns of polymorphism and linkage disequilibrium in cultivated barley

    PubMed Central

    Comadran, Jordi; Ramsay, Luke; MacKenzie, Katrin; Hayes, Patrick; Close, Timothy J.; Muehlbauer, Gary; Stein, Nils

    2010-01-01

    We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the ‘genetic centromeres’. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1466-7) contains supplementary material, which is available to authorized users. PMID:21076812

  1. 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...

  2. A FORTRAN program for the calculation and analysis of two-locus linkage disequilibrium coefficients.

    PubMed

    Black, W C; Krafsur, E S

    1985-08-01

    A FORTRAN program was written that calculates composite linkage disequilibrium coefficients from genotypic data. Chi-square tests determine whether coefficients calculated for allele and locus pairs are significantly greater than zero. A subroutine is provided that partitions the variance in linkage disequilibrium into within- and between-subpopulation components. Output obtained from analysis of allozyme data collected from natural subpopulations of the house fly (Musca domestica L.) are included to illustrate features of the program.

  3. 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.

  4. Disequilibrium patterns of the peptide transporter loci within the HLA class II region

    SciTech Connect

    Klitz, W.; Stephens, C.J.; Carrington, M.

    1994-09-01

    Disequilibrium between genetic markers is expected to decline monotonically with recombinational map distance. We present evidence from the HLA class II region which seems to violate this principle. Pairwise disequilibrium values from a sample of northern Europeans were calculated for six loci ranging in physical separation from 7 kb to 550 kb. The histocompatibility loci DRB1, DQA1 and DQB1 located on the distal end of the class II region behave as a single evolutionary unit within which extremely high linkage disequilibrium exists. Lower but significant levels of disequilibrium are present between these loci and DPB1 located at the proximal edge of the HLA complex. The peptide transporter loci TAP1 and TAP2, located in the intervening region, reveal no disequilibrium with each other and low or negligible disequilibrium with the flanking loci. This evidence suggests either a high rate of gene conversion in the TAP loci which mixes TAP alleles among haplotypes while maintaining the flanking markers, or recombinational hot spots near and between the TAP loci operating in combination with selection to preserve particular combinations of alleles at the flanking histocompatibility loci. Whatever explanation proves correct, this work demonstrates that the lack of association of TAP alleles with a DR-DQ associated disease cannot be used as evidence for a centromeric boundary of influence on that disease.

  5. Demographic history and linkage disequilibrium in human populations.

    PubMed

    Laan, M; Pääbo, S

    1997-12-01

    In the human genome, linkage disequilibrium (LD)--the non-random association of alleles at chromosomal loci--has been studied mainly in regions surrounding disease genes on affected chromosomes. Consequently, little information is available on the distribution of LD across anonymous genomic regions in the general population. However, demographic history is expected to influence the extent of overall LD across the genome, so a population that has been of constant size will display higher levels of LD than a population that has expanded. In support of this, the extent of LD between anonymous loci on chromosome 4 in chimpanzees (as a model of a population of constant size) has been compared to that in Finns (as a model of an expanded population; refs 8,9) and found to exhibit more LD than in the latter population. In Europe, studies of mitochondrial (mt) DNA sequences have suggested that most populations have experienced expansion, whereas the Saami in northern Fenno-Scandinavia have been of constant size (Table 1). Thus, in northern Europe, populations with radically different demographic histories live in close geographic proximity to each other. We studied the allelic associations between anonymous microsatellite loci on the X chromosome in the Saami and neighbouring populations and found dramatically higher levels of LD in the Saami than in other populations in the region. This indicates that whereas recently expanded populations, such as the Finns, are well suited to map single disease genes affected by recent mutations, populations that have been of constant size, such as the Saami, may be much better suited to map genes for complex traits that are caused by older mutations.

  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. Magma Chamber Dynamics Recorded by Mineral Disequilibrium. Evidences and Questions.

    NASA Astrophysics Data System (ADS)

    Wagner, C.; Deloule, E.

    2004-05-01

    Clinopyroxenes (cpx) are one of the phases commonly used for tracing shallow-level processes in magma reservoirs. They are likely phases to constrain and record the magmatic evolution, as they are liquidus phases over a wide range of temperature and composition, and incorporate trace elements in sufficient amounts to be analysed. We discuss here the potentiality and limits for reconstructing magma chamber dynamics from a study of disequilibrium cpx assemblages from alkaline rocks from North Morocco. Cpx are Al-rich diopside and salite enriched in incompatible elements. Salite and diopside occur indifferently as resorbed cores or rims, and their respective composition is identical in both cases. The Al distribution between octahedral and tetrahedral sites shows that cores and rims follow a trend of low-pressure origin. This supports shallow-level crystallization for all cpx, including the cores, which then do not represent xenocrysts extracted from the wall-rock during ascent. The heterogeneous cpx population may result from : 1) a thermally and compositionally zoned reservoir in which salite crystallized from the mush layer (T = 950oC) and diopside from the main magma body (T = 1150oC). Residence times of 1 to 15 years have been estimated for cores and rims respectively, constraining the movement of the cpx in and out of the mush layer. 2) mixing processes: as both diopside and salite cores are present, mixing must have occurred subsequent the crystallization of both types of cpx in their respective magmas. Oscillatory zoning of diopsidic and salitic compositions suggests repeated mixing episodes (up to four cycles of crystallization interrupted by episodes of mixing between more or less evolved melts). Different scenarii will be proposed. Particularly, we discuss the importance of crystal-chemical controls (crystal lattice model) and liquid composition/structure on partitioning of some elements (HFSE, REE, Sr) between cpx and melt for using with confidence the cpx

  8. 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

  9. Short-lived radioactivity and magma genesis

    NASA Astrophysics Data System (ADS)

    Gill, James; Condomines, Michel

    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 U-238, Th-230, and Ra-226 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.

  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. Extreme landscape disequilibrium and slow erosion during rapid mountain building

    NASA Astrophysics Data System (ADS)

    Ouimet, W. B.; Byrne, T. B.; Huang, C.; Bierman, P. R.; Lee, Y. H.; Hsu, W. H.; Hsieh, M. L.; Van Soest, M. C.

    2015-12-01

    In this study, we examine topography and erosion in Taiwan, where high rates of tectonic convergence, easily erodible bedrock, and a highly erosive climate have produced some of the steepest landscapes and highest erosion rates in the world. Through a combined analysis of topography throughout the Central Range and cosmogenic radionulcide 10Be erosion rates measured in quartz purified from river sediment, we show that Taiwan preserves broad (up to 10-20 km2) areas of anomalous, low slope, low relief terrain and exhibits a wide range of short-term (103-104 yr) 10Be erosion rates (0.1 to ~10 mm/yr) within topography that has been exhuming at 3-5 mm/yr for at least the past 1.5 Ma. The extreme landscape disequilibrium observed in Taiwan highlights the variation in erosion and morphology that mountain belts can exhibit despite strong tectonic forcing and a highly erosive climate. The wide range in cosmogenic erosion rates observed in Taiwan is a direct consequence of the presence of low slope, low relief topography within a rapid uplifting and exhuming orogen. Low relief, slowly eroding areas are consistently found at high elevations near the main topographic divide of the Central Range and in the upstream headwaters where it is more likely to preserve relict topography. Their existence in combination with constant, rapid background exhumation suggest that Taiwan has seen large scale shifts in mean elevation over the last 2 Ma, a conclusion that challenges classic notion of orogeny evolution in Taiwan, the archetype example of arc-continent collision and rapid mountain around the world. Conversely, because Taiwan exhibits rapid rock uplift, frequent landslides and high rates of erosion, it may be the type landscape where dynamic landscape process of river capture and in situ formation of low relief landscape allow for the highest range of millennial scale erosion rates anywhere in the world. Either way, this study highlights that spatial variation erosion rate and

  12. Linkage disequilibrium reveals different demographic history in egg laying chickens

    PubMed Central

    2010-01-01

    Background The availability of larger-scale SNP data sets in the chicken genome allows to achieve a higher resolution of the pattern of linkage disequilibrium (LD). In this study, 36 k and 57 k genotypes from two independent genotyping chips were used to systematically characterize genome-wide extent and structure of LD in the genome of four chicken populations. In total, we analyzed genotypes of 454 animals from two commercial and two experimental populations of white and brown layers which allows to some extent a generalization of the results. Results The number of usable SNPs in this study was 19 k to 37 k in brown layers and 8 k to 19 k in white layers. Our analyzes showed a large difference of LD between the lines of white and brown layers. A mean value of r2 = 0.73 ± 0.36 was observed in pair-wise distances of < 25 Kb for commercial white layers, and it dropped to 0.60 ± 0.38 with distances of 75 to 120 Kb, the interval which includes the average inter-marker space in this line. In contrast, an overall mean value of r2= 0.32 ± 0.33 was observed for SNPs less than 25 Kb apart from each other and dropped to 0.21 ± 0.26 at a distance of 100 kb in commercial brown layers. There was a remarkable similarity of the LD patterns among the two populations of white layers. The same was true for the two populations of brown layers, while the LD pattern between white and brown layers was clearly different. Inferring the population demographic history from LD data resulted in a larger effective population size in brown than white populations, reflecting less inbreeding among brown compared to white egg layers. Conclusions We report comprehensive LD map statistics for the genome of egg laying chickens with an up to 3 times higher resolution compared to the maps available so far. The results were found to be consistent between analyzes based on the parallel SNP chips and across different populations (commercial vs. experimental) within the brown and the white layers. It

  13. Discordant patterns of linkage disequilibrium of the peptide-transporter loci within the HLA class II region

    SciTech Connect

    Klitz, W.; Grote, M.; Stephens, J.C.

    1995-12-01

    Disequilibrium between genetic markers is expected to decline monotonically with recombinational map distance. We present evidence from the HLA class II region that seems to violate this principle. Pairwise disequilibrium values were calculated for six loci ranging in physical separation from 15 kb to 550 kb. The histocompatibility loci DRB1, DQA1, and DQBI, located on the distal end of the class II region, behave as a single evolutionary unit within which extremely high linkage disequilibrium exists. Lower but still significant levels of disequilibrium are present between these loci and DPB1, located at the proximal edge of the HLA complex. The peptide-transporter loci TAP1 and TAP2, located in the intervening region, reveal no disequilibrium with each other and low or negligible disequilibrium with the flanking loci. The action of two genetic processes is required to account for this phenomenon: a recombinational hotspot operating between TAP1 and TAP2, to eliminate disequilibrium between these loci, and at the same time selection operating on particular combinations of alleles across the DR-DP region, to create disequilibrium in the favored haplotypes. The forces producing the patterns of disequilibrium observed here have implications for the mapping of trait loci and disease genes: markers of TAP1, for example, would give a false impression as to the influence of DPB1 on a trait known to be associated with DQB1. 44 refs., 2 figs., 3 tabs.

  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. A Novel Diagnosis of Chemical Disequilibrium in Extrasolar Planet and Substellar Object Atmospheres

    NASA Astrophysics Data System (ADS)

    Line, Michael R.; Yung, Y. L.

    2013-10-01

    With recent advancements in spectroscopic capabilities, characterization of the temperatures and compositions of extra-solar planets is becoming more prevalent. One outstanding issue one can address with temperature and abundance determinations is the role that disequilibrium plays in sculpting the atmospheric compositions. A variety of disequilibrium models now exist in the literature to explore various planets and the effects that photochemistry and vertical mixing have on the molecular abundances. In this investigation we introduce a novel approach to diagnosing disequilibrium without the need of sophisticated photochemical/kinetics models. In short, we define an “equilibrium” line as a function of a representative planet temperature. If we can determine the abundances of H2O, CH4, CO, and H2, we can evaluate a simple analytic formula to quickly assess whether or not the atmospheric composition is in disequilibrium. We verify the usefulness of this approach with state-of-the-art chemistry-transport models and find that, as expected, cooler planets tend to show the strongest signs of disequilibrium.

  16. 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.

  17. Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis.

    PubMed

    Marsden, Clare Diana; Lee, Yoosook; Kreppel, Katharina; Weakley, Allison; Cornel, Anthony; Ferguson, Heather M; Eskin, Eleazar; Lanzaro, Gregory C

    2014-01-10

    Association mapping is a widely applied method for elucidating the genetic basis of phenotypic traits. However, factors such as linkage disequilibrium and levels of genetic diversity influence the power and resolution of this approach. Moreover, the presence of population subdivision among samples can result in spurious associations if not accounted for. As such, it is useful to have a detailed understanding of these factors before conducting association mapping experiments. Here we conducted whole-genome sequencing on 24 specimens of the malaria mosquito vector, Anopheles arabiensis, to further understanding of patterns of genetic diversity, population subdivision and linkage disequilibrium in this species. We found high levels of genetic diversity within the An. arabiensis genome, with ~800,000 high-confidence, single- nucleotide polymorphisms detected. However, levels of nucleotide diversity varied significantly both within and between chromosomes. We observed lower diversity on the X chromosome, within some inversions, and near centromeres. Population structure was absent at the local scale (Kilombero Valley, Tanzania) but detected between distant populations (Cameroon vs. Tanzania) where differentiation was largely restricted to certain autosomal chromosomal inversions such as 2Rb. Overall, linkage disequilibrium within An. arabiensis decayed very rapidly (within 200 bp) across all chromosomes. However, elevated linkage disequilibrium was observed within some inversions, suggesting that recombination is reduced in those regions. The overall low levels of linkage disequilibrium suggests that association studies in this taxon will be very challenging for all but variants of large effect, and will require large sample sizes.

  18. 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

  19. 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

  20. Linkage disequilibrium between the ELA and the A blood group systems in Standardbred horses.

    PubMed

    Bailey, E

    1983-01-01

    The linkage group formed by the ELA and A blood group system in horses was studied in American Standardbred horses. The distance between the ELA locus and the A blood group locus was measured as 1.61 centimorgans, observing only the haplotypes contributed by the sires. Strong linkage disequilibrium was found in pacing Standardbred horses for ELA-W1 with Aa, ELA-W5 with Ab and ELA-W10 with Ab. Linkage disequilibrium was apparent at both the population and family level. Among trotting Standardbred horses, linkage disequilibrium was found for ELA-W1 with Aa and for ELA-W10 with Ab. It was not possible to investigate linkage relationships in Thoroughbred horses because of the high frequency of Aa and low frequency of other A system markers.

  1. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data.

    PubMed

    Maruki, Takahiro; Lynch, Michael

    2014-08-01

    Rapidly improving sequencing technologies provide unprecedented opportunities for analyzing genome-wide patterns of polymorphisms. In particular, they have great potential for linkage-disequilibrium analyses on both global and local genetic scales, which will substantially improve our ability to derive evolutionary inferences. However, there are some difficulties with analyzing high-throughput sequencing data, including high error rates associated with base reads and complications from the random sampling of sequenced chromosomes in diploid organisms. To overcome these difficulties, we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations indicate that the estimator is nearly unbiased with a sampling variance at high coverage asymptotically approaching the value expected when all relevant information is accurately estimated. The estimator does not require phasing of haplotypes and enables the estimation of linkage disequilibrium even when all individual reads cover just single polymorphic sites.

  2. 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.

  3. A linkage disequilibrium-based approach to selecting disease-associated rare variants.

    PubMed

    Talluri, Rajesh; Shete, Sanjay

    2013-01-01

    Rare variants have increasingly been cited as major contributors in the disease etiology of several complex disorders. Recently, several approaches have been proposed for analyzing the association of rare variants with disease. These approaches include collapsing rare variants, summing rare variant test statistics within a particular locus to improve power, and selecting a subset of rare variants for association testing, e.g., the step-up approach. We found that (a) if the variants being pooled are in linkage disequilibrium, the standard step-up method of selecting the best subset of variants results in loss of power compared to a model that pools all rare variants and (b) if the variants are in linkage equilibrium, performing a subset selection using step-based selection methods results in a gain of power of association compared to a model that pools all rare variants. Therefore, we propose an approach to selecting the best subset of variants to include in the model that is based on the linkage disequilibrium pattern among the rare variants. The proposed linkage disequilibrium-based variant selection model is flexible and borrows strength from the model that pools all rare variants when the rare variants are in linkage disequilibrium and from step-based selection methods when the variants are in linkage equilibrium. We performed simulations under three different realistic scenarios based on: (1) the HapMap3 dataset of the DRD2 gene, and CHRNA3/A5/B4 gene cluster (2) the block structure of linkage disequilibrium, and (3) linkage equilibrium. We proposed a permutation-based approach to control the type 1 error rate. The power comparisons after controlling the type 1 error show that the proposed linkage disequilibrium-based subset selection approach is an attractive alternative method for subset selection of rare variants.

  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. Radioactive decay.

    PubMed

    Groch, M W

    1998-01-01

    When a parent radionuclide decays to its daughter radionuclide by means of alpha, beta, or isomeric transition, the decay follows an exponential form, which is characterized by the decay constant lambda. The decay constant represents the probability per unit time that a single radioatom will decay. The decay equation can be used to provide a useful expression for radionuclide decay, the half-life, the time when 50% of the radioatoms present will have decayed. Radiotracer half-life has direct implications in nuclear imaging, radiation therapy, and radiation safety because radionuclide half-life affects the ability to evaluate tracer kinetics and create appropriate nuclear images and also affects organ, tumor, and whole-body radiation dose. The number of radioatoms present in a sample is equal to the activity, defined as the number of transitions per unit time, divided by the decay constant; the mass of radioatoms present in a sample can be calculated to determine the specific activity (activity per unit mass). The dynamic relationship between the number of parent and daughter atoms present over time may lead to radioactive equilibrium, which takes two forms--secular and transient--and has direct relevance to generator-produced radionuclides.

  6. 230Th- 238U disequilibrium systematics in oceanic tholeiites from 21°N on the East Pacific Rise

    NASA Astrophysics Data System (ADS)

    Newman, S.; Finkel, R. C.; MacDougall, J. D.

    1983-10-01

    Significant disequilibrium occurs between 230Th and its parent, 238U, in a suite of fresh basalt glasses from the RISE Project study area at 21°N on the East Pacific Rise. The ( 230Th/ 232Th) activity ratios observed for eight of nine samples from the crest of the axis at this site are constant within analytical uncertainty, with a value of 1.22. This observed homogeneity of ( 230Th/ 232Th) has two possible interpretations. First, the measured ( 230Th/ 232Th) can be considered to indicate a mantle-source for the RISE basalts with Th/U of 2.5. This interpretation, however, conflicts with the proposed correlation between ( 230Th/ 232Th) and 87Sr/ 86Sr [1] which predicts that ( 230Th/ 232Th) should equal 1.33 at the RISE site. A second possible interpretation is that radioactive decay of 230Th, in the basalts themselves or in a magma chamber, has decreased ( 230Th/ 232Th) from 1.33 to the observed values. The required time span is 11,000 to > 100,000 years. However, petrologic arguments rule against long residence time in a magma chamber, and the spreading rate of this section of the East Pacific Rise (6 cm/yr) predicts that the maximum age for axis basalts is 27,000 years. Both interpretations of the measured ( 230Th/ 232Th) imply a low Th/U ratio for the RISE basalt source and suggest that the MORB source at this location is depleted in Th with respect to U relative to primitive mantle or bulk earth. In spite of their constant ( 230Th/ 232Th), the basalts from 21°N have wide ranges of measured Th/U and thorium and uranium concentrations, in apparent conflict with the common assumption that these two elements have very small, similar crystal-liquid partition coefficients. Participation of an accessory phase with high Th and U concentrations during partial melting or fractional crystallization appears to be required to explain this anomaly. Major and other trace element compositions provide more information about petrogenetic processes. Although fractional

  7. Specification and estimation of multi-market disequilibrium model: An application to the US auto and gasoline markets

    SciTech Connect

    Mustafa, M.

    1988-01-01

    This dissertation presents a tractable estimation procedures for a multi-market disequilibrium model and applies to the US automobile and gasoline markets. The model of the two interrelated markets is a desegregated disequilibrium model that has a system of interrelated demand equations in one market. This is the first specification in either the theoretical and empirical literature of multi-market disequilibrium with lagged endogenous variables. Using the minimum-distance method, it is possible to estimate far richer models than is computationally feasible with maximum likelihood. The estimated model reveals a spill-over effect from gasoline market disequilibrium into automobile market: the evidence of a spill-over from the automobile into the gasoline market is weaker. When a disequilibrium framework is used, the estimates of elasticities in automobile and gasoline markets are more efficient and are significantly different from the estimates obtained from an equilibrium model.

  8. 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 ...

  9. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

    PubMed

    Slavov, Gancho T; DiFazio, Stephen P; Martin, Joel; Schackwitz, Wendy; Muchero, Wellington; Rodgers-Melnick, Eli; Lipphardt, Mindie F; Pennacchio, Christa P; Hellsten, Uffe; Pennacchio, Len A; Gunter, Lee E; Ranjan, Priya; Vining, Kelly; Pomraning, Kyle R; Wilhelm, Larry J; Pellegrini, Matteo; Mockler, Todd C; Freitag, Michael; Geraldes, Armando; El-Kassaby, Yousry A; Mansfield, Shawn D; Cronk, Quentin C B; Douglas, Carl J; Strauss, Steven H; Rokhsar, Dan; Tuskan, Gerald A

    2012-11-01

    • Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed. PMID:22861491

  10. 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...

  11. 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…

  12. 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...

  13. A comparison of linkage disequilibrium measures for fine-scale mapping

    SciTech Connect

    Devlin, B.; Risch, N.

    1995-09-20

    Linkage mapping generally localizes disease genes to 1-to 2-cM regions of chromosome. In theory, further refinement of location can be achieved by population-based studies of linkage diequilibrium between disease locus alleles at adjacent markers. One approach to localization, dubbed simple disequilibrium mapping, is to determine the relative location of the disease locus by plotting disequilibrium values against marker locations. We investigate the simple mapping properties of five disequilibrium measures, the correlation coefficient {Delta}, Lewontin`s D`, the robust formulation of the population attribute risk {delta}, Yule`s Q, and Kaplan and Weir`s proportional difference d under the assumption of initial complete disequilibrium between disease and marker loci. The studies indicate that {delta} is a superior measure for fine mapping because it is directly related to the recombination fraction between the disease and the marker sampled at a rate higher than their population frequencies, as in a case-control study. D` yields results of comparable to those of {delta} in many realistic settings. Of the remaining three measures, Q,{Delta}, and d, Q yields the best results. From simulations of short-term evolution, all measures show some sensitivity to marker allele frequencies; however, as predicted by analytic results, Q, {Delta}, and d exhibit the greatest sensitivity to variation in marker allele frequencies across loci. 56 refs., 1 fig., 6 tabs.

  14. 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...

  15. Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

    SciTech Connect

    Purandare, S.M.; Viskochil, D.H.; Cawthon, R.

    1996-07-01

    Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

  16. Linkage disequilibrium among RFLPs at the insulin-receptor locus despite intervening alu repeat sequences

    SciTech Connect

    Elbein, S.C. )

    1992-11-01

    Multiple mutations of the insulin receptor (INSR) gene have been identified in individuals with extreme insulin resistance. These mutations have included recombination events between Alu repeat units in the tyrosine kinase-encoding [beta]-chain region of the gene. To evaluate the influence of Alu and dinucleotide repetitive sequences on recombination events within the insulin receptor gene, the author examined the degree of linkage disequilibrium between RFLP pairs spanning the gene. The author established 228 independent haplotypes for seven RFLPs (two each for PstI, RsaI, and SstI and one for MspI and 172 independent haplotypes which included an additional RFLP with BglII) from 19 pedigrees. These RFLPs span >130 kb of this gene, and it was previously demonstrated that multiple Alu sequences separate RFLP pairs. Observed haplotype frequencies deviated significantly from those predicted. Pairwise analysis of RFLP showed high levels of linkage disequilibrium among RFLP in the [beta]-chain region of the insulin receptor, but not between [alpha]-chain RFLPs and those of the [beta]-chain. Disequilibrium was present among [beta]-chain RFLPs, despite separation by one or more Alu repeat sequences. The very strong linkage disequilibrium which was present in sizable regions of the INSR gene despite the presence of both Alu and microsatellite repeats suggested that these regions do not have a major impact on recombinations at this locus. 25 refs., 1 fig., 5 tabs.

  17. 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.

  18. 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…

  19. Conditional asymmetric linkage disequilibrium (ALD): extending the biallelic r2 measure.

    PubMed

    Thomson, Glenys; Single, Richard M

    2014-09-01

    For multiallelic loci, standard measures of linkage disequilibrium provide an incomplete description of the correlation of variation at two loci, especially when there are different numbers of alleles at the two loci. We have developed a complementary pair of conditional asymmetric linkage disequilibrium (ALD) measures. Since these measures do not assume symmetry, they more accurately describe the correlation between two loci and can identify heterogeneity in genetic variation not captured by other symmetric measures. For biallelic loci the ALD are symmetric and equivalent to the correlation coefficient r. The ALD measures are particularly relevant for disease-association studies to identify cases in which an analysis can be stratified by one of more loci. A stratified analysis can aid in detecting primary disease-predisposing genes and additional disease genes in a genetic region. The ALD measures are also informative for detecting selection acting independently on loci in high linkage disequilibrium or on specific amino acids within genes. For SNP data, the ALD statistics provide a measure of linkage disequilibrium on the same scale for comparisons among SNPs, among SNPs and more polymorphic loci, among haplotype blocks of SNPs, and for fine mapping of disease genes. The ALD measures, combined with haplotype-specific homozygosity, will be increasingly useful as next-generation sequencing methods identify additional allelic variation throughout the genome.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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 ...

  5. 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

  6. 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.

  7. 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.

  8. Polymorphic L1 retrotransposons are frequently in strong linkage disequilibrium with neighboring SNPs.

    PubMed

    Higashino, Saneyuki; Ohno, Tomoyuki; Ishiguro, Koichi; Aizawa, Yasunori

    2014-05-10

    L1 retrotransposons have been the major driver of structural variation of the human genome. L1 insertion polymorphism (LIP)-mediated genomic variation can alter the transcriptome and contribute to the divergence of human phenotypes. To assess this possibility, a genome-wide association study (GWAS) including LIPs is required. Toward this ultimate goal, the present study examined linkage disequilibrium between six LIPs and their neighboring single nucleotide polymorphisms (SNPs). Genomic PCR and sequencing of L1-plus and -minus alleles from different donors revealed that all six LIPs were in strong linkage disequilibrium with at least one SNP. In addition, comparison of syntenic regions containing the identified SNP nucleotides was performed among modern humans (L1-plus and -minus alleles), archaic humans and non-human primates, revealing two different evolutionary schemes that might have resulted in the observed strong SNP-LIP linkage disequilibria. This study provides an experimental framework and guidance for a future SNP-LIP integrative GWAS.

  9. On an extended interpretation of linkage disequilibrium in genetic case-control association studies.

    PubMed

    Dickhaus, Thorsten; Stange, Jens; Demirhan, Haydar

    2015-11-01

    We are concerned with statistical inference for 2 × C × K contingency tables in the context of genetic case-control association studies. Multivariate methods based on asymptotic Gaussianity of vectors of test statistics require information about the asymptotic correlation structure among these test statistics under the global null hypothesis. In the case of C=2, we show that for a wide variety of test statistics this asymptotic correlation structure is given by the standardized linkage disequilibrium matrix of the K loci under investigation. Three popular choices of test statistics are discussed for illustration. In the case of C=3, the standardized composite linkage disequilibrium matrix is the limiting correlation matrix of the K locus-specific Cochran-Armitage trend test statistics.

  10. Mendelian inheritance, genetic linkage, and genotypic disequilibrium at microsatellite loci in Genipa americana L. (Rubiaceae).

    PubMed

    Manoel, R O; Freitas, M L M; Tambarussi, E V; Cambuim, J; Moraes, M L T; Sebbenn, A M

    2015-07-27

    Genipa americana is a tropical tree species that is widely distributed in the humid tropical and subtropical regions of Central and South America. This study investigated Mendelian inheritance, genetic linkage, and genotypic disequilibrium at six microsatellite loci developed for G. americana. Adult trees (188) and regenerants (163) were sampled and genotyped in a fragmented population of the species. We also genotyped open-pollinated seeds from 12 seed-trees during reproductive events in 2010 and 2011. Significant deviations from the expected 1:1 Mendelian segregation were detected in 29.5% of the tests. Significant genetic linkage between pairwise loci was detected in 54.4% of the tests, but no genotypic disequilibrium was detected between pairwise loci for adult trees and regenerants. Overall, the results indicate that the six loci analyzed may be used in studies of G. americana's genetic diversity and structure, its mating system, and in parentage analyses.

  11. Significance of linkage disequilibrium between the fragile X locus and its flanking markers

    SciTech Connect

    Chiurazzi, P.; Neri, G.; Macpherson, J.

    1996-07-12

    The identification of several microsatellite markers flanking the FRAXA locus was instrumental in the positional cloning of the FMR1 gene. These markers can still be valuable in family studies, e.g., as additional evidence in prenatal diagnosis. Additionally, they were employed to verify the presence of any significant gametic disequilibrium between the fragile X mutation and some haplotypes, although the high mutation rate predicted from early segregation studies implied that new mutants would arise on almost every chromosomal background. Thus, the discovery of linkage disequilibrium encompassing the fragile X locus has been surprising. Here, we review the available evidence of such gametic association and underline its implications for the mutational mechanism. 50 refs., 1 fig., 2 tabs.

  12. Linkage disequilibrium in Huntington's disease: an improved localisation for the gene.

    PubMed

    Snell, R G; Lazarou, L P; Youngman, S; Quarrell, O W; Wasmuth, J J; Shaw, D J; Harper, P S

    1989-11-01

    The search for the Huntington's disease gene has recently concentrated on the telomere of the short arm of chromosome 4. The evidence suggesting this position has been based on single crossover events, but there is conflicting evidence regarding the position of the gene relative to the most terminal markers. We have found significant linkage disequilibrium between the markers D4S98 (probe BS731B-C) and D4S95 (probe BS674E-D) and HD, which supports a localisation for the gene proximal to D4S90 and makes a telomeric localisation unlikely. This disequilibrium may also prove to be important in the future in allowing modification of risk estimates based on genetic linkage.

  13. Mendelian inheritance, genetic linkage, and genotypic disequilibrium at microsatellite loci in Genipa americana L. (Rubiaceae).

    PubMed

    Manoel, R O; Freitas, M L M; Tambarussi, E V; Cambuim, J; Moraes, M L T; Sebbenn, A M

    2015-01-01

    Genipa americana is a tropical tree species that is widely distributed in the humid tropical and subtropical regions of Central and South America. This study investigated Mendelian inheritance, genetic linkage, and genotypic disequilibrium at six microsatellite loci developed for G. americana. Adult trees (188) and regenerants (163) were sampled and genotyped in a fragmented population of the species. We also genotyped open-pollinated seeds from 12 seed-trees during reproductive events in 2010 and 2011. Significant deviations from the expected 1:1 Mendelian segregation were detected in 29.5% of the tests. Significant genetic linkage between pairwise loci was detected in 54.4% of the tests, but no genotypic disequilibrium was detected between pairwise loci for adult trees and regenerants. Overall, the results indicate that the six loci analyzed may be used in studies of G. americana's genetic diversity and structure, its mating system, and in parentage analyses. PMID:26345742

  14. Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.

    PubMed

    Jacobs, Guy S; Sluckin, Tim J; Kivisild, Toomas

    2016-08-01

    During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's [Formula: see text] and [Formula: see text]) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly's [Formula: see text] offers high power, but is outperformed by a novel statistic that we test, which we call [Formula: see text] We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics-[Formula: see text] Kelly's [Formula: see text] and [Formula: see text]-are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While [Formula: see text] replicates most candidates when recombination map data are not available, the [Formula: see text] and [Formula: see text] statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available. PMID:27516617

  15. Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.

    PubMed

    Jacobs, Guy S; Sluckin, Tim J; Kivisild, Toomas

    2016-08-01

    During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's [Formula: see text] and [Formula: see text]) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly's [Formula: see text] offers high power, but is outperformed by a novel statistic that we test, which we call [Formula: see text] We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics-[Formula: see text] Kelly's [Formula: see text] and [Formula: see text]-are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While [Formula: see text] replicates most candidates when recombination map data are not available, the [Formula: see text] and [Formula: see text] statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available.

  16. Haplotype analysis finds linkage disequilibrium in the IL-12 gene in patients with HCV.

    PubMed

    Houldsworth, Annwyne; Metzner, Magdalena; Hodgkinson, Andrea; Shaw, Steve; Kaminski, Edward; Demaine, Andy G; Cramp, Matthew E

    2015-07-01

    HCV is a major cause of liver disease worldwide. IL-12 plays an essential role in the balance of T helper 1 (Th1) differentiation versus a T helper 2 (Th2) driven response from its naïve precursor. Linkage disequilibrium measures the degree to which alleles at two loci are associated and the non-random associations between alleles at two loci. Haplotypes of the three IL-12B loci studied were determined in the patient cases and the normal healthy control subjects. The frequency of the 12 possible IL-12B haplotypes on the 3 loci was determined in subjects heterozygous at only one of the loci within the studied haplotype. Haplotype frequencies were compared between the patient groups and controls (n = 49) to determine if any preferential combination of markers occurred using chi-squared and applying the Bonferroni correction. 45 HCV RNA negative patients; 88 HCV RNA positive patients; and 15 uninfected cases at high risk of HCV infection (EU) were studied. The haplotype "C" SNP of the 3'UTR with the "E" 4 bp deletion of the intron 4 region was in linkage disequilibrium (χ(2)  = 45.15, P < 0.001, 95% CL). The haplotype analysis of the insertion allele of the promoter with the deletion allele of the intron 4("E") IL-12B polymorphism showed linkage disequilibrium (χ(2)  = 5.64, P = 0.02). Linkage disequilibrium of polymorphisms is reported in the IL-12 gene in patients with HCV infection and contributes to the understanding of patient genotype and expected production of IL-12, responding to infection.

  17. 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

  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. 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.

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

    PubMed

    Chen, Yongsheng; Blanco, Michael; Ji, Qing; Frei, Ursula Karoline; Lübberstedt, Thomas

    2014-05-01

    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 this locus between exotic populations sampled within the Germplasm Enhancement of Maize (GEM) project and 70 inbred lines. In total, we investigated 55 exotic COMT alleles and discovered more than 400 polymorphisms in a 2.2 kb region with pairwise nucleotide diversity (π) up to 0.017, much higher than reported π values of various genes in inbred lines. The ratio of non-synonymous to synonymous SNPs was 3:1 in exotic populations, and significantly higher than the 1:1 ratio for inbred lines. Selection tests detected selection signature in this gene in both pools, but with different evolution patterns. The linkage disequilibrium decay in exotic populations was at least four times more rapid than for inbred lines with r²>0.1 persisting only up to 100 bp. In conclusion, the alleles sampled in the GEM Project offer a valuable genetic resource to broaden genetic variation for the COMT gene, and likely other genes, in inbred background. Moreover, the low linkage disequilibrium makes this material suitable for high resolution association analyses.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Comparisons between radioactive and non-radioactive gas lantern mantles.

    PubMed

    Furuta, E; Yoshizawa, Y; Aburai, T

    2000-12-01

    Gas lantern mantles containing radioactive thorium have been used for more than 100 years. Although thorium was once believed to be indispensable for giving a bright light, non-radioactive mantles are now available. From the radioactivities of the daughter nuclides, we estimated the levels of radioactivity of 232Th and 228Th in 11 mantles. The mantles contained various levels of radioactivity from background levels to 1410 +/- 140 Bq. Our finding that radioactive and non-radioactive mantles are equally bright suggests that there is no advantage in using radioactive mantles. A remaining problem is that gas lantern mantles are sold without any information about radioactivity.

  6. Radioactive Waste Management Basis

    SciTech Connect

    Perkins, B K

    2009-06-03

    The purpose of this Radioactive Waste Management Basis is to describe the systematic approach for planning, executing, and evaluating the management of radioactive waste at LLNL. The implementation of this document will ensure that waste management activities at LLNL are conducted in compliance with the requirements of DOE Order 435.1, Radioactive Waste Management, and the Implementation Guide for DOE Manual 435.1-1, Radioactive Waste Management Manual. Technical justification is provided where methods for meeting the requirements of DOE Order 435.1 deviate from the DOE Manual 435.1-1 and Implementation Guide.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

    SciTech Connect

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

    1994-10-01

    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 {ge}.3 between admixed parent populations) to produce an efficient approach (>95% ascertainment) for locating genes not easily tracked in human pedigrees. 321 refs., 8 figs., 7 tabs.

  13. Constraints on melt movement beneath the East Pacific Rise from 230Th-238U disequilibrium.

    PubMed

    Zou, Haibo; Zindler, Alan; Niu, Yaoling

    2002-01-01

    We report 230Th-238U disequilibrium data on mid-ocean ridge basalts recovered 5 to 40 kilometers off the ridge axis near 9 degrees 30'N of the East Pacific Rise. These data indicate near-symmetrical eruptions of normal mid-ocean ridge basalts (NMORBs) and incompatible element-enriched mid-ocean ridge basalts (EMORBs) as far as 20 kilometers off axis. Our results suggest large-scale subsurface lateral transport of NMORB melt at 19 to 21 centimeters per year and also provide constraints on the petrogenesis of EMORBs of off-axis origin.

  14. [Electro-encephalographic study of the disequilibrium syndrome during bicarbonate dialysis and acetate dialysis].

    PubMed

    Hampl, H; Klopp, H W; Michels, N; Mahiout, A; Schilling, H; Wolfgruber, M; Schiller, R; Hanefeld, F; Kessel, M

    1983-01-01

    Continuous long-time electroencephalographic (EEG) monitoring was performed during AHD and BHD in 20 patients. Persisting normal basic activity of the EEG without neurological symptoms could be found only during the course of BHD. However, in AHD, during the decrease of arterial CO2 tension (PaCO2) we registered EEG disturbances with moderate to severe slowing down, dysrythmic activity and high voltage discharges. The decrease in PaCO2 and the deterioration in EEG activity in the patients during AHD was concomitant with severe neurological alterations, e.g. the typical symptoms of so-called "disequilibrium" causing a cessation of dialysis in 3 patients.

  15. Electroencephalogram investigations of the disequilibrium syndrome during bicarbonate and acetate dialysis.

    PubMed

    Hampl, H; Klopp, H W; Michels, N; Mahiout, A; Schilling, H; Wolfgruber, M; Schiller, R; Hanefeld, F; Kessel, M

    1983-01-01

    Continuous long-time electroencephalographic (EEG) monitoring was performed during acetate and bicarbonate dialysis in 20 patients. Persisting normal basic activity of the EEG without neurological symptoms was found only during the course of bicarbonate dialysis. However, in acetate dialysis, during the decrease of arterial CO2 tension (PaCO2), we registered EEG disturbances with moderate to severe slowing, dysrhythmic activity and high voltage discharges. The decrease in PaCO2 and the deterioration in EEG activity in the patients during acetate dialysis was concomitant with severe neurological alterations, e.g. the typical symptoms of so-called 'disequilibrium' causing a cessation of dialysis in three patients.

  16. Prediction of multi-locus inbreeding coefficients and relation to linkage disequilibrium in random mating populations.

    PubMed

    Hill, William G; Weir, Bruce S

    2007-09-01

    An algorithm to predict the level of identity by descent simultaneously at multiple loci is presented, which can in principle be extended to any number of loci. The model assumes a random mating population, with random association of haplotypes. The relationship is shown between coefficients of multi-locus identity or non-identity by descent and moments of multi-locus linkage disequilibrium. Thus, these moments can be computed from the multilocus identity or, using algorithms derived previously to predict the disequilibria moments, vice-versa. The results can be applied to predict multi-locus identity in, for example, gene mapping.

  17. 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.

  18. The uranium and thorium decay series nuclides in Mt. St. Helens effusives

    NASA Astrophysics Data System (ADS)

    Bennett, J. T.; Krishnaswami, S.; Turekian, K. K.; Melson, W. G.; Hopson, C. A.

    1982-08-01

    The concentrations of the radionuclides 238U, 230Th, 226Ra, 210Pb, 210Po, 232Th, 228Ra and 228Th and the abundances of major elements were determined in samples from all major eruptions of Mt. St. Helens from May 18, 1980 through June 21, 1981. During this time the effusives changed from plagioclase-phyric dacite to a more andesitic composition but the concentrations of U and Th series nuclides were measurably invariant. The average 232Th/ 238U weight ratio in the rocks is 2.4 and the 230Th/ 232Th activity ratio equals the 238U/ 232Th activity ratio indicating no fractionation of U from Th during magma genesis. 226Ra activity is in excess (˜40% on average) of its parent 230Th whereas 228Ra is in radioactive equilibrium with its parent 232Th, constraining the time of magma formation between 30 and 10 4 years prior to eruption. The 210Pb/ 226Ra activity ratios in the samples average 1.0, with a 20% scatter on either side, but allowing for volatile 210Pb loss at time of eruption excess 210Pb over 226Ra is inferred, indicating that the time of magma formation was within the last 150 years. 210Po was virtually absent in the samples immediately after eruption, indicating its total loss by volatilization during eruption. The quantity of 210Po volatilized during the May 18, 1980 event is estimated to be in the range of 300 Ci from the effusives and as much as 5000 Ci total including losses from heated slide material. The 222Rn activity volatilized should have been comparable to the 210Po activity released.

  19. Radioactive waste disposal package

    DOEpatents

    Lampe, Robert F.

    1986-01-01

    A radioactive waste disposal package comprising a canister for containing vitrified radioactive waste material and a sealed outer shell encapsulating the canister. A solid block of filler material is supported in said shell and convertible into a liquid state for flow into the space between the canister and outer shell and subsequently hardened to form a solid, impervious layer occupying such space.

  20. Radioactive waste disposal package

    DOEpatents

    Lampe, Robert F.

    1986-11-04

    A radioactive waste disposal package comprising a canister for containing vitrified radioactive waste material and a sealed outer shell encapsulating the canister. A solid block of filler material is supported in said shell and convertible into a liquid state for flow into the space between the canister and outer shell and subsequently hardened to form a solid, impervious layer occupying such space.

  1. A Remote Radioactivity Experiment

    ERIC Educational Resources Information Center

    Jona, Kemi; Vondracek, Mark

    2013-01-01

    Imagine a high school with very few experimental resources and limited budgets that prevent the purchase of even basic laboratory equipment. For example, many high schools do not have the means of experimentally studying radioactivity because they lack Geiger counters and/or good radioactive sources. This was the case at the first high school one…

  2. Radioactive Wastes. Revised.

    ERIC Educational Resources Information Center

    Fox, Charles H.

    This publication is one of a series of information booklets for the general public published by the United States Atomic Energy Commission. This booklet deals with the handling, processing and disposal of radioactive wastes. Among the topics discussed are: The Nature of Radioactive Wastes; Waste Management; and Research and Development. There are…

  3. 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

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

    PubMed

    Wang, Yi-Hong; Upadhyaya, Hari D; Burrell, A Millie; Sahraeian, Sayed Mohammad Ebrahim; Klein, Robert R; Klein, Patricia E

    2013-05-20

    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 13,390 single-nucleotide polymorphims. The single-nucleotide polymorphisms were produced using a highly multiplexed genotyping-by-sequencing methodology. Genetic structure was established using principal component, Neighbor-Joining phylogenetic, and Bayesian cluster analyses. These analyses indicated that the mini-core collection was structured along both geographic origin and sorghum race classification. Examples of the former were accessions from Southern Africa, East Asia, and Yemen. Examples of the latter were caudatums with widespread geographical distribution, durras from India, and guineas from West Africa. Race bicolor, the most primitive and the least clearly defined sorghum race, clustered among other races and formed only one clear bicolor-centric cluster. Genome-wide linkage disequilibrium analyses showed linkage disequilibrium decayed, on average, within 10-30 kb, whereas the short arm of SBI-06 contained a linkage disequilibrium block of 20.33 Mb, confirming a previous report of low recombination on this chromosome arm. Four smaller but equally significant linkage disequilibrium blocks of 3.5-35.5 kb were detected on chromosomes 1, 2, 9, and 10. We examined the genes encoded within each block to provide a first look at candidates such as homologs of GS3 and FT that may indicate a selective sweep during sorghum domestication.

  5. An analysis of linkage disequilibrium in the interleukin-1 gene cluster, using a novel grouping method for multiallelic markers.

    PubMed Central

    Cox, A; Camp, N J; Nicklin, M J; di Giovine, F S; Duff, G W

    1998-01-01

    In population- and family-based association studies, it is useful to have some knowledge of the patterns of linkage disequilibrium that exist between markers in candidate regions. When such studies are carried out with multiallelic markers, it is often convenient to group the alleles into a biallelic system, for analysis. In this study, we specifically examined the interleukin-1 (IL-1) gene cluster on chromosome 2, a region containing candidates for many inflammatory and autoimmune disorders. Data were collected on eight markers, four of which were multiallelic. Using these data, we investigated the effect of three allele-grouping strategies, including a novel method, on the detection of linkage disequilibrium. The novel approach, termed the "delta method," measures the deviation from the expected haplotype frequencies under linkage equilibrium, for each allelic combination. This information is then used to group the alleles, in an attempt to avoid the grouping together of alleles at one locus that are in opposite disequilibrium with the same allele at the second locus. The estimate haplotype frequencies (EH) program was used to estimate haplotype frequencies and the disequilibrium measure. In our data it was found that the delta method compared well with the other two strategies. Using this method, we found that there was a reasonable correlation between disequilibrium and physical distance in the region (r=-.540, P=.001, one-tailed). We also identified a common, eight-locus haplotype of the IL-1 gene cluster. PMID:9545388

  6. Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles.

    PubMed Central

    Schaeffer, S W; Walthour, C S; Toleno, D M; Olek, A T; Miller, E L

    2001-01-01

    A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%. PMID:11606543

  7. Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor

    PubMed Central

    Wang, Yi-Hong; Upadhyaya, Hari D.; Burrell, A. Millie; Sahraeian, Sayed Mohammad Ebrahim; Klein, Robert R.; Klein, Patricia E.

    2013-01-01

    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 13,390 single-nucleotide polymorphims. The single-nucleotide polymorphisms were produced using a highly multiplexed genotyping-by-sequencing methodology. Genetic structure was established using principal component, Neighbor-Joining phylogenetic, and Bayesian cluster analyses. These analyses indicated that the mini-core collection was structured along both geographic origin and sorghum race classification. Examples of the former were accessions from Southern Africa, East Asia, and Yemen. Examples of the latter were caudatums with widespread geographical distribution, durras from India, and guineas from West Africa. Race bicolor, the most primitive and the least clearly defined sorghum race, clustered among other races and formed only one clear bicolor-centric cluster. Genome-wide linkage disequilibrium analyses showed linkage disequilibrium decayed, on average, within 10−30 kb, whereas the short arm of SBI-06 contained a linkage disequilibrium block of 20.33 Mb, confirming a previous report of low recombination on this chromosome arm. Four smaller but equally significant linkage disequilibrium blocks of 3.5−35.5 kb were detected on chromosomes 1, 2, 9, and 10. We examined the genes encoded within each block to provide a first look at candidates such as homologs of GS3 and FT that may indicate a selective sweep during sorghum domestication. PMID:23704283

  8. 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

  9. 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.

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

    PubMed Central

    Trachtenberg, E A; Erlich, H A; Rickards, O; DeStefano, G F; Klitz, W

    1995-01-01

    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 evenness 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. PMID:7668268

  11. Disequilibrium of 13CO2 fluxes between photosynthesis and respiration in North American temperate forest biomes

    NASA Astrophysics Data System (ADS)

    Lai, C.; Ehleringer, J.; Schauer, A.; Tans, P.; Hollinger, D.; Paw U, K.; Wofsy, S.

    2003-12-01

    We report the first weekly dataset of seasonal and interannual variability in δ 13C of CO2 fluxes from dominant forest ecosystems in the US. We observed large variations in the δ 13C of respired biosphere-atmosphere fluxes (δ 13CR) across 3 temperate coniferous and deciduous forest ecosystems (-24.9 +/- 0.4 to -31.3 +/- 0.6 per mil). Values of δ 13CR were significantly correlated with growing-season soil water availability. By analyzing daytime flask measurements collected at the top of canopies, we estimated an annual mean, flux-weighted δ 13C of net ecosystem CO2 exchange fluxes (δ 13Cnet). Combining δ 13CR and δ 13Cnet, along with eddy-covariance measured fluxes, we estimated regional discrimination against 13C during photosynthesis (Δ A) for these 3 forest ecosystems. Our approach allows for examination of the interannual correlations between gross primary production fluxes and Δ A that could potentially modulate atmospheric 13C budget. The results showed that C3 forests in temperate regions in the U.S. exhibited a slight isotopic disequilibrium (< 1 per mil) on an annual basis, despite significant seasonal variations in respired δ 13CO2 values (> 3 per mil). Such subtle isotopic disequilibrium however, when associated with enormous one-way gross fluxes, can effectively affect atmospheric 13C budget.

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    PubMed

    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.

  17. 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.

  18. 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.

  19. 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.

  20. Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes.

    PubMed

    Wu, Weiwei; Hao, Honglei; Liu, Qiuling; Han, Xian; Wu, Yeda; Cheng, Jianding; Lu, Dejian

    2014-09-01

    The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

    PubMed

    Houle, David; Márquez, Eladio J

    2015-06-10

    We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r(2) ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.

  7. 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

  8. 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.

  9. Mendelian inheritance, genetic linkage, and genotypic disequilibrium at nine microsatellite loci of Cariniana legalis (Mart.) O. Kuntze.

    PubMed

    Tambarussi, E V; Vencovsky, R; Freitas, M L M; Sebbenn, A M

    2013-11-11

    Cariniana legalis is one of the largest tropical trees with a wide distribution in the Brazilian Atlantic rainforest. We investigated the Mendelian inheritance, genetic linkage, and genotypic disequilibrium at seven microsatellite loci specifically isolated for C. legalis, and at two previously developed heterologous microsatellite loci. Forty to 100 open-pollinated seeds were collected from 22 seed-trees in two populations. Using the Bonferroni correction, no remarkable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected in the nine loci studied. Only 3.7% of the tests were significant for investigations of the Mendelian proportions. On the other hand, only 2.8% of tests for linkage detection showed significance. In addition, among all pairwise tests used for investigating linkage disequilibrium, significance was found in 9.7% of the locus pairs. Our results show clear evidence that the nine simple sequence repeat loci can be used without restriction in genetic diversity, mating system, and parentage analyses.

  10. A Remote Radioactivity Experiment

    NASA Astrophysics Data System (ADS)

    Jona, Kemi; Vondracek, Mark

    2013-01-01

    Imagine a high school with very few experimental resources and limited budgets that prevent the purchase of even basic laboratory equipment. For example, many high schools do not have the means of experimentally studying radioactivity because they lack Geiger counters and/or good radioactive sources. This was the case at the first high school one of us (MV) worked at, and after talking with numerous colleagues we know this is still the case at many schools. What options are there then for physics teachers to allow their students to experimentally investigate certain characteristics of radioactivity, such as how distance affects the intensity of radiation coming from a radioactive source? There are computer simulations that can be run, or perhaps the teacher has a light sensor and tries to make an analogy between the intensity of light from a light bulb and the intensity of radiation from a radioactive source based on geometric arguments to get an inverse-square law. But for many there is no direct experimental option if one does not possess a Geiger counter and good radioactive sample. It is for that teacher and class of students that an online, remote radioactivity experiment was created.

  11. 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

  12. Diffusion-controlled growth and degree of disequilibrium of garnet porphyroblasts: is diffusion-controlled growth of porphyroblasts common?

    NASA Astrophysics Data System (ADS)

    Miyazaki, Kazuhiro

    2015-12-01

    Rate-limiting processes and the degree of disequilibrium during metamorphic mineral growth are key controls on the rate of dehydration and hydration in the Earth's crust. This paper examines diffusion-controlled growth and the degree of disequilibrium of garnet porphyroblasts in the Tsukuba metamorphic rocks of central Japan. The analyzed porphyroblasts have irregular and branching morphologies with clear diffusional haloes, indicating that they grew in a diffusion-controlled regime. Mathematical analysis shows that the dominant wavelength of the interface of a garnet porphyroblast is dependent on the extent of supersaturation (Δ ζ), which is an index for the degree of disequilibrium. Using the calculated upper and lower limits of the dominant wavelength, the value of Δ ζ is estimated to be 0.05 × 10-1-0.16, which corresponds to a Gibbs free energy (Δ G r ) overstep of 0.9-27 kJ per mole of garnet (12 oxygen atoms) and a temperature overstep (Δ T) of 1.7-50 °C. Using the average value of the dominant wavelength, the following results are obtained: Δ ζ = 0.15 × 10-1, Δ G r = 2.7 kJ per mole of garnet, and Δ T = 5 °C. These values bring into question the importance of diffusion-controlled growth of garnet porphyroblasts, as highly irregular and branching garnet porphyroblasts are rare in most metamorphic belts. After significant overstepping for the nucleation of garnet, the garnet porphyroblasts grow at a high degree of disequilibrium. However, a high degree of disequilibrium under diffusion-controlled growth would be characterized by diffusional instability. The results indicate that garnet porphyroblasts that lack an irregular and branching morphology may grow at a high degree of disequilibrium under interface-controlled growth, provided they are set in a medium where the diffusion and supply of constituent elements are sufficient, such as a sufficient volume of metamorphic fluid.

  13. Behaviour of nuclides and U-series disequilibrium in clayey sediments: application to the Late Jurassic record from the eastern Paris basin

    NASA Astrophysics Data System (ADS)

    Casanova, J.; Négrel, Ph.; Innocent, C.; Brulhet, J.

    2003-04-01

    We present a record of U-series disequilibrium covering the Callovo-Oxfordian-Thitonian times of the Late Jurassic carbonated platform from the eastern part of the Paris basin. The Callovo-Oxfordian clayey layer is the potential host rock for reconnaissance work carried out by Andra (e.g., Agence Nationale de Gestion des Déchets Radioactifs) in eastern France, the objective of which is the designing and building of an underground research laboratory to study the aptitude of the clay-marl Callovo-Oxfordian layer for the storage of radioactive wastes. We analyse U and Th trace elements on both the labile fraction (extracted by cold HCl) and the total bulk sediments. The Th contents are extremely low in the Oxfordian shelf reef carbonates (<10 ppb) with respect to the Kimmeridgian-Tithonian clayey marls and the Callovian-Oxfordian argilites (up to 10 ppm). In contrast, the uranium contents are much more homogenous (1 ppm ±0.8) along the section. With respect to bulk concentrations, the nuclide contents in the labile component are particularly low in the Callovian-Oxfordian argilites. This behaviour suggests that given the extremely low permeability of the rock, any groundwater circulation of solutes could only have taken place by diffusion - a very slow mechanism that favours water-rock interactions. For U-series analyses (measured by alpha-spectrometry), a total of 43 bulk-rock samples were preferentially microdrilled from the fine-grained lithologies, although the heterogeneity of carbonate facies within sections necessitated occasional sampling of coarser grained lithologies. Within the carbonate-rich part (Oxfordian to Tithonian) of the section, the 234U/238U ratios slightly fluctuate from secular equilibrium and are interpreted as preferential 234U-solution processes related to groundwater circulation. Preferential removal of 234U in this zone is also indicated by some 230Th/234U activity ratios higher than unity. In contrast, most of the samples from the

  14. Radioactive iodine uptake

    MedlinePlus

    ... much radioactive iodine is taken up by your thyroid gland in a certain time period. A similar test ... over the area of your neck where the thyroid gland is located. The probe detects the location and ...

  15. Understanding radioactive waste

    SciTech Connect

    Murray, R.L.

    1981-12-01

    This document contains information on all aspects of radioactive wastes. Facts are presented about radioactive wastes simply, clearly and in an unbiased manner which makes the information readily accessible to the interested public. The contents are as follows: questions and concerns about wastes; atoms and chemistry; radioactivity; kinds of radiation; biological effects of radiation; radiation standards and protection; fission and fission products; the Manhattan Project; defense and development; uses of isotopes and radiation; classification of wastes; spent fuels from nuclear reactors; storage of spent fuel; reprocessing, recycling, and resources; uranium mill tailings; low-level wastes; transportation; methods of handling high-level nuclear wastes; project salt vault; multiple barrier approach; research on waste isolation; legal requiremnts; the national waste management program; societal aspects of radioactive wastes; perspectives; glossary; appendix A (scientific American articles); appendix B (reference material on wastes). (ATT)

  16. Radioactive gold ring dermatitis

    SciTech Connect

    Miller, R.A.; Aldrich, J.E. )

    1990-08-01

    A superficial squamous cell carcinoma developed in a woman who wore a radioactive gold ring for more than 30 years. Only part of the ring was radioactive. Radiation dose measurements indicated that the dose to basal skin layer was 2.4 Gy (240 rad) per week. If it is assumed that the woman continually wore her wedding ring for 37 years since purchase, she would have received a maximum dose of approximately 4600 Gy.

  17. Temporary Personal Radioactivity

    ERIC Educational Resources Information Center

    Myers, Fred

    2012-01-01

    As part of a bone scan procedure to look for the spread of prostate cancer, I was injected with radioactive technetium. In an effort to occupy/distract my mind, I used a Geiger counter to determine if the radioactive count obeyed the inverse-square law as a sensor was moved away from my bladder by incremental distances. (Contains 1 table and 2…

  18. Dynamic radioactive particle source

    DOEpatents

    Moore, Murray E.; Gauss, Adam Benjamin; Justus, Alan Lawrence

    2012-06-26

    A method and apparatus for providing a timed, synchronized dynamic alpha or beta particle source for testing the response of continuous air monitors (CAMs) for airborne alpha or beta emitters is provided. The method includes providing a radioactive source; placing the radioactive source inside the detection volume of a CAM; and introducing an alpha or beta-emitting isotope while the CAM is in a normal functioning mode.

  19. Container for radioactive materials

    DOEpatents

    Fields, Stanley R.

    1985-01-01

    A container for housing a plurality of canister assemblies containing radioactive material and disposed in a longitudinally spaced relation within a carrier to form a payload package concentrically mounted within the container. The payload package includes a spacer for each canister assembly, said spacer comprising a base member longitudinally spacing adjacent canister assemblies from each other and a sleeve surrounding the associated canister assembly for centering the same and conducting heat from the radioactive material in a desired flow path.

  20. 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

  1. 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

  2. Significant linkage disequilibrium between the Huntington disease gene and the loci D4S10 and D4S95 in the Dutch population

    SciTech Connect

    Skraastad, M.I.; Van de Vosse, E.; Belfroid, R.; Hoeld, K.; Vegter-van der Vlis, M.; Bakker, E.; van Ommen, G.J.B. ); Sandkuijl, L.A. )

    1992-10-01

    Significant linkage disequilibrium has been found between the Huntington disease (HD) gene and DNA markers located around D4S95 and D4S98. The linkage-disequilibrium studies favor the proximal location of the HD gene, in contrast to the conflicting results of recombination analyses. The authors have analyzed 45 Dutch HD families with 19 DNA markers and have calculated the strength of linkage disequilibrium. Highly significant linkage disequilibrium has been detected with D4S95, consistent with the studies in other populations. In contrast with most other studies, however, the area of linkage disequilibrium extends from D4S10 proximally to D4S95, covering 1,100 kb. These results confirm that the HD gene most likely maps near D4S95. 28 refs., 1 fig., 2 tabs.

  3. Radioactive disequilibria in mineralised fracture samples from two uranium occurrences in northern Sweden

    USGS Publications Warehouse

    Smellie, John A.T.; Rosholt, J.N.

    1984-01-01

    Mineralised fractures from two uranium occurrences in northern Sweden were examined mineralogically and isotopically to establish the presence or absence of radioactive equilibrium that may indicate recent rock-water interaction processes based on the natural mobility of uranium (i.e.; during the last 0.5 Ma). The results show evidence of radioactive disequilibrium in six of the nine samples investigated. Disequilibria are attributable to solution to solid 234U recoil gain (weakly mineralised zones adjacent to the main mineralisation) and solid to solution 234U recoil loss (moderate to highly mineralised zones). The absence of significant 238U loss in the samples emphasises the reducing conditions at the sampled depths. ?? 1984.

  4. Improved confidence intervals for the linkage disequilibrium method for estimating effective population size.

    PubMed

    Jones, A T; Ovenden, J R; Wang, Y-G

    2016-10-01

    The linkage disequilibrium method is currently the most widely used single sample estimator of genetic effective population size. The commonly used software packages come with two options, referred to as the parametric and jackknife methods, for computing the associated confidence intervals. However, little is known on the coverage performance of these methods, and the published data suggest there may be some room for improvement. Here, we propose two new methods for generating confidence intervals and compare them with the two in current use through a simulation study. The new confidence interval methods tend to be conservative but outperform the existing methods for generating confidence intervals under certain circumstances, such as those that may be encountered when making estimates using large numbers of single-nucleotide polymorphisms.

  5. 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.

  6. Disequilibrium Chemistry in the Solar Nebula and Early Solar System: Implications for the Chemistry of Comets

    NASA Astrophysics Data System (ADS)

    Fegley, Bruce, Jr.

    1997-12-01

    A growing body of observations demonstrates that comets, like the chondritic meteorites, are disequilibrium assemblages, whose chemistry and molecular composition cannot be explained solely on the basis of models of equilibrium condensation in the solar nebula. These observations include: (1) The coexistence of reduced (e.g., CH4 and organics) and oxidized (e.g., CO, CO2, and H2CO) carbon compounds observed in the gas and dust emitted by comet P/Halley; (2) The coexistence of reduced (e.g., NH3) and oxidized (e.g., N2) nitrogen compounds in the gas emitted by comet P/Halley; (3) The observation of large amounts of formaldehyde in the gas emitted by comet P/Halley (H2CO/H2O approx. 1.5 - 4%) and by comet Machholz (1988j). Formaldehyde would be rapidly destroyed by thermal processing in the solar nebula and must be formed by some disequilibrating process either in the solar nebula or in some presolar environment. (4) The observation of large amounts of the oxidized carbon gases CO and CO2 in comet P/Halley at levels far exceeding those predicted by chemical equilibrium models of solar nebula carbon chemistry. In fact, oxidized carbon gases (CO+ C02 + H2CO) are the most abundant volatile (after water vapor) emitted by comet P/Halley. (5) The observation of HCN, which is not a predicted low temperature condensate in the solar nebula (e.g., Lewis 1972), in comet P/Halley (e.g., Schloerb et al. 1987) and in comet Kohoutek. (6) The observation of S2, which is argued to be a parent molecule vaporized from the nucleus, in comet IRAS-Araki-Alcock (1983d) by A'Hearn et aL (1983) and Feldman et al. (1984). This molecule is not an equilibrium condensate in the solar nebula and must result from disequilibrium chemistry. (7) The deduction that organic grains (C-H-O-N particles) comprise about 30% of the dust emitted by comet P/Halley and that about 75% of the total carbon inventory of Halley is in these grains also implies substantial disequilibrium chemistry. (8) The deductions

  7. Refining the analysis of a whole genome linkage disequilibrium association map: the United Kingdom results.

    PubMed

    Yeo, Tai Wai; Roxburgh, Richard; Maranian, Mel; Singlehurst, Sara; Gray, Julia; Hensiek, Anke; Setakis, Efrosini; Compston, Alastair; Sawcer, Stephen

    2003-10-01

    Individual genotyping of the 10 most promising markers identified in our previously reported screen for linkage disequilibrium (LD) in multiple sclerosis identified a number of effects which confound the analysis and are of general importance in the interpretation of results obtained using microsatellite markers typed in pooled DNA. In order to identify and characterise these effects, we individually genotyped 529 promising markers in 16 trio families. We then devised adapting factors, which were designed to correct for these confounders. This more extensive analysis of the previously published UK data set and the repeat analyses incorporating these adaptations led to the identification of two novel markers that may be associated with multiple sclerosis in this population, providing a close correlation between the results of pooled analysis and individual typing.

  8. 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.

  9. Improved confidence intervals for the linkage disequilibrium method for estimating effective population size.

    PubMed

    Jones, A T; Ovenden, J R; Wang, Y-G

    2016-10-01

    The linkage disequilibrium method is currently the most widely used single sample estimator of genetic effective population size. The commonly used software packages come with two options, referred to as the parametric and jackknife methods, for computing the associated confidence intervals. However, little is known on the coverage performance of these methods, and the published data suggest there may be some room for improvement. Here, we propose two new methods for generating confidence intervals and compare them with the two in current use through a simulation study. The new confidence interval methods tend to be conservative but outperform the existing methods for generating confidence intervals under certain circumstances, such as those that may be encountered when making estimates using large numbers of single-nucleotide polymorphisms. PMID:27005004

  10. Bayesian model selection for multiple QTLs mapping combining linkage disequilibrium and linkage.

    PubMed

    Jiang, Dan; Ma, Guoda; Yang, Runqing; Li, Keshen; Fang, Ming

    2014-01-01

    Linkage disequilibrium (LD) mapping is able to localize quantitative trait loci (QTL) within a rather small region (e.g. 2 cM), which is much narrower than linkage analysis (LA, usually 20 cM). The multilocus LD method utilizes haplotype information around putative mutation and takes historical recombination events into account, and thus provides a powerful method for further fine mapping. However, sometimes there are more than one QTLs in the region being studied. In this study, the Bayesian model selection implemented via the Markov chain Monte Carlo (MCMC) method is developed for fine mapping of multiple QTLs using haplotype information in a small region. The method combines LD as well as linkage information. A series of simulation experiments were conducted to investigate the behavior of the method. The results showed that this new multiple QTLs method was more efficient in separating closely linked QTLs than single-marker association studies. PMID:25579473

  11. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

    SciTech Connect

    Slavov, Gancho; DiFazio, Stephen P; Martin, Joel R; Schackwitz, Wendy; Muchero, Wellington; Rodgers-Melnick, Eli; Lipphardt, Mindie; Pennacchio, Christa; Hellsten, Uffe; Pennacchio, Len; Gunter, Lee; Ranjan, Priya; Strauss, Steven; Rokhsar, Daniel; Tuskan, Gerald A

    2012-01-01

    Population genomics of forest trees provides crucial information for breeding, conservation, and bioenergy feedstock development. As part of a large-scale association study, we resequenced 16 genomes of the model tree Populus trichocarpa to an average depth of 39 . Analyses of the resulting data revealed surprisingly extensive population genetic structure and decay of linkage disequilibrium over much larger physical distances than the expected based on previous, smaller-scale studies. Rates of recombination varied widely across the genome but were largely predictable based on DNA sequence and methylation patterns. Our results suggest that genomewide association studies and accurate prediction of phenotypes from DNA data are more feasible in Populus than previously assumed, thereby laying the foundation for a step change in our understanding of tree biology.

  12. Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations.

    PubMed Central

    Service, S K; Lang, D W; Freimer, N B; Sandkuijl, L A

    1999-01-01

    Linkage disequilibrium (LD) mapping may be a powerful means for genome screening to identify susceptibility loci for common diseases. A new statistical approach for detection of LD around a disease gene is presented here. This method compares the distribution of haplotypes in affected individuals versus that expected for individuals descended from a common ancestor who carried a mutation of the disease gene. Simulations demonstrate that this method, which we term "ancestral haplotype reconstruction" (AHR), should be powerful for genome screening of phenotypes characterized by a high degree of etiologic heterogeneity, even with currently available marker maps. AHR is best suited to application in isolated populations where affected individuals are relatively recently descended (< approximately 25 generations) from a common disease mutation-bearing founder. PMID:10330361

  13. Bayesian model selection for multiple QTLs mapping combining linkage disequilibrium and linkage.

    PubMed

    Jiang, Dan; Ma, Guoda; Yang, Runqing; Li, Keshen; Fang, Ming

    2014-09-19

    Linkage disequilibrium (LD) mapping is able to localize quantitative trait loci (QTL) within a rather small region (e.g. 2 cM), which is much narrower than linkage analysis (LA, usually 20 cM). The multilocus LD method utilizes haplotype information around putative mutation and takes historical recombination events into account, and thus provides a powerful method for further fine mapping. However, sometimes there are more than one QTLs in the region being studied. In this study, the Bayesian model selection implemented via the Markov chain Monte Carlo (MCMC) method is developed for fine mapping of multiple QTLs using haplotype information in a small region. The method combines LD as well as linkage information. A series of simulation experiments were conducted to investigate the behavior of the method. The results showed that this new multiple QTLs method was more efficient in separating closely linked QTLs than single-marker association studies.

  14. 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.

  15. Linkage disequilibrium in the insulin gene region: size variation at the 5' flanking polymorphism and bimodality among "class I" alleles.

    PubMed Central

    McGinnis, R. E.; Spielman, R. S.

    1994-01-01

    The 5' flanking polymorphism (5'FP), a hypervariable region at the 5' end of the insulin gene, has "class 1" alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). We report that precise sizing of the 5'FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. We also examined 5'FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5'FP, we found that one allele exhibits near-total association with the upper component of the 5'FP class 1 distribution. Such associations represent a little-known but potentially widespread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. PMID:7915880

  16. 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...

  17. 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.

  18. 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…

  19. 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

  20. 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

  1. Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions.

    PubMed

    Adetunji, Ibraheem; Willems, Glenda; Tschoep, Hendrik; Bürkholz, Alexandra; Barnes, Steve; Boer, Martin; Malosetti, Marcos; Horemans, Stefaan; van Eeuwijk, Fred

    2014-03-01

    Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.

  2. 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.

  3. A powerful one degree of freedom approach to mapping genes with linkage disequilibrium

    SciTech Connect

    Terwilliger, J.D. |; Ott, J.

    1994-09-01

    A novel procedure for detecting linkage disequilibrium is proposed which has only one degree of freedom irrespective of the number of alleles at the marker locus under consideration. In this test, all marker allele frequencies are determined as a function of the true marker allele frequencies, the recombination fraction between marker and disease, and the number of generations since an initial disease mutation was introduced into the population. Under the restrictive assumption of one initial founder mutation occuring in the population under study, it is possible to predict the marker allele frequency in the case sample as follows: p{sub n}=p{sub n{minus}1}(1-{theta}) + q{sub n{minus}1}{theta}, where p{sub n} is the frequency in the case sample of the allele in generation n, and q{sub n} is the frequency of said marker allele in the control sample. Then a test of linkage disequilibrium can be parametrized as a function of {theta} using a {open_quotes}LOD{close_quotes} score statistic as log{sub 10}[L({theta})/L({theta}=0.5)], where the allele frequencies in generation 0, and the number of generations since introduction of the allele to the population are treated as nuisance parameters and estimated separately in numerator and denominator, thus leaving us with a test statistic on one df, irrespective of the number of alleles at the marker locus. While the assumptions are often not reasonable, violations of said assumptions will simply have the effect of making the test less powerful. Still, the test is consistently more powerful than the standard 2 x n table chi-square test of association for multi-allelic marker systems. Multiple founders, non-zero mutation rates, and an extension to multipoint association tests are under development.

  4. Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions.

    PubMed

    Adetunji, Ibraheem; Willems, Glenda; Tschoep, Hendrik; Bürkholz, Alexandra; Barnes, Steve; Boer, Martin; Malosetti, Marcos; Horemans, Stefaan; van Eeuwijk, Fred

    2014-03-01

    Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material. PMID:24292512

  5. A Global Perspective on Genetic Variation at the ADH Genes Reveals Unusual Patterns of Linkage Disequilibrium and Diversity

    PubMed Central

    Osier, Michael V.; Pakstis, Andrew J.; Soodyall, Himla; Comas, David; Goldman, David; Odunsi, Adekunle; Okonofua, Friday; Parnas, Josef; Schulz, Leslie O.; Bertranpetit, Jaume; Bonne-Tamir, Batsheva; Lu, Ru-Band; Kidd, Judith R.; Kidd, Kenneth K.

    2002-01-01

    Variants of different Class I alcohol dehydrogenase (ADH) genes have been shown to be associated with an effect that is protective against alcoholism. Previous work from our laboratory has shown that the two sites showing the association are in linkage disequilibrium and has identified the ADH1B Arg47His site as causative, with the ADH1C Ile349Val site showing association only because of the disequilibrium. Here, we describe an initial study of the nature of linkage disequilibrium and genetic variation, in population samples from different regions of the world, in a larger segment of the ADH cluster (including the three Class I ADH genes and ADH7). Linkage disequilibrium across ∼40 kb of the Class I ADH cluster is moderate to strong in all population samples that we studied. We observed nominally significant pairwise linkage disequilibrium, in some populations, between the ADH7 site and some Class I ADH sites, at moderate values and at a molecular distance as great as 100 kb. Our data indicate (1) that most ADH-alcoholism association studies have failed to consider many sites in the ADH cluster that may harbor etiologically significant alleles and (2) that the relevance of the various ADH sites will be population dependent. Some individual sites in the Class I ADH cluster show Fst values that are among the highest seen among several dozen unlinked sites that were studied in the same subset of populations. The high Fst values can be attributed to the discrepant frequencies of specific alleles in eastern Asia relative to those in other regions of the world. These alleles are part of a single haplotype that exists at high (>65%) frequency only in the eastern-Asian samples. It seems unlikely that this haplotype, which is rare or unobserved in other populations, reached such high frequency because of random genetic drift alone. PMID:12050823

  6. Genetic Structure and the Search for Genotype-Phenotype Relationships: An Example from Disequilibrium in the Apo B Gene Region

    PubMed Central

    Zerba, K. E.; Kessling, A. M.; Davignon, J.; Sing, C. F.

    1991-01-01

    We analyzed allelic associations (disequilibria) for four restriction fragment length polymorphisms (RFLPs) in the region of the 43-kb Apo B gene in a sample of 233 unrelated individuals from Montreal, Canada, sampled for health. This total sample (T) included 160 individuals of known French Canadian (FC) ancestry. We present a rigorous application of current methodology to these samples, including estimation of type II error probabilities and correlations between markers for estimates of disequilibria. We then consider the utility of these estimates of allelic disequilibria for the interpretation of genotype-phenotype relations. Significant deviations from Hardy-Weinberg equilibrium were not predicted by proximity to other markers in disequilibrium. We found significant quadri-allelic disequilibrium for two marker pairs despite absence of significant deviations from Hardy-Weinberg equilibrium for either marker or tri-allelic disequilibrium, respectively. Altogether these results underscore the complexity of the genotypic structure of the data. A combination of nonevolutionary factors, including sampling for health, small sample size and data exclusion due to methodological constraints of not successfully typing all members of the sample for every RFLP, is a likely explanation for this complexity. These types of factors are common to many RFLP studies. Patterns of composite di-allelic disequilibrium indicated that some RFLP allele pairs may have a longer shared evolutionary history than others and that disequilibrium is not predicted by distance between RFLPs. Type II error probabilities were generally much higher than those for type I errors. Correlations between marker pairs for disequilibria were generally not high. We show from a review of 14 published studies of association between the XbaI RFLP and variation in a total of 15 lipid traits that deviations from Hardy-Weinberg equilibrium can cause substantial differences in the estimation of variability

  7. Radioactivity in food crops

    SciTech Connect

    Drury, J.S.; Baldauf, M.F.; Daniel, E.W.; Fore, C.S.; Uziel, M.S.

    1983-05-01

    Published levels of radioactivity in food crops from 21 countries and 4 island chains of Oceania are listed. The tabulation includes more than 3000 examples of 100 different crops. Data are arranged alphabetically by food crop and geographical origin. The sampling date, nuclide measured, mean radioactivity, range of radioactivities, sample basis, number of samples analyzed, and bibliographic citation are given for each entry, when available. Analyses were reported most frequently for /sup 137/Cs, /sup 40/K, /sup 90/Sr, /sup 226/Ra, /sup 228/Ra, plutonium, uranium, total alpha, and total beta, but a few authors also reported data for /sup 241/Am, /sup 7/Be, /sup 60/Co, /sup 55/Fe, /sup 3/H, /sup 131/I, /sup 54/Mn, /sup 95/Nb, /sup 210/Pb, /sup 210/Po, /sup 106/Ru, /sup 125/Sb, /sup 228/Th, /sup 232/Th, and /sup 95/Zr. Based on the reported data it appears that radioactivity from alpha emitters in food crops is usually low, on the order of 0.1 Bq.g/sup -1/ (wet weight) or less. Reported values of beta radiation in a given crop generally appear to be several orders of magnitude greater than those of alpha emitters. The most striking aspect of the data is the great range of radioactivity reported for a given nuclide in similar food crops with different geographical origins.

  8. Trapping radioactive ions

    NASA Astrophysics Data System (ADS)

    Kluge, H.-J.; Blaum, K.

    2004-12-01

    Trapping devices for atomic and nuclear physics experiments with radioactive ions are becoming more and more important at accelerator facilities. While about ten years ago only one online Penning trap experiment existed, namely ISOLTRAP at ISOLDE/CERN, meanwhile almost every radioactive beam facility has installed or plans an ion trap setup. This article gives an overview on ion traps in the operation, construction or planing phase which will be used for fundamental studies with short-lived radioactive nuclides such as mass spectrometry, laser spectroscopy and nuclear decay spectroscopy. In addition, this article summarizes the use of gas cells and radiofrequency quadrupole (Paul) traps at different facilities as a versatile tool for ion beam manipulation like retardation, cooling, bunching, and cleaning.

  9. Radioactivity of Consumer Products

    NASA Astrophysics Data System (ADS)

    Peterson, David; Jokisch, Derek; Fulmer, Philip

    2006-11-01

    A variety of consumer products and household items contain varying amounts of radioactivity. Examples of these items include: FiestaWare and similar glazed china, salt substitute, bananas, brazil nuts, lantern mantles, smoke detectors and depression glass. Many of these items contain natural sources of radioactivity such as Uranium, Thorium, Radium and Potassium. A few contain man-made sources like Americium. This presentation will detail the sources and relative radioactivity of these items (including demonstrations). Further, measurements of the isotopic ratios of Uranium-235 and Uranium-238 in several pieces of china will be compared to historical uses of natural and depleted Uranium. Finally, the presenters will discuss radiation safety as it pertains to the use of these items.

  10. Radioactive mixed waste disposal

    SciTech Connect

    Jasen, W.G.; Erpenbeck, E.G.

    1993-02-01

    Various types of waste have been generated during the 50-year history of the Hanford Site. Regulatory changes in the last 20 years have provided the emphasis for better management of these wastes. Interpretations of the Atomic Energy Act of 1954 (AEA), the Resource Conservation and Recovery Act of 1976 (RCRA), and the Hazardous and Solid Waste Amendments (HSWA) have led to the definition of radioactive mixed wastes (RMW). The radioactive and hazardous properties of these wastes have resulted in the initiation of special projects for the management of these wastes. Other solid wastes at the Hanford Site include low-level wastes, transuranic (TRU), and nonradioactive hazardous wastes. This paper describes a system for the treatment, storage, and disposal (TSD) of solid radioactive waste.

  11. Container for radioactive materials

    DOEpatents

    Fields, S.R.

    1984-05-30

    A container is claimed for housing a plurality of canister assemblies containing radioactive material. The several canister assemblies are stacked in a longitudinally spaced relation within a carrier to form a payload concentrically mounted within the container. The payload package includes a spacer for each canister assembly, said spacer comprising a base member longitudinally spacing adjacent canister assemblies from each other and sleeve surrounding the associated canister assembly for centering the same and conducting heat from the radioactive material in a desired flow path. 7 figures.

  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. 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

  14. 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

  15. Radioactivity test (image)

    MedlinePlus

    ... type of nuclear test performed to evaluate thyroid function. The patient ingests radioactive iodine (I-123 or I-131) capsules or liquid. After a time (usually 6 and 24-hours later), a gamma probe is placed over the thyroid gland to ...

  16. TABLE OF RADIOACTIVE ELEMENTS.

    SciTech Connect

    HOLDEN,N.E.

    2001-06-29

    For those chemical elements which have no stable nuclides with a terrestrial isotopic composition, the data on radioactive half-lives and relative atomic masses for the nuclides of interest and importance have been evaluated and the recommended values and uncertainties are listed.

  17. Viewer Makes Radioactivity "Visible"

    NASA Technical Reports Server (NTRS)

    Yin, L. I.

    1983-01-01

    Battery operated viewer demonstrates feasibility of generating threedimensional visible light simulations of objects that emit X-ray or gamma rays. Ray paths are traced for two pinhold positions to show location of reconstructed image. Images formed by pinholes are converted to intensified visible-light images. Applications range from radioactivity contamination surveys to monitoring radioisotope absorption in tumors.

  18. Radioactivity: A Natural Phenomenon.

    ERIC Educational Resources Information Center

    Ronneau, C.

    1990-01-01

    Discussed is misinformation people have on the subject of radiation. The importance of comparing artificial source levels of radiation to natural levels is emphasized. Measurements of radioactivity, its consequences, and comparisons between the risks induced by radiation in the environment and from artificial sources are included. (KR)

  19. AIR RADIOACTIVITY MONITOR

    DOEpatents

    Bradshaw, R.L.; Thomas, J.W.

    1961-04-11

    The monitor is designed to minimize undesirable background buildup. It consists of an elongated column containing peripheral electrodes in a central portion of the column, and conduits directing an axial flow of radioactively contaminated air through the center of the column and pure air through the annular portion of the column about the electrodes. (AEC)

  20. Radioactive Decay - An Analog.

    ERIC Educational Resources Information Center

    McGeachy, Frank

    1988-01-01

    Presents an analog of radioactive decay that allows the student to grasp the concept of half life and the exponential nature of the decay process. The analog is devised to use small, colored, plastic poker chips or counters. Provides the typical data and a graph which supports the analog. (YP)

  1. Radioactivity and foods

    SciTech Connect

    Olszyna-Marzys, A.E. )

    1991-01-01

    The purpose of this article is to describe and contrast two relationships between radiation and food--on the one hand, beneficial preservation of food by controlled exposure to ionizing radiation; and, on the other, contamination of food by accidental incorporation of radioactive nuclides within the food itself. In food irradiation, electrons or electromagnetic radiation is used to destroy microorganisms and insects or prevent seed germination. The economic advantages and health benefits of sterilizing food in this manner are clear, and numerous studies have confirmed that under strictly controlled conditions no undersirable changes or induced radioactivity is produced in the irradiated food. An altogether different situation is presented by exposure of food animals and farming areas to radioactive materials, as occurred after the major Soviet nuclear reactor accident at Chenobyl. This article furnishes the basic information needed to understand the nature of food contamination associated with that event and describes the work of international organizations seeking to establish appropriate safe limits for levels of radioactivity in foods.

  2. Environmental Radioactivity, Temperature, and Precipitation.

    ERIC Educational Resources Information Center

    Riland, Carson A.

    1996-01-01

    Reports that environmental radioactivity levels vary with temperature and precipitation and these effects are due to radon. Discusses the measurement of this environmental radioactivity and the theory behind it. (JRH)

  3. Episodic Holocene eruption of the Salton Buttes rhyolites, California, from paleomagnetic, U-Th, and Ar/Ar dating

    USGS Publications Warehouse

    Wright, Heather M.; Vazquez, Jorge A.; Champion, Duane E.; Calvert, Andrew T.; Mangan, Margaret T.; Stelten, Mark E.; Cooper, Kari M.; Herzig, Charles; Schriener Jr., Alexander

    2015-01-01

    In the Salton Trough, CA, five rhyolite domes form the Salton Buttes: Mullet Island, Obsidian Butte, Rock Hill, North and South Red Hill, from oldest to youngest. Results presented here include 40Ar/39Ar anorthoclase ages, 238U-230Th zircon crystallization ages, and comparison of remanent paleomagnetic directions with the secular variation curve, which indicate that all domes are Holocene. 238U-230Th zircon crystallization ages are more precise than but within uncertainty of 40Ar/39Ar anorthoclase ages, suggesting that zircon crystallization proceeded until shortly before eruption in all cases except one. Remanent paleomagnetic directions require three eruption periods: (1) Mullet Island, (2) Obsidian Butte, and (3) Rock Hill, North Red Hill, and South Red Hill. Borehole cuttings logs document up to two shallow tephra layers. North and South Red Hills likely erupted within 100 years of each other, with a combined 238U-230Th zircon isochron age of: 2.83 ± 0.60 ka (2 sigma); paleomagnetic evidence suggests this age predates eruption by hundreds of years (1800 cal BP). Rock Hill erupted closely in time to these eruptions. The Obsidian Butte 238U-230Th isochron age (2.86 ± 0.96 ka) is nearly identical to the combined Red Hill age, but its Virtual Geomagnetic Pole position suggests a slightly older age. The age of aphyric Mullet Island dome is the least well constrained: zircon crystals are resorbed and the paleomagnetic direction is most distinct; possible Mullet Island ages include ca. 2300, 5900, 6900, and 7700 cal BP. Our results constrain the duration of Salton Buttes volcanism to between ca. 5900 and 500 years.

  4. Episodic Holocene eruption of the Salton Buttes rhyolites, California, from paleomagnetic, U-Th, and Ar/Ar dating

    NASA Astrophysics Data System (ADS)

    Wright, Heather M.; Vazquez, Jorge A.; Champion, Duane E.; Calvert, Andrew T.; Mangan, Margaret T.; Stelten, Mark; Cooper, Kari M.; Herzig, Charles; Schriener, Alexander

    2015-04-01

    In the Salton Trough, CA, five rhyolite domes form the Salton Buttes: Mullet Island, Obsidian Butte, Rock Hill, North and South Red Hill, from oldest to youngest. Results presented here include 40Ar/39Ar anorthoclase ages, 238U-230Th zircon crystallization ages, and comparison of remanent paleomagnetic directions with the secular variation curve, which indicate that all domes are Holocene. 238U-230Th zircon crystallization ages are more precise than but within uncertainty of 40Ar/39Ar anorthoclase ages, suggesting that zircon crystallization proceeded until shortly before eruption in all cases except one. Remanent paleomagnetic directions require three eruption periods: (1) Mullet Island, (2) Obsidian Butte, and (3) Rock Hill, North Red Hill, and South Red Hill. Borehole cuttings logs document up to two shallow tephra layers. North and South Red Hills likely erupted within 100 years of each other, with a combined 238U-230Th zircon isochron age of: 2.83 ± 0.60 ka (2 sigma); paleomagnetic evidence suggests this age predates eruption by hundreds of years (1800 cal BP). Rock Hill erupted closely in time to these eruptions. The Obsidian Butte 238U-230Th isochron age (2.86 ± 0.96 ka) is nearly identical to the combined Red Hill age, but its Virtual Geomagnetic Pole position suggests a slightly older age. The age of aphyric Mullet Island dome is the least well constrained: zircon crystals are resorbed and the paleomagnetic direction is most distinct; possible Mullet Island ages include ca. 2300, 5900, 6900, and 7700 cal BP. Our results constrain the duration of Salton Buttes volcanism to between ca. 5900 and 500 years.

  5. Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes

    PubMed Central

    2004-01-01

    To dissect the haplotype structure of candidate genes for disease association studies, it is important to understand the nature of genetic variation at these loci in different populations. We present a survey of haplotype structure and linkage disequilibrium of chemokine and chemokine receptor genes in 11 geographically-distinct population samples (n = 728). Chemokine proteins are involved in intercellular signalling and the immune response. These molecules are important modulators of human immunodeficiency virus (HIV)-1 infection and the progression of the acquired immune deficiency syndrome, tumour development and the metastatic process of cancer. To study the extent of genetic variation in this gene family, single nucleotide polymorphisms (SNPs) from 13 chemokine and chemokine receptor genes were genotyped using the 5' nuclease assay (TaqMan). SNP haplotypes, estimated from unphased genotypes using the Expectation-Maximization-algorithm, are described in a cluster of four CC-chemokine receptor genes (CCR3, CCR2, CCR5 and CCRL2) on chromosome 3p21, and a cluster of three CC-chemokine genes [MPIF-1 (CCL23) PARC (CCL18) and MIP- 1α (CCL3)] on chromosome 17q11-12. The 32 base pair (bp) deletion in exon 4 of CCR5 was also included in the haplotype analysis of 3p21. A total of 87.5 per cent of the variation of 14 biallelic loci scattered over 150 kilobases of 3p21 is explained by 11 haplotypes which have a frequency of at least 1 per cent in the total sample. An analysis of haplotype blocks in this region indicates recombination between CCR2 and CCR5, although long-range pairwise linkage disequilibrium across the region appears to remain intact on two common haplotypes. A reduced-median network demonstrates a clear relationship between 3p21 haplotypes, rooted by the putative ancestral haplotype determined by direct sequencing of four primate species. Analysis of six SNPs on 17q11-12 indicates that 97.5 per cent of the variation is explained by 15 haplotypes

  6. 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

  7. Localization of an ataxia-telangiectasia gene by linkage disequilibrium in the Costa Rican population

    SciTech Connect

    Uhrhammer, N.A.; Lange, E.; Gatti, R.A.

    1994-09-01

    Linkage disequilibrium (LD) was studied in 27 Costa Rican families with ataxia-telangiectasia. Previous studies indicate that the ATA and ATC gene(s) are on chromosome 11q22.3, between D11S1819 and D11S927. We studied the ordered loci D11-S1816, S1817, S1343, S1819, S384, S535, S1295, S1818, S927, S1300 and S1004 by PCR and Southern blotting. We noted moderate LD at the more distant markers S1816, S1300, and S1004. LD was higher at markers closer to A-T, and also where A-T was associated with rarer alleles. This broad region of disequilibrium did not by itself contribute to further localization of the A-T gene(s). We analyzed 54 affected chromosomal haplotypes. The most common haplotype occurred 34 times, including some that had recombined outside the known A-T region. Other haplotypes occurred seven times, five times, two occurred twice, and the four remaining were unique. The most common haplotype had `broken` at S927 in five different patients, placing A-T proximal to this marker. We looked for recombination events in 15 of the families to further localize A-T. We observed one family with a recombination event placing A-T distal to S1819. A second family appears to either not link to 11q22.3 or to have a double-crossover between the markers S384 and S927; two affected sibs share haplotypes for the entire region studied, and a normal sib shared the same two haplotypes. Since all or part of this A-T haplotype occurs in 32 other, unrelated, Costa Rican patients, we anticipate a double-crossover in the 1600 kb between the informative flanking markers. All other families show segregation patterns consistent with placing A-T at 11q22.3. These results demonstrate that the major A-T gene in the Costa Rican population is located between S1819 and S927 at 11q22.3.

  8. Method for calcining radioactive wastes

    DOEpatents

    Bjorklund, William J.; McElroy, Jack L.; Mendel, John E.

    1979-01-01

    This invention relates to a method for the preparation of radioactive wastes in a low leachability form by calcining the radioactive waste on a fluidized bed of glass frit, removing the calcined waste to melter to form a homogeneous melt of the glass and the calcined waste, and then solidifying the melt to encapsulate the radioactive calcine in a glass matrix.

  9. 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.

  10. 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.

  11. Linkage disequilibrium utilized to establish a refined genetic position of the Salla disease locus on 6q14-q15

    SciTech Connect

    Schleutker, J.; Laine, A.P.; Haataja, L. |

    1995-05-20

    Salla disease (SD), an inherited free sialic acid storage disorder, is caused by impaired transport of free sialic acid across the lyosomal membrane. Clinical characteristics of the disease include severe psychomotor retardation and some neurological abnormalities. The authors report detailed linkage analyses of 50 Finnish SD families that localize the SD disease gene to a refined chromosomal area on 6q14-q15. The highest lod score of 17.30 was obtained with a microsatellite marker of locus D6S280. When linkage disequilibrium was adopted in the linkage analyses, they could further assign the SD locus to the immediate vicinity of marker locus D6S406. Linkage disequilibrium facilitated further restriction of the critical chromosomal region to approximately 80 kb, well within the limits of positional cloning techniques. 31 refs., 3 figs., 3 tabs.

  12. Studies of linkage in populations. XIII. A unique cause of linkage disequilibrium in natural populations of Drosophila robusta.

    PubMed

    Levitan, M; Etges, W J

    1998-06-01

    Natural populations of Drosophila robusta are polymorphic for chromosomal gene arrangements in most of its range, the deciduous forests of North America east of the Rocky Mountains. Many of the gene arrangements are the result of paracentric inversions on both arms of the metacentric second chromosome. They are frequently in linkage disequilibrium, determined in many areas largely, or entirely, by differing frequencies of cis and trans forms of the double heterokaryotypes and their component linkage combinations. Presence and degree of linkage disequilibrium in these populations varies with locality and gender, with males from southern localities exhibiting the largest deviation from equilibrium. Analysis of the extensive karyotype data encompassing the entire species range collected over the past 50 years shows that natural selection is primarily responsible for maintaining these complex polymorphisms.

  13. 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

  14. 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

  15. Dynamic dialog between cytokeratin 18 and annexin A1 in breast cancer: a transcriptional disequilibrium.

    PubMed

    Araujo, Thaise G; Marangoni, Karina; Rocha, Rafael M; Maia, Yara C P; Araujo, Galber R; Alcântar, Tânia M; Alves, Patrícia T; Calábria, Luanda; Neves, Adriana F; Soares, Fernando A; Goulart, Luiz R

    2014-09-01

    Cytokeratins (CKs) constitute the cytoskeletal network and are regulated by post-translational modifications, acting not only as a mechanical support, but also in cell signaling and regulatory processes. Signaling is mediated by CK-associated proteins, such as Annexin A1 (ANXA1), a ligand of the CK18/CK8 complex. ANXA1 has a pivotal role in cellular and immunological responses, and together with CK18 have been implicated in several processes related to malignant transformation in breast cancer (BC). Our aim was to demonstrate how their interaction might be linked to BC development. We investigated transcript levels, protein expression and distribution for both targets in breast tissues of 92 patients (42 BCs and 50 benign diseases) using qPCR and immunohistochemistry, respectively. ANXA1 and CK18 mRNAs were inversely correlated, and their ratio in each TNM stage significantly differentiated BC from benign diseases (OR=5.62). These differences did not mirror tissue protein levels, but a significant dichotomous protein distribution in tumor tissues was observed, differing from the expected co-localization observed during cell homeostasis. The disequilibrium of transcriptional levels between ANXA1/CK18 and alterations in their tissue distribution are present either in initial events or tumor progression, which suggest a critical event in BC. The broken dialog between ANXA1 and CK18 in normal breast tissues may play a critical role in BC development, and together may be used as combined targets for BC diagnostics. PMID:25028131

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. Haplotype and linkage disequilibrium analysis of the CRMP1 and EVC genes.

    PubMed

    Sivakumaran, Theru A; Lesperance, Marci M

    2004-11-01

    In this report, we present the haplotype and linkage disequilibrium (LD) pattern in the Collapsin Response Mediator Protein 1 (CRMP1) and Ellis-van Creveld syndrome (EVC) gene region. We genotyped eight different single nucleotide polymorphisms (SNPs) in the CRMP1 and EVC genes in 90 control individuals of diverse ethnicity. The minor allele frequencies ranged from 3.3-49.4%, with most having a frequency >25%. A total of 37 haplotypes were derived from these eight polymorphisms, with only one haplotype having a frequency >10%. Pairwise LD analysis showed a weak but significant LD between markers located about 243 kb apart in this region. The LD was significant between markers spaced about 208 kb apart in EVC, whereas no LD was found between a pair of markers located about 5 kb apart in CRMP1. However, in general, LD correlated with the distance between loci. The CRMP1 and EVC genes are located near WFS1, the Wolfram syndrome type 1 gene, in which mutations also cause low frequency sensorineural hearing loss (LFSNHL). The haplotypes obtained from these polymorphisms will be useful to track the segregation of phenotypes in families with Ellis-van Creveld syndrome, Weyers acrodental dysostosis, LFSNHL and Wolfram syndrome type 1.

  3. Patterns of linkage disequilibrium of LRRK2 across different races: implications for genetic association studies.

    PubMed

    Li, Huihua; Teo, Yik Ying; Tan, Eng King

    2013-01-01

    Genome Wide Association Studies (GWASs) have identified trait-associated polymorphisms via a hypothesis-free approach. However, it is challenging when attempting to reproduce GWAS findings in different populations as it fundamentally relies on the similar patterns of linkage disequilibrium (LD) between the unknown causal variants and the genotyped single nucleotide polymorphisms (SNPs). To address this potential limitation, we examined the regional LD pattern of leucine-rich repeat kinase 2 (LRRK2) gene, which is responsible for both autosomal dominant and sporadic Parkinson's disease (PD), in Caucasians (CEU), Japanese (JPT) and Chinese (CHB) from HapMap and Chinese (CHS), Malays (MAS) and Indians (INS) from the Singapore Genome Variation Project (SGVP) utilizing the traditional heatmaps and targeted analysis of LRRK2 gene via Monte Carlo simulation through varLD scores of these ethnic groups. Both heatmaps and targeted analysis showed that LD pattern of JPT was different from that of INS (P=0.0001); while LD pattern of CEU was different from that in Asian except for INS (all P=0.0001). Our study suggests that there is a higher chance to detect associations between PD and those trait-associated SNPs of LRRK2 gene found in Caucasian studies in INS, while those found in Japanese studies are likely to be better replicated among CHB.

  4. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

    PubMed Central

    Hohenlohe, Paul A.; Bassham, Susan; Currey, Mark; Cresko, William A.

    2012-01-01

    Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations. PMID:22201169

  5. Linkage disequilibrium and association studies in higher plants: present status and future prospects.

    PubMed

    Gupta, Pushpendra K; Rustgi, Sachin; Kulwal, Pawan L

    2005-03-01

    During the last two decades, DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant systems. Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis. Although this approach of association analysis has already been used for studies on genetics of complex traits (including different diseases) in humans, its use in plants has just started. In the present review, we first define and distinguish between LD and association mapping, and then briefly describe various measures of LD and the two methods of its depiction. We then give a list of different factors that affect LD without discussing them, and also discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in plant genomics research and summarize the present status of LD research in different plant genomes. In the end, we discuss briefly the future prospects of LD research in plants, and give a list of softwares that are useful in LD research, which is available as electronic supplementary material (ESM).

  6. 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

  7. 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.

  8. 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

  9. Disequilibrium response of permafrost thaw to climate warming in Canada over 1850-2100

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Chen, Wenjun; Riseborough, Daniel W.

    2008-01-01

    Climate warming would induce permafrost thaw. However, the response of permafrost to atmospheric climate change could take from a few years to millennia. In this study, we simulated the transient changes in ground thermal regimes and permafrost status in Canada over 1850-2100 at a half-degree latitude/longitude resolution using a process-based model. The results show that the ground thermal regimes were in strong disequilibrium, with much stronger warming near the surface than in deeper ground. The reduction in permafrost extent (20.5-24.0%) by the end of the 21st century was much smaller than equilibrium projections, but permafrost thaw would continue after the 21st century even if air temperature stops increasing. Permafrost thaw from the top was very significant, and the area with supra-permafrost taliks increased exponentially, especially during the 21st century. This marked permafrost thaw from the top could have significant impacts on hydrology, landscape, soil biogeochemistry, ecosystems, and infrastructure.

  10. 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

  11. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region.

    PubMed

    Kauppi, Liisa; Sajantila, Antti; Jeffreys, Alec J

    2003-01-01

    Recombination, demographic history, drift and selection influence the extent of linkage disequilibrium (LD) in the human genome, but their relative contributions remain unclear. To investigate the effect of meiotic recombination versus population history on LD, three populations with different demographic histories (UK north Europeans, Saami and Zimbabweans) were genotyped for high-frequency single-nucleotide polymorphisms (SNPs) across a 75 kb DNA segment of the MHC class II region. This region spans three well-characterized recombination hotspots and a 60 kb long LD block. Despite a high level of underlying haplotype diversity and considerable divergence in haplotype composition between populations, all three populations showed very similar patterns of LD. Surprisingly, the entire 60 kb LD block was present even in Africans, although it was relatively difficult to detect owing to a systematic deficiency of high frequency SNPs. In contrast, DNA within recombination hotspots did not show this low nucleotide diversity in Africans. Thus, while population history has some influence on LD, our findings suggest that recombination hotspots play a major global role in shaping LD patterns as well as helping to maintain localized SNP diversity in this region of the MHC.

  12. Dissecting the genetics of complex inheritance: linkage disequilibrium mapping provides insight into Crohn disease.

    PubMed

    Elding, Heather; Lau, Winston; Swallow, Dallas M; Maniatis, Nikolas

    2011-12-01

    Family studies for Crohn disease (CD) report extensive linkage on chromosome 16q and pinpoint NOD2 as a possible causative locus. However, linkage is also observed in families that do not bear the most frequent NOD2 causative mutations, but no other signals on 16q have been found so far in published genome-wide association studies. Our aim is to identify this missing genetic contribution. We apply a powerful genetic mapping approach to the Wellcome Trust Case-Control Consortium and the National Institute of Diabetes and Digestive and Kidney Diseases genome-wide association data on CD. This method takes into account the underlying structure of linkage disequilibrium (LD) by using genetic distances from LD maps and provides a location for the causal agent. We find genetic heterogeneity within the NOD2 locus and also show an independent and unsuspected involvement of the neighboring gene, CYLD. We find associations with the IRF8 region and the region containing CDH1 and CDH3, as well as substantial phenotypic and genetic heterogeneity for CD itself. The genes are known to be involved in inflammation and immune dysregulation. These findings provide insight into the genetics of CD and suggest promising directions for understanding disease heterogeneity. The application of this method thus paves the way for understanding complex inheritance in general, leading to the dissection of different pathways and ultimately, personalized treatment.

  13. Upwelling in the Atlantic sector of the Southern Ocean inferred from helium isotope disequilibrium

    NASA Astrophysics Data System (ADS)

    Buß, A.; Huhn, O.; Sültenfuß, J.; Rhein, M.

    2012-04-01

    Upwelling plays an important role regarding the physical and biogeochemical characteristics of the mixed layer, and it may also counteract the uptake of atmospheric gases like CO2. However, estimates of upwelling velocities are rare, particularly in the Southern Ocean. Since upwelling velocities are too small to be measured directly - in the order of a few meters per day - an indirect method to infer upwelling velocities from the helium isotope disequilibrium in the mixed layer is applied here instead. The main source of 3He to the ocean is hydrothermal venting and thus a significant excess of 3He in the mixed layer can only be maintained by vertical motion. Helium isotope data - measured from 1986 to 2009 - in the Antarctic Circumpolar Current (ACC) and the Weddell Sea shows a significant excess of 3He in the mixed layer from which upwelling velocities will be inferred. Here, first results of upwelling estimates inferred from helium isotope disequilibria in the ACC and the Weddell Sea will be presented.

  14. Linkage Disequilibrium Mapping via Cladistic Analysis of Single-Nucleotide Polymorphism Haplotypes

    PubMed Central

    Durrant, Caroline; Zondervan, Krina T.; Cardon, Lon R.; Hunt, Sarah; Deloukas, Panos; Morris, Andrew P.

    2004-01-01

    We present a novel approach to disease-gene mapping via cladistic analysis of single-nucleotide polymorphism (SNP) haplotypes obtained from large-scale, population-based association studies, applicable to whole-genome screens, candidate-gene studies, or fine-scale mapping. Clades of haplotypes are tested for association with disease, exploiting the expected similarity of chromosomes with recent shared ancestry in the region flanking the disease gene. The method is developed in a logistic-regression framework and can easily incorporate covariates such as environmental risk factors or additional unlinked loci to allow for population structure. To evaluate the power of this approach to detect disease-marker association, we have developed a simulation algorithm to generate high-density SNP data with short-range linkage disequilibrium based on empirical patterns of haplotype diversity. The results of the simulation study highlight substantial gains in power over single-locus tests for a wide range of disease models, despite overcorrection for multiple testing. PMID:15148658

  15. Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes.

    PubMed

    Durrant, Caroline; Zondervan, Krina T; Cardon, Lon R; Hunt, Sarah; Deloukas, Panos; Morris, Andrew P

    2004-07-01

    We present a novel approach to disease-gene mapping via cladistic analysis of single-nucleotide polymorphism (SNP) haplotypes obtained from large-scale, population-based association studies, applicable to whole-genome screens, candidate-gene studies, or fine-scale mapping. Clades of haplotypes are tested for association with disease, exploiting the expected similarity of chromosomes with recent shared ancestry in the region flanking the disease gene. The method is developed in a logistic-regression framework and can easily incorporate covariates such as environmental risk factors or additional unlinked loci to allow for population structure. To evaluate the power of this approach to detect disease-marker association, we have developed a simulation algorithm to generate high-density SNP data with short-range linkage disequilibrium based on empirical patterns of haplotype diversity. The results of the simulation study highlight substantial gains in power over single-locus tests for a wide range of disease models, despite overcorrection for multiple testing.

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

    PubMed

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

    2015-04-01

    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.

  17. 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.

  18. The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection.

    PubMed

    Liu, Hongjun; Zhou, Huangkai; Wu, Yongsheng; Li, Xiao; Zhao, Jing; Zuo, Tao; Zhang, Xuan; Zhang, Yongzhong; Liu, Sisi; Shen, Yaou; Lin, Haijian; Zhang, Zhiming; Huang, Kaijian; Lübberstedt, Thomas; Pan, Guangtang

    2015-01-01

    Genomic selection is a promising research area due to its practical application in breeding. In this study, impact of realized genetic relationship and linkage disequilibrium (LD) on marker density and training population size required was investigated and their impact on practical application was further discussed. This study is based on experimental data of two populations derived from the same two founder lines (B73, Mo17). Two populations were genotyped with different marker sets at different density: IBM Syn4 and IBM Syn10. A high-density marker set in Syn10 was imputed into the Syn4 population with low marker density. Seven different prediction scenarios were carried out with a random regression best linear unbiased prediction (RR-BLUP) model. The result showed that the closer the real genetic relationship between training and validation population, the fewer markers were required to reach a good prediction accuracy. Taken the short-term cost for consideration, relationship information is more valuable than LD information. Meanwhile, the result indicated that accuracies based on high LD between QTL and markers were more stable over generations, thus LD information would provide more robust prediction capacity in practical applications.

  19. Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits.

    PubMed

    Hill, W G; Mäki-Tanila, A

    2015-04-01

    Linkage disequilibrium (LD) influences the genetic variation in a quantitative trait contributed by two or more loci, with positive LD increasing the variance. The magnitude of LD also affects the relative magnitude of dominance and epistatic variation. We quantify the extent of the non-additive variance expected within populations, deriving analytical expressions for simple models and using numerical simulation in finite population more generally. As LD generates non-independence among loci, a simple partition into additive, dominance and epistatic components is not possible, so we merely distinguish between additive and non-additive components based on comparing covariances among close relatives, such as full sibs, half sibs and offspring-parent. As tight linkage is needed to yield substantial LD in outbred populations, we ignore recombination in the generation used to estimate components and it is analogous to a multi-allelic model. The expected magnitude of the non-additive variance is generally increased but not greatly so by the LD in outbred populations. Thus, as found in previous studies for unlinked loci, independent of the type and strength of gene interaction, the epistatic variance contributes little to the total.

  20. Genome-wide linkage disequilibrium in nine-spined stickleback populations.

    PubMed

    Yang, Ji; Shikano, Takahito; Li, Meng-Hua; Merilä, Juha

    2014-08-12

    Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.

  1. Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium.

    PubMed

    Nishio, M; Satoh, M

    2015-10-01

    The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP-LD). In the three GBLUP-LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP-LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation data. When quantitative trait loci (QTL) were located at weak LD regions, the predictive abilities of the three GBLUP-LD methods were superior to those of GBLUP and Bayesian lasso except when the number of QTL was small. In particular, the superiority of GBLUP-LD increased with decreasing trait heritability. The rates of QTL at weak LD regions would increase when selection by GBLUP continues; this consequently decreases the predictive ability of GBLUP. Thus, the GBLUP-LD could be applicable for populations selected by GBLUP for a long time. However, if QTL were located at strong LD regions, the accuracies of three GBLUP-LD methods were lower than GBLUP and Bayesian lasso.

  2. 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.

  3. Linkage disequilibrium mapping places the gene causing familial Mediterranean fever close to D16S246

    SciTech Connect

    Levy, E. N.; Aksentijevich, I.; Pras, E.

    1996-03-01

    This report presents refined genetic mapping data for the gene causing familial Mediterranean fever (FMF), a recessively inherited disorder of inflammation. We sampled 65 Jewish, Armenian, and Arab families and typed them for eight markers from chromosome 16p. Using a new algorithm that permits multipoint calculations for a dense map of markers in consanguineous families, we obtained a maximal LOD score of 49.2 at a location 1.6 cM centromeric to D16S246. A specific haplotype at D16S283-D16S94-D16S246 was found in 76% of Moroccan and 32% of non-Moroccan Jewish carrier chromosomes, but this haplotype was not overrepresented in Armenian or Arab FMF carriers. Moreover, the 2.5-kb allele at D16S246 was significantly associated with FMF in Moroccan and non-Moroccan Jews but not in Armenians or Arabs. Since the Moroccan Jewish community represents a relatively recently established and genetically isolated founder population, we analyzed the Moroccan linkage-disequilibrium data by using Luria-Delbruck formulas and simulations based on a Poisson branching process. These methods place the FMF susceptibility gene within 0.305 cM of D16S246 (2-LOD-unit range 0.02-0.64 cM). 41 refs., 3 figs., 5 tabs.

  4. The TDT and other family-based tests for linkage disequilibrium and association

    SciTech Connect

    Spielman, R.S.; Ewens, W.J.

    1996-11-01

    The transmission/disequilibrium test (TDT) was introduced several years ago by Spielman et al. as a test for linkage between a complex disease and a genetic marker. The original intended use of the TDT was to test for linkage with a marker located near a candidate gene, in cases where disease association already had been found. However, even if prior evidence for association is absent, the TDT is valid and can be used to test any marker (or a set of markers) for which data are available from parents and one or more affected offspring. Other tests that focus on association itself - but that, like the TDT, are applied to data from nuclear families - also have been proposed. In addition, several papers have appeared recently that discuss extensions and properties of these tests and of the TDT. Since the aim of both the TDT and the association tests is to locate genes that contribute to disease susceptibility, a number of questions about their differences have arisen. In this review, we compare the properties of the TDT with those of family-based tests of association, and we comment on issues regarding the use of these tests. 22 refs., 2 tabs.

  5. 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.

  6. 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.

  7. ArchiLD: hierarchical visualization of linkage disequilibrium in human populations.

    PubMed

    Melchiotti, Rossella; Rötzschke, Olaf; Poidinger, Michael

    2014-01-01

    Linkage disequilibrium (LD) is an essential metric for selecting single-nucleotide polymorphisms (SNPs) to use in genetic studies and identifying causal variants from significant tag SNPs. The explosion in the number of polymorphisms that can now be genotyped by commercial arrays makes the interpretation of triangular correlation plots, commonly used for visualizing LD, extremely difficult in particular when large genomics regions need to be considered or when SNPs in perfect LD are not adjacent but scattered across a genomic region. We developed ArchiLD, a user-friendly graphical application for the hierarchical visualization of LD in human populations. The software provides a powerful framework for analyzing LD patterns with a particular focus on blocks of SNPs in perfect linkage as defined by r(2). Thanks to its integration with the UCSC Genome Browser, LD plots can be easily overlapped with additional data on regulation, conservation and expression. ArchiLD is an intuitive solution for the visualization of LD across large or highly polymorphic genomic regions. Its ease of use and its integration with the UCSC Genome Browser annotation potential facilitates the interpretation of association results and enables a more informed selection of tag SNPs for genetic studies.

  8. 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

    2016-04-07

    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.

  9. 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

  10. 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

  11. 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

  12. Equivalence by descent: pedigree analysis with inbreeding and gametic phase disequilibrium.

    PubMed

    Denniston, C

    2000-01-01

    In the presence of gametic phase disequilibrium and inbreeding, multiple locus genotype frequencies cannot be written solely in terms of identity by descent (IBD) probabilities. Following Cockerham & Weir (1973) we introduce the concept of 'equivalence by descent' (EBD), an extension of the concept of IBD to include non-allelic genes. Two genes are said to be EBD if they derive ultimately from the same founding gamete of a pedigree. Allelic genes that are EBD are also IBD. For two loci 11 EBD probabilities, the 'J-coefficients,' are required and for three loci 117 J-coefficients are required to write genotype probabilities. It is shown how the 117 J-coefficients for three loci can be reduced to a basic set of 37. Computer programs, written in the algebraic programming language, MAPLE, are described which are capable of calculating the two- and three-locus J-coefficients for any pedigree, subject only to size limitations. The MAPLE packages are available from the author upon request.

  13. Gravel threshold of motion: a state function of sediment transport disequilibrium?

    NASA Astrophysics Data System (ADS)

    Johnson, Joel P. L.

    2016-08-01

    In most sediment transport models, a threshold variable dictates the shear stress at which non-negligible bedload transport begins. Previous work has demonstrated that nondimensional transport thresholds (τc*) vary with many factors related not only to grain size and shape, but also with characteristics of the local bed surface and sediment transport rate (qs). I propose a new model in which qs-dependent τc*, notated as τc(qs)*, evolves as a power-law function of net erosion or deposition. In the model, net entrainment is assumed to progressively remove more mobile particles while leaving behind more stable grains, gradually increasing τc(qs)* and reducing transport rates. Net deposition tends to fill in topographic lows, progressively leading to less stable distributions of surface grains, decreasing τc(qs)* and increasing transport rates. Model parameters are calibrated based on laboratory flume experiments that explore transport disequilibrium. The τc(qs)* equation is then incorporated into a simple morphodynamic model. The evolution of τc(qs)* is a negative feedback on morphologic change, while also allowing reaches to equilibrate to sediment supply at different slopes. Finally, τc(qs)* is interpreted to be an important but nonunique state variable for morphodynamics, in a manner consistent with state variables such as temperature in thermodynamics.

  14. Effect of initial linkage disequilibrium and epistasis on fixation probability in a small population, with two segregating loci.

    PubMed

    Ohta, T

    1968-06-01

    The probability of ultimate fixation was studied for 2 loci small populations by the method of Monte Carlo simulation and also partly by analytical treatment. The analytical solutions for fixation probability known at present and the difficulty of their application to more complex situations were discussed. Monte Carlo experiments were carried out for large values ofN e s 1,N e s 2 andN e ε, for which the analytical solutions have not been obtained.One of the main purposes was to investigate the effect of initial linkage disequilibrium (D) on fixation probability. Whens 1,s 2 and ε are 0, the effect of disequilibrium is given by {1-2N e c/(2N e c+1)}D withKIMURA'S model and {1-2N e c/(2 N e c-c+1)}D with the model ofKARLIN andMCGREGOR. When |N e s 1| and |N e s 2| were small and ε=0, the effect of disequilibrium was shown to be almost the same as in the selectively neutral case (formulas 8). When those parameters are not small, the effect of disequilibrium is larger because of the rapid approach to fixation.Another purpose of this study was to investigate the effect of epistasis on fixation probability.KIMURA obtained the solution for joint fixation ofA andB when the selective advantage is given to genotypeAB as the joint effect ofA andB. The present study has verified his formula and showed that linkage does not affectu(AB) under initial linkage equilibrium. Also some cases of additive × additive epistasis were studied. PMID:24442309

  15. 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.

  16. Linkage disequilibrium at the human dopamine D2 receptor locus (DRD2) in three populations from Taiwan

    SciTech Connect

    Ko, H.C.; Lu, R.B.; Chang, F.M.

    1994-09-01

    There are now at least several polymorphisms distributed across the coding regions of DRD2. The TaqI A and B systems are roughly 30 kb apart; the TaqI A system is about 10 kb downstream from the last exon and the TaqI B system is about 5 kb upstream of exon 2 (which contains the initiation codon). Previous studies in U.S. Blacks and Caucasians have show significant linkage disequilibrium. We have studied three ethnic groups living on Taiwan: Chinese Han (44 individuals), Atayal (41 individuals) and Ami (40 individuals). All three groups show significant linkage disequilibrium between the TaqI A and TaqI B systems. The haplotype frequencies differ significantly among the three groups, Blacks and Caucasians; the magnitude of disequilibrium also differs among the six. However, all six groups show a pattern of higher than expected frequencies of A1B1 and A2B2, and lower than expected frequencies of A1B2 and A2B1.

  17. [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.

  18. Kinetics of Radioactive Decay

    NASA Astrophysics Data System (ADS)

    Nagy, S.

    At present there are over 3,000 known nuclides (see the Appendix in Vol. 2 on the “Table of the Nuclides”), 265 of which are stable, while the rest, i.e., more than 90% of them, are radioactive. The chemical applications of the specific isotopes of chemical elements are mostly connected with the latter group, including quite a number of metastable nuclear isomers, making the kinetics of radioactive decay an important chapter of nuclear chemistry. After giving a phenomenological and then a statistical interpretation of the exponential law, the various combinations of individual decay processes as well as the cases of equilibrium and nonequilibrium will be discussed. Half-life systematics of the different decay modes detailed in Chaps. 2 and 4 of this volume are also summarized.

  19. Sources of radioactive ions

    SciTech Connect

    Alonso, J.R.

    1985-05-01

    Beams of unstable nuclei can be formed by direct injection of the radioactive atoms into an ion source, or by using the momentum of the primary production beam as the basis for the secondary beam. The effectiveness of this latter mechanism in secondary beam formation, i.e., the quality of the emerging beam (emittance, intensity, energy spread), depends critically on the nuclear reaction kinematics, and on the magnitude of the incident beam energy. When this beam energy significantly exceeds the energies typical of the nuclear reaction process, many of the qualities of the incident beam can be passed on to the secondary beam. Factors affecting secondary beam quality are discussed, along with techniques for isolating and purifying a specific secondary product. The ongoing radioactive beam program at the Bevalac is used as an example, with applications, present performance and plans for improvements.

  20. Radioactive ion detector

    DOEpatents

    Bower, K.E.; Weeks, D.R.

    1997-08-12

    Apparatus for detecting the presence, in aqueous media, of substances which emit alpha and/or beta radiation and determining the oxidation state of these radioactive substances, that is, whether they are in cationic or anionic form. In one embodiment, a sensor assembly has two elements, one comprised of an ion-exchange material which binds cations and the other comprised of an ion-exchange material which binds anions. Each ion-exchange element is further comprised of a scintillation plastic and a photocurrent generator. When a radioactive substance to which the sensor is exposed binds to either element and emits alpha or beta particles, photons produced in the scintillation plastic illuminate the photocurrent generator of that element. Sensing apparatus senses generator output and thereby indicates whether cationic species or anionic species or both are present and also provides an indication of species quantity. 2 figs.

  1. Radioactive ion detector

    DOEpatents

    Bower, Kenneth E.; Weeks, Donald R.

    1997-01-01

    Apparatus for detecting the presence, in aqueous media, of substances which emit alpha and/or beta radiation and determining the oxidation state of these radioactive substances, that is, whether they are in cationic or anionic form. In one embodiment, a sensor assembly has two elements, one comprised of an ion-exchange material which binds cations and the other comprised of an ion-exchange material which binds anions. Each ion-exchange element is further comprised of a scintillation plastic and a photocurrent generator. When a radioactive substance to which the sensor is exposed binds to either element and emits alpha or beta particles, photons produced in the scintillation plastic illuminate the photocurrent generator of that element. Sensing apparatus senses generator output and thereby indicates whether cationic species or anionic species or both are present and also provides an indication of species quantity.

  2. Table of radioactive elements

    SciTech Connect

    Holden, N.E.

    1985-01-01

    As has been the custom in the past, the Commission publishes a table of relative atomic masses and halflives of selected radionuclides. The information contained in this table will enable the user to calculate the atomic weight for radioactive materials with a variety of isotopic compositions. The atomic masses have been taken from the 1984 Atomic Mass Table. Some of the halflives have already been documented.

  3. PROCESSING OF RADIOACTIVE WASTE

    DOEpatents

    Johnson, B.M. Jr.; Barton, G.B.

    1961-11-14

    A process for treating radioactive waste solutions prior to disposal is described. A water-soluble phosphate, borate, and/or silicate is added. The solution is sprayed with steam into a space heated from 325 to 400 deg C whereby a powder is formed. The powder is melted and calcined at from 800 to 1000 deg C. Water vapor and gaseous products are separated from the glass formed. (AEC)

  4. Radioactive waste storage issues

    SciTech Connect

    Kunz, D.E.

    1994-08-15

    In the United States we generate greater than 500 million tons of toxic waste per year which pose a threat to human health and the environment. Some of the most toxic of these wastes are those that are radioactively contaminated. This thesis explores the need for permanent disposal facilities to isolate radioactive waste materials that are being stored temporarily, and therefore potentially unsafely, at generating facilities. Because of current controversies involving the interstate transfer of toxic waste, more states are restricting the flow of wastes into - their borders with the resultant outcome of requiring the management (storage and disposal) of wastes generated solely within a state`s boundary to remain there. The purpose of this project is to study nuclear waste storage issues and public perceptions of this important matter. Temporary storage at generating facilities is a cause for safety concerns and underscores, the need for the opening of permanent disposal sites. Political controversies and public concern are forcing states to look within their own borders to find solutions to this difficult problem. Permanent disposal or retrievable storage for radioactive waste may become a necessity in the near future in Colorado. Suitable areas that could support - a nuclear storage/disposal site need to be explored to make certain the health, safety and environment of our citizens now, and that of future generations, will be protected.

  5. Radioactive deposits of Nevada

    USGS Publications Warehouse

    Lovering, T.G.

    1953-01-01

    Thirty-five occurrences of radioactive rocks had been reported from Nevada prior to 1952. Twenty-five of these had been investigated by the U. S. Geological Survey and the U. S. Atomic Energy Commission. Of those investigated, uranium minerals were identified in 13; two contained a thorium mineral (monazite); the source of radioactivity on 7 properties was not ascertained; and one showed no abnormal radioactivity. Of the other reported occurrences, one is said to contain uraniferous hydrocarbons and 9 are placers containing thorian monazite. Pitchblende occurs at two localities; the East Walker River area, and the Stalin's Present prospect, where it is sparsely disseminated in tabular bodies cutting granitic rocks. Other uranium minerals found in the state include: carnotite, tyuyamunite, autunite, torbernite, gummite, uranophane, kasolite, and an unidentified mineral which may be dumontit. Monazite is the only thorium mineral of possible economic importance that has been reported. From an economic standpoint 9 only 4 of the properties examined showed reserves of uranium ore in 1952; these are: the Green Monster mine, which shipped 5 tons of ore to Marysvale, Utah, during 1951, the Majuba Hill mine, the Stalin's Present prospect, and the West Willys claim in the Washington district. Reserves of ore grade are small on all of these properties and probably cannot be developed commercially unless an ore-buying station is set up nearby. No estimate has been made of thorium reserves and no commercial deposits of thorium are known.

  6. Radioactive deposits of Nevada

    USGS Publications Warehouse

    Lovering, T.G.

    1954-01-01

    Thirty-five occurrences of radioactive rocks had been reported from Nevada prior to 1952. Twenty-five of these had been investigated by personnel of the U. S. Geological Surveyor of the U. S. Atomic Energy Commission. Of those investigated, uranium minerals were identified at 13 sites; two sites contained a thorium mineral (monazite); the source of radioactivity on nine properties was not ascertained, and one showed no abnormal radioactivity. Of the other reported occurrences, one is said to contain uraniferous hydrocarbons and nine are placers containing thorian monazite. Pitchblende occurs at two localities, the East Walker River area, and the Stalin's Present prospect, where it is sparsely disseminated in tabular bodies cutting granitic rocks. Other uranium minerals found in the state include: carnotite, tyuyamunite, autunite, torbernite, gummite, uranophane, kasolite, and an unidentified mineral which may be dumontite. Monazite is the only thorium mineral of possible economic importance that has been reported. From an economic standpoint, only four of the properties examined showed reserves of uranium ore in 1952; these are: the Green Monster mine, which shipped 5 tons of ore to Marysvale, Utah, during 1951; the Majuba Hill mine; the Stalin's Present prospect; and the West Willys claim in the Washington district. No estimate has been made of thorium reserves and no commercial deposits of thorium are known.

  7. ASSESSMENT OF RADIOACTIVE AND NON-RADIOACTIVE CONTAMINANTS FOUND IN LOW LEVEL RADIOACTIVE WASTE STREAMS

    SciTech Connect

    R.H. Little, P.R. Maul, J.S.S. Penfoldag

    2003-02-27

    This paper describes and presents the findings from two studies undertaken for the European Commission to assess the long-term impact upon the environment and human health of non-radioactive contaminants found in various low level radioactive waste streams. The initial study investigated the application of safety assessment approaches developed for radioactive contaminants to the assessment of nonradioactive contaminants in low level radioactive waste. It demonstrated how disposal limits could be derived for a range of non-radioactive contaminants and generic disposal facilities. The follow-up study used the same approach but undertook more detailed, disposal system specific calculations, assessing the impacts of both the non-radioactive and radioactive contaminants. The calculations undertaken indicated that it is prudent to consider non-radioactive, as well as radioactive contaminants, when assessing the impacts of low level radioactive waste disposal. For some waste streams with relatively low concentrations of radionuclides, the potential post-closure disposal impacts from non-radioactive contaminants can be comparable with the potential radiological impacts. For such waste streams there is therefore an added incentive to explore options for recycling the materials involved wherever possible.

  8. Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations

    PubMed Central

    Hu, Xin-Sheng; Hu, Yang

    2015-01-01

    Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI) possess more significant zygotic LDs for the double-homozygotes (DAABB) than any other significant zygotic LDs (DAABb, DAaBB, and DAaBb), while non-Africa populations generally have more significant DAaBb’s than any other significant zygotic LDs (DAABB, DAABb, and DAaBB). Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for DAABB and DAaBb than for DAaBB and DAABb in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia), which helps to understand geographical genomic medicine. PMID:26126177

  9. A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions

    PubMed Central

    Berger, Swetlana; Schlather, Martin; de los Campos, Gustavo; Weigend, Steffen; Preisinger, Rudolf; Erbe, Malena; Simianer, Henner

    2015-01-01

    The understanding of non-random association between loci, termed linkage disequilibrium (LD), plays a central role in genomic research. Since causal mutations are generally not included in genomic marker data, LD between those and available markers is essential for capturing the effects of causal loci on localizing genes responsible for traits. Thus, the interpretation of association studies requires a detailed knowledge of LD patterns. It is well known that most LD measures depend on minor allele frequencies (MAF) of the considered loci and the magnitude of LD is influenced by the physical distances between loci. In the present study, a procedure to compare the LD structure between genomic regions comprising several markers each is suggested. The approach accounts for different scaling factors, namely the distribution of MAF, the distribution of pair-wise differences in MAF, and the physical extent of compared regions, reflected by the distribution of pair-wise physical distances. In the first step, genomic regions are matched based on similarity in these scaling factors. In the second step, chromosome- and genome-wide significance tests for differences in medians of LD measures in each pair are performed. The proposed framework was applied to test the hypothesis that the average LD is different in genic and non-genic regions. This was tested with a genome-wide approach with data sets for humans (Homo sapiens), a highly selected chicken line (Gallus gallus domesticus) and the model plant Arabidopsis thaliana. In all three data sets we found a significantly higher level of LD in genic regions compared to non-genic regions. About 31% more LD was detected genome-wide in genic compared to non-genic regions in Arabidopsis thaliana, followed by 13.6% in human and 6% chicken. Chromosome-wide comparison discovered significant differences on all 5 chromosomes in Arabidopsis thaliana and on one third of the human and of the chicken chromosomes. PMID:26517830

  10. Extent and Distribution of Linkage Disequilibrium in the Old Order Amish

    PubMed Central

    Van Hout, Cristopher V; Levin, Albert M; Rampersaud, Evadnie; Shen, Haiqing; O'Connell, Jeffrey R; Mitchell, Braxton D; Shuldiner, Alan R; Douglas, Julie A

    2010-01-01

    Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02–0.09, and for autosomal SNPs 10–20 kb apart with common alleles (minor allele frequency≥0.05), the LD measure r2 was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA (∼88%) at r2≥0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations. PMID:19697356

  11. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

    PubMed

    Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

    2012-08-01

    White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

  12. Carbon and oxygen isotopic disequilibrium during calcification of Globigerina bulloides in the Southern ocean

    NASA Astrophysics Data System (ADS)

    K, P.; Ghosh, P.; N, A.

    2015-12-01

    Oxygen and carbon isotopes in planktonic foraminifera Globigerina bulloides recovered from the water column of 0-1000 m depth across the meridional transect i.e. 10°N to 53°S of Indian ocean were compared with the available data from the core-top samples across the same transect. We also recorded in situ temperatures of the water column based on probe (CTD) profiles. The δ18O and δ13C values measured in the core top samples matches with the tow results. The equilibrium δ18O of calcite calculated from known temperature and δ18O of water column allowed us to compare the observed δ18O of formaminieral shell with the expected equilibrium values. Our comparison of carbonate composition in the samples between 10°N till 40°S showed excellent match with the expected equilibrium δ18O values established from the water collected at depth range of ~75-200m, however beyond 40°S the disequilibrium was pronounced with heavier δ18O (enriched by ~1.5‰) recorded in the carbonate as compared with the expected equilibrium δ18O values established from water. This observation was further verified with δ13C measurement of shell carbonates comparing with the equilibrium δ13C of calcite calculated with known temperature and δ13C of dissolved inorganic carbon in the water column. The δ13C of the shell carbonate was found heavier as compared to the expected equilibrium δ13C. Both δ18O and δ13C showed simultaneous enrichment signature in the region beyond 40°S suggesting role of processes such as leaching along with dissolution of shell carbonate in a relatively acidic condition.

  13. Modeling reactive transport of organic compounds in groundwater using a partial redox disequilibrium approach

    NASA Astrophysics Data System (ADS)

    McNab, W. W.; Narasimhan, T. N.

    1994-09-01

    The chemical transformation of organic contaminants in natural groundwater systems is clearly dependent upon local geochemistry which determines the thermodynamically favorable degradation reactions and the nature of local microbial populations. Conversely, groundwater geochemistry may be impacted significantly in terms of pH and redox couple speciation by the chemical transformation of sufficient quantities of organic compounds. Therefore an understanding of the coupling between degradation reactions, local geochemistry, and chemical transport is essential in predicting the chemical evolution of contaminated aquifers. Equilibrium-based reactive chemical transport models are usually not utilized for problems involving the transport of degradable organic compounds due to slow reaction kinetics and the persistence of intermediate degradation products. In this study we propose a reactive geochemical transport model which considers these types of degradation reactions. An expert system approach is used to postulate a set of sequential, first-order degradation reactions for the organic compounds based upon thermodynamic considerations and user-defined rules. Redox disequilibrium provides the driving force for the abiotic or microbially mediated transformation of the organic compounds as well as the associated response of groundwater geochemistry. Coupling between local inorganic geochemistry and reacting organic compounds is achieved by assuring conservation of operational valence and mass balance. The composite geochemical model is in turn coupled with an integral finite difference transport algorithm using a two-step sequential solution approach. The transport equation is solved separately for each inorganic aqueous species, complex, and dissolved organic species, allowing a high degree of flexibility in problem definition. We apply the model to an illustrative example problem concerning the introduction of aromatic hydrocarbons and chlorinated ethenes into an

  14. Modeling reactive transport of organic compounds in groundwater using a partial redox disequilibrium approach

    SciTech Connect

    McNab, W.W. Jr.; Narasimhan, T.N. )

    1994-09-01

    The chemical transformation of organic contaminants in natural groundwater systems is clearly dependent upon local geochemistry which determines the thermodynamically favorable degradation reactions and the nature of local microbial populations. Conversely, groundwater geochemistry may be impacted significantly in terms of pH and redox couple speciation by the chemical transformation of sufficient quantities of organic compounds. Therefore an understanding of the coupling between degradation reactions, local geochemistry, and chemical transport is essential in predicting the chemical evolution of contaminated aquifers. Equilibrium-based reactive chemical transport models are usually not utilized for problems involving the transport of degradable organic compounds due to slow reaction kinetics and the persistence of intermediate degradation products. In this study we propose a reactive geochemical transport model which considers these types of degradation reactions. An expert system approach is used to postulate a set of sequential, first-order degradation reactions for the organic compounds based upon thermodynamic considerations and user-defined rules. Redox disequilibrium provides the driving force for the abiotic or microbially mediated transformation of the organic compounds as well as the associated response of groundwater geochemistry. Coupling between local inorganic geochemistry and reacting organic compounds is achieved by assuring conservation of operation valence and mass balance. The composite geochemical model is in turn coupled with an integral finite difference transport algorithm using a two-step sequential solution approach. The transport equation is solved separately for each inorganic aqueous species, complex, and dissolved organic species, allowing degree of flexibility in problem definition. 58 refs., 18 figs., 2 tabs.

  15. Accuracy of genomic prediction in switchgrass (Panicum virgatum L.) improved by accounting for linkage disequilibrium

    DOE PAGES

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

    2016-02-11

    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,more » 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. Furthermore, some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.« less

  16. Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

    PubMed Central

    Waples, Robin S.; Antao, Tiago; Luikart, Gordon

    2014-01-01

    Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: N^b was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw N^b based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems). PMID:24717176

  17. Extent of Linkage Disequilibrium in the Domestic Cat, Felis silvestris catus, and Its Breeds

    PubMed Central

    Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A.

    2013-01-01

    Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits. PMID:23308248

  18. Assessment of Linkage Disequilibrium in Potato Genome With Single Nucleotide Polymorphism Markers

    PubMed Central

    Simko, Ivan; Haynes, Kathleen G.; Jones, Richard W.

    2006-01-01

    The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that have been analyzed so far for the extent of LD, cultivated potato (Solanum tuberosum L.), an outcrossing species, is a highly heterozygous autotetraploid. The favored genotypes of modern cultivars are maintained by vegetative propagation through tubers. As a first step in the LD analysis, we surveyed both coding and noncoding regions of 66 DNA fragments from 47 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with experimental SNP detection. The total length of all analyzed fragments was >25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (θ = 11.5 × 10−3) and diversity (π = 14.6 × 10−3) was high compared to the other plant species. The overall Tajima's D value (0.5) was not significant, but indicates a deficit of low-frequency alleles relative to expectation. To eliminate the possibility that an elevated D value occurs due to population subdivision, we assessed the population structure with probabilistic statistics. The analysis did not reveal any significant subdivision, indicating a relatively homogenous population structure. However, the analysis of individual fragments revealed the presence of subgroups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show relatively fast decay of LD in the short range (r2 = 0.208 at 1 kb) but slow decay afterward (r2 = 0.137 at ∼70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of ∼10 cM. We speculate that two conflicting factors play a vital role in shaping LD in potato: the outcrossing mating type and the very limited number of meiotic generations. PMID:16783002

  19. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

    PubMed

    Alhaddad, Hasan; Khan, Razib; Grahn, Robert A; Gandolfi, Barbara; Mullikin, James C; Cole, Shelley A; Gruffydd-Jones, Timothy J; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A

    2013-01-01

    Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

  20. Linkage disequilibrium studies of dentatorubral-pallidoluysian atrophy (DRPLA) in Japan

    SciTech Connect

    Kishimoto, T. |; Peterson, A.; Freimer, N.

    1994-09-01

    Dentatorbral-pallidolluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder which is almost unknown outside of Japan. The molecular basis of this disorder was recently demonstrated to be an expansion of a CAG repeat, within a previously unknown gene. This genetic mechanism, trinucleotide repeat expansion, has now been shown to be the basis of several neurological diseases. For many of these disorders, population studies have indicated that individuals with predisposition to expansion demonstrate conservation of haplotypes for polymorphic markers which flank the trinucleotide repeat, suggesting that predisposing mutations occurred on a small number of founding chromosomes. For most of the disorders associated with unstable repeats, prevalence is not mainly limited to a single population, and therefore it is unlikely that a single region can be identified which is completely conserved in all patients. However, for DRPLA, the Japanese predominance suggests that investigating patterns of linkage disequilibrium and haplotype conservation may be especially instructive. We have collected a sample consisting of 8 unrelated Japanese DRPLA patients and 74 unrelated members of the general Japanese population, and have genotyped these individuals for the DRPLA trinucleotide repeat; all of the patients demonstrate the expansion. In addition, 6 individuals from the general population have CAG repeat numbers in the high normal/predisposing size range. By typing 8 microsatellite markers from a 7 cM region between D12S99 and D12S77, we have identified a haplotype, consisting of four markers, which appears to be partially conserved in the DRPLA patients. Future work will focus on more complete reconstruction of the predisposing haplotype with additional markers.

  1. Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster.

    PubMed

    Garud, Nandita R; Petrov, Dmitri A

    2016-06-01

    The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ∼10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.

  2. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.

    PubMed

    Kovi, Mallikarjuna Rao; Fjellheim, Siri; Sandve, Simen R; Larsen, Arild; Rudi, Heidi; Asp, Torben; Kent, Matthew Peter; Rognli, Odd Arne

    2015-01-01

    Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two F st outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  3. Effective population size, extended linkage disequilibrium and signatures of selection in the rare dog breed lundehund.

    PubMed

    Pfahler, Sophia; Distl, Ottmar

    2015-01-01

    The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2 = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed = 0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.

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

    PubMed

    Abdurakhmonov, Ibrokhim Y; Saha, Sukumar; Jenkins, Jonnie N; Buriev, Zabardast T; Shermatov, Shukhrat E; Scheffler, Brain E; Pepper, Alan E; Yu, John Z; Kohel, Russell J; Abdukarimov, Abdusattor

    2009-07-01

    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. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r (2) >or= 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r (2) >or= 0.2 was reduced to approximately 5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at 'moderate to strong' and 'strong to very strong' evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources. PMID:19067183

  5. Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle

    PubMed Central

    2012-01-01

    Background Linkage disequilibrium (LD) between genes at linked or independent loci can occur at gametic and zygotic levels known asgametic LD and zygotic LD, respectively. Gametic LD is well known for its roles in fine-scale mapping of quantitative trait loci, genomic selection and evolutionary inference. The less-well studied is the zygotic LD and its components that can be also estimated directly from the unphased SNPs. Results This study was set up to investigate the genome-wide extent and patterns of zygotic LD and its components in a crossbred cattle population using the genomic data from the Illumina BovineSNP50 beadchip. The animal population arose from repeated crossbreeding of multiple breeds and selection for growth and cow reproduction. The study showed that similar genomic structures in gametic and zygotic LD were observed, with zygotic LD decaying faster than gametic LD over marker distance. The trigenic and quadrigenic disequilibria were generally two- to three-fold smaller than the usual digenic disequilibria (gametic or composite LD). There was less power of testing for these high-order genic disequilibria than for the digenic disequilibria. The power estimates decreased with the marker distance between markers though the decay trend is more obvious for the digenic disequilibria than for high-order disequilibria. Conclusions This study is the first major genome-wide survey of all non-allelic associations between pairs of SNPs in a cattle population. Such analysis allows us to assess the relative importance of gametic LD vs. all other non-allelic genic LDs regardless of whether or not the population is in HWE. The observed predominance of digenic LD (gametic or composite LD) coupled with insignificant high-order trigenic and quadrigenic disequilibria supports the current intensive focus on the use of high-density SNP markers for genome-wide association studies and genomic selection activities in the cattle population. PMID:22827586

  6. Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

    PubMed Central

    Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

    2015-01-01

    Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

  7. The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes

    PubMed Central

    2014-01-01

    Background The extent of linkage disequilibrium (LD) between molecular markers impacts genome-wide association studies and implementation of genomic selection. The availability of high-density single nucleotide polymorphism (SNP) genotyping platforms makes it possible to investigate LD at an unprecedented resolution. In this work, we characterised LD decay in breeds of beef cattle of taurine, indicine and composite origins and explored its variation across autosomes and the X chromosome. Findings In each breed, LD decayed rapidly and r2 was less than 0.2 for marker pairs separated by 50 kb. The LD decay curves clustered into three groups of similar LD decay that distinguished the three main cattle types. At short distances between markers (< 10 kb), taurine breeds showed higher LD (r2 = 0.45) than their indicine (r2 = 0.25) and composite (r2 = 0.32) counterparts. This higher LD in taurine breeds was attributed to a smaller effective population size and a stronger bottleneck during breed formation. Using all SNPs on only the X chromosome, the three cattle types could still be distinguished. However for taurine breeds, the LD decay on the X chromosome was much faster and the background level much lower than for indicine breeds and composite populations. When using only SNPs that were polymorphic in all breeds, the analysis of the X chromosome mimicked that of the autosomes. Conclusions The pattern of LD mirrored some aspects of the history of breed populations and showed a sharp decay with increasing physical distance between markers. We conclude that the availability of the HD chip can be used to detect association signals that remained hidden when using lower density genotyping platforms, since LD dropped below 0.2 at distances of 50 kb. PMID:24661366

  8. PERSPECTIVE: Fireworks and radioactivity

    NASA Astrophysics Data System (ADS)

    Breitenecker, Katharina

    2009-09-01

    both reaction products and unburnt constituents of a pyrotechnic mixture. One major environmental concern in pyrotechnics focuses on the emission of heavy metals. This is the topic discussed in the article by Georg Steinhauser and Andreas Musilek in this issue [4]. A possible interrelationship between respiratory effects and fireworks emissions of barium-rich aerosols was also raised last year [5]. In recent years the potential hazard of naturally occurring radioactive material has become of importance to the scientific community. Naturally occurring radionuclides can be of terrestrial or cosmological origin. Terrestrial radionuclides were present in the presolar cloud that later contracted in order to build our solar system. These radionuclides—mainly heavy metals—and their non-radioactive isotopes are nowadays fixed in the matrix of the Earth's structure. Usually, their percentage is quite small compared to their respective stable isotopes—though there are exceptions like in the case of radium. The problem with environmental pollution due to naturally occurring radioactive material begins when this material is concentrated due to mining and milling, and later further processed [6]. Environmental pollution due to radioactive material goes back as far as the Copper and Iron Ages, when the first mines were erected in order to mine ores (gold, silver, copper, iron, etc), resulting in naturally occurring radioactive material being set free with other dusts into the atmosphere. So where is the link between pyrotechnics and radioactivity? In this article presented by Georg Steinhauser and Andreas Musilek [4], the pyrotechnic ingredients barium nitrate and strontium nitrate are explored with respect to their chemical similarities to radium. The fundamental question, therefore, was whether radium can be processed together with barium and strontium. If so, the production and ignition of these pyrotechnic ingredients could cause atmospheric pollution with radium aerosols

  9. Study of proton radioactivities

    SciTech Connect

    Davids, C.N.; Back, B.B.; Henderson, D.J.

    1995-08-01

    About a dozen nuclei are currently known to accomplish their radioactive decay by emitting a proton. These nuclei are situated far from the valley of stability, and mark the very limits of existence for proton-rich nuclei: the proton drip line. A new 39-ms proton radioactivity was observed following the bombardment of a {sup 96}Ru target by a beam of 420-MeV {sup 78}Kr. Using the double-sided Si strip detector implantation system at the FMA, a proton group having an energy of 1.05 MeV was observed, correlated with the implantation of ions having mass 167. The subsequent daughter decay was identified as {sup 166}Os by its characteristic alpha decay, and therefore the proton emitter is assigned to the {sup 167}Ir nucleus. Further analysis showed that a second weak proton group from the same nucleus is present, indicating an isomeric state. Two other proton emitters were discovered recently at the FMA: {sup 171}Au and {sup 185}Bi, which is the heaviest known proton radioactivity. The measured decay energies and half-lives will enable the angular momentum of the emitted protons to be determined, thus providing spectroscopic information on nuclei that are beyond the proton drip line. In addition, the decay energy yields the mass of the nucleus, providing a sensitive test of mass models in this extremely proton-rich region of the chart of the nuclides. Additional searches for proton emitters will be conducted in the future, in order to extend our knowledge of the location of the proton drip line.

  10. Radioactive and magnetic investigations

    NASA Technical Reports Server (NTRS)

    Heye, D.; Beiersdorf, H.

    1979-01-01

    Age and growth pattern determination of manganese nodules were explored. Two methods are discussed: (1) measurement of the presence of radioactive iodine isotopes; which is effective only up to 3.105 years, and (2) measurements of magnetism. The growth rates of three nodules were determined. The surface of the nodule was recent, and the overall age of the nodule could be determined with accuracy of better than 30%. Measurement of paleomagnetic effect was attempted to determine wider age ranges, however, the measured sign changes could not be interpreted as paleomagnetic reversals.

  11. Radioactive waste material disposal

    DOEpatents

    Forsberg, Charles W.; Beahm, Edward C.; Parker, George W.

    1995-01-01

    The invention is a process for direct conversion of solid radioactive waste, particularly spent nuclear fuel and its cladding, if any, into a solidified waste glass. A sacrificial metal oxide, dissolved in a glass bath, is used to oxidize elemental metal and any carbon values present in the waste as they are fed to the bath. Two different modes of operation are possible, depending on the sacrificial metal oxide employed. In the first mode, a regenerable sacrificial oxide, e.g., PbO, is employed, while the second mode features use of disposable oxides such as ferric oxide.

  12. Radioactive waste material disposal

    DOEpatents

    Forsberg, C.W.; Beahm, E.C.; Parker, G.W.

    1995-10-24

    The invention is a process for direct conversion of solid radioactive waste, particularly spent nuclear fuel and its cladding, if any, into a solidified waste glass. A sacrificial metal oxide, dissolved in a glass bath, is used to oxidize elemental metal and any carbon values present in the waste as they are fed to the bath. Two different modes of operation are possible, depending on the sacrificial metal oxide employed. In the first mode, a regenerable sacrificial oxide, e.g., PbO, is employed, while the second mode features use of disposable oxides such as ferric oxide. 3 figs.

  13. Material for radioactive protection

    DOEpatents

    Taylor, R.S.; Boyer, N.W.

    A boron containing burn resistant, low-level radiation protection material useful, for example, as a liner for radioactive waste disposal and storage, a component for neutron absorber, and a shield for a neutron source is described. The material is basically composed of borax in the range of 25 to 50%, coal tar in the range of 25 to 37.5%, with the remainder being an epoxy resin mix. A preferred composition is 50% borax, 25% coal tar and 25% epoxy resin. The material is not susceptible to burning and is about 1/5 the cost of existing radiation protection material utilized in similar applications.

  14. Levels of radioactivity in Qatar

    SciTech Connect

    Al-Thani, A.A.; Abdul-Majid, S.; Mohammed, K.

    1995-12-31

    The levels of natural and man-made radioactivity in soil and seabed were measured in Qatar to assess radiation exposure levels and to evaluate any radioactive contamination that may have reached the country from fallout or due to the Chernobyl accident radioactivity release. Qatar peninsula is located on the Arabian Gulf, 4500 km from Chernobyl, and has an area of {approximately}11,600 km{sup 2} and a population of {approximately}600,000.

  15. U-series zircon age constraints on the plumbing system and magma residence times of the Changbai volcano, China/North Korea border

    NASA Astrophysics Data System (ADS)

    Zou, Haibo; Fan, Qicheng; Zhang, Hongfu; Schmitt, Axel K.

    2014-07-01

    The Changbai (or Baitoushan, Paektu) volcano on the China/North Korea border is best known for its climactic caldera-forming eruption of 100 km3 of comendite materials 1000 years (1 ka) ago. The polygenetic Changbai volcano also erupted moderate-volume pre-caldera comendite lava at ~ 4 ka and small-volume post-caldera trachyte ignimbrite at ~ 0.3 ka. Here we report 238U-230Th disequilibrium ages of zircons from lavas and ignimbrites of the pre-caldera (~ 4 ka), syn-caldera (1 ka), and post-caldera (~ 0.3 ka) events. The zircon isochron ages are 12.2 ± 1.1 ka (2σ) for the 4-ka comendite lava and 12.2 ± 1.7 ka for the 1-ka comendite ignimbrite. Zircons from the 0.3-ka trachyte ignimbrite exhibit 3 respective peaks at 2.6 ± 1.8 ka, 130 ± 10 ka and > 230 ka. The indistinguishable zircon ages for the 4-ka pre-caldera eruption of comendite lava and the 1-ka caldera-forming eruption of comendite pumice and ignimbrite suggest that the 4-ka lava provides an early sampling of a much larger magma body at depth and thus serves as a kind of petrologic early-warning signal. In addition, the 4-ka lava may represent the lowest-temperature magma in the roof zone of a thermally zoned magma chamber that usually escapes first. The distinctive multi-modal zircon age distributions of the 0.3-ka trachytic eruption, however, reveal that this post-caldera eruption tapped a different magma body and indicate that Changbai's magmatic plumbing system had changed after the 1-ka caldera-forming climactic eruption. Our results suggest very short zircon and magma residence times for the Changbai volcano (8 kyr for the 4-ka eruption, 11-12 kyr for the 1-ka eruption and 2.3 kyr for the 0.3-ka eruption).

  16. Uranium and radium diffusion in organic-rich sediments (sapropels)

    NASA Astrophysics Data System (ADS)

    Gourgiotis, A.; Reyss, J.-L.; Frank, N.; Guihou, A.; Anagnostou, C.

    2011-09-01

    Among the late Quaternary Mediterranean sapropels, the S5 (125 ka) is one of the best preserved due to its high organic carbon content that has limited postdepositional oxidation. The high uranium content in this sapropel, >40 dpm g-1, makes this layer interesting for studying uranium series disequilibrium in organic-rich sediments. For this reason, the present work provides isotopic measurements of the U decay series in a S5 sapropel by applying more precise mass spectrometric methods, TIMS/MC-ICPMS, and gamma spectrometry. Assuming that U in the sapropel mostly originated from seawater the (234U/238U), (230Th/238U), (226Ra/230Th) and (231Pa/235U) activity ratios show systematic deviations from the theoretical values for a closed-system evolution of the U series over the 125 ka since sapropel formation. The radiogenic 234Urad and 226Ra show clear evidence of migration in the sapropel with modeled diffusion coefficients of (7.1 ± 1.1) × 10-12 cm2 s-1 and (1.6 ± 0.2) × 10-10 cm2 s-1, respectively. The diffusion of 234Urad cannot explain the high (230Th/238U) and (231Pa/235U) activity ratios observed in the sapropel. Two possible mechanisms or a combination of both are proposed for explaining the irregular (230Th/238U) and (231Pa/235U) activity profiles in sapropel S5. The first one is an enhanced export flux of 230Thxs and 231Paxs excesses exceeding the production rate in seawater, during the time of sapropel formation, and the second one is diffusion of authigenic Uauth in the sapropel. However, the ambiguous determination of 230Thxs and 231Paxs in the sapropel and the poorly understood processes that might lead to Uauth migration in anoxic sediments still limit a final explanation for the deviation of (230Th/238U) and (231Pa/235U) activity ratios from their expected theoretical values.

  17. Regolith production rates calculated with uranium-series isotopes at Susquehanna/Shale Hills Critical Zone Observatory

    NASA Astrophysics Data System (ADS)

    Ma, Lin; Chabaux, Francois; Pelt, Eric; Blaes, Estelle; Jin, Lixin; Brantley, Susan

    2010-08-01

    In the Critical Zone where rocks and life interact, bedrock equilibrates to Earth surface conditions, transforming to regolith. The factors that control the rates and mechanisms of formation of regolith, defined here as material that can be augered, are still not fully understood. To quantify regolith formation rates on shale lithology, we measured uranium-series (U-series) isotopes ( 238U, 234U, and 230Th) in three weathering profiles along a planar hillslope at the Susquehanna/Shale Hills Observatory (SSHO) in central Pennsylvania. All regolith samples show significant U-series disequilibrium: ( 234U/ 238U) and ( 230Th/ 238U) activity ratios range from 0.934 to 1.072 and from 0.903 to 1.096, respectively. These values display depth trends that are consistent with fractionation of U-series isotopes during chemical weathering and element transport, i.e., the relative mobility decreases in the order 234U > 238U > 230Th. The activity ratios observed in the regolith samples are explained by i) loss of U-series isotopes during water-rock interactions and ii) re-deposition of U-series isotopes downslope. Loss of U and Th initiates in the meter-thick zone of "bedrock" that cannot be augered but that nonetheless consists of up to 40% clay/silt/sand inferred to have lost K, Mg, Al, and Fe. Apparent equivalent regolith production rates calculated with these isotopes for these profiles decrease exponentially from 45 m/Myr to 17 m/Myr, with increasing regolith thickness from the ridge top to the valley floor. With increasing distance from the ridge top toward the valley, apparent equivalent regolith residence times increase from 7 kyr to 40 kyr. Given that the SSHO experienced peri-glacial climate ˜ 15 kyr ago and has a catchment-wide averaged erosion rate of ˜ 15 m/Myr as inferred from cosmogenic 10Be, we conclude that the hillslope retains regolith formed before the peri-glacial period and is not at geomorphologic steady state. Both chemical weathering reactions of clay

  18. Radioactive waste processing apparatus

    DOEpatents

    Nelson, Robert E.; Ziegler, Anton A.; Serino, David F.; Basnar, Paul J.

    1987-01-01

    Apparatus for use in processing radioactive waste materials for shipment and storage in solid form in a container is disclosed. The container includes a top, and an opening in the top which is smaller than the outer circumference of the container. The apparatus includes an enclosure into which the container is placed, solution feed apparatus for adding a solution containing radioactive waste materials into the container through the container opening, and at least one rotatable blade for blending the solution with a fixing agent such as cement or the like as the solution is added into the container. The blade is constructed so that it can pass through the opening in the top of the container. The rotational axis of the blade is displaced from the center of the blade so that after the blade passes through the opening, the blade and container can be adjusted so that one edge of the blade is adjacent the cylindrical wall of the container, to insure thorough mixing. When the blade is inside the container, a substantially sealed chamber is formed to contain vapors created by the chemical action of the waste solution and fixant, and vapors emanating through the opening in the container.

  19. Exploring Radioactive Decay and Geochronology through Hydrostatic Principles

    NASA Astrophysics Data System (ADS)

    Claiborne, L. L.; Miller, C. F.

    2008-12-01

    results and/or designing an experiment to address complex decay chains, where the daughter products are radioactive themselves. This permits them to investigate connections between 'activity' and equilibrium and to understand how disequilibrium can develop and be used for dating. In order to evaluate the success of the activity, each student participates in pre and post assessment including stating their confidence in their understanding of the concept.

  20. The age of human mutation: Genealogical and linkage disequilibrium analysis of the CLN5 mutation in the Finnish population

    SciTech Connect

    Varilo, T; Savukoski, M.; Peltonen, L.

    1996-03-01

    Variant late infantile neuronal ceroid lipofuscinosis (vLINCL) is an autosomal recessive progressive encephalopathy of childhood enriched in the western part of Finland, with a local incidence of 1/1,500. We recently assigned the locus for vLINCL, CLN5, to 13q21.1-q32. In the present study, the haplotype analysis of Finnish CLN5 chromosomes provides evidence that one single mutation causes vLINCL in the Finnish population. Eight microsatellite markers closely linked to the CLN5 gene on chromosome 13q were analyzed, to study identity by descent by shared haplotype analysis. One single haplotype formed by flanking markers D13S160 and D13S162 in strong linkage disequilibrium (P < .0001) was present in 81% of disease-bearing chromosomes. Allele 4 at the marker locus D13S162 was detected in 94% of disease-bearing chromosomes. To evaluate the age of the CLN5 mutation by virtue of its restricted geographical distribution, church records were used to identify the common ancestors for 18 vLINCL families diagnosed in Finland. The pedigrees of the vLINCL ancestors merged on many occasions, which also supports a single founder mutation that obviously happened 20-30 generations ago (i.e., {approximately}500 years ago) in this isolated population. Linkage disequilibrium was detected with seven markers covering an extended genetic distance of 11 cM, which further supports the young age of the CLN5 mutation. When the results of genealogical and linkage disequilibrium studies were combined, the CLN5 gene was predicted to lie {approximately}200-400 kb (total range 30-1,360 kb) from the closest marker D13S162. 29 refs., 2 figs., 5 tabs.

  1. DISEQUILIBRIUM CARBON, OXYGEN, AND NITROGEN CHEMISTRY IN THE ATMOSPHERES OF HD 189733b AND HD 209458b

    SciTech Connect

    Moses, Julianne I.; Visscher, C.; Fortney, J. J.; Showman, A. P.; Lewis, N. K.; Griffith, C. A.; Klippenstein, S. J.; Shabram, M.; Friedson, A. J.; Marley, M. S.; Freedman, R. S.

    2011-08-10

    We have developed a one-dimensional photochemical and thermochemical kinetics and diffusion model to study the effects of disequilibrium chemistry on the atmospheric composition of 'hot-Jupiter' exoplanets. Here we investigate the coupled chemistry of neutral carbon, hydrogen, oxygen, and nitrogen species on HD 189733b and HD 209458b and we compare the model results with existing transit and eclipse observations. We find that the vertical profiles of molecular constituents are significantly affected by transport-induced quenching and photochemistry, particularly on the cooler HD 189733b; however, the warmer stratospheric temperatures on HD 209458b help maintain thermochemical equilibrium and reduce the effects of disequilibrium chemistry. For both planets, the methane and ammonia mole fractions are found to be enhanced over their equilibrium values at pressures of a few bar to less than an mbar due to transport-induced quenching, but CH{sub 4} and NH{sub 3} are photochemically removed at higher altitudes. Disequilibrium chemistry also enhances atomic species, unsaturated hydrocarbons (particularly C{sub 2}H{sub 2}), some nitriles (particularly HCN), and radicals like OH, CH{sub 3}, and NH{sub 2}. In contrast, CO, H{sub 2}O, N{sub 2}, and CO{sub 2} more closely follow their equilibrium profiles, except at pressures {approx}<1 {mu}bar, where CO, H{sub 2}O, and N{sub 2} are photochemically destroyed and CO{sub 2} is produced before its eventual high-altitude destruction. The enhanced abundances of CH{sub 4}, NH{sub 3}, and HCN are expected to affect the spectral signatures and thermal profiles of HD 189733b and other relatively cool, transiting exoplanets. We examine the sensitivity of our results to the assumed temperature structure and eddy diffusion coefficients and discuss further observational consequences of these models.

  2. 224Ra:228Th disequilibrium in coastal sediments: Implications for solute transfer across the sediment-water interface

    NASA Astrophysics Data System (ADS)

    Cai, Pinghe; Shi, Xiangming; Moore, Williard S.; Peng, Shiyun; Wang, Guizhi; Dai, Minhan

    2014-01-01

    We utilized 224Ra/228Th disequilibrium in the sediment to investigate processes that regulate solute transfer across the sediment-water interface. Depth profiles of dissolved and surface-bound 224Ra and 228Th in the upper 0-20 cm sediment column were measured using a delayed coincidence counter during a cruise to the Yangtze estuary from 15 to 24 August 2011. Along with 224Ra and 228Th, depth profiles of 234Th were collected to determine the bioturbation rate in the sediment. At most study sites, a significant deficit of 224Ra relative to 228Th was observed in the upper 0-10 cm. In contrast, 224Ra was in excess with respect to 228Th in the upper 0-5 cm at the river mouth, possibly due to redistribution of 224Ra from the mid-salinity region. By modeling the 224Ra depth profiles in the sediment using the general diagenetic equation, we demonstrated that in most cases molecular diffusion and bioturbation together can account for only ∼20-30% of the measured flux of 224Ra. We concluded that other mechanisms, especially irrigation, must be invoked to explain the remnant 70% of the observed deviation of 224Ra relative to 228Th. On the basis of the 224Ra/228Th disequilibrium in the sediment and a concept of increased surface area for exchange by irrigation as developed by early investigators, we proposed a new approach - the 224Ra/228Th disequilibrium approach to quantify the transfer rate of other dissolved species across the sediment-water interface. We have utilized this new approach to determine the benthic consumption rate of dissolved O2. The result reveals that benthic consumption is an important loss term of dissolved O2 in the Yangtze estuary and must be considered as one of the mechanisms that lead to hypoxia in this area.

  3. Disequilibrium of Blood Coagulation and Fibrinolytic System in Patients With Coronary Artery Ectasia.

    PubMed

    Wu, Wei; Liu, Ruifeng; Chen, Lianfeng; Chen, Houzao; Zhang, Shuyang

    2016-02-01

    Thrombus formation and myocardial infarction are not uncommon in patients with coronary artery ectasia (CAE). In light of this, the present study aims to systemically evaluate the blood coagulation and fibrinolytic systems in CAE patients. In this study, we enrolled 30 patients with CAE, 30 patients with coronary atherosclerosis disease (CAD), and 29 subjects with normal coronary arteries (control). The coagulation system was evaluated using a routine coagulation function test performed in the hospital laboratory before coronary angiography, and measurements included prothrombin time, international normalized ratio, activated partial thromboplastin time, fibrinogen time, and thrombin time. The evaluation of the fibrinolytic system included measurements of D-dimer, euglobulin lysis time, plasminogen activator inhibitor 1, plasminogen, plasminogen activity assay, α1-antitrypsin (α1-AT), α2 plasmin inhibitor (α2-PI), and α2-macroglobulin (α2-MG). Alpha1-AT, α2-PI, and α2-MG also inhibit activities of 3 neutrophil serine proteases, namely human neutrophil elastase (HNE), cathepsin G (CG), and proteinase 3 (PR3); therefore, the plasma levels of these 3 proteinases were also evaluated.In CAE patients, the circulating coagulation system was normal. For the fibrinolytic system, a decrease of plasminogen activity was observed (P = 0.029) when compared with CAD patients, and the concentrations of α1-AT (both P < 0.001), α2-PI (P = 0.002 and P = 0.025), and α2-MG (P = 0.034 and P < 0.001) were significantly elevated when compared with CAD patients and normal controls. Moreover, the plasma levels of HNE (both P < 0.001) and CG (P = 0.027 and 0.016) in CAE patients were also significantly higher than those of the CAD and control groups. There was no difference in plasma PR3 concentration among these 3 groups.Disequilibrium of the coagulation/fibrinolytic system may contribute to thrombus formation and clinical coronary events in

  4. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties

    PubMed Central

    2010-01-01

    Background Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim was an in-depth study of the extent, distribution and structure of peach genetic variation in North American and European commercial varieties as well as old Spanish varieties and several founders used in the early USA peach breeding programmes. For this we genotyped 224 peach cultivars using 50 SSRs evenly distributed along the 8 linkage groups of the Prunus reference map. Results Genetic distance analysis based on SSRs divided the peach cultivars in three main groups based mainly on their fruit characteristics: melting flesh peaches, melting flesh nectarines and non-melting varieties. Whereas non-melting flesh peaches had a higher number of alleles than melting peaches and nectarines, they were more homozygous. With some exceptions ('Admiral Dewey', 'Early Crawford' and 'Chinese Cling'), the founder US cultivars clustered together with the commercial melting peaches, indicating that their germplasm is well represented in modern cultivars. Population structure analysis showed a similar subdivision of the sample into subpopulations. Linkage disequilibrium (LD) analysis in three unstructured, or barely structured, subpopulations revealed a high level of LD conservation in peach extending up to 13-15 cM. Conclusions Using a much larger set of SSRs, our results confirm previous observations on peach variability and population structure and provide additional tools for breeding and breeders' rights enforcement. SSR data are also used for the estimation of marker mutation rates and allow pedigree inferences, particularly with founder genotypes of the currently grown cultivars, which are useful to understand the evolution of peach as a crop. Results on LD

  5. Disequilibrium of Blood Coagulation and Fibrinolytic System in Patients With Coronary Artery Ectasia

    PubMed Central

    Wu, Wei; Liu, Ruifeng; Chen, Lianfeng; Chen, Houzao; Zhang, Shuyang

    2016-01-01

    Abstract Thrombus formation and myocardial infarction are not uncommon in patients with coronary artery ectasia (CAE). In light of this, the present study aims to systemically evaluate the blood coagulation and fibrinolytic systems in CAE patients. In this study, we enrolled 30 patients with CAE, 30 patients with coronary atherosclerosis disease (CAD), and 29 subjects with normal coronary arteries (control). The coagulation system was evaluated using a routine coagulation function test performed in the hospital laboratory before coronary angiography, and measurements included prothrombin time, international normalized ratio, activated partial thromboplastin time, fibrinogen time, and thrombin time. The evaluation of the fibrinolytic system included measurements of D-dimer, euglobulin lysis time, plasminogen activator inhibitor 1, plasminogen, plasminogen activity assay, α1-antitrypsin (α1-AT), α2 plasmin inhibitor (α2-PI), and α2-macroglobulin (α2-MG). Alpha1-AT, α2-PI, and α2-MG also inhibit activities of 3 neutrophil serine proteases, namely human neutrophil elastase (HNE), cathepsin G (CG), and proteinase 3 (PR3); therefore, the plasma levels of these 3 proteinases were also evaluated. In CAE patients, the circulating coagulation system was normal. For the fibrinolytic system, a decrease of plasminogen activity was observed (P = 0.029) when compared with CAD patients, and the concentrations of α1-AT (both P < 0.001), α2-PI (P = 0.002 and P = 0.025), and α2-MG (P = 0.034 and P < 0.001) were significantly elevated when compared with CAD patients and normal controls. Moreover, the plasma levels of HNE (both P < 0.001) and CG (P = 0.027 and 0.016) in CAE patients were also significantly higher than those of the CAD and control groups. There was no difference in plasma PR3 concentration among these 3 groups. Disequilibrium of the coagulation/fibrinolytic system may contribute to thrombus formation and clinical coronary

  6. Magma storage depths in the Eastern Volcanic Zone of Iceland: disentangling disequilibrium and tuning thermobarometers

    NASA Astrophysics Data System (ADS)

    Neave, D.; Maclennan, J.; Thordarson, T.; Hartley, M. E.; Buisman, I.; Namur, O.; Halldorsson, S. A.

    2015-12-01

    The Eastern Volcanic Zone (EVZ) is the most volcanically productive of Iceland's neovolcanic zones. In addition to being the source of numerous small but disruptive eruptions, such Eyjafjallajökull in 2010 and Grímsvötn in 2011, the EVZ is notable for generating very large eruptions such as the environmentally impacting Laki eruption in 1783-84 and the widely dispersed Saksunarvatn Ash. Thus, investigating the plumbing systems of volcanoes in the EVZ not only reveals information about magma reservoir behaviour and crustal structure, but also has important implications for hazard management. However, in order to obtain reliable estimates of pre-eruptive magma storage conditions and depths from minerals a number of conditions need to be met first. Firstly, all estimates of pre-eruptive conditions need to be placed into petrogenetic frameworks that consider the extensive disequilibrium that results not only from fractionation, but also from magma mixing and crystal mush entrainment. Secondly, it is important to verify that the mineral-melt equilibrium, i.e. thermobarometeric, models used are well calibrated at the expected conditions of magma storage. Using a range of techniques including QEMSCAN imaging, textural analysis and geochemical microanalysis of crystals, glasses and melt inclusions, we present internally consistent models of magma evolution and storage for a number of eruptions in the EVZ, including Laki and the 10ka Grímsvötn tephra series (i.e. Saksunarvatn Ash). All eruptions studied preserve evidence of mixing and crystallisation of primitive melts in the mid-crust (8-20 km) followed by crystallisation of evolved and, in general, more incompatible element-enriched melts in the shallow crust (0-8 km) shortly before eruption. Substantial uncertainties in storage depths nevertheless remain because of incomplete calibration of clinopyroxene-melt equilibria at mid-crustal pressures. As part of an ongoing experimental campaign on Icelandic magma

  7. Microsatellites haplotyping of CF chromosomes shows linkage disequilibrium and several founder effects in Brittany (France)

    SciTech Connect

    Raguenes, O.; Ferec, C.; Mercier, B.

    1994-09-01

    A large study on cystic fibrosis (CF) is underway in Brittany (France). It is based on 902 CF patients distributed in 795 families who were or are still followed at the {open_quotes}Centre Helio-Marin{close_quotes} in Roscoff and/or were subjected to a molecular analysis at the {open_quotes}Centre de Biogenetique{close_quotes} in Brest. At present, the CF mutations have been identified in 309 patients born in Brittany, most of them of Celtic origin. A microsatellite (MS) study using IVS 17b TA, IVS 17b CA and IVS 8 CA was also completed in 63 CF patients and their parents (carriers of the {Delta}F508 mutation or the G551D mutation or the 1078delT mutation or the W846X mutation). All the 21 chromosomes carrying the 1078delT mutation had the same MS haplotype (16-21-13), which was also found on 9 of the 83 non-CF chromosomes analyzed. All the 16 chromosomes with the G551D mutation carried another MS haplotype (16-7-17), which was also found on 13.3% of the non-CF chromosomes. All the 6 chromosomes with the W846X mutation carried the 16-32-13 haplotype, also found on 6.0% of the non-CF chromosomes. Sixteen different MS haplotypes were found among the 74 chromosomes carrying the{Delta}F508 mutation, three of them representing 74.3% (55/74) of the chromosomes. These were the 23-31-13 haplotype (31/74 - 41.9%), the 17-31-13 haplotype (11/74 - 14.9%), and the 17-32-13 haplotype (13/74 - 17.6%). These results show that the CF mutations observed in Brittany are in linkage disequilibrium with the MS haplotypes. They also suggest that their presence in Brittany is the consequence of several founder effects.

  8. Disequilibrium of Blood Coagulation and Fibrinolytic System in Patients With Coronary Artery Ectasia.

    PubMed

    Wu, Wei; Liu, Ruifeng; Chen, Lianfeng; Chen, Houzao; Zhang, Shuyang

    2016-02-01

    Thrombus formation and myocardial infarction are not uncommon in patients with coronary artery ectasia (CAE). In light of this, the present study aims to systemically evaluate the blood coagulation and fibrinolytic systems in CAE patients. In this study, we enrolled 30 patients with CAE, 30 patients with coronary atherosclerosis disease (CAD), and 29 subjects with normal coronary arteries (control). The coagulation system was evaluated using a routine coagulation function test performed in the hospital laboratory before coronary angiography, and measurements included prothrombin time, international normalized ratio, activated partial thromboplastin time, fibrinogen time, and thrombin time. The evaluation of the fibrinolytic system included measurements of D-dimer, euglobulin lysis time, plasminogen activator inhibitor 1, plasminogen, plasminogen activity assay, α1-antitrypsin (α1-AT), α2 plasmin inhibitor (α2-PI), and α2-macroglobulin (α2-MG). Alpha1-AT, α2-PI, and α2-MG also inhibit activities of 3 neutrophil serine proteases, namely human neutrophil elastase (HNE), cathepsin G (CG), and proteinase 3 (PR3); therefore, the plasma levels of these 3 proteinases were also evaluated.In CAE patients, the circulating coagulation system was normal. For the fibrinolytic system, a decrease of plasminogen activity was observed (P = 0.029) when compared with CAD patients, and the concentrations of α1-AT (both P < 0.001), α2-PI (P = 0.002 and P = 0.025), and α2-MG (P = 0.034 and P < 0.001) were significantly elevated when compared with CAD patients and normal controls. Moreover, the plasma levels of HNE (both P < 0.001) and CG (P = 0.027 and 0.016) in CAE patients were also significantly higher than those of the CAD and control groups. There was no difference in plasma PR3 concentration among these 3 groups.Disequilibrium of the coagulation/fibrinolytic system may contribute to thrombus formation and clinical coronary events in

  9. Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations.

    PubMed

    Franssen, Susanne U; Nolte, Viola; Tobler, Ray; Schlötterer, Christian

    2015-02-01

    Whole-genome resequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed. Until now only Pool-Seq (whole-genome sequencing of pools of individuals) data were available, which do not provide sufficient information about the correlation between linked sites. We address this problem in two complementary analyses of three replicate Drosophila melanogaster populations evolving to a new hot temperature environment for almost 70 generations. In the first analysis, we sequenced 58 haploid genomes from the founder population and evolved flies at generation 67. We show that during the experiment linkage disequilibrium (LD) increased almost uniformly over much greater distances than typically seen in Drosophila. In the second analysis, Pool-Seq time series data of the three replicates were combined with haplotype information from the founder population to follow blocks of initial haplotypes over time. We identified 17 selected haplotype-blocks that started at low frequencies in the base population and increased in frequency during the experiment. The size of these haplotype-blocks ranged from 0.082 to 4.01 Mb. Moreover, between 42% and 46% of the top candidate single nucleotide polymorphisms from the comparison of founder and evolved populations fell into the genomic region covered by the haplotype-blocks. We conclude that LD in such rising haplotype-blocks results in long range hitchhiking over multiple kilobase-sized regions. LD in such haplotype-blocks is therefore a major factor contributing to an excess of candidate loci

  10. Pseudovitamin D deficient rickets (PDDR). Linkage disequilibrium mapping in young populations

    SciTech Connect

    Labuda, M.; Korab-Laskowska, M.; Labuda, D.

    1994-09-01

    PDDR is an autosomal recessive disorder with elevated prevalence in French Canadians. The condition is believed to be due to a deficient renal 25(OH)-vitamin D 1-alpha hydroxylase, but its underlying molecular defect is unknown. By linkage analysis we have earlier mapped PDDR to human chromosome 12q14. Using recently developed microsatellite markers we narrowed down the disease locus to a 5.6 cM interval between two clusters of loci: 234tf12, 207yh10, 249vf9, 329zh9, on proximal, and 259zc9 and 184yf2 on the distal side. Further refinement of the PDDR locus was obtained from analysis of those markers on 85 French Canadian PDDR chromosomes by linkage disequilibrium (LD). Ten-marker haplotype analysis for all chromosomes allowed to divide this sample into two groups, one of Saguenay-Lac St. Jean-Charlevoix (SLSJ-Ch), the other from Nova Scotia and New Brunswick (NS, NB). All SLSJ-Ch PDDR chromosomes shared an identical haplotype for markers 172x38, 184yf2, 259zc9, pointing to a single founder in this population. In the NS, NB group, the founder effect was also pronounced; however, the link of 2 PDDR chromosomes to either of these groups remains to be elucidated. In the absence of recombination in 12 generations of the SLSJ-Ch population, the genetic distance between PDDR and markers 172xd8, 184yf2, 259zc9 was estimated to be less than 0.4 cM. Finally the marker 207va9 was found to be the closest proximal one based on one recombination in a Polish PDDR family, its CEPH map position as well as its localization on the same YAC together with the distal markers 184yf2, 309xh1 and the marker 172xd8, probably the closest to the PDDR gene. Our study clearly shows the potential of LD for mapping human disorders in populations as young as 10-12 generations. Here it allowed narrowing PDDR position down to a single YAC.

  11. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

    PubMed Central

    2009-01-01

    Background The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs). Results At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r2 for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10 kb. Conclusion Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The

  12. MICA, MICB Polymorphisms and Linkage Disequilibrium with HLA-B in a Chinese Mongolian Population.

    PubMed

    Wang, W Y; Tian, W; Zhu, F M; Liu, X X; Li, L X; Wang, F

    2016-06-01

    In this study, polymorphisms of major histocompatibility complex class I chain-related genes A and B (MICA and MICB) and human leucocyte antigen (HLA)-B gene were investigated for 158 unrelated Chinese Mongolian subjects recruited from central Inner Mongolia Autonomous Region, northern China, by polymerase chain reaction-sequence-based typing (PCR-SBT) and cloning. Collectively, 79 alleles, including 20 MICA, 12 MICB and 47 HLA-B alleles, were identified. MICA*008:01 (21.2%), MICB*005:02 (48.1%) and HLA-B*51:01 (7.91%) were the most common alleles. Significant global linkage disequilibrium (LD) was detected between HLA-B and MICA, HLA-B and MICB, and MICA and MICB loci (all P < 0.000001). The most frequent haplotypes were HLA-B*51:01-MICA*009:01 (7.28%), HLA-B*58:01-MICB*008 (6.96%), MICA*010-MICB*005:02 (13.92%) and HLA-B*58:01-MICA*002:01-MICB*008 (6.96%). HLA-B-MICA haplotypes such as HLA-B*50:01-MICA*009:02 were associated with single MICB allele. Some HLA-B-MICA haplotypes were associated with multiple MICB alleles, including HLA-B*51:01-MICA*009:01. One novel MICB allele, MICB*031, was identified, which has possibly arisen from MICB*002:01 through single mutation event. We also confirmed the existence of a recently recognized MICA allele, MICA*073, whose ethnic origin has not been previously described. Genotype distributions at MICA, MICB and HLA-B were consistent with a neutrality model. Our results provide new insight into MIC genetic polymorphisms in Chinese ethnic groups. Findings shown here are important from an anthropologic perspective and will inform future studies of the potential role of MIC genes in allogeneic organ transplantation and HLA-linked disease association in populations of related ancestry.

  13. MICA, MICB Polymorphisms and Linkage Disequilibrium with HLA-B in a Chinese Mongolian Population.

    PubMed

    Wang, W Y; Tian, W; Zhu, F M; Liu, X X; Li, L X; Wang, F

    2016-06-01

    In this study, polymorphisms of major histocompatibility complex class I chain-related genes A and B (MICA and MICB) and human leucocyte antigen (HLA)-B gene were investigated for 158 unrelated Chinese Mongolian subjects recruited from central Inner Mongolia Autonomous Region, northern China, by polymerase chain reaction-sequence-based typing (PCR-SBT) and cloning. Collectively, 79 alleles, including 20 MICA, 12 MICB and 47 HLA-B alleles, were identified. MICA*008:01 (21.2%), MICB*005:02 (48.1%) and HLA-B*51:01 (7.91%) were the most common alleles. Significant global linkage disequilibrium (LD) was detected between HLA-B and MICA, HLA-B and MICB, and MICA and MICB loci (all P < 0.000001). The most frequent haplotypes were HLA-B*51:01-MICA*009:01 (7.28%), HLA-B*58:01-MICB*008 (6.96%), MICA*010-MICB*005:02 (13.92%) and HLA-B*58:01-MICA*002:01-MICB*008 (6.96%). HLA-B-MICA haplotypes such as HLA-B*50:01-MICA*009:02 were associated with single MICB allele. Some HLA-B-MICA haplotypes were associated with multiple MICB alleles, including HLA-B*51:01-MICA*009:01. One novel MICB allele, MICB*031, was identified, which has possibly arisen from MICB*002:01 through single mutation event. We also confirmed the existence of a recently recognized MICA allele, MICA*073, whose ethnic origin has not been previously described. Genotype distributions at MICA, MICB and HLA-B were consistent with a neutrality model. Our results provide new insight into MIC genetic polymorphisms in Chinese ethnic groups. Findings shown here are important from an anthropologic perspective and will inform future studies of the potential role of MIC genes in allogeneic organ transplantation and HLA-linked disease association in populations of related ancestry. PMID:27028549

  14. Uranium-series disequilibrium, sedimentation, diatom frustules, and paleoclimate change in Lake Baikal

    USGS Publications Warehouse

    Edgington, D.N.; Robbins, J.A.; Colman, Steven M.; Orlandini, K.A.; Gustin, M.-P.

    1996-01-01

    The large volume of water, approximately one-fifth of the total surface fresh water on the planet, contained in Lake Baikal in southeastern Siberia is distinguished by having a relatively high concentration of uranium (ca. 2 nM), and, together with the surface sediments, an unusually high 234U/238U alpha activity ratio of 1.95. About 80% of the input of uranium to the lake, with a 234U/238U ratio of 2.0, comes from the Selenga River. Profiles of uranium, as well as the extent of isotopic disequilibrium in a 9 m sediment core collected on Academic Ridge, generally show high values during interglacial periods corresponding to high diatom frustule numbers (DiFr) and biogenic silica (BSi) data that have been reported elsewhere. During glacial periods (low DiFr and BSi), uranium progeny (234U and 230Th) were in secular equilibrium with low concentrations of their parent 238U. Radionuclide distributions were interpreted in terms of a quantitative model allowing for adsorption of riverine inputs of uranium onto two classes of sedimenting particles with differing 238U/232Th ratios and uranium progeny in secular equilibrium. If the 234U/238U activity ratio of adsorbed uranium has remained constant, mean sedimentation rates can be independently estimated as 3.6 ?? 0.6 and 3.7 ?? 0.9 cm ?? kyr-1 for the decay of 234U and in-growth of 230Th, respectively. These rates are consistent with a mean rate of 3.76 cm ?? kyr-1, calculated by optimization of the correspondence between adsorbed 238U and ??18O in dated oceanic sediments. The adsorbed uranium apparently tracks variable river flow during interglacials and is drastically reduced during periods of glaciation. Evidently, uranium has not been significantly redistributed within Baikal sediments over at least the past 250 kyr and is a unique, biologically non-essential, tracer for climate-sensitive processes, which provide their own internal geochronometers, potentially useful for ages up to 1 Myr BP.

  15. Uranium disequilibrium as a hydrological aid in studying the salinization processes in the Southeastern Coastal Plain of Israel.

    PubMed

    Avisar, D; Kronfeld, J

    2009-01-01

    Saline waters, of unknown origin, have been encountered in the basal portions of the phreatic Coastal Plain aquifer of Israel. (234)U/(238)U disequilibrium was used to trace their origin to the evaporate layers within the Saqiye aquiclude, the most saline, and the warmest (up to 42 degrees C) waters are also those that have the highest uranium concentrations combined with low (234)U/(238)U activity ratios, derived as the ascending brines traverse underlying uranium-rich Senonian phosphorites, in secular equilibrium along fault conduits.

  16. Anonymous marker loci within 400 kb of HLA-A generate haplotypes in linkage disequilibrium with the hemochromatosis gene (HFE)

    SciTech Connect

    Yaouanq, J.; Perichon, M.; Treut, A.L.; Kahloun, A.E.; Mauvieux, V.; Blayau, M.; Jouanolle, A.M.; Chauvel, B.; Le Gall, J.Y.; David, V. )

    1994-02-01

    The hemochromatosis gene (HFE) maps to 6p21.3 and is less than 1 cM from the HLA class I gene; however, the precise physical location of the gene has remained elusive and controversial. The unambiguous identification of a crossover event within hemochromatosis families is very difficult; it is particularly hampered by the variability of the phenotypic expression as well as by the sex- and age-related penetrance of the disease. For these considerations, traditional linkage analysis could prove of limited value in further refining the extrapolated physical position of HFE. The authors therefore embarked upon a linkage-disequilibrium analysis of HFE and normal chromosomes for the Brittany population. In this report, 66 hemochromatosis families yielding 151 hemochromatosis chromosomes and 182 normal chromosomes were RFLP-typed with a battery of probes, including two newly derived polymorphic markers from the 6.7 and HLA-F loci located 150 and 250 kb telomeric to HLA-A, respectively. The results suggest a strong peak of existing linkage disequilibrium focused within the i82-to-6.7 interval (approximately 250 kb). The zone of linkage disequilibrium is flanked by the i97 locus, positioned 30 kb proximal to i82, and the HLA-F gene, found 250 kb distal to HLA-A, markers of which display no significant association with HFE. These data support the possibility that HFE resides within the 400-kb expanse of DNA between i97 and HLA-F. Alternatively, the very tight association of HLA-A3 and allele 1 of the 6.7 locus, both of which are comprised by the major ancestral or founder HFE haplotype in Brittany, supports the possibility that the disease gene may reside immediately telomeric to the 6.7 locus within the linkage-disequilibrium zone. Additionally, hemochromatosis haplotypes possessing HLA-A11 and the low-frequency HLA-F polymorphism (allele 2) are supportive of a separate founder chromosome containing a second, independently arising mutant allele. 69 refs., 1 fig., 5 tabs.

  17. [Determination of natural radioactive nuclides in the travertine samples from Tamagawa hot spring].

    PubMed

    Hashimoto, T; Masumura, S; Takahashi, K; Sotobayashi, T

    1982-07-01

    The determination of natural radioactive nuclides was carried out for 7 travertine samples collected from Tamagawa hot spring by means of the non-distructive gamma-ray spectrometry and of the alpha-ray spectrometry. From the former measurements, the relative activity strength, due to 223Ra, 226Ra, and 228Th, and their ratios was obtained in comparison with the photopeak strength due to respective daughters, 228Ac, 214Bi, and 212Pb, and with the results from a monazite sand standard. One travertine sample was engaged to the alpha-ray spectrometric determination of Th isotopes after the chemical purification using a 234Th-yield tracer. On the basis of the resultant absolute content of 228Th, the 228Ra and 228Th contents in the remainder samples were evaluated to be the range of 3 approximately 80 Bq (81 approximately 2160 pCi)/g and 2 approximately 20 Bq (54 approximately pCi)/g respectively. These radioactive nuclides were verified to exist almost within a Hokutolite small crystals up to 90% and there are apparently the radioactive disequilibrium relations between 228Ra and 228Th among freshly deposited travertines. The presence of 227Ac in Hokutolite was also suggested from the detection of 227Th owing to 215Po-alpha peak. PMID:7178540

  18. Stefan Meyer: Pioneer of Radioactivity

    NASA Astrophysics Data System (ADS)

    Reiter, Wolfgang L.

    2001-03-01

    Stefan Meyer was one of the pioneers in radioactivity research and director of the Vienna Radium Institute, the first institution in the world devoted exclusively to radioactivity. I give here a biographical sketch of Meyer and of some of his colleagues and an overview of the research activities at the Radium Institute.

  19. Radioactive elements in stellar atmospheres

    SciTech Connect

    Gopka, Vira; Yushchenko, Alexander; Goriely, Stephane; Shavrina, Angelina; Kang, Young Woon

    2006-07-12

    The identification of lines of radioactive elements (Tc, Pm and elements with 83radioactive decay of Th and U in the upper levels of stellar atmospheres, contamination of stellar atmosphere by recent SN explosion, and spallation reactions.

  20. Heavy fragment radioactivities

    SciTech Connect

    Price, P.B.

    1987-12-10

    This recently discovered mode of radioactive decay, like alpha decay and spontaneous fission, is believed to involve tunneling through the deformation-energy barrier between a very heavy nucleus and two separated fragments the sum of whose masses is less than the mass of the parent nucleus. In all known cases the heavier of the two fragments is close to doubly magic /sup 208/Pb, and the lighter fragment has even Z. Four isotopes of Ra are known to emit /sup 14/C nuclei; several isotopes of U as well as /sup 230/Th and /sup 231/Pa emit Ne nuclei; and /sup 234/U exhibits four hadronic decay modes: alpha decay, spontaneous fission, Ne decay and Mg decay.

  1. Low Radioactivity in CANDLES

    SciTech Connect

    Kishimoto, T.; Ogawa, I.; Hazama, R.; Yoshida, S.; Umehara, S.; Matsuoka, K.; Sakai, H.; Yokoyama, D.; Mukaida, K.; Ichihara, K.; Tatewaki, Y.; Kishimoto, K.; Hirano, Y.; Yanagisawa, A.; Ajimura, S.

    2005-09-08

    CANDLES is the project to search for double beta decay of 48Ca by using CaF2 crystals. Double beta decay of 48Ca has the highest Q value among all nuclei whose double beta decay is energetically allowed. This feature makes the study almost background free and becomes important once the study is limited by the backgrounds. We studied double beta decays of 48Ca by using ELEGANTS VI detector system which features CaF2(Eu) crystals. We gave the best limit on the lifetime of neutrino-less double beta decay of 48Ca although further development is vital to reach the neutrino mass of current interest for which CANDLES is designed. In this article we present how CANDLES can achieve low radioactivity, which is the key for the future double beta decay experiment.

  2. Radioactive waste processing apparatus

    DOEpatents

    Nelson, R.E.; Ziegler, A.A.; Serino, D.F.; Basnar, P.J.

    1985-08-30

    Apparatus for use in processing radioactive waste materials for shipment and storage in solid form in a container is disclosed. The container includes a top, and an opening in the top which is smaller than the outer circumference of the container. The apparatus includes an enclosure into which the container is placed, solution feed apparatus for adding a solution containing radioactive waste materials into the container through the container opening, and at least one rotatable blade for blending the solution with a fixing agent such as cement or the like as the solution is added into the container. The blade is constructed so that it can pass through the opening in the top of the container. The rotational axis of the blade is displaced from the center of the blade so that after the blade passes through the opening, the blade and container can be adjusted so that one edge of the blade is adjacent the cylindrical wall of the container, to insure thorough mixing. When the blade is inside the container, a substantially sealed chamber is formed to contain vapors created by the chemical action of the waste solution and fixant, and vapors emanating through the opening in the container. The chamber may be formed by placing a removable extension over the top of the container. The extension communicates with the apparatus so that such vapors are contained within the container, extension and solution feed apparatus. A portion of the chamber includes coolant which condenses the vapors. The resulting condensate is returned to the container by the force of gravity.

  3. PERSPECTIVE: Fireworks and radioactivity

    NASA Astrophysics Data System (ADS)

    Breitenecker, Katharina

    2009-09-01

    both reaction products and unburnt constituents of a pyrotechnic mixture. One major environmental concern in pyrotechnics focuses on the emission of heavy metals. This is the topic discussed in the article by Georg Steinhauser and Andreas Musilek in this issue [4]. A possible interrelationship between respiratory effects and fireworks emissions of barium-rich aerosols was also raised last year [5]. In recent years the potential hazard of naturally occurring radioactive material has become of importance to the scientific community. Naturally occurring radionuclides can be of terrestrial or cosmological origin. Terrestrial radionuclides were present in the presolar cloud that later contracted in order to build our solar system. These radionuclides—mainly heavy metals—and their non-radioactive isotopes are nowadays fixed in the matrix of the Earth's structure. Usually, their percentage is quite small compared to their respective stable isotopes—though there are exceptions like in the case of radium. The problem with environmental pollution due to naturally occurring radioactive material begins when this material is concentrated due to mining and milling, and later further processed [6]. Environmental pollution due to radioactive material goes back as far as the Copper and Iron Ages, when the first mines were erected in order to mine ores (gold, silver, copper, iron, etc), resulting in naturally occurring radioactive material being set free with other dusts into the atmosphere. So where is the link between pyrotechnics and radioactivity? In this article presented by Georg Steinhauser and Andreas Musilek [4], the pyrotechnic ingredients barium nitrate and strontium nitrate are explored with respect to their chemical similarities to radium. The fundamental question, therefore, was whether radium can be processed together with barium and strontium. If so, the production and ignition of these pyrotechnic ingredients could cause atmospheric pollution with radium aerosols

  4. Environmental radioactive intercomparison program and radioactive standards program

    SciTech Connect

    Dilbeck, G.

    1993-12-31

    The Environmental Radioactivity Intercomparison Program described herein provides quality assurance support for laboratories involved in analyzing public drinking water under the Safe Drinking Water Act (SDWA) Regulations, and to the environmental radiation monitoring activities of various agencies. More than 300 federal and state nuclear facilities and private laboratories participate in some phase of the program. This presentation describes the Intercomparison Program studies and matrices involved, summarizes the precision and accuracy requirements of various radioactive analytes, and describes the traceability determinations involved with radioactive calibration standards distributed to the participants. A summary of program participants, sample and report distributions, and additional responsibilities of this program are discussed.

  5. Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson).

    PubMed

    Macbeth, Gilbert Michael; Broderick, Damien; Buckworth, Rik C; Ovenden, Jennifer R

    2013-03-11

    Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. But, pitfalls are predicted when the effective size is large, as estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes around 5000. This was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest standard deviation of Ne estimates occurred when low frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or non-breeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were above 24,000.

  6. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    PubMed

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-01-01

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations. PMID:27525897

  7. Disequilibrium between [sup 226]Ra and supported [sup 210]Pb in a sediment core from a shallow Florida lake

    SciTech Connect

    Brenner, M.; Peplov, A.J.; Schelske, C.L. )

    1994-07-01

    [sup 210]Pb dating can be used to assign ages in lake sediment cores, calculate rates of sediment accumulation, and determine the timing of recent changes in lake-watershed ecosystems. We used low-background gamma counting to measure [sup 226]Ra and total [sup 210]Pb activity in a core from Lake Rowell, Florida. [sup 226]Ra activity was high and strongly variable throughout the core, even exceeding total [sup 210]Pb activity in recently deposited sediments. We traced one source of Ra-rich sediments to the only inflow, Alligator Creek, where stream-bottom deposits display disequilibrium between [sup 226]Ra and supported [sup 210]Pb. High and variable [sup 226]Ra activity in the Lake Rowell profile argues for direct estimates of in situ Ra in lake sediment cores from disturbed watersheds that have Ra-bearing bedrock. Isotopic disequilibrium between [sup 226]Ra and supported [sup 210]Pb makes it difficult to distinguish between supported and unsupported [sup 210]Pb activity throughout the Lake Rowell core and would require special assumptions and nonconventional dating models to establish age-depth relationships. 78 refs., 3 figs., 1 tab.

  8. Linkage disequilibrium and haplotype studies of chromosome 8p 11. 1-21. 1 markers and Werner syndrome

    SciTech Connect

    Yu, Chang-En; Schellenberg, G.D.; Oshima, Junko; Martin, G.M.; Goddard, K.A.B.; Wijsman, E.M. ); Miki, Tetsuro; Nakura, Jun; Ogihara, Toshio ); Poot, M.; Hoehn, H. )

    1994-08-01

    Werner syndrome (WS) is an autosomal recessive disorder, characterized as a progeroid syndrome, previously mapped to the 8p 11.2-21.1 region. Because WS is so rare, and because many patients are from consanguineous marriages, fine localization of the gene by traditional meiotic mapping methods is unlikely to succeed. Here the authors present the results of a search for a region that exhibits linkage disequilibrium with the disorder, under the assumption that identification of such a region may provide an alternative method of narrowing down the location of WRN, the gene responsible for WS. They present allele frequencies in Japanese and Caucasian cases and controls for D8S137, D8S131, D8S87, D8S278, D8S259, D8S283, fibroblast growth factor receptor 1, ankyrin 1, D8S339, and two polymorphisms in glutathione reductase (GSR), covering [approximately] 16.5 cM in total. They show that three of the markers examined - D8S339 and both polymorphisms in the GSR locus - show strong statistically significant evidence of disequilibrium with WRN in the Japanese population but not in the Caucasian population. In addition, they show that a limited number of haplotypes are associated with the disease in both populations and that these haplotypes define clusters of apparently related haplotypes that may identify as many as eight or nine independent WRN mutations in these two populations. 36 refs., 1 fig., 4 tabs.

  9. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    PubMed

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-07-29

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

  10. Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes

    SciTech Connect

    van Endert, P.M.; Lopez, M.T.; Patel, S.D.; McDevitt, H.O. ); Monaco, J.J. )

    1992-12-01

    Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes.

  11. Radioactive deposits in California

    USGS Publications Warehouse

    Walker, George W.; Lovering, Tom G.

    1954-01-01

    Reconnaissance examination by Government geologists of many areas, mine properties, and prospects in California during the period between 1948 and 1953 has confirmed the presence of radioactive materials in place at more than 40 localities. Abnormal radioactivity at these localities is due to concentrations of primary and secondary uranium minerals, to radon gas, radium (?), and to thorium minerals. Of the known occurrences only three were thought to contain uranium oxide (uranitite or pitchblende), 4 contained uranium-bearing columbate, tantalate, or titanate minerals, 12 contained secondary uranium minerals, such as autunite, carnotite, and torbernite, one contained radon gas, 7 contained thorium minerals, and, at the remaining 16 localities, the source of the anomalous radiation was not positively determined. The occurrences in which uranium oxide has been tentatively identified include the Rathgeb mine (Calaveras County), the Yerih group of claims (San Bernardino County), and the Rainbow claim (Madera County). Occurrences of secondary uranium minerals are largely confined to the arid desert regions of south-eastern California including deposits in San Bernardino, Kern, Inyo, and Imperial Counties. Uranium-bearing columbate, tantalate, or titanate minerals have been reported from pegmatite and granitic rock in southeastern and eastern California. Thorium minerals have been found in vein deposits in eastern San Bernardino County and from pegmatites and granitic rocks in various parts of southeastern California; placer concentrations of thorium minerals are known from nearly all areas in the State that are underlain, in part, by plutonic crystalline rocks. The primary uranium minerals occur principally as minute accessory crystals in pegmatite or granitic rock, or with base-metal sulfide minerals in veins. Thorium minerals also occur as accessory crystals in pegmatite or granitic rock, in placer deposits derived from such rock, and, at Mountain Pass, in veins

  12. Automatic Searching Radioactive Sources by Airborne Radioactive Survey Using Multicopter

    NASA Astrophysics Data System (ADS)

    Rim, H.; Eun, S. B.; Kim, K.; Park, S.; Jung, H. K.

    2015-12-01

    In order to prepare emergency situation lost a dangerous radioelement source in advance and to search a radioactive source automatically, we develop airborne radioelement survey system by multicopter. This multicopter radioelement survey system consists of a small portable customized BGO (Bismuth Germanate Oxide) detector, video recording part, wireless connecting part to ground pilot, GPS, and several equipments for automatic flight. This system is possible to search flight by preprogramed lines. This radioactive detecting system are tested to find intentional hidden source, The performance of detecting a source is well proved with very low flight altitude in spite of depending on the magnitude of radioelement sources. The advantage of multicopter system, one of UAV (Unmanned Aerial Vehicle), is to avoid the potential of close access to a dangerous radioactive source by using fully automatic searching capability. In this paper, we introduce our multicopter system for detecting radioactive source and synthetic case history for demonstrating this system.

  13. Final disposal of radioactive waste

    NASA Astrophysics Data System (ADS)

    Freiesleben, H.

    2013-06-01

    In this paper the origin and properties of radioactive waste as well as its classification scheme (low-level waste - LLW, intermediate-level waste - ILW, high-level waste - HLW) are presented. The various options for conditioning of waste of different levels of radioactivity are reviewed. The composition, radiotoxicity and reprocessing of spent fuel and their effect on storage and options for final disposal are discussed. The current situation of final waste disposal in a selected number of countries is mentioned. Also, the role of the International Atomic Energy Agency with regard to the development and monitoring of international safety standards for both spent nuclear fuel and radioactive waste management is described.

  14. RADIOACTIVE CONCENTRATOR AND RADIATION SOURCE

    DOEpatents

    Hatch, L.P.

    1959-12-29

    A method is presented for forming a permeable ion exchange bed using Montmorillonite clay to absorb and adsorb radioactive ions from liquid radioactive wastes. A paste is formed of clay, water, and a material that fomns with clay a stable aggregate in the presence of water. The mixture is extruded into a volume of water to form clay rods. The rods may then be used to remove radioactive cations from liquid waste solutions. After use, the rods are removed from the solution and heated to a temperature of 750 to 1000 deg C to fix the ratioactive cations in the clay.

  15. SELF SINTERING OF RADIOACTIVE WASTES

    DOEpatents

    McVay, T.N.; Johnson, J.R.; Struxness, E.G.; Morgan, K.Z.

    1959-12-29

    A method is described for disposal of radioactive liquid waste materials. The wastes are mixed with clays and fluxes to form a ceramic slip and disposed in a thermally insulated container in a layer. The temperature of the layer rises due to conversion of the energy of radioactivity to heat boillng off the liquid to fomn a dry mass. The dry mass is then covered with thermal insulation, and the mass is self-sintered into a leach-resistant ceramic cake by further conversion of the energy of radioactivity to heat.

  16. Star formation and extinct radioactivities

    NASA Technical Reports Server (NTRS)

    Cameron, A. G. W.

    1984-01-01

    An assessment is made of the evidence for the existence of now-extinct radioactivities in primitive solar system material, giving attention to implications for the early stages of sun and solar system formation. The characteristics of possible disturbances in dense molecular clouds which can initiate the formation of cloud cores is discussed, with emphasis on these disturbances able to generate fresh radioactivities. A one-solar mass red giant star on the asymptotic giant branch appears to have been the best candidate to account for the short-lived extinct radioactivities in the early solar system.

  17. Radioactive Waste Management

    NASA Astrophysics Data System (ADS)

    Baisden, P. A.; Atkins-Duffin, C. E.

    Issues related to the management of radioactive wastes are presented with specific emphasis on high-level wastes generated as a result of energy and materials production using nuclear reactors. The final disposition of these high-level wastes depends on which nuclear fuel cycle is pursued, and range from once-through burning of fuel in a light water reactor followed by direct disposal in a geologic repository to more advanced fuel cycles (AFCs) where the spent fuel is reprocessed or partitioned to recover the fissile material (primarily 235U and 239Pu) as well as the minor actinides (MAs) (neptunium, americium, and curium) and some long-lived fission products (e.g., 99Tc and 129I). In the latter fuel cycle, the fissile materials are recycled through a reactor to produce more energy, the short-lived fission products are vitrified and disposed of in a geologic repository, and the minor actinides and long-lived fission products are converted to less radiotoxic or otherwise stable nuclides by a process called transmutation. The advantages and disadvantages of the various fuel cycle options and the challenges to the management of nuclear wastes they represent are discussed.

  18. Radioactive decay data tables

    SciTech Connect

    Kocher, D.C.

    1981-01-01

    The estimation of radiation dose to man from either external or internal exposure to radionuclides requires a knowledge of the energies and intensities of the atomic and nuclear radiations emitted during the radioactive decay process. The availability of evaluated decay data for the large number of radionuclides of interest is thus of fundamental importance for radiation dosimetry. This handbook contains a compilation of decay data for approximately 500 radionuclides. These data constitute an evaluated data file constructed for use in the radiological assessment activities of the Technology Assessments Section of the Health and Safety Research Division at Oak Ridge National Laboratory. The radionuclides selected for this handbook include those occurring naturally in the environment, those of potential importance in routine or accidental releases from the nuclear fuel cycle, those of current interest in nuclear medicine and fusion reactor technology, and some of those of interest to Committee 2 of the International Commission on Radiological Protection for the estimation of annual limits on intake via inhalation and ingestion for occupationally exposed individuals.

  19. Process for treating radioactive waste

    SciTech Connect

    Chino, K.; Kawamura, F.; Kikuchi, M.; Yusa, H.

    1982-11-30

    N-beta-(Aminoethyl)-gamma-aminopropyltrimethoxysilane (NH2(CH2)2NH(CH2)3SI(OCH3)3) as a silane coupling agent and SiO(2 -x)(ONa)x/2(OH)x/2 as colloidal silica are mixed into a radioactive liquid waste containing sodium sulfate as a main component, coming from a boiling water-type, nuclear power plant as an effluent. The resulting mixed radioactive liquid waste is supplied into a vessel provided with a rotating shaft with blades. The rotating shaft is revolved while heating the radioactive liquid waste in the vessel, thereby making the radioactive liquid waste into powder. The resulting powder containing the silane coupling agent and the colloidal silica is shaped into pellets by a pelletizer. The pellets having a low hygroscopicity and a high strength are obtained.

  20. Radioactive stilbene derivatives in radioimmunoassay

    SciTech Connect

    Jouquey, A.; Touyer, G.

    1985-07-16

    Novel radioactive stilbene derivatives marked with iodine 125 or 131 possessing an iodine acceptor group and marked with iodine 125 or 131 and their preparation and antigens obtained therefrom and a process for preparing said antigens.

  1. Naturally Occurring Radioactive Materials (NORM)

    SciTech Connect

    Gray, P.

    1997-02-01

    This paper discusses the broad problems presented by Naturally Occuring Radioactive Materials (NORM). Technologically Enhanced naturally occuring radioactive material includes any radionuclides whose physical, chemical, radiological properties or radionuclide concentration have been altered from their natural state. With regard to NORM in particular, radioactive contamination is radioactive material in an undesired location. This is a concern in a range of industries: petroleum; uranium mining; phosphorus and phosphates; fertilizers; fossil fuels; forestry products; water treatment; metal mining and processing; geothermal energy. The author discusses in more detail the problem in the petroleum industry, including the isotopes of concern, the hazards they present, the contamination which they cause, ways to dispose of contaminated materials, and regulatory issues. He points out there are three key programs to reduce legal exposure and problems due to these contaminants: waste minimization; NORM assesment (surveys); NORM compliance (training).

  2. Radioactive waste material melter apparatus

    DOEpatents

    Newman, D.F.; Ross, W.A.

    1990-04-24

    An apparatus for preparing metallic radioactive waste material for storage is disclosed. The radioactive waste material is placed in a radiation shielded enclosure. The waste material is then melted with a plasma torch and cast into a plurality of successive horizontal layers in a mold to form a radioactive ingot in the shape of a spent nuclear fuel rod storage canister. The apparatus comprises a radiation shielded enclosure having an opening adapted for receiving a conventional transfer cask within which radioactive waste material is transferred to the apparatus. A plasma torch is mounted within the enclosure. A mold is also received within the enclosure for receiving the melted waste material and cooling it to form an ingot. The enclosure is preferably constructed in at least two parts to enable easy transport of the apparatus from one nuclear site to another. 8 figs.

  3. Radioactive waste material melter apparatus

    DOEpatents

    Newman, Darrell F.; Ross, Wayne A.

    1990-01-01

    An apparatus for preparing metallic radioactive waste material for storage is disclosed. The radioactive waste material is placed in a radiation shielded enclosure. The waste material is then melted with a plasma torch and cast into a plurality of successive horizontal layers in a mold to form a radioactive ingot in the shape of a spent nuclear fuel rod storage canister. The apparatus comprises a radiation shielded enclosure having an opening adapted for receiving a conventional transfer cask within which radioactive waste material is transferred to the apparatus. A plasma torch is mounted within the enclosure. A mold is also received within the enclosure for receiving the melted waste material and cooling it to form an ingot. The enclosure is preferably constructed in at least two parts to enable easy transport of the apparatus from one nuclear site to another.

  4. Radioactivity of the Cooling Water

    DOE R&D Accomplishments Database

    Wigner, E. P.

    1943-03-01

    The most important source of radioactivity at the exit manifold of the pile will be due to O{sup 19}, formed by neutron absorption of O{sup 18}. A recent measurement of Fermi and Weil permits to estimate that it will be safe to stay about 80 minutes daily close to the exit manifolds without any shield. Estimates are given for the radioactivities from other sources both in the neighborhood and farther away from the pile.

  5. Fluid-present disequilibrium melting in Neoarchean arc-related migmatites of Daeijak Island, western Gyeonggi Massif, Korea

    NASA Astrophysics Data System (ADS)

    Lee, Yuyoung; Cho, Moonsup

    2013-10-01

    The melting process of meta-igneous rocks was investigated via field, petrographic and geochemical analyses of the Neoarchean (~ 2.51 Ga) migmatite complex in Daeijak Island, western Gyeonggi Massif. This complex consists primarily of garnet-free amphibolites and tonalitic migmatites, both of which contain hornblende, plagioclase and quartz as major constituents. Neosomes and leucosomes in the migmatite have dioritic-tonalitic and tonalitic-trondhjemitic compositions, respectively. Compositions of hornblende (XFe = 0.39-0.42) and plagioclase (An24-27) vary little between the neosomes and leucosomes. The amphibolites show distinct depletions in Nb, Ta, Zr, and Ti relative to large ion lithophile elements, suggesting an arc-related origin for their basaltic protolith. Leucosomes have lower contents of K2O, MgO, FeO*, TiO2, Zr, Rb, and rare earth elements (REE) than amphibolites and neosomes, but are higher in SiO2, Na2O, and Sr contents. Leucosomes and neosomes have positive [(Eu/Eu*)N = 1.32-7.26] and negative (0.71-0.97) Eu anomalies, respectively, which are attributed to the variable degree of plagioclase fractionation during the partial melting. The P-T condition for the migmatite formation was estimated to be ~ 700-730 °C and 4.7-5.5 kbar, primarily based on the hornblende-plagioclase thermobarometry and phase equilibria. Various lines of textural evidence, such as the channel flow of melt along migmatitic layers and the segregation of melt into shear bands or boudin necks suggest a syn-deformation crystallization of melt. Chemical disequilibrium in migmatites is documented not only by petrographic and geochemical data but also by the REE modeling between melt product and source rock. Disequilibrium process is most likely attributed to the rapidity of melt extraction or migration, compared to chemical diffusion rate. In summary, the fluid-present disequilibrium melting of dioritic-tonalitic protoliths has produced tonalitic-trondhjemitic leucosomes in a dynamic

  6. Storage depot for radioactive material

    DOEpatents

    Szulinski, Milton J.

    1983-01-01

    Vertical drilling of cylindrical holes in the soil, and the lining of such holes, provides storage vaults called caissons. A guarded depot is provided with a plurality of such caissons covered by shielded closures preventing radiation from penetrating through any linear gap to the atmosphere. The heat generated by the radioactive material is dissipated through the vertical liner of the well into the adjacent soil and thus to the ground surface so that most of the heat from the radioactive material is dissipated into the atmosphere in a manner involving no significant amount of biologically harmful radiation. The passive cooling of the radioactive material without reliance upon pumps, personnel, or other factor which might fail, constitutes one of the most advantageous features of this system. Moreover this system is resistant to damage from tornadoes or earthquakes. Hermetically sealed containers of radioactive material may be positioned in the caissons. Loading vehicles can travel throughout the depot to permit great flexibility of loading and unloading radioactive materials. Radioactive material can be shifted to a more closely spaced caisson after ageing sufficiently to generate much less heat. The quantity of material stored in a caisson is restricted by the average capacity for heat dissipation of the soil adjacent such caisson.

  7. 49 CFR 172.556 - RADIOACTIVE placard.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 2 2011-10-01 2011-10-01 false RADIOACTIVE placard. 172.556 Section 172.556... SECURITY PLANS Placarding § 172.556 RADIOACTIVE placard. (a) Except for size and color, the RADIOACTIVE... on the RADIOACTIVE placard must be white in the lower portion with a yellow triangle in the...

  8. 49 CFR 172.556 - RADIOACTIVE placard.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 2 2012-10-01 2012-10-01 false RADIOACTIVE placard. 172.556 Section 172.556... SECURITY PLANS Placarding § 172.556 RADIOACTIVE placard. (a) Except for size and color, the RADIOACTIVE... on the RADIOACTIVE placard must be white in the lower portion with a yellow triangle in the...

  9. 49 CFR 172.556 - RADIOACTIVE placard.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 2 2014-10-01 2014-10-01 false RADIOACTIVE placard. 172.556 Section 172.556... SECURITY PLANS Placarding § 172.556 RADIOACTIVE placard. (a) Except for size and color, the RADIOACTIVE... on the RADIOACTIVE placard must be white in the lower portion with a yellow triangle in the...

  10. 49 CFR 172.556 - RADIOACTIVE placard.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false RADIOACTIVE placard. 172.556 Section 172.556... SECURITY PLANS Placarding § 172.556 RADIOACTIVE placard. (a) Except for size and color, the RADIOACTIVE... on the RADIOACTIVE placard must be white in the lower portion with a yellow triangle in the...

  11. 49 CFR 172.556 - RADIOACTIVE placard.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 2 2013-10-01 2013-10-01 false RADIOACTIVE placard. 172.556 Section 172.556... SECURITY PLANS Placarding § 172.556 RADIOACTIVE placard. (a) Except for size and color, the RADIOACTIVE... on the RADIOACTIVE placard must be white in the lower portion with a yellow triangle in the...

  12. Uranium series disequilibrium in a young surficial uranium deposit, northeastern Washington, U.S.A.

    USGS Publications Warehouse

    Zielinski, R.A.; Bush, C.A.; Rosholt, J.N.

    1986-01-01

    A recently discovered ore-grade accumulation of U in organic-rich sediments of late Quaternary age provides an opportunity for studying the early association of U, U-daughters, and organic matter in a natural setting. The U occurs in valley-fill sediments of peat, peaty clay, silt, and sand along the north fork of Flodelle Creek, Stevens County, Washington. Radiometric techniques (delayed neutron, high-resolution gamma-ray spectrometry, thin-source alpha spectrometry) were employed to determine the abundance and distribution of U-series nuclides, the extent of secular equilibrium within the U decay series, and the apparent U-series ages of U incorporation. Sixteen lithologically distinct intervals were sampled from a 292 cm core. Uranium contents range from 140 to 2790 ppm and are positively correlated with organic contents. Measured alpha activity ratios of 234U/238U (1.31-1.38) are very similar to those reported in coexisting waters, suggesting a rather constant isotopic composition of introduced U. Much lower Th contents of <10-40 ppm are controlled by the type and abundance of silicate detritus. The youth of the host sediments (<15 000 a) and the paucity of associated radioactivity suggested large excesses of U relative to radioactive daughters and such excesses were observed, particularly in the shallowest intervals. Apparent ages of U emplacement determined by the (alpha) activity ratio of 230Th daughter to 234U parent show a general increase with depth and fair agreement with estimated depositional ages. This observation suggests dominantly syndepositional or early post depositional emplacement of U followed by decay-generated buildup of 230Th daughter with time. However, interval by interval comparisons of the relative abundances of other daughters, particularly 226Ra and 210Pb, indicate variability caused by processes other than closed-system growth and decay, probably because chemically diverse daughters that are decay-generated in situ have differing

  13. Heat transfer to two-phase air/water mixtures flowing in small tubes with inlet disequilibrium

    NASA Technical Reports Server (NTRS)

    Janssen, J. M.; Florschuetz, L. W.; Fiszdon, J. P.

    1986-01-01

    The cooling of gas turbine components was the subject of considerable research. The problem is difficult because the available coolant, compressor bleed air, is itself quite hot and has relatively poor thermophysical properties for a coolant. Injecting liquid water to evaporatively cool the air prior to its contact with the hot components was proposed and studied, particularly as a method of cooling for contingency power applications. Injection of a small quantity of cold liquid water into a relatively hot coolant air stream such that evaporation of the liquid is still in process when the coolant contacts the hot component was studied. No approach was found whereby heat transfer characteristics could be confidently predicted for such a case based solely on prior studies. It was not clear whether disequilibrium between phases at the inlet to the hot component section would improve cooling relative to that obtained where equilibrium was established prior to contact with the hot surface.

  14. High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep.

    PubMed

    Song, S V; Downes, S; Parker, T; Oakeshott, J G; Robin, C

    2015-11-01

    Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of 'selective sweeps'. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus.

  15. Characterization and polymerase chain reaction (PCR) detection of an Alu deletion polymorphism in total linkage disequilibrium with myotonic dystrophy

    SciTech Connect

    Mahadevan, M.S. ); Foitzik, M.A. ); Surh, L.C.; Korneluk, R.G. Univ. of Ottawa )

    1993-02-01

    The mutation causing myotonic dystrophy has been identified as an unstable trinucleotide CRG repeat located in the 3[prime] untranslated region of a gene putatively encoding a serine-threonine protein kinase. The mutation has been reported to be in total linkage disequilibrium with an insertion/deletion polymorphism located within the kinase gene. To determine the nature of this polymorphism, we have sequenced this genomic fragment and have found that the sequence of this region consists of five consecutive Alu repeats. Further analysis suggests that the smaller of two alleles is actually due to a proposed deletion event that resulted in the loss of an equivalent of three Alu repeats. We have developed a PCR-based assay to detect this polymorphism, the closest, distal marker to the DM mutation. 12 refs., 2 figs.

  16. High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep.

    PubMed

    Song, S V; Downes, S; Parker, T; Oakeshott, J G; Robin, C

    2015-11-01

    Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of 'selective sweeps'. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus. PMID:26174024

  17. The membrane stress response buffers the lethal effects of lipid disequilibrium by reprogramming the protein homeostasis network

    PubMed Central

    Thibault, Guillaume; Shui, Guanghou; Kim, Woong; McAlister, Graeme C.; Ismail, Nurzian; Gygi, Steven P.; Wenk, Markus R.; Ng, Davis T.W.

    2012-01-01

    SUMMARY Lipid composition can differ widely among organelles and even between leaflets of a membrane. Lipid homeostasis is critical because disequilibrium can have disease outcomes. Despite their importance, mechanisms maintaining lipid homeostasis remain poorly understood. Here, we establish a model system to study the global effects of lipid imbalance. Quantitative lipid profiling was integral to monitor changes to lipid composition and for system validation. Applying global transcriptional and proteomic analyses, a dramatically altered biochemical landscape was revealed from adaptive cells. The resulting composite regulation we term the “membrane stress response” (MSR) confers compensation, not through restoration of lipid composition, but by remodeling the protein homeostasis network. To validate its physiological significance, we analyzed the unfolded protein response (UPR), one facet of the MSR and a key regulator of protein homeostasis. We demonstrate that the UPR maintains protein biogenesis, quality control, and membrane integrity—functions otherwise lethally compromised in lipid dysregulated cells. PMID:23000174

  18. Linkage disequilibrium in the insulin gene region: Size variation at the 5{prime} flanking polymorphism and bimodality among {open_quotes}Class I{close_quotes} alleles

    SciTech Connect

    McGinnis, R.E.; Spielman, R.S.

    1994-09-01

    The 5{prime} flanking polymorphism (5{prime}FP), a hypervariable region at the 5{prime} end of the insulin gene, has {open_quotes}class 1{close_quotes} alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). The authors report that precise sizing of the 5{prime}FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. They also examined 5{prime}FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5{prime}FP, they found that one allele exhibits near-total association with the upper component of the 5FP class 1 distribution. Such associations represent a little-known but potentially wide-spread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. 22 refs., 5 figs., 6 tabs.

  19. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

  20. Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large datasets containing single nucleotide polymorphisms (SNPs) are used to analyze genome-wide diversity in a robust collection of cultivars from representative accessions, across the world. The extent of linkage disequilibrium (LD) within a population determines the number of markers required fo...

  1. Toward localization of the Werner syndrome gene by linkage disequilibrium and ancestral haplotyping: Lessons learned from analysis of 35 chromosome 8p11.1-21.1 markers

    SciTech Connect

    Goddard, K.A.B.; Wijsman, E.M.; Martin, G.M.

    1996-06-01

    Werner syndrome (WS) is an autosomal recessive disorder characterized by premature onset of a number of age-related diseases. The gene for WS, WRN, has been mapped to the 8p11.1-21.1 region with further localization through linkage disequilibrium mapping. Here we present the results of linkage disequilibrium and ancestral haplotype analyses of 35 markers to further refine the location of WRN. We identified an interval in this region in which 14 of 18 markers tested show significant evidence of linkage disequilibrium in at least one of the two populations tested. Analysis of extended and partial haplotypes covering 21 of the markers studied supports the existence of both obligate and probable ancestral recombinant events which localize WRN almost certainly to the interval between DSS2196 and D8S2186, and most likely to the narrower interval between D8S2168 and D8S2186. These haplotype analyses also suggest that there are multiple WRN mutations in each of the two populations under study. We also present a comparison of approaches to performing disequilibrium tests with multiallelic markers, and show that some commonly used approximations for such tests perform poorly in comparison to exact probability tests. Finally, we discuss some of the difficulties introduced by the high mutation rate at microsatellite markers which influence our ability to use ancestral haplotype analysis to localize disease genes. 51 refs., 6 figs., 7 tabs.

  2. [Investigation of radioactivity measurement of medical radioactive waste].

    PubMed

    Koizumi, Kiyoshi; Masuda, Kazutaka; Kusakabe, Kiyoko; Kinoshita, Fujimi; Kobayashi, Kazumi; Yamamoto, Tetsuo; Kanaya, Shinichi; Kida, Tetsuo; Yanagisawa, Masamichi; Iwanaga, Tetsuo; Ikebuchi, Hideharu; Kusama, Keiji; Namiki, Nobuo; Okuma, Hiroshi; Fujimura, Yoko; Horikoshi, Akiko; Tanaka, Mamoru

    2004-11-01

    To explore the possibility of which medical radioactive wastes could be disposed as general wastes after keeping them a certain period of time and confirming that their radioactivity reach a background level (BGL), we made a survey of these wastes in several nuclear medicine facilities. The radioactive wastes were collected for one week, packed in a box according to its half-life, and measured its radioactivity by scintillation survey meter with time. Some wastes could reach a BGL within 10 times of half-life, but 19% of the short half-life group (group 1) including 99mTc and 123I, and 8% of the middle half-life group (group 2) including 67Ga, (111)In, and 201Tl did not reach a BGL within 20 times of half-life. A reason for delaying the time of reaching a BGL might be partially attributed to high initial radiation dose rate or heavy package weight. However, mixing with the nuclides of longer half-life was estimated to be the biggest factor affecting this result. When disposing medical radioactive wastes as general wastes, it is necessary to avoid mixing with radionuclide of longer half-life and confirm that it reaches a BGL by actual measurement.

  3. Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping.

    PubMed

    Nimmakayala, Padma; Abburi, Venkata L; Abburi, Lavanya; Alaparthi, Suresh Babu; Cantrell, Robert; Park, Minkyu; Choi, Doil; Hankins, Gerald; Malkaram, Sridhar; Reddy, Umesh K

    2014-08-01

    Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R(2) of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.

  4. Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping.

    PubMed

    Nimmakayala, Padma; Abburi, Venkata L; Abburi, Lavanya; Alaparthi, Suresh Babu; Cantrell, Robert; Park, Minkyu; Choi, Doil; Hankins, Gerald; Malkaram, Sridhar; Reddy, Umesh K

    2014-08-01

    Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R(2) of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum. PMID:24585251

  5. Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

    PubMed Central

    Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

    2012-01-01

    Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod. PMID:22428056

  6. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

    PubMed

    Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

    2015-09-01

    Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species. PMID:25573196

  7. A tetranucleotide repeat (D4S1652) is linked to facioscapulohumeral dystrophy and shows no linkage disequilibrium with the disease

    SciTech Connect

    Mathews, K.D.; Bailey, H.L.; Mills, K.A.

    1994-09-01

    Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant dystrophy which is associated with a deletion in a subtelomeric repeat element on 4q35. The gene has not yet been identified. The probe detecting this deletion (D4F104S1) is not chromosome 4-specific, and at least one large family has been identified which is not linked to chromosome 4. Thus, persymptomatic/prenatal diagnosis can only be provided to families that are proven to be chromosome 4-linked or where a new mutation is demonstrated. The markers available to demonstrate linkage to chromosome 4, D4S139, D4S163, and D4F35S1, are VNTRs. We have used D4S1652, a tetranucleotide repeat recently identified by the Cooperative Human Linkage Center, in our FSHD families. We found it is completely linked to the 4q35 VNTRs and to the disease phenotype. Physical mapping, using radiation hybrids and somatic cell hybrids, places D4S1652 between D4S139, an interval of approximately 1 Mb. We have used D4S1652 to look for linkage disequilibrium in our FSHD patient population. This result is of interest because of our hypothesis that the deletion in the subtelomeric repeat element alters transcription of a more proximal gene through a position effect. Previously available markers have been unsatisfactory for this experiment because of difficulty comparing numerous VNTR alleles across families. We observed 4, easily distinguished, D4S1652 alleles in our families. We studied 14 chromosomes associated with disease phenotype and 55 chromosomes from nontransmitting parents. We found no evidence for linkage disequilibrium ({chi}{sup 2}=1.313, nonsignificant). This result will need confirmation with a larger patient population, but is consistent with the clinical observation that there is a high rate of a new mutation in this disorder.

  8. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

    PubMed

    Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

    2015-09-01

    Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.

  9. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

    PubMed

    Sved, John A; Cameron, Emilie C; Gilchrist, A Stuart

    2013-01-01

    There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-1)2, rather than the usual factor 1+1/(2S-1) for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

  10. Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population.

    PubMed

    Zhao, Yunlei; Wang, Hongmei; Chen, Wei; Li, Yunhai

    2014-01-01

    Understanding the population structure and linkage disequilibrium in an association panel can effectively avoid spurious associations and improve the accuracy in association mapping. In this study, one hundred and fifty eight elite cotton (Gossypium hirsutum L.) germplasm from all over the world, which were genotyped with 212 whole genome-wide marker loci and phenotyped with an disease nursery and greenhouse screening method, were assayed for population structure, linkage disequilibrium, and association mapping of Verticillium wilt resistance. A total of 480 alleles ranging from 2 to 4 per locus were identified from all collections. Model-based analysis identified two groups (G1 and G2) and seven subgroups (G1a-c, G2a-d), and differentiation analysis showed that subgroup having a single origin or pedigree was apt to differentiate with those having a mixed origin. Only 8.12% linked marker pairs showed significant LD (P<0.001) in this association panel. The LD level for linked markers is significantly higher than that for unlinked markers, suggesting that physical linkage strongly influences LD in this panel, and LD level was elevated when the panel was classified into groups and subgroups. The LD decay analysis for several chromosomes showed that different chromosomes showed a notable change in LD decay distances for the same gene pool. Based on the disease nursery and greenhouse environment, 42 marker loci associated with Verticillium wilt resistance were identified through association mapping, which widely were distributed among 15 chromosomes. Among which 10 marker loci were found to be consistent with previously identified QTLs and 32 were new unreported marker loci, and QTL clusters for Verticillium wilt resistanc on Chr.16 were also proved in our study, which was consistent with the strong linkage in this chromosome. Our results would contribute to association mapping and supply the marker candidates for marker-assisted selection of Verticillium wilt

  11. Linkage disequilibrium between a 5q13 microsatellite null allele and SMA indicates complex but stable deletions/duplications

    SciTech Connect

    Surhk, L.C.; Aubry, H.L.; MacKenzie, A.E.

    1994-09-01

    SMA is a recessively inherited degeneration of alpha motor neurons presenting in three distinct types with diverse onsets ranging from infancy (type I) to childhood (types II and III). All forms have been mapped to chromosome 5q13.1. We have developed PCR primers for two distinct microsatellite repeats (MSR), CATT-40G1 and CATT-192F7. These subloci are constituents of a previously reported 5q13.1 complex CA dinucleotide MSR, CATT-1, with four or more copies per chromosome. Type 1 SMA families (n=35) were examined because stricter clinical criteria permitted greater diagnostic accuracy and, possibly, greater mutational homogeneity. One allele per chromosome is amplified with the 40G1 and 192F7 subloci-specific primers out of a total of 3 and 7 possible alleles, respectively. Significant linkage disequilibrium was observed between the disease phenotype and the 40G1 null allele ({chi}{sup 2}=38.23) and 192F7 allele with 19 CA repeats ({chi}{sup 2}=6.62) in contrast to two markers D5S435 ({chi}{sup 2}=.42) and D5S351 ({chi}{sup 2}=.16), which have been shown to flank the SMA locus at less than 1% recombination. The null alleles present in both subloci appeared to be due to stable deletions rather than isolated DNA sequence polymorphisms. In contrast to recent reports, no evidence of de novo rearrangements were observed. Furthermore, duplications of these subloci have been observed in three normal chromosomes. Our data are consistent with unequal cross-overs generating deletions/duplications which not only account for the complexity being observed in the genomic walk within the critical SMA region, but could also be causally related SMA mutations. Results of similar linkage disequilibrium analyses employing 3 additional 5q13.1 microsatellites will also be presented.

  12. Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia.

    PubMed

    Edea, Z; Dadi, H; Kim, S-W; Park, J-H; Shin, G-H; Dessie, T; Kim, K-S

    2014-10-01

    Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D' and r(2) between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r(2) and D' values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers.

  13. Estimating Effective Population Size from Linkage Disequilibrium between Unlinked Loci: Theory and Application to Fruit Fly Outbreak Populations

    PubMed Central

    Sved, John A; Cameron, Emilie C.; Gilchrist, A. Stuart

    2013-01-01

    There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The ‘Burrows composite index’ is introduced in a novel way with a ‘composite haplotype table’. We show that in a sample of diploid size , the mean value of or from the composite haplotype table is biased by a factor of , rather than the usual factor for a conventional haplotype table. But analysis of population data using these formulae leads to estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to , and find that this factor leads to a bias in the estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered with lower variance than the original , and one that is also insensitive to null alleles. The resulting formulae are used to provide estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown. PMID:23894410

  14. Thorium-uranium disequilibrium dating of Late Quaternary ferruginous concretions and rinds

    NASA Astrophysics Data System (ADS)

    Short, Stephen A.; Lowson, Richard T.; Ems, John; Price, David M.

    1989-06-01

    Radioactive ferruginous nodules from the Alligator Rivers Uranium Province, Northern Territory, Australia, were systematically examined by optical microscopy, XRD, alpha- and fission-track autoradiography, and analysed for U, Th, Ra and major stable elements. Correlation of autoradiographs with microscopic structure and analyses of selective extractions confirmed that U and Th were strongly associated with Fe oxides. Fission-track autoradiography showed no concentration gradient evidence for postdepositional leaching of uranium. Strong acid leaching studies showed that irreversibly adsorbed U, and authigenic 234U and 230Th, but not 226Ra, are quantitatively retained by accumulated oxide/oxyhydroxide. Correlation of the groundwater activity ratio with oxidic 234U/ 238U activity ratios indicated the latter was radiogenically consistent with oxidic 230Th/ 234U activity ratios < 1. Dense, accumulated Fe/Mn oxide matrices are apparently capable of forming radiogenic closed systems in respect of the 230U → 234U → 230Th decay set. 234U/ 238U and 230Th/ 234U activity ratios were used to derive similar mean ages of rinds for four nodules in the same horizon. Th/U ages were also determined, using a Th-index detrital correction method previously used for impure carbonates, of pedogenic Fe/Mn accumulations having background concentrations of U and Th from other locations in Australia. These ages were compared with TL and 14C ages of the-host sediments. The comparisions suggest that Th/U dating could be used to age indurated layers of Fe/Mn oxides in soil horizons < 350 ka old.

  15. Radioactive Nanomaterials for Multimodality Imaging

    PubMed Central

    Chen, Daiqin; Dougherty, Casey A.; Yang, Dongzhi; Wu, Hongwei; Hong, Hao

    2016-01-01

    Nuclear imaging techniques, including primarily positron emission tomography (PET) and single-photon emission computed tomography (SPECT), can provide quantitative information for a biological event in vivo with ultra-high sensitivity, however, the comparatively low spatial resolution is their major limitation in clinical application. By convergence of nuclear imaging with other imaging modalities like computed tomography (CT), magnetic resonance imaging (MRI) and optical imaging, the hybrid imaging platforms can overcome the limitations from each individual imaging technique. Possessing versatile chemical linking ability and good cargo-loading capacity, radioactive nanomaterials can serve as ideal imaging contrast agents. In this review, we provide a brief overview about current state-of-the-art applications of radioactive nanomaterials in the circumstances of multimodality imaging. We present strategies for incorporation of radioisotope(s) into nanomaterials along with applications of radioactive nanomaterials in multimodal imaging. Advantages and limitations of radioactive nanomaterials for multimodal imaging applications are discussed. Finally, a future perspective of possible radioactive nanomaterial utilization is presented for improving diagnosis and patient management in a variety of diseases. PMID:27227167

  16. Using short-lived nuclides of the U- and Th-series to probe the kinetics of colloid migration in forested soils

    NASA Astrophysics Data System (ADS)

    Rihs, Sophie; Prunier, Jonathan; Thien, Bruno; Lemarchand, Damien; Pierret, Marie-Claire; Chabaux, François

    2011-12-01

    The recent chemical dynamics of a podzolic forest soil section (from the Strengbach watershed, France) was investigated using U- and Th-series nuclides. Analyses of ( 238U), ( 230Th), ( 226Ra), ( 232Th), ( 228Ra) and ( 228Th) activities in the soil particles, the seepage waters, and the mature leaves of the beech trees growing on this soil were performed by TIMS or gamma spectrometry. The simultaneous analysis of the different soil ( sl) compartments allows to demonstrate that a preferential Th leaching over Ra must be assumed to explain the ( 226Ra/ 230Th), ( 228Ra/ 232Th) and ( 228Th/ 228Ra) disequilibria recorded in the soil particles. The overall Ra- and Th- transfer schemes are entirely consistent with the prevailing acido-complexolysis weathering mechanism in podzols. Using a continuous open-system leaching model, the ( 226Ra/ 230Th) and ( 228Ra/ 232Th) disequilibria measured in the different soil layers enable dating of the contemporary processes occurring in this soil. In this way, we have determined that a preferential Th-leaching from the shallow Ah horizon, due to a strong complexation with organic colloids, began fairly recently (18 years ago at most). The continual increase in pH recorded in precipitations over the last 20 years is assumed to be the cause of this enhanced organic complexation. A lower soil horizon (50-60 cm) is also affected by preferential Th leaching, though lasting over several centuries at least, with a much smaller leaching rate. The migration of Th isotopes through this soil section might hence be used as a tracer for the organic colloids migration and the induced radioactive disequilibria demonstrate to be useful for assessing the colloidal migration kinetics in a forested soil. Ra and Th isotopic ratios also appear to be valuable tracers of some mineral-water-plant interactions occurring in soil. The ( 228Ra/ 226Ra) ratio enables discrimination of the Ra flux originating from leaf degradation from that originating from mineral

  17. Radioactivity in bottled mineral waters.

    PubMed

    Martín Sánchez, A; Rubio Montero, M P; Gómez Escobar, V; Jurado Vargas, M

    1999-06-01

    Consumption of bottled mineral water is a growing practice and is sometimes a necessity rather than a choice. In this work, a study of the radioactive content of a wide selection of commercial bottled mineral waters for human intake was carried out. The origins of the analyzed waters were very different, coming from various locations in France, Portugal and Spain. Their total alpha and beta activity concentrations were determined and also gamma spectrometry was used to detect some radionuclides. In some cases, the waters presented high values of the total alpha and beta activity concentrations surpassing the reference levels established by the CSN, the Spanish. Regulatory Organization. In these cases, a determination of uranium and 226Ra was also performed by using low-level liquid scintillation counting. The results revealed a strong correlation between radioactive content and dry residue, and lead one to conclude that high radioactive content is mainly related to the mineralization in waters of underground origin.

  18. Sorting of solid radioactive wastes

    SciTech Connect

    Marek, J.; Pecival, I.; Hejtman, J.; Wildman, J.; Cechak, T.

    1993-12-31

    In the nuclear power plants solid radioactive wastes are produced during regular operation and during small repairs. It is necessary to sort them into the highly contaminated wastes for which a special procedure for storage is necessary and waste that is not radioactive and can be stored in the environment under specific regulations. The aim of the project was to propose and to construct equipment, which is able to sort the waste with a high degree of reliability and to distinguish highly contaminated wastes from wastes which are less dangerous to the environment. The sensitivity of the detection system was tested by a mathematical model. The radioactive wastes from the primary part of the nuclear power plant can have three composition types. Details of the composition of the radioisotopes mixture are presented.

  19. Radioactive dating of the elements

    NASA Technical Reports Server (NTRS)

    Cowan, John J.; Thielemann, Friedrich-Karl; Truran, James W.

    1991-01-01

    The extent to which an accurate determination of the age of the Galaxy, and thus a lower bound on the age of the universe, can be obtained from radioactive dating is discussed. Emphasis is given to the use of the long-lived radioactive nuclei Re-187, Th-232, U-238, and U-235. The nature of the production sites of these and other potential Galactic chronometers is examined along with their production ratios. Age determinations from models of nucleocosmochronology are reviewed and compared with age determination from stellar sources and age constraints form cosmological considerations.

  20. Storage containers for radioactive material

    DOEpatents

    Groh, E.F.; Cassidy, D.A.; Dates, L.R.

    1980-07-31

    A radioactive material storage system is claimed for use in the laboratory having a flat base plate with a groove in one surface thereof and a hollow pedestal extending perpendicularly away from the other surface thereof, a sealing gasket in the groove, a cover having a filter therein and an outwardly extending flange which fits over the plate, the groove and the gasket, and a clamp for maintaining the cover and the plate sealed together. The plate and the cover and the clamp cooperate to provide a storage area for radioactive material readily accessible for use or inventory. Wall mounts are provided to prevent accidental formation of critical masses during storage.

  1. Storage containers for radioactive material

    DOEpatents

    Groh, Edward F.; Cassidy, Dale A.; Dates, Leon R.

    1981-01-01

    A radioactive material storage system for use in the laboratory having a flat base plate with a groove in one surface thereof and a hollow pedestal extending perpendicularly away from the other surface thereof, a sealing gasket in the groove, a cover having a filter therein and an outwardly extending flange which fits over the plate, the groove and the gasket, and a clamp for maintaining the cover and the plate sealed together, whereby the plate and the cover and the clamp cooperate to provide a storage area for radioactive material readily accessible for use or

  2. Induced radioactivity in LDEF components

    NASA Technical Reports Server (NTRS)

    Harmon, B. A.; Fishman, G. J.; Parnell, T. A.; Laird, C. E.

    1992-01-01

    A systematic study of the induced radioactivity of the Long Duration Exposure Facility (LDEF) is being carried out in order to gather information about the low earth orbit radiation environment and its effects on materials. The large mass of the LDEF spacecraft, its stabilized configuration, and long mission duration have presented an opportunity to determine space radiation-induced radioactivities with a precision not possible before. Data presented include preliminary activities for steel and aluminum structural samples, and activation subexperiment foils. Effects seen in the data show a clear indication of the trapped proton anisotropy in the South Atlantic Anomaly and suggest contributions from different sources of external radiation fluxes.

  3. LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs

    PubMed Central

    2012-01-01

    Background Complex human diseases may be associated with many gene interactions. Gene interactions take several different forms and it is difficult to identify all of the interactions that are potentially associated with human diseases. One approach that may fill this knowledge gap is to infer previously unknown gene interactions via identification of non-physical linkages between different mutations (or single nucleotide polymorphisms, SNPs) to avoid hitchhiking effect or lack of recombination. Strong non-physical SNP linkages are considered to be an indication of biological (gene) interactions. These interactions can be physical protein interactions, regulatory interactions, functional compensation/antagonization or many other forms of interactions. Previous studies have shown that mutations in different genes can be linked to the same disorders. Therefore, non-physical SNP linkages, coupled with knowledge of SNP-disease associations may shed more light on the role of gene interactions in human disorders. A user-friendly web resource that integrates information about non-physical SNP linkages, gene annotations, SNP information, and SNP-disease associations may thus be a good reference for biomedical research. Findings Here we extracted the SNPs located within the promoter or exonic regions of protein-coding genes from the HapMap database to construct a database named the Linkage-Disequilibrium-based Gene Interaction database (LDGIdb). The database stores 646,203 potential human gene interactions, which are potential interactions inferred from SNP pairs that are subject to long-range strong linkage disequilibrium (LD), or non-physical linkages. To minimize the possibility of hitchhiking, SNP pairs inferred to be non-physically linked were required to be located in different chromosomes or in different LD blocks of the same chromosomes. According to the genomic locations of the involved SNPs (i.e., promoter, untranslated region (UTR) and coding region (CDS)), the

  4. Radioactivity and the Biology Teacher

    ERIC Educational Resources Information Center

    Hornsey, D. J.

    1974-01-01

    Discusses minimum necessary nuclear fundamentals of radioactive isotopes such as levels of activity, specific activity and the use of carrier materials. Corrections that need to be taken into account in using an isotope to obtain a valid result are also described and statistics for a valid result are included. (BR)

  5. Nuclear structure from radioactive decay

    SciTech Connect

    Wood, J.L.

    1990-09-30

    This report discusses the nuclear structure of the following isotopes as a result of radioactive decays: neutron-deficient iridium isotopes; neutron-deficient platinum isotopes; neutron-deficient gold isotopes; neutron-deficient mercury isotopes; neutron-deficient thallium isotopes; neutron-deficient lead isotopes; neutron-deficient promethium isotopes; and neutron-deficient samarium isotopes.

  6. RadioActive101 Practices

    ERIC Educational Resources Information Center

    Brites, Maria José; Ravenscroft, Andrew; Dellow, James; Rainey, Colin; Jorge, Ana; Santos, Sílvio Correia; Rees, Angela; Auwärter, Andreas; Catalão, Daniel; Balica, Magda; Camilleri, Anthony F.

    2014-01-01

    In keeping with the overarching RadioActive101 (RA101) spirit and ethos, this report is the product of collaborative and joined-up thinking from within the European consortium spread across five countries. As such, it is not simply a single voice reporting on the experiences and knowledge gained during the project. Rather it is a range of…

  7. High-Level Radioactive Waste.

    ERIC Educational Resources Information Center

    Hayden, Howard C.

    1995-01-01

    Presents a method to calculate the amount of high-level radioactive waste by taking into consideration the following factors: the fission process that yields the waste, identification of the waste, the energy required to run a 1-GWe plant for one year, and the uranium mass required to produce that energy. Briefly discusses waste disposal and…

  8. Electrodynamic radioactivity detector for microparticles

    NASA Astrophysics Data System (ADS)

    Ward, T. L.; Davis, E. J.; Jenkins, R. W., Jr.; McRae, D. D.

    1989-03-01

    A new technique for the measurement of the radioactive decay of single microparticles has been demonstrated. Although the experiments were made with droplets of order 20 μm in diameter, microparticles in the range 0.1-100 μm can be accommodated. An electrodynamic balance and combination light-scattering photometer were used to measure the charge-loss rate and size of a charged microsphere suspended in a laser beam by superposed ac and dc electrical fields. The charged particle undergoes charge loss in the partially ionized gas atmosphere which results from radioactive decay of 14C-tagged compounds, and the rate of charge loss is proportional to the rate of decay here. The charge on a particle was determined by measuring the dc voltage necessary to stably suspend the particle against gravity while simultaneously determining the droplet size by light-scattering techniques. The parameters which affect the operation of the electrodynamic balance as a radioactivity detector are examined, and the limits of its sensitivity are explored. Radioactivity levels as low as 120 pCi have been measured, and it appears that by reducing the background contamination inside our balance activity levels on the order of 10 pCi can be detected. This new technique has application in the measurement of activity levels and source discrimination of natural and man-made aerosols and smokes and is also useful for studies involving specifically labeled radio-chemical probes.

  9. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

    PubMed Central

    2014-01-01

    Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

  10. Inorganic carbon uptake during photosynthesis. II. Uptake by isolated Asparagus mesophyll cells during isotopic disequilibrium. [Asparagus sprengeri

    SciTech Connect

    Espie, G.S.; Owttrim, G.W.; Colman, B.

    1986-04-01

    The species of inorganic carbon (CO/sub 2/ or HCO/sub 3//sup -/) taken up as a source of substrate for photosynthetic fixation by isolated Asparagus sprengeri mesophyll cells is investigated. Discrimination between CO/sub 2/ or HCO/sub 3//sup -/ transport, during steady state photosynthesis, is achieved by monitoring the changes (by /sup 14/C fixation) which occur in the specific activity of the intracellular pool of inorganic carbon when the inorganic carbon present in the suspending medium is in a state of isotopic disequilibrium. Quantitative comparisons between theoretical (CO/sub 2/ or HCO/sub 3//sup -/ transport) and experimental time-courses of /sup 14/C incorporation, over the pH range of 5.2 to 7.5, indicate that the specific activity of extracellular CO/sub 2/, rather than HCO/sub 3//sup -/, is the appropriate predictor of the intracellular specific activity. It is concluded, therefore, that CO/sub 2/ is the major source of exogenous inorganic carbon taken up by Asparagus cells. However, at high pH (8.5), a component of net DIC uptake may be attributable to HCO/sub 3//sup -/ transport, as the incorporation of /sup 14/C during isotopic disequilibrium exceeds the maximum possible incorporation predicted on the basis of CO/sub 2/ uptake alone. The contribution of HCO/sub 3//sup -/ to net inorganic carbon uptake (pH 8.5) is variable, ranging from 5 to 16%, but is independent of the extracellular HCO/sub 3//sup -/ concentration. The evidence for direct HCO/sub 3//sup -/ transport is subject to alternative explanations and must, therefore, be regarded as equivocal. Nonlinear regression analysis of the rate of /sup 14/C incorporation as a function of time indicates the presence of a small extracellular resistance to the diffusion of CO/sub 2/, which is partially alleviated by a high extracellular concentration of HCO/sub 3//sup -/.

  11. Clumped isotope disequilibrium during rapid CO2 uptake and carbonate precipitation in subaerial alkaline springs associated with ongoing serpentinization

    NASA Astrophysics Data System (ADS)

    Falk, E. S.; Guo, W.; Kelemen, P. B.

    2014-12-01

    Ongoing serpentinization in tectonically exposed ultramafic bodies is manifested at the surface in alkaline springs (pH >11). Where these high-pH waters come in contact with CO2 at the surface, rapid calcite precipitation forms extensive travertines. We study natural travertine samples from Oman and synthetic witherite (BaCO3) from high-pH experiments to identify disequilibrium signals in δ18O, δ13C and clumped isotopes (measured as Δ47) that characterize rapid uptake of atmospheric CO2 and carbonate precipitation from high pH fluids. Kinetic effects preclude the use of clumped or oxygen isotopes for carbonate thermometry in these environments, but trends in δ18O, δ13C and Δ47 could help identify extinct alkaline systems or distinguish CO2 sources. Oman travertines formed at peridotite-hosted alkaline springs have long been known to exhibit a large range of kinetically depleted δ18O and δ13C values. We find fresh carbonate precipitated at these alkaline springs also exhibit large enrichments in Δ47 that covary with the depletions in δ18O and δ13C, thought to arise during hydroxylation of CO2 in high-pH fluids. Witherite precipitated during rapid CO2 uptake and carbonate precipitation in high pH experiments also exhibits disequilibrium values in δ18O, δ13C and Δ47, with the Δ47 of carbonate precipitates strongly affected by the Δ47 the reactant CO2. δ18O, δ13C and Δ47 trends could serve as a marker for carbonates formed in subaerial alkaline environments and track carbon sources in these systems. For example, the δ18O-δ13C slope in carbonates from Martian meteorites is similar to that observed in carbonates from terrestrial alkaline springs, so if corresponding enrichments in Δ47 could be identified in Martian carbonates, it could suggest that alkaline springs were present on the surface of Mars. Clumped isotope signals could also help distinguish carbon sources: kinetic enrichments in Δ47 would be absent or diminished in high-pH carbonates

  12. Linkage disequilibrium between the juvenile neuronal ceroid lipofuscinosis gene and marker loci on chromosome 16p12. 1

    SciTech Connect

    Lerner, T.J.; MacCormack, K.; Gleitsman, J.; Schlumpf, K.; Breakefield, X.O.; Gusella, J.F.; Haines, J.L. )

    1994-01-01

    The neuronal ceroid lipofuscinoses (NCL; Batten disease) are a collection of autosomal recessive disorders characterized by the accumulation of autofluorescent lipopigments in the neurons and other cell types. Clinically, these disorders are characterized by progressive encephalopathy, loss of vision, and seizures. CLN3, the gene responsible for juvenile NCL, has been mapped to a 15-cM region flanked by the marker loci D16S148 and D16S150 on human chromosome 16. CLN2, the gene causing the late-infantile form of NCL (LNCL), is not yet mapped. The authors have used highly informative dinucleoide repeat markers mapping between D16S148 and D16S150 to refine the localization of CLN3 and to test for linkage to CLN2. The authors find significant linkage disequilibrium between CLN3 and the dinucleotide repeat marker loci D16S288 (X[sup 2](7) = 46.5, P < .005), D16S298 (X[sup 2](6) = 36.6, P < .005), and D16S299 (X[sup 2](7) = 73.8, P < .005), and also a novel RFLP marker at the D16S272 locus (X[sup 2](1) = 5.7, P = .02). These markers all map to 16p12.1. The D16S298/D16S299 haplotype [open quotes]5/4[close quotes] is highly overrepresented, accounting for 54% of CLN3 chromosomes as compared with 8% of control chromosomes (X[sup 2] = 117, df = 1, P < .001). Examination of the haplotypes suggests that the CLN3 locus can be narrowed to the region immediately surrounding these markers in 16p12.1. Analysis of D16S299 in LNCL pedigrees supports the previous finding that CLN3 and CLN2 are different genetic loci. This study also indicates that dinucleotide repeat markers play a valuable role in disequilibrium studies. 23 refs., 1 fig., 4 tabs.

  13. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    PubMed

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in

  14. Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack)

    PubMed Central

    2012-01-01

    Background Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines. Results The principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes. Conclusions Our results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye

  15. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    PubMed

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in

  16. Radioactive Waste Incineration: Status Report

    SciTech Connect

    Diederich, A.R.; Akins, M.J.

    2008-07-01

    Incineration is generally accepted as a method of reducing the volume of radioactive waste. In some cases, the resulting ash may have high concentrations of materials such as Plutonium or Uranium that are valuable materials for recycling. Incineration can also be effective in treating waste that contains hazardous chemicals as well as radioactive contamination. Despite these advantages, the number of operating incinerators currently in the US currently appears to be small and potentially declining. This paper describes technical, regulatory, economic and political factors that affect the selection of incineration as a preferred method of treating radioactive waste. The history of incinerator use at commercial and DOE facilities is summarized, along with the factors that have affected each of the sectors, thus leading to the current set of active incinerator facilities. In summary: Incineration has had a long history of use in radioactive waste processing due to their ability to reduce the volume of the waste while destroying hazardous chemicals and biological material. However, combinations of technical, regulatory, economic and political factors have constrained the overall use of incineration. In both the Government and Private sectors, the trend is to have a limited number of larger incineration facilities that treat wastes from a multiple sites. Each of these sector is now served by only one or two incinerators. Increased use of incineration is not likely unless there is a change in the factors involved, such as a significant increase in the cost of disposal. Medical wastes with low levels of radioactive contamination are being treated effectively at small, local incineration facilities. No trend is expected in this group. (authors)

  17. 46 CFR 147.100 - Radioactive materials.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... (NRC) under 10 CFR parts 30 and 34. (b) Stowage of radioactive materials must conform to the... 46 Shipping 5 2010-10-01 2010-10-01 false Radioactive materials. 147.100 Section 147.100 Shipping... Stowage and Other Special Requirements for Particular Materials § 147.100 Radioactive materials....

  18. 49 CFR 175.705 - Radioactive contamination.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 2 2014-10-01 2014-10-01 false Radioactive contamination. 175.705 Section 175.705... Regulations Applicable According to Classification of Material § 175.705 Radioactive contamination. (a) A... (radioactive) materials that may have been released from their packagings. (b) When contamination is present...

  19. 49 CFR 175.705 - Radioactive contamination.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 2 2013-10-01 2013-10-01 false Radioactive contamination. 175.705 Section 175.705... Regulations Applicable According to Classification of Material § 175.705 Radioactive contamination. (a) A... (radioactive) materials that may have been released from their packagings. (b) When contamination is present...

  20. 49 CFR 175.705 - Radioactive contamination.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Radioactive contamination. 175.705 Section 175.705... Regulations Applicable According to Classification of Material § 175.705 Radioactive contamination. (a) A... (radioactive) materials that may have been released from their packagings. (b) When contamination is present...

  1. 49 CFR 175.705 - Radioactive contamination.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 2 2011-10-01 2011-10-01 false Radioactive contamination. 175.705 Section 175.705... Regulations Applicable According to Classification of Material § 175.705 Radioactive contamination. (a) A... (radioactive) materials that may have been released from their packagings. (b) When contamination is present...

  2. 49 CFR 175.705 - Radioactive contamination.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 2 2012-10-01 2012-10-01 false Radioactive contamination. 175.705 Section 175.705... Regulations Applicable According to Classification of Material § 175.705 Radioactive contamination. (a) A... (radioactive) materials that may have been released from their packagings. (b) When contamination is present...

  3. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  4. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  5. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  6. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  7. 46 CFR 147.100 - Radioactive materials.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... (NRC) under 10 CFR parts 30 and 34. (b) Stowage of radioactive materials must conform to the... 46 Shipping 5 2011-10-01 2011-10-01 false Radioactive materials. 147.100 Section 147.100 Shipping... Stowage and Other Special Requirements for Particular Materials § 147.100 Radioactive materials....

  8. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  9. 46 CFR 147.100 - Radioactive materials.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... (NRC) under 10 CFR parts 30 and 34. (b) Stowage of radioactive materials must conform to the... 46 Shipping 5 2014-10-01 2014-10-01 false Radioactive materials. 147.100 Section 147.100 Shipping... Stowage and Other Special Requirements for Particular Materials § 147.100 Radioactive materials....

  10. 46 CFR 147.100 - Radioactive materials.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... (NRC) under 10 CFR parts 30 and 34. (b) Stowage of radioactive materials must conform to the... 46 Shipping 5 2012-10-01 2012-10-01 false Radioactive materials. 147.100 Section 147.100 Shipping... Stowage and Other Special Requirements for Particular Materials § 147.100 Radioactive materials....

  11. 46 CFR 147.100 - Radioactive materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... (NRC) under 10 CFR parts 30 and 34. (b) Stowage of radioactive materials must conform to the... 46 Shipping 5 2013-10-01 2013-10-01 false Radioactive materials. 147.100 Section 147.100 Shipping... Stowage and Other Special Requirements for Particular Materials § 147.100 Radioactive materials....

  12. A model that helps explain Sr-isotope disequilibrium between feldspar phenocrysts and melt in large-volume silicic magma systems

    USGS Publications Warehouse

    Duffield, W.A.; Ruiz, J.

    1998-01-01

    Feldspar phenocrysts of silicic volcanic rocks are commonly in Sr-isotopic disequilibrium with groundmass. In some cases the feldspar is more radiogenic, and in others it is less radiogenic. Several explanations have been published previously, but none of these is able to accommodate both senses of disequilibrium. We present a model by which either more- or less-radiogenic feldspar (or even both within a single eruptive unit) can originate. The model requires a magma body open to interaction with biotite- and feldspar-bearing wall rock. Magma is incrementally contaminated as wall rock melts incongruently. Biotite preferentially melts first, followed by feldspar. Such melting behavior, which is supported by both field and experimental studies, first contaminates magma with a relatively radiogenic addition, followed by a less-radiogenic addition. Feldspar phenocrysts lag behind melt (groundmass of volcanic rock) in incorporating the influx of contaminant, thus resulting in Sr-isotopic disequilibrium between the crystals and melt. The sense of disequilibrium recorded in a volcanic rock depends on when eruption quenches the contamination process. This model is testable by isotopic fingerprinting of individual feldspar crystals. For a given set of geologic boundary conditions, specific core-to-rim Sr-isotopic profiles are expectable. Moreover, phenocrysts that nucleate at different times during the contamination process should record different and predictable parts of the history. Initial results of Sr-isotopic fingerprinting of sanidine phenocrysts from the Taylor Creek Rhyolite are consistent with the model. More tests of the model are desirable.Feldspar phenocrysts of silicic volcanic rocks are commonly in Sr-isotopic disequilibrium with groundmass. In some cases the feldspar is more radiogenic, and in others it is less radiogenic. Several explanations have been published previously, but none of these is able to accommodate both senses of disequilibrium. We present a

  13. Evidence, from family studies, for linkage disequilibrium between TGFA and a gene for nonsyndromic cleft lip with or without cleft palate

    SciTech Connect

    Feng, Hongshu; Lee, A.; Gasser, D.L.; Sassani, R.; Bartlett, S.P.; Buetow, K.H.; Hecht, J.T.; Malcolm, S.; Winter, R.M.; Vintiner, G.M.

    1994-11-01

    The inheritance of alleles of the transforming growth factor alpha (TGFA) locus has been studied in families affected with cleft lip with or without cleft palate (CL/P), by using the transmission/disequilibrium test described by Spielman and colleagues. Only heterozygous parents with an affected child can be included in this test, but within such families a significantly greater frequency of C2 alleles were transmitted to affected children than would be expected by chance. There was no evidence that the total number of C2 alleles transmitted to affected and unaffected children differed significantly from random segregation. These data provide evidence from within families that a gene for susceptibility to CL/P is in significant linkage disequilibrium with the C2 allele of the TGFA locus. 30 refs., 1 fig., 2 tabs.

  14. Linkage disequilibrium analysis in young populations: pseudo-vitamin D-deficiency rickets and the founder effect in French Canadians.

    PubMed

    Labuda, M; Labuda, D; Korab-Laskowska, M; Cole, D E; Zietkiewicz, E; Weissenbach, J; Popowska, E; Pronicka, E; Root, A W; Glorieux, F H

    1996-09-01

    Pseudo-vitamin D-deficiency rickets (PDDR) was mapped close to D12S90 and between proximal D12S312 and distal (D12S305, D12S104) microsatellites that were subsequently found on a single YAC clone. Analysis of a complex haplotype in linkage disequilibrium (LD) with the disease discriminated among distinct founder effects in French Canadian populations in Acadia and in Charlevoix-Saguenay-Lac-Saint-Jean (Ch-SLSJ), as well as an earlier one in precolonial Europe. A simple demographic model suggested the historical age of the founder effect in Ch-SLSJ to be approximately 12 generations. The corresponding LD data are consistent with this figure when they are analyzed within the framework of Luria-Delbrück model, which takes into account the population growth. Population sampling due to a limited number of first settlers and the rapid demographic expansion appear to have played a major role in the founding of PDDR in Ch-SLSJ and, presumably, other genetic disorders endemic to French Canada. Similarly, the founder effect in Ashkenazim, coinciding with their early settlement in medieval Poland and subsequent expansion eastward, could explain the origin of frequent genetic diseases in this population. PMID:8751865

  15. Genetic Coadaptation in the Chromosomal Polymorphism of DROSOPHILA SUBOBSCURA. I. Seasonal Changes of Gametic Disequilibrium in a Natural Population

    PubMed Central

    Fontdevila, A.; Zapata, C.; Alvarez, G.; Sanchez, L.; Méndez, J.; Enriquez, I.

    1983-01-01

    Seasonal changes in gene arrangement and allozyme frequencies have been investigated in Drosophila subobscura for several years. Some arrangements (Ost and O3+4+7) show seasonal variation, which suggests that chromosomal polymorphism is flexible in this species. Seasonal changes in allozyme frequencies for Lap and Pept-1 loci, both located within the same inversions of chromosome O, are significant only inside the Ost arrangement, but not inside O3+4 arrangement. This arrangement-dependent response of allozyme generates variation in arrangement-allozyme disequilibrium. The historical hypothesis on the maintenance of disequilibria cannot explain these seasonal changes, and some kind of natural selection must be invoked. Association between Lap and Pept-1 is also seasonal inside Ost but not inside O3+4. We propose that Ost probably consists of a finite array of supergenes that are differentially favored in each season by natural selection. The present evidence on this supergene selection and other genetic, biogeographic and phylogenetic data points to O3+4 as the most primitive gene order among the present arrangements. PMID:17246183

  16. sup 13 C and sup 18 O isotopic disequilibrium in biological carbonates: II. In vitro simulation of kinetic isotope effects

    SciTech Connect

    McConnaughey, T. )

    1989-01-01

    Biological carbonates are built largely from CO{sub 2}, which diffuses across the skeletogenic membrane and reacts to form HCO{sub 3}{sup {minus}}. Kinetic discrimination against the heavy isotopes {sup 18}O and {sup 13}C during CO{sub 2} hydration and hydroxylation apparently causes most of the isotopic disequilibrium observed in biological carbonates. These kinetic isotope effects are expressed when the extracytosolic calcifying solution is thin and alkaline, and HCO{sub 3}{sup {minus}} precipitates fairly rapidly as CaCO{sub 3}. In vitro simulation of the calcifying environment produced heavy isotope depletions qualitatively similar to, but somewhat more extreme than, those seen in biological carbonates. Isotopic equilibration during biological calcification occurs through CO{sub 2} exchange across the calcifying membrane and by admixture ambient waters (containing HCO{sub 3}{sup {minus}}) into the calcifying fluids. Both mechanisms tend to produce linear correlations between skeletal {delta}{sup 13}C and {delta}{sup 18}O.

  17. Dacite formation at Ilopango Caldera, El Salvador: U-series disequilibrium and implications for petrogenetic processes and magma storage time

    NASA Astrophysics Data System (ADS)

    Garrison, Jennifer M.; Reagan, Mark K.; Sims, Kenneth W. W.

    2012-06-01

    Ilopango Caldera was formed ˜1810 years ago by eruption of the Tierra Blanca Joven (TBJ) dacite (70 km3) in central El Salvador. A subsequent eruption in 1880 produced a cluster of dacite domes in the center of Lago Ilopango that contain olive-bearing enclaves of basaltic andesite. The purpose of this study is to use trace element, isotope, and U-series data from the TBJ and 1880 eruptions to assess petrogenesis and the timescale of magma storage. We find that although the range of trace element data in the TBJ dacite can be reproduced by simple crystal fractionation of a plagioclase- and amphibole-rich mineral assemblage, the87Sr/86Sr and 207Pb/204Pb data suggest that the 1880 basaltic andesite enclave has a different source than the dacites. This is consistent with U-series data that show the TBJ dacites have lower (230Th/232Th) than the 1880 basaltic andesite enclave (1.5 versus 1.6, respectively). All Ilopango rocks have 230Th excesses, and the range in (238U/232Th) of the TBJ dacites can be modeled by crystal fractionation of a mineral assemblage including accessory zircon and allanite from a magma that is similar in composition to the enclave. Mineral isochrons yield crystallization ages of <10,000 years, and disequilibrium (226Ra/230Th) values suggest a similarly short residence time. Our data suggest that the large volumes of erupted dacite at Ilopango Caldera are generated very rapidly.

  18. Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

    PubMed

    Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J; Xiao, Yingjie; Liu, Kede

    2016-01-01

    High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.

  19. Distribution of long-range linkage disequilibrium and Tajima's D values in Scandinavian populations of Norway Spruce (Picea abies).

    PubMed

    Larsson, Hanna; Källman, Thomas; Gyllenstrand, Niclas; Lascoux, Martin

    2013-05-20

    The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima's D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.

  20. Assortative mating drives linkage disequilibrium between sperm and egg recognition protein loci in the sea urchin Strongylocentrotus purpuratus.

    PubMed

    Stapper, Andres Plata; Beerli, Peter; Levitan, Don R

    2015-04-01

    Sperm and eggs have interacting proteins on their surfaces that influence their compatibility during fertilization. These proteins are often polymorphic within species, producing variation in gamete affinities. We first demonstrate the fitness consequences of various sperm bindin protein (Bindin) variants in the sea urchin Strongylocentrotus purpuratus, and assortative mating between males and females based on their sperm Bindin genotype. This empirical finding of assortative mating based on sperm Bindin genotype could arise by linkage disequilibrium (LD) between interacting sperm and egg recognition loci. We then examine sequence variation in eight exons of the sea urchin egg receptor for sperm Bindin (EBR1). We find little evidence of LD among the eight exons of EBR1, yet strong evidence for LD between sperm Bindin and EBR1 overall, and varying degrees of LD between sperm Bindin among the eight exons. We reject the alternate hypotheses of LD driven by shared evolutionary histories, population structure, or close physical linkage between these interacting loci on the genome. The most parsimonious explanation for this pattern of LD is that it represents selection driven by assortative mating based on interactions among these sperm and egg loci. These findings indicate the importance of ongoing sexual selection in the maintenance of protein polymorphisms and LD, and more generally highlight how LD can be used as an indication of current mate choice, as opposed to historic selection. PMID:25618458

  1. Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing

    PubMed Central

    Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J.; Xiao, Yingjie; Liu, Kede

    2016-01-01

    High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome “Darmor-bzh.” The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS. PMID:26730738

  2. A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes.

    PubMed

    Chen, W M; Deng, H W

    2001-07-01

    Transmission disequilibrium test (TDT) is a nuclear family-based analysis that can test linkage in the presence of association. It has gained extensive attention in theoretical investigation and in practical application; in both cases, the accuracy and generality of the power computation of the TDT are crucial. Despite extensive investigations, previous approaches for computing the statistical power of the TDT are neither accurate nor general. In this paper, we develop a general and highly accurate approach to analytically compute the power of the TDT. We compare the results from our approach with those from several other recent papers, all against the results obtained from computer simulations. We show that the results computed from our approach are more accurate than or at least the same as those from other approaches. More importantly, our approach can handle various situations, which include (1) families that consist of one or more children and that have any configuration of affected and nonaffected sibs; (2) families ascertained through the affection status of parent(s); (3) any mixed sample with different types of families in (1) and (2); (4) the marker locus is not a disease susceptibility locus; and (5) existence of allelic heterogeneity. We implement this approach in a user-friendly computer program: TDT Power Calculator. Its applications are demonstrated. The approach and the program developed here should be significant for theoreticians to accurately investigate the statistical power of the TDT in various situations, and for empirical geneticists to plan efficient studies using the TDT.

  3. Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

    PubMed

    Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J; Xiao, Yingjie; Liu, Kede

    2016-01-01

    High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS. PMID:26730738

  4. Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus.

    PubMed

    Tarazona-Santos, E; Tishkoff, S A

    2005-02-01

    Interleukin-13 (IL-13) is a cytokine involved in Th2 immune response, which plays a role in susceptibility to infection by extracellular parasites as well as complex diseases of the immune system such as asthma and allergies. To determine the pattern of genetic diversity at the IL13 gene, we sequenced 3950 bp encompassing the IL13 gene and its promoter in 264 chromosomes from individuals originating from East and West Africa, Europe, China and South America. Thirty-one single-nucleotide polymorphisms (SNPs) arranged in 88 haplotypes were indentified, including the nonsynonymous substitution Arg130Gln in exon 4, which differs in frequency across ethnic groups. We show that genetic diversity and linkage disequilibrium (LD) are not evenly distributed across the gene and that sites in the 5' and 3' regions of the gene show strong differentiation among continental groups. We observe a divergent pattern of haplotype variation and LD across geographic regions and we identify a set of htSNPs that will be useful for functional genetic association studies of complex disease. We use several statistical tests to distinguish the effects of natural selection and demographic history on patterns of genetic diversity at the IL13 locus.

  5. Assortative mating drives linkage disequilibrium between sperm and egg recognition protein loci in the sea urchin Strongylocentrotus purpuratus.

    PubMed

    Stapper, Andres Plata; Beerli, Peter; Levitan, Don R

    2015-04-01

    Sperm and eggs have interacting proteins on their surfaces that influence their compatibility during fertilization. These proteins are often polymorphic within species, producing variation in gamete affinities. We first demonstrate the fitness consequences of various sperm bindin protein (Bindin) variants in the sea urchin Strongylocentrotus purpuratus, and assortative mating between males and females based on their sperm Bindin genotype. This empirical finding of assortative mating based on sperm Bindin genotype could arise by linkage disequilibrium (LD) between interacting sperm and egg recognition loci. We then examine sequence variation in eight exons of the sea urchin egg receptor for sperm Bindin (EBR1). We find little evidence of LD among the eight exons of EBR1, yet strong evidence for LD between sperm Bindin and EBR1 overall, and varying degrees of LD between sperm Bindin among the eight exons. We reject the alternate hypotheses of LD driven by shared evolutionary histories, population structure, or close physical linkage between these interacting loci on the genome. The most parsimonious explanation for this pattern of LD is that it represents selection driven by assortative mating based on interactions among these sperm and egg loci. These findings indicate the importance of ongoing sexual selection in the maintenance of protein polymorphisms and LD, and more generally highlight how LD can be used as an indication of current mate choice, as opposed to historic selection.

  6. Linkage disequilibrium analysis in young populations: Pseudo-vitamin D-deficiency rickets and the founder effect in French Canadians

    SciTech Connect

    Labuda, M.; Glorieux, F.H.; Labuda, D.; Korab-Laskowska, M.

    1996-09-01

    Pseudo-vitamin D-deficiency rickets (PDDR) was mapped close to D12S90 and between proximal D12S312 and distal (D12S305, D12S104) microsatellites that were subsequently found on a single YAC clone. Analysis of a complex haplotype in linkage disequilibrium (LD) with the disease discriminated among distinct founder effects in French Canadian populations in Acadia and in Charlevoix-Saguenay-Lac-Saint-Jean (Ch-SLSJ), as well as an earlier one in precolonial Europe. A simple demographic model suggested the historical age of the founder effect in Ch-SLSJ to be {approximately}12 generations. The corresponding LD data are consistent with this figure when they are analyzed within the framework of Luria-Delbruck model, which takes into account the population growth. Population sampling due to a limited number of first settlers and the rapid demographic expansion appear to have played a major role in the founding of PDDR in Ch-SLSJ and, presumably, other genetic disorders endemic to French Canada. Similarly, the founder effect in Ashkenazim, coinciding with their early settlement in medieval Poland and subsequent expansion eastward, could explain the origin of frequent genetic diseases in this population. 48 refs., 5 figs., 2 tabs.

  7. Linkage disequilibrium between the FES, D15S127, and BLM loci in Ashkenazi Jews with Bloom syndrome

    SciTech Connect

    Ellis, N.A.; Roe, A.M.; Kozloski, J.; Proytcheva, M.; Falk, C.; German, J.

    1994-09-01

    Bloom syndrome (BS) is more common in the Ashkenazi Jewish than in any other population. Approximately 1 in 110 Ashkenazi Jews carries blm, the BS mutation. The locus mutated in BS, BLM, maps to chromosome subband 15q26.1, tightly linked to the proto-oncogene FES. The authors have investigated the basis for the increased frequency of blm in the Ashkenazim by genotyping polymorphic microsatellite loci tightly linked to BLM in affected and unaffected individuals from Ashkenazi Jewish and non-Ashkenazi populations. A striking association of the C3 allele at FES with blm ({Delta} = .422; p = 5.52 x 10{sup {minus}7}) and of the 145-bp and 147-bp alleles at D15S127 with blm ({Delta} = .392 and {Delta} = .483, respectively; p = 2.8 x 10{sup {minus}5} and p = 5.4 x 10{sup {minus}7}, respectively) was detected in Ashkenazi Jews with BS. This linkage disequilibrium constitutes strong support for a founder-effect hypothesis; the chromosome in the hypothetical founder who carried blm also carried the C3 allele at FES and either the 145-bp or the 147-bp allele at D15S127. 32 refs., 1 fig., 5 tabs.

  8. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    PubMed

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  9. Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens.

    PubMed

    Beissinger, T M; Gholami, M; Erbe, M; Weigend, S; Weigend, A; de Leon, N; Gianola, D; Simianer, H

    2016-02-01

    A whole-genome scan for identifying selection acting on pairs of linked loci is proposed and implemented. The scan is based on , one of Ohta's 1982 measures of between-population linkage disequilibrium (LD). An approximate empirical null distribution for the statistic is suggested. Although the partitioning of LD into between-population components was originally used to investigate epistatic selection, we demonstrate that values of may also be influenced by single-locus selective sweeps with linkage but no epistasis. The proposed scan is implemented in a diverse panel of chickens including 72 distinct breeds genotyped at 538 298 single-nucleotide polymorphisms. In all, 1723 locus pairs are identified as putatively corresponding to a selective sweep or epistatic selection. These pairs of loci generally cluster to form overlapping or neighboring signals of selection. Known variants that were expected to have been under selection in the panel are identified, as well as an assortment of novel regions that have putatively been under selection in chickens. Notably, a promising pair of genes located 8 MB apart on chromosome 9 are identified based on as demonstrating strong evidence of dispersive epistatic selection between populations.

  10. A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci.

    PubMed

    Hollenbeck, C M; Portnoy, D S; Gold, J R

    2016-10-01

    Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP data set are unlinked. The approach is applied to an empirical data set of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.

  11. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

    PubMed Central

    Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca e; Mundim, Gabriel Borges

    2016-01-01

    Abstract The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

  12. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

    PubMed

    Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca E; Mundim, Gabriel Borges

    2016-03-01

    The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

  13. Effect of two- and three-locus linkage disequilibrium on the power to detect marker/phenotype associations.

    PubMed

    Nielsen, Dahlia M; Ehm, Margaret G; Zaykin, Dmitri V; Weir, Bruce S

    2004-10-01

    There has been much recent interest in describing the patterns of linkage disequilibrium (LD) along a chromosome. Most empirical studies that have examined this issue have concentrated on LD between collections of pairs of markers and have not considered the joint effect of a group of markers beyond these pairwise connections. Here, we examine many different patterns of LD defined by both pairwise and joint multilocus LD terms. The LD patterns we considered were chosen in part by examining those seen in real data. We examine how changes in these patterns affect the power to detect association when performing single-marker and haplotype-based case-control tests, including a novel haplotype test based on contrasting LD between affected and unaffected individuals. Through our studies we find that differences in power between single-marker tests and haplotype-based tests in general do not appear to be large. Where moderate to high levels of multilocus LD exist, haplotype tests tend to be more powerful. Single-marker tests tend to prevail when pairwise LD is high. For moderate pairwise values and weak multilocus LD, either testing strategy may come out ahead, although it is also quite likely that neither has much power. PMID:15514073

  14. Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor.

    PubMed Central

    Hamblin, Martha T; Mitchell, Sharon E; White, Gemma M; Gallego, Javier; Kukatla, Rakesh; Wing, Rod A; Paterson, Andrew H; Kresovich, Stephen

    2004-01-01

    Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome. PMID:15166170

  15. A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep.

    PubMed

    Miller, J M; Poissant, J; Kijas, J W; Coltman, D W

    2011-03-01

    The development of genomic resources for wild species is still in its infancy. However, cross-species utilization of technologies developed for their domestic counterparts has the potential to unlock the genomes of organisms that currently lack genomic resources. Here, we apply the OvineSNP50 BeadChip, developed for domestic sheep, to two related wild ungulate species: the bighorn sheep (Ovis canadensis) and the thinhorn sheep (Ovis dalli). Over 95% of the domestic sheep markers were successfully genotyped in a sample of fifty-two bighorn sheep while over 90% were genotyped in two thinhorn sheep. Pooling the results from both species identified 868 single-nucleotide polymorphisms (SNPs), 570 were detected in bighorn sheep, while 330 SNPs were identified in thinhorn sheep. The total panel of SNPs was able to discriminate between the two species, assign population of origin for bighorn sheep and detect known relationship classes within one population of bighorn sheep. Using an informative subset of these SNPs (n=308), we examined the extent of genome-wide linkage disequilibrium (LD) within one population of bighorn sheep and found that high levels of LD persist over 4 Mb.

  16. Refined mapping of a gene responsible for Fukuyama-type congenital muscular dystrophy: Evidence for strong linkage disequilibrium

    SciTech Connect

    Toda, Tatsushi; Ikegawa, Shiro; Okui, Keiko; Nakamura, Yusuke; Kanazawa, Ichiro; Kondo, Eri; Saito, Kayoko; Fukuyama, Yukio; Yoshioka, Mieko; Kumagai, Toshiyuki

    1994-11-01

    Fukuyama-type congenital muscular dystrophy (FCMD), the second most common form of childhood muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy associated with an anomaly of the brain. After our initial mapping of the FCMD locus to chromosome 9q31-33, we further defined the locus within a region of {approximately}5 cM between loci D9S127 and CA246, by homozygosity mapping in patients born to consanguineous marriages and by recombination analyses in other families. We also found evidence for strong linkage disequilibrium between FCMD and a polymorphic microsatellite marker, mfd220, which showed no recombination and a lod score of (Z) 17.49. A {open_quotes}111-bp{close_quotes} allele for the mfd220 was observed in 22 (34%) of 64 FCMD chromosomes, but it was present in only 1 of 120 normal chromosomes. This allelic association with FCMD was highly significant ({chi}{sup 2} = 50.7; P < .0001). Hence, we suspect that the FCMD gene could lie within a few hundred kilobases of the mfd220 locus. 32 refs., 2 figs., 2 tabs.

  17. Particulate organic carbon export fluxes on Chukchi Shelf, western Arctic Ocean, derived from 210Po/210Pb disequilibrium

    NASA Astrophysics Data System (ADS)

    He, Jianhua; Yu, Wen; Lin, Wuhui; Men, Wu; Chen, Liqi

    2015-05-01

    Fluxes of particulate organic carbon (POC) were derived from 210Po/210Pb disequilibrium during the 4th Chinese National Arctic Research Expedition (CHINARE-4) from July 1 to September 28, 2010. Average residence times of particulate 210Po in the euphotic zone were -16.00 a to 1.54 a, which are higher than those of dissolved 210Po (-6.89 a to -0.70 a). Great excesses of dissolved 210Po were observed at all stations, with an average 210Po/210Pb ratio of 1.91±0.20, resulting from 210Pb atmospheric deposition after sea ice melt. POC fluxes from the euphotic zone were estimated by two methods (E and B) in the irreversible scavenging model. Estimated POC fluxes were 945-126 mmol C/(m2·a) and 1 848-109 mmol C/(m2·a) by methods E and B, respectively, both decreasing from low to high latitude. The results are comparable to previous works for the same region, indicating efficient biological pumping in the Chukchi Sea. The results can improve understanding of the carbon cycle in the western Arctic Ocean.

  18. Sexual antagonism and meiotic drive cause stable linkage disequilibrium and favour reduced recombination on the X chromosome.

    PubMed

    Rydzewski, W T; Carioscia, S A; Liévano, G; Lynch, V D; Patten, M M

    2016-06-01

    Sexual antagonism and meiotic drive are sex-specific evolutionary forces with the potential to shape genomic architecture. Previous theory has found that pairing two sexually antagonistic loci or combining sexual antagonism with meiotic drive at linked autosomal loci augments genetic variation, produces stable linkage disequilibrium (LD) and favours reduced recombination. However, the influence of these two forces has not been examined on the X chromosome, which is thought to be enriched for sexual antagonism and meiotic drive. We investigate the evolution of the X chromosome under both sexual antagonism and meiotic drive with two models: in one, both loci experience sexual antagonism; in the other, we pair a meiotic drive locus with a sexually antagonistic locus. We find that LD arises between the two loci in both models, even when the two loci freely recombine in females and that driving haplotypes will be enriched for male-beneficial alleles, further skewing sex ratios in these populations. We introduce a new measure of LD, Dz', which accounts for population allele frequencies and is appropriate for instances where these are sex specific. Both models demonstrate that natural selection favours modifiers that reduce the recombination rate. These results inform observed patterns of congealment found on driving X chromosomes and have implications for patterns of natural variation and the evolution of recombination rates on the X chromosome.

  19. Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis).

    PubMed

    Huynh, L Y; Maney, D L; Thomas, J W

    2011-04-01

    Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2(m)) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2(m) polymorphism is a complex inversion spanning > 100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2(m) polymorphism, we generated sequence from 8 ZAL2(m) and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2(m), resulting in uniformly high levels of genetic differentiation (F(ST)=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ~104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2(m) homozygotes are exceedingly rare in the population, occurring at a frequency of < 1%, we detected evidence of historical recombination between ZAL2(m) chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.

  20. Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study.

    PubMed

    van den Berg, Irene; Boichard, Didier; Guldbrandtsen, Bernt; Lund, Mogens S

    2016-01-01

    Sequence data are expected to increase the reliability of genomic prediction by containing causative mutations directly, especially in cases where low linkage disequilibrium between markers and causative mutations limits prediction reliability, such as across-breed prediction in dairy cattle. In practice, the causative mutations are unknown, and prediction with only variants in perfect linkage disequilibrium with the causative mutations is not realistic, leading to a reduced reliability compared to knowing the causative variants. Our objective was to use sequence data to investigate the potential benefits of sequence data for the prediction of genomic relationships, and consequently reliability of genomic breeding values. We used sequence data from five dairy cattle breeds, and a larger number of imputed sequences for two of the five breeds. We focused on the influence of linkage disequilibrium between markers and causative mutations, and assumed that a fraction of the causative mutations was shared across breeds and had the same effect across breeds. By comparing the loss in reliability of different scenarios, varying the distance between markers and causative mutations, using either all genome wide markers from commercial SNP chips, or only the markers closest to the causative mutations, we demonstrate the importance of using only variants very close to the causative mutations, especially for across-breed prediction. Rare variants improved prediction only if they were very close to rare causative mutations, and all causative mutations were rare. Our results show that sequence data can potentially improve genomic prediction, but careful selection of markers is essential. PMID:27317779