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Sample records for quantitative autoradiographic mapping

  1. Quantitative autoradiographic microimaging in the development and evaluation of radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Som, P. [Brookhaven National Lab., Upton, NY (United States); Oster, Z.H. [State Univ. of New York, Stony Brook, NY (United States)

    1994-04-01

    Autoradiographic (ARG) microimaging is the method for depicting biodistribution of radiocompounds with highest spatial resolution. ARG is applicable to gamma, positron and negatron emitting radiotracers. Dual or multiple-isotope studies can be performed using half-lives and energies for discrimination of isotopes. Quantitation can be performed by digital videodensitometry and by newer filmless technologies. ARG`s obtained at different time intervals provide the time dimension for determination of kinetics.

  2. Decreased benzodiazepine receptor binding in epileptic El mice: A quantitative autoradiographic study

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    Shirasaka, Y.; Ito, M.; Tsuda, H.; Shiraishi, H.; Oguro, K.; Mutoh, K.; Mikawa, H. (Kyoto Univ. (Japan))

    1990-09-01

    Benzodiazepine receptors and subtypes were examined in El mice and normal ddY mice with a quantitative autoradiographic technique. Specific (3H)flunitrazepam binding in stimulated El mice, which had experienced repeated convulsions, was significantly lower in the cortex and hippocampus than in ddY mice and unstimulated El mice. In the amygdala, specific ({sup 3}H)flunitrazepam binding in stimulated El mice was lower than in ddY mice. There was a tendency for the ({sup 3}H)flunitrazepam binding in these regions in unstimulated El mice to be intermediate between that in stimulated El mice and that in ddY mice, but there was no significant difference between unstimulated El mice and ddY mice. ({sup 3}H)Flunitrazepam binding displaced by CL218,872 was significantly lower in the cortex of stimulated El mice than in that of the other two groups, and in the hippocampus of stimulated than of unstimulated El mice. These data suggest that the decrease in ({sup 3}H)flunitrazepam binding in stimulated El mice may be due mainly to that of type 1 receptor and may be the result of repeated convulsions.

  3. Quantitative autoradiographic analysis of muscarinic receptor subtypes and their role in representational memory

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    Messer, W.S.

    1986-01-01

    Autoradiographic techniques were used to examine the distribution of muscarinic receptors in rat brain slices. Agonist and selective antagonist binding were examined by measuring the ability for unlabeled ligands to inhibit (/sup 3/H)-1-QNB labeling of muscarinic receptors. The distribution of high affinity pirenzepine binding sites (M/sub 1/ subtype) was distinct from the distribution of high affinity carbamylcholine sites, which corresponded to the M/sub 2/ subtype. In a separate assay, the binding profile for pirenzepine was shown to differ from the profile for scopolamine, a classical muscarinic antagonist. Muscarinic antagonists, when injected into the Hippocampus, impaired performance of a representational memory task. Pirenzepine, the M/sub 1/ selective antagonist, produced representational memory deficits. Scopolamine, a less selective muscarinic antagonist, caused increases in running times in some animals which prevented a definitive interpretation of the nature of the impairment. Pirenzepine displayed a higher affinity for the hippocampus and was more effective in producing a selective impairment of representational memory than scopolamine. The data indicated that cholinergic activity in the hippocampus was necessary for representation memory function.

  4. Quantitive DNA Fiber Mapping

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    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  5. Quantitative autoradiographic assessment of sup 55 Fe-RBC distribution in rat brain

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    Lin, S.Z.; Nakata, H.; Tajima, A.; Gruber, K.; Acuff, V.; Patlak, C.; Fenstermacher, J. (State Univ. of New York, Stony Brook (USA))

    1990-11-01

    A simple in vivo technique of labeling erythrocytes (RBCs) with {sup 55}Fe was developed for quantitative autoradiography (QAR). This procedure involved injecting 5-6 ml of ({sup 55}Fe)ferrous citrate solution (1 mCi/ml) intraperitoneally into donor rats. The number of labeled RBCs reached a maximum at around 7 days and declined very slowly thereafter. Labeled RBCs were harvested from donor rats and used for RBC volume measurement in awake rats. Brain radioactivity was assayed by QAR, which yielded spatial resolution of greater than 50 microns. Tight nearly irreversible binding of {sup 55}Fe to RBCs was found in vivo and in vitro. More than 99.5% of the {sup 55}Fe in the blood of donor rats was bound to RBCs. Because of this, labeled blood can be taken from donors and injected into recipients without further preparation. The tissue absorption of {sup 55}Fe emissions was the same in gray and white matter. Microvascular RBC volumes measured with {sup 55}Fe-labeled RBCs agreed with those assayed with {sup 51}Cr-labeled RBCs for many, but not all, brain areas. In conclusion, {sup 55}Fe-RBCs can be readily prepared by this technique and accurately quantitated in brain tissue by QAR.

  6. Corticosterone modulation of neurotransmitter receptors in rat hippocampus: a quantitative autoradiographic study

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    Biegon, A. (Hoffmann-La Roche, Inc., Nutley, NJ (USA). Dept. of Pharmacology); Rainbow, T.C. (Pennsylvania Univ., Philadelphia (USA). School of Medicine); McEwen, B.S. (Rockefeller Univ., New York (USA))

    1985-04-22

    The effect of adrenalectomy (ADX) and corticosterone (CORT) replacement on neurotransmitter receptors was studied in dorsal hippocampus of rat using quantitative autoradiography. ADX for one week causes an increase in (/sup 3/H)5-HT binding to 5-HT/sub 1/ receptors which is significant in the CA1 cell field. CORT treatment of ADX rats for 3-5 days results in localized reductions of (/sup 3/H)5-HT binding including a partial reversal of the increase observed after ADX in CA1. CORT treatment of ADX animals also decreases binding of (/sup 3/H)QNB to muscarinic receptors in the dorsal hippocampus, with a significant effect in an area designated as subiculum. No influence of CORT was detected on (/sup 3/H)prazosin binding to alpha/sub 1/ adrenergic receptors in dorsal hippocampus. Possible mechanisms for hormone effects on neurotransmitter receptor levels are discussed.

  7. Effects of methylmercury on muscarinic receptors in the mouse brain: A quantitative autoradiographic study

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    Lee, Haesung; Yee, S.; Geddes, J.; Choi, Byung, H. (Ewha Women' s Univ., Seoul (Korea) Univ. of California, Irvine (United States))

    1991-03-11

    Methylmercury (MeHg) is reported to inhibit several stages of cholinergic neurotransmission in brain tissue in-vitro and in-vivo. To examine whether or not behavioral disturbances and/or selective vulnerability of specific neuronal groups in MeHg poisoning may be related to MeHg effects on cholinergic receptors in specific regions of the brain, the density and distribution of muscarinic receptors in the brains of C57BL/6J mice were determined following repeated injections of 5 mg/kg of methylmercuric chloride (MMC). The receptor densities in six cortical laminae of seven cerebral cortical regions, hippocampus and striatum were quantitated by computer-assisted imaging system following in-vitro labeling with ({sup 3}H)-pirenzepine (M1) and ({sup 3}H)N-methyl scopolamine (M2). The results showed heterogeneous distribution of M1 and M2 sites in different regions of the brain, and significant reduction in the density of both receptor subtypes following MeHg poisoning in many cortical and subcortical regions. However, the changes in the density were variable in different laminae even in the same cortical regions. Prominent reductions in M1 densities were noted in the temporal and entorhinal cortices, CA3 and hilar regions of the hippocampus as compared to control, whereas the reduction in M2 receptor density was most prominently noted in the frontal, perirhinal and entorhinal cortices, and CA1 and hilar regions of the hippocampus. Thus, it is apparent that MeHg significantly affects muscarinic receptors in the mouse brain, and that these data when used in conjunction with immunocytochemical and other morphological studies would provide further insights into the mechanisms of neurotoxic effects of MeHg.

  8. Interval Mapping of Multiple Quantitative Trait Loci

    NARCIS (Netherlands)

    Jansen, Ritsert C.

    1993-01-01

    The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple Q

  9. Whole body autoradiographic and quantitative tissue distribution studies with /sup 14/C-cefotaxime in the rat

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    Stevens, L.A.; Ings, R.M.J.; Fromson, J.M.; Coombes, J.D.

    1984-01-01

    The absorption, distribution and elimination of radioactivity following intravenous (i.v.) or intramuscular (i.m.) administration of /sup 14/C-cefotaxime (/sup 14/C-HR 756) to the rat has been examined by qualitative and quantitative techniques. After i.v. and i.m. doses to male albino animals radioactivity was extensively distributed throughout the body and rapidly eliminated with a predominant half-life of approximately 30 to 40 min. Maximum plasma levels for the i.m. dose were reached within 20 min and approximately 85% of the dose was recovered from the urine (74%) and faeces (11%) within 8 h after dosing. In all quantitative studies 100+-5% of the dose was recovered within 24 h. Whole body autoradiography studies showed good distribution of radioactivity from the blood into the tissues including lung, liver, kidney, heart, bone marrow and the gastrointestinal tract. Lowest levels were seen in the eye and brain. There was limited placental transfer of radioactivity in 14-days pregnant animals although by day 18 of the gestation period radioactivity was detected in the foetus but distribution into individual organs and tissues could not be seen. There was no evidence to show that retention of radioactivity in pigmented tissues had occurred nor was there any suggestion of accumulation of radioactivity in any organ or tissues as a consequence of multiple dosing /sup 14/C-cefotaxime.

  10. Quantitative Autoradiographic Study on Receptor Regulation in the Basal Ganglia in Rat Model of Levodopa-induced Motor Complications

    Institute of Scientific and Technical Information of China (English)

    Yan XU; Zhentao ZHANG; Kairong QIN; Stella M.Papa; Xuebing CAO

    2009-01-01

    In order to study neurotransmitter receptor regulation in the basal ganglia involved in the functional changes underlying levodopa-induced motor complications,quantitative autoradiography was used to observe receptor bindings of dopamine D1 and D2,N-methyl-D-aspartate (NMDA),amino-3-hydroxy-5-methylisoxazole propionic acid (AMPA) and amino butyric acid (GABA) in the basal ganglia of rats that had unilateral nigrostriatal lesions and had been chronically treated with levodopa until motor complications developed.The rats were randomly assigned to three groups:normal,denervated and treatment-complicated groups.The results showed that response duration to levodopa became progressively shorter and abnormal involuntary movement (AIM) score was progressively increased during the course of levodopa treatment.Chronic treatment augmented DI receptors more than denervation,and reduced D2 receptors that were also increased by dopamine denervation.Striatal NMDA receptors were substantially up-regulated in the treatment-complicated group.Levodopa treatment did not change receptors of nigral AMPA,pailidai GABA,and subthalamic GABA,which remained the same as that in denervation group.However,chronic treatment reversed the increase ofnigral GABA receptors caused by the lesion.It was concluded that a shortening of response duration and AIM mimicked levodopa-induced motor complications of Parkinson's patients.These data suggested that up-regulation of dopamine D1 and NMDA receptors in the striatum leads to an imbalance of stimulation through the striatal output pathways,which is associated with levodopa-induced motor complications.

  11. Quantitative Proteome Mapping of Nitrotyrosines

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    Bigelow, Diana J.; Qian, Weijun

    2008-02-10

    An essential first step in the understanding disease and environmental perturbations is the early and quantitative detection of the increased levels of the inflammatory marker nitrotyrosine, as compared with its endogenous levels within the tissue or cellular proteome. Thus, methods that successfully address a proteome-wide quantitation of nitrotyrosine and related oxidative modifications can provide early biomarkers of risk and progression of disease as well as effective strategies for therapy. Multidimensional separations LC coupled with tandem mass spectrometry (LC-MS/MS) has, in recent years, significantly expanded our knowledge of human (and mammalian model system) proteomes including some nascent work in identification of post-translational modifications. In the following review, we discuss the application of LC-MS/MS for quantitation and identification of nitrotyrosine-modified proteins within the context of complex protein mixtures presented in mammalian proteomes.

  12. Mapping Quantitative Trait Loci in Yeast.

    Science.gov (United States)

    Liti, Gianni; Warringer, Jonas; Blomberg, Anders

    2017-08-01

    Natural Saccharomyces strains isolated from the wild differ quantitatively in molecular and organismal phenotypes. Quantitative trait loci (QTL) mapping is a powerful approach for identifying sequence variants that alter gene function. In yeast, QTL mapping has been used in designed crosses to map functional polymorphisms. This approach, outlined here, is often the first step in understanding the molecular basis of quantitative traits. New large-scale sequencing surveys have the potential to directly associate genotypes with organismal phenotypes, providing a broader catalog of causative genetic variants. Additional analysis of intermediate phenotypes (e.g., RNA, protein, or metabolite levels) can produce a multilayered and integrated view of individual variation, producing a high-resolution view of the genotype-phenotype map. © 2017 Cold Spring Harbor Laboratory Press.

  13. Quantitative Mapping of Large Area Graphene Conductance

    DEFF Research Database (Denmark)

    Buron, Jonas Christian Due; Petersen, Dirch Hjorth; Bøggild, Peter

    2012-01-01

    We present quantitative mapping of large area graphene conductance by terahertz time-domain spectroscopy and micro four point probe. We observe a clear correlation between the techniques and identify the observed systematic differences to be directly related to imperfections of the graphene sheet...

  14. Quantitative Susceptibility Mapping in Parkinson's Disease

    Science.gov (United States)

    Seiler, Stephan; Deistung, Andreas; Schweser, Ferdinand; Franthal, Sebastian; Homayoon, Nina; Katschnig-Winter, Petra; Koegl-Wallner, Mariella; Pendl, Tamara; Stoegerer, Eva Maria; Wenzel, Karoline; Fazekas, Franz; Ropele, Stefan; Reichenbach, Jürgen Rainer; Schmidt, Reinhold; Schwingenschuh, Petra

    2016-01-01

    Background Quantitative susceptibility mapping (QSM) and R2* relaxation rate mapping have demonstrated increased iron deposition in the substantia nigra of patients with idiopathic Parkinson’s disease (PD). However, the findings in other subcortical deep gray matter nuclei are converse and the sensitivity of QSM and R2* for morphological changes and their relation to clinical measures of disease severity has so far been investigated only sparsely. Methods The local ethics committee approved this study and all subjects gave written informed consent. 66 patients with idiopathic Parkinson’s disease and 58 control subjects underwent quantitative MRI at 3T. Susceptibility and R2* maps were reconstructed from a spoiled multi-echo 3D gradient echo sequence. Mean susceptibilities and R2* rates were measured in subcortical deep gray matter nuclei and compared between patients with PD and controls as well as related to clinical variables. Results Compared to control subjects, patients with PD had increased R2* values in the substantia nigra. QSM also showed higher susceptibilities in patients with PD in substantia nigra, in the nucleus ruber, thalamus, and globus pallidus. Magnetic susceptibility of several of these structures was correlated with the levodopa-equivalent daily dose (LEDD) and clinical markers of motor and non-motor disease severity (total MDS-UPDRS, MDS-UPDRS-I and II). Disease severity as assessed by the Hoehn & Yahr scale was correlated with magnetic susceptibility in the substantia nigra. Conclusion The established finding of higher R2* rates in the substantia nigra was extended by QSM showing superior sensitivity for PD-related tissue changes in nigrostriatal dopaminergic pathways. QSM additionally reflected the levodopa-dosage and disease severity. These results suggest a more widespread pathologic involvement and QSM as a novel means for its investigation, more sensitive than current MRI techniques. PMID:27598250

  15. Comparison of quantitative autoradiographic and xenon-133 clearance methods: correlation of gray and white matter cerebral blood flow with compartmental blood flow indices

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    Tuor, U.I.; Fitch, W.; Graham, D.I.; Mendelow, A.D.

    1986-08-01

    The relationships between CBF in gray and white matter to those of the fast and slow components of xenon-133 clearance curves remain uncertain. CBF was measured in 13 anaesthetized baboons under a variety of conditions, using both the xenon-133 clearance technique and (14C)iodoantipyrine quantitative autoradiography. There was a linear relationship between CBF, as determined by the stochastic (height/area) analysis of the clearance curve, and mean CBF determined from the autoradiograms (r = 0.94, p less than 0.001, slope = 0.86 +/- 0.09). There was also a linear correlation between the fast-flow component (measured with xenon-133) and blood flow in the cerebral gray matter (measured with (14C)iodoantipyrine) (r = 0.92, p less than 0.001, slope = 0.69 +/- 0.15) and between the slow-flow component (with xenon-133) and blood flow in white matter (with (14C)iodoantipyrine) (r = 0.79, p less than 0.01, slope = 0.81 +/- 0.10). In the primate brain, the fast- and slow-flow indices therefore appear to be representative of CBF in gray matter and white matter, respectively, whereas the stochastic analysis provides a stable measure of mean CBF within the tissue monitored.

  16. Effects of fixation and demineralization on the intensity of autoradiographic labelling over the periodontal ligament of the mouse incisor after administration of [3H]-proline

    NARCIS (Netherlands)

    Beertsen, W.; Tonino, G.J.M.

    1975-01-01

    The effect of different histological procedures on the autoradiographic grain count over the periodontal ligament was studied quantitatively in autoradiographs made eight hours after administration of [3H]-proline. The lower jaws of 9 mice were fixed in Bouin's fixative, in 10 per cent formalin or i

  17. Chromatic Image Analysis For Quantitative Thermal Mapping

    Science.gov (United States)

    Buck, Gregory M.

    1995-01-01

    Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.

  18. Dynamic Quantitative T1 Mapping in Orthotopic Brain Tumor Xenografts

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    Kelsey Herrmann

    2016-04-01

    Full Text Available Human brain tumors such as glioblastomas are typically detected using conventional, nonquantitative magnetic resonance imaging (MRI techniques, such as T2-weighted and contrast enhanced T1-weighted MRI. In this manuscript, we tested whether dynamic quantitative T1 mapping by MRI can localize orthotopic glioma tumors in an objective manner. Quantitative T1 mapping was performed by MRI over multiple time points using the conventional contrast agent Optimark. We compared signal differences to determine the gadolinium concentration in tissues over time. The T1 parametric maps made it easy to identify the regions of contrast enhancement and thus tumor location. Doubling the typical human dose of contrast agent resulted in a clearer demarcation of these tumors. Therefore, T1 mapping of brain tumors is gadolinium dose dependent and improves detection of tumors by MRI. The use of T1 maps provides a quantitative means to evaluate tumor detection by gadolinium-based contrast agents over time. This dynamic quantitative T1 mapping technique will also enable future quantitative evaluation of various targeted MRI contrast agents.

  19. Towards adaptable, interactive and quantitative paleogeographic maps

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    N. Wright

    2012-07-01

    Full Text Available A variety of paleogeographic atlases have been constructed, with applications from paleoclimate, ocean circulation and faunal radiation models to resource exploration; yet their uncertainties remain difficult to assess, as they are generally presented as low-resolution static maps. We present a methodology for ground-truthing paleogeographic maps, by linking the GPlates plate reconstruction tool to the global Paleobiology Database and a Phanerozoic plate motion model. We develop a spatio-temporal data mining workflow to compare a Phanerozoic Paleogeographic Atlas of Australia with biogeographic indicators. The agreement between fossil data and paleogeographic maps is quite good, but the methodology also highlights key inconsistencies. The Early Devonian paleogeography of southeastern Australia insufficiently describes the Emsian inundation that is supported by biogeography. Additionally, the Cretaceous inundation of eastern Australia retreats by 110 Ma according to the paleogeography, but the biogeography indicates that inundation prevailed until at least 100 Ma. Paleobiogeography can also be used to refine Gondwana breakup and the extent of pre-breakup Greater India can be inferred from the southward limit of inundation along western Australia. Although paleobiology data provide constraints only for paleoenvironments with high preservation potential of organisms, our approach enables the use of additional proxy data to generate improved paleogeographic reconstructions.

  20. A quantitative analysis of IRAS maps of molecular clouds

    Science.gov (United States)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  1. An autoradiographic study of neurotensin receptors in the human hypothalamus.

    Science.gov (United States)

    Najimi, Mohamed; Sarrieau, Alain; Kopp, Nicolas; Chigr, Fatiha

    2014-03-01

    The aim of the present investigation was to determine a detailed mapping of neurotensin (NT) in the human hypothalamus, the brain region involved in neuroendocrine control. For this, we investigated the presence and the distribution of neurotensin binding sites in the human hypothalamus, using an in vitro quantitative autoradiography technique and the selective radioligand monoiodo-Tyr3-neurotensin (2000Ci/mM). This study was performed on nine adult human postmortem hypothalami. We first determined the biochemical kinetics of the binding and found that binding affinity constants were of high affinity and do not differ significantly between all cases investigated. Our analysis of the autoradiographic distribution shows that NT binding sites are widely distributed throughout the rostrocaudal extent of the hypothalamus. However, the distribution of NT binding sites is not homogenous and regional variations exist. In general, the highest densities are mainly present in the anterior hypothalamic level, particularly in the preoptic region and the anterior boarding limit (i.e. the diagonal band of Broca). Important NT binding site densities are also present at the mediobasal hypothalamic level, particularly in the paraventricular, parafornical and dorsomedial nuclei. At the posterior level, relatively moderate densities could be observed in the mammillary complex subdivisions, apart from the supramammillary nucleus and the posterior hypothalamic area. In conclusion, the present study demonstrates the occurrence of high concentrations of NT binding sites in various structures in many regions in the human adult hypothalamus, involved in the control of neuroendocrine and/or neurovegetative functions. Copyright © 2013 Elsevier GmbH. All rights reserved.

  2. Autoradiographic Mapping of 5-HT(1B/1D) Binding Sites in the Rhesus Monkey Brain Using [carbonyl-C]zolmitriptan.

    Science.gov (United States)

    Lindhe, Orjan; Almqvist, Per; Kågedal, Matts; Gustafsson, Sven-Åke; Bergström, Mats; Nilsson, Dag; Antoni, Gunnar

    2011-01-01

    Zolmitriptan is a serotonin 5-HT(1B/1D) receptor agonist that is an effective and well-tolerated drug for migraine treatment. In a human positron emission tomography study, [(11)C]zolmitriptan crossed the blood-brain barrier but no clear pattern of regional uptake was discernable. The objective of this study was to map the binding of [(11)C]zolmitriptan in Rhesus monkey brain using whole hemisphere in vitro autoradiography with [(11)C]zolmitriptan as a radioligand. In saturation studies, [(11)C]zolmitriptan showed specific (90%) binding to a population of high-affinity binding sites (Kd 0.95-5.06 nM). There was regional distribution of binding sites with the highest density in the ventral pallidum, followed by the external globus pallidus, substantia nigra, visual cortex, and nucleus accumbens. In competitive binding studies with 5-HT(1) receptor antagonists, [(11)C]zolmitriptan binding was blocked by selective 5-HT(1B) and 5-HT(1D) ligands in all target areas. There was no appreciable change in binding with the addition of a 5-HT(1A) receptor antagonist.

  3. Autoradiographic Mapping of 5-H T 1B/1D Binding Sites in the Rhesus Monkey Brain Using [carbonyl-11C]zolmitriptan

    Science.gov (United States)

    Lindhe, Örjan; Almqvist, Per; Kågedal, Matts; Gustafsson, Sven-Åke; Bergström, Mats; Nilsson, Dag; Antoni, Gunnar

    2011-01-01

    Zolmitriptan is a serotonin 5-HT1B/1D receptor agonist that is an effective and well-tolerated drug for migraine treatment. In a human positron emission tomography study, [11C]zolmitriptan crossed the blood-brain barrier but no clear pattern of regional uptake was discernable. The objective of this study was to map the binding of [11C]zolmitriptan in Rhesus monkey brain using whole hemisphere in vitro autoradiography with [11C]zolmitriptan as a radioligand. In saturation studies, [11C]zolmitriptan showed specific (90%) binding to a population of high-affinity binding sites (Kd 0.95–5.06 nM). There was regional distribution of binding sites with the highest density in the ventral pallidum, followed by the external globus pallidus, substantia nigra, visual cortex, and nucleus accumbens. In competitive binding studies with 5-HT1 receptor antagonists, [11C]zolmitriptan binding was blocked by selective 5-HT1B and 5-HT1D ligands in all target areas. There was no appreciable change in binding with the addition of a 5-HT1A receptor antagonist. PMID:22013519

  4. Autoradiographic Mapping of 5-HT1B/1D Binding Sites in the Rhesus Monkey Brain Using [carbonyl-11C]zolmitriptan

    Directory of Open Access Journals (Sweden)

    Örjan Lindhe

    2011-01-01

    Full Text Available Zolmitriptan is a serotonin 5-HT1B/1D receptor agonist that is an effective and well-tolerated drug for migraine treatment. In a human positron emission tomography study, [11C]zolmitriptan crossed the blood-brain barrier but no clear pattern of regional uptake was discernable. The objective of this study was to map the binding of [11C]zolmitriptan in Rhesus monkey brain using whole hemisphere in vitro autoradiography with [11C]zolmitriptan as a radioligand. In saturation studies, [11C]zolmitriptan showed specific (90% binding to a population of high-affinity binding sites (Kd 0.95–5.06 nM. There was regional distribution of binding sites with the highest density in the ventral pallidum, followed by the external globus pallidus, substantia nigra, visual cortex, and nucleus accumbens. In competitive binding studies with 5-HT1 receptor antagonists, [11C]zolmitriptan binding was blocked by selective 5-HT1B and 5-HT1D ligands in all target areas. There was no appreciable change in binding with the addition of a 5-HT1A receptor antagonist.

  5. Autoradiographic localization of benzodiazepine receptor downregulation

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    Tietz, E.I.; Rosenberg, H.C.; Chiu, T.H.

    1986-01-01

    Regional differences in downregulation of brain benzodiazepine receptors were studied using a quantitative autoradiographic method. Rats were given a 4-week flurazepam treatment known to cause tolerance and receptor downregulation. A second group of rats was given a similar treatment, but for only 1 week. A third group was given a single acute dose of diazepam to produce a brain benzodiazepine-like activity equivalent to that found after the chronic treatment. Areas studied included hippocampal formation, cerebral cortex, superior colliculus, substantia nigra, dorsal geniculate nucleus, lateral amygdala and lateral hypothalamus. There was a regional variation in the degree of downregulation after 1 week of flurazepam treatment, ranging from 12% to 25%. Extending the flurazepam treatment to 4 weeks caused little further downregulation in those areas studied, except for the pars reticulata of the substantia nigra, which showed a 13% reduction in (/sup 3/H)flunitrazepam binding after 1 week and a 40% reduction after 4 weeks of treatment. In a few areas, such as the lateral hypothalamus, no significant change in binding was found after 4 weeks. Acute diazepam treatment caused no change in binding. This latter finding as well as results obtained during the development of the methodology show that downregulation was not an artifact due to residual drug content of brain slices. The regional variations in degree and rate of downregulation suggest areas that may be most important for benzodiazepine tolerance and dependence and may be related to the varying time courses for tolerance to different benzodiazepine actions.

  6. Quantitative genetic-interaction mapping in mammalian cells

    Science.gov (United States)

    Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

    2013-01-01

    Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

  7. Functional mapping imprinted quantitative trait loci underlying developmental characteristics

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    Li Gengxin

    2008-03-01

    Full Text Available Abstract Background Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL mapping focusing on single trait analysis. Recent studies have shown that most imprinted genes in mammals play an important role in controlling embryonic growth and post-natal development. For a developmental character such as growth, current approach is less efficient in dissecting the dynamic genetic effect of imprinted genes during individual ontology. Results Functional mapping has been emerging as a powerful framework for mapping quantitative trait loci underlying complex traits showing developmental characteristics. To understand the genetic architecture of dynamic imprinted traits, we propose a mapping strategy by integrating the functional mapping approach with genomic imprinting. We demonstrate the approach through mapping imprinted QTL controlling growth trajectories in an inbred F2 population. The statistical behavior of the approach is shown through simulation studies, in which the parameters can be estimated with reasonable precision under different simulation scenarios. The utility of the approach is illustrated through real data analysis in an F2 family derived from LG/J and SM/J mouse stains. Three maternally imprinted QTLs are identified as regulating the growth trajectory of mouse body weight. Conclusion The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits.

  8. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...

  9. Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae.

    Science.gov (United States)

    Swinnen, Steve; Thevelein, Johan M; Nevoigt, Elke

    2012-03-01

    Saccharomyces cerevisiae has become a favorite production organism in industrial biotechnology presenting new challenges to yeast engineers in terms of introducing advantageous traits such as stress tolerances. Exploring subspecies diversity of S. cerevisiae has identified strains that bear industrially relevant phenotypic traits. Provided that the genetic basis of such phenotypic traits can be identified inverse engineering allows the targeted modification of production strains. Most phenotypic traits of interest in S. cerevisiae strains are quantitative, meaning that they are controlled by multiple genetic loci referred to as quantitative trait loci (QTL). A straightforward approach to identify the genetic basis of quantitative traits is QTL mapping which aims at the allocation of the genetic determinants to regions in the genome. The application of high-density oligonucleotide arrays and whole-genome re-sequencing to detect genetic variations between strains has facilitated the detection of large numbers of molecular markers thus allowing high-resolution QTL mapping over the entire genome. This review focuses on the basic principle and state of the art of QTL mapping in S. cerevisiae. Furthermore we discuss several approaches developed during the last decade that allow down-scaling of the regions identified by QTL mapping to the gene level. We also emphasize the particular challenges of QTL mapping in nonlaboratory strains of S. cerevisiae.

  10. Quantitative susceptibility mapping: current status and future directions.

    Science.gov (United States)

    Haacke, E Mark; Liu, Saifeng; Buch, Sagar; Zheng, Weili; Wu, Dongmei; Ye, Yongquan

    2015-01-01

    Quantitative susceptibility mapping (QSM) is a new technique for quantifying magnetic susceptibility. It has already found various applications in quantifying in vivo iron content, calcifications and changes in venous oxygen saturation. The accuracy of susceptibility mapping is dependent on several factors. In this review, we evaluate the entire process of QSM from data acquisition to individual data processing steps. We also show preliminary results of several new concepts introduced in this review in an attempt to improve the quality and accuracy for certain steps. The uncertainties in estimating susceptibility differences using susceptibility maps, phase images, and T2* maps are analyzed and compared. Finally, example clinical applications are presented. We conclude that QSM holds great promise in quantifying iron and becoming a standard clinical tool.

  11. Experiment K-7-18: Effects of Spaceflight in the Muscle Adductor Longus of Rats Flown in the Soviet Biosatellite Cosmos 2044. Part 2; Quantitative Autoradiographic Analysis of Gaba (Benzodiazepine) and Muscarinic (Cholinergic) Receptors in the Forebrain of Rats Flown on Cosmos 2044

    Science.gov (United States)

    Wu, L.; Daunton, N. G.; Krasnov, I. B.; DAmelio, F.; Hyde, T. M.; Sigworth, S. K.

    1994-01-01

    Quantitative autoradiographic analysis of receptors for GABA and acetylcholine in the forebrain of rats flown on COSMOS 2044 was undertaken as part of a joint US-Soviet study to determine the effects of microgravity on the central nervous system, and in particular on the sensory and motor portions of the forebrain. Changes in binding of these receptors in tissue from animals exposed to microgravity would provide evidence for possible changes in neural processing as a result of exposure to microgravity. Tritium-labelled diazepam and Quinuclidinyl-benzilate (QNB) were used to visualize GABA (benzodiazepine) and muscarinic (cholinergic) receptors, respectively. The density of tritium-labelled radioligands bound to various regions in the forebrain of both flight and control animals were measured from autoradiograms. Data from rats flown in space and from ground-based control animals that were not exposed to microgravity were compared.

  12. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei; Meng; Huihui; Li; Luyan; Zhang; Jiankang; Wang

    2015-01-01

    QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

  13. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei Meng; Huihui Li; Luyan Zhang; Jiankang Wang

    2015-01-01

    QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight func-tionalities are integrated in this software package: (1) BIN:binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci;(5) BIP:mapping of additive, dominant, and digenic epistasis genes;(6) MET:QTL-by-environment interaction analysis;(7) CSL:mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  14. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Directory of Open Access Journals (Sweden)

    Lei Meng

    2015-06-01

    Full Text Available QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL in biparental populations. Eight functionalities are integrated in this software package: (1 BIN: binning of redundant markers; (2 MAP: construction of linkage maps in biparental populations; (3 CMP: consensus map construction from multiple linkage maps sharing common markers; (4 SDL: mapping of segregation distortion loci; (5 BIP: mapping of additive, dominant, and digenic epistasis genes; (6 MET: QTL-by-environment interaction analysis; (7 CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8 NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  15. nowCOAST's Map Service for NOAA Quantitative Precipitation Estimates (Time Enabled)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Map Information: This nowCOAST time-enabled map service provides maps depicting the NWS Multi-Radar Multi-Sensor (MRMS) quantitative precipitation estimate mosaics...

  16. A quantitative transcriptome reference map of the normal human brain.

    Science.gov (United States)

    Caracausi, Maria; Vitale, Lorenza; Pelleri, Maria Chiara; Piovesan, Allison; Bruno, Samantha; Strippoli, Pierluigi

    2014-10-01

    We performed an innovative systematic meta-analysis of 60 gene expression profiles of whole normal human brain, to provide a quantitative transcriptome reference map of it, i.e. a reference typical value of expression for each of the 39,250 known, mapped and 26,026 uncharacterized (unmapped) transcripts. To this aim, we used the software named Transcriptome Mapper (TRAM), which is able to generate transcriptome maps based on gene expression data from multiple sources. We also analyzed differential expression by comparing the brain transcriptome with those derived from human foetal brain gene expression, from a pool of human tissues (except the brain) and from the two normal human brain regions cerebellum and cerebral cortex, which are two of the main regions severely affected when cognitive impairment occurs, as happens in the case of trisomy 21. Data were downloaded from microarray databases, processed and analyzed using TRAM software and validated in vitro by assaying gene expression through several magnitude orders by 'real-time' reverse transcription polymerase chain reaction (RT-PCR). The excellent agreement between in silico and experimental data suggested that our transcriptome maps may be a useful quantitative reference benchmark for gene expression studies related to the human brain. Furthermore, our analysis yielded biological insights about those genes which have an intrinsic over-/under-expression in the brain, in addition offering a basis for the regional analysis of gene expression. This could be useful for the study of chromosomal alterations associated to cognitive impairment, such as trisomy 21, the most common genetic cause of intellectual disability.

  17. Linkage disequilibrium interval mapping of quantitative trait loci

    Directory of Open Access Journals (Sweden)

    de Rochambeau Hubert

    2006-03-01

    Full Text Available Abstract 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.

  18. Mapping Quantitative Trait Loci Controlling Endosperm Traits with Molecular Marker

    Institute of Scientific and Technical Information of China (English)

    XU Chen-wu; LI Tao; SUN Chang-sen; GU Shi-liang

    2002-01-01

    Based on the genetic models for triploid endosperm traits and on the methods for mapping diploid quantitative traits loci (QTLs), the genetic constitutions, components of means and genetic variances of QTL controlling endosperm traits under flanking marker genotypes of different generations were presented. From these results, a multiple linear regression method for mapping QTL underlying endosperm traits in cereals was proposed, which used the means of endosperm traits under flanking marker genotypes as a dependent variable, the coefficient of additive effect ( d ) and dominance effect ( h 1 and/or h2 ) of a putative QTL in a given interval as independent variables. This method can work at any position in a genome covered by markers and increase the estimation precision of QTL location and their effects by eliminating the interference of other relative QTLs. This method can also be easily used in other uneven data such as markers and quantitative traits detected or measured in plants and tissues different either in generations or at chromosomal ploidy levels, and in endosperm traits controlled by complicated genetic models considering the effects produced by genotypes of both maternal plants and seeds on them.

  19. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

    Directory of Open Access Journals (Sweden)

    Xu Shizhong

    2011-05-01

    Full Text Available Abstract Background The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. Results We developed a fast empirical Bayesian LASSO (EBLASSO method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. Conclusions The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  20. QUANTITATIVE RISK MAPPING OF URBAN GAS PIPELINE NETWORKS USING GIS

    Directory of Open Access Journals (Sweden)

    P. Azari

    2017-09-01

    Full Text Available Natural gas is considered an important source of energy in the world. By increasing growth of urbanization, urban gas pipelines which transmit natural gas from transmission pipelines to consumers, will become a dense network. The increase in the density of urban pipelines will influence probability of occurring bad accidents in urban areas. These accidents have a catastrophic effect on people and their property. Within the next few years, risk mapping will become an important component in urban planning and management of large cities in order to decrease the probability of accident and to control them. Therefore, it is important to assess risk values and determine their location on urban map using an appropriate method. In the history of risk analysis of urban natural gas pipeline networks, the pipelines has always been considered one by one and their density in urban area has not been considered. The aim of this study is to determine the effect of several pipelines on the risk value of a specific grid point. This paper outlines a quantitative risk assessment method for analysing the risk of urban natural gas pipeline networks. It consists of two main parts: failure rate calculation where the EGIG historical data are used and fatal length calculation that involves calculation of gas release and fatality rate of consequences. We consider jet fire, fireball and explosion for investigating the consequences of gas pipeline failure. The outcome of this method is an individual risk and is shown as a risk map.

  1. Autoradiographic localization of estrogen binding sites in human mammary lesions

    Energy Technology Data Exchange (ETDEWEB)

    Buell, R.H.

    1984-01-01

    The biochemical assay of human mammary carcinomas for estrogen receptors is of proven clinical utility, but the cellular localization of estrogen binding sites within these lesions is less certain. The author describes the identification of estrogen binding sites as visualized by thaw-mount autoradiography after in vitro incubation in a series of 17 benign and 40 malignant human female mammary lesions. The results on the in vitro incubation method compared favorably with data from in vivo studies in mouse uterus, a well-characterized estrogen target organ. In noncancerous breast biopsies, a variable proportion of epithelial cells contained specific estrogen binding sites. Histologically identifiable myoepithelial and stromal cells were, in general, unlabeled. In human mammary carcinomas, biochemically estrogen receptor-positive, labeled and unlabeled neoplastic epithelial cells were identified by autoradiography. Quantitative results from the autoradiographic method compared favorably with biochemical data.

  2. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

    Directory of Open Access Journals (Sweden)

    Esteras Cristina

    2012-02-01

    Full Text Available Abstract Background Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP, was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL. Results We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo × Scallop (subsp. ovifera. The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research

  3. In vivo quantitative susceptibility mapping (QSM in Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Julio Acosta-Cabronero

    Full Text Available BACKGROUND: This study explores the magnetostatic properties of the Alzheimer's disease brain using a recently proposed, magnetic resonance imaging, postprocessed contrast mechanism. Quantitative susceptibility mapping (QSM has the potential to monitor in vivo iron levels by reconstructing magnetic susceptibility sources from field perturbations. However, with phase data acquired at a single head orientation, the technique relies on several theoretical approximations and requires fast-evolving regularisation strategies. METHODS: In this context, the present study describes a complete methodological framework for magnetic susceptibility measurements with a review of its theoretical foundations. FINDINGS AND SIGNIFICANCE: The regional and whole-brain cross-sectional comparisons between Alzheimer's disease subjects and matched controls indicate that there may be significant magnetic susceptibility differences for deep brain nuclei--particularly the putamen--as well as for posterior grey and white matter regions. The methodology and findings described suggest that the QSM method is ready for larger-scale clinical studies.

  4. Ex vivo quantitative multiparametric MRI mapping of human meniscus degeneration

    Energy Technology Data Exchange (ETDEWEB)

    Nebelung, Sven; Kuhl, Christiane; Truhn, Daniel [Aachen University Hospital, Department of Diagnostic and Interventional Radiology, Aachen (Germany); Tingart, Markus; Jahr, Holger [Aachen University Hospital, Department of Orthopaedics, Aachen (Germany); Pufe, Thomas [RWTH Aachen University, Institute of Anatomy and Cell Biology, Aachen (Germany)

    2016-12-15

    To evaluate the diagnostic performance of T1, T1ρ, T2, T2*, and UTE-T2* (ultrashort-echo time-enhanced T2*) mapping in the refined graduation of human meniscus degeneration with histology serving as standard-of-reference. This IRB-approved intra-individual comparative ex vivo study was performed on 24 lateral meniscus body samples obtained from 24 patients undergoing total knee replacement. Samples were assessed on a 3.0-T MRI scanner using inversion-recovery (T1), spin-lock multi-gradient-echo (T1ρ), multi-spin-echo (T2) and multi-gradient-echo (T2* and UTE-T2*) sequences to determine relaxation times of quantitative MRI (qMRI) parameters. Relaxation times were calculated on the respective maps, averaged to the entire meniscus and to its zones. Histologically, samples were analyzed on a four-point score according to Williams (0-III). QMRI results and Williams (sub)scores were correlated using Spearman's ρ, while Williams grade-dependent differences were assessed using Kruskal-Wallis and Dunn's tests. Sensitivities and specificities in the detection of intact (Williams grade [WG]-0) and severely degenerate meniscus (WG-II-III) were calculated. Except for T2*, significant increases in qMRI parameters with increasing Williams grades were observed. T1, T1ρ, T2, and UTE-T2* exhibited high sensitivity and variable specificity rates. Significant marked-to-strong correlations were observed for these parameters with each other, with histological WGs and the subscores tissue integrity and cellularity. QMRI mapping holds promise in the objective evaluation of human meniscus. Although sufficient discriminatory power of T1, T1ρ, T2, and UTE-T2* was only demonstrated for the histological extremes, these data may aid in the future MRI-based parameterization and quantification of human meniscus degeneration. (orig.)

  5. Current Approaches Toward Quantitative Mapping of the Interactome.

    Science.gov (United States)

    Buntru, Alexander; Trepte, Philipp; Klockmeier, Konrad; Schnoegl, Sigrid; Wanker, Erich E

    2016-01-01

    Protein-protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.

  6. Quantitative Map of Proteome Dynamics during Neuronal Differentiation

    Directory of Open Access Journals (Sweden)

    Christian K. Frese

    2017-02-01

    Full Text Available Neuronal differentiation is a multistep process that shapes and re-shapes neurons by progressing through several typical stages, including axon outgrowth, dendritogenesis, and synapse formation. To systematically profile proteome dynamics throughout neuronal differentiation, we took cultured rat hippocampal neurons at different developmental stages and monitored changes in protein abundance using a combination of stable isotope labeling and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS. Almost one third of all 4,500 proteins quantified underwent a more than 2-fold expression change during neuronal differentiation, indicating extensive remodeling of the neuron proteome. To highlight the strength of our resource, we studied the neural-cell-adhesion molecule 1 (NCAM1 and found that it stimulates dendritic arbor development by promoting actin filament growth at the dendritic growth cone. We anticipate that our quantitative map of neuronal proteome dynamics is a rich resource for further analyses of the many identified proteins in various neurodevelopmental processes.

  7. Quantitative Susceptibility Mapping and Dynamic Contrast Enhanced Quantitative Perfusion in Cerebral Cavernous Angiomas

    Science.gov (United States)

    Mikati, Abdul Ghani; Tan, Huan; Shenkar, Robert; Li, Luying; Zhang, Lingjiao; Guo, Xiaodong; Shi, Changbin; Liu, Tian; Wang, Yi; Shah, Akash; Edelman, Robert; Christoforidis, Gregory; Awad, Issam

    2015-01-01

    Background Hyperpermeability and iron deposition are two central pathophysiological phenomena in human cerebral cavernous malformation (CCM) disease. Here we used two novel magnetic resonance imaging (MRI) techniques to establish a relationship between these phenomena. Methods Subjects with CCM disease (4 sporadic and 18 familial) underwent MRI imaging using the Dynamic Contrast Enhanced Quantitative Perfusion (DCEQP) and Quantitative Susceptibility Mapping (QSM) techniques that measure hemodynamic factors of vessel leak and iron deposition respectively, previously demonstrated in CCM disease. Regions of interest encompassing the CCM lesions were analyzed using these techniques Results Susceptibility measured by QSM was positively correlated with permeability of lesions measured using DCEQP (r=0.49, p=<0.0001). The correlation was not affected by factors including familial predisposition, lesion volume, the contrast agent and the use of statin medication. Susceptibility was correlated with lesional blood volume (r=0.4, p=0.0001), but not with lesional blood flow. Conclusion The correlation between QSM and DCEQP suggests that the phenomena of permeability and iron deposition are related in CCM; hence “more leaky lesions” also manifest a more cumulative iron burden. These techniques might be used as biomarkers to monitor the course of this disease and the effect of therapy. PMID:24302484

  8. Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

    NARCIS (Netherlands)

    Jansen, R.C.; Ooijen, J.W. van; Stam, P.; Lister, C.; Dean, C.

    1995-01-01

    The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment

  9. Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci

    NARCIS (Netherlands)

    Meuwissen, T.H.E.; Goddard, M.E.

    2000-01-01

    A multimarker linkage disequilibrium mapping method was developed for the fine mapping of quantitative trait loci (QTL) using a dense marker map. The method compares the expected covariances between haplotype effects given a postulated QTL position to the covariances that are found in the data. The

  10. Quantitative Architectural Analysis: A New Approach to Cortical Mapping

    Science.gov (United States)

    Schleicher, Axel; Morosan, Patricia; Amunts, Katrin; Zilles, Karl

    2009-01-01

    Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological…

  11. Quantitative Architectural Analysis: A New Approach to Cortical Mapping

    Science.gov (United States)

    Schleicher, Axel; Morosan, Patricia; Amunts, Katrin; Zilles, Karl

    2009-01-01

    Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological…

  12. nowCOAST's Map Service for NOAA NWS NDFD Gridded Forecasts of 6-Hr Quantitative Precipitation Amount (inches) (Time Offsets)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Map Information: This nowCOAST time-offsets map service provides maps depicting the NWS 6-hr quantitative precipitation [amount] forecasts (QPF) from the National...

  13. Development of the glucocorticoid receptor system in the rat limbic brain. 2. An autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Meaney, M.J.; Sapolsky, R.M.; McEwen, B.S. (Rockefeller Univ., New York (USA))

    1985-02-01

    The authors report the results of an autoradiographic analysis of the postnatal development of the hippocampal glucocorticoid receptor system in the rat brain. Quantitative analysis of the autoradiograms revealed a varied pattern of gradual development towards adult receptor concentrations during the second week of life. Receptor concentrations in the dentate gyrus increased dramatically between Days 9 and 15, while the changes during this period in the pyramidal layers of Ammon's horn seemed to reflect both structural changes in these regions as well as increases in receptor concentrations.

  14. Genetic mapping of quantitative trait loci in plants - a novel statistical approach.

    NARCIS (Netherlands)

    Jansen, R.C.

    1995-01-01

    Quantitative variation is a feature of many important traits such as yield, quality and disease resistance in crop plants and farm animals, and diseases in humans. The genetic mapping, understanding and manipulation of quantitative trait loci (QTLs) are therefore of prime importance. Only by using g

  15. High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

    Science.gov (United States)

    Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

    2017-07-14

    Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

  16. Combined expression trait correlations and expression quantitative trait locus mapping.

    Directory of Open Access Journals (Sweden)

    Hong Lan

    2006-01-01

    Full Text Available Coordinated regulation of gene expression levels across a series of experimental conditions provides valuable information about the functions of correlated transcripts. The consideration of gene expression correlation over a time or tissue dimension has proved valuable in predicting gene function. Here, we consider correlations over a genetic dimension. In addition to identifying coregulated genes, the genetic dimension also supplies us with information about the genomic locations of putative regulatory loci. We calculated correlations among approximately 45,000 expression traits derived from 60 individuals in an F2 sample segregating for obesity and diabetes. By combining the correlation results with linkage mapping information, we were able to identify regulatory networks, make functional predictions for uncharacterized genes, and characterize novel members of known pathways. We found evidence of coordinate regulation of 174 G protein-coupled receptor protein signaling pathway expression traits. Of the 174 traits, 50 had their major LOD peak within 10 cM of a locus on Chromosome 2, and 81 others had a secondary peak in this region. We also characterized a Riken cDNA clone that showed strong correlation with stearoyl-CoA desaturase 1 expression. Experimental validation confirmed that this clone is involved in the regulation of lipid metabolism. We conclude that trait correlation combined with linkage mapping can reveal regulatory networks that would otherwise be missed if we studied only mRNA traits with statistically significant linkages in this small cross. The combined analysis is more sensitive compared with linkage mapping alone.

  17. Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11

    DEFF Research Database (Denmark)

    Schulman, N F; Sahana, G; Iso-Touru, T;

    2009-01-01

    Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red......, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis...

  18. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    Science.gov (United States)

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  19. Quantitative Mapping of Mechanisms for Photoinitiated Coating Degradation

    DEFF Research Database (Denmark)

    Kiil, Søren

    2015-01-01

    This work concerns the mathematical modeling of photoinitiated coating degradation. Using experimental evidence available, some of the most importantassumptions underlying existing models for the rmoset coatings are analyzed and suggestions for further work provided. A modeling approach that can...... be used toimplement the various effects of water on the degradation mechanisms of cross-linked coatings is also presented and experiments to test the approach are suggested. Additionally, simulations with an existing degradation model for an epoxy–amine coating are used to map the influence of model...... parameters on the lag time (i.e., the time passing prior to the onset of erosion) and the stable erosion rate. The simulation results can be used in the optimization of UV radiation-induced intercoat adhesion losses, which are often observed in multilayer coating systems based on top coated epoxy coatings...

  20. Quantitative mapping of intracellular cations in the human amniotic membrane

    Science.gov (United States)

    Moretto, Ph.; Llabador, Y.; Simonoff, M.; Razafindrabe, L.; Bara, M.; Guiet-Bara, A.

    1993-05-01

    The effect of magnesium and taurine on the permeability of cell membranes to monovalent cations has been investigated using the Bordeaux nuclear microprobe. PIXE and RBS techniques have been used to provide quantitative measurements and ion distributions in the isolated amniotic membrane. This physiological model for cellular exchanges allowed us to reveal the distribution of most elements involved in cellular pathways and the modifications under different experimental conditions of incubation in physiological fluids. The PIXE microanalysis provided an original viewpoint on these mechanisms. Following this first study, the amnion compact lamina was found to play a role which was not, up to now, taken into account in the interpretation of electrophysiological experimentations. The release of some ionic species, such as K +, from the epithelial cells, during immersion in isotonic fluids, could have been hitherto underestimated.

  1. Quantitative Mapping of Precursory Seismic Quiescence Before Large Aftershocks

    Science.gov (United States)

    Neukomm, S.; Wiemer, S.; Giardini, D.

    2002-12-01

    A relative decrease of aftershock activity before the occurrence of large aftershocks to M6+ mainshocks is one of only few earthquake precursors accepted for the IASPEI preliminary list of significant earthquake precursors. If one considers earthquake rate to be dependent on stressing rate, aftershocks sequences offer in fact an ideal environment to detect precursory quiescence before large earthquakes: The numerous aftershocks allow a much higher spatial and temporal resolution of transients in seismicity than possible with the average background rate of micro-earthquakes. Past studies of precursory quiescence before larger aftershocks, however, have largely been based on bulk value. The aim of this study is to map the temporal and spatial variability of activity rate within several rich aftershock sequences, and, possibly, exploit the results for improving real time probabilistic aftershock hazard assessment. We introduce a new algorithm based on fitting the modified Omori law to the aftershock sequences. At arbitrarily chosen grid points, the Omori parameters of the sub-samples containing all aftershock within 5 or 10 km of the node are estimated at time t. We calculate the number of aftershocks N +/- dN in the time interval t + dt using the relevant four Omori parameters (p, c and k) parameters and their corresponding standard deviations estimated using a bootstrap analysis. The difference between the forecasted and the observed number of aftershocks, normalized by the standard deviation of the forecast, is our estimator of rate change. The algorithm is tested on synthetic aftershock sequences containing artificial quiescences in order to calibrate the free parameters for optimal detection of precursory quiescence. We then perform our spatial and temporal mapping for several prominent Californian and Japanese aftershock sequences (Landers, Hector Mine, Northridge, Loma Prieta, Kobe, Western Tottori and Hokkaido). Preliminary results suggest that we cannot

  2. Mapping Quantitative Trait Loci for Palatability of Milled Rice

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Quantitative trait loci (QTLs) controlling palatability in rice were identified using a set of 98 backcross inbred lines (BILs) population derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath. The palatability scores of the population measured by RQ1/Plus Rice Analyzer, showed a continuous and transgressive segregative distribution with a range from 66 to 92. Four putative QTLs for palatability, qPAL-5, qPAL-7, qPAL-8a and qPAL-8b, were detected on chromosome 5, 7 and 8, and they accounted 7.83, 7.03, 11.58 and 7.19% of the total phenotypic variation, respectively. Three alleles qPAL-5, qPAL-7 and qPAL-8b from Kasalath increased the palatability score, whereas only one Nipponbare allele qPAL-8a increased the score. Eight transgressive lines in palatability were selected to make a comparison between phenotypic and genotypic classes. The result explained the possibility of positive QTLs pyramiding through marker-assisted selection of highly palatable rice.

  3. Current approaches towards quantitative mapping of the interactome

    Directory of Open Access Journals (Sweden)

    Alexander eBuntru

    2016-05-01

    Full Text Available Protein-protein interactions (PPIs play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid (Y2H system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as DULIP, FRET or LUMIER with BACON. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.

  4. Mapping Quantitative Trait Loci Underlying Function-Valued Traits Using Functional Principal Component Analysis and Multi-Trait Mapping

    Directory of Open Access Journals (Sweden)

    Il-Youp Kwak

    2016-01-01

    Full Text Available We previously proposed a simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. In order to better handle the case of noisy phenotype measurements and accommodate the correlation structure among time points, we propose an alternative approach that maintains much of the simplicity and speed of the regression-based method. We overcome noisy measurements by replacing the observed data with a smooth approximation. We then apply functional principal component analysis, replacing the smoothed phenotype data with a small number of principal components. Quantitative trait locus mapping is applied to these dimension-reduced data, either with a multi-trait method or by considering the traits individually and then taking the average or maximum LOD score across traits. We apply these approaches to root gravitropism data on Arabidopsis recombinant inbred lines and further investigate their performance in computer simulations. Our methods have been implemented in the R package, funqtl.

  5. Mapping of imprinted quantitative trait loci using immortalized F2 populations.

    Directory of Open Access Journals (Sweden)

    Yongxian Wen

    Full Text Available Mapping of imprinted quantitative trait loci (iQTLs is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM and composite interval mapping (CIM based on conventional low-density genetic maps and point mapping (PM and composite point mapping (CPM based on ultrahigh-density genetic maps, using an immortalized F2 (imF2 population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

  6. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.

    Science.gov (United States)

    Georgi, Laura; Johnson-Cicalese, Jennifer; Honig, Josh; Das, Sushma Parankush; Rajah, Veeran D; Bhattacharya, Debashish; Bassil, Nahla; Rowland, Lisa J; Polashock, James; Vorsa, Nicholi

    2013-03-01

    The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

  7. New Imaging Frontiers in Cardiology: Fast and Quantitative Maps from Raw Data.

    Science.gov (United States)

    Santarelli, Maria Filomena; Vanello, Nicola; Scipioni, Michele; Valvano, Giuseppe; Landini, Luigi

    2017-03-28

    Among the novelties in the field of cardiovascular imaging, the construction of quantitative maps in a fast and efficient way is one of the most interesting aspects of the clinical research. Quantitative parametric maps are typically obtained by post processing dynamic images, that is, sets of images usually acquired in different temporal intervals, where several images with different contrasts are obtained. Magnetic resonance (MR) imaging, and emission tomography (positron emission and single photon emission) are the imaging techniques best suited for the formation of quantitative maps. In this review article we present several methods that can be used for obtaining parametric maps, in a fast way, starting from the acquired raw data. We describe both methods commonly used in clinical research, and more innovative methods that build maps directly from the raw data, without going through the image reconstruction. We briefly described recently developed methods in magnetic resonance (MR) imaging that accelerate further the MR raw data generation, based on appropriate sub-sampling of k-space; then, we described recently developed methods for generating MR parametric maps. With regard to the emission tomography techniques, we gave an overview of both conventional methods, and more recently developed direct estimation algorithms for parametric image reconstruction from dynamic positron emission tomography data. We have provided an overview of the possible approaches that can be followed to realize useful parametric maps from imaging raw data. We moved from the conventional approaches to more recent and efficient methods for accelerating the raw data generation and the of parametric maps formation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. Evaluation and Quantitative trait loci mapping of resistance to powdery mildew in lettuce

    Science.gov (United States)

    Lettuce (Lactuca sativa L.) is the major leafy vegetable that is susceptible to powdery mildew disease under greenhouse and field conditions. We mapped quantitative trait loci (QTLs) for resistance to powdery mildew under greenhouse conditions in an interspecific population derived from a cross betw...

  9. Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

    NARCIS (Netherlands)

    Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

    1999-01-01

    A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

  10. A General Monte Carlo Method for Mapping Multiple Quantitative Trait Loci

    NARCIS (Netherlands)

    Jansen, Ritsert C.

    1996-01-01

    In this paper we address the mapping of multiple quantitative trait loci (QTLs) in line crosses for which the genetic data are highly incomplete. Such complicated situations occur, for instance, when dominant markers are used or when unequally informative markers are used in experiments with outbred

  11. Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

    Science.gov (United States)

    Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

    2016-08-01

    Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

  12. Spatial access priority mapping (SAPM) with fishers: a quantitative GIS method for participatory planning.

    Science.gov (United States)

    Yates, Katherine L; Schoeman, David S

    2013-01-01

    Spatial management tools, such as marine spatial planning and marine protected areas, are playing an increasingly important role in attempts to improve marine management and accommodate conflicting needs. Robust data are needed to inform decisions among different planning options, and early inclusion of stakeholder involvement is widely regarded as vital for success. One of the biggest stakeholder groups, and the most likely to be adversely impacted by spatial restrictions, is the fishing community. In order to take their priorities into account, planners need to understand spatial variation in their perceived value of the sea. Here a readily accessible, novel method for quantitatively mapping fishers' spatial access priorities is presented. Spatial access priority mapping, or SAPM, uses only basic functions of standard spreadsheet and GIS software. Unlike the use of remote-sensing data, SAPM actively engages fishers in participatory mapping, documenting rather than inferring their priorities. By so doing, SAPM also facilitates the gathering of other useful data, such as local ecological knowledge. The method was tested and validated in Northern Ireland, where over 100 fishers participated in a semi-structured questionnaire and mapping exercise. The response rate was excellent, 97%, demonstrating fishers' willingness to be involved. The resultant maps are easily accessible and instantly informative, providing a very clear visual indication of which areas are most important for the fishers. The maps also provide quantitative data, which can be used to analyse the relative impact of different management options on the fishing industry and can be incorporated into planning software, such as MARXAN, to ensure that conservation goals can be met at minimum negative impact to the industry. This research shows how spatial access priority mapping can facilitate the early engagement of fishers and the ready incorporation of their priorities into the decision-making process

  13. Spatial access priority mapping (SAPM with fishers: a quantitative GIS method for participatory planning.

    Directory of Open Access Journals (Sweden)

    Katherine L Yates

    Full Text Available Spatial management tools, such as marine spatial planning and marine protected areas, are playing an increasingly important role in attempts to improve marine management and accommodate conflicting needs. Robust data are needed to inform decisions among different planning options, and early inclusion of stakeholder involvement is widely regarded as vital for success. One of the biggest stakeholder groups, and the most likely to be adversely impacted by spatial restrictions, is the fishing community. In order to take their priorities into account, planners need to understand spatial variation in their perceived value of the sea. Here a readily accessible, novel method for quantitatively mapping fishers' spatial access priorities is presented. Spatial access priority mapping, or SAPM, uses only basic functions of standard spreadsheet and GIS software. Unlike the use of remote-sensing data, SAPM actively engages fishers in participatory mapping, documenting rather than inferring their priorities. By so doing, SAPM also facilitates the gathering of other useful data, such as local ecological knowledge. The method was tested and validated in Northern Ireland, where over 100 fishers participated in a semi-structured questionnaire and mapping exercise. The response rate was excellent, 97%, demonstrating fishers' willingness to be involved. The resultant maps are easily accessible and instantly informative, providing a very clear visual indication of which areas are most important for the fishers. The maps also provide quantitative data, which can be used to analyse the relative impact of different management options on the fishing industry and can be incorporated into planning software, such as MARXAN, to ensure that conservation goals can be met at minimum negative impact to the industry. This research shows how spatial access priority mapping can facilitate the early engagement of fishers and the ready incorporation of their priorities into the

  14. Quantitative Trait Loci Mapping of Leaf Morphological Traits and Chlorophyll Content in Cultivated Tetraploid Cotton

    Institute of Scientific and Technical Information of China (English)

    Xian-Liang SONG; Wang-Zhen GUO; Zhi-Guo HAN; Tian-Zhen ZHANG

    2005-01-01

    Genetic mapping provides a powerful tool for quantitative trait loci (QTL) analysis at the molecular level. A simple sequence repeat (SSR) genetic map containing 590 markers and a BC1 population from two cultivated tetraploid cotton (Gossypium hirsutum L.) cultivars, namely TM-1 and Hai 7124 (G.barbadense L.), were used to map and analyze QTL using the composite interval mapping (CIM) method.Thirty one QTLs, 10 for lobe length, 13 for lobe width, six for lobe angle, and two for leaf chlorophyll content,were detected on 15 chromosomes or linkage groups at logarithm of odds (LOD) ≥ 2.0, of which 15 were found for leaf morphology at LOD ≥.3.0. The genetic effects of the QTL were estimated. These results are fundamental for marker-assisted selection (MAS) of these traits in tetraploid cotton breeding.

  15. Mapping and Analysis of Quantitative Trait Loci Controlling Seed Dormancy in Rice

    Institute of Scientific and Technical Information of China (English)

    JIANG Ling; ZHANG Wen-wei; ZHAI Hu-qu; WAN Jian-min

    2005-01-01

    Seed dormancy is one of the most important traits related to the rice grain quality and seeds application, because it is associated with pre-harvest sprouting, resulting in a downgrading of quality and severe limitations in end-use application.The recent development of DNA markers and linkage maps of rice has made possible mapping of individual genes associated with complex seed dormancy traits, analyzing the genetics effects of individual genes and genotype-byenvironment interactions. Up to now, numerous quantitative trait loci (QTLs) associated with seed dormancy in rice have been identified and mapped in the molecular genetic map by different populations. In this review, we focus on the genetic base of seed dormancy in rice, especially compare QTLs controlling seed dormancy reported up to now, analyze the expression and stability of QTLs controlling seed dormancy, and discuss the present problems. Finally we show a new pathway to further research on seed dormancy.

  16. A Sequential Quantitative Trait Locus Fine-Mapping Strategy Using Recombinant-Derived Progeny

    Institute of Scientific and Technical Information of China (English)

    Qin Yang; Dongfeng Zhang; Mingliang Xu

    2012-01-01

    A thorough understanding of the quantitative trait loci (QTLs) that underlie agronomically important traits in crops would greatly increase agricultural productivity.Although advances have been made in QTL cloning,the majority of QTLs remain unknown because of their low heritability and minor contributions to phenotypic performance.Here we summarize the key advantages and disadvantages of current QTL fine-mapping methodologies,and then introduce a sequential QTL fine-mapping strategy based on both genotypes and phenotypes of progeny derived from recombinants.With this mapping strategy,experimental errors could be dramatically diminished so as to reveal the authentic genetic effect of target QTLs.The number of progeny required to detect QTLs at various R2 values was calculated,and the backcross generation suitable to start QTL fine-mapping was also estimated.This mapping strategy has proved to be very powerful in narrowing down QTL regions,particularly minor-effect QTLs,as revealed by fine-mapping of various resistance QTLs in maize.Application of this sequential QTL mapping strategy should accelerate cloning of agronomically important QTLs,which is currently a substantial challenge in crops.

  17. Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

    DEFF Research Database (Denmark)

    Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

    2016-01-01

    Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far...... approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity...... been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new...

  18. Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle

    OpenAIRE

    Kelly, Scott A; Nehrenberg, Derrick L.; Hua, Kunjie; Garland, Theodore; Pomp, Daniel

    2014-01-01

    Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to v...

  19. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  20. Model selection for quantitative trait loci mapping in a full-sib family

    Directory of Open Access Journals (Sweden)

    Chunfa Tong

    2012-01-01

    Full Text Available Statistical methods for mapping quantitative trait loci (QTLs in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation, F2 cross (1:2:1 segregation and full cross (1:1:1:1 segregation. Akaike's information criterion (AIC, the Bayesian information criterion (BIC and the Laplace-empirical criterion (LEC were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.

  1. Exploring discrepancies between quantitative validation results and the geomorphic plausibility of statistical landslide susceptibility maps

    Science.gov (United States)

    Steger, Stefan; Brenning, Alexander; Bell, Rainer; Petschko, Helene; Glade, Thomas

    2016-06-01

    Empirical models are frequently applied to produce landslide susceptibility maps for large areas. Subsequent quantitative validation results are routinely used as the primary criteria to infer the validity and applicability of the final maps or to select one of several models. This study hypothesizes that such direct deductions can be misleading. The main objective was to explore discrepancies between the predictive performance of a landslide susceptibility model and the geomorphic plausibility of subsequent landslide susceptibility maps while a particular emphasis was placed on the influence of incomplete landslide inventories on modelling and validation results. The study was conducted within the Flysch Zone of Lower Austria (1,354 km2) which is known to be highly susceptible to landslides of the slide-type movement. Sixteen susceptibility models were generated by applying two statistical classifiers (logistic regression and generalized additive model) and two machine learning techniques (random forest and support vector machine) separately for two landslide inventories of differing completeness and two predictor sets. The results were validated quantitatively by estimating the area under the receiver operating characteristic curve (AUROC) with single holdout and spatial cross-validation technique. The heuristic evaluation of the geomorphic plausibility of the final results was supported by findings of an exploratory data analysis, an estimation of odds ratios and an evaluation of the spatial structure of the final maps. The results showed that maps generated by different inventories, classifiers and predictors appeared differently while holdout validation revealed similar high predictive performances. Spatial cross-validation proved useful to expose spatially varying inconsistencies of the modelling results while additionally providing evidence for slightly overfitted machine learning-based models. However, the highest predictive performances were obtained for

  2. Quantitative mapping by remote sensing of an ocean acid-waste dump

    Science.gov (United States)

    Ohlhorst, C. W.

    1978-01-01

    Results from quantitative analysis show that airplane remotely sensed spectral data can be used to quantify and map an acid-waste dump in terms of its particulate iron concentration. These same data, however, could not be used to map the dump in terms of total suspended solids, organic suspended solids, or inorganic suspended solids concentrations. A single-variable equation using the ratio of band 2 (440 to 490 nm) radiance to band 4 (540 to 580 nm) radiance was used to quantify the iron concentration in the acid-waste dump. The acid waste that was mapped varied in age from freshly dumped to 31/2 hr. Particulate iron concentrations in the acid waste were estimated to range up to 1.1 mg/l at a depth of 0.46 m. A classification technique was developed to identify pixels in the data set affected by sun glitter.

  3. Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

    Science.gov (United States)

    Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

    2014-06-01

    Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions.

  4. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    In fine mapping of a large-scale experimental population where collection of phenotypes are very expensive, difficult to record or time-demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage...... disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...

  5. A method for estimating and removing streaking artifacts in quantitative susceptibility mapping.

    Science.gov (United States)

    Li, Wei; Wang, Nian; Yu, Fang; Han, Hui; Cao, Wei; Romero, Rebecca; Tantiwongkosi, Bundhit; Duong, Timothy Q; Liu, Chunlei

    2015-03-01

    Quantitative susceptibility mapping (QSM) is a novel MRI method for quantifying tissue magnetic property. In the brain, it reflects the molecular composition and microstructure of the local tissue. However, susceptibility maps reconstructed from single-orientation data still suffer from streaking artifacts which obscure structural details and small lesions. We propose and have developed a general method for estimating streaking artifacts and subtracting them from susceptibility maps. Specifically, this method uses a sparse linear equation and least-squares (LSQR)-algorithm-based method to derive an initial estimation of magnetic susceptibility, a fast quantitative susceptibility mapping method to estimate the susceptibility boundaries, and an iterative approach to estimate the susceptibility artifact from ill-conditioned k-space regions only. With a fixed set of parameters for the initial susceptibility estimation and subsequent streaking artifact estimation and removal, the method provides an unbiased estimate of tissue susceptibility with negligible streaking artifacts, as compared to multi-orientation QSM reconstruction. This method allows for improved delineation of white matter lesions in patients with multiple sclerosis and small structures of the human brain with excellent anatomical details. The proposed methodology can be extended to other existing QSM algorithms.

  6. Quantitative validation of sensory mapping in persistent postherniorrhaphy inguinal pain patients undergoing triple neurectomy.

    Science.gov (United States)

    Bjurström, M F; Álvarez, R; Nicol, A L; Olmstead, R; Amid, P K; Chen, D C

    2017-04-01

    Neurectomy of the inguinal nerves may be considered for selected refractory cases of chronic postherniorrhaphy inguinal pain (CPIP). There is to date a paucity of easily applicable clinical tools to identify neuropathic pain and examine the neurosensory effects of remedial surgery. The present quantitative sensory testing (QST) pilot study evaluates a sensory mapping technique. Longitudinal (preoperative, immediate postoperative, and late postoperative) dermatomal sensory mapping and a comprehensive QST protocol were conducted in CPIP patients with unilateral, predominantly neuropathic inguinodynia presenting for triple neurectomy (n = 13). QST was conducted in four areas on the affected, painful side and in one contralateral comparison site. QST variables were compared according to sensory mapping outcomes: (o)/normal sensation, (+)/pain, and (-)/numbness. Diagnostic ability of the sensory mapping outcomes to detect QST-assessed allodynia or hypoesthesia was estimated through calculation of specificity and sensitivity values. Preoperatively, patients exhibited mechanical hypoesthesia and allodynia and pressure allodynia and hyperalgesia in painful areas mapped (+) (p mapping outcome (+) demonstrated high ability to detect mechanical allodynia [sensitivity 0.74 (95% CI 0.61-0.86), specificity 0.94 (0.84-1.00)] and pressure allodynia [sensitivity 0.96 (0.89-1.00), specificity 1.00 (1.00-1.00)], but not thermal allodynia. Postoperatively, mapped areas of numbness (-) were associated with mechanical and thermal hypoesthesia (p mapping provides an accurate clinical neuropathic assessment with strong correlation to QST findings of preoperative mechanical and pressure allodynia, and postoperative mechanical and thermal hypoesthesia in CPIP patients undergoing neurectomy.

  7. Improving fieldwork by using GIS for quantitative exploration, data management and digital mapping

    Science.gov (United States)

    Marra, Wouter; Alberti, Koko; van de Grint, Liesbeth; Karssenberg, Derek

    2016-04-01

    Fieldwork is an essential part of teaching geosciences. The essence of a fieldwork is to study natural phenomena in its proper context. Fieldworks dominantly utilize a learning-by-experiencing learning style and are often light on abstract thinking skills. We introduce more of the latter skills to a first-year fieldwork of several weeks by using Geographical Information Systems (GIS). We use simple techniques as the involved students had no prior experience with GIS. In our project, we introduced new tutorials prior to the fieldwork where students explored their research area using aerial photos, satellite images, an elevation model and slope-map using Google Earth and QGIS. The goal of these tutorials was to get acquainted with the area, plan the first steps of the fieldwork, and formulate hypotheses in form of a preliminary map based on quantitative data. During the actual fieldwork, half of the students processed and managed their field data using GIS, used elevation data as additional data source, and made digital geomorphological maps. This was in contrast to the other half of the students that used classic techniques with paper maps. We evaluated the learning benefits by two questionnaires (one before and one after the fieldwork), and a group interview with students that used GIS in the field. Students liked the use of Google Earth and GIS, and many indicate the added value of using quantitative maps. The hypotheses and fieldwork plans of the students were quickly superseded by insights during the fieldwork itself, but making these plans and hypotheses in advance improved the student's ability to perform empirical research. Students were very positive towards the use of GIS for their fieldwork, mainly because they experienced it as a modern and relevant technique for research and the labour market. Tech-savvy students were extra motivated and explored additional methods. There were some minor technical difficulties with using GIS during the fieldwork, but

  8. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  9. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins.

    Science.gov (United States)

    Hong, Qiuting; Ruhaak, L Renee; Stroble, Carol; Parker, Evan; Huang, Jincui; Maverakis, Emanual; Lebrilla, Carlito B

    2015-12-04

    A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.

  10. An improved procedure of mapping a quantitative trait locus via the EM algorithm using posterior probabilities

    Indian Academy of Sciences (India)

    Saurabh Ghosh; Partha P. Majumder

    2000-08-01

    Mapping a locus controlling a quantitative genetic trait (e.g. blood pressure) to a specific genomic region is of considerable contemporary interest. Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically analysed to estimate the recombination fraction, , between the putative quantitative trait locus and a genetic marker. One of the major complications in estimating for a quantitative trait in humans is the lack of haplotype information on members of families. We have devised a computationally simple two-stage method of estimation of in the absence of haplotypic information using the expectation-maximization (EM) algorithm. In the first stage, parameters of the quantitative trait locus (QTL) are estimated on the basis of data of a sample of unrelated individuals and a Bayes's rule is used to classify each parent into a QTL genotypic class. In the second stage, we have proposed an EM algorithm for obtaining the maximum-likelihood estimate of based on data of informative families (which are identified upon inferring parental QTL genotypes performed in the first stage). The purpose of this paper is to investigate whether, instead of using genotypically `classified' data of parents, the use of posterior probabilities of QT genotypes of parents at the second stage yields better estimators. We show, using simulated data, that the proposed procedure using posterior probabilities is statistically more efficient than our earlier classification procedure, although it is computationally heavier.

  11. Quantitative EPMA Compositional Mapping of NWA 2995: Characterization, and Petrologic Interpretation of Mafic Clasts

    Science.gov (United States)

    Carpenter, P. K.; Hahn, T. M.; Korotev, R. L.; Ziegler, R. A.; Jolliff, B. L.

    2017-01-01

    We present the first fully quantitative compositional maps of lunar meteorite NWA 2995 using electron microprobe stage mapping, and compare selected clast mineralogy and chemistry. NWA 2995 is a feldspathic fragmental breccia containing numerous highland fine grained lithologies, including anorthosite, norite, olivine basalt, subophitic basalt, gabbro, KREEP-like basalt, granulitic and glassy impact melts, coarse-grained mineral fragments, Fe-Ni metal, and glassy matrix [1]. Chips of NWA 2995, representing these diverse materials, were analyzed by INAA and fused-bead electron-probe microanalysis (EPMA); comparison of analytical data suggests grouping of lunar meteorites NWA 2995, 2996, 3190, 4503, 5151, and 5152. The mean composition of NWA 2995 corresponds to a 2:1 mixture of feldspathic and mare material, with approximately 5% KREEP component [2]. Clast mineral chemistry and petrologic interpretation of paired stone NWA 2996 has been reported by Mercer et al. [3], and Gross et al. [4]. This study combines advances in quantitative EPMA compositional mapping and data analysis, as applied to selected mafic clasts in a polished section of NWA 2995, to investigate the origin of mafic lithic components and to demonstrate a procedural framework for petrologic analysis.

  12. TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees.

    Science.gov (United States)

    Pan, Feng; McMillan, Leonard; Pardo-Manuel De Villena, Fernando; Threadgill, David; Wang, Wei

    2009-01-01

    The goal of genome wide association (GWA) mapping in modern genetics is to identify genes or narrow regions in the genome that contribute to genetically complex phenotypes such as morphology or disease. Among the existing methods, tree-based association mapping methods show obvious advantages over single marker-based and haplotype-based methods because they incorporate information about the evolutionary history of the genome into the analysis. However, existing tree-based methods are designed primarily for binary phenotypes derived from case/control studies or fail to scale genome-wide. In this paper, we introduce TreeQA, a quantitative GWA mapping algorithm. TreeQA utilizes local perfect phylogenies constructed in genomic regions exhibiting no evidence of historical recombination. By efficient algorithm design and implementation, TreeQA can efficiently conduct quantitative genom-wide association analysis and is more effective than the previous methods. We conducted extensive experiments on both simulated datasets and mouse inbred lines to demonstrate the efficiency and effectiveness of TreeQA.

  13. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.

    Science.gov (United States)

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-06-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.

  14. Mapping quantitative trait loci for binary trait in the F2:3 design

    Indian Academy of Sciences (India)

    Chengsong Zhu; Yuan-Ming Zhang; Zhigang Guo

    2008-12-01

    In the analysis of inheritance of quantitative traits with low heritability, an F2:3 design that genotypes plants in F2 and phenotypes plants in F2:3 progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F2:3 design have been well developed, those for binary traits of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F2:3 design. The fundamental idea was: the F2 plants were genotyped, all phenotypic values of each F2:3 progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte–Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F2:3 design is more efficient than classical F2 design, even though only a single progeny is collected from each F2:3 family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F2:3 design.

  15. Fine mapping of multiple interacting quantitative trait loci using combined linkage disequilibrium and linkage information

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Quantitative trait loci (QTL) and their additive, dominance and epistatic effects play a critical role in complex trait variation. It is often infeasible to detect multiple interacting QTL due to main effects often being confounded by interaction effects.Positioning interacting QTL within a small region is even more difficult. We present a variance component approach nested in an empirical Bayesian method, which simultaneously takes into account additive, dominance and epistatic effects due to multiple interacting QTL. The covariance structure used in the variance component approach is based on combined linkage disequilibrium and linkage (LDL) information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously fine map interacting QTL using the proposed approach. The present method combined with LDL information can efficiently detect QTL and their dominance and epistatic effects, making it possible to simultaneously fine map main and epistatic QTL.

  16. Foundations of MRI phase imaging and processing for Quantitative Susceptibility Mapping (QSM)

    Energy Technology Data Exchange (ETDEWEB)

    Schweser, Ferdinand [New York State Univ., Buffalo, NY (United States). Buffalo Neuroimaging Analysis Center; New York State Univ., Buffalo, NY (United States). MRI Clinical and Translational Research Center; Deistung, Andreas [Jena Univ. (Germany). Medical Physics Group; Reichenbach, Juergen R. [Jena Univ. (Germany). Medical Physics Group; Jena Univ. (Germany). Michael Stifel Center for Data-driven and Simulation Science Jena

    2016-05-01

    Quantitative Susceptibility Mapping (QSM) is a novel MRI based technique that relies on estimates of the magnetic field distribution in the tissue under examination. Several sophisticated data processing steps are required to extract the magnetic field distribution from raw MRI phase measurements. The objective of this review article is to provide a general overview and to discuss several underlying assumptions and limitations of the pre-processing steps that need to be applied to MRI phase data before the final field-to-source inversion can be performed. Beginning with the fundamental relation between MRI signal and tissue magnetic susceptibility this review covers the reconstruction of magnetic field maps from multi-channel phase images, background field correction, and provides an overview of state of the art QSM solution strategies.

  17. Genetic mapping of quantitative trait loci for milk production in sheep.

    Science.gov (United States)

    Mateescu, R G; Thonney, M L

    2010-10-01

    A backcross pedigree using dairy East Friesian rams and non-dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test-day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here.

  18. Mapping Quantitative Field Resistance Against Apple Scab in a 'Fiesta' x 'Discovery' Progeny.

    Science.gov (United States)

    Liebhard, R; Koller, B; Patocchi, A; Kellerhals, M; Pfammatter, W; Jermini, M; Gessler, C

    2003-04-01

    ABSTRACT Breeding of resistant apple cultivars (Malus x domestica) as a disease management strategy relies on the knowledge and understanding of the underlying genetics. The availability of molecular markers and genetic linkage maps enables the detection and the analysis of major resistance genes as well as of quantitative trait loci (QTL) contributing to the resistance of a genotype. Such a genetic linkage map was constructed, based on a segregating population of the cross between apple cvs. Fiesta (syn. Red Pippin) and Discovery. The progeny was observed for 3 years at three different sites in Switzerland and field resistance against apple scab (Venturia inaequalis) was assessed. Only a weak correlation was detected between leaf scab and fruit scab. A QTL analysis was performed, based on the genetic linkage map consisting of 804 molecular markers and covering all 17 chromosomes of apple. With the maximum likelihood-based interval mapping method, eight genomic regions were identified, six conferring resistance against leaf scab and two conferring fruit scab resistance. Although cv. Discovery showed a much stronger resistance against scab in the field, most QTL identified were attributed to the more susceptible parent 'Fiesta'. This indicated a high degree of homozygosity at the scab resistance loci in 'Discovery', preventing their detection in the progeny due to the lack of segregation.

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

    Directory of Open Access Journals (Sweden)

    Pérez-Enciso Miguel

    2003-09-01

    Full Text Available Abstract 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.

  20. Multi-QTL mapping for quantitative traits using epistatic distorted markers.

    Directory of Open Access Journals (Sweden)

    Shang-Qian Xie

    Full Text Available The interaction between segregation distortion loci (SDL has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4.

  1. Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection.

    Science.gov (United States)

    Li, Zitong; Sillanpää, Mikko J

    2012-08-01

    Quantitative trait loci (QTL)/association mapping aims at finding genomic loci associated with the phenotypes, whereas genomic selection focuses on breeding value prediction based on genomic data. Variable selection is a key to both of these tasks as it allows to (1) detect clear mapping signals of QTL activity, and (2) predict the genome-enhanced breeding values accurately. In this paper, we provide an overview of a statistical method called least absolute shrinkage and selection operator (LASSO) and two of its generalizations named elastic net and adaptive LASSO in the contexts of QTL mapping and genomic breeding value prediction in plants (or animals). We also briefly summarize the Bayesian interpretation of LASSO, and the inspired hierarchical Bayesian models. We illustrate the implementation and examine the performance of methods using three public data sets: (1) North American barley data with 127 individuals and 145 markers, (2) a simulated QTLMAS XII data with 5,865 individuals and 6,000 markers for both QTL mapping and genomic selection, and (3) a wheat data with 599 individuals and 1,279 markers only for genomic selection.

  2. Regional quantitative analysis of cortical surface maps of FDG PET images

    CERN Document Server

    Protas, H D; Hayashi, K M; Chin Lung, Yu; Bergsneider, M; Sung Cheng, Huang

    2006-01-01

    Cortical surface maps are advantageous for visualizing the 3D profile of cortical gray matter development and atrophy, and for integrating structural and functional images. In addition, cortical surface maps for PET data, when analyzed in conjunction with structural MRI data allow us to investigate, and correct for, partial volume effects. Here we compared quantitative regional PET values based on a 3D cortical surface modeling approach with values obtained directly from the 3D FDG PET images in various atlas-defined regions of interest (ROIs; temporal, parietal, frontal, and occipital lobes). FDG PET and 3D MR (SPGR) images were obtained and aligned to ICBM space for 15 normal subjects. Each image was further elastically warped in 2D parameter space of the cortical surface, to align major cortical sulci. For each point within a 15 mm distance of the cortex, the value of the PET intensity was averaged to give a cortical surface map of FDG uptake. The average PET values on the cortical surface map were calcula...

  3. Quantitative retinal blood flow mapping from fluorescein videoangiography using tracer kinetic modeling.

    Science.gov (United States)

    Tichauer, Kenneth M; Guthrie, Micah; Hones, Logan; Sinha, Lagnojita; St Lawrence, Keith; Kang-Mieler, Jennifer J

    2015-05-15

    Abnormal retinal blood flow (RBF) has been associated with numerous retinal pathologies, yet existing methods for measuring RBF predominantly provide only relative measures of blood flow and are unable to quantify volumetric blood flow, which could allow direct patient to patient comparison. This work presents a methodology based on linear systems theory and an image-based arterial input function to quantitatively map volumetric blood flow from standard fluorescein videoangiography data, and is therefore directly translatable to the clinic. Application of the approach to fluorescein retinal videoangiography in rats (4 control, 4 diabetic) demonstrated significantly higher RBF in 4-5 week diabetic rats as expected from the literature.

  4. Developing and applying quantitative skills maps for STEM curricula, with a focus on different modes of learning

    Science.gov (United States)

    Reid, Jackie; Wilkes, Janelle

    2016-08-01

    Mapping quantitative skills across the science, technology, engineering and mathematics (STEM) curricula will help educators identify gaps and duplication in the teaching, practice and assessment of the necessary skills. This paper describes the development and implementation of quantitative skills mapping tools for courses in STEM at a regional university that offers both on-campus and distance modes of study. Key elements of the mapping project included the identification of key graduate quantitative skills, the development of curriculum mapping tools to record in which unit(s) and at what level of attainment each quantitative skill is taught, practised and assessed, and identification of differences in the way quantitative skills are developed for on-campus and distance students. Particular attention is given to the differences that are associated with intensive schools, which consist of concentrated periods of face-to-face learning over a three-four day period, and are available to distance education students enrolled in STEM units. The detailed quantitative skills mapping process has had an impact on the review of first-year mathematics units, resulted in crucial changes to the curriculum in a number of courses, and contributed to a more integrated approach, and a collective responsibility, to the development of students' quantitative skills for both face-to-face and online modes of learning.

  5. Spatially quantitative seafloor habitat mapping: example from the northern South Carolina inner continental shelf

    Science.gov (United States)

    Ojeda, Germán Y.; Gayes, Paul T.; Van Dolah, Robert F.; Schwab, William C.

    2004-03-01

    Naturally occurring hard bottom areas provide the geological substrate that can support diverse assemblages of sessile benthic organisms, which in turn, attract many reef-dwelling fish species. Alternatively, defining the location and extent of bottom sand bodies is relevant for potential nourishment projects as well as to ensure that transient sediment does not affect reef habitats, particularly in sediment-starved continental margins. Furthermore, defining sediment transport pathways documents the effects these mobile bedforms have on proximal reef habitats. Thematic mapping of these substrates is therefore crucial in safeguarding critical habitats and offshore resources of coastal nations. This study presents the results of a spatially quantitative mapping approach based on classification of sidescan-sonar imagery. By using bottom video for image-to-ground control, digital image textural features for pattern recognition, and an artificial neural network for rapid, quantitative, multivariable decision-making, this approach resulted in recognition rates of hard bottom as high as 87%. The recognition of sand bottom was less successful (31%). This approach was applied to a large (686 km 2), high-quality, 2-m resolution sidescan-sonar mosaic of the northern South Carolina inner continental shelf. Results of this analysis indicate that both surficial sand and hard bottoms of variable extent are present over the study area. In total, 59% of the imaged area was covered by hard bottom, while 41% was covered by sand. Qualitative spatial correlation between bottom type and bathymetry appears possible from comparison of our interpretive map and available bathymetry. Hard bottom areas tend to be located on flat, low-lying areas, and sandy bottoms tend to reside on areas of positive relief. Published bio-erosion rates were used to calculate the potential sediment input from the mapped hard bottom areas rendering sediment volumes that may be as high as 0.8 million m 3/yr for

  6. Whole-brain quantitative mapping of metabolites using short echo 3D-proton- MRSI

    Science.gov (United States)

    Lecocq, Angèle; Le Fur, Yann; Maudsley, Andrew A; Le Troter, Arnaud; Sheriff, Sulaiman; Sabati, Mohamad; Donnadieu, Maxime; Confort-Gouny, Sylviane; Cozzone, Patrick J.; Guye, Maxime; Ranjeva, Jean-Philippe

    2014-01-01

    Purpose To improve the extent over which whole brain quantitative 3D-MRSI maps can be obtained and be used to explore brain metabolism in a population of healthy volunteers. Materials and Methods Two short TE (20 ms) acquisitions of 3D Echo Planar Spectroscopic Imaging at two orientations, one in the anterior commissure – posterior commissure (AC-PC) plane and the second tilted in the AC-PC +15° plane were obtained at 3T in a group of ten healthy volunteers. B1+, B1−, and B0 correction procedures and normalization of metabolite signals with quantitative water proton density measurements were performed. A combination of the two spatially normalized 3D-MRSI, using a weighted mean based on the pixel wise standard deviation metabolic maps of each orientation obtained from the whole group, provided metabolite maps for each subject allowing regional metabolic profiles of all parcels of the automated anatomical labeling (AAL) atlas to be obtained. Results The combined metabolite maps derived from the two acquisitions reduced the regional inter-subject variance. The numbers of AAL regions showing NAA SD/Mean ratios lower than 30% increased from 17 in the AC-PC orientation and 41 in the AC-PC+15° orientation, to a value of 76 regions out of 116 for the combined NAA maps. Quantitatively, regional differences in absolute metabolite concentrations (mM) over the whole brain were depicted such as in the GM of frontal lobes (cNAA=10.03+1.71, cCho=1.78±0.55, cCr=7.29±1.69; cmIns=5.30±2.67) and in cerebellum (cNAA=5.28±1.77, cCho=1.60±0.41, cCr=6.95±2.15; cmIns=3.60±0.74). Conclusion A double-angulation acquisition enables improved metabolic characterization over a wide volume of the brain. PMID:25431032

  7. The potential of Fuzzy Cognitive Maps for semi-quantitative scenario development, with an example from Brazil

    NARCIS (Netherlands)

    Kok, K.

    2009-01-01

    The main drawback of the Story-and-Simulation approach is the weak link between qualitative and quantitative scenarios. A semi-quantitative tool, Fuzzy Cognitive Mapping, is introduced as a possible improvement. An example from the Brazilian Amazon shows that by including an integrated set of factor

  8. Quantitative trait locus (QTL mapping reveals a role for unstudied genes in Aspergillus virulence.

    Directory of Open Access Journals (Sweden)

    Julian K Christians

    Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.

  9. Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum)

    Indian Academy of Sciences (India)

    Min Wang; Chengqi Li; Qinglian Wang

    2014-08-01

    Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5 /chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for marker-assisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

  10. Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum).

    Science.gov (United States)

    Wang, Min; Li, Chengqi; Wang, Qinglian

    2014-08-01

    Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5/chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for markerassisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

  11. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch

    Directory of Open Access Journals (Sweden)

    Cristian Araneda

    2012-01-01

    Full Text Available Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss, various quantitative trait loci (QTL that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch. The four loci were identified in females from two populations (early and late spawners produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC that were strongly associated with spawning time in coho salmon (p < 0.0002 were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10 with a suggestive association (p = 0.00035 mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

  12. Analyzing the texture changes in the quantitative phase maps of adipocytes

    Science.gov (United States)

    Roitshtain, Darina; Sharabani-Yosef, Orna; Gefen, Amit; Shaked, Natan T.

    2016-03-01

    We present a new analysis tool for studying texture changes in the quantitative phase maps of live cells acquired by wide-field interferometry. The sensitivity of wide-field interferometry systems to small changes in refractive index enables visualizing cells and inner cell organelles without the using fluorescent dyes or other cell-invasive approaches, which may affect the measurement and require external labeling. Our label-free texture-analysis tool is based directly on the optical path delay profile of the sample and does not necessitate decoupling refractive index and thickness in the cell quantitative phase profile; thus, relevant parameters can be calculated using a single-frame acquisition. Our experimental system includes low-coherence wide-field interferometer, combined with simultaneous florescence microscopy system for validation. We used this system and analysis tool for studying lipid droplets formation in adipocytes. The latter demonstration is relevant for various cellular functions such as lipid metabolism, protein storage and degradation to viral replication. These processes are functionally linked to several physiological and pathological conditions, including obesity and metabolic diseases. Quantification of these biological phenomena based on the texture changes in the cell phase map has a potential as a new cellular diagnosis tool.

  13. An improved method for retrospective motion correction in quantitative T2* mapping.

    Science.gov (United States)

    Nöth, Ulrike; Volz, Steffen; Hattingen, Elke; Deichmann, Ralf

    2014-05-15

    A new method for motion correction of T2*-weighted data and resulting quantitative T2* maps is presented. For this method, additional data sets with a reduced number of phase encoding steps covering the k-space centre are acquired. Motion correction is based on a 3-step procedure: (1) calculation of improved input data sets with reduced artefact levels from the original data, (2) creation of a target data set free of movement artefacts on the basis of the improved input data sets, and (3) fitting of original data to the target data set, yielding an optimum combination of acquired k-space data which suppresses lines affected by movement. The method was tested on healthy subjects performing pre-trained movement. Motion correction was successful unless the same k-space line was affected by movement in all data sets acquired on a specific subject. The method was applied to patients suffering from subarachnoid haemorrhage (group 1) or tumours (group 2) with accompanying edema in the brain. Motion correction improved the interpretability of T2*-weighted patient data and resulting quantitative T2* maps considerably by allowing a clear delineation between ventricle and edema and a clear localisation of haemorrhage (group 1) or a clear delineation of tumour accompanying edema (group 2) which was not possible in data affected by movement.

  14. Molecular Imaging of Tumors Using a Quantitative T1 Mapping Technique via Magnetic Resonance Imaging

    Directory of Open Access Journals (Sweden)

    Kelsey Herrmann

    2015-07-01

    Full Text Available Magnetic resonance imaging (MRI of glioblastoma multiforme (GBM with molecular imaging agents would allow for the specific localization of brain tumors. Prior studies using T1-weighted MR imaging demonstrated that the SBK2-Tris-(Gd-DOTA3 molecular imaging agent labeled heterotopic xenograft models of brain tumors more intensely than non-specific contrast agents using conventional T1-weighted imaging techniques. In this study, we used a dynamic quantitative T1 mapping strategy to more objectively compare intra-tumoral retention of the SBK2-Tris-(Gd-DOTA3 agent over time in comparison to non-targeted control agents. Our results demonstrate that the targeted SBK2-Tris-(Gd-DOTA3 agent, a scrambled-Tris-(Gd-DOTA3 control agent, and the non-specific clinical contrast agent Optimark™ all enhanced flank tumors of human glioma cells with similar maximal changes on T1 mapping. However, the retention of the agents differs. The non-specific agents show significant recovery within 20 min by an increase in T1 while the specific agent SBK2-Tris-(Gd-DOTA3 is retained in the tumors and shows little recovery over 60 min. The retention effect is demonstrated by percent change in T1 values and slope calculations as well as by calculations of gadolinium concentration in tumor compared to muscle. Quantitative T1 mapping demonstrates the superior binding and retention in tumors of the SBK2-Tris-(Gd-DOTA3 agent over time compared to the non-specific contrast agent currently in clinical use.

  15. Identifying hazard parameter to develop quantitative and dynamic hazard map of an active volcano in Indonesia

    Science.gov (United States)

    Suminar, Wulan; Saepuloh, Asep; Meilano, Irwan

    2016-05-01

    Analysis of hazard assessment to active volcanoes is crucial for risk management. The hazard map of volcano provides information to decision makers and communities before, during, and after volcanic crisis. The rapid and accurate hazard assessment, especially to an active volcano is necessary to be developed for better mitigation on the time of volcanic crises in Indonesia. In this paper, we identified the hazard parameters to develop quantitative and dynamic hazard map of an active volcano. The Guntur volcano in Garut Region, West Java, Indonesia was selected as study area due population are resided adjacent to active volcanoes. The development of infrastructures, especially related to tourism at the eastern flank from the Summit, are growing rapidly. The remote sensing and field investigation approaches were used to obtain hazard parameters spatially. We developed a quantitative and dynamic algorithm to map spatially hazard potential of volcano based on index overlay technique. There were identified five volcano hazard parameters based on Landsat 8 and ASTER imageries: volcanic products including pyroclastic fallout, pyroclastic flows, lava and lahar, slope topography, surface brightness temperature, and vegetation density. Following this proposed technique, the hazard parameters were extracted, indexed, and calculated to produce spatial hazard values at and around Guntur Volcano. Based on this method, the hazard potential of low vegetation density is higher than high vegetation density. Furthermore, the slope topography, surface brightness temperature, and fragmental volcanic product such as pyroclastics influenced to the spatial hazard value significantly. Further study to this proposed approach will be aimed for effective and efficient analyses of volcano risk assessment.

  16. Quantitative Susceptibility Mapping Indicates a Disturbed Brain Iron Homeostasis in Neuromyelitis Optica – A Pilot Study

    Science.gov (United States)

    Granado, Vanessa; Rueda, Fernanda; Deistung, Andreas; Reichenbach, Juergen R.; Tukamoto, Gustavo; Gasparetto, Emerson Leandro; Schweser, Ferdinand

    2016-01-01

    Dysregulation of brain iron homeostasis is a hallmark of many neurodegenerative diseases and can be associated with oxidative stress. The objective of this study was to investigate brain iron in patients with Neuromyelitis Optica (NMO) using quantitative susceptibility mapping (QSM), a quantitative iron-sensitive MRI technique. 12 clinically confirmed NMO patients (6 female and 6 male; age 35.4y±14.2y) and 12 age- and sex-matched healthy controls (7 female and 5 male; age 33.9±11.3y) underwent MRI of the brain at 3 Tesla. Quantitative maps of the effective transverse relaxation rate (R2*) and magnetic susceptibility were calculated and a blinded ROI-based group comparison analysis was performed. Normality of the data and differences between patients and controls were tested by Kolmogorov-Smirnov and t-test, respectively. Correlation with age was studied using Spearman’s rank correlation and an ANCOVA-like analysis. Magnetic susceptibility values were decreased in the red nucleus (p0.95; between -15 and -22 ppb depending on reference region) with a trend toward increasing differences with age. R2* revealed significantly decreased relaxation in the optic radiations of five of the 12 patients (p<0.0001; -3.136±0.567 s-1). Decreased relaxation in the optic radiation is indicative for demyelination, which is in line with previous findings. Decreased magnetic susceptibility in the red nucleus is indicative for a lower brain iron concentration, a chemical redistribution of iron into less magnetic forms, or both. Further investigations are necessary to elucidate the pathological cause or consequence of this finding. PMID:27171423

  17. Brain abnormalities in bipolar disorder detected by quantitative T1ρ mapping.

    Science.gov (United States)

    Johnson, C P; Follmer, R L; Oguz, I; Warren, L A; Christensen, G E; Fiedorowicz, J G; Magnotta, V A; Wemmie, J A

    2015-02-01

    Abnormal metabolism has been reported in bipolar disorder, however, these studies have been limited to specific regions of the brain. To investigate whole-brain changes potentially associated with these processes, we applied a magnetic resonance imaging technique novel to psychiatric research, quantitative mapping of T1 relaxation in the rotating frame (T1ρ). This method is sensitive to proton chemical exchange, which is affected by pH, metabolite concentrations and cellular density with high spatial resolution relative to alternative techniques such as magnetic resonance spectroscopy and positron emission tomography. Study participants included 15 patients with bipolar I disorder in the euthymic state and 25 normal controls balanced for age and gender. T1ρ maps were generated and compared between the bipolar and control groups using voxel-wise and regional analyses. T1ρ values were found to be elevated in the cerebral white matter and cerebellum in the bipolar group. However, volumes of these areas were normal as measured by high-resolution T1- and T2-weighted magnetic resonance imaging. Interestingly, the cerebellar T1ρ abnormalities were normalized in participants receiving lithium treatment. These findings are consistent with metabolic or microstructural abnormalities in bipolar disorder and draw attention to roles of the cerebral white matter and cerebellum. This study highlights the potential utility of high-resolution T1ρ mapping in psychiatric research.

  18. Echo time-dependent quantitative susceptibility mapping contains information on tissue properties.

    Science.gov (United States)

    Sood, Surabhi; Urriola, Javier; Reutens, David; O'Brien, Kieran; Bollmann, Steffen; Barth, Markus; Vegh, Viktor

    2017-05-01

    Magnetic susceptibility is a physical property of matter that varies depending on chemical composition and abundance of different molecular species. Interest is growing in mapping of magnetic susceptibility in the human brain using magnetic resonance imaging techniques, but the influences affecting the mapped values are not fully understood. We performed quantitative susceptibility mapping on 7 Tesla (T) multiple echo time gradient recalled echo data and evaluated the trend in 10 regions of the human brain. Temporal plots of susceptibility were performed in the caudate, pallidum, putamen, thalamus, insula, red nucleus, substantia nigra, internal capsule, corpus callosum, and fornix. We implemented an existing three compartment signal model and used optimization to fit the experimental result to assess the influences that could be responsible for our findings. The temporal trend in susceptibility is different for different brain regions, and subsegmentation of specific regions suggests that differences are likely to be attributable to variations in tissue structure and composition. Using a signal model, we verified that a nonlinear temporal behavior in experimentally computed susceptibility within imaging voxels may be the result of the heterogeneous composition of tissue properties. Decomposition of voxel constituents into meaningful parameters may lead to informative measures that reflect changes in tissue microstructure. Magn Reson Med 77:1946-1958, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  19. Quantitative NumART2* mapping in functional MRI studies at 1.5 T.

    Science.gov (United States)

    Hagberg, Gisela E; Bianciardi, Marta; Patria, Fabiana; Indovina, Iole

    2003-12-01

    Quantitative mapping of the effective transverse relaxation time, T2* and proton density was performed in a motor activation functional MRI (fMRI) study using multi-echo, echo planar imaging (EPI) and NumART2* (Numerical Algorithm for Real time T2*). Comparisons between NumART2* and conventional single echo EPI with an echo time of 64 ms were performed for five healthy participants examined twice. Simulations were also performed to address specific issues associated with the two techniques, such as echo time-dependent signal variation. While the single echo contrast varied with the baseline T2* value, relative changes in T2* remained unaffected. Statistical analysis of the T2* maps yielded fMRI activation patterns with an improved statistical detection relative to conventional EPI but with less activated voxels, suggesting that NumART2* has superior spatial specificity. Two effects, inflow and dephasing, that may explain this finding were investigated. Particularly, a statistically significant increase in proton density was found in a brain area that was detected as activated by conventional EPI but not by NumART2* while no such changes were observed in brain areas that showed stimulus correlated signal changes on T2* maps.

  20. Simple but novel test method for quantitatively comparing robot mapping algorithms using SLAM and dead reckoning

    Science.gov (United States)

    Davey, Neil S.; Godil, Haris

    2013-05-01

    This article presents a comparative study between a well-known SLAM (Simultaneous Localization and Mapping) algorithm, called Gmapping, and a standard Dead-Reckoning algorithm; the study is based on experimental results of both approaches by using a commercial skid-based turning robot, P3DX. Five main base-case scenarios are conducted to evaluate and test the effectiveness of both algorithms. The results show that SLAM outperformed the Dead Reckoning in terms of map-making accuracy in all scenarios but one, since SLAM did not work well in a rapidly changing environment. Although the main conclusion about the excellence of SLAM is not surprising, the presented test method is valuable to professionals working in this area of mobile robots, as it is highly practical, and provides solid and valuable results. The novelty of this study lies in its simplicity. The simple but novel test method for quantitatively comparing robot mapping algorithms using SLAM and Dead Reckoning and some applications using autonomous robots are being patented by the authors in U.S. Patent Application Nos. 13/400,726 and 13/584,862.

  1. Quantitative Trait Loci Mapping for Bacterial Blight Resistance in Rice Using Bulked Segregant Analysis

    Directory of Open Access Journals (Sweden)

    Xueying Han

    2014-07-01

    Full Text Available Oryza meyeriana is highly resistant to rice bacterial blight (BB and this resistance trait has been transferred to cultivated rice (O. sativa using asymmetric somatic hybridization. However, no resistance genes have yet been cloned. In the present study, a progeny of the somatic hybridization with high BB resistance was crossed with a rice cultivar with high BB susceptibility to develop an F2 population. Using bulked segregant analysis (BSA, 17 polymorphic markers that were linked to rice BB resistance were obtained through scanning a total of 186 simple sequence repeats (SSR and sequence-tagged site (STS markers, evenly distributed on 12 chromosomes. A genetic linkage map was then constructed based on the 17 linkage markers and the F2 segregating population, which was followed by mapping for quantitative trait loci (QTLs for BB resistance. Three QTLs were identified on chromosomes 1, 3 and 5, respectively, and the alleles of the resistant parent at any of the QTLs increased BB resistance. All of the three QTLs had a strong effect on resistance, explaining about 21.5%, 12.3% and 39.2% of the resistance variance, respectively. These QTLs were different from the loci of the BB resistance genes that have been identified in previous studies. The QTLs mapped in this work will facilitate the isolation of novel BB resistance genes and their utilization in rice resistance breeding.

  2. Mapping and Quantitative Trait Loci Analysis of Verticillium Wilt Resistance Genes in Cotton

    Institute of Scientific and Technical Information of China (English)

    Hong-Mei Wang; Zhong-Xu Lin; Xian-Long Zhang; Wei Chen; Xiao-Ping Guo; Yi-Chun Nie; Yun-Hai Li

    2008-01-01

    Verticillium wilt is one of the most serious constraints to cotton production in almost all of the cotton-growing countries. In this study, "XinLuZao1" (XLZ1), a susceptible cultivar Gossypium hirsutum L. and "Hai7124" (H7124), a resistant line G. barbadense, and their F2:3 families were used to map and study the disease Index induced by verticillium wilt. A total of 430 SSR loci were mapped into 41 linkage groups; the map spanned 3 745.9 cM and the average distance between adjacent loci was 8.71 cM. Four and five quantitative trait loci (QTLs) were detected based on the disease index investigated on July 22 and August 24 in 2004, respectively. These nine QTLs explained 10.63-28.83% of the phenotypic variance, six of them were located on the D sub-genome. Two QTLs located In the same marker intervals may partly explain the significant correlation of the two traits. QTLs explaining large phenotypic variation were identified in this study, which may be quite useful in cotton anti-disease breeding.

  3. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  4. Noninvasive Assessment of Oxygen Extraction Fraction in Chronic Ischemia Using Quantitative Susceptibility Mapping at 7 Tesla.

    Science.gov (United States)

    Uwano, Ikuko; Kudo, Kohsuke; Sato, Ryota; Ogasawara, Kuniaki; Kameda, Hiroyuki; Nomura, Jun-Ichi; Mori, Futoshi; Yamashita, Fumio; Ito, Kenji; Yoshioka, Kunihiro; Sasaki, Makoto

    2017-08-01

    The oxygen extraction fraction (OEF) is an effective metric to evaluate metabolic reserve in chronic ischemia. However, OEF is considered to be accurately measured only when using positron emission tomography (PET). Thus, we investigated whether OEF maps generated by magnetic resonance quantitative susceptibility mapping (QSM) at 7 Tesla enabled detection of OEF changes when compared with those obtained with PET. Forty-one patients with chronic stenosis/occlusion of the unilateral internal carotid artery or middle cerebral artery were examined using 7 Tesla-MRI and PET scanners. QSM images were obtained from 3-dimensional T2*-weighted images, using a multiple dipole-inversion algorithm. OEF maps were generated based on susceptibility differences between venous structures and brain tissues on QSM images. OEF ratios of the ipsilateral middle cerebral artery territory against the contralateral side were calculated on the QSM-OEF and PET-OEF images, using an anatomic template. The OEF ratio in the middle cerebral artery territory showed significant correlations between QSM-OEF and PET-OEF maps (r=0.69; P1.09, as determined by receiver operating characteristic analysis, showed a sensitivity and specificity of 0.82 and 0.86, respectively, for the substantial increase in the PET-OEF ratio. Absolute QSM-OEF values were significantly correlated with PET-OEF values in the patients with increased PET-OEF. OEF ratios on QSM-OEF images at 7 Tesla showed a good correlation with those on PET-OEF images in patients with unilateral steno-occlusive internal carotid artery/middle cerebral artery lesions, suggesting that noninvasive OEF measurement by MRI can be a substitute for PET. © 2017 American Heart Association, Inc.

  5. Automatic segmentation method of striatum regions in quantitative susceptibility mapping images

    Science.gov (United States)

    Murakawa, Saki; Uchiyama, Yoshikazu; Hirai, Toshinori

    2015-03-01

    Abnormal accumulation of brain iron has been detected in various neurodegenerative diseases. Quantitative susceptibility mapping (QSM) is a novel contrast mechanism in magnetic resonance (MR) imaging and enables the quantitative analysis of local tissue susceptibility property. Therefore, automatic segmentation tools of brain regions on QSM images would be helpful for radiologists' quantitative analysis in various neurodegenerative diseases. The purpose of this study was to develop an automatic segmentation and classification method of striatum regions on QSM images. Our image database consisted of 22 QSM images obtained from healthy volunteers. These images were acquired on a 3.0 T MR scanner. The voxel size was 0.9×0.9×2 mm. The matrix size of each slice image was 256×256 pixels. In our computerized method, a template mating technique was first used for the detection of a slice image containing striatum regions. An image registration technique was subsequently employed for the classification of striatum regions in consideration of the anatomical knowledge. After the image registration, the voxels in the target image which correspond with striatum regions in the reference image were classified into three striatum regions, i.e., head of the caudate nucleus, putamen, and globus pallidus. The experimental results indicated that 100% (21/21) of the slice images containing striatum regions were detected accurately. The subjective evaluation of the classification results indicated that 20 (95.2%) of 21 showed good or adequate quality. Our computerized method would be useful for the quantitative analysis of Parkinson diseases in QSM images.

  6. Mapping quantitative trait loci (QTLs for fatty acid composition in an interspecific cross of oil palm

    Directory of Open Access Journals (Sweden)

    Sharma Mukesh

    2009-08-01

    Full Text Available Abstract Background Marker Assisted Selection (MAS is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026 and a Nigerian E. guinneensis (T128. A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis map, 252 markers (199 AFLP, 38 RFLP and 15 SSR could be ordered in 21 linkage groups (1815 cM. Interval mapping and multiple-QTL model (MQM mapping (also known as composite interval mapping, CIM were used to detect quantitative trait loci (QTLs controlling oil quality (measured in terms of iodine value and fatty acid composition. At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV, myristic acid (C14:0, palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1 and linoleic acid (C18:2 content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3

  7. Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing

    Science.gov (United States)

    Georges, M.; Nielsen, D.; Mackinnon, M.; Mishra, A.; Okimoto, R.; Pasquino, A. T.; Sargeant, L. S.; Sorensen, A.; Steele, M. R.; Zhao, X.; Womack, J. E.; Hoeschele, I.

    1995-01-01

    We have exploited ``progeny testing'' to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score >/= 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding. PMID:7713441

  8. Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing

    Energy Technology Data Exchange (ETDEWEB)

    Georges, M.; Nielsen, D.; Mackinnon, M.; Mishra, A.; Okimoto, R.; Sargeant, L.S.; Steele, M.R.; Zhao, X. [Genmark Inc., Salt Lake City, UT (United States); Pasquino, A.T. [Virginia Polytechnic Institute and State Univ., Blacksburg, VA (United States)

    1995-02-01

    We have exploited {open_quotes}progeny testing{close_quotes} to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of >150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score {ge} 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding. 44 refs., 4 figs., 3 tabs.

  9. Quantitative Trait Loci (QTLs mapping for growth traits in the mouse: A review

    Directory of Open Access Journals (Sweden)

    Medrano Juan F

    2001-03-01

    Full Text Available Abstract The attainment of a specific mature body size is one of the most fundamental differences among species of mammals. Moreover, body size seems to be the central factor underlying differences in traits such as growth rate, energy metabolism and body composition. An important proportion of this variability is of genetic origin. The goal of the genetic analysis of animal growth is to understand its "genetic architecture", that is the number and position of loci affecting the trait, the magnitude of their effects, allele frequencies and types of gene action. In this review, the different strategies developed to identify and characterize genes involved in the regulation of growth in the mouse are described, with emphasis on the methods developed to map loci contributing to the regulation of quantitative traits (QTLs.

  10. Mapping of thermal injury in biologic tissues using quantitative pathologic techniques

    Science.gov (United States)

    Thomsen, Sharon L.

    1999-05-01

    Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.

  11. Quantitative EEG Brain Mapping In Psychotropic Drug Development, Drug Treatment Selection, and Monitoring.

    Science.gov (United States)

    Itil, Turan M.; Itil, Kurt Z.

    1995-05-01

    Quantification of standard electroencephalogram (EEG) by digital computers [computer-analyzed EEG (CEEG)] has transformed the subjective analog EEG into an objective scientific method. Until a few years ago, CEEG was only used to assist in the development of psychotropic drugs by means of the quantitative pharmaco EEG. Thanks to the computer revolution and the accompanying reductions in cost of quantification, CEEG can now also be applied in psychiatric practice. CEEG can assist the physician in confirming clinical diagnoses, selecting psychotropic drugs for treatment, and drug treatment monitoring. Advancements in communications technology allow physicians and researchers to reduce the costs of acquiring a high-technology CEEG brain mapping system by utilizing the more economical telephonic services.

  12. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

    2014-01-20

    Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

  13. Quantitative analysis of myocardial ischemia by technetium-99m sestamibi exercise scintigraphy. A new method for change rate mapping

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Shigeru; Kuwahara, Taishi; Tanada, Shuji [Ehime Univ., Shigenobu, Ehime (Japan). School of Medicine; Higashino, Hiroshi; Hamamoto, Ken

    1997-11-01

    In order to quantitatively assess the extent and severity of myocardial ischemia by Tc-99m sestamibi exercise myocardial scintigraphy, we developed a new method of change rate (CR) mapping and examined its efficiency. CR was calculated to divide the counts per pixel in the stress polar map by that in the rest polar map at each corresponding pixel. The CR map showed the CR values at each pixel. To correct the differences between the stress and rest images for the dose of Tc-99m sestamibi administered, the mean counts per pixel in the stress polar map and the rest map were adjusted to the same level. Regarding the regions in which the CR value was less than 1 as ischemia, we compared the abilities of the CR map and the polar map to detect coronary artery stenosis in 5 patients with angina pectoris. The sensitivity for coronary artery stenosis was 80% in the CR map, and 40% in the polar map. The specificity for both was 75%. We concluded that the CR map was effective in assessing the extent and severity of myocardial ischemia in Tc-99m sestamibi exercise myocardial scintigraphy. (author)

  14. Quantitative Trait Loci Mapping for Chlorophyll Fluorescence and Associated Traits in Wheat (Triticum aestivum)

    Institute of Scientific and Technical Information of China (English)

    De-Long Yang; Rui-Lian Jing; Xiao-Ping Chang; Wei Li

    2007-01-01

    Parameters of chlorophyll fluorescence kinetics (PCFKs) under drought stress condition are generally used to characterize instincts for dehydration tolerance in wheat (Triticum aestivum L.). Therefore, it is important to map quantitative trait loci (QTLs) for PCFKs in wheat genetic improvement for drought tolerance. A doubled haploid (DH)population with 150 lines, derived from a cross between two common wheat varieties, Hanxuan 10 and Lumai 14,was used to analyze the correlation between PCFKs and chlorophyll content (ChlC) and to map QTLs at the grainfilling stage under conditions of both rainfed (drought stress, DS) and well-watered (WW), respectively. QTLs for these traits were detected by QTLMapper version 1.0 based on the composite interval mapping method of the mixed-linear model. The results showed a very significant positive correlation between Fy, Fm, Fv/Fm and Fv/Fo.The correlation coefficients were generally higher under WW than under DS. Also, there was a significant or a highly significant positive correlation between Fv, Fm, Fv/Fm, Fv/Fo and ChlC. The correlation coefficients were higher in the DS group than the WW group. A total of 14 additive QTLs (nine QTLs detected under DS and five QTLs under WW)and 25 pairs of eplstatic QTLs (15 pairs detected under DS and 10 pairs under WW) for PCFKs were mapped on chromosomes 6A, 7A, 1B, 3B, 4D and 7D. The contributions of additive QTLs for PCFKs to phenotype variation were from 8.40% to 72.72%. Four additive QTLs (two QTLs detected under DS and WW apiece) controlling ChlC were mapped on chromosomes 1A, 5A and 7A. The contributions of these QTLs for ChlC to phenotype variation were from 7.27% to 11.68%. Several QTL clusters were detected on chromosomes 1B, 7A and 7D, but no shared chromosomal regions for them were identified under different water regimes, indicating that these QTLs performed different expression patterns under rainfed and well-watered conditions.

  15. Mapping Bone Mineral Density Obtained by Quantitative Computed Tomography to Bone Volume Fraction

    Science.gov (United States)

    Pennline, James A.; Mulugeta, Lealem

    2017-01-01

    Methods for relating or mapping estimates of volumetric Bone Mineral Density (vBMD) obtained by Quantitative Computed Tomography to Bone Volume Fraction (BVF) are outlined mathematically. The methods are based on definitions of bone properties, cited experimental studies and regression relations derived from them for trabecular bone in the proximal femur. Using an experimental range of values in the intertrochanteric region obtained from male and female human subjects, age 18 to 49, the BVF values calculated from four different methods were compared to the experimental average and numerical range. The BVF values computed from the conversion method used data from two sources. One source provided pre bed rest vBMD values in the intertrochanteric region from 24 bed rest subject who participated in a 70 day study. Another source contained preflight vBMD values from 18 astronauts who spent 4 to 6 months on the ISS. To aid the use of a mapping from BMD to BVF, the discussion includes how to formulate them for purpose of computational modeling. An application of the conversions would be used to aid in modeling of time varying changes in vBMD as it relates to changes in BVF via bone remodeling and/or modeling.

  16. A computational approach for functional mapping of quantitative trait loci that regulate thermal performance curves.

    Directory of Open Access Journals (Sweden)

    John Stephen Yap

    Full Text Available Whether and how thermal reaction norm is under genetic control is fundamental to understand the mechanistic basis of adaptation to novel thermal environments. However, the genetic study of thermal reaction norm is difficult because it is often expressed as a continuous function or curve. Here we derive a statistical model for dissecting thermal performance curves into individual quantitative trait loci (QTL with the aid of a genetic linkage map. The model is constructed within the maximum likelihood context and implemented with the EM algorithm. It integrates the biological principle of responses to temperature into a framework for genetic mapping through rigorous mathematical functions established to describe the pattern and shape of thermal reaction norms. The biological advantages of the model lie in the decomposition of the genetic causes for thermal reaction norm into its biologically interpretable modes, such as hotter-colder, faster-slower and generalist-specialist, as well as the formulation of a series of hypotheses at the interface between genetic actions/interactions and temperature-dependent sensitivity. The model is also meritorious in statistics because the precision of parameter estimation and power of QTLdetection can be increased by modeling the mean-covariance structure with a small set of parameters. The results from simulation studies suggest that the model displays favorable statistical properties and can be robust in practical genetic applications. The model provides a conceptual platform for testing many ecologically relevant hypotheses regarding organismic adaptation within the Eco-Devo paradigm.

  17. Streaking Artifact Reduction for Quantitative Susceptibility Mapping of Sources with Large Dynamic Range

    Science.gov (United States)

    Wei, Hongjiang; Dibb, Russell; Zhou, Yan; Sun, Yawen; Xu, Jianrong; Wang, Nian; Liu, Chunlei

    2015-01-01

    Quantitative susceptibility mapping (QSM) is a novel MRI technique for measuring tissue magnetic susceptibility in 3D. While there are numerous algorithms developed to solve this ill-posed inverse problem, estimating susceptibility maps with a wide range of values is still problematic. In cases such as large veins, contrast agent uptake, and intracranial hemorrhages, extreme susceptibility values in focal areas cause severe streaking artifacts. To enable the reduction of these artifacts while preserving subtle susceptibility contrast, a two-level QSM reconstruction algorithm (STAR-QSM) was developed in this study by tuning a regularization parameter to automatically reconstruct both large and small susceptibility values. Compared to current state-of-the-art QSM methods such as iLSQR, STAR-QSM significantly reduced streaking artifacts while preserving sharp boundaries for blood vessels of mouse brains in vivo and fine anatomical details of high resolution mouse brains ex vivo. Brain image data from patients with cerebral hematoma and multiple sclerosis further illustrated the superiority of this method in reducing streaking artifacts caused by large susceptibility sources while maintaining sharp anatomical details. STAR-QSM is implemented in STI Suite, a comprehensive shareware for susceptibility imaging and quantification. PMID:26313885

  18. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

    2015-10-01

    Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.

  19. A computational approach for functional mapping of quantitative trait loci that regulate thermal performance curves.

    Science.gov (United States)

    Yap, John Stephen; Wang, Chenguang; Wu, Rongling

    2007-06-20

    Whether and how thermal reaction norm is under genetic control is fundamental to understand the mechanistic basis of adaptation to novel thermal environments. However, the genetic study of thermal reaction norm is difficult because it is often expressed as a continuous function or curve. Here we derive a statistical model for dissecting thermal performance curves into individual quantitative trait loci (QTL) with the aid of a genetic linkage map. The model is constructed within the maximum likelihood context and implemented with the EM algorithm. It integrates the biological principle of responses to temperature into a framework for genetic mapping through rigorous mathematical functions established to describe the pattern and shape of thermal reaction norms. The biological advantages of the model lie in the decomposition of the genetic causes for thermal reaction norm into its biologically interpretable modes, such as hotter-colder, faster-slower and generalist-specialist, as well as the formulation of a series of hypotheses at the interface between genetic actions/interactions and temperature-dependent sensitivity. The model is also meritorious in statistics because the precision of parameter estimation and power of QTLdetection can be increased by modeling the mean-covariance structure with a small set of parameters. The results from simulation studies suggest that the model displays favorable statistical properties and can be robust in practical genetic applications. The model provides a conceptual platform for testing many ecologically relevant hypotheses regarding organismic adaptation within the Eco-Devo paradigm.

  20. Quantitative trait locus mapping for seed mineral concentrations in two Arabidopsis thaliana recombinant inbred populations.

    Science.gov (United States)

    Waters, Brian M; Grusak, Michael A

    2008-01-01

    Biofortification of foods, achieved by increasing the concentrations of minerals such as iron (Fe) and zinc (Zn), is a goal of plant scientists. Understanding genes that influence seed mineral concentration in a model plant such as Arabidopsis could help in the development of nutritionally enhanced crop cultivars. Quantitative trait locus (QTL) mapping for seed concentrations of calcium (Ca), copper (Cu), Fe, potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and Zn was performed using two recombinant inbred line (RIL) populations, Columbia (Col) x Landsberg erecta (Ler) and Cape Verde Islands (Cvi) x Ler, grown on multiple occasions. QTL mapping was also performed using data from silique hulls and the ratio of seed:hull mineral concentration of the Cvi x Ler population. Over 100 QTLs that affected seed mineral concentration were identified. Twenty-nine seed QTLs were found in more than one experiment, and several QTLs were found for both seed and hull mineral traits. A number of candidate genes affecting seed mineral concentration are discussed. These results indicate that A. thaliana is a suitable and convenient model for discovery of genes that affect seed mineral concentration. Some strong QTLs had no obvious candidate genes, offering the possibility of identifying unknown genes that affect mineral uptake and translocation to seeds.

  1. Mapping of quantitative trait loci for oil content in cottonseed kernel.

    Science.gov (United States)

    Alfred, Quampah; Liu, Hai Ying; Xu, Hai Ming; Li, Jin Rong; Wu, Jian Guo; Zhu, Shui Jin; Shi, Chun Hai

    2012-01-01

    Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of cottonseed oil among other vegetable oils. Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. In the current experiment, an IF(2) population of cottonseed kernels from the random crossing of 188 intraspecific recombinant inbred lines which were derived from the hybrid of two parents, HS46 and MARCABUCAG8US-1-88, were used to simultaneously locate QTLs for oil content in the embryo and maternal plant genomes. The four QTLs found to be associated with oil content in cottonseed were: qOC-18-1 on chromosome 18; qOC-LG-11 on linkage group 11; qOC-18-2 on chromosome 18; and qOC-22 on chromosome 22. At a high selection threshold of 0.05, there was strong evidence linking the QTLs above the oil content in cottonseed. Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects from the tetraploid maternal plant genome were found to be significant contributors to genetic variation in cottonseed oil content.

  2. Large-scale in silico mapping of complex quantitative traits in inbred mice.

    Directory of Open Access Journals (Sweden)

    Pengyuan Liu

    Full Text Available Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.

  3. Mapping of quantitative trait loci for oil content in cottonseed kernel

    Indian Academy of Sciences (India)

    Quampah Alfred; Hai Ying Liu; Hai Ming Xu; Jin Rong Li; Jian Guo Wu; Shui Jin Zhu; Chun Hai Shi

    2012-12-01

    Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of cottonseed oil among other vegetable oils. Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. In the current experiment, an IF2 population of cottonseed kernels from the random crossing of 188 intraspecific recombinant inbred lines which were derived from the hybrid of two parents, HS46 and MARCABUCAG8US-1-88, were used to simultaneously locate QTLs for oil content in the embryo and maternal plant genomes. The four QTLs found to be associated with oil content in cottonseed were: qOC-18-1 on chromosome 18; qOC-LG-11 on linkage group 11; qOC-18-2 on chromosome 18; and qOC-22 on chromosome 22. At a high selection threshold of 0.05, there was strong evidence linking the QTLs above the oil content in cottonseed. Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects from the tetraploid maternal plant genome were found to be significant contributors to genetic variation in cottonseed oil content.

  4. Susceptibility-weighted imaging and quantitative susceptibility mapping in the brain.

    Science.gov (United States)

    Liu, Chunlei; Li, Wei; Tong, Karen A; Yeom, Kristen W; Kuzminski, Samuel

    2015-07-01

    Susceptibility-weighted imaging (SWI) is a magnetic resonance imaging (MRI) technique that enhances image contrast by using the susceptibility differences between tissues. It is created by combining both magnitude and phase in the gradient echo data. SWI is sensitive to both paramagnetic and diamagnetic substances which generate different phase shift in MRI data. SWI images can be displayed as a minimum intensity projection that provides high resolution delineation of the cerebral venous architecture, a feature that is not available in other MRI techniques. As such, SWI has been widely applied to diagnose various venous abnormalities. SWI is especially sensitive to deoxygenated blood and intracranial mineral deposition and, for that reason, has been applied to image various pathologies including intracranial hemorrhage, traumatic brain injury, stroke, neoplasm, and multiple sclerosis. SWI, however, does not provide quantitative measures of magnetic susceptibility. This limitation is currently being addressed with the development of quantitative susceptibility mapping (QSM) and susceptibility tensor imaging (STI). While QSM treats susceptibility as isotropic, STI treats susceptibility as generally anisotropic characterized by a tensor quantity. This article reviews the basic principles of SWI, its clinical and research applications, the mechanisms governing brain susceptibility properties, and its practical implementation, with a focus on brain imaging.

  5. Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers.

    Science.gov (United States)

    Ragognetti, B N N; Stafuzza, N B; Silva, T B R; Chud, T C S; Grupioni, N V; Cruz, V A R; Peixoto, J O; Nones, K; Ledur, M C; Munari, D P

    2015-12-21

    Selection among broilers for performance traits is resulting in locomotion problems and bone disorders, once skeletal structure is not strong enough to support body weight in broilers with high growth rates. In this study, genetic parameters were estimated for body weight at 42 days of age (BW42), and tibia traits (length, width, and weight) in a population of broiler chickens. Quantitative trait loci (QTL) were identified for tibia traits to expand our knowledge of the genetic architecture of the broiler population. Genetic correlations ranged from 0.56 ± 0.18 (between tibia length and BW42) to 0.89 ± 0.06 (between tibia width and weight), suggesting that these traits are either controlled by pleiotropic genes or by genes that are in linkage disequilibrium. For QTL mapping, the genome was scanned with 127 microsatellites, representing a coverage of 2630 cM. Eight QTL were mapped on Gallus gallus chromosomes (GGA): GGA1, GGA4, GGA6, GGA13, and GGA24. The QTL regions for tibia length and weight were mapped on GGA1, between LEI0079 and MCW145 markers. The gene DACH1 is located in this region; this gene acts to form the apical ectodermal ridge, responsible for limb development. Body weight at 42 days of age was included in the model as a covariate for selection effect of bone traits. Two QTL were found for tibia weight on GGA2 and GGA4, and one for tibia width on GGA3. Information originating from these QTL will assist in the search for candidate genes for these bone traits in future studies.

  6. A Quantitative Visual Mapping and Visualization Approach for Deep Ocean Floor Research

    Science.gov (United States)

    Hansteen, T. H.; Kwasnitschka, T.

    2013-12-01

    Geological fieldwork on the sea floor is still impaired by our inability to resolve features on a sub-meter scale resolution in a quantifiable reference frame and over an area large enough to reveal the context of local observations. In order to overcome these issues, we have developed an integrated workflow of visual mapping techniques leading to georeferenced data sets which we examine using state-of-the-art visualization technology to recreate an effective working style of field geology. We demonstrate a microbathymetrical workflow, which is based on photogrammetric reconstruction of ROV imagery referenced to the acoustic vehicle track. The advantage over established acoustical systems lies in the true three-dimensionality of the data as opposed to the perspective projection from above produced by downward looking mapping methods. A full color texture mosaic derived from the imagery allows studies at resolutions beyond the resolved geometry (usually one order of magnitude below the image resolution) while color gives additional clues, which can only be partly resolved in acoustic backscatter. The creation of a three-dimensional model changes the working style from the temporal domain of a video recording back to the spatial domain of a map. We examine these datasets using a custom developed immersive virtual visualization environment. The ARENA (Artificial Research Environment for Networked Analysis) features a (lower) hemispherical screen at a diameter of six meters, accommodating up to four scientists at once thus providing the ability to browse data interactively among a group of researchers. This environment facilitates (1) the development of spatial understanding analogue to on-land outcrop studies, (2) quantitative observations of seafloor morphology and physical parameters of its deposits, (3) more effective formulation and communication of working hypotheses.

  7. Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Siwo Geoffrey

    2010-10-01

    Full Text Available Abstract Background Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration. Results Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle. Conclusions We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c, a Zinc finger transcription factor (PFL0465c both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c.

  8. Quantitative mapping of hemodynamics in the lung, brain, and dorsal window chamber-grown tumors using a novel, automated algorithm.

    Science.gov (United States)

    Fontanella, Andrew N; Schroeder, Thies; Hochman, Daryl W; Chen, Raymond E; Hanna, Gabi; Haglund, Michael M; Rajaram, Narasimhan; Frees, Amy E; Secomb, Timothy W; Palmer, Gregory M; Dewhirst, Mark W

    2013-11-01

    Hemodynamic properties of vascular beds are of great interest in a variety of clinical and laboratory settings. However, there presently exists no automated, accurate, technically simple method for generating blood velocity maps of complex microvessel networks. Here, we present a novel algorithm that addresses the problem of acquiring quantitative maps by applying pixel-by-pixel cross-correlation to video data. Temporal signals at every spatial coordinate are compared with signals at neighboring points, generating a series of correlation maps from which speed and direction are calculated. User-assisted definition of vessel geometries is not required, and sequential data are analyzed automatically, without user bias. Velocity measurements were validated against the dual-slit method and against in vitro capillary flow with known velocities. The algorithm was tested in three different biological models in order to demonstrate its versatility. The hemodynamic maps presented here demonstrate an accurate, quantitative method of analyzing dynamic vascular systems. © 2013 John Wiley & Sons Ltd.

  9. Autoradiographic visualization of CNS receptors for vasoactive intestinal peptide

    Energy Technology Data Exchange (ETDEWEB)

    Shaffer, M.M.; Moody, T.W.

    1986-03-01

    Receptors for VIP were characterized in the rat CNS. /sup 125/I-VIP bound with high affinity to rat brain slices. Binding was time dependent and specific. Pharmacology studies indicated that specific /sup 125/I-VIP binding was inhibited with high affinity by VIP and low affinity by secretin and PHI. Using in vitro autoradiographic techniques high grain densities were present in the dentate gyrus, pineal gland, supraoptic and suprachiasmatic nuclei, superficial gray layer of the superior colliculus and the area postrema. Moderate grain densities were present in the olfactory bulb and tubercle, cerebral cortex, nucleus accumbens, caudate putamen, interstitial nucleus of the stria terminalis, paraventricular thalamic nucleus, medial amygdaloid nucleus, subiculum and the medial geniculate nucleus. Grains were absent in the corpus callosum and controls treated with 1 microM unlabeled VIP. The discrete regional distribution of VIP receptors suggest that it may function as an important modulator of neural activity in the CNS.

  10. Statistical distributions of test statistics used for quantitative trait association mapping in structured populations

    Directory of Open Access Journals (Sweden)

    Teyssèdre Simon

    2012-11-01

    generalized in this work. The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate. The power of the quantitative transmission/disequilibrium test was low. In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.

  11. A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

    National Research Council Canada - National Science Library

    Raman, Harsh; Raman, Rosy; Kilian, Andrzej; Detering, Frank; Long, Yan; Edwards, David; Parkin, Isobel A P; Sharpe, Andrew G; Nelson, Matthew N; Larkan, Nick; Zou, Jun; Meng, Jinling; Aslam, M Naveed; Batley, Jacqueline; Cowling, Wallace A; Lydiate, Derek

    2013-01-01

    Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive...

  12. Autoradiographic and ultrastructural studies on the human fibro-atheromatous plaque

    Energy Technology Data Exchange (ETDEWEB)

    Villaschi, S.; Spagnoli, L.G. (Universita degli Studi, Rome (Italy). Istituto di Anatomia ed Istologia Patologica)

    1983-07-01

    Foam cells, either myogenic or macrophagic, are commonly detected in experimental and human fibro-atheromatous plaques. Their role in human atherosclerosis is not yet understood. This paper reports on a preliminary autoradiographic study combined with ultrastructural observations in the human fibro-atheromatous plaque. Most of the autoradiographic silver grains appeared on foam cells and monocytelike cells, thus suggesting a local proliferation of these cells.

  13. Regeneration of the vagus nerve after highly selective vagotomy, an autoradiographic study in the ferret stomach .

    OpenAIRE

    Al Muhtaseb, M. H. [محمد هاشم المحتسب; Abu-Khalaf, M.

    1995-01-01

    This study investigates the regeneration of the vagal nerve fibres after highly selective vagotomy in the ferret stomach by using the autoradiographic technique. Autoradiographic examination of the body of the stomach in the acute experimental animals has failed to show any labelled nerve fibres after highly selective vagotomy while the pylorus has shown many labelled nerve fibres . These observations indicate that the highly selective vagotomy has been performed properly and adequately. ...

  14. Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a (TM-1xHai 7124)xTM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.

  15. Mapping of quantitative trait loci associated with partial resistance to phytophthora sojae and flooding tolerance in soybean

    Science.gov (United States)

    Phytophthora root rot (PRR) caused by Phytophthora sojae Kaufm. & Gerd. and flooding can limit growth and productivity, of soybean [Glycine max (L.) Merr.], especially on poorly drained soils. The primary objective of this research project was to map quantitative trait loci (QTL) associated with f...

  16. Using multiple spectral feature analysis for quantitative pH mapping in a mining environment

    Science.gov (United States)

    Kopačková, Veronika

    2014-05-01

    The pH is one of the major chemical parameters affecting the results of remediation programs carried out at abandoned mines and dumps and one of the major parameters controlling heavy metal mobilization and speciation. This study is concerned with testing the feasibility of estimating surface pH on the basis of airborne hyperspectral (HS) data (HyMap). The work was carried on the Sokolov lignite mine, as it represents a site with extreme material heterogeneity and high pH gradients. First, a geochemical conceptual model of the site was defined. Pyrite, jarosite or lignite were the diagnostic minerals of very low pH (6.5). It was found that these minerals have absorption feature parameters which are common for both forms, individual minerals as well as parts of the mixtures, while the shift to longer wavelengths of the absorption maximum centered between 0.90 and 1.00 μm is the main parameter that allows differentiation among the ferric minerals. The multi range spectral feature fitting (MRSFF) technique was employed to map the defined end-members indicating certain pH ranges in the HS image datasets. This technique was found to be sensitive enough to assess differences in the desired spectral parameters (e.g., absorption shape, depth and indirectly maximum absorption wavelength position). Furthermore, the regression model using the fit images, the results of MRSFF, as inputs was constructed (R2 = 0.61, Rv2 = 0.76) to estimate the surface pH. This study represents one of the few approaches employing image spectroscopy for quantitative pH modeling in a mining environment and the achieved results demonstrate the potential application of hyperspectral remote sensing as an efficient method for environmental monitoring.

  17. Mapping Quantitative Trait Loci (QTL) for Resistance to Late Blight in Tomato.

    Science.gov (United States)

    Panthee, Dilip R; Piotrowski, Ann; Ibrahem, Ragy

    2017-07-22

    Late blight caused by Phytophthora infestans (Montagne, Bary) is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL) conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS). The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC) at Mills River, NC, and Mountain Research Staion (MRS) at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD) scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter's Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.

  18. Mapping Quantitative Trait Loci (QTL for Resistance to Late Blight in Tomato

    Directory of Open Access Journals (Sweden)

    Dilip R. Panthee

    2017-07-01

    Full Text Available Late blight caused by Phytophthora infestans (Montagne, Bary is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS. The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC at Mills River, NC, and Mountain Research Staion (MRS at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter’s Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.

  19. Quantitative mapping and statistical evaluation of fracture minerals in the granitic bedrock at Forsmark, Sweden

    Science.gov (United States)

    Löfgren, Martin; Sidborn, Magnus

    2016-10-01

    This article provides quantitative data on occurrences and amounts of fracture minerals that coat discrete fractures in granitic rock at the Forsmark site in Sweden. The data are useful for retardation modelling of radionuclide and other contaminants, and for groundwater composition calculations. In a unique campaign, 2071 open fractures in groundwater conducting rock have been mapped with respect to chlorite, calcite, and pyrite. In total 767 m of drill core has been studied from very shallow rock down to ~1000 m depth. The occurrences of fracture minerals, their thicknesses, and their fractions of surface coverage have been recorded for up to eight layers for each fracture. Detection limits are, for each layer, 0.1 mm for the thickness and 1 % for the surface coverage, except for pyrite crystals where surface coverages down to 0.01 % are detectable. The abundance of data has permitted statistical treatment, using parametric and non-parametric methods. Parametric fittings have been made to log-normal, truncated log-normal, and beta distributions. Chlorite, calcite, and pyrite were found in 57 %, 52 %, and 10 % of all mapped fractures, respectively. The fracture mineral thickness was 0.1 mm for calcite, 0.2 mm for chlorite, and 2 μm for pyrite, as averaged over the fracture surface area. For 50 % and 99 % of all fractures the total fracture coating thickness was less than 0.1 mm and 1 mm, respectively, which is important for diffusion resistance estimates. Average surface coverages were 18 % for calcite, 38 % for chlorite, and 0.5 % for pyrite. These data may be used for calculating the reaction capacity of flow paths.

  20. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus.

    Science.gov (United States)

    Tian, Meilin; Li, Yangping; Jing, Jing; Mu, Chuang; Du, Huixia; Dou, Jinzhuang; Mao, Junxia; Li, Xue; Jiao, Wenqian; Wang, Yangfan; Hu, Xiaoli; Wang, Shi; Wang, Ruijia; Bao, Zhenmin

    2015-10-06

    Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.

  1. Use of /sup 75/Se tracer and autoradiographic techniques in the study of schistosomiasis

    Energy Technology Data Exchange (ETDEWEB)

    Chandiwana, S.K. (New York State Veterinary Coll., Ithaca, NY (USA))

    1988-12-01

    The paper provides an overview of recent studies on the use of /sup 75/Se to tag larval schistosomes and to monitor their migration and distribution patterns in naive mice and those previously exposed to cercariae. The principles and techniques of radioassay and autoradiography in studying various aspects of /sup 75/Se-labelled larval schistosomes are described. The main shortcoming of radioassay in monitoring location and movement of labelled schistosomula is that some of the label dissociates from the schistosomula and accumulates in host tissues, notably the liver. Dissociated label is indistinguishable from schistosomula-bound label making monitoring of parasite migration extremely difficult. This difficulty is overcome by compressed tissue autoradiography where labelled schistosomula can be seen as reduced silver foci on an autoradiographic film, whereas dissociated label is too diffusely distributed to produce such reduced silver foci. Furthermore, using autoradiography, quantitative information on parasite migration in normal and immunized laboratory animals can be obtained that would be impossible using traditional recovery techniques. In addition to using /sup 75/Se tracer in migration studies, the radio-isotope has potential for elucidating various aspects of schistosome transmission ecology and snail population dynamics in natural waters. (author).

  2. Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain

    Science.gov (United States)

    Fang, Jinsheng; Bao, Lijun; Li, Xu; van Zijl, Peter C. M.; Chen, Zhong

    2017-08-01

    Background field removal is an important MR phase preprocessing step for quantitative susceptibility mapping (QSM). It separates the local field induced by tissue magnetic susceptibility sources from the background field generated by sources outside a region of interest, e.g. brain, such as air-tissue interface. In the vicinity of air-tissue boundary, e.g. skull and paranasal sinuses, where large susceptibility variations exist, present background field removal methods are usually insufficient and these regions often need to be excluded by brain mask erosion at the expense of losing information of local field and thus susceptibility measures in these regions. In this paper, we propose an extension to the variable-kernel sophisticated harmonic artifact reduction for phase data (V-SHARP) background field removal method using a region adaptive kernel (R-SHARP), in which a scalable spherical Gaussian kernel (SGK) is employed with its kernel radius and weights adjustable according to an energy ;functional; reflecting the magnitude of field variation. Such an energy functional is defined in terms of a contour and two fitting functions incorporating regularization terms, from which a curve evolution model in level set formation is derived for energy minimization. We utilize it to detect regions of with a large field gradient caused by strong susceptibility variation. In such regions, the SGK will have a small radius and high weight at the sphere center in a manner adaptive to the voxel energy of the field perturbation. Using the proposed method, the background field generated from external sources can be effectively removed to get a more accurate estimation of the local field and thus of the QSM dipole inversion to map local tissue susceptibility sources. Numerical simulation, phantom and in vivo human brain data demonstrate improved performance of R-SHARP compared to V-SHARP and RESHARP (regularization enabled SHARP) methods, even when the whole paranasal sinus regions

  3. Precise Temperature Mapping of GaN-Based LEDs by Quantitative Infrared Micro-Thermography

    Science.gov (United States)

    Chang, Ki Soo; Yang, Sun Choel; Kim, Jae-Young; Kook, Myung Ho; Ryu, Seon Young; Choi, Hae Young; Kim, Geon Hee

    2012-01-01

    A method of measuring the precise temperature distribution of GaN-based light-emitting diodes (LEDs) by quantitative infrared micro-thermography is reported. To reduce the calibration error, the same measuring conditions were used for both calibration and thermal imaging; calibration was conducted on a highly emissive black-painted area on a dummy sapphire wafer loaded near the LED wafer on a thermoelectric cooler mount. We used infrared thermal radiation images of the black-painted area on the dummy wafer and an unbiased LED wafer at two different temperatures to determine the factors that degrade the accuracy of temperature measurement, i.e., the non-uniform response of the instrument, superimposed offset radiation, reflected radiation, and emissivity map of the LED surface. By correcting these factors from the measured infrared thermal radiation images of biased LEDs, we determined a precise absolute temperature image. Consequently, we could observe from where the local self-heat emerges and how it distributes on the emitting area of the LEDs. The experimental results demonstrated that highly localized self-heating and a remarkable temperature gradient, which are detrimental to LED performance and reliability, arise near the p-contact edge of the LED surface at high injection levels owing to the current crowding effect. PMID:22666050

  4. Precise Temperature Mapping of GaN-Based LEDs by Quantitative Infrared Micro-Thermography

    Directory of Open Access Journals (Sweden)

    Geon Hee Kim

    2012-04-01

    Full Text Available A method of measuring the precise temperature distribution of GaN-based light-emitting diodes (LEDs by quantitative infrared micro-thermography is reported. To reduce the calibration error, the same measuring conditions were used for both calibration and thermal imaging; calibration was conducted on a highly emissive black-painted area on a dummy sapphire wafer loaded near the LED wafer on a thermoelectric cooler mount. We used infrared thermal radiation images of the black-painted area on the dummy wafer and an unbiased LED wafer at two different temperatures to determine the factors that degrade the accuracy of temperature measurement, i.e., the non-uniform response of the instrument, superimposed offset radiation, reflected radiation, and emissivity map of the LED surface. By correcting these factors from the measured infrared thermal radiation images of biased LEDs, we determined a precise absolute temperature image. Consequently, we could observe from where the local self-heat emerges and how it distributes on the emitting area of the LEDs. The experimental results demonstrated that highly localized self-heating and a remarkable temperature gradient, which are detrimental to LED performance and reliability, arise near the p-contact edge of the LED surface at high injection levels owing to the current crowding effect.

  5. Quantitative trait loci (QTL mapping for growth traits on bovine chromosome 14

    Directory of Open Access Journals (Sweden)

    Marcelo Miyata

    2007-03-01

    Full Text Available Quantitative trait loci (QTL mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. We analyzed the birth weight and weight at 60 days QTL segregating on bovine chromosome BTA14 in a F2 resource population using genotypes produced from seven microsatellite markers. Phenotypes were derived from 346 F2 progeny produced from crossing Bos indicus Gyr x Holstein Bos taurus F1 parents. Interval analysis to detect QTL for birth weight revealed the presence of a QTL (p < 0.05 at 1 centimorgan (cM from the centromere with an additive effect of 1.210 ± 0.438 kg. Interval analysis for weight at 60 days revealed the presence of a QTL (p < 0.05 at 0 cM from the centromere with an additive effect of 2.122 ± 0.735 kg. The region to which the QTL were assigned is described in the literature as responsible for some growth traits, milk yield, milk composition, fat deposition and has also been related to reproductive traits such as daughter pregnancy rate and ovulation rate. The effects of the QTL described on other traits were not investigated.

  6. Trace element mapping in Parkinsonian brain by quantitative ion beam microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Barapatre, Nirav, E-mail: barapatre@physik.uni-leipzig.d [Nukleare Festkoerperphysik, Universitaet Leipzig, Linnestr. 5, 04103 Leipzig (Germany); Morawski, Markus [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnalle 59, 04109 Leipzig (Germany); Butz, Tilman; Reinert, Tilo [Nukleare Festkoerperphysik, Universitaet Leipzig, Linnestr. 5, 04103 Leipzig (Germany)

    2010-06-15

    The role of iron in the pathogenesis of the Parkinson's disease (PD) is a current subject of research in Neurochemistry, since an abnormal increase in iron is reported in the substantia nigra (SN) of Parkinsonian patients. A severe loss of the cells containing dopamine in the SN in the PD has also drawn attention towards the function of a browny-black pigment called neuromelanin, which accumulates predominantly in these dopaminergic neurons. The neuromelanin has an ability to chelate metal ions, which, in free state, may cause considerable damage to cells by reacting with their lipid-rich membranes. However, it could also potentiate free radical production if it releases the bound metal ions. The highly sensitive and non-destructive micro-PIXE method suits best to quantify and map the trace elements in the SN. The accuracy in charge measurement for such microanalysis studies is of utmost importance for quantitative analysis. Since a Faraday cup is usually placed behind the thin biological sample to measure the charge, the primary and the secondary electrons, knocked out from the sample by traversing ion beam, hamper an exact charge determination. Hence, a new non-interceptive technique was developed for precise charge measurement and for continuous monitoring of beam current.

  7. Bayesian model choice and search strategies for mapping interacting quantitative trait Loci.

    Science.gov (United States)

    Yi, Nengjun; Xu, Shizhong; Allison, David B

    2003-01-01

    Most complex traits of animals, plants, and humans are influenced by multiple genetic and environmental factors. Interactions among multiple genes play fundamental roles in the genetic control and evolution of complex traits. Statistical modeling of interaction effects in quantitative trait loci (QTL) analysis must accommodate a very large number of potential genetic effects, which presents a major challenge to determining the genetic model with respect to the number of QTL, their positions, and their genetic effects. In this study, we use the methodology of Bayesian model and variable selection to develop strategies for identifying multiple QTL with complex epistatic patterns in experimental designs with two segregating genotypes. Specifically, we develop a reversible jump Markov chain Monte Carlo algorithm to determine the number of QTL and to select main and epistatic effects. With the proposed method, we can jointly infer the genetic model of a complex trait and the associated genetic parameters, including the number, positions, and main and epistatic effects of the identified QTL. Our method can map a large number of QTL with any combination of main and epistatic effects. Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated. PMID:14573494

  8. Trace element mapping in Parkinsonian brain by quantitative ion beam microscopy

    Science.gov (United States)

    Barapatre, Nirav; Morawski, Markus; Butz, Tilman; Reinert, Tilo

    2010-06-01

    The role of iron in the pathogenesis of the Parkinson's disease (PD) is a current subject of research in Neurochemistry, since an abnormal increase in iron is reported in the substantia nigra (SN) of Parkinsonian patients. A severe loss of the cells containing dopamine in the SN in the PD has also drawn attention towards the function of a browny-black pigment called neuromelanin, which accumulates predominantly in these dopaminergic neurons. The neuromelanin has an ability to chelate metal ions, which, in free state, may cause considerable damage to cells by reacting with their lipid-rich membranes. However, it could also potentiate free radical production if it releases the bound metal ions. The highly sensitive and non-destructive micro-PIXE method suits best to quantify and map the trace elements in the SN. The accuracy in charge measurement for such microanalysis studies is of utmost importance for quantitative analysis. Since a Faraday cup is usually placed behind the thin biological sample to measure the charge, the primary and the secondary electrons, knocked out from the sample by traversing ion beam, hamper an exact charge determination. Hence, a new non-interceptive technique was developed for precise charge measurement and for continuous monitoring of beam current.

  9. Mapping of quantitative trait loci (QTL) for production, resistance and tolerance traits in Salix. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics

    2004-05-01

    Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.

  10. Quantitative Susceptibility Mapping Reveals an Association between Brain Iron Load and Depression Severity

    Directory of Open Access Journals (Sweden)

    Shun Yao

    2017-08-01

    Full Text Available Previous studies have detected abnormal serum ferritin levels in patients with depression; however, the results have been inconsistent. This study used quantitative susceptibility mapping (QSM for the first time to examine brain iron concentration in depressed patients and evaluated whether it is related to severity. We included three groups of age- and gender-matched participants: 30 patients with mild-moderate depression (MD, 14 patients with major depression disorder (MDD and 20 control subjects. All participants underwent MR scans with a 3D gradient-echo sequence reconstructing for QSM and performed the 17-item Hamilton Depression Rating Scale (HDRS test. In MDD, the susceptibility value in the bilateral putamen was significantly increased compared with MD or control subjects. In addition, a significant difference was also observed in the left thalamus in MDD patients compared with controls. However, the susceptibility values did not differ between MD patients and controls. The susceptibility values positively correlated with the severity of depression as indicated by the HDRS scores. Our results provide evidence that brain iron deposition may be associated with depression and may even be a biomarker for investigating the pathophysiological mechanism of depression.

  11. Mapping of quantitative trait loci using the skew-normal distribution

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In standard interval mapping (IM) of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. When this assumption of normality is violated, the most commonly adopted strategy is to use the previous model after data transformation. However, an appropriate transformation may not exist or may be difficult to find. Also this approach can raise interpretation issues. An interesting alternative is to consider a skew-normal mixture model in standard IM, and the resulting method is here denoted as skew-normal IM. This flexible model that includes the usual symmetric normal distribution as a special case is important, allowing continuous variation from normality to non-normality. In this paper we briefly introduce the main peculiarities of the skew-normal distribution. The maximum likelihood estimates of parameters of the skew-normal distribution are obtained by the expectation-maximization (EM) algorithm. The proposed model is illustrated with real data from an intercross experiment that shows a significant departure from the normality assumption. The performance of the skew-normal IM is assessed via stochastic simulation. The results indicate that the skew-normal IM has higher power for QTL detection and better precision of QTL location as compared to standard IM and nonparametric IM.

  12. Quantitative evaluation of myocardial function by a volume-normalized map generated from relative blood flow

    Energy Technology Data Exchange (ETDEWEB)

    Fukami, Tadanori [Department of Bio-system Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992-8510 (Japan); Sato, Hidenori [Department of Bio-system Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992-8510 (Japan); Wu, Jin [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Lwin, Thet-Thet- [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Yuasa, Tetsuya [Department of Bio-system Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992-8510 (Japan); Kawano, Satoru [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Iida, Keiji [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Akatsuka, Takao [Department of Bio-system Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992-8510 (Japan); Hontani, Hidekata [Department of Computer Science and Engineering, Nagoya Institute of Technology, Aichi 466-8555 (Japan); Takeda, Tohoru [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Tamura, Masao [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan); Yokota, Hiroshi [Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575 (Japan)

    2007-07-21

    Our study aimed to quantitatively evaluate blood flow in the left ventricle (LV) of apical hypertrophic cardiomyopathy (APH) by combining wall thickness obtained from cardiac magnetic resonance imaging (MRI) and myocardial perfusion from single-photon emission computed tomography (SPECT). In this study, we considered paired MRI and myocardial perfusion SPECT from ten patients with APH and ten normals. Myocardial walls were detected using a level set method, and blood flow per unit myocardial volume was calculated using 3D surface-based registration between the MRI and SPECT images. We defined relative blood flow based on the maximum in the whole myocardial region. Accuracies of wall detection and registration were around 2.50 mm and 2.95 mm, respectively. We finally created a bull's-eye map to evaluate wall thickness, blood flow (cardiac perfusion) and blood flow per unit myocardial volume. In patients with APH, their wall thicknesses were over 10 mm. Decreased blood flow per unit myocardial volume was detected in the cardiac apex by calculation using wall thickness from MRI and blood flow from SPECT. The relative unit blood flow of the APH group was 1/7 times that of the normals in the apex. This normalization by myocardial volume distinguishes cases of APH whose SPECT images resemble the distributions of normal cases.

  13. Towards quantitative molecular mapping of cells by Raman microscopy: using AFM for decoupling molecular concentration and cell topography.

    Science.gov (United States)

    Boitor, Radu; Sinjab, Faris; Strohbuecker, Stephanie; Sottile, Virginie; Notingher, Ioan

    2016-06-23

    Raman micro-spectroscopy (RMS) is a non-invasive technique for imaging live cells in vitro. However, obtaining quantitative molecular information from Raman spectra is difficult because the intensity of a Raman band is proportional to the number of molecules in the sampled volume, which depends on the local molecular concentration and the thickness of the cell. In order to understand these effects, we combined RMS with atomic force microscopy (AFM), a technique that can measure accurately the thickness profile of the cells. Solution-based calibration models for RNA and albumin were developed to create quantitative maps of RNA and proteins in individual fixed cells. The maps were built by applying the solution-based calibration models, based on partial least squares fitting (PLS), on raster-scan Raman maps, after accounting for the local cell height obtained from the AFM. We found that concentrations of RNA in the cytoplasm of mouse neuroprogenitor stem cells (NSCs) were as high as 25 ± 6 mg ml(-1), while proteins were distributed more uniformly and reached concentrations as high as ∼50 ± 12 mg ml(-1). The combined AFM-Raman datasets from fixed cells were also used to investigate potential improvements for normalization of Raman spectral maps. For all Raman maps of fixed cells (n = 10), we found a linear relationship between the scores corresponding to the first component (PC1) and the cell height profile obtained by AFM. We used PC1 scores to reconstruct the relative height profiles of independent cells (n = 10), and obtained correlation coefficients with AFM maps higher than 0.99. Using this normalization method, qualitative maps of RNA and protein were used to obtain concentrations for live NSCs. While this study demonstrates the potential of using AFM and RMS for measuring concentration maps for individual NSCs in vitro, further studies are required to establish the robustness of the normalization method based on principal component analysis when comparing

  14. A composite method for mapping quantitative trait loci without interference of female achiasmatic and gender effects in silkworm, Bombyx mori.

    Science.gov (United States)

    Li, C; Zuo, W; Tong, X; Hu, H; Qiao, L; Song, J; Xiong, G; Gao, R; Dai, F; Lu, C

    2015-08-01

    The silkworm, Bombyx mori, is an economically important insect that was domesticated more than 5000 years ago. Its major economic traits focused on by breeders are quantitative traits, and an accurate and efficient QTL mapping method is necessary to explore their genetic architecture. However, current widely used QTL mapping models are not well suited for silkworm because they ignore female achiasmate and gender effects. In this study, we propose a composite method combining rational population selection and special mapping methods to map QTL in silkworm. By determining QTL for cocoon shell weight (CSW), we demonstrated the effectiveness of this method. In the CSW mapping process, only 56 markers were used and five loci or chromosomes were detected, more than in previous studies. Additionally, loci on chromosomes 1 and 11 dominated and accounted for 35.10% and 15.03% of the phenotypic variance respectively. Unlike previous studies, epistasis was detected between loci on chromosomes 11 and 22. These mapping results demonstrate the power and convenience of this method for QTL mapping in silkworm, and this method may inspire the development of similar approaches for other species with special genetic characteristics.

  15. Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross.

    Science.gov (United States)

    Zhang, Luyan; Li, Huihui; Ding, Junqiang; Wu, Jianyu; Wang, Jiankang

    2015-12-01

    In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.

  16. The quantitative evaluation of the Clinical and Translational Science Awards (CTSA) program based on science mapping and scientometric analysis.

    Science.gov (United States)

    Zhang, Yin; Wang, Lei; Diao, Tianxi

    2013-12-01

    The Clinical and Translational Science Awards (CTSA) program is one of the most important initiatives in translational medical funding. The quantitative evaluation of the efficiency and performance of the CTSA program has a significant referential meaning for the decision making of global translational medical funding. Using science mapping and scientometric analytic tools, this study quantitatively analyzed the scientific articles funded by the CTSA program. The results of the study showed that the quantitative productivities of the CTSA program had a stable increase since 2008. In addition, the emerging trends of the research funded by the CTSA program covered clinical and basic medical research fields. The academic benefits from the CTSA program were assisting its members to build a robust academic home for the Clinical and Translational Science and to attract other financial support. This study provided a quantitative evaluation of the CTSA program based on science mapping and scientometric analysis. Further research is required to compare and optimize other quantitative methods and to integrate various research results. © 2013 Wiley Periodicals, Inc.

  17. Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens.

    Science.gov (United States)

    Aronova, M A; Kim, Y C; Pivovarova, N B; Andrews, S B; Leapman, R D

    2009-02-01

    Although electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) provides high sensitivity for measuring the important element, calcium, in biological specimens, the technique has been difficult to apply routinely, because of long acquisition times required. Here we describe a refinement of the complementary analytical technique of energy-filtered transmission electron microscopy (EFTEM), which enables rapid imaging of large cellular regions and measurement of calcium concentrations approaching physiological levels. Extraction of precise quantitative information is possible by averaging large numbers of pixels that are contained in organelles of interest. We employ a modified two-window approach in which the behavior of the background signal in the EELS spectrum can be modeled as a function of specimen thickness t expressed in terms of the inelastic mean free path lambda. By acquiring pairs of images, one above and one below the Ca L(2,3) edge, together with zero-loss and unfiltered images, which are used to determine a relative thickness (t/lambda) map, it is possible to correct the Ca L(2,3) signal for plural scattering. We have evaluated the detection limits of this technique by considering several sources of systematic errors and applied this method to determine mitochondrial total calcium concentrations in freeze-dried cryosections of rapidly frozen stimulated neurons. By analyzing 0.1 microm2 areas of specimen regions that do not contain calcium, it was found that the standard deviation in the measurement of Ca concentrations was about 20 mmol/kg dry weight, corresponding to a Ca:C atomic fraction of approximately 2 x 10(-4). Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data.

  18. Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens

    Energy Technology Data Exchange (ETDEWEB)

    Aronova, M.A. [Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bldg. 13, Rm. 3N17, 9000 Rockville Pike, Bethesda, MD 20892 (United States); Kim, Y.C. [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 (United States); Pivovarova, N.B.; Andrews, S.B. [Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States); Leapman, R.D. [Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bldg. 13, Rm. 3N17, 9000 Rockville Pike, Bethesda, MD 20892 (United States)], E-mail: leapmanr@mail.nih.gov

    2009-02-15

    Although electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) provides high sensitivity for measuring the important element, calcium, in biological specimens, the technique has been difficult to apply routinely, because of long acquisition times required. Here we describe a refinement of the complementary analytical technique of energy-filtered transmission electron microscopy (EFTEM), which enables rapid imaging of large cellular regions and measurement of calcium concentrations approaching physiological levels. Extraction of precise quantitative information is possible by averaging large numbers of pixels that are contained in organelles of interest. We employ a modified two-window approach in which the behavior of the background signal in the EELS spectrum can be modeled as a function of specimen thickness t expressed in terms of the inelastic mean free path {lambda}. By acquiring pairs of images, one above and one below the Ca L{sub 2,3} edge, together with zero-loss and unfiltered images, which are used to determine a relative thickness (t/{lambda}) map, it is possible to correct the Ca L{sub 2,3} signal for plural scattering. We have evaluated the detection limits of this technique by considering several sources of systematic errors and applied this method to determine mitochondrial total calcium concentrations in freeze-dried cryosections of rapidly frozen stimulated neurons. By analyzing 0.1 {mu}m{sup 2} areas of specimen regions that do not contain calcium, it was found that the standard deviation in the measurement of Ca concentrations was about 20 mmol/kg dry weight, corresponding to a Ca:C atomic fraction of approximately 2x10{sup -4}. Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data.

  19. Analysis of training sample selection strategies for regression-based quantitative landslide susceptibility mapping methods

    Science.gov (United States)

    Erener, Arzu; Sivas, A. Abdullah; Selcuk-Kestel, A. Sevtap; Düzgün, H. Sebnem

    2017-07-01

    All of the quantitative landslide susceptibility mapping (QLSM) methods requires two basic data types, namely, landslide inventory and factors that influence landslide occurrence (landslide influencing factors, LIF). Depending on type of landslides, nature of triggers and LIF, accuracy of the QLSM methods differs. Moreover, how to balance the number of 0 (nonoccurrence) and 1 (occurrence) in the training set obtained from the landslide inventory and how to select which one of the 1's and 0's to be included in QLSM models play critical role in the accuracy of the QLSM. Although performance of various QLSM methods is largely investigated in the literature, the challenge of training set construction is not adequately investigated for the QLSM methods. In order to tackle this challenge, in this study three different training set selection strategies along with the original data set is used for testing the performance of three different regression methods namely Logistic Regression (LR), Bayesian Logistic Regression (BLR) and Fuzzy Logistic Regression (FLR). The first sampling strategy is proportional random sampling (PRS), which takes into account a weighted selection of landslide occurrences in the sample set. The second method, namely non-selective nearby sampling (NNS), includes randomly selected sites and their surrounding neighboring points at certain preselected distances to include the impact of clustering. Selective nearby sampling (SNS) is the third method, which concentrates on the group of 1's and their surrounding neighborhood. A randomly selected group of landslide sites and their neighborhood are considered in the analyses similar to NNS parameters. It is found that LR-PRS, FLR-PRS and BLR-Whole Data set-ups, with order, yield the best fits among the other alternatives. The results indicate that in QLSM based on regression models, avoidance of spatial correlation in the data set is critical for the model's performance.

  20. Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle.

    Science.gov (United States)

    Kelly, Scott A; Nehrenberg, Derrick L; Hua, Kunjie; Garland, Theodore; Pomp, Daniel

    2014-08-15

    Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to voluntary exercise, body composition, and changes in body composition as a result of exercise. Using brain tissue in a subset of the G4 (n = 244), we have also previously reported expression QTL (eQTL) colocalizing with the QTL for the higher-level phenotypes. Here, we examined the transcriptional landscape of hind limb muscle tissue via global mRNA expression profiles. Correlations revealed an ∼1,168% increase in significant relationships between muscle transcript expression levels and the same exercise and body composition phenotypes examined previously in the brain. The exercise trait most often significantly correlated with gene expression in the brain was running duration while in the muscle it was maximum running speed. This difference may indicate that time spent engaging in exercise behavior may be more influenced by central (neurobiological) mechanisms, while intensity of exercise may be largely controlled by peripheral mechanisms. Additionally, we used subsets of cis-acting eQTL, colocalizing with QTL, to identify candidate genes based on both positional and functional evidence. We discuss three plausible candidate genes (Insig2, Prcp, Sparc) and their potential regulatory role.

  1. Quantitative Susceptibility Mapping Suggests Altered Brain Iron in Premanifest Huntington Disease.

    Science.gov (United States)

    van Bergen, J M G; Hua, J; Unschuld, P G; Lim, I A L; Jones, C K; Margolis, R L; Ross, C A; van Zijl, P C M; Li, X

    2016-05-01

    In patients with premanifest (nonsymptomatic) and advanced Huntington disease, changes in brain iron levels in the basal ganglia have been previously reported, especially in the striatum. Quantitative susceptibility mapping by using MR phase imaging allows in vivo measurements of tissue magnetic susceptibility, which has been shown to correlate well with iron levels in brain gray matter and is believed to be more specific than other imaging-based iron measures. The purpose of this study was to investigate the use of magnetic susceptibility as a biomarker of disease progression. Fifteen subjects with premanifest Huntington disease and 16 age-matched healthy controls were scanned at 7T. Magnetic susceptibility, effective relaxation, and tissue volume in deep gray matter structures were quantified and compared with genetic and clinical measures. Subjects with premanifest Huntington disease showed significantly higher susceptibility values in the caudate nucleus, putamen, and globus pallidus, indicating increased iron levels in these structures. Significant decreases in magnetic susceptibility were found in the substantia nigra and hippocampus. In addition, significant volume loss (atrophy) and an increase effective relaxation were observed in the caudate nucleus and putamen. Susceptibility values in the caudate nucleus and putamen were found to be inversely correlated with structure volumes and directly correlated with the genetic burdens, represented by cytosine-adenine-guanine repeat age-product-scaled scores. The significant magnetic susceptibility differences between subjects with premanifest Huntington disease and controls and their correlation with genetic burden scores indicate the potential use of magnetic susceptibility as a biomarker of disease progression in premanifest Huntington disease. © 2016 by American Journal of Neuroradiology.

  2. Atomic Force Microscopy of Red-Light Photoreceptors Using PeakForce Quantitative Nanomechanical Property Mapping

    Science.gov (United States)

    Kroeger, Marie E.; Sorenson, Blaire A.; Thomas, J. Santoro; Stojković, Emina A.; Tsonchev, Stefan; Nicholson, Kenneth T.

    2014-01-01

    Atomic force microscopy (AFM) uses a pyramidal tip attached to a cantilever to probe the force response of a surface. The deflections of the tip can be measured to ~10 pN by a laser and sectored detector, which can be converted to image topography. Amplitude modulation or “tapping mode” AFM involves the probe making intermittent contact with the surface while oscillating at its resonant frequency to produce an image. Used in conjunction with a fluid cell, tapping-mode AFM enables the imaging of biological macromolecules such as proteins in physiologically relevant conditions. Tapping-mode AFM requires manual tuning of the probe and frequent adjustments of a multitude of scanning parameters which can be challenging for inexperienced users. To obtain high-quality images, these adjustments are the most time consuming. PeakForce Quantitative Nanomechanical Property Mapping (PF-QNM) produces an image by measuring a force response curve for every point of contact with the sample. With ScanAsyst software, PF-QNM can be automated. This software adjusts the set-point, drive frequency, scan rate, gains, and other important scanning parameters automatically for a given sample. Not only does this process protect both fragile probes and samples, it significantly reduces the time required to obtain high resolution images. PF-QNM is compatible for AFM imaging in fluid; therefore, it has extensive application for imaging biologically relevant materials. The method presented in this paper describes the application of PF-QNM to obtain images of a bacterial red-light photoreceptor, RpBphP3 (P3), from photosynthetic R. palustris in its light-adapted state. Using this method, individual protein dimers of P3 and aggregates of dimers have been observed on a mica surface in the presence of an imaging buffer. With appropriate adjustments to surface and/or solution concentration, this method may be generally applied to other biologically relevant macromolecules and soft materials. PMID

  3. Taking stock of four decades of quantitative research on stakeholder participation and evaluation use: a systematic map.

    Science.gov (United States)

    Daigneault, Pierre-Marc

    2014-08-01

    Stakeholder participation and evaluation use have attracted a lot of attention from practitioners, theorists and researchers. A common hypothesis is that participation is positively associated with evaluation use. Whereas the number of empirical studies conducted on this topic is impressive, quantitative research has held a minority position within this scientific production. This study mobilizes systematic review methods to 'map' the empirical literature that has quantitatively studied participation and use. The goal is to take stock and assess the strength of evidence of this literature (but not to synthesize the findings) and, based on this assessment, to provide directions for future research.

  4. Quantitative T1 and T2 mapping in recurrent glioblastomas under bevacizumab: earlier detection of tumor progression compared to conventional MRI

    Energy Technology Data Exchange (ETDEWEB)

    Lescher, Stephanie; Jurcoane, Alina; Veit, Andreas [Hospital of Goethe University, Institute of Neuroradiology, Frankfurt am Main (Germany); Baehr, Oliver [Hospital of Goethe University, Department of Neurology, Dr. Senckenberg Institute of Neurooncology, Frankfurt am Main (Germany); Deichmann, Ralf [Brain Imaging Center, Center for Imaging in Neuroscience, Frankfurt am Main (Germany); Hattingen, Elke [Hospital of Goethe University, Institute of Neuroradiology, Frankfurt am Main (Germany); Hospital of University Bonn, Instiute of Neuroradiology, Bonn (Germany)

    2014-10-07

    Treatment with the humanized anti-vascular endothelial growth factor (VEGF) antibody bevacizumab in glioblastoma patients suppresses contrast enhancement via the reduction of vascular permeability, which does not necessarily indicate real reduction of tumor cell mass. Therefore, other imaging criteria are needed to recognize tumor growth under bevacizumab more reliably. It is still unknown, whether quantitative T1 mapping is useful to monitor the effects of anti-angiogenic therapy or to indicate a tumor progression earlier and more reliable compared to conventional magnetic resonance imaging (MRI) sequences. This raised the question whether quantitative T1 mapping is more suitable to monitor treatment effects of bevacizumab. Conventional and quantitative MRI was performed on six consecutive patients with recurrent glioblastoma before treatment with bevacizumab and every 8 weeks thereafter until further tumor progression. Quantitative T1 maps before and after intravenous application of contrast agent and quantitative T2 maps were performed to calculate serial differential maps and subtraction maps from one time point, subtracting contrast-enhanced T1 maps from non-contrast T1 maps. In five illustrative cases, tumor progression was documented earlier in differential T1 relaxation time (DiffT1) and T2 relaxation time (DiffT2) maps before changes in the conventional MRI studies were obvious. Four patients showed previous prolongation of T1 relaxation time in the DiffT1 maps, suggesting tumor progression, and subtraction maps revealed faint contrast enhancement matching with the areas of T1 prolongation. Our results emphasize that quantitative relaxation time mapping could be a promising method for tumor monitoring in glioblastoma patients under anti-angiogenic therapy. Quantitative T1 mapping seems to detect enhancing tumor earlier than conventional contrast-enhanced T1-weighted images. (orig.)

  5. Tissue fixation and autoradiographic negative chemography in rat oral epithelium

    Energy Technology Data Exchange (ETDEWEB)

    Prime, S.S.; MacDonald, D.G. (Glasgow Dental Hospital (UK))

    1983-01-01

    The effect of routine methods of tissue fixation on autoradiographic negative chemography was investigated in adult rat palatal and tongue epithelia following the incorporation of /sup 3/H thymidine in vivo. Tissues fixed in formalin or Bouin's without acetic acid demonstrated more negative chemography than those fixed in Bouin's fluid, formol-acetic-methanol or Carnoy's solutions. These findings were associated with the lowest silver grain counts per nucleus in the formalin fixed tissues, low grain counts in tissues fixed in Bouin's without acetic acid, but the addition of acetic acid to make complete Bouin's fluid gave results similar to those following fixation with Carnoy's solution. The highest silver grain counts were obtained with tissues fixed in formol-acetic-methanol. The relationship between negative chemography and the labelling indices of tissues was unclear except where the negative chemographic effects were severe. Formalin fixed tissues showed the maximum negative chemographic effects and the lowest labelling indices. Carnoy's solution appeared to be the fixative of choice for cell kinetic studies of oral epithelium.

  6. PETROMAP: MS-DOS software package for quantitative processing of X-ray maps of zoned minerals

    Science.gov (United States)

    Cossio, Roberto; Borghi, Alessandro

    1998-10-01

    This paper shows an application of energy dispersive spectrometry (EDS) for digital acquisition of multi-element X-ray compositional maps of minerals in polished thin sections. A square matrix of n EDS spectra with known X, Y coordinates is collected, converted and exported to a personal computer. Each spectrum of the matrix is processed and the apparent concentration of each analyzed element is calculated by means of PETROMAP, a program written in Quick-Basic which applies a quantitative ZAF/FLS correction. The results of processing are comparable to the conventional quantitative microprobe analyses, with similar counting statistics. The output is a numerical matrix, compatible with the most popular graphic and spreadsheet programs from which it is possible to produce two-dimensional wt% oxide, mole fractions and mineral end-members pseudocolored or black/white maps. The procedure has been tested using a metamorphic garnet of the medium-grade Stilo unit (Calabrian Arc, Southern Italy).

  7. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Directory of Open Access Journals (Sweden)

    Melody K Morris

    2011-03-01

    Full Text Available Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL, converts a prior knowledge network (obtained from literature or interactome databases into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a generating experimentally testable biological hypotheses concerning pathway crosstalk, (b establishing capability for quantitative prediction of protein activity, and (c prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  8. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Science.gov (United States)

    Morris, Melody K; Saez-Rodriguez, Julio; Clarke, David C; Sorger, Peter K; Lauffenburger, Douglas A

    2011-03-01

    Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL), converts a prior knowledge network (obtained from literature or interactome databases) into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a) generating experimentally testable biological hypotheses concerning pathway crosstalk, (b) establishing capability for quantitative prediction of protein activity, and (c) prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  9. [Quantitative topographic characterization of the myoelectric activity distribution of the masseter muscle: mapping of spectral EMG parameters].

    Science.gov (United States)

    Scholle, H C; Schumann, N P; Anders, C; Mey, E

    1992-09-01

    A new method for quantitative characterization of myoelectrical masseter activity distribution by mapping of spectral EMG-parameters is described. The surface electromyograms of M. masseter were monopolarly recorded (16 channels). On the basis of registered EMG intervals (512 ms) the spectral EMG power of several frequency bands was calculated (Fast Fourier Transformation). The spectral EMG parameters between the 16 electrode positions were estimated by linear interpolation (4-nearest neighbours algorithm). Afterwards the spectral EMG parameters were fitted in a grey-tone or colour scale with 10 intervals. The so obtained EMG activity maps ("EMG-Maps") permit a quantitative-topographic characterization of myoelectrical masseter activity during different functional load procedures. The frequency range which is to consider in masseter surface-EMG investigations encloses frequencies between 15 and 500 Hz. The topography of EMG activation pattern of M. masseter is only described in a comprehensive manner when the electrode array consists of 16 electrodes and more. During defined motor tasks like clenching with controlled forces the reproducibility of EMG-Maps which respect to the topography of EMG activity pattern is very high. The absolute values of spectral EMG power as well as power changes of selected band ranges during clenching correlate to the extent of chewing forces.

  10. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Reppert, Mike [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); Tokmakoff, Andrei, E-mail: tokmakoff@uchicago.edu [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States)

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  11. Mapping of quantitative trait loci affecting quality and production traits in egg layers

    NARCIS (Netherlands)

    Tuiskula-Haavisto, M.; Honkatukia, M.; Vilkki, J.; Koning, de D.J.; Schulman, N.F.; Maki-Tanila, A.

    2002-01-01

    A mapping population segregating for egg quality traits was created by a line cross between two egg layer lines and screened by a genome scan. The F2 generation consisted of 307 hens, which were scored for egg quality and production traits. The mapping population was genotyped for 99 microsatellite

  12. Comparison and quantitative verification of mapping algorithms for whole genome bisulfite sequencing

    Science.gov (United States)

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitat...

  13. High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Stam, Piet

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data, whi

  14. Autoradiographic localization of specific [3H]dexamethasone binding in fetal lung.

    Science.gov (United States)

    Beer, D G; Butley, M S; Cunha, G R; Malkinson, A M

    1984-10-01

    The cellular and subcellular localization of specific [3H]dexamethasone binding was examined in fetal mouse lung at various stages of development and in human fetal lung at 8 weeks of gestation using a rapid in vitro steroid incubation technique followed by thaw-mount autoradiography. Competition studies with unlabeled steroids demonstrate the specificity of [3H]dexamethasone labeling, and indicate that fetal lung mesenchyme is a primary glucocorticoid target during lung development. Quantitative binding studies, involving incubation of intact tissue with competing ligand and subsequent subcellular fractionation, show this to be specific, nuclear binding characteristic of glucocorticoid receptors. Autoradiographs of [3H]dexamethasone binding in lung tissue at early stages of development demonstrate that the mesenchyme directly adjacent to the more proximal portions of the bronchiolar network is heavily labeled. In contrast, the epithelium which will later differentiate into bronchi and bronchioles, is relatively unlabeled. Distal portions of the growing epithelium, destined to become alveolar ducts and alveoli, do show nuclear localization of [3H]dexamethasone. Because of the known importance of the mesenchyme in controlling lung development and the ability of glucocorticoids to stimulate lung development, these results suggest that many of the growth-promoting effects of glucocorticoids may be mediated through the mesenchyme. In addition, by utilizing a technique which allows the simultaneous examination of extracellular matrix components and [3H]dexamethasone binding, a relationship is observed between extensive mesenchymal [3H]dexamethasone binding and extensive extracellular matrix accumulation. Since glucocorticoids stimulate the synthesis of many extracellular matrix components, these results suggest a role for these hormones in affecting mesenchymal-epithelial interactions during lung morphogenesis.

  15. Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.

    Science.gov (United States)

    Assunção, Ana G L; Pieper, Bjorn; Vromans, Jaap; Lindhout, Pim; Aarts, Mark G M; Schat, Henk

    2006-01-01

    Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL.

  16. Quantitative assessment of errors in monitoring landcover changes by comparison of maps

    Directory of Open Access Journals (Sweden)

    Jean Francois Mas

    2012-02-01

    Full Text Available Many studies aimed at assessing land-cover changes are based upon the comparison of maps elaborated in different dates. This comparison allows the calculation of change rates as well as to generate more detailed data such as the transition matrix and the change map. In this study, we evaluated the errors incurred when comparing maps elaborated at different scales, obtained through independent digitalisation processes, elaborated using different classification schemes or when the maps were elaborated with inputs from different dates. Errors derived from the difference of scale or from the map-digitalisation processes led to false changes with a similar or greater scale to that of true changes. The comparison of maps based on different classification schemes invalidated the results of the comparison. By contrast, the different approaches used to tackle the issue of maps with multiple dates produced similar results. The paper discusses some methods aimed at reducing these problems and evaluating the reliability of multi-temporal databases.

  17. 7 Tesla quantitative hip MRI: T1, T2 and T2* mapping of hip cartilage in healthy volunteers

    Energy Technology Data Exchange (ETDEWEB)

    Lazik, Andrea; Theysohn, Jens M.; Geis, Christina [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Johst, Soeren; Kraff, Oliver [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Ladd, Mark E. [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); German Cancer Research Center (DKFZ), Medical Physics in Radiology, Heidelberg (Germany); Quick, Harald H. [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital Essen, High Field and Hybrid MR Imaging, Essen (Germany)

    2016-05-15

    To evaluate the technical feasibility and applicability of quantitative MR techniques (delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T2 mapping, T2* mapping) at 7 T MRI for assessing hip cartilage. Hips of 11 healthy volunteers were examined at 7 T MRI with an 8-channel radiofrequency transmit/receive body coil using multi-echo sequences for T2 and T2* mapping and a dual flip angle gradient-echo sequence before (T1{sub 0}) and after intravenous contrast agent administration (T1{sub Gd}; 0.2 mmol/kg Gd-DTPA{sup 2-} followed by 0.5 h of walking and 0.5 h of rest) for dGEMRIC. Relaxation times of cartilage were measured manually in 10 regions of interest. Pearson's correlations between R1{sub delta} = 1/T1{sub Gd} - 1/T1{sub 0} and T1{sub Gd} and between T2 and T2* were calculated. Image quality and the delineation of acetabular and femoral cartilage in the relaxation time maps were evaluated using discrete rating scales. High correlations were found between R1{sub delta} and T1{sub Gd} and between T2 and T2* relaxation times (all p < 0.01). All techniques delivered diagnostic image quality, with best delineation of femoral and acetabular cartilage in the T2* maps (mean 3.2 out of a maximum of 4 points). T1, T2 and T2* mapping of hip cartilage with diagnostic image quality is feasible at 7 T. To perform dGEMRIC at 7 T, pre-contrast T1 mapping can be omitted. (orig.)

  18. Simultaneous Quantitative MRI Mapping of T1, T2* and Magnetic Susceptibility with Multi-Echo MP2RAGE

    Science.gov (United States)

    Kober, Tobias; Möller, Harald E.; Schäfer, Andreas

    2017-01-01

    The knowledge of relaxation times is essential for understanding the biophysical mechanisms underlying contrast in magnetic resonance imaging. Quantitative experiments, while offering major advantages in terms of reproducibility, may benefit from simultaneous acquisitions. In this work, we demonstrate the possibility of simultaneously recording relaxation-time and susceptibility maps with a prototype Multi-Echo (ME) Magnetization-Prepared 2 RApid Gradient Echoes (MP2RAGE) sequence. T1 maps can be obtained using the MP2RAGE sequence, which is relatively insensitive to inhomogeneities of the radio-frequency transmit field, B1+. As an extension, multiple gradient echoes can be acquired in each of the MP2RAGE readout blocks, which permits the calculation of T2* and susceptibility maps. We used computer simulations to explore the effects of the parameters on the precision and accuracy of the mapping. In vivo parameter maps up to 0.6 mm nominal resolution were acquired at 7 T in 19 healthy volunteers. Voxel-by-voxel correlations and the test-retest reproducibility were used to assess the reliability of the results. When using optimized paramenters, T1 maps obtained with ME-MP2RAGE and standard MP2RAGE showed excellent agreement for the whole range of values found in brain tissues. Simultaneously obtained T2* and susceptibility maps were of comparable quality as Fast Low-Angle SHot (FLASH) results. The acquisition times were more favorable for the ME-MP2RAGE (≈ 19 min) sequence as opposed to the sum of MP2RAGE (≈ 12 min) and FLASH (≈ 10 min) acquisitions. Without relevant sacrifice in accuracy, precision or flexibility, the multi-echo version may yield advantages in terms of reduced acquisition time and intrinsic co-registration, provided that an appropriate optimization of the acquisition parameters is performed. PMID:28081157

  19. Lumbar intervertebral disc abnormalities: comparison of quantitative T2 mapping with conventional MR at 3.0 T

    Energy Technology Data Exchange (ETDEWEB)

    Trattnig, Siegfried [Medical University of Vienna, Department of Radiology, MR Centre-Highfield MR, Vienna (Austria); Ludwig Boltzmann Institute for Clinical and Experimental Traumatology, Austrian Cluster for Tissue Regeneration, Vienna (Austria); Stelzeneder, David; Goed, Sabine; Reissegger, Michael [Medical University of Vienna, Department of Radiology, MR Centre-Highfield MR, Vienna (Austria); Mamisch, Tallal C. [Inselspital Berne, Orthopedic Surgery Department, Berne (Switzerland); Paternostro-Sluga, Tatjana [Medical University of Vienna, Department of Physical Medicine and Rehabilitation, Vienna (Austria); Weber, Michael [Medical University of Vienna, Department of Radiology, Vienna (Austria); Szomolanyi, Pavol [Medical University of Vienna, Department of Radiology, MR Centre-Highfield MR, Vienna (Austria); Slovak Academy of Sciences, Department of Imaging Methods, Institute of Measurement Science, Bratislava (Slovakia); Welsch, Goetz H. [Medical University of Vienna, Department of Radiology, MR Centre-Highfield MR, Vienna (Austria); University Hospital of Erlangen, Department of Trauma Surgery, Erlangen (Germany)

    2010-11-15

    To assess the relationship of morphologically defined lumbar disc abnormalities with quantitative T2 mapping. Fifty-three patients, mean age 39 years, with low back pain were examined by MRI at 3 T (sagittal T1-fast spin echo (FSE), three-plane T2-FSE for morphological MRI, multi-echo spin echo for T2 mapping). All discs were classified morphologically. Regions of interest (ROIs) for the annulus were drawn. The space in between was defined as the nucleus pulposus (NP). To evaluate differences between the classified groups, univariate ANOVA with post hoc Games-Howell and paired two-tailed t tests were used. In 265 discs we found 39 focal herniations, 10 annular tears, 123 bulging discs and 103 ''normal discs''. T2 values of the NP between discs with annular tear and all other groups were statistically significantly different (all p {<=} 0.01). Discs with annular tears showed markedly lower NP T2 values than discs without. The difference in NP T2 values between discs with focal herniation and normal discs (p = 0.005) was statistically significant. There was no difference in NP T2 values between bulging and herniated discs (p = 0.11) Quantitative T2 mapping of the nucleus pulposus of the intervertebral disc in the lumbar spine at 3 T reveals significant differences in discs with herniation and annular tears compared with discs without these abnormalities. (orig.)

  20. Modeling and mapping of cadmium in soils based on qualitative and quantitative auxiliary variables in a cadmium contaminated area.

    Science.gov (United States)

    Cao, Shanshan; Lu, Anxiang; Wang, Jihua; Huo, Lili

    2017-02-15

    The aim of this study was to measure the improvement in mapping accuracy of spatial distribution of Cd in soils by using geostatistical methods combined with auxiliary factors, especially qualitative variables. Significant correlations between Cd content and correlation environment variables that are easy to obtain (such as topographic factors, distance to residential area, land use types and soil types) were analyzed systematically and quantitatively. Based on 398 samples collected from a Cd contaminated area (Hunan Province, China), we estimated the spatial distribution of Cd in soils by using spatial interpolation models, including ordinary kriging (OK), and regression kriging (RK) with each auxiliary variable, all quantitative variables (RKWQ) and all auxiliary variables (RKWA). Results showed that mapping with RK was more consistent with the sampling data of the spatial distribution of Cd in the study area than mapping with OK. The performance indicators (smaller mean error, mean absolute error, root mean squared error values and higher relative improvement of RK than OK) indicated that the introduction of auxiliary variables can improve the prediction accuracy of Cd in soils for which the spatial structure could not be well captured by point-based observation (nugget to sill ratio=0.76) and strong relationships existed between variables to be predicted and auxiliary variables. The comparison of RKWA with RKWQ further indicated that the introduction of qualitative variables improved the prediction accuracy, and even weakened the effects of quantitative factors. Furthermore, the significantly different relative improvement with similar R(2) and varying spatial dependence showed that a reasonable choice of auxiliary variables and analysis of spatial structure of regression residuals are equally important to ensure accurate predictions. Copyright © 2016. Published by Elsevier B.V.

  1. [Autoradiographic investigations on postnatal proliferative activity of the telencephalic and diencephalic matrix-zones in the axolotl (Ambystoma mexicanum), with special references to the olfactory organ (author's transl)].

    Science.gov (United States)

    Richter, W; Kranz, D

    1981-01-01

    The localization and proliferative activity of the matrix-zones has been investigated in the telencephalon and in the diencephalon of 21 axolotls (Ambystoma mexicanum) by means of autoradiographs, after injection of tritiated thymidine at different stages of the postnatal life. There are no previous detailed autoradiographical reports on postnatal brain development in the axolotl. Matrix-zones (i.e. ventricular and subventricular zone) exist in the dorsal part and in the ventral part of the telencephalon, we have found these also in the diencephalon in the wall of the preoptic recessus and ventrally of the habenula. The quantitative part of this study indicates high values of the labeling-index in the early postnatal stages. Then, the labeling-index decreases, but also in 3 years old specimens labeled cells were observed in the matrix-zones of the telencephalon; therefore a few of proliferative capacity remains in the central nervous system of adult axolotls. Labeled cells were also found in the olfactory organ of early postnatal and adult axolotls; these are neuroblasts which have relevance for the regeneration of the forebrain.

  2. Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait.

    Science.gov (United States)

    Yu, Xiaona; Choi, Su Ryun; Ramchiary, Nirala; Miao, Xinyang; Lee, Su Hee; Sun, Hae Jeong; Kim, Sunggil; Ahn, Chun Hee; Lim, Yong Pyo

    2013-10-01

    Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbred lines '835' (susceptible) and 'B2' (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.

  3. Surface-Enhanced Raman Spectroscopy Based Quantitative Bioassay on Aptamer-Functionalized Nanopillars Using Large-Area Raman Mapping

    DEFF Research Database (Denmark)

    Yang, Jaeyoung; Palla, Mirko; Bosco, Filippo

    2013-01-01

    Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars......-to-spot variation in conventional SERS quantification. Furthermore, we have developed an analytical model capable of predicting experimental intensity distributions on the substrates for reliable quantification of biomolecules. Lastly, we have calculated the minimum needed area of Raman mapping for efficient...

  4. A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Apllication to Multiple Cattle Families

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Johnson, David L.; Arendonk, Johan A.M. van

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  5. A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families.

    NARCIS (Netherlands)

    Jansen, R.C.; Johnson, D.L.; Arendonk, van J.A.M.

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  6. A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Application to Multiple Cattle Families

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Johnson, David L.; Arendonk, Johan A.M. van

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  7. Rapid spin-lattice relaxation time mapping incorporating flip angle calibration in quantitative magnetic resonance imaging

    Institute of Scientific and Technical Information of China (English)

    Zhongliang Zu; Qi Liu; Yanming Yu; Song Gao; Shanglian Bao

    2008-01-01

    Driven equilibrium single pulse observation of T1(DESPOT1)is a rapid spin-lattice relaxation constant(T1)mapping technique in magnetic resonance imaging(MRI).However,DESPOT1 is very sensitive to flip angle(FA)inhomogeneity,resulting in T1 inaccuracy.Here,a five-point DESPOTl method is proposed to reduce the sensitivity to FA inhomogeneity through FA measurement and calibra-tion.Phantom and in vivo experiments are performed to validate the technique.As a result.a rapid and accurate T1 mapping is acquired by using the proposed five-point DESPOT1 method.

  8. Quantitative trait loci mapping for flowering time in a switchgrass pseudo-F2 population

    Science.gov (United States)

    Flowering is an important developmental event in switchgrass (Panicum virgatum) because the onset of flowering causes the cessation of vegetative growth and biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify ...

  9. Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches

    NARCIS (Netherlands)

    Jannink, Jean-Luc; Jansen, Ritsert

    2001-01-01

    The discovery of epistatically interacting QTL is hampered by the intractability and low power to detect QTL in multidimensional genome searches. We describe a new method that maps epistatic QTL by identifying loci of high QTL by genetic background interaction. This approach allows detection of QTL

  10. Mapping of multiple quantitative trait loci by simple regression in half-sib designs

    NARCIS (Netherlands)

    Koning, de D.J.; Schulman, N.; Elo, K.; Moisio, S.; Kinos, R.; Vilkki, J.; Maki-Tanila, A.

    2001-01-01

    Detection of QTL in outbred half-sib family structures has mainly been based on interval mapping of single QTL on individual chromosomes. Methods to account for linked and unlinked QTL have been developed, but most of them are only applicable in designs with inbred species or pose great demands on c

  11. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Jannink, Jean-Luc; Beavis, William D.

    2003-01-01

    Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping quanti

  12. Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches

    NARCIS (Netherlands)

    Jannink, Jean-Luc; Jansen, Ritsert

    2001-01-01

    The discovery of epistatically interacting QTL is hampered by the intractability and low power to detect QTL in multidimensional genome searches. We describe a new method that maps epistatic QTL by identifying loci of high QTL by genetic background interaction. This approach allows detection of QTL

  13. Mapping quantitative trait loci for plant adaptation and morphology traits in wheat using single nucleotide polymorphisms

    Science.gov (United States)

    Wheat (Triticum aestivum L.) morphological and adaptation-related traits that are controlled by quantitative traits loci (QTL) define potential growing areas of a wheat cultivar. To dissect the QTL for heading date (HD), lodging resistance (LR), shattering resistance (SR), cold tolerance (CT), plant...

  14. Using GIS in an Earth Sciences Field Course for Quantitative Exploration, Data Management and Digital Mapping

    Science.gov (United States)

    Marra, Wouter A.; van de Grint, Liesbeth; Alberti, Koko; Karssenberg, Derek

    2017-01-01

    Field courses are essential for subjects like Earth Sciences, Geography and Ecology. In these topics, GIS is used to manage and analyse spatial data, and offers quantitative methods that are beneficial for fieldwork. This paper presents changes made to a first-year Earth Sciences field course in the French Alps, where new GIS methods were…

  15. Mapping Quantitatively Regional Drug Absorption in Canines with IntelliCap System

    NARCIS (Netherlands)

    Becker, D.; Schütz, H.; Beyerbach, A.; Zou, H.; Shimizu, J.; Iordanov, V.P.

    2011-01-01

    Quantitative regional absorption of a drug under development was studied by using the novel IntelliCap system. IntelliCap is an orally swallowable programmable drug delivery capsule and capable of real-time monitoring of physiological conditions (pH, temperature), consequently allowing localization

  16. Meta-Analysis of Results from Quantitative Trait Loci Mapping Studies on Pig Chromosome 4

    NARCIS (Netherlands)

    Moraes Silva, De K.M.; Bastiaansen, J.W.M.; Knol, E.F.; Merks, J.W.M.; Lopes, P.S.; Guimaraes, R.M.; Arendonk, van J.A.M.

    2011-01-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this

  17. mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

    Science.gov (United States)

    Teo, Guoshou; Kim, Sinae; Tsou, Chih-Chiang; Collins, Ben; Gingras, Anne-Claude; Nesvizhskii, Alexey I; Choi, Hyungwon

    2015-11-03

    Data independent acquisition (DIA) mass spectrometry is an emerging technique that offers more complete detection and quantification of peptides and proteins across multiple samples. DIA allows fragment-level quantification, which can be considered as repeated measurements of the abundance of the corresponding peptides and proteins in the downstream statistical analysis. However, few statistical approaches are available for aggregating these complex fragment-level data into peptide- or protein-level statistical summaries. In this work, we describe a software package, mapDIA, for statistical analysis of differential protein expression using DIA fragment-level intensities. The workflow consists of three major steps: intensity normalization, peptide/fragment selection, and statistical analysis. First, mapDIA offers normalization of fragment-level intensities by total intensity sums as well as a novel alternative normalization by local intensity sums in retention time space. Second, mapDIA removes outlier observations and selects peptides/fragments that preserve the major quantitative patterns across all samples for each protein. Last, using the selected fragments and peptides, mapDIA performs model-based statistical significance analysis of protein-level differential expression between specified groups of samples. Using a comprehensive set of simulation datasets, we show that mapDIA detects differentially expressed proteins with accurate control of the false discovery rates. We also describe the analysis procedure in detail using two recently published DIA datasets generated for 14-3-3β dynamic interaction network and prostate cancer glycoproteome. The software was written in C++ language and the source code is available for free through SourceForge website http://sourceforge.net/projects/mapdia/.This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression.

    Science.gov (United States)

    Chen, Jinmiao; Xue, Yuezhen; Poidinger, Michael; Lim, Thimothy; Chew, Sung Hock; Pang, Chai Ling; Abastado, Jean-Pierre; Thierry, Françoise

    2014-08-01

    Two classes of Human papillomaviruses (HPV) infect the anogenital track: high risk viruses that are associated with risk of cervical cancer and low risk types that drive development of benign lesions, such as condylomas. In the present study, we established quantitative transcriptional maps of the viral genome in clinical lesions associated with high risk HPV16 or low risk HPV6b. Marked qualitative and quantitative changes in the HPV16 transcriptome were associated with progression from low to high grade lesions. Specific transcripts encoding essential regulatory proteins such as E7, E2, E1^E4 and E5 were identified. We also identified intrinsic differences between the HPV6b-associated condyloma transcript map and that of the HPV16-associated low grade CIN specifically regarding promoter usage. Characterization and quantification of HPV transcripts in patient samples thus establish the impact of viral transcriptional regulation on the status of HPV-associated lesions and may therefore help in defining new biologically-relevant prognosis markers. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Detection of cerebral microbleeds with quantitative susceptibility mapping in the ArcAbeta mouse model of cerebral amyloidosis

    Science.gov (United States)

    Klohs, Jan; Deistung, Andreas; Schweser, Ferdinand; Grandjean, Joanes; Dominietto, Marco; Waschkies, Conny; Nitsch, Roger M; Knuesel, Irene; Reichenbach, Jürgen R; Rudin, Markus

    2011-01-01

    Cerebral microbleeds (CMBs) are findings in patients with neurological disorders such as cerebral amyloid angiopathy and Alzheimer's disease, and are indicative of an underlying vascular pathology. A diagnosis of CMBs requires an imaging method that is capable of detecting iron-containing lesions with high sensitivity and spatial accuracy in the presence of potentially confounding tissue abnormalities. In this study, we investigated the feasibility of quantitative magnetic susceptibility mapping (QSM), a novel technique based on gradient-recalled echo (GRE) phase data, for the detection of CMBs in the arcAβ mouse, a mouse model of cerebral amyloidosis. Quantitative susceptibility maps were generated from phase data acquired with a high-resolution T2*-weighted GRE sequence at 9.4 T. We examined the influence of different regularization parameters on susceptibility computation; a proper adjustment of the regularization parameter minimizes streaking artifacts and preserves fine structures. In the present study, it is shown that QSM provides increased detection sensitivity of CMBs and improved contrast when compared with GRE magnitude imaging. Furthermore, QSM corrects for the blooming effect observed in magnitude and phase images and depicts both the localization and spatial extent of CMBs with high accuracy. Therefore, QSM may become an important tool for diagnosing CMBs in neurological diseases. PMID:21847134

  20. Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat ( Triticum aestivum L.).

    Science.gov (United States)

    Börner, A.; Schumann, E.; Fürste, A.; Cöster, H.; Leithold, B.; Röder, S.; Weber, E.

    2002-11-01

    A set of 114 recombinant inbred lines of the 'International Triticeae Mapping Initiative' mapping population was grown during the seasons 1997, 1998, 1999 and 2000 under several environments. Twenty morphological (glume colour, awn colour, waxiness, leaf erectness, peduncle length), agronomical (ear emergence time, flowering time, grain filling time, ear length, plant height, lodging, grain number, thousand-grain-weight, grain weight per ear, grain protein content, winter hardiness) and disease resistance (powdery mildew, yellow rust, leaf rust, fusarium) traits were studied. Not all traits were scored in each experiment. In total 210 QTLs with a LOD threshold of >2.0 (minor QTLs) were detected of which 64 reached a LOD score of >3.0 (major QTLs). Often QTLs were detected in comparable positions in different experiments. Homologous and homoeologous relationships of the detected QTLs, and already described major genes or QTLs determining the same traits in wheat or other Triticeae members, are discussed.

  1. Quantitative mapping of rainfall rates over the oceans utilizing Nimbus-5 ESMR data

    Science.gov (United States)

    Rao, M. S. V.; Abbott, W. V.

    1976-01-01

    The electrically scanning microwave radiometer (ESMR) data from the Nimbus 5 satellite was used to deduce estimates of precipitation amount over the oceans. An atlas of the global oceanic rainfall was prepared and the global rainfall maps analyzed and related to available ground truth information as well as to large scale processes in the atmosphere. It was concluded that the ESMR system provides the most reliable and direct approach yet known for the estimation of rainfall over sparsely documented, wide oceanic regions.

  2. Quantitative suspended sediment mapping using aircraft remotely sensed multispectral data. [in Virginia

    Science.gov (United States)

    Johnson, R. W.

    1975-01-01

    Suspended sediment is an important environmental parameter for monitoring water quality, water movement, and land use. Quantitative suspended sediment determinations were made from analysis of aircraft remotely sensed multispectral digital data. A statistical analysis and derived regression equation were used to determine and plot quantitative suspended sediment concentration contours in the tidal James River, Virginia, on May 28, 1974. From the analysis, a single band, Band 8 (0.70-0.74 microns), was adequate for determining suspended sediment concentrations. A correlation coefficient of 0.89 was obtained with a mean inaccuracy of 23.5 percent for suspended sediment concentrations up to about 50 mg/l. Other water quality parameters - secchi disc depth and chlorophyll - also had high correlations with the remotely sensed data. Particle size distribution had only a fair correlation with the remotely sensed data.

  3. Towards quantitative electrostatic potential mapping of working semiconductor devices using off-axis electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Yazdi, Sadegh, E-mail: sadegh.yazdi@cen.dtu.dk [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Center for Electron Nanoscopy, Technical University of Denmark, DK 2800 Lyngby (Denmark); Kasama, Takeshi; Beleggia, Marco; Samaie Yekta, Maryam [Center for Electron Nanoscopy, Technical University of Denmark, DK 2800 Lyngby (Denmark); McComb, David W. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210 (United States); Twitchett-Harrison, Alison C. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Dunin-Borkowski, Rafal E. [Center for Electron Nanoscopy, Technical University of Denmark, DK 2800 Lyngby (Denmark); Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany)

    2015-05-15

    Pronounced improvements in the understanding of semiconductor device performance are expected if electrostatic potential distributions can be measured quantitatively and reliably under working conditions with sufficient sensitivity and spatial resolution. Here, we employ off-axis electron holography to characterize an electrically-biased Si p–n junction by measuring its electrostatic potential, electric field and charge density distributions under working conditions. A comparison between experimental electron holographic phase images and images obtained using three-dimensional electrostatic potential simulations highlights several remaining challenges to quantitative analysis. Our results illustrate how the determination of reliable potential distributions from phase images of electrically biased devices requires electrostatic fringing fields, surface charges, specimen preparation damage and the effects of limited spatial resolution to be taken into account.

  4. Towards quantitative electrostatic potential mapping of working semiconductor devices using off-axis electron holography

    DEFF Research Database (Denmark)

    Yazdi, Sadegh; Kasama, Takeshi; Beleggia, Marco;

    2015-01-01

    Pronounced improvements in the understanding of semiconductor device performance are expected if electrostatic potential distributions can be measured quantitatively and reliably under working conditions with sufficient sensitivity and spatial resolution. Here, we employ off-axis electron...... holography to characterize an electrically-biased Si p-. n junction by measuring its electrostatic potential, electric field and charge density distributions under working conditions. A comparison between experimental electron holographic phase images and images obtained using three-dimensional electrostatic...

  5. Quantitative Mapping of Reversible Mitochondrial Complex I Cysteine Oxidation in a Parkinson Disease Mouse Model*

    OpenAIRE

    Danielson, Steven R.; Held, Jason M.; Oo, May; Riley, Rebeccah; Gibson, Bradford W.; Andersen, Julie K.

    2011-01-01

    Differential cysteine oxidation within mitochondrial Complex I has been quantified in an in vivo oxidative stress model of Parkinson disease. We developed a strategy that incorporates rapid and efficient immunoaffinity purification of Complex I followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. This method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in muri...

  6. Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.

    Science.gov (United States)

    Creech, Amanda L; Taylor, Jordan E; Maier, Verena K; Wu, Xiaoyun; Feeney, Caitlin M; Udeshi, Namrata D; Peach, Sally E; Boehm, Jesse S; Lee, Jeannie T; Carr, Steven A; Jaffe, Jacob D

    2015-01-15

    Epigenetic control of genome function is an important regulatory mechanism in diverse processes such as lineage commitment and environmental sensing, and in disease etiologies ranging from neuropsychiatric disorders to cancer. Here we report a robust, high-throughput targeted, quantitative mass spectrometry (MS) method to rapidly profile modifications of the core histones of chromatin that compose the epigenetic landscape, enabling comparisons among cells with differing genetic backgrounds, genomic perturbations, and drug treatments. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Identification of quantitative trait loci for salinity tolerance in rice (Oryza sativa L.) using IR29/Hasawi mapping population

    Indian Academy of Sciences (India)

    J. B. BIZIMANA; A. LUZI-KIHUPI; ROSEMARY W. MURORI; R. K. SINGH

    2017-09-01

    Salinity is the second most important abiotic stress after drought that hampers rice production, especially in south and Southeast Asia. Breeding approach supplemented with molecular markers-assisted selection is the most promising approach in terms of efficiency to increase the productivity under salt-affected soils. Thirty-day-old rice seedlings of 300 F5:6 recombinant-inbred lines derived from a cross between the salt sensitive, IR29 (indica), and a salt tolerant, Hasawi (aus), were used to identify quantitative trait loci (QTLs) linked to salinity tolerance. One hundred and ninety four polymorphic SNP markers were used to construct a genetic linkage map involving 142 selected RILs that covered 1441.96 cM genome with an average distance of 7.88 cM between loci. Twentynew QTLs (LOD > 3) were identified on chromosomes 1, 2, 4, 6, 8, 9 and 12 using composite interval mapping with R2 as high as >20% with LODvalue of 7.21. Many earlier studies reported big qSaltol for seedling stage salinity tolerance in rice is on short arm of chromosome 1 but none of the QTL in our study was on qSaltol or nearby position, therefore, Hasawi conferred salinity tolerance in RILs due to novel QTLs. It is suggested to fine map the novel QTLs so that the level of salinity tolerance could be further enhanced by pyramiding of the different QTLs in one genetic background through marker-assisted selection.

  8. Study on mapping Quantitative Trait Loci for animal complex binary traits using Bayesian-Markov chain Monte Carlo approach

    Institute of Scientific and Technical Information of China (English)

    LIU; Jianfeng; ZHANG; Yuan; ZHANG; Qin; WANG; Lixian; ZHANG; Jigang

    2006-01-01

    It is a challenging issue to map Quantitative Trait Loci (QTL) underlying complex discrete traits, which usually show discontinuous distribution and less information, using conventional statistical methods. Bayesian-Markov chain Monte Carlo (Bayesian-MCMC) approach is the key procedure in mapping QTL for complex binary traits, which provides a complete posterior distribution for QTL parameters using all prior information. As a consequence, Bayesian estimates of all interested variables can be obtained straightforwardly basing on their posterior samples simulated by the MCMC algorithm. In our study, utilities of Bayesian-MCMC are demonstrated using simulated several animal outbred full-sib families with different family structures for a complex binary trait underlied by both a QTL and polygene. Under the Identity-by-Descent-Based variance component random model, three samplers basing on MCMC, including Gibbs sampling, Metropolis algorithm and reversible jump MCMC, were implemented to generate the joint posterior distribution of all unknowns so that the QTL parameters were obtained by Bayesian statistical inferring. The results showed that Bayesian-MCMC approach could work well and robust under different family structures and QTL effects. As family size increases and the number of family decreases, the accuracy of the parameter estimates will be improved. When the true QTL has a small effect, using outbred population experiment design with large family size is the optimal mapping strategy.

  9. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

    Science.gov (United States)

    Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M

    2007-01-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

  10. Mapping quantitative trait loci controlling early growth in a (longleaf pine x slash pine) x slash pine BC(1) family.

    Science.gov (United States)

    Weng, C.; Kubisiak, L.; Nelson, D.; Stine, M.

    2002-04-01

    Random amplified polymorphic DNA (RAPD) markers were employed to map the genome and quantitative trait loci controlling the early growth of a pine hybrid F(1) tree ( Pinus palustris Mill. x P. elliottii Engl.) and a recurrent slash pine tree ( P. elliottii Engl.) in a (longleaf pine x slash pine) x slash pine BC(1) family consisting of 258 progeny. Of the 150 hybrid F(1) parent-specific RAPD markers, 133 were mapped into 17 linkage groups covering a genetic distance of 1,338.2 cM. Of the 116 slash pine parent-specific RAPD markers, 83 were mapped into 19 linkage groups covering a genetic distance of 994.6 cM. A total of 11 different marker intervals were found to be significantly associated with 13 of the 20 traits on height and diameter growth using MAPMAKER/QTL. Nine of the eleven marker intervals were unique to the hybrid parent 488 genome, and two were unique to the recurrent parent 18-27 genome. The amount of phenotypic variance explained by the putative QTLs ranged from 3.6% to 11.0%. Different QTLs were detected at different ages. Two marker intervals from the hybrid parent 488 were found to have QTL by environment interactions.

  11. High-resolution three-dimensional quantitative map of the macromolecular proton fraction distribution in the normal rat brain

    Directory of Open Access Journals (Sweden)

    Anna V. Naumova

    2017-02-01

    Full Text Available The presented dataset provides a normative high-resolution three-dimensional (3D macromolecular proton fraction (MPF map of the healthy rat brain in vivo and source images used for its reconstruction. The images were acquired using the protocol described elsewhere (Naumova, et al. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields. Neuroimage (2016 doi: 10.1016/j.neuroimage.2016.09.036. The map was reconstructed from three source images with different contrast weightings (proton density, T1, and magnetization transfer using the single-point algorithm with a synthetic reference image. Source images were acquired from a living animal on an 11.7 T small animal MRI scanner with isotropic spatial resolution of 170 µm3 and total acquisition time about 1.5 h. The 3D dataset can be used for multiple purposes including interactive viewing of rat brain anatomy, measurements of reference MPF values in various brain structures, and development of image processing techniques for the rodent brain segmentation. It also can serve as a gold standard image for implementation and optimization of rodent brain MRI protocols.

  12. Forage Species Suitability Mapping for China Using Topographic, Climatic and Soils Spatial Data and Quantitative Plant Tolerances

    Institute of Scientific and Technical Information of China (English)

    David B Hannaway; LI Xiang-lin; Christopher Daly; CAO Wei-xing; LUO Wei-hong; WEI Yu-rong; ZHANG Wei-li; XU Ai-guo; LU Chang-ai; SHI Xue-zheng

    2005-01-01

    Selecting plants adapted to the climatic and soil conditions of specific locations is essential for environmental protection and economic sustainability of agricultural and pastoral systems. This is particularly true for countries like China with a diversity of climates and soils and intended uses. Currently, proper species selection is difficult due to the absence of computer-based selection tools. Climate and soil GIS layers, matched with a matrix of plant characteristics through rules describing species tolerances would greatly improve the selection process. Better matching will reduce environmental hazards and economic risks associated with sub-optimal plant selection and performance. GIS-based climate and soil maps have been developed for China. A matrix of quantitative species tolerances has been developed for example forage species and used in combination with an internet map server that allows customized map creation. A web-based decision support system has been developed to provide current information and links to original data sources, supplementary materials, and selection strategies.

  13. Statistical analysis of results from the quantitative mapping of fracture minerals in Laxemar. Site descriptive modelling - complementary studies

    Energy Technology Data Exchange (ETDEWEB)

    Loefgren, Martin (Niressa AB, Norsborg (Sweden)); Sidborn, Magnus (Kemakta Konsult AB, Stockholm (Sweden))

    2010-12-15

    Within the Laxemar site investigation campaign, quantitative mapping of different fracture minerals has been performed. This has been done by studying fracture surfaces of drill core sections from many different boreholes at the Laxemar site /Eklund and Mattsson 2008/. The drill core mapping was focused on the rock in the vicinity of flow anomalies detected by the Posiva Flow Log (PFL). The quantitative mapping was performed only on open fractures. The fracture minerals that were mapped are calcite, chlorite, clay minerals (as a group), hematite, and pyrite. In this present report, data from the quantitative mineral mapping campaign are refined, sorted into different data subsets, and analysed by parametric and non-parametric statistical methods. The data subsets are associated with 17 different rock volumes, representing different elevations, rock domains, fracture domains, and groups of deformation zones. In total 1,852 fractures were mapped at the site, and the most frequent mineral was calcite. Its amount could be quantitatively estimated in 51% of the mapped fractures. Of the other minerals, chlorite was quantitatively estimated in 46%, pyrite in 19%, clay minerals in 16%, and hematite in 0.05% of the mapped fractures. For fractures where the averaged fracture mineral thickness, d{sub mean} [mm], and visible coverage, C{sub vis} [%], could be quantitatively estimated, the following arithmetic means were found: calcite = 0.25 mm and 22%, chlorite = 0.29 mm and 41%, pyrite =1.3 mum and 0.2%, and clay minerals = 0.15 mm and 35%. These quantities are based on visual inspection of fracture surfaces and do not include the contribution from non-consolidated fracture fillings. It is shown that there is significant spatial variability of d{sub mean} and C{sub vis} within the examined rock volumes. Furthermore, the non-parametric analyses indicate that there are differences in d{sub mean} and C{sub vis} between the different rock volumes. Even so, the differences are

  14. Rapid, Quantitative Mapping of Anti-HIV Type 1 Envelope Serum Antibody Specificities

    OpenAIRE

    Powell, Rebecca L.R.; Lindsay, Ross W.B.; Wilson, Aaron; Carpov, Alexei; Rabinovich, Svetlana; Hoffenberg, Simon; Caulfield, Michael J.

    2013-01-01

    A new generation of extremely broad and potent neutralizing antibodies (bNAbs) has been isolated from HIV-infected subjects. This has refocused interest in the sites of vulnerability targeted by these bNAbs and in the potential for designing Envelope (Env) immunogens that display these sites. Standard methods for evaluating HIV-1 vaccine candidates do not enable epitope mapping on the HIV Env spike, the target for NAbs. To meet the need for rapid analysis of Ab specificity, we designed a mult...

  15. Linkage Map Construction and Quantitative Trait Loci Analysis for Bolting Based on a Double Haploid Population of Brassica rapa

    Institute of Scientific and Technical Information of China (English)

    Xu Yang; Yang-Jun Yu; Feng-Lan Zhang; Zhi-Rong Zou; Xiu-Yun Zhao; De-Shuang Zhang; Jia-Bing Xu

    2007-01-01

    Early bolting of Chinese cabbage (Brassica rapa L.) during spring cultivation often has detrimental effects on the yield and quality of the harvested products. Breeding late bolting varieties is a major objective of Chinese cabbage breeding programs. in order to analyze the genetic basis of bolting traits, a genetic map of B. rapa was constructed based on amplified fragment-length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), simple sequence repeat (SSR), random amplification of polymorphic DNA (RAPD), and isozyme markers. Marker analysis was carried out on 81 double haploid (DH) lines obtained by mlcrospore culture from F1 progeny of two homozygous parents: B. rapa L. ssp. pekinensis (BY) (an extra-early bolting Chinese cabbage line) and B. rapa L. ssp. rapifera (MM) (an extra-late bolting European turnip line). A total of 326 markers including 130 AFLPs, 123 SRAPs, 16 SSRs, 43RAPDs and 14 isozymes were used to construct a linkage map with 10 linkage groups covering 882 cM with an average distance of 2.71 cM between loci. The bolting trait of each DH line was evaluated by the bolting index under controlled conditions. Quantitative trait loci (QTL) analysis was conducted using multiple QTL model mapping with MapQTL5.0 software. Eight QTLs controlling bolting resistance were identified. These QTLs, accounting for 14.1% to 25.2% of the phenotyplc variation with positive additive effects, were distributed into three linkage groups. These results provide useful information for molecular marker-assisted selection of late bolting traits in Chinese cabbage breeding programs.

  16. Modeling and Mapping of Soil Salinity with Reflectance Spectroscopy and Landsat Data Using Two Quantitative Methods (PLSR and MARS

    Directory of Open Access Journals (Sweden)

    Said Nawar

    2014-11-01

    Full Text Available The monitoring of soil salinity levels is necessary for the prevention and mitigation of land degradation in arid environments. To assess the potential of remote sensing in estimating and mapping soil salinity in the El-Tina Plain, Sinai, Egypt, two predictive models were constructed based on the measured soil electrical conductivity (ECe and laboratory soil reflectance spectra resampled to Landsat sensor’s resolution. The models used were partial least squares regression (PLSR and multivariate adaptive regression splines (MARS. The results indicated that a good prediction of the soil salinity can be made based on the MARS model (R2 = 0.73, RMSE = 6.53, and ratio of performance to deviation (RPD = 1.96, which performed better than the PLSR model (R2 = 0.70, RMSE = 6.95, and RPD = 1.82. The models were subsequently applied on a pixel-by-pixel basis to the reflectance values derived from two Landsat images (2006 and 2012 to generate quantitative maps of the soil salinity. The resulting maps were validated successfully for 37 and 26 sampling points for 2006 and 2012, respectively, with R2 = 0.72 and 0.74 for 2006 and 2012, respectively, for the MARS model, and R2 = 0.71 and 0.73 for 2006 and 2012, respectively, for the PLSR model. The results indicated that MARS is a more suitable technique than PLSR for the estimation and mapping of soil salinity, especially in areas with high levels of salinity. The method developed in this paper can be used for other satellite data, like those provided by Landsat 8, and can be applied in other arid and semi-arid environments.

  17. Quantitative trait loci mapping of phenotypic plasticity and genotype-environment interactions in plant and insect performance.

    Science.gov (United States)

    Tétard-Jones, C; Kertesz, M A; Preziosi, R F

    2011-05-12

    Community genetic studies generally ignore the plasticity of the functional traits through which the effect is passed from individuals to the associated community. However, the ability of organisms to be phenotypically plastic allows them to rapidly adapt to changing environments and plasticity is commonly observed across all taxa. Owing to the fitness benefits of phenotypic plasticity, evolutionary biologists are interested in its genetic basis, which could explain how phenotypic plasticity is involved in the evolution of species interactions. Two current ideas exist: (i) phenotypic plasticity is caused by environmentally sensitive loci associated with a phenotype; (ii) phenotypic plasticity is caused by regulatory genes that simply influence the plasticity of a phenotype. Here, we designed a quantitative trait loci (QTL) mapping experiment to locate QTL on the barley genome associated with barley performance when the environment varies in the presence of aphids, and the composition of the rhizosphere. We simultaneously mapped aphid performance across variable rhizosphere environments. We mapped main effects, QTL × environment interaction (QTL×E), and phenotypic plasticity (measured as the difference in mean trait values) for barley and aphid performance onto the barley genome using an interval mapping procedure. We found that QTL associated with phenotypic plasticity were co-located with main effect QTL and QTL×E. We also located phenotypic plasticity QTL that were located separately from main effect QTL. These results support both of the current ideas of how phenotypic plasticity is genetically based and provide an initial insight into the functional genetic basis of how phenotypically plastic traits may still be important sources of community genetic effects.

  18. Spatially resolved quantitative mapping of thermomechanical properties and phase transition temperatures using scanning probe microscopy

    Science.gov (United States)

    Jesse, Stephen; Kalinin, Sergei V; Nikiforov, Maxim P

    2013-07-09

    An approach for the thermomechanical characterization of phase transitions in polymeric materials (polyethyleneterephthalate) by band excitation acoustic force microscopy is developed. This methodology allows the independent measurement of resonance frequency, Q factor, and oscillation amplitude of a tip-surface contact area as a function of tip temperature, from which the thermal evolution of tip-surface spring constant and mechanical dissipation can be extracted. A heating protocol maintained a constant tip-surface contact area and constant contact force, thereby allowing for reproducible measurements and quantitative extraction of material properties including temperature dependence of indentation-based elastic and loss moduli.

  19. Microscopy imaging and quantitative phase contrast mapping in turbid microfluidic channels by digital holography.

    Science.gov (United States)

    Paturzo, Melania; Finizio, Andrea; Memmolo, Pasquale; Puglisi, Roberto; Balduzzi, Donatella; Galli, Andrea; Ferraro, Pietro

    2012-09-07

    We show that sharp imaging and quantitative phase-contrast microcopy is possible in microfluidics in flowing turbid media by digital holography. In fact, in flowing liquids with suspended colloidal particles, clear vision is hindered and cannot be recovered by any other microscopic imaging technique. On the contrary, using digital holography, clear imaging is possible thanks to the Doppler frequency shift experienced by the photons scattered by the flowing colloidal particles, which do not contribute to the interference process, i.e. the recorded hologram. The method is illustrated and imaging results are demonstrated for pure phase objects, i.e. biological cells in microfluidic channels.

  20. Assessing the accuracy of hyperspectral and multispectral satellite imagery for categorical and Quantitative mapping of salinity stress in sugarcane fields

    Science.gov (United States)

    Hamzeh, Saeid; Naseri, Abd Ali; AlaviPanah, Seyed Kazem; Bartholomeus, Harm; Herold, Martin

    2016-10-01

    This study evaluates the feasibility of hyperspectral and multispectral satellite imagery for categorical and quantitative mapping of salinity stress in sugarcane fields located in the southwest of Iran. For this purpose a Hyperion image acquired on September 2, 2010 and a Landsat7 ETM+ image acquired on September 7, 2010 were used as hyperspectral and multispectral satellite imagery. Field data including soil salinity in the sugarcane root zone was collected at 191 locations in 25 fields during September 2010. In the first section of the paper, based on the yield potential of sugarcane as influenced by different soil salinity levels provided by FAO, soil salinity was classified into three classes, low salinity (1.7-3.4 dS/m), moderate salinity (3.5-5.9 dS/m) and high salinity (6-9.5) by applying different classification methods including Support Vector Machine (SVM), Spectral Angle Mapper (SAM), Minimum Distance (MD) and Maximum Likelihood (ML) on Hyperion and Landsat images. In the second part of the paper the performance of nine vegetation indices (eight indices from literature and a new developed index in this study) extracted from Hyperion and Landsat data was evaluated for quantitative mapping of salinity stress. The experimental results indicated that for categorical classification of salinity stress, Landsat data resulted in a higher overall accuracy (OA) and Kappa coefficient (KC) than Hyperion, of which the MD classifier using all bands or PCA (1-5) as an input performed best with an overall accuracy and kappa coefficient of 84.84% and 0.77 respectively. Vice versa for the quantitative estimation of salinity stress, Hyperion outperformed Landsat. In this case, the salinity and water stress index (SWSI) has the best prediction of salinity stress with an R2 of 0.68 and RMSE of 1.15 dS/m for Hyperion followed by Landsat data with an R2 and RMSE of 0.56 and 1.75 dS/m respectively. It was concluded that categorical mapping of salinity stress is the best option

  1. Mapping of quantitative trait loci for the bolting trait in Brassica rapa under vernalizing conditions.

    Science.gov (United States)

    Wang, Y G; Zhang, L; Ji, X H; Yan, J F; Liu, Y T; Lv, X X; Feng, H

    2014-05-23

    Premature bolting can occur occasionally during spring cultivation of heading Chinese cabbage in East Asia when the plants encounter low temperatures (vernalization), leading to economic loss. Breeding bolting-resistant cultivars is the best choice for solving this problem. We looked for QTLs responsible for varietal differences in the bolting trait in Brassica rapa under environmental conditions that promote vernalization. To achieve this goal, we constructed a linkage map with 107 simple sequence repeats and 54 insertion/deletion markers based on a segregating population of 186 F2 individuals. The resulting map consisted of 10 linkage groups and covered a total length of 947.1 cM, with an average genetic distance of 5.84 cM between adjacent markers. QTL analysis of the bolting trait was performed by two phenotypic evaluations (bolting index and flowering time) based on the scores in an F2 population in the spring of 2010, and scores in F2:3 families in autumn 2010 and spring 2011, respectively. Twenty-six QTLs that controlled bolting were detected, accounting for 2.6 to 31.2% of the phenotypic variance. The detected QTLs with large effects co-localized mainly on linkage groups A02, A06, and A07. These QTLs may provide useful information for marker-assisted selection in a breeding program for late bolting or bolting-resistant cultivars in B. rapa crops.

  2. Quantitative Trait Loci Mapping of Dark-Induced Senescence in Winter Wheat (Triticum aestivum)

    Institute of Scientific and Technical Information of China (English)

    Hongwei Li; Fanyun Lin; Gui Wang; Ruilian Jing; Qi Zheng; Bin Li; Zhensheng Li

    2012-01-01

    In order to explore the genetics of dark-induced senescence in winter wheat (Triticum aestivum L.),aquantitative trait loci (QTL) analysis was carried out in a doubled haploid population developed from across between the varieties Hanxuan 10 (HX) and Lumai 14 (LM).The senescence parameters chlorophyll content (Chl a+b,Chl a,and Chl b),original fluorescence (Fo),maximum fluorescence level (Fm),maximum photochemical efficiency (Fv/Fm),and ratio of variable fluorescence to original fluorescence (Fv/Fo) were evaluated in the second leaf of whole three-leaf seedlings subjected to 7 d of darkness.A total of 43 QTLs were identified that were associated with dark-induced senescence using composite interval mapping.These QTLs were mapped to 20 loci distributed on 11 chromosomes:1B,1D,2A,2B,3B,3D,5D,6A,6B,7A,and 7B.The phenotypic variation explained by each QTL ranged from 7.5% to 19.4%.Eleven loci coincided with two or more of the analyzed parameters.In addition,14 loci co-located or were linked with previously reported QTLs regulating flag leaf senescence,tolerance to high light stress,and grain protein content (Gpc),separately.

  3. Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype.

    Directory of Open Access Journals (Sweden)

    Akiko Watanabe

    2007-11-01

    Full Text Available Deficits in prepulse inhibition (PPI are a biological marker for schizophrenia. To unravel the mechanisms that control PPI, we performed quantitative trait loci (QTL analysis on 1,010 F2 mice derived by crossing C57BL/6 (B6 animals that show high PPI with C3H/He (C3 animals that show low PPI. We detected six major loci for PPI, six for the acoustic startle response, and four for latency to response peak, some of which were sex-dependent. A promising candidate on the Chromosome 10-QTL was Fabp7 (fatty acid binding protein 7, brain, a gene with functional links to the N-methyl-D-aspartic acid (NMDA receptor and expression in astrocytes. Fabp7-deficient mice showed decreased PPI and a shortened startle response latency, typical of the QTL's proposed effects. A quantitative complementation test supported Fabp7 as a potential PPI-QTL gene, particularly in male mice. Disruption of Fabp7 attenuated neurogenesis in vivo. Human FABP7 showed altered expression in schizophrenic brains and genetic association with schizophrenia, which were both evident in males when samples were divided by sex. These results suggest that FABP7 plays a novel and crucial role, linking the NMDA, neurodevelopmental, and glial theories of schizophrenia pathology and the PPI endophenotype, with larger or overt effects in males. We also discuss the results from the perspective of fetal programming.

  4. Scintillation autoradiographic localization of 1,25-dihydroxyvitamin D/sub 3/ in chick intestine. [Tritium tracer techniques

    Energy Technology Data Exchange (ETDEWEB)

    Jones, P.G.; Haussler, M.R.

    1979-02-01

    The intracellular binding site of 1,25-dihydroxyvitamin D/sub 3/ (1,25(OH)/sub 2/D/sub 3/) was determined via biochemical analysis of radioactive 1,25(OH)/sub 2/D/sub 3/ association with various chick tissues and then by direct autoradiography. When vitamin D-deficient chicks were injected intracardially with doses of tritiated 1,25(OH)/sub 2/D/sub 3/ and killed 2 h later, 2 to 3 times more radioactivity was found in the intestinal mucosa than was present in equal weights of pancreas, parathyroid, or liver tissue. Very little tritium was found in muscle tissue. The intestinally localized radioactivity was predominantly associated with the nuclear chromatin fraction, and binding of 1,25(OH)/sub 2/(/sup 3/H)D/sub 3/ to the nucleus was maximal 2 h after injection and at a dose of at least 0.52 nmol. Using this dose and time period, autoradiographic studies were done on duodenum and thoracic muscle of rachitic chicks injected with radioactive 1,25(OH)/sub 2/D/sub 3/ (11.2 Ci/mol). Thin sections of tissue were prepared for thaw and dry mount scintillation autoradiography as well as simple dip-coating autoradiography. After exposure for 4 to 6 months, a preferential concentration and retention of tritium-labeled 1,25(OH)/sub 2/D/sub 3/ was evident in the nuclei of intestinal villi and in the crypt of Lieberkuehn cells when each of the autoradiographic techniques was utilized. Quantitation of the labeled hormone confirms the significant nuclear accumulation in both villi and crypt cells. No such nuclear concentration of silver grains was observed in thoracic muscle cells, and the intestinal localization was abolished when a 100-fold excess of unlabeled 1,25(OH)/sub 2/D/sub 3/ was injected simultaneously with the radioactive hormone. It is concluded that 1,25(OH)/sub 2/D/sub 3/ is bound in a tissue-selective fashion to a high affinity, low capacity site within the nucleus of its intestinal target organ.

  5. Autoradiographic characterization of L-(/sup 3/H)glutamate binding sites in the central nervous system

    Energy Technology Data Exchange (ETDEWEB)

    Greenamyre, J.T.

    1986-01-01

    A quantitative autoradiographic technique was developed to study L-(/sup 3/H(glutamate binding in sections of central nervous system tissue. This technique circumvented some problems associated with conventional receptor binding methodologies and allowed direct assessment of regional distribution, numbers and affinities of glutamate binding sites. The sensitivity and high degree of anatomical resolution attainable by autoradiography obviated the need for pooled samples of microdissected specimens. Under assay conditions, (/sup 4/H)glutamate bound rapidly and reversibly to sections of rat brain and was not metabolized appreciably. The distribution of glutamate binding sites corresponded to the projection areas of putative glutamatergic pathways. Thus, there was heavy glutamate binding in regions where there is evidence for glutamatergic innervation and little binding in nuclei which apparently do not receive glutamatergic input. Scatchard and Hill plots suggested that glutamate was interacting with a single population of sites; however, competition studies revealed binding site heterogeneity. Anatomical and pharmacological evidence suggested that the NMDA-, high affinity quisqualate-, and kainate-sensitive glutamate binding sites may correspond to physiologically-defined NMDA, quisqualate and kainate receptors.

  6. Quantitative mapping of collagen fiber alignment in thick tissue samples using transmission polarized-light microscopy.

    Science.gov (United States)

    Yakovlev, Dmitry D; Shvachkina, Marina E; Sherman, Maria M; Spivak, Andrey V; Pravdin, Alexander B; Yakovlev, Dmitry A

    2016-07-01

    Immersion optical clearing makes it possible to use transmission polarized-light microscopy for characterization of thick (200 to 2000  μm) layers of biological tissues. We discuss polarization properties of thick samples in the context of the problem of characterization of collagen fiber alignment in connective tissues such as sclera and dermis. Optical chirality caused by azimuthal variations of the macroscopic (effective) optic axis of the medium across the sample thickness should be considered in polarization mapping of thick samples of these tissues. We experimentally evaluate to what extent the optical chirality affects the measurement results in typical situations and show under what conditions it can be easily taken into account and does not hinder, but rather helps, in characterization of collagen fiber alignment.

  7. Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy.

    Science.gov (United States)

    Graham, Emmelyn M; Iwai, Kaoru; Uchiyama, Seiichi; de Silva, A Prasanna; Magennis, Steven W; Jones, Anita C

    2010-05-21

    The use of a water-soluble, thermo-responsive polymer as a highly sensitive fluorescence-lifetime probe of microfluidic temperature is demonstrated. The fluorescence lifetime of poly(N-isopropylacrylamide) labelled with a benzofurazan fluorophore is shown to have a steep dependence on temperature around the polymer phase transition and the photophysical origin of this response is established. The use of this unusual fluorescent probe in conjunction with fluorescence lifetime imaging microscopy (FLIM) enables the spatial variation of temperature in a microfluidic device to be mapped, on the micron scale, with a resolution of less than 0.1 degrees C. This represents an increase in temperature resolution of an order of magnitude over that achieved previously by FLIM of temperature-sensitive dyes.

  8. Quantitative analysis of the Stratus optical coherence tomography fast macular thickness map reports

    Directory of Open Access Journals (Sweden)

    Domalpally Amitha

    2010-01-01

    Full Text Available The cross sectional optical coherence tomography images have an important role in evaluating retinal diseases. The reports generated by the Stratus fast macular thickness scan protocol are useful for both clinical and research purposes. The centerpoint thickness is an important outcome measure for many therapeutic trials related to macular disease. The data is susceptible to artifacts such as decentration and boundary line errors and could be potentially erroneous. An understanding of how the data is generated is essential before utilizing the data. This article describes the interpretation of the fast macular thickness map report, assessment of the quality of an optical coherence tomography image and identification of the artifacts that could influence the numeric data.

  9. Association Mapping of Quantitative Trait Loci for Mineral Element Contents in Whole Grain Rice (Oryza sativa L.).

    Science.gov (United States)

    Huang, Yan; Sun, Chengxiao; Min, Jie; Chen, Yaling; Tong, Chuan; Bao, Jinsong

    2015-12-23

    Mineral elements in brown rice grain play an important role in human health. In this study, variations in the content of iron (Fe), zinc (Zn), selenium (Se), cadmium (Cd), and lead (Pb) in 378 accessions of brown rice were investigated, and association mapping was used to detect the quantitative trait loci (QTLs) responsible for the variation. Among seven subpopulations, the mean values of Zn and Cd in the japonica group were significantly higher than in the indica groups. The population structure accounted for from 5.7% (Se) to 22.1% (Pb) of the total variation. Correlation analyses showed that Pb was positively correlated with the other minerals (P rice grain by marker-assisted selection (MAS).

  10. A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis.

    Science.gov (United States)

    Grimsrud, Paul A; Carson, Joshua J; Hebert, Alex S; Hubler, Shane L; Niemi, Natalie M; Bailey, Derek J; Jochem, Adam; Stapleton, Donald S; Keller, Mark P; Westphall, Michael S; Yandell, Brian S; Attie, Alan D; Coon, Joshua J; Pagliarini, David J

    2012-11-07

    Mitochondria are dynamic organelles that play a central role in a diverse array of metabolic processes. Elucidating mitochondrial adaptations to changing metabolic demands and the pathogenic alterations that underlie metabolic disorders represent principal challenges in cell biology. Here, we performed multiplexed quantitative mass spectrometry-based proteomics to chart the remodeling of the mouse liver mitochondrial proteome and phosphoproteome during both acute and chronic physiological transformations in more than 50 mice. Our analyses reveal that reversible phosphorylation is widespread in mitochondria, and is a key mechanism for regulating ketogenesis during the onset of obesity and type 2 diabetes. Specifically, we have demonstrated that phosphorylation of a conserved serine on Hmgcs2 (S456) significantly enhances its catalytic activity in response to increased ketogenic demand. Collectively, our work describes the plasticity of this organelle at high resolution and provides a framework for investigating the roles of proteome restructuring and reversible phosphorylation in mitochondrial adaptation.

  11. Joint 2D and 3D phase processing for quantitative susceptibility mapping: application to 2D echo-planar imaging.

    Science.gov (United States)

    Wei, Hongjiang; Zhang, Yuyao; Gibbs, Eric; Chen, Nan-Kuei; Wang, Nian; Liu, Chunlei

    2017-04-01

    Quantitative susceptibility mapping (QSM) measures tissue magnetic susceptibility and typically relies on time-consuming three-dimensional (3D) gradient-echo (GRE) MRI. Recent studies have shown that two-dimensional (2D) multi-slice gradient-echo echo-planar imaging (GRE-EPI), which is commonly used in functional MRI (fMRI) and other dynamic imaging techniques, can also be used to produce data suitable for QSM with much shorter scan times. However, the production of high-quality QSM maps is difficult because data obtained by 2D multi-slice scans often have phase inconsistencies across adjacent slices and strong susceptibility field gradients near air-tissue interfaces. To address these challenges in 2D EPI-based QSM studies, we present a new data processing procedure that integrates 2D and 3D phase processing. First, 2D Laplacian-based phase unwrapping and 2D background phase removal are performed to reduce phase inconsistencies between slices and remove in-plane harmonic components of the background phase. This is followed by 3D background phase removal for the through-plane harmonic components. The proposed phase processing was evaluated with 2D EPI data obtained from healthy volunteers, and compared against conventional 3D phase processing using the same 2D EPI datasets. Our QSM results were also compared with QSM values from time-consuming 3D GRE data, which were taken as ground truth. The experimental results show that this new 2D EPI-based QSM technique can produce quantitative susceptibility measures that are comparable with those of 3D GRE-based QSM across different brain regions (e.g. subcortical iron-rich gray matter, cortical gray and white matter). This new 2D EPI QSM reconstruction method is implemented within STI Suite, which is a comprehensive shareware for susceptibility imaging and quantification. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

    Directory of Open Access Journals (Sweden)

    Wang Xiaoqiang

    2012-04-01

    Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i

  13. Quantitative Trait Locus Mapping of Salt Tolerance and Identification of Salt-Tolerant Genes in Brassica napus L

    Directory of Open Access Journals (Sweden)

    Lina Lang

    2017-06-01

    Full Text Available Salinity stress is one of typical abiotic stresses that seriously limit crop production. In this study, a genetic linkage map based on 532 molecular markers covering 1341.1 cM was constructed to identify the loci associated with salt tolerance in Brassica napus. Up to 45 quantitative trait loci (QTLs for 10 indicators were identified in the F2:3 populations. These QTLs can account for 4.80–51.14% of the phenotypic variation. A major QTL, qSPAD5 on LG5 associated with chlorophyll can be detected in three replicates. Two intron polymorphic (IP markers in this QTL region were developed successfully to narrow down the QTL location to a region of 390 kb. A salt tolerance related gene Bra003640 was primary identified as the candidate gene in this region. The full length of the candidate gene was 1,063 bp containing three exons and two introns in B. napus L. The open reading frame (ORF is 867 bp and encodes 287 amino acids. Three amino acid differences (34, 54, and 83 in the conserved domain (B-box were identified. RT-qPCR analysis showed that the gene expression had significant difference between the two parents. The study laid great foundation for salt tolerance related gene mapping and cloning in B. napus L.

  14. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations.

    Science.gov (United States)

    Schielzeth, Holger; Husby, Arild

    2014-07-01

    A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.

  15. Inheritance and quantitative trail loci mapping of adventitious root numbers in cucumber seedlings under waterlogging conditions.

    Science.gov (United States)

    Xu, Xuewen; Ji, Jing; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

    2017-04-01

    The hypocotyl-derived adventitious root (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis has not been adequately understood. In the present study, a mixed major gene plus polygene inheritance model was used to analyze AR numbers (ARN) 7 days after waterlogging treatment in six generations (P1, P2, F1, B1, B2, and F2), using cucumber waterlogging tolerant line Zaoer-N and sensitive Pepino as parents. The results showed that the genetic model D-4, mixed one negative dominance major gene and additive-dominance polygenes, is the best-fitting genetic model for waterlogging-triggered ARN phenotype. A genetic linkage map spanning 550.8 cM and consisting of 149 simple sequence repeat (SSR) markers segregating into seven linkage groups was constructed. Three QTLs (ARN3.1, ARN5.1, and ARN6.1) distributed on chromosomes 3, 5, and 6 were identified by composite interval mapping. The major-effect QTL, ARN6.1, located between SSR12898 and SSR04751, was the only locus detected in three seasons, with least likelihood (LOD) scores of 8.8, 10.4, and 9.5 and account for 17.6, 24, and 19.8% of the phenotypic variance, respectively. Using five additional single nucleotide polymorphism (SNP) makers, the ARN6.1 was narrowed down to a 0.79 Mb interval franked by SSR12898 and SNP25558853. Illumina RNA-sequencing data generated on hypocotyls of two parents 48 h after waterlogging treatment revealed 15 genes in the 0.79 Mb interval were differentially expressed, including Csa6G503880 encoding a salicylic acid methyl transferase-like protein, Csa6G504590 encoding a cytochrome P450 monooxygenase, and Csa6G505230 encoding a heavy metal-associated protein. Our findings shed light on the genetic architecture underlying adventitious rooting during waterlogging stress in cucumber, and provide a list of potential gene targets for further elucidating waterlogging tolerance in plants.

  16. Mapping irrigation potential from renewable groundwater in Africa - a quantitative hydrological approach

    Science.gov (United States)

    Altchenko, Y.; Villholth, K. G.

    2015-02-01

    Groundwater provides an important buffer to climate variability in Africa. Yet, groundwater irrigation contributes only a relatively small share of cultivated land, approximately 1% (about 2 × 106 hectares) as compared to 14% in Asia. While groundwater is over-exploited for irrigation in many parts in Asia, previous assessments indicate an underutilized potential in parts of Africa. As opposed to previous country-based estimates, this paper derives a continent-wide, distributed (0.5° spatial resolution) map of groundwater irrigation potential, indicated in terms of fractions of cropland potentially irrigable with renewable groundwater. The method builds on an annual groundwater balance approach using 41 years of hydrological data, allocating only that fraction of groundwater recharge that is in excess after satisfying other present human needs and environmental requirements, while disregarding socio-economic and physical constraints in access to the resource. Due to high uncertainty of groundwater environmental needs, three scenarios, leaving 30, 50 and 70% of recharge for the environment, were implemented. Current dominating crops and cropping rotations and associated irrigation requirements in a zonal approach were applied in order to convert recharge excess to potential irrigated cropland. Results show an inhomogeneously distributed groundwater irrigation potential across the continent, even within individual countries, mainly reflecting recharge patterns and presence or absence of cultivated cropland. Results further show that average annual renewable groundwater availability for irrigation ranges from 692 to 1644 km3 depending on scenario. The total area of cropland irrigable with renewable groundwater ranges from 44.6 to 105.3 × 106 ha, corresponding to 20.5 to 48.6% of the cropland over the continent. In particular, significant potential exists in the semi-arid Sahel and eastern African regions which could support poverty alleviation if developed

  17. Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data.

    Science.gov (United States)

    Sillanpää, Mikko J; Hoti, Fabian

    2007-12-01

    A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the log-normal survival time or censored/selected traits. A great benefit of the approach is that it enables the utilization of multiple-QTL models, is easy to incorporate into different data designs (experimental and outbred populations), and can potentially be extended to epistatic models. In inbred lines, the method exploits the fact that the parental mating type and the linkage phases (haplotypes) are known by definition. In outbred populations, two-generation data are needed, for example, selected offspring and one of the parents (the sires) in breeding material. The idea is to statistically (computationally) generate a fully complementary, maximally dissimilar, observation for each offspring in the sample. Bayesian data augmentation is then used to sample the space of possible trait values for the pseudoobservations. The benefits of the approach are illustrated using simulated data sets and a real data set on the survival of F(2) mice following infection with Listeria monocytogenes.

  18. Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice.

    Science.gov (United States)

    Xie, Lixia; Tan, Zhengwei; Zhou, Yuan; Xu, Rongbao; Feng, Laibao; Xing, Yongzhong; Qi, Xiaoquan

    2014-08-01

    Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments.

  19. Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

    Institute of Scientific and Technical Information of China (English)

    Lixia Xie; Zhengwei Tan; Yuan Zhou; Rongbao Xu; Laibao Feng; Yongzhong Xing; Xiaoquan Qi

    2014-01-01

    Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establish-ment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-tempera-ture-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive al eles for increased seed vigor in both normal and low-temperature germination environments.

  20. Electron microscopic and autoradiographic analysis of the distribution of the vagus nerve in the ferret stomach

    OpenAIRE

    Al Muhtaseb, M. H. [محمد هاشم المحتسب; Kittani, H. F.

    1999-01-01

    In this study, tritiated leucine was injected into the vagal dorsal motor nucleus after acute and chronic partial vagotomy. The method of sampling of the stomach, application of % 2 test and the analysis of the electron microscopic autoradiographs revealed that the distribution of silver grains over the axon profiles were uniformly distributed over the body and pyloric areas of the stomach. Also a % test showed that the number of grains is independent of the area chosen. Statistical analysis ...

  1. TU-C-12A-02: Development of a Multiparametric Statistical Response Map for Quantitative Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bosca, R [The University of Texas Graduate School of Biomedical Sciences, Houston, TX (United States); The University of Texas MD Anderson Cancer Center, Houston, TX (United States); Mahajan, A; Brown, PD; Stafford, RJ [The University of Texas MD Anderson Cancer Center, Houston, TX (United States); Johnson, VE [Texas A' M University, College Station, TX (United States); Dong, L [Scripps Proton Therapy Center, San Diego, CA (United States); Jackson, EF [University of Wisconsin, Madison, WI (United States)

    2014-06-15

    Purpose: Quantitative imaging biomarkers (QIB) are becoming increasingly utilized in early phase clinical trials as a means of non-invasively assessing treatment response and associated response heterogeneity. The aim of this study was to develop a flexible multiparametric statistical framework to predict voxel-by-voxel response of several potential MRI QIBs. Methods: Patients with histologically proven glioblastomas (n=11) were treated with chemoradiation (with/without bevacizumab) and underwent one baseline and two mid-treatment (3–4wks) MRIs. Dynamic contrast-enhanced (3D FSPGR, 6.3sec/phase, 0.1 mmol/kg Gd-DTPA), dynamic susceptibility contrast (2D GRE-EPI, 1.5sec/phase, 0.2mmol/kg Gd-DTPA), and diffusion tensor (2D DW-EPI, b=0, 1200 s/mm{sup 2}, 27 directions) imaging acquisitions were obtained during each study. Mid-treatment and pre-treatment images were rigidly aligned, and regions of partial response (PR), stable disease (SD), and progressive disease (PD) were contoured in consensus by two experienced radiation oncologists. Voxels in these categories were used to train ordinal (PR

  2. Bone quantitative susceptibility mapping using a chemical species-specific R2* signal model with ultrashort and conventional echo data.

    Science.gov (United States)

    Dimov, Alexey V; Liu, Zhe; Spincemaille, Pascal; Prince, Martin R; Du, Jiang; Wang, Yi

    2017-03-05

    To develop quantitative susceptibility mapping (QSM) of bone using an ultrashort echo time (UTE) gradient echo (GRE) sequence for signal acquisition and a bone-specific effective transverse relaxation rate ( R2*) to model water-fat MR signals for field mapping. Three-dimensional radial UTE data (echo times ≥ 40 μs) was acquired on a 3 Tesla scanner and fitted with a bone-specific signal model to map the chemical species and susceptibility field. Experiments were performed ex vivo on a porcine hoof and in vivo on healthy human subjects (n = 7). For water-fat separation, a bone-specific model assigning R2* decay mostly to water was compared with the standard models that assigned the same decay for both fat and water. In the ex vivo experiment, bone QSM was correlated with CT. Compared with standard models, the bone-specific R2* method significantly reduced errors in the fat fraction within the cortical bone in all tested data sets, leading to reduced artifacts in QSM. Good correlation was found between bone CT and QSM values in the porcine hoof (R(2)  = 0.77). Bone QSM was successfully generated in all subjects. The QSM of bone is feasible using UTE with a conventional echo time GRE acquisition and a bone-specific R2* signal model. Magn Reson Med 000:000-000, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  3. Quantitative mapping of particulate iron in an ocean dump using remotely sensed data

    Science.gov (United States)

    Ohlhorst, C. W.; Bahn, G. S.

    1978-01-01

    A remote sensing experiment was conducted at the industrial acid waste ocean dump site located approximately 38 n mi SE of Cape Henlopen, Delaware, to see if there was a relationship between aircraft remotely sensed spectral signatures and the iron concentration measured in the plume. Results are presented which show that aircraft remotely sensed spectral data can be used to quantify and map an acid waste dump in terms of its particulate iron concentration. A single variable equation using the ratio of band 2 (440-490 nm) radiance to band 4 (540-580 nm) radiance was used to quantify the acid plume and the surrounding water. The acid waste varied in age from freshly dumped to 3 1/2 hours old. Particulate iron concentrations in the acid waste were estimated to range up to 1.1 mg/liter at the 0.46 meter depth. A classification technique was developed to remove sunglitter-affected pixels from the data set.

  4. Quantitative analysis of scale of aeromagnetic data raises questions about geologic-map scale

    Science.gov (United States)

    Nykanen, V.; Raines, G.L.

    2006-01-01

    A recently published study has shown that small-scale geologic map data can reproduce mineral assessments made with considerably larger scale data. This result contradicts conventional wisdom about the importance of scale in mineral exploration, at least for regional studies. In order to formally investigate aspects of scale, a weights-of-evidence analysis using known gold occurrences and deposits in the Central Lapland Greenstone Belt of Finland as training sites provided a test of the predictive power of the aeromagnetic data. These orogenic-mesothermal-type gold occurrences and deposits have strong lithologic and structural controls associated with long (up to several kilometers), narrow (up to hundreds of meters) hydrothermal alteration zones with associated magnetic lows. The aeromagnetic data were processed using conventional geophysical methods of successive upward continuation simulating terrane clearance or 'flight height' from the original 30 m to an artificial 2000 m. The analyses show, as expected, that the predictive power of aeromagnetic data, as measured by the weights-of-evidence contrast, decreases with increasing flight height. Interestingly, the Moran autocorrelation of aeromagnetic data representing differing flight height, that is spatial scales, decreases with decreasing resolution of source data. The Moran autocorrelation coefficient scems to be another measure of the quality of the aeromagnetic data for predicting exploration targets. ?? Springer Science+Business Media, LLC 2007.

  5. Quantitative chemical mapping of sodium acrylate- and N-vinylpyrrolidone-enhanced alginate microcapsules.

    Science.gov (United States)

    Araki, Tohru; Hitchcock, Adam P; Shen, Feng; Chang, Patricia L; Wang, Maggie; Childs, Ronald F

    2005-01-01

    Alginate microcapsules enclosing recombinant cells secreting therapeutic products have been used successfully to treat several murine models of human diseases. The mechanical and chemical properties of these alginate capsules can be improved by the addition and in situ photo-polymerization of sodium acrylate and N-vinylpyrrolidone in the alginate capsule. The purpose of this modification was to form additional covalent cross-links. In this work we have used scanning transmission X-ray microscopy (STXM) to probe the nature and location of the chemical modifications in the modified capsules by comparison with unmodified capsules. Analysis of X-ray image sequences and selected area spectra has been used to map the calcium gradient in capsules, to identify the presence of polyacrylate throughout the capsules and the localization of poly-N-vinylpyrrolidone in the outer regions of the alginate capsules. The differences in the spatial distributions of these species have led to better understanding of the chemical modifications that provide a mechanically more stable capsule structure.

  6. Quantitative T2 mapping of white matter: applications for ageing and cognitive decline

    Science.gov (United States)

    Knight, Michael J.; McCann, Bryony; Tsivos, Demitra; Dillon, Serena; Coulthard, Elizabeth; Kauppinen, Risto A.

    2016-08-01

    In MRI, the coherence lifetime T2 is sensitive to the magnetic environment imposed by tissue microstructure and biochemistry in vivo. Here we explore the possibility that the use of T2 relaxometry may provide information complementary to that provided by diffusion tensor imaging (DTI) in ageing of healthy controls (HC), Alzheimer’s disease (AD) and mild cognitive impairment (MCI). T2 and diffusion MRI metrics were quantified in HC and patients with MCI and mild AD using multi-echo MRI and DTI. We used tract-based spatial statistics (TBSS) to evaluate quantitative MRI parameters in white matter (WM). A prolonged T2 in WM was associated with AD, and able to distinguish AD from MCI, and AD from HC. Shorter WM T2 was associated with better cognition and younger age in general. In no case was a reduction in T2 associated with poorer cognition. We also applied principal component analysis, showing that WM volume changes independently of  T2, MRI diffusion indices and cognitive performance indices. Our data add to the evidence that age-related and AD-related decline in cognition is in part attributable to WM tissue state, and much less to WM quantity. These observations suggest that WM is involved in AD pathology, and that T2 relaxometry is a potential imaging modality for detecting and characterising WM in cognitive decline and dementia.

  7. Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines.

    Science.gov (United States)

    Crowgey, Erin L; Matlock, Andrea; Venkatraman, Vidya; Fert-Bober, Justyna; Van Eyk, Jennifer E

    2017-01-01

    Data-independent acquisition mass spectrometry (DIA-MS) strategies and applications provide unique advantages for qualitative and quantitative proteome probing of a biological sample allowing constant sensitivity and reproducibility across large sample sets. These advantages in LC-MS/MS are being realized in fundamental research laboratories and for clinical research applications. However, the ability to translate high-throughput raw LC-MS/MS proteomic data into biological knowledge is a complex and difficult task requiring the use of many algorithms and tools for which there is no widely accepted standard and best practices are slowly being implemented. Today a single tool or approach inherently fails to capture the full interpretation that proteomics uniquely supplies, including the dynamics of quickly reversible chemically modified states of proteins, irreversible amino acid modifications, signaling truncation events, and, finally, determining the presence of protein from allele-specific transcripts. This chapter highlights key steps and publicly available algorithms required to translate DIA-MS data into knowledge.

  8. Regional Myocardial Substrate Uptake in Hypertensive Rats: A Quantitative Autoradiographic Measurement

    Science.gov (United States)

    Yonekura, Yoshiharu; Bertrand Brill, A.; Som, Prantika; Yamamoto, Kazutaka; Srivastava, Suresh C.; Iwai, Junichi; Elmaleh, David R.; Livni, Eli; Strauss, H. William; Goodman, Mark M.; Knapp, Furn F.

    1985-03-01

    Severe hypertension causes global and regional changes in myocardial perfusion and substrate utilization. Regional perfusion and fatty acid utilization were evaluated by dual-tracer autoradiography in normotensive and hypertensive rats of the Dahl strain. The regional distributions of perfusion and fatty acid utilization were homogeneous in normotensive rats. Severe hypertension was associated with a homogeneous pattern of regional perfusion, but fatty acid utilization was focally decreased in the free wall of the left ventricle. The decrease in fatty acid uptake was associated with a concomitant increase in glucose utilization. These findings suggest that severe hypertension is associated with uniform myocardial perfusion and focal alterations in the substrates used for the performance of myocardial work.

  9. Quantitative analysis of autoradiographic image intensification using Thiourea-S35

    Science.gov (United States)

    Askins, B. S.; Odell, C. R.

    1980-01-01

    Photographic images enhanced by the method of Thiourea-S35 autoradiography are evaluated in terms of signal-to-noise ratio, detective quantum efficiency (DQE), and Wiener spectrum analysis using digitized images. It is determined that the original signal-to-noise ratio is not degraded by the intensification process which allows an increase in the practical working DQE as a function of density. These results apply at all spatial frequencies that were tested. The advantage given by autoradiography is the ability to produce usable images from emulsions originally exposed to the low densities corresponding to maximum DQE and movement of faint image densities above the level of the threshold for detection.

  10. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.

    Directory of Open Access Journals (Sweden)

    Schaffer Arthur

    2011-07-01

    Full Text Available Abstract Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L. over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS. Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org, an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability

  11. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    Science.gov (United States)

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

  12. A new algebraic method for quantitative proton density mapping using multi-channel coil data.

    Science.gov (United States)

    Cordes, Dietmar; Yang, Zhengshi; Zhuang, Xiaowei; Sreenivasan, Karthik; Mishra, Virendra; Hua, Le H

    2017-08-01

    A difficult problem in quantitative MRI is the accurate determination of the proton density, which is an important quantity in measuring brain tissue organization. Recent progress in estimating proton density in vivo has been based on using the inverse linear relationship between the longitudinal relaxation rate T1 and proton density. In this study, the same type of relationship is being used, however, in a more general framework by constructing 3D basis functions to model the receiver bias field. The novelty of this method is that the basis functions developed are suitable to cover an entire range of inverse linearities between T1 and proton density. The method is applied by parcellating the human brain into small cubes with size 30mm x 30mm x 30mm. In each cube the optimal set of basis functions is determined to model the receiver coil sensitivities using multi-channel (32 element) coil data. For validation, we use arbitrary data from a numerical phantom where the data satisfy the conventional MR signal equations. Using added noise of different magnitude and realizations, we show that the proton densities obtained have a bias close to zero and also low noise sensitivity. The obtained root-mean-square-error rate is less than 0.2% for the estimated proton density in a realistic 3D simulation. As an application, the method is used in a small cohort of MS patients, and proton density values for specific brain structures are determined. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry

    Science.gov (United States)

    Galland, Nicolas; Kone, Soleymane; Le Questel, Jean-Yves

    2012-10-01

    A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.

  14. Quantitative analysis of axonal fiber activation evoked by deep brain stimulation via activation density heat maps

    Directory of Open Access Journals (Sweden)

    Christian J. Hartmann

    2015-02-01

    Full Text Available Background: Cortical modulation is likely to be involved in the various therapeutic effects of deep brain stimulation (DBS. However, it is currently difficult to predict the changes of cortical modulation during clinical adjustment of DBS. Therefore, we present a novel quantitative approach to estimate anatomical regions of DBS-evoked cortical modulation. Methods: Four different models of the subthalamic nucleus (STN DBS were created to represent variable electrode placements (model I: dorsal border of the posterolateral STN; model II: central posterolateral STN; model III: central anteromedial STN; model IV: dorsal border of the anteromedial STN. Axonal fibers of passage near each electrode location were reconstructed using probabilistic tractography and modeled using multi-compartment cable models. Stimulation-evoked activation of local axon fibers and corresponding cortical projections were modeled and quantified. Results: Stimulation at the border of the STN (models I and IV led to a higher degree of fiber activation and associated cortical modulation than stimulation deeply inside the STN (models II and III. A posterolateral target (models I and II was highly connected to cortical areas representing motor function. Additionally, model I was also associated with strong activation of fibers projecting to the cerebellum. Finally, models III and IV showed a dorsoventral difference of preferentially targeted prefrontal areas (models III: middle frontal gyrus; model IV: inferior frontal gyrus.Discussion: The method described herein allows characterization of cortical modulation across different electrode placements and stimulation parameters. Furthermore, knowledge of anatomical distribution of stimulation-evoked activation targeting cortical regions may help predict efficacy and potential side effects, and therefore can be used to improve the therapeutic effectiveness of individual adjustments in DBS patients.

  15. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry.

    Science.gov (United States)

    Galland, Nicolas; Kone, Soleymane; Le Questel, Jean-Yves

    2012-10-01

    A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.

  16. Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4.

    Science.gov (United States)

    Silva, K M; Bastiaansen, J W M; Knol, E F; Merks, J W M; Lopes, P S; Guimarães, S E F; van Arendonk, J A M

    2011-06-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.

  17. Population average T2 MRI maps reveal quantitative regional transformations in the degenerating rabbit intervertebral disc that vary by lumbar level.

    Science.gov (United States)

    Martin, John T; Collins, Christopher M; Ikuta, Kensuke; Mauck, Robert L; Elliott, Dawn M; Zhang, Yeija; Anderson, D Greg; Vaccaro, Alexander R; Albert, Todd J; Arlet, Vincent; Smith, Harvey E

    2015-01-01

    Magnetic resonance imaging (MRI) with T2-weighting is routinely performed to assess intervertebral disc degeneration. Standard clinical evaluations of MR images are qualitative, however, and do not focus on region-specific alterations in the disc. Utilizing a rabbit needle puncture model, T2 mapping was performed on injured discs to develop a quantitative description of the degenerative process following puncture. To do so, an 18G needle was inserted into four discs per rabbit (L3/L4 to L6/L7) and T2 maps were generated pre- and 4 weeks post-injury. Individual T2 maps were normalized to a disc-specific coordinate system and then averaged for pre- and post-injury population composite T2 maps. We also developed a method to automatically segment the nucleus pulposus by fitting the NP region of the T2 maps with modified 2-D and 3-D Gaussian distribution functions. Puncture injury produced alterations in MR signal intensity in a region-specific manner mirroring human degeneration. Population average T2 maps provided a quantitative representation of the injury response, and identified deviations of individual degenerate discs from the pre-injury population. We found that the response to standardized injury was modest at lower lumbar levels, likely as a result of increased disc dimensions. These tools will be valuable for the quantitative characterization of disc degeneration in future clinical and pre-clinical studies. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  18. Genome-wide association mapping of quantitative traits in a breeding population of sugarcane.

    Science.gov (United States)

    Racedo, Josefina; Gutiérrez, Lucía; Perera, María Francisca; Ostengo, Santiago; Pardo, Esteban Mariano; Cuenya, María Inés; Welin, Bjorn; Castagnaro, Atilio Pedro

    2016-06-24

    Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. Previous sugarcane genome-wide association analyses (GWAS) have found few molecular markers associated with relevant traits at plant-cane stage. The aim of this study was to establish an appropriate GWAS to find molecular markers associated with yield related traits consistent across harvesting seasons in a breeding population. Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY) and sugar content (SC) at two locations during three successive crop cycles. GWAS mapping was applied within a novel mixed-model framework accounting for population structure with Principal Component Analysis scores as random component. A total of 43 markers significantly associated with CY in plant-cane, 42 in first ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were associated with CY in 2 years. Additionally, 38 significant associations for SC were detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker-trait association was found significant for the 3 years of the study, while twelve markers presented association for 2 years. In the multi-QTL model several markers with large allelic substitution effect were found. Sequences of four DArT markers showed high similitude and e-value with coding sequences of Sorghum bicolor, confirming the high gene microlinearity between sorghum and sugarcane. In contrast with other sugarcane GWAS studies reported earlier, the novel methodology to analyze multi-QTLs through successive crop cycles used in the present study allowed us to find several markers associated with relevant traits. Combining existing phenotypic trial data and genotypic DArT and TRAP marker characterizations within a GWAS approach including population structure as

  19. Osteochondritis dissecans of the capitellum: lesion size and pattern analysis using quantitative 3-dimensional computed tomography and mapping technique.

    Science.gov (United States)

    Bexkens, Rens; Oosterhoff, Jacobien H; Tsai, Tsung-Yuan; Doornberg, Job N; van den Bekerom, Michel P J; Eygendaal, Denise; Oh, Luke S

    2017-09-01

    The goals of this study were to evaluate the reliability of a quantitative 3-dimensional computed tomography (Q3DCT) technique for measurement of the capitellar osteochondritis dissecans (OCD) surface area, to analyze OCD distribution using a mapping technique, and to investigate associations between Q3DCT lesion quantification and demographic characteristics and/or clinical examination findings. We identified patients with capitellar OCD who presented to our orthopedic sports medicine practice between January 2001 and January 2016 and who had undergone a preoperative computed tomography scan (slice thickness ≤1.25 mm). A total of 17 patients with a median age of 15 years (range, 12-23 years) were included in this study. Three-dimensional polygon models were reconstructed after osseous structures were marked in 3 planes. Surface areas of the OCD lesion as well as the capitellum were measured. Observer agreement was assessed with the intraclass correlation coefficient (ICC). Heat maps were created to visualize OCD distribution. Measurements of the OCD surface area showed almost perfect intraobserver agreement (ICC, 0.99; confidence interval [CI], 0.98-0.99) and interobserver agreement (ICC, 0.93; CI, 0.86-0.97). Measurements of the capitellar surface area also showed almost perfect intraobserver agreement (ICC, 0.97;CI, 0.91-0.99) and interobserver agreement (ICC, 0.86; CI, 0.46-0.96). The median OCD surface area was 101 mm(2) (range, 49-217 mm(2)). On the basis of OCD heat mapping, the posterolateral zone of the capitellum was most frequently affected. OCDs in which the lateral wall was involved were associated with larger lesion size (P = .041), longer duration of symptoms (P = .030), and worse elbow extension (P = .013). The ability to quantify the capitellar OCD surface area and lesion location in a reliable manner using Q3DCT and a mapping technique should be considered when detailed knowledge of lesion size and location is desired

  20. Characterization of Benign Myocarditis Using Quantitative Delayed-Enhancement Imaging Based on Molli T1 Mapping.

    Science.gov (United States)

    Toussaint, Marcel; Gilles, Raymond J; Azzabou, Noura; Marty, Benjamin; Vignaud, Alexandre; Greiser, Andreas; Carlier, Pierre G

    2015-10-01

    Delayed contrast enhancement after injection of a gadolinium-chelate (Gd-chelate) is a reference imaging method to detect myocardial tissue changes. Its localization within the thickness of the myocardial wall allows differentiating various pathological processes such as myocardial infarction (MI), inflammatory myocarditis, and cardiomyopathies. The aim of the study was first to characterize benign myocarditis using quantitative delayed-enhancement imaging and then to investigate whether the measure of the extracellular volume fraction (ECV) can be used to discriminate between MI and myocarditis.In 6 patients with acute benign myocarditis (32.2 ± 13.8 year-old, subepicardial late gadolinium enhancement [LGE]) and 18 patients with MI (52.3 ± 10.9 year-old, subendocardial/transmural LGE), myocardial T1 was determined using the Modified Look-Locker Imaging (MOLLI) sequence at 3 Tesla before and after Gd-chelate injection. T1 values were compared in LGE and normal regions of the myocardium. The myocardial T1 values were normalized to the T1 of blood, and the ECV was calculated from T1 values of myocardium and blood pre- and post-Gd injection.In both myocarditis and MI, the T1 was lower in LGE regions than in normal regions of the left ventricle. T1 of LGE areas was significantly higher in myocarditis than in MI (446.8 ± 45.8 vs 360.5 ± 66.9 ms, P = 0.003) and ECV was lower in myocarditis than in MI (34.5 ± 3.3 vs 53.8 ± 13.0 %, P = 0.004).Both inflammatory process and chronic fibrosis induce LGE (subepicardial in myocarditis and subendocardial in MI). The present study demonstrates that the determination of T1 and ECV is able to differentiate the 2 histological patterns.Further investigation will indicate whether the severity of ECV changes might help refine the predictive risk of LGE in myocarditis.

  1. Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1

    Science.gov (United States)

    Hancock, Dana B.; Levy, Joshua L.; Gaddis, Nathan C.; Glasheen, Cristie; Saccone, Nancy L.; Page, Grier P.; Hulse, Gary; Wildenauer, Dieter; Kelty, Erin; Schwab, Sibylle; Degenhardt, Louisa; Martin, Nicholas G.; Montgomery, Grant W.; Attia, John; Holliday, Elizabeth G.; McEvoy, Mark; Scott, Rodney J.; Bierut, Laura J.; Nelson, Elliot C.; Kral, Alex; Johnson, Eric O.

    2015-01-01

    Background No opioid receptor, mu 1 (OPRM1) gene polymorphisms, including the functional single nucleotide polymorphism (SNP) rs1799971, have been conclusively associated with heroin/other opioid addiction, despite their biological plausibility. We used evidence of polymorphisms altering OPRM1 expression in normal human brain tissue to nominate and then test associations with heroin addiction. Methods We tested 103 OPRM1 SNPs for association with OPRM1 mRNA expression in prefrontal cortex from 224 European Americans and African Americans of the BrainCloud cohort. We then tested the 16 putative cis-quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in the Urban Health Study and two replication cohorts, totaling 16,729 European Americans, African Americans, and Australians of European ancestry. Results Four putative cis-eQTL SNPs were significantly associated with heroin addiction in the Urban Health Study (smallest P=8.9×10−5): rs9478495, rs3778150, rs9384169, and rs562859. Rs3778150, located in OPRM1 intron 1, was significantly replicated (P=6.3×10−5). Meta-analysis across all case-control cohorts resulted in P=4.3×10−8: the rs3778150-C allele (frequency=16%-19%) being associated with increased heroin addiction risk. Importantly, the functional SNP allele rs1799971-A was associated with heroin addiction only in the presence of rs3778150-C (P=1.48×10−6 for rs1799971-A/rs3778150-C and P=0.79 for rs1799971-A/rs3778150-T haplotypes). Lastly, replication was observed for six other intron 1 SNPs which had prior suggestive associations with heroin addiction (smallest P=2.7×10−8 for rs3823010). Conclusions Our findings show that common OPRM1 intron 1 SNPs have replicable associations with heroin addiction. The haplotype structure of rs3778150 and nearby SNPs may underlie the inconsistent associations between rs1799971 and heroin addiction. PMID:25744370

  2. A method for quantitative mapping of thick oil spills using imaging spectroscopy

    Science.gov (United States)

    Clark, Roger N.; Swayze, Gregg A.; Leifer, Ira; Livo, K. Eric; Kokaly, Raymond F.; Hoefen, Todd; Lundeen, Sarah; Eastwood, Michael; Green, Robert O.; Pearson, Neil; Sarture, Charles; McCubbin, Ian; Roberts, Dar; Bradley, Eliza; Steele, Denis; Ryan, Thomas; Dominguez, Roseanne; ,

    2010-01-01

    In response to the Deepwater Horizon oil spill in the Gulf of Mexico, a method of near-infrared imaging spectroscopic analysis was developed to map the locations of thick oil floating on water. Specifically, this method can be used to derive, in each image pixel, the oil-to-water ratio in oil emulsions, the sub-pixel areal fraction, and its thicknesses and volume within the limits of light penetration into the oil (up to a few millimeters). The method uses the shape of near-infrared (NIR) absorption features and the variations in the spectral continuum due to organic compounds found in oil to identify different oil chemistries, including its weathering state and thickness. The method is insensitive to complicating conditions such as moderate aerosol scattering and reflectance level changes from other conditions, including moderate sun glint. Data for this analysis were collected by the NASA Airborne Visual Infrared Imaging Spectrometer (AVIRIS) instrument, which was flown over the oil spill on May 17, 2010. Because of the large extent of the spill, AVIRIS flight lines could cover only a portion of the spill on this relatively calm, nearly cloud-free day. Derived lower limits for oil volumes within the top few millimeters of the ocean surface directly probed with the near-infrared light detected in the AVIRIS scenes were 19,000 (conservative assumptions) to 34,000 (aggressive assumptions) barrels of oil. AVIRIS covered about 30 percent of the core spill area, which consisted of emulsion plumes and oil sheens. Areas of oil sheen but lacking oil emulsion plumes outside of the core spill were not evaluated for oil volume in this study. If the core spill areas not covered by flight lines contained similar amounts of oil and oil-water emulsions, then extrapolation to the entire core spill area defined by a MODIS (Terra) image collected on the same day indicates a minimum of 66,000 to 120,000 barrels of oil was floating on the surface. These estimates are preliminary and

  3. Quantitative multi-parameter mapping of R1, PD*, MT and R2* at 3T: a multi-center validation

    Directory of Open Access Journals (Sweden)

    Nikolaus eWeiskopf

    2013-06-01

    Full Text Available Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1mm high-resolution maps of the longitudinal relaxation rate (R1=1/T1, effective proton density (PD*, magnetization transfer saturation (MT and effective transverse relaxation rate (R2*=1/T2*. MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV for typical morphometric measures (i.e., gray matter probability maps used in voxel-based morphometry and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1% and 8%, respectively, except for the inter-site CoV of R2* (< 20%. The gray matter probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived gray matter probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.

  4. Towards quantitative off-axis electron holographic mapping of the electric field around the tip of a sharp biased metallic needle

    DEFF Research Database (Denmark)

    Beleggia, Marco; Kasama, Takeshi; Larson, D. J.

    2014-01-01

    We apply off-axis electron holography and Lorentz microscopy in the transmission electron microscope to map the electric field generated by a sharp biased metallic tip. A combination of experimental data and modelling provides quantitative information about the potential and the field around the ...

  5. High-throughput computer vision introduces the time axis to a quantitative trait map of a plant growth response.

    Science.gov (United States)

    Moore, Candace R; Johnson, Logan S; Kwak, Il-Youp; Livny, Miron; Broman, Karl W; Spalding, Edgar P

    2013-11-01

    Automated image acquisition, a custom analysis algorithm, and a distributed computing resource were used to add time as a third dimension to a quantitative trait locus (QTL) map for plant root gravitropism, a model growth response to an environmental cue. Digital images of Arabidopsis thaliana seedling roots from two independently reared sets of 162 recombinant inbred lines (RILs) and one set of 92 near isogenic lines (NILs) derived from a Cape Verde Islands (Cvi) × Landsberg erecta (Ler) cross were collected automatically every 2 min for 8 hr following induction of gravitropism by 90° reorientation of the sample. High-throughput computing (HTC) was used to measure root tip angle in each of the 1.1 million images acquired and perform statistical regression of tip angle against the genotype at each of the 234 RIL or 102 NIL DNA markers independently at each time point using a standard stepwise procedure. Time-dependent QTL were detected on chromosomes 1, 3, and 4 by this mapping method and by an approach developed to treat the phenotype time course as a function-valued trait. The QTL on chromosome 4 was earliest, appearing at 0.5 hr and remaining significant for 5 hr, while the QTL on chromosome 1 appeared at 3 hr and thereafter remained significant. The Cvi allele generally had a negative effect of 2.6-4.0%. Heritability due to the QTL approached 25%. This study shows how computer vision and statistical genetic analysis by HTC can characterize the developmental timing of genetic architectures.

  6. Major Gene Identiifcation and Quantitative Trait Locus Mapping for Yield-Related Traits in Upland Cotton (Gossypium hirsutum L.)

    Institute of Scientific and Technical Information of China (English)

    XIA Zhe; ZHANG Xin; LIU Yang-yang; JIA Zi-fang; ZHAO Hai-hong; LI Cheng-qi; WANG Qing-lian

    2014-01-01

    Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genesfor cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cross of Baimian 1×TM-1. In addition to boll size and seed index, the major genes for the other ifve traits were detected:one each for seed yield, lint percentage, boll number, lint index; and two for lint yield. Quantitative trait locus/loci (QTL) mapping was performed in the F2 and F2:3 populations of above cross through molecular marker technology, and a total of 50 QTL (26 suggestive and 24 signiifcant) for yield-related traits were detected. Four common QTL were discovered: qLP-3b(F2)/qLP-3(F2:3)andqLP-19b (F2)/qLP-19(F2:3) for lint percentage, qBN-17(F2)/qBN-17(F2:3)for boll number, and qBS-26b(F2)/qBS-26(F2:3) for boll size. Especially, qLP-3b(F2)/qLP-3(F2:3), not only had LOD scores>3 but also exceeded the permutation threshold (5.13 and 5.29, respectively), correspondingly explaining 23.47 and 29.55% of phenotypic variation. This QTL should be considered preferentially in marker assisted selection (MAS). Segregation analysis and QTL mapping could mutually complement and verify, which provides a theoretical basis for genetic improvement of cotton yield-related traits by using major genes (QTL).

  7. Changes in brain iron concentration after exposure to high-altitude hypoxia measured by quantitative susceptibility mapping.

    Science.gov (United States)

    Chen, Lin; Cai, Congbo; Yang, Tianhe; Lin, Jianzhong; Cai, Shuhui; Zhang, Jiaxing; Chen, Zhong

    2017-02-15

    Hypoxia can induce physiological changes. This study aims to explore effects of high-altitude (HA) hypoxia on cerebral iron concentration. Twenty-nine healthy sea-level participants were tested shortly before and after approximately 4-week adaptation to the HA environment at fQinghai-Tibet Plateau (4200m), and were re-investigated after re-adaptation to the sea-level environment one year later. Iron concentration was quantified with quantitative susceptibility mapping (QSM), and the results were compared with transverse relaxation rate (R(*)2) measurements. The variations of magnetic susceptibility indicate that the iron concentration in gray matter regions, especially in basal ganglia, including caudate nucleus, putamen, globus pallidus and substantia nigra, increases significantly after HA exposure. This increase appears consistent with the conclusion from R(*)2 value variations. However, unlike QSM, the R(*)2 value fails to demonstrate the statistical difference of iron content in red nucleus. The re-investigation results show that most variations are recovered after sea-level re-adaptation for one year. Additionally, hemisphere- and gender-related differences in iron concentration changes were analyzed among cerebral regions. The results show greater possibilities in the right hemisphere and females. Further studies based on diffusion tensor imaging (DTI) suggest that the fractional anisotropy increases and the mean diffusivity decreases after HA exposure in six deep gray matter nuclei, with linear dependence on iron concentration only in putamen. In conclusion, the magnetic susceptibility value can serve as a quantitative marker of brain iron, and variations of regional susceptibility reported herein indicate that HA hypoxia can result in significant iron deposition in most deep gray matter regions. Additionally, the linear dependence of DTI metrics on iron concentration in putamen indicates a potential relationship between ferritin and water diffusion.

  8. Mapping quantitative trait loci for nitrogen uptake and utilization efficiency in rice (Oryza sativa L.) at different nitrogen fertilizer levels.

    Science.gov (United States)

    Dai, G J; Cheng, S H; Hua, Z T; Zhang, M L; Jiang, H B; Feng, Y; Shen, X H; Su, Y A; He, N; Ma, Z B; Ma, X Q; Hou, S G; Wang, Y R

    2015-09-08

    Genetic improvement is the fundamental basis for improving nitrogen-use efficiency. A better understanding of genetic factors controlling nitrogen uptake and utilization is required for crop genetic improvement. In this study, we identified the quantitative trait loci (QTLs) associated with traits of nitrogen uptake and utilization by using the single-sequence repeat marker method and a recombinant inbred line (RIL) population derived from a super hybrid Xieyou9308. All the traits investigated were inherited quantitatively by continuous variation and showed normal distribution in phenotype with transgressive segregation in the RIL population. Most of the traits were significantly correlated with each other except for nitrogen absorption ability (NAA) with nitrogen harvest index (NHI) and NHI with agricultural nitrogen-absorption efficiency (ANAE). At logarithmic odds value of 2.3, total 13 candidate QTLs, including 4 for NAA, 2 for NHI, 2 for physiological nitrogen-use efficiency, 1 for agricultural nitrogen-use efficiency (ANUE), and 4 for ANAE, were detected and mapped on chromosomes 2, 3, 4, 5, 8, 9, 10, and 12. Significant pleiotropic effect or neighboring expression of QTLs was observed among traits. At position 64.8 cM on chromosome 4 near the marker RM5757, there was a QTL cluster of NAA, ANUE, and ANAE, and at chromosome 5 near the marker RM5968, there was a QTL cluster of NAA and ANUE. The QTL clusters might provide partial explanation and genetic mechanism for the observed correlations between nitrogen uptake and utilization efficiency traits and might form a basis for future breeding programs.

  9. From HYSOMA to ENSOMAP - A new open source tool for quantitative soil properties mapping based on hyperspectral imagery from airborne to spaceborne applications

    Science.gov (United States)

    Chabrillat, Sabine; Guillaso, Stephane; Rabe, Andreas; Foerster, Saskia; Guanter, Luis

    2016-04-01

    Soil spectroscopy from the visible-near infrared to the short wave infrared has been shown to be a proven method for the quantitative prediction of key soil surface properties in the laboratory, field, and up to airborne studies for exposed soils in appropriate surface conditions. With the upcoming launch of the next generation of spaceborne hyperspectral sensors within the next 3 to 5 years (EnMAP, HISUI, PRISMA, SHALOM), a great potential for the global mapping and monitoring of soil properties is appearing. This potential can be achieved only if adequate software tools are available, as shown by the increasing demand for the availability/accessibility of hyperspectral soil products from the geoscience community that have neither the capacity nor the expertise to deliver these soil products. In this context, recently many international efforts were tuned toward the development of robust and easy-to-access soil algorithms to allow non-remote sensing experts to obtain geoscience information based on non-expensive software packages where repeatability of the results is an important prerequisite. In particular, several algorithms for geological and mineral mapping were recently released such as the U.S. Geological Survey Processing Routines in IDL for Spectroscopic Measurements (PRISM) software, or the GFZ EnMAP Geological Mapper. For quantitative soil mapping and monitoring, the HYSOMA (Hyperspectral Soil Mapper) software interface was developed at GFZ under the EUFAR (www.eufar.net) and the EnMAP (www.enmap.org) programs. HYSOMA was specifically oriented toward digital soil mapping applications and has been distributed since 2012 for free as IDL plug-ins under the IDL-virtual machine at www.gfz-potsdam.de/hysoma under a close source license. The HYSOMA interface focuses on fully automatic generation of semi-quantitative soil maps such as soil moisture, soil organic matter, iron oxide, clay content, and carbonate content. With more than 100 users around the world

  10. Enhancing k-space quantitative susceptibility mapping by enforcing consistency on the cone data (CCD) with structural priors.

    Science.gov (United States)

    Wen, Yan; Wang, Yi; Liu, Tian

    2016-02-01

    The inversion from the magnetic field to the magnetic susceptibility distribution is ill-posed because the dipole kernel, which relates the magnetic susceptibility to the magnetic field, has zeroes at a pair of cone surfaces in the k-space, leading to streaking artifacts on the reconstructed quantitative susceptibility maps (QSM). A method to impose consistency on the cone data (CCD) with structural priors is proposed to improve the solutions of k-space methods. The information in the cone region is recovered by enforcing structural consistency with structural prior, while information in the noncone trust region is enforced to be consistent with the magnetic field measurements in k-space. This CCD method was evaluated by comparing the initial results of existing QSM algorithms to the QSM results after CCD enhancement with respect to the COSMOS results in simulation, phantom, and in vivo human brain. The proposed method demonstrated suppression of streaking artifacts and the resulting QSM showed better agreement with reference standard QSM compared with other k-space based methods. By enforcing consistency with structural priors in the cone region, the missing data in the cone can be recovered and the streaking artifacts in QSM can be suppressed. © 2015 Wiley Periodicals, Inc.

  11. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.

    Directory of Open Access Journals (Sweden)

    Heather E Wheeler

    2009-10-01

    Full Text Available Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We sequentially used transcriptional profiling and expression quantitative trait loci (eQTL mapping to narrow down which genes to test for association with kidney aging. We first performed whole-genome transcriptional profiling to find 630 genes that change expression with age in the kidney. Using two methods to detect eQTLs, we found 101 of these age-regulated genes contain expression-associated SNPs. We tested the eQTLs for association with kidney aging, measured by glomerular filtration rate (GFR using combined data from the Baltimore Longitudinal Study of Aging (BLSA and the InCHIANTI study. We found a SNP association (rs1711437 in MMP20 with kidney aging (uncorrected p = 3.6 x 10(-5, empirical p = 0.01 that explains 1%-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans.

  12. Qualitative and quantitative analysis of specific polysaccharides in Dendrobium huoshanense by using saccharide mapping and chromatographic methods.

    Science.gov (United States)

    Deng, Yong; Chen, Ling-Xiao; Han, Bang-Xing; Wu, Ding-Tao; Cheong, Kit-Leong; Chen, Nai-Fu; Zhao, Jing; Li, Shao-Ping

    2016-09-10

    Qualitative and quantitative analysis of specific polysaccharides from ten batches of Dendrobium huoshanense were performed using high performance size exclusion chromatography coupled with multi-angle laser light scattering and refractive index detector (HPSEC-MALLS-RID), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) and saccharide mapping based on polysaccharides analysis by using carbohydrate gel electrophoresis (PACE) and high performance thin layer chromatography (HPTLC). Results showed that molecular weights, the radius of gyrations, and contents of specific polysaccharides in D. huoshanense were ranging from 1.16×10(5) to 2.17×10(5)Da, 38.8 to 52.1nm, and 9.9% to 19.9%, respectively. Furthermore, the main monosaccharide compositions were Man and Glc. Indeed, the main glycosidic linkages were β-1,4-Manp and β-1,4-Glcp, and substituted with acetyl groups at O-2 and O-3 of 1,4-linked Manp. Moreover, results showed that PACE and HPTLC fingerprints of partial acidic and enzymatic hydrolysates of specific polysaccharides were similar, which are helpful to better understand the specific polysaccharides in D. huoshanense and beneficial to improve their quality control. These approaches could also be routinely used for quality control of polysaccharides in other medicinal plants. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Quantitative trait loci mapping for leaf length and leaf width in rice cv. IR64 derived lines.

    Science.gov (United States)

    Farooq, Muhammad; Tagle, Analiza G; Santos, Rizza E; Ebron, Leodegario A; Fujita, Daisuke; Kobayashi, Nobuya

    2010-06-01

    The present study was conducted to identify quantitative trait loci (QTLs) for leaf size traits in IR64 introgression lines (INLs). For this purpose, selected F(2) populations derived from crosses between recurrent parent IR64 and its derived INLs, unique for leaf length and leaf width, were used to confirm QTLs. A total of eight QTLs, mapped on three chromosomes, were identified for the four leaf size traits in six F(2) populations. A QTL for leaf length, qLLnpt-1, in HKL69 was identified around simple sequence repeat (SSR) marker RM3709 on chromosome 1. Two QTLs for flag leaf length, qFLLnpt-2 and qFLLnpt-4, in HFG39 were indentified on chromosomes 2 and 4, respectively. For flag leaf width, a QTL, qFLWnpt-4, in HFG39 was identified around RM17483 on chromosome 4. While another QTL for flag leaf width, qFLWnpt-1, in HFG27 was identified around RM3252 on chromosome 1. A QTL for leaf width, qLWnpt-2, in HKL75 was identified around RM7451 on chromosome 2. For leaf width, two QTLs, qLWnpt-4a, qLWnpt-4b, in HKL48 and HKL99 were identified around RM7208 and RM6909, respectively on chromosome 4. Results from this study suggest the possibilities to use marker-assisted selection and pyramiding these QTLs to improve rice water productivity.

  14. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.

    Science.gov (United States)

    Wheeler, Heather E; Metter, E Jeffrey; Tanaka, Toshiko; Absher, Devin; Higgins, John; Zahn, Jacob M; Wilhelmy, Julie; Davis, Ronald W; Singleton, Andrew; Myers, Richard M; Ferrucci, Luigi; Kim, Stuart K

    2009-10-01

    Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We sequentially used transcriptional profiling and expression quantitative trait loci (eQTL) mapping to narrow down which genes to test for association with kidney aging. We first performed whole-genome transcriptional profiling to find 630 genes that change expression with age in the kidney. Using two methods to detect eQTLs, we found 101 of these age-regulated genes contain expression-associated SNPs. We tested the eQTLs for association with kidney aging, measured by glomerular filtration rate (GFR) using combined data from the Baltimore Longitudinal Study of Aging (BLSA) and the InCHIANTI study. We found a SNP association (rs1711437 in MMP20) with kidney aging (uncorrected p = 3.6 x 10(-5), empirical p = 0.01) that explains 1%-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans.

  15. Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian information criterion.

    Science.gov (United States)

    Ball, R D

    2001-11-01

    We describe an approximate method for the analysis of quantitative trait loci (QTL) based on model selection from multiple regression models with trait values regressed on marker genotypes, using a modification of the easily calculated Bayesian information criterion to estimate the posterior probability of models with various subsets of markers as variables. The BIC-delta criterion, with the parameter delta increasing the penalty for additional variables in a model, is further modified to incorporate prior information, and missing values are handled by multiple imputation. Marginal probabilities for model sizes are calculated, and the posterior probability of nonzero model size is interpreted as the posterior probability of existence of a QTL linked to one or more markers. The method is demonstrated on analysis of associations between wood density and markers on two linkage groups in Pinus radiata. Selection bias, which is the bias that results from using the same data to both select the variables in a model and estimate the coefficients, is shown to be a problem for commonly used non-Bayesian methods for QTL mapping, which do not average over alternative possible models that are consistent with the data.

  16. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    Energy Technology Data Exchange (ETDEWEB)

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O' Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes

  17. Mapping quantitative trait loci conferring resistance to rice black-streaked virus in maize (Zea mays L.).

    Science.gov (United States)

    Luan, Junwen; Wang, Fei; Li, Yujie; Zhang, Bin; Zhang, Juren

    2012-08-01

    Maize rough dwarf disease (MRDD) is one of the most serious virus diseases of maize worldwide, and it causes great reduction of maize production. In China, the pathogen was shown to be rice black-streaked virus (RBSDV). Currently, MRDD has spread broadly and leads to significant loss in China. However, there has been little research devoted to this disease. Our aims were to identify the markers and loci underlying resistance to this virus disease. In this study, segregation populations were constructed from two maize elite lines '90110', which is highly resistant to MRDD and 'Ye478', which is highly susceptible to MRDD. The F(2) and BC(1) populations were used for bulk sergeant analysis (BSA) to identify resistance-related markers. One hundred and twenty F(7:9) RILs were used for quantitative trait loci (QTL) mapping through the experiment of multiple environments over 3 years. Natural occurrence and artificial inoculation were both used and combined to determine the phenotype of plants. Five QTL, qMRD2, qMRD6, qMRD7, qMRD8 and qMRD10 were measured in the experiments. The qMRD8 on chromosome 8 was proved to be one major QTL conferring resistance to RBSDV disease in almost all traits and environments, which explained 12.0-28.9 % of the phenotypic variance for disease severity in this present study.

  18. Exercise training reinstates cortico-cortical sensorimotor functional connectivity following striatal lesioning: Development and application of a subregional-level analytic toolbox for perfusion autoradiographs of the rat brain

    Science.gov (United States)

    Peng, Yu-Hao; Heintz, Ryan; Wang, Zhuo; Guo, Yumei; Myers, Kalisa; Scremin, Oscar; Maarek, Jean-Michel; Holschneider, Daniel

    2014-12-01

    Current rodent connectome projects are revealing brain structural connectivity with unprecedented resolution and completeness. How subregional structural connectivity relates to subregional functional interactions is an emerging research topic. We describe a method for standardized, mesoscopic-level data sampling from autoradiographic coronal sections of the rat brain, and for correlation-based analysis and intuitive display of cortico-cortical functional connectivity (FC) on a flattened cortical map. A graphic user interface “Cx-2D” allows for the display of significant correlations of individual regions-of-interest, as well as graph theoretical metrics across the cortex. Cx-2D was tested on an autoradiographic data set of cerebral blood flow (CBF) of rats that had undergone bilateral striatal lesions, followed by 4 weeks of aerobic exercise training or no exercise. Effects of lesioning and exercise on cortico-cortical FC were examined during a locomotor challenge in this rat model of Parkinsonism. Subregional FC analysis revealed a rich functional reorganization of the brain in response to lesioning and exercise that was not apparent in a standard analysis focused on CBF of isolated brain regions. Lesioned rats showed diminished degree centrality of lateral primary motor cortex, as well as neighboring somatosensory cortex--changes that were substantially reversed in lesioned rats following exercise training. Seed analysis revealed that exercise increased positive correlations in motor and somatosensory cortex, with little effect in non-sensorimotor regions such as visual, auditory, and piriform cortex. The current analysis revealed that exercise partially reinstated sensorimotor FC lost following dopaminergic deafferentation. Cx-2D allows for standardized data sampling from images of brain slices, as well as analysis and display of cortico-cortical FC in the rat cerebral cortex with potential applications in a variety of autoradiographic and histologic

  19. Exercise training reinstates cortico-cortical sensorimotor functional connectivity following striatal lesioning: Development and application of a subregional-level analytic toolbox for perfusion autoradiographs of the rat brain

    Directory of Open Access Journals (Sweden)

    Yu-Hao ePeng

    2014-12-01

    Full Text Available Current rodent connectome projects are revealing brain structural connectivity with unprecedented resolution and completeness. How subregional structural connectivity relates to subregional functional interactions is an emerging research topic. We describe a method for standardized, mesoscopic-level data sampling from autoradiographic coronal sections of the rat brain, and for correlation-based analysis and intuitive display of cortico-cortical functional connectivity (FC on a flattened cortical map. A graphic user interface Cx-2D allows for the display of significant correlations of individual regions-of-interest, as well as graph theoretical metrics across the cortex. Cx-2D was tested on an autoradiographic data set of cerebral blood flow (CBF of rats that had undergone bilateral striatal lesions, followed by 4 weeks of aerobic exercise training or no exercise. Effects of lesioning and exercise on cortico-cortical FC were examined during a locomotor challenge in this rat model of Parkinsonism. Subregional FC analysis revealed a rich functional reorganization of the brain in response to lesioning and exercise that was not apparent in a standard analysis focused on CBF of isolated brain regions. Lesioned rats showed diminished degree centrality of lateral primary motor cortex, as well as neighboring somatosensory cortex–-changes that were substantially reversed in lesioned rats following exercise training. Seed analysis revealed that exercise increased positive correlations in motor and somatosensory cortex, with little effect in non-sensorimotor regions such as visual, auditory, and piriform cortex. The current analysis revealed that exercise partially reinstated sensorimotor FC lost following dopaminergic deafferentation. Cx-2D allows for standardized data sampling from images of brain slices, as well as analysis and display of cortico-cortical FC in the rat cerebral cortex with potential applications in a variety of autoradiographic and

  20. A semi-quantitative technique for mapping potential aquifer productivity on the national scale: example of England and Wales (UK)

    Science.gov (United States)

    Abesser, Corinna; Lewis, Melinda

    2015-12-01

    The development and validation of aquifer productivity and depth-to-source maps for England and Wales are described. Aquifer productivity maps can provide valuable support for the assessment, planning and management of groundwater and renewable heat energy resources. Aquifer productivity is often mapped using geostatistical interpolation techniques such as kriging, but these techniques tend to be unsuitable for mapping at the national scale due to the high data (and time) demands. A methodology is outlined for mapping aquifer productivity at the national scale using existing national-scale data sets. Pumping test data are used to characterise the potential borehole yields that different geological formations of varying lithologies and ages can provide. Based on this analysis and using expert knowledge, the corresponding map codes on the geological map are assigned to potential productivity classes. The subsurface (concealed) extent of aquifer units is mapped from geophysical data, and together with the attributed geological map, provide the bedrock-aquifer productivity map. Drilling and pumping costs can be an important consideration when evaluating the feasibility of developing a groundwater source. Thus, a map of the approximate depth to source is developed alongside the aquifer productivity map. The maps are validated using independent data sets, and map performance is compared against performance from maps derived by random and uniform attribution. The results show that the maps successfully predict potential productivity and approximate depth to the water source, although utility of the depth-to-source map could be improved by increasing the vertical discretisation at which depth intervals are mapped.

  1. Plasticity-related binding of GABA and muscarinic receptor sites in piriform cortex of rat: An autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, A.P.; Westrum, L.E. (Univ. of Washington, Seattle (USA))

    1989-09-01

    This study has used the recently developed in vitro quantitative autoradiographic technique to examine the effects of olfactory bulb (OB) removal on receptor-binding sites in the deafferented piriform cortex (PC) of the rat. The gamma-aminobutyric acid-benzodiazepine receptor (GABA-BZR)- and muscarinic cholinergic receptor (MChR)-binding sites in layer I of PC were localized using (3H)flunitrazepam and (3H)quinuclidinyl benzilate as ligands, respectively. From the resultant autoradiograms the optical densities were measured using a Drexel-DUMAS image analysis system. The densities of BZR and MChR-binding sites were markedly increased in the PC ipsilateral to the lesion as compared to the contralateral side in those subjects that were operated in adulthood (Postnatal Day 100, PN 100). Comparisons between the unoperated and PN 100 operated animals also showed significant increases in the deafferented PC. In the animals operated on the day of birth (PN 0) no significant differences were seen between the operated and the contralateral PC. The difference between the PN 0 deafferented PC and the unoperated controls shows a slight decrease in BZR density in the former group; however, in case of the MChR there is a slight increase on the side of the lesion. These results demonstrate that deafferentation of PC by OB removal appears to modulate both the BZR-binding sites that are coupled with the GABA-A receptor complex and the MChR-binding sites. The results also suggest that possibility of a role for these neurotransmitter receptor-binding sites in plasticity following deafferentation.

  2. Hide and seek: a comparative autoradiographic in vitro investigation of the adenosine A3 receptor

    Energy Technology Data Exchange (ETDEWEB)

    Haeusler, D.; Fuchshuber, F.; Girschele, F.; Hacker, M.; Wadsak, W.; Mitterhauser, Markus [Medical University of Vienna, Department of Biomedical Imaging and Image-guided Therapy, Vienna (Austria); Grassinger, L. [University of Applied Sciences Wiener Neustadt, Department of Biomedical Analytics, Wiener Neustadt (Austria); Hoerleinsberger, W.J. [Medical University of Vienna, Department of Biomedical Imaging and Image-guided Therapy, Vienna (Austria); University of Vienna, Cognitive Science Research Platform, Vienna (Austria); Hoeftberger, R.; Leisser, I. [Medical University of Vienna, Institute of Neurology, Vienna (Austria); Shanab, K.; Spreitzer, H. [University of Vienna, Department of Drug and Natural Product Synthesis, Vienna (Austria); Gerdenitsch, W. [Medical University of Vienna, Institute of Biomedicinal Research, Vienna (Austria)

    2015-05-01

    Since the adenosine A3 receptor (A3R) is considered to be of high clinical importance in the diagnosis and treatment of ischaemic conditions (heart and brain), glaucoma, asthma, arthritis, cancer and inflammation, a suitable and selective A3R PET tracer such as [{sup 18}F]FE rate at SUPPY would be of high clinical value for clinicians as well as patients. A3R was discovered in the late 1990s, but there is still little known regarding its distribution in the CNS and periphery. Hence, in autoradiographic experiments the distribution of A3R in human brain and rat tissues was investigated and the specific binding of the A3R antagonist FE rate at SUPPY and MRS1523 compared. Immunohistochemical staining (IHC) experiments were also performed to validate the autoradiographic findings. For autoradiographic competition experiments human post-mortem brain and rat tissues were incubated with [{sup 125}I]AB-MECA and highly selective compounds to block the other adenosine receptor subtypes. Additionally, IHC was performed with an A3 antibody. Specific A3R binding of MRS1523 and FE rate at SUPPY was found in all rat peripheral tissues examined with the highest amounts in the spleen (44.0 % and 46.4 %), lung (44.5 % and 45.0 %), heart (39.9 % and 42.9 %) and testes (27.4 % and 29.5 %, respectively). Low amounts of A3R were found in rat brain tissues (5.9 % and 5.6 %, respectively) and human brain tissues (thalamus 8.0 % and 9.1 %, putamen 7.8 % and 8.2 %, cerebellum 6.0 % and 7.8 %, hippocampus 5.7 % and 5.6 %, caudate nucleus 4.9 % and 6.4 %, cortex 4.9 % and 6.3 %, respectively). The outcome of the A3 antibody staining experiments complemented the results of the autoradiographic experiments. The presence of A3R protein was verified in central and peripheral tissues by autoradiography and IHC. The specificity and selectivity of FE rate at SUPPY was confirmed by direct comparison with MRS1523, providing further evidence that [{sup 18}F]FE rate at SUPPY may be a suitable A3 PET

  3. Whole-body autoradiographic microimaging: Applications in radiopharmaceutical and drug research

    Energy Technology Data Exchange (ETDEWEB)

    Som, P.; Sacker, D.F.

    1991-12-31

    The whole-body autoradiographic (WBARG) microimaging technique is used for evaluation of the temporo-spatial distribution of radiolabeled molecules in intact animals as well as to determine the sites of accumulation of parent compounds and their metabolites. This technique is also very useful to determine the metabolism of a compound, toxicity, and effects of therapeutic interventions on the distribution of a compound in the whole body, by studying animals at different time intervals after injection of the radiolabeled compound. This report discusses various aspects of WBARG.

  4. Whole-body autoradiographic microimaging: Applications in radiopharmaceutical and drug research

    Energy Technology Data Exchange (ETDEWEB)

    Som, P.; Sacker, D.F.

    1991-01-01

    The whole-body autoradiographic (WBARG) microimaging technique is used for evaluation of the temporo-spatial distribution of radiolabeled molecules in intact animals as well as to determine the sites of accumulation of parent compounds and their metabolites. This technique is also very useful to determine the metabolism of a compound, toxicity, and effects of therapeutic interventions on the distribution of a compound in the whole body, by studying animals at different time intervals after injection of the radiolabeled compound. This report discusses various aspects of WBARG.

  5. Ultrastructural and autoradiographic studies of the role of nucleolar vacuoles in soybean root meristem.

    OpenAIRE

    Dariusz Stepiński

    2004-01-01

    Ultrastructural and autoradiographic studies of nucleoli in soybean root meristematic cells in seedlings: (1) grown for 3 days at 25 degrees C (control), (2) grown for three days at 25 degrees C and for 4 days at 10 degrees C, and (3) grown as in (2) and recovered for 1 day at 25 degrees C were carried out. Control nucleoli had dense structure and a few small nucleolar vacuoles. Chilled plant nucleoli had less dense structure and no vacuoles. Nucleoli of plants recovered at 25 degrees C had b...

  6. Quantitative autoradiography of alpha particle emission in geo-materials using the Beaver™ system

    Science.gov (United States)

    Sardini, Paul; Angileri, Axel; Descostes, Michael; Duval, Samuel; Oger, Tugdual; Patrier, Patricia; Rividi, Nicolas; Siitari-Kauppi, Marja; Toubon, Hervé; Donnard, Jérôme

    2016-10-01

    In rocks or artificial geo-materials, radioactive isotopes emitting alpha particles are dispersed according to the mineralogy. At hand specimen scale, the achievement of quantitative chemical mapping of these isotopes takes on a specific importance. Knowledge of the distribution of the uranium and thorium series radionuclides is of prime interest to several disciplines, from the geochemistry of uranium deposits, to the dispersion of uranium mill tailings in the biosphere. The disequilibrium of these disintegration chains is also commonly used for dating. However, some prime importance isotopes, such as 226Ra, are complicated to localize in geo-materials. Because of its high specific activity, 226Ra is found in very low concentrations ( ppq), preventing its accurate localization in rock forming minerals. This paper formulates a quantitative answer to the following question: at hand specimen scale, how can alpha emitters in geo-materials be mapped quantitatively? In this study, we tested a new digital autoradiographic method (called the Beaver™) based on a Micro Patterned Gaseous Detector (MPGD) in order to quantitatively map alpha emission at the centimeter scale rock section. Firstly, for two thin sections containing U-bearing minerals at secular equilibrium, we compared the experimental and theoretical alpha count rates, measured by the Beaver™ and calculated from the uranium content, respectively. We found that they are very similar. Secondly, for a set of eight homemade standards made up of a mixture of inactive sand and low-radioactivity mud, we compared the count rates obtained by the Beaver™ and by an alpha spectrometer. The results indicate (i) a linearity between both count rates, and (ii) that the count obtained by the Beaver™ can be estimated from the count obtained by the alpha spectrometry using a factor of 0.82.

  7. Quantitative Trait Loci and Candidate Genes for Neutrophil Recruitment in Sterile Inflammation Mapped in AXB-BXA Recombinant Inbred Mice.

    Directory of Open Access Journals (Sweden)

    Quyen Cheng

    Full Text Available Neutrophil recruitment (NR to sites of sterile inflammation plays a key role in tissue damage and healing potential of lesions characteristic to non-infectious inflammatory diseases. Previous studies suggested significant genetic control of neutrophil survival, function, and migration in inflammatory responses to endogenous and exogenous stimuli. We have mapped the murine genome for quantitative trait loci (QTLs harbouring genetic determinants that regulate NR in SI using a murine model of chemically-induced peritonitis. NR was quantified in 16 AXB-BXA recombinant inbred strains and their progenitors, A/J (A and C57BL/6J (B. A continuous distribution of NR was found among the strains, with parent B showing higher NR and parent A showing lower NR (3.0-fold difference, p=0.05. Within the progeny strains, a 5.5-fold difference in NR was observed between the lowest, BXA1, and the highest responders AXB19 (p<0.001. This data was analyzed using GeneNetwork, which linked NR to one significant QTL on chromosome 12 (Peritoneal Neutrophil Recruitment 1, PNR1 and two suggestive QTLs (PNR2, PNR3 on chromosomes 12 and 16 respectively. Sixty-four candidate genes within PNR1 were cross-referenced with currently published data, mRNA expression from two NR microarrays, and single nucleotide polymorphism analysis. The present study brings new light into the genetics of NR in response to cell injury and highlights potential candidate genes Hif1α, Fntb, and Prkch and their products for further studies on neutrophil infiltration and inflammation resolution in sterile inflammation.

  8. Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat.

    Science.gov (United States)

    Singh, A; Pandey, M P; Singh, A K; Knox, R E; Ammar, K; Clarke, J M; Clarke, F R; Singh, R P; Pozniak, C J; Depauw, R M; McCallum, B D; Cuthbert, R D; Randhawa, H S; Fetch, T G

    2013-02-01

    Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding.

  9. Quantitative nanoscale water mapping in frozen-hydrated skin by low-loss electron energy-loss spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yakovlev, Sergey [Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, NJ 07030 (United States); Misra, Manoj; Shi, Shanling [Unilever Research and Development, Trumbull, CT 06611 (United States); Firlar, Emre [Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, NJ 07030 (United States); Libera, Matthew, E-mail: mlibera@stevens.edu [Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, NJ 07030 (United States)

    2010-06-15

    Spatially resolved low-loss electron energy-loss spectroscopy (EELS) is a powerful method to quantitatively determine the water distribution in frozen-hydrated biological materials at high spatial resolution. However, hydrated tissue, particularly its hydrophilic protein-rich component, is very sensitive to electron radiation. This sensitivity has traditionally limited the achievable spatial resolution because of the relatively high noise associated with low-dose data acquisition. We show that the damage caused by high-dose data acquisition affects the accuracy of a multiple-least-squares (MLS) compositional analysis because of inaccuracies in the reference spectrum used to represent the protein. Higher spatial resolution combined with more accurate compositional analysis can be achieved if a reference spectrum is used that better represents the electron-beam-damaged protein component under frozen-hydrated conditions rather than one separately collected from dry protein under low-dose conditions. We thus introduce a method to extract the best-fitting protein reference spectrum from an experimental spectrum dataset. This method can be used when the MLS-fitting problem is sufficiently constrained so that the only unknown is the reference spectrum for the protein component. We apply this approach to map the distribution of water in cryo-sections obtained from frozen-hydrated tissue of porcine skin. The raw spectral data were collected at doses up to 10{sup 5} e/nm{sup 2} despite the fact that observable damage begins at doses as low as 10{sup 3} e/nm{sup 2}. The resulting spatial resolution of 10 nm is 5-10 times better than that in previous studies of frozen-hydrated tissue and is sufficient to resolve sub-cellular water fluctuations as well as the inter-cellular lipid-rich regions of skin where water-mediated processes are believed to play a significant role in the phenotype of keratinocytes in the stratum corneum.

  10. Mapping of quantitative trait loci for fiber and lignin contents from an interspecific cross Oryza sativa×Oryza rufipogon

    Institute of Scientific and Technical Information of China (English)

    Jian-kun XIE; Xiang-li KONG; Jie CHEN; Biao-lin HU; Piao WEN; Jie-yun ZHUANG; Jin-song BAO

    2011-01-01

    Rice straw is always regarded as a by-product of rice production,but it could be a significant energy source for ruminant animals.Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering.The common wild rice,Oryza rufipogon Griff.,which is considered to be the progenitor of Oryza sativa,has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement.In the present study,the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF),neutral detergent fiber (NDF),acid detergent lignin (ADL),and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR).The results indicated that all four traits tested were continuously distributed among the BILs,but many BILs showed transgressive segregation.A total of 16 QTLs were identified for the four traits,but no QTLs were in common in two environments,suggesting that environment has dramatic effects on fiber and lignin syntheses.Compared to the QTL positions for grain yield-related traits,there were no unfavorable correlations between grain yield components and cell wall traits in this population.The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.

  11. Autoradiographic localization of beta-adrenoreceptors in rat uterus

    Energy Technology Data Exchange (ETDEWEB)

    Tolszczuk, M.; Pelletier, G.

    1988-12-01

    The inhibitory effects of catecholamines on uterine smooth muscle are known to be mediated through beta-adrenergic receptors. To investigate further the distribution of these receptors in the rat uterus, we utilized in vitro autoradiography using ( SVI)-cyanopindolol (CYP), a specific beta-receptor ligand that has equal activity for both beta 1- and beta 2-receptor subtypes. The specificity of the labeling and the characterization of receptor subtypes in different cell types were achieved by displacement of radioligand with increasing concentrations of zinterol, a beta-adrenergic agonist with preferential affinity for the beta 2-adrenoreceptor subtype, and practolol, a beta-adrenergic antagonist that binds preferentially to the beta 1-subtype. Quantitative estimation of ligand binding was performed by densitometry. It was shown that the vast majority of beta-adrenoreceptors were of the beta 2-subtype and were found in high concentration not only in the myometrium but also in the endometrial and serosal epithelia. Specific labeling was also observed in glandular elements. These results suggest that beta-adrenoreceptors might be involved in different functions in the uterus.

  12. A major gene mapped on chromosome XII is the main factor of a quantitatively inherited resistance to Meloidogyne fallax in Solanum sparsipilum.

    Science.gov (United States)

    Kouassi, Abou Bakari; Bakari, Kouassi Abou; Kerlan, Marie-Claire; Marie-Claire, Kerlan; Caromel, Bernard; Bernard, Caromel; Dantec, Jean-Paul; Jean-Paul, Dantec; Fouville, Didier; Didier, Fouville; Manzanares-Dauleux, Maria; Maria, Manzanares-Dauleux; Ellissèche, Daniel; Daniel, Ellissèche; Mugniéry, Didier; Didier, Mugniéry

    2006-02-01

    Meloidogyne fallax is an emerging pest in Europe and represents a threat for potato production. We report the mapping of genetic factors controlling a quantitative resistance against M. fallax identified in the Solanum sparsipilum genotype 88S.329.15. When infected, this genotype develops a necrotic reaction at the feeding site of the juveniles and totally prevents their development to the female stage. A "F1" diploid progeny consisting of 128 individuals was obtained using the potato (S. tuberosum) dihaploid genotype BF15 H1 as female progenitor. Sixty-eight hybrid genotypes displayed necrosis at the feeding site of the juveniles and 60 other genotypes showed no defence reaction. This suggested a monogenic control of the resistance. However, when considering the number of nematode females developed in their roots, a continuous distribution was observed for both "necrotic" and "non-necrotic" hybrid genotypes, indicating a polygenic control of the resistance. A linkage map of each parental genotype was constructed using AFLP markers. The necrotic reaction (NR) was mapped as a qualitative trait on chromosome XII of the resistant genotype 88S.329.15. Quantitative trait locus (QTL) analysis for the number of nematode females developed per "F1" plant genotype was performed using the QTL cartographer software. No QTL was detected on the linkage map of the susceptible parent. A QTL explaining 94.5% of the phenotypic variation was mapped on chromosome XII of the resistant progenitor. This QTL, named MfaXIIspl, was mapped in a genomic region collinear to the map position of the Mi-3 gene conferring resistance to Meloidogyne incognita in tomato. It corresponds to the NR locus.

  13. Diagnosis of Acute Global Myocarditis Using Cardiac MRI with Quantitative T1 and T2 Mapping: Case Report and Literature Review

    Energy Technology Data Exchange (ETDEWEB)

    Park, Chul Hwan [Department of Radiology and Research Institute of Radiological Science, Yonsei University Health System, Seoul 135-720 (Korea, Republic of); Choi, Eui-Young [Division of Cardiology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 135-720 (Korea, Republic of); Greiser, Andreas [Healthcare Sector, Siemens AG, Erlangen D-91052 (Germany); Paek, Mun Young [Siemens Ltd., Seoul 120-837 (Korea, Republic of); Hwang, Sung Ho; Kim, Tae Hoon [Department of Radiology and Research Institute of Radiological Science, Yonsei University Health System, Seoul 135-720 (Korea, Republic of)

    2013-07-01

    The diagnosis of myocarditis can be challenging given that symptoms, clinical exam findings, electrocardiogram results, biomarkers, and echocardiogram results are often non-specific. Endocardial biopsy is an established method for diagnosing myocarditis, but carries the risk of complications and false negative results. Cardiac magnetic resonance imaging (MRI) has become the primary non-invasive imaging tool in patients with suspected myocarditis. Myocarditis can be diagnosed by using three tissue markers including edema, hyperemia/capillary leak, and necrosis/fibrosis. The interpretation of cardiac MR findings can be confusing, especially when the myocardium is diffusely involved. Using T1 and T2 maps, the diagnosis of myocarditis can be made even in cases of global myocarditis with the help of quantitative analysis. We herein describe a case of acute global myocarditis which was diagnosed by using quantitative T1 and T2 mapping.

  14. Autoradiographic determination of marginal leakage of a pressed glass ceramic inlay.

    Science.gov (United States)

    Canay, R S; Hersek, N E; Uzun, G; Ercan, M T

    1997-09-01

    The marginal integrity and microleakage of pressed glass ceramic inlays were evaluated using autoradiography. IPS/Empress ceramic inlays were fabricated for 10 human molar mandibular teeth. After adjusting the inlays, they were etched with 37% phosphoric acid gel for 30 s and silanized with Monobond S for 30 s. Before cementation with dual cure resin cement the inlays and cavity walls were gently covered with a thin layer of bonding agent. When the cementation process was completed the samples were cycled 300 times between a 55 degrees C hot bath and a 5 degrees C cold bath. The samples were placed in each bath for 60 s, with 5 s intervals between immersions, then the specimens were immersed in an aqueous solution of Ca-45. After 24 h the inlay and tooth assemblies were removed, rinsed with water and placed in cold-cured acrylic resin, then sectioned through the long axis for autoradiographic analysis. According to the penetration of Ca-45, the microleakage level was scored for each section. The results indicated slight penetration of Ca-45 on autoradiographic films.

  15. Autoradiographic demonstration of oxytocin-binding sites in the macula densa

    Energy Technology Data Exchange (ETDEWEB)

    Stoeckel, M.E.; Freund-Mercier, M.J. (Centre National de la Recherche Scientifique, Strasbourg (France))

    1989-08-01

    Specific oxytocin (OT)-binding sites were localized in the rat kidney with use of a selective {sup 125}I-labeled OT antagonist ({sup 125}I-OTA). High concentrations of OT binding sites were detected on the juxtaglomerular apparatus with use of the conventional film autoradiographic technique. No labeling occurred on other renal structures. The cellular localization of the OT binding sites within the juxtaglomerular apparatus was studied in light microscope autoradiography, on semithin sections from paraformaldehyde-fixed kidney slices incubated in the presence of {sup 125}I-OTA. These preparations revealed selective labeling of the macula densa, mainly concentrated at the basal pole of the cells. Control experiments showed first that {sup 125}I-OTA binding characteristics were not noticeably altered by prior paraformaldehyde fixation of the kidneys and second that autoradiographic detection of the binding sites was not impaired by histological treatments following binding procedures. In view of the role of the macula densa in the tubuloglomerular feedback, the putative OT receptors of this structure might mediate the stimulatory effect of OT on glomerular filtration.

  16. Site of anticonvulsant action on sodium channels: autoradiographic and electrophysiological studies in rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Worley, P.F.; Baraban, J.M.

    1987-05-01

    The anticonvulsants phenytoin and carbamazepine interact allosterically with the batrachotoxin binding site of sodium channels. In the present study, we demonstrate an autoradiographic technique to localize the batrachotoxin binding site on sodium channels in rat brain using (/sup 3/H)batrachotoxinin-A 20-alpha-benzoate (BTX-B). Binding of (/sup 3/H)BTX-B to brain sections is dependent on potentiating allosteric interactions with scorpion venom and is displaced by BTX-B (Kd approximately 200 nM), aconitine, veratridine, and phenytoin with the same rank order of potencies as described in brain synaptosomes. The maximum number of (/sup 3/H)BTX-B binding sites in forebrain sections also agrees with biochemical determinations. Autoradiographic localizations indicate that (/sup 3/H)BTX-B binding sites are not restricted to cell bodies and axons but are present in synaptic zones throughout the brain. For example, a particularly dense concentration of these sites in the substantia nigra is associated with afferent terminals of the striatonigral projection. By contrast, myelinated structures possess much lower densities of binding sites. In addition, we present electrophysiological evidence that synaptic transmission, as opposed to axonal conduction, is preferentially sensitive to the action of aconitine and veratridine. Finally, the synaptic block produced by these sodium channel activators is inhibited by phenytoin and carbamazepine at therapeutic anticonvulsant concentrations.

  17. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci.

    Science.gov (United States)

    Liu, Z H; Anderson, J A; Hu, J; Friesen, T L; Rasmussen, J B; Faris, J D

    2005-08-01

    Efficient user-friendly methods for mapping plant genomes are highly desirable for the identification of quantitative trait loci (QTLs), genotypic profiling, genomic studies, and marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. Target region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects a large number of loci from a single reaction without extensive pre-PCR processing of samples. In the investigation reported here, we used both SSRs and TRAPs to generate over 700 markers for the construction of a genetic linkage map in a hard red spring wheat intervarietal recombinant inbred population. A framework map consisting of 352 markers accounted for 3,045 cM with an average density of one marker per 8.7 cM. On average, SSRs detected 1.9 polymorphic loci per reaction, while TRAPs detected 24. Both marker systems were suitable for assigning linkage groups to chromosomes using wheat aneuploid stocks. We demonstrated the utility of the maps by identifying major QTLs for days to heading and reduced plant height on chromosomes 5A and 4B, respectively. Our results indicate that TRAPs are highly efficient for genetic mapping in wheat. The maps developed will be useful for the identification of quality and disease resistance QTLs that segregate in this population.

  18. Large area quantitative X-ray mapping of (U,Pu)O 2 nuclear fuel pellets using wavelength dispersive electron probe microanalysis

    Science.gov (United States)

    Brémier, S.; Haas, D.; Somers, J.; Walker, C. T.

    2003-04-01

    The work presented is an example of how large area compositional mapping (≥1 mm 2) can be used to provide quantitative information on element distribution and specimen homogeneity. High-resolution was accomplished by producing a collage of X-ray maps acquired using classical conditions; magnification ×400, spatial resolution 256×256 pixels. The individual images, each measuring roughly 250×250 μm, were converted to quantitative maps using the HIMAX® software package and the XMAS® matrix correction from SAMx. The quantitative gray-level large area X-ray picture was pieced together using the 'Multiple Image Alignment' function of the ANALYSIS® image processing software. This software was also used to convert the gray-level pictures to false color images. The specimens investigated were transverse sections of MOX fuel pellets. Results are presented for the distribution of Pu by area fraction and cumulative area fraction, the size distribution of regions of high Pu concentration and average separation of these regions.

  19. Quantitative lithofacies palaeogeography

    Institute of Scientific and Technical Information of China (English)

    Zeng-Zhao; Feng; Xiu-Juan; Zheng; Zhi-Dong; Bao; Zhen-Kui; Jin; Sheng-He; Wu; You-Bin; He; Yong-Min; Peng; Yu-Qing; Yang; Jia-Qiang; Zhang; Yong-Sheng; Zhang

    2014-01-01

    Quantitative lithofacies palaeogeography is an important discipline of palaeogeography.It is developed on the foundation of traditional lithofacies palaeogeography and palaeogeography,the core of which is the quantitative lithofacies palaeogeographic map.Quantity means that in the palaeogeographic map,the division and identification of each palaeogeographic unit are supported by quantitative data and quantitative fundamental maps.Our lithofacies palaeogeographic maps are quantitative or mainly quantitative.A great number of quantitative lithofacies palaeogeographic maps have been published,and articles and monographs of quantitative lithofacies palaeogeography have been published successively,thus the quantitative lithofacies palaeogeography was formed and established.It is an important development in lithofacies palaeogeography.In composing quantitative lithofacies palaeogeographic maps,the key measure is the single factor analysis and multifactor comprehensive mapping method—methodology of quantitative lithofacies palaeogeography.In this paper,the authors utilize two case studies,one from the Early Ordovician of South China and the other from the Early Ordovician of Ordos,North China,to explain how to use this methodology to compose the quantitative lithofacies palaeogeographic maps,and to discuss the palaeogeographic units in these maps.Finally,three characteristics,i.e.,quantification,multiple orders and multiple types,of quantitative lithofacies palaeogeographic maps are conclusively discussed.

  20. Autoradiographic localization of 5-hydroxytryptamine and noradrenaline in the central nervous system of Lithobius forficatus L. (Myriapoda; Chilopoda)

    NARCIS (Netherlands)

    Descamps, Michel; Joly, Robert; Jamault-Navarro, Catherine

    1985-01-01

    Using the ability of selective uptake by the neurons of their own secreted amines, two 3H labeled neurotransmitters were used: 5-hydroxytryptamine (5 HT, serotonin) and noradrenaline (NA). Autoradiographic study was conducted on semithin and on ultrathin sections. In the brain, 3H-5 HT labeling is o

  1. Quantitative T1 and proton density mapping with direct calculation of radiofrequency coil transmit and receive profiles from two-point variable flip angle data.

    Science.gov (United States)

    Baudrexel, Simon; Reitz, Sarah C; Hof, Stephanie; Gracien, René-Maxime; Fleischer, Vinzenz; Zimmermann, Hilga; Droby, Amgad; Klein, Johannes C; Deichmann, Ralf

    2016-03-01

    Quantitative T1 mapping of brain tissue is frequently based on the variable flip angle (VFA) method, acquiring spoiled gradient echo (GE) datasets at different excitation angles. However, accurate T1 calculation requires a knowledge of the sensitivity profile B1 of the radiofrequency (RF) transmit coil. For an additional derivation of proton density (PD) maps, the receive coil sensitivity profile (RP) must also be known. Mapping of B1 and RP increases the experiment duration, which may be critical when investigating patients. In this work, a method is presented for the direct calculation of B1 and RP from VFA data. Thus, quantitative maps of T1 , PD, B1 and RP can be obtained from only two spoiled GE datasets. The method is based on: (1) the exploitation of the linear relationship between 1/PD and 1/T1 in brain tissue and (2) the assumption of smoothly varying B1 and RP, so that a large number of data points can be fitted across small volume elements where B1 and RP are approximately constant. The method is tested and optimized on healthy subjects. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Quantitative Trait Loci Mapping of Maize Yield and Its Components Under Different Water Treatments at Flowering Time

    Institute of Scientific and Technical Information of China (English)

    Gui-He Lu; Yi-Rong Zhang; Jing-Rui Dai; Ji-Hua Tang; Jian-Bing Yan; Xi-Qing Ma; Jian-Sheng Li; Shao-Jiang Chen; Jian-Cang Ma; Zhan-Xian Liu; Li-Zhu E

    2006-01-01

    Drought or water stress is a serious agronomic problem resulting in maize (Zea mays L.) yield loss throughout the world. Breeding hybrids with drought tolerance is one important approach for solving this problem. However, lower efficiency and a longer period of breeding hybrids are disadvantages of traditional breeding programs. It is generally recognized that applying molecular marker techniques to traditional breeding programs could improve the efficiency of the breeding of drought-tolerant maize. To provide useful information for use in studies of maize drought tolerance,the mapping and tagging of quantitative trait loci (QTL) for yield and its components were performed in the present study on the basis of the principle of a mixed linear model. Two hundred and twenty-one recombinant inbred lines (RIL) of Yuyu 22 were grown under both well-watered and water-stressed conditions. In the former treatment group, plants were well irrigated, whereas those in the latter treatment group were stressed at flowering time.Ten plants of each genotype were grown in a row that was 3.00 m×0.67 m (length×width). The results show that a few of the QTL were the same (one additive QTL for ear length, two additive QTL and one pair of epistatic QTL for kernel number per row, one additive QTL for kernel weight per plant), whereas most of other QTL were different between the two different water treatment groups. It may be that genetic expression differs under the two different water conditions. Furthermore, differences in the additive and epistatic QTL among the traits under water-stressed conditions indicate that genetic expression also differs from trait to trait.Major and minor QTL were detected for the traits,except for kernel number per row, under water-stressed conditions. Thus, the genetic mechanism of drought tolerance in maize is complex because the additive and epistatic QTL exist at the same time and the major and minor QTL all contribute to phenotype under water

  3. Cerebral Microbleeds in Multiple Sclerosis Evaluated on Susceptibility-weighted Images and Quantitative Susceptibility Maps: A Case-Control Study.

    Science.gov (United States)

    Zivadinov, Robert; Ramasamy, Deepa P; Benedict, Ralph R H; Polak, Paul; Hagemeier, Jesper; Magnano, Christopher; Dwyer, Michael G; Bergsland, Niels; Bertolino, Nicola; Weinstock-Guttman, Bianca; Kolb, Channa; Hojnacki, David; Utriainen, David; Haacke, E Mark; Schweser, Ferdinand

    2016-12-01

    Purpose To assess cerebral microbleed (CMB) prevalence in patients with multiple sclerosis (MS) and clinically isolated syndrome (CIS) and associations with clinical outcomes. Materials and Methods CMBs are associated with aging and neurodegenerative disorders. The prevalence of CMBs has not previously been well established. In this study, 445 patients with MS (266 with relapsing-remitting MS, 138 with secondary progressive MS, and 41 with primary progressive MS), 45 patients with CIS, 51 patients with other neurological diseases, and 177 healthy control subjects (HCs) underwent 3-T magnetic resonance (MR) imaging and clinical examinations. A subset of 168 patients with MS and 50 HCs underwent neuropsychological testing. Number of CMBs was assessed on susceptibility-weighted minimum intensity projections by using the Microbleed Anatomic Rating Scale; volume was calculated by using quantitative susceptibility maps. Differences between groups were analyzed with the χ(2) test, Fisher exact test, Student t test, and analysis of variance; associations of CMBs with clinical and other MR imaging outcomes were explored with correlation and regression analyses. Because CMB frequency increases with age, prevalence was investigated in participants at least 50 years of age and younger than 50 years. Results Significantly more patients with MS than HCs had CMBs (19.8% vs 7.4%, respectively; P = .01) in the group at least 50 years old. A trend toward greater presence of CMBs was found in patients with MS (P = .016) and patients with CIS who were younger than 50 years (P = .039) compared with HCs. In regression analysis adjusted for age, hypertension, and normalized brain volume, increased number of CMBs was significantly associated with increased physical disability in the MS population (R(2) = 0.23, P CMBs was significantly associated with deteriorated auditory and verbal learning and memory (P = .006) and visual information processing speed trends (P = .049) in patients with

  4. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

    Science.gov (United States)

    In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

  5. Quantitative evaluation of fMRI retinotopic maps, from V1 to V4, for cognitive experiments

    Directory of Open Access Journals (Sweden)

    Cecile eBordier

    2015-05-01

    Full Text Available FMRI retinotopic mapping is a non-invasive technique for the delineation of low-level visual areas in individual subjects. It generally relies upon the analysis of functional responses to periodic visual stimuli that encode eccentricity or polar angle in the visual field. This technique is used in vision research when the precise assignation of brain activation to retinotopic areas is an issue. It involves processing steps computed with different algorithms and embedded in various software suites. Manual intervention may be needed for some steps. Although the diversity of the available processing suites and manual interventions may potentially introduce some differences in the final delineation of visual areas, no documented comparison between maps obtained with different procedures has been reported in the literature. To explore the effect of the processing steps on the quality of the maps obtained, we used two tools, BALC, which relies on a fully automated procedure, and BrainVoyager, where areas are delineated by hand on the brain surface. To focus on the mapping procedures specifically, we used the same SPM pipeline for pretreatment and the same tissue segmentation tool. We document the consistency and differences of the fMRI retinotopic maps obtained from routine retinotopy experiments on ten subjects. The maps obtained by skilled users are never fully identical. However, the agreement between the maps, around 80% for low-level areas, is probably sufficient for most applications. Our results also indicate that assigning cognitive activations, following a specific experiment (here, color perception, to individual retinotopic maps is not free of errors. We provide measurements of this error, that may help for the cautious interpretation of cognitive activation projection onto fMRI retinotopic maps. On average, the magnitude of the error is about 20%, with much larger differences in a few subjects.

  6. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

  7. Dose rate mapping and quantitative analysis of radioactive deposition with simple monitoring instruments in Finland after the Chernobyl accident.

    Energy Technology Data Exchange (ETDEWEB)

    Koivukoski, J. [Ministry of the Interior, Rescue Dept., Helsinki (Finland); Paatero, J. [Finnish Meteorological Inst., Helsinki (Finland)], E-mail: janne.koivukoski@intermin.fi

    2013-03-01

    This article reviews the Finnish dose-rate mapping equipment and the system to process the obtained results, which were used immediately after the 1986 Chernobyl accident. We present the results of the external gamma-radiation monitoring carried out with simple civil-defence gamma monitoring instruments and compare them with the subsequent deposition mapping performed with research-grade instruments. The analysis shows that the quality of radiation mapping is good enough for decision makers to direct protective measures to the right areas. This review also demonstrates that a simple stationary external gamma radiation monitoring network can be effectively used for early warning in radiation emergency situations. (orig.)

  8. Statistical parametric mapping of stimuli-evoked changes in quantitative blood flow using extended-focus optical coherence microscopy (Conference Presentation)

    Science.gov (United States)

    Marchand, Paul J.; Bouwens, Arno; Shamaei, Vincent; Nguyen, David; Extermann, Jerome; Bolmont, Tristan; Lasser, Theo

    2016-03-01

    Magnetic Resonance Imaging has revolutionised our understanding of brain function through its ability to image human cerebral structures non-invasively over the entire brain. By exploiting the different magnetic properties of oxygenated and deoxygenated blood, functional MRI can indirectly map areas undergoing neural activation. Alongside the development of fMRI, powerful statistical tools have been developed in an effort to shed light on the neural pathways involved in processing of sensory and cognitive information. In spite of the major improvements made in fMRI technology, the obtained spatial resolution of hundreds of microns prevents MRI in resolving and monitoring processes occurring at the cellular level. In this regard, Optical Coherence Microscopy is an ideal instrumentation as it can image at high spatio-temporal resolution. Moreover, by measuring the mean and the width of the Doppler spectra of light scattered by moving particles, OCM allows extracting the axial and lateral velocity components of red blood cells. The ability to assess quantitatively total blood velocity, as opposed to classical axial velocity Doppler OCM, is of paramount importance in brain imaging as a large proportion of cortical vascular is oriented perpendicularly to the optical axis. We combine here quantitative blood flow imaging with extended-focus Optical Coherence Microscopy and Statistical Parametric Mapping tools to generate maps of stimuli-evoked cortical hemodynamics at the capillary level.

  9. 多QTL定位的压缩估计方法%Shrinkage Estimation Method for Mapping Multiple Quantitative Trait Loci

    Institute of Scientific and Technical Information of China (English)

    章元明

    2006-01-01

    本文综述了多标记分析和多QTL定位的压缩估计方法.对于前者,Xu(Genetics,2003,163:789-801)首先提出了Bayesian压缩估计方法.其关键在于让每个效应有一个特定的方差参数,而该方差又服从一定的先验分布,以致能从资料中估计之.由此,能够同时估计大量分子标记基因座的遗传效应,即使大多数标记的效应是可忽略的.然而,对于上位性遗传模型,其运算时间还是过长.为此,笔者将上述思想嵌入极大似然法,提出了惩罚最大似然方法.模拟研究显示:该方法能处理变量个数大于样本容量10倍左右的线性遗传模型.对于后者,本文详细介绍了基于固定区间和可变区间的Bayesian压缩估计方法.固定区间方法可处理中等密度的分子标记资料;可变区间方法则可分析高密度分子标记资料,甚至是上位性遗传模型.对于上位性检测,已介绍的惩罚最大似然方法和可变区间Bayesian压缩估计方法可供利用.应当指出,压缩估计方法在今后的eQTL和QTN定位以及基因互作网络分析等研究中也是有应用价值的.%In this article, shrinkage estimation method for multiple-marker analysis and for mapping multiple quantitative trait loci (QTL) was reviewed. For multiple-marker analysis, Xu (Genetics, 2003, 163:789-801) developed a Bayesian shrinkage estimation (BSE) method. The key to the success of this method is to allow each marker effect have its own variance parameter, which in turn has its own prior distribution so that the variance can be estimated from the data. Under this hierarchical model, a large number of markers can be handled although most of them may have negligible effects. Under epistatic genetic model, however, the running time is very long. To overcome this problem, a novel method of incorporating the idea described above into maximum likelihood,known as penalized likelihood method, was proposed. A simulated study showed that this method can

  10. Autoradiographic localization of adenosine receptors in rat brain using (/sup 3/H)cyclohexyladenosine

    Energy Technology Data Exchange (ETDEWEB)

    Goodman, R.R.; Synder, S.H.

    1982-09-01

    Adenosine (A1) receptor binding sites have been localized in rat brain by an in vitro light microscopic autoradiographic method. The binding of (/sup 3/H)N6-cyclohexyladenosine to slide-mounted rat brain tissue sections has the characteristics of A1 receptors. It is saturable with high affinity and has appropriate pharmacology and stereospecificity. The highest densities of adenosine receptors occur in the molecular layer of the cerebellum, the molecular and polymorphic layers of the hippocampus and dentate gyrus, the medial geniculate body, certain thalamic nuclei, and the lateral septum. High densities also are observed in certain layers of the cerebral cortex, the piriform cortex, the caudate-putamen, the nucleus accumbens, and the granule cell layer of the cerebellum. Most white matter areas, as well as certain gray matter areas, such as the hypothalamus, have negligible receptor concentrations. These localizations suggest possible central nervous system sites of action of adenosine.

  11. Calcitonin receptors in the rat mesencephalon mediate its analgesic actions: autoradiographic and behavioral analyses

    Energy Technology Data Exchange (ETDEWEB)

    Fabbri, A.; Pert, C.B.; Pert, A.; Fraioli, F.

    1985-09-23

    Autoradiographic analyses of salmon calcitonin (sCT) binding in the rat mesencephalon revealed an exceptionally high concentration of receptors in the ventral and ventrolateral segments of the periaqueductal gray matter (PAG) extending along the entire rostralcaudal axis. Relatively heavy labeling was also seen along a band extending ventrolaterally through the mesencephalic reticular formation. Other receptor-rich areas include the nucleus linearis, pars compacta and lateralis of the substantia nigra, locus coeruleus, parabrachial nuclei and nucleus raphe pontis of the pontine reticular formation. The biological effects are consistent with the potencies of both peptides in displacing SVI-sCT from slide-mounted sections of rat PAG. Naloxone failed to antagonize sCT-induced analgesia, suggesting an opiate independent mechanism for this peptide in elicting analgesia. (Auth.). 60 refs.; 9 figs.

  12. Light microscopic and autoradiographic study of non-irradiated and irradiated ocular wounds

    Energy Technology Data Exchange (ETDEWEB)

    Chakravarthy, U.; Gardiner, T.A.; Archer, D.B.; Maguire, C.J. (Queen' s Univ., Belfast, Northern Ireland (UK). Dept. of Opthalmology; Royal Victoria Hospital, Belfast, Northern Ireland (UK). Eye and Ear Clinic)

    1989-01-01

    Focal gamma irradiation was used to limit the intraocular extension of scar tissue which typically occurs after posterior perforating injury to the eye. Standard posterior perforating injuries were created in the right eye of forty-eight rabbits, half of which had the site of perforation focally irradiated using a Cobalt 60 ophthalmic plaque. Non-irradiated wounds healed with profuse formation of highly cellular and vascularised granulation tissue which invaded the vitreous to form contractile vitreo-retinal membranes. In irradiated eyes vitreo-retinal membrane formation was infrequent; the wounds showing only sparse granulation tissue with little or no extension into the vitreous cavity. Autoradiographic studies carried out in a second group of 40 animals showed that the episclera was the main source of the proliferating fibroblasts, and call counts confirmed that the inflammatory and repair responses in irradiated wounds were both delayed and attenuated. (author).

  13. Autoradiographic detection of HPRT variants of human lymphocytes resistant to RNA synthesis inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Jones, I.M.; Zetterberg, G.; Strout, C.L.; Carrano, A.V.

    1985-01-01

    The feasibility of using RNA synthesis in freshly isolated, human peripheral blood lymphocytes to detect 6-thioguanine (TG)- and 8-azaguanine (AG)-resistant variants in an autoradiographic assay similar to that of Strauss and Albertini (1979) has been evaluated. In phytohemagglutinin (PHA)-stimulated cultures RNA synthesis and HPRT activity began well in advance of DNA synthesis and increased in parallel during the first 44 h of culture. Introduction of TG or AG with PHA at the beginning of culture completely inhibited DNA synthesis during the first 44 h and reduced RNA synthesis to low levels within 24 h. When TG or AG was added after cells had been in culture for 38 h, DNA synthesis was reduced quickly while RNA synthesis was inhibited more slowly. An autoradiographic assay is described in which freshly isolated lymphocytes are cultured with PHA for 24 h, with or without TG or AG, then labeled with (/sup 3/H)uridine for 1 h. TG-resistant and AG-resistant variant frequencies for 2 normal individuals and a Lesch-Nyhan individual were determined with this assay. The variant frequencies for the normal individuals ranged from 0.46 to 10.6 x 10/sup -5/ depending upon the selective conditions used. All the Lesch-Nyhan cells were resistant to 0.2 ..mu..M-2 mM AG; some were sensitive to 0.2 mM TG and most were sensitive to 2.0 mM TG. 24 references, 3 figures, 1 table.

  14. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields.

    Science.gov (United States)

    Naumova, Anna V; Akulov, Andrey E; Khodanovich, Marina Yu; Yarnykh, Vasily L

    2017-02-15

    A well-known problem in ultra-high-field MRI is generation of high-resolution three-dimensional images for detailed characterization of white and gray matter anatomical structures. T1-weighted imaging traditionally used for this purpose suffers from the loss of contrast between white and gray matter with an increase of magnetic field strength. Macromolecular proton fraction (MPF) mapping is a new method potentially capable to mitigate this problem due to strong myelin-based contrast and independence of this parameter of field strength. MPF is a key parameter determining the magnetization transfer effect in tissues and defined within the two-pool model as a relative amount of macromolecular protons involved into magnetization exchange with water protons. The objectives of this study were to characterize the two-pool model parameters in brain tissues in ultra-high magnetic fields and introduce fast high-field 3D MPF mapping as both anatomical and quantitative neuroimaging modality for small animal applications. In vivo imaging data were obtained from four adult male rats using an 11.7T animal MRI scanner. Comprehensive comparison of brain tissue contrast was performed for standard R1 and T2 maps and reconstructed from Z-spectroscopic images two-pool model parameter maps including MPF, cross-relaxation rate constant, and T2 of pools. Additionally, high-resolution whole-brain 3D MPF maps were obtained with isotropic 170µm voxel size using the single-point synthetic-reference method. MPF maps showed 3-6-fold increase in contrast between white and gray matter compared to other parameters. MPF measurements by the single-point synthetic reference method were in excellent agreement with the Z-spectroscopic method. MPF values in rat brain structures at 11.7T were similar to those at lower field strengths, thus confirming field independence of MPF. 3D MPF mapping provides a useful tool for neuroimaging in ultra-high magnetic fields enabling both quantitative tissue

  15. Towards quantitative off-axis electron holographic mapping of the electric field around the tip of a sharp biased metallic needle

    Energy Technology Data Exchange (ETDEWEB)

    Beleggia, M. [Center for Electron Nanoscopy, Technical University of Denmark, Kongens Lyngby (Denmark); Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin (Germany); Kasama, T. [Center for Electron Nanoscopy, Technical University of Denmark, Kongens Lyngby (Denmark); Larson, D. J.; Kelly, T. F. [CAMECA Instruments, Inc., Madison, Wisconsin 53711 (United States); Dunin-Borkowski, R. E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungzentrum Jülich, Jülich (Germany); Pozzi, G. [Department of Physics and Astronomy, University of Bologna, Bologna (Italy)

    2014-07-14

    We apply off-axis electron holography and Lorentz microscopy in the transmission electron microscope to map the electric field generated by a sharp biased metallic tip. A combination of experimental data and modelling provides quantitative information about the potential and the field around the tip. Close to the tip apex, we measure a maximum field intensity of 82 MV/m, corresponding to a field k factor of 2.5, in excellent agreement with theory. In order to verify the validity of the measurements, we use the inferred charge density distribution in the tip region to generate simulated phase maps and Fresnel (out-of-focus) images for comparison with experimental measurements. While the overall agreement is excellent, the simulations also highlight the presence of an unexpected astigmatic contribution to the intensity in a highly defocused Fresnel image, which is thought to result from the geometry of the applied field.

  16. Quantitative analysis of aircraft multispectral-scanner data and mapping of water-quality parameters in the James River in Virginia

    Science.gov (United States)

    Johnson, R. W.; Bahn, G. S.

    1977-01-01

    Statistical analysis techniques were applied to develop quantitative relationships between in situ river measurements and the remotely sensed data that were obtained over the James River in Virginia on 28 May 1974. The remotely sensed data were collected with a multispectral scanner and with photographs taken from an aircraft platform. Concentration differences among water quality parameters such as suspended sediment, chlorophyll a, and nutrients indicated significant spectral variations. Calibrated equations from the multiple regression analysis were used to develop maps that indicated the quantitative distributions of water quality parameters and the dispersion characteristics of a pollutant plume entering the turbid river system. Results from further analyses that use only three preselected multispectral scanner bands of data indicated that regression coefficients and standard errors of estimate were not appreciably degraded compared with results from the 10-band analysis.

  17. From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits.

    Science.gov (United States)

    Slate, Jon

    2013-05-01

    Quantitative trait locus (QTL) mapping is frequently used in evolutionary studies to understand the genetic architecture of continuously varying traits. The majority of studies have been conducted in specially created crosses, in which genetic differences between parental lines are identified by linkage analysis. Detecting QTL segregating within populations is more problematic, especially in wild populations, because these populations typically have complicated and unbalanced multigenerational pedigrees. However, QTL mapping can still be conducted in such populations using a variance components mixed model approach, and the advent of appropriate statistical frameworks and better genotyping methods mean that the approach is gaining popularity. In this study it is shown that all studies described to date report evidence of QTL of major effect on trait variation, but that these findings are probably caused by inflated estimates of QTL effect sizes due to the Beavis effect. Using simulations I show that even the most powerful studies conducted to date are likely to give misleading descriptions of the genetic architecture of a trait. I show that an interpretation of a mapping study of beak color in the zebra finch (Taeniopygia guttata), that suggested genetic variation was determined by a small number of loci of large effect, which are possibly maintained by antagonistic pleiotropy, is likely to be incorrect. More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture.

  18. Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages

    Institute of Scientific and Technical Information of China (English)

    LIU Fengxia; SUN Chuanqing; TAN Lubin; FU Yongcai; LI Dejun; WANG Xiangkun

    2003-01-01

    An advanced backcross population of rice was used to identify the quantitative trait locus (QTL) controlling the cold-tolerance at booting to flowering stages. The recipient, Guichao 2 (GC2), was a commercial Indica rice; the donor Dongxiang common wild rice, was an accession of common wild rice (DXCWR, Oryza rufipogon Griff.). Three QTLs for cold-tolerance were detected on chromosomes 1, 6and 11. Two of them coming from DXCWR could enhance the cold-tolerance of the backcross progenies. Moreover, one sterility QTL that could reduce the seed set rate of the backcross progenies by 78% was mapped on chromosome 5.

  19. Identification of quantitative trait locus (QTL) linked to dorsal fin length from preliminary linkage map of molly fish, Poecilia sp.

    Science.gov (United States)

    Keong, Bun Poh; Siraj, Siti Shapor; Daud, Siti Khalijah; Panandam, Jothi Malar; Rahman, Arina Nadia Abdul

    2014-02-15

    A preliminary linkage map was constructed by applying backcross and testcross strategy using microsatellite (SSR) markers developed for Xiphophorus and Poecilia reticulata in ornamental fish, molly Poecilia sp. The linkage map having 18 SSR loci consisted of four linkage groups that spanned a map size of 516.1cM. Association between genotypes and phenotypes was tested in a random fashion and QTL for dorsal fin length was found to be linked to locus Msb069 on linkage group 2. Coincidentally, locus Msb069 was also reported as putative homologue primer pairs containing SSRs repeat motif which encoded hSMP-1, a sex determining locus. Dorsal fin length particularly in males of Poecilia latipinna is an important feature during courtship display. Therefore, we speculate that both dorsal fin length and putative hSMP-1 gene formed a close proximity to male sexual characteristics.

  20. Quantitative analysis of terrain units mapped in the northern quarter of Venus from Venera 15/16 data

    Science.gov (United States)

    Schaber, G. G.

    1991-01-01

    The contacts between 34 geological/geomorphic terrain units in the northern quarter of Venus mapped from Venera 15/16 data were digitized and converted to a Sinusoidal Equal-Area projection. The result was then registered with a merged Pioneer Venus/Venera 15/16 altimetric database, root mean square (rms) slope values, and radar reflectivity values derived from Pioneer Venus. The resulting information includes comparisons among individual terrain units and terrain groups to which they are assigned in regard to percentage of map area covered, elevation, rms slopes, distribution of suspected craters greater than 10 km in diameter.

  1. Comparison of quantitative trait loci for adaptive traits between oak and chestnut based on an expressed sequence tag consensus map.

    Science.gov (United States)

    Casasoli, Manuela; Derory, Jeremy; Morera-Dutrey, Caroline; Brendel, Oliver; Porth, Ilga; Guehl, Jean-Marc; Villani, Fiorella; Kremer, Antoine

    2006-01-01

    A comparative genetic and QTL mapping was performed between Quercus robur L. and Castanea sativa Mill., two major forest tree species belonging to the Fagaceae family. Oak EST-derived markers (STSs) were used to align the 12 linkage groups of the two species. Fifty-one and 45 STSs were mapped in oak and chestnut, respectively. These STSs, added to SSR markers previously mapped in both species, provided a total number of 55 orthologous molecular markers for comparative mapping within the Fagaceae family. Homeologous genomic regions identified between oak and chestnut allowed us to compare QTL positions for three important adaptive traits. Colocation of the QTL controlling the timing of bud burst was significant between the two species. However, conservation of QTL for height growth was not supported by statistical tests. No QTL for carbon isotope discrimination was conserved between the two species. Putative candidate genes for bud burst can be identified on the basis of colocations between EST-derived markers and QTL.

  2. Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris)

    Science.gov (United States)

    Root rot diseases of bean (Phaseolus vulgaris L.) are a constraint to dry and snap bean production. We developed the RR138 RIL mapping population from the cross of OSU5446, a susceptible line that meets current snap bean processing industry standards, and RR6950, a root rot resistant dry bean in th...

  3. Using molecular markers to map multiple quantitative trait loci: models for backcross, recombinant inbred, and doubled haploid progeny.

    Science.gov (United States)

    Knapp, S J

    1991-03-01

    To maximize parameter estimation efficiency and statistical power and to estimate epistasis, the parameters of multiple quantitative trait loci (QTLs) must be simultaneously estimated. If multiple QTL affect a trait, then estimates of means of QTL genotypes from individual locus models are statistically biased. In this paper, I describe methods for estimating means of QTL genotypes and recombination frequencies between marker and quantitative trait loci using multilocus backcross, doubled haploid, recombinant inbred, and testcross progeny models. Expected values of marker genotype means were defined using no double or multiple crossover frequencies and flanking markers for linked and unlinked quantitative trait loci. The expected values for a particular model comprise a system of nonlinear equations that can be solved using an interative algorithm, e.g., the Gauss-Newton algorithm. The solutions are maximum likelihood estimates when the errors are normally distributed. A linear model for estimating the parameters of unlinked quantitative trait loci was found by transforming the nonlinear model. Recombination frequency estimators were defined using this linear model. Certain means of linked QTLs are less efficiently estimated than means of unlinked QTLs.

  4. Genetic mapping and confirmation of quantitative trait loci for seed protein and oil contents and seed weight in soybean

    Science.gov (United States)

    Demand for soybean [Glycine max (L.) Merr.] meal has increased worldwide and soybean importers often offer premiums for soybean containing higher contents of protein and oil. Objectives were to detect quantitative trait loci (QTL) associated with soybean seed protein, oil, and seed weight in a soyb...

  5. Usefulness of R2* maps generated by iterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence for cerebral artery dissection

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Ayumi; Shinohara, Yuki; Fujii, Shinya; Miyoshi, Fuminori; Kuya, Keita; Ogawa, Toshihide [Tottori University, Division of Radiology, Department of Pathophysiological, and Therapeutic Science, Faculty of Medicine, Yonago (Japan); Yamashita, Eijiro [Tottori University Hospital, Division of Clinical Radiology, Yonago (Japan)

    2015-09-15

    Acute intramural hematoma resulting from cerebral artery dissection is usually visualized as a region of intermediate signal intensity on T1-weighted images (WI). This often causes problems with distinguishing acute atheromatous lesions from surrounding parenchyma and dissection. The present study aimed to determine whether or not R2* maps generated by the iterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence (IDEAL IQ) can distinguish cerebral artery dissection more effectively than three-dimensional variable refocusing flip angle TSE T1WI (T1-CUBE) and T2*WI. We reviewed data from nine patients with arterial dissection who were assessed by MR images including R2* maps, T2*WI, T1-CUBE, and 3D time-of-flight (TOF)-MRA. We visually assessed intramural hematomas in each patient as positive (clearly visible susceptibility effect reflecting intramural hematoma as hyperintensity on R2* map and hypointensity on T2*WI), negative (absent intramural hematoma), equivocal (difficult to distinguish between intramural hematoma and other paramagnetic substances such as veins, vessel wall calcification, or hemorrhage) and not evaluable (difficult to determine intramural hematoma due to susceptibility artifacts arising from skull base). Eight of nine patients were assessed during the acute phase. Lesions in all eight patients were positive for intramural hematoma corresponding to dissection sites on R2* maps, while two lesions were positive on T2*WI and three lesions showed high-intensity on T1-CUBE reflected intramural hematoma during the acute phase. R2* maps generated using IDEAL IQ can detect acute intramural hematoma associated with cerebral artery dissection more effectively than T2*WI and earlier than T1-CUBE. (orig.)

  6. Quantitative T2 mapping for detecting myocardial edema after reperfusion of myocardial infarction: validation and comparison with T2-weighted images.

    Science.gov (United States)

    Park, Chul Hwan; Choi, Eui-Young; Kwon, Hyuck Moon; Hong, Bum Kee; Lee, Byoung Kwon; Yoon, Young Won; Min, Pil-Ki; Greiser, Andreas; Paek, Mun Young; Yu, Wei; Sung, Yon Mi; Hwang, Sung Ho; Hong, Yoo Jin; Kim, Tae Hoon

    2013-06-01

    This study evaluates the clinical usefulness of T2 mapping for the detection of myocardial edema in the re-perfused acute myocardial infarction (MI). Cardiac MRIs were reviewed in 20 patients who had acute MI after reperfusion therapy. The regional T2 values and T2-weighted image (T2WI) signal intensities (SI) were measured in the infarcted and remote zones of the myocardium. Patients were divided into three groups according to the signal patterns of the infarcted myocardium on the T2WIs. The T2 values of the infarcted zones were compared on the T2 maps among the three groups. Validation of the T2 values was performed in the normal myocardium of seven healthy volunteers. There were no significant differences in mean T2WI-SI or T2 values in the normal myocardium of healthy volunteers compared to the remote myocardium of acute MI patients (p > 0.05). Mean SI on the T2WIs was significantly higher in the infarcted myocardium (81.3 ± 37.6) than in the remote myocardium (63.8 ± 18.1) (p infarcted myocardium, compared to the remote myocardium. The T2 maps showed that T2 values in the infarcted myocardium had mostly increased, regardless of group, with values of 71 ± 9 ms in group 1, 64.9 ± 7.4 ms in group 2, and 61.4 ± 8.5 ms in group 3. T2 mapping is superior to T2WI for detecting areas of high SI in the infarcted myocardium. Therefore, quantitative T2 mapping sequences may be more useful and reliable in identifying myocardial edema in the infarcted myocardium than T2WI.

  7. Quantitative assay for the detection of the V617F variant in the Janus kinase 2 (JAK2 gene using the Luminex xMAP technology

    Directory of Open Access Journals (Sweden)

    Gaudet Daniel

    2010-04-01

    Full Text Available Abstract Background The availability of clinically valid biomarkers contribute to improve the diagnosis and clinical management of diseases. A valine-to-phenylalanine substitution at position 617 (V617F in the Janus kinase 2 (JAK2 gene has been recently associated with key signaling abnormalities in the transduction of haemopoietic growth-factor receptors and is now considered as a useful clinical marker of myeloproliferative neoplasms. Several methods have recently been reported to detect the JAK2 V617F point mutation and show variable sensitivity. Methods Using the Luminex xMAP technology, we developed a quantitative assay to detect the JAK2V617F variant. The method was based on polymerase chain reaction (PCR followed by hybridization to specific probes coupled with internally dyed microspheres. The assay comprises 3 steps: genomic DNA extraction, end point PCR reaction, direct hybridization of PCR fragments and quantification. It has been tested with different sources of nucleic acid. Results Applied to whole blood samples, this quantitative assay showed a limit of detection of 2%. A highly sensitive allele-specific primer extension reaction performed in parallel allowed to validate the results and to identify the specimens with values below 2%. Conclusion Direct hybridization assay using the Luminex xMAP technology allows sensitive quantification of JAK2V617F from blood spots. It is simple and can be easily performed in a clinical setting.

  8. Quantitative MRI characterization of arthroscopically verified supraspinatus pathology: comparison of tendon tears, tendinosis and asymptomatic supraspinatus tendons with T2 mapping.

    Science.gov (United States)

    Ganal, Edmund; Ho, Charles P; Wilson, Katharine J; Surowiec, Rachel K; Smith, W Sean; Dornan, Grant J; Millett, Peter J

    2016-07-01

    Quantitative MRI T2 mapping is a non-invasive imaging technique sensitive to biochemical changes, but no studies have evaluated T2 mapping in pathologic rotator cuff tendons. It was sought to evaluate the efficacy of T2 mapping in detecting differences in the supraspinatus tendon (SST) among patients with tendinosis, partial tears and minimally retracted full-thickness tears, relative to asymptomatic volunteers. The pathologic cohort consisted of two arthroscopically verified groups: tendinosis and a tear group of partial tears or minimally retracted full-thickness tears, and was compared to an asymptomatic cohort with no prior history of shoulder pathology. The SST was manually segmented from the footprint to the medial humeral head in the coronal and sagittal planes and divided into six clinically relevant subregions. Mean T2 values and inter- and intra-rater reliability were assessed. In the anterolateral subregion, the tear group exhibited significantly higher mean T2 values (43.9 ± 12.7 ms) than the tendinosis (34.9 ± 3.9 ms; p = 0.006) and asymptomatic (33.6 ± 5.3 ms; p = 0.015) groups. In the posterolateral subregion, the tear group had higher mean T2 values (45.2 ± 13.7) than the asymptomatic group (34.7 ± 6.7; p = 0.012). Inter- and intra-rater reliability was mostly excellent (ICC > 0.75). T2 mapping is an accurate non-invasive method to identify quantitatively early rotator cuff pathology. The lateral region in the coronal plane in particular may differentiate partial and small minimally retracted full-thickness tears from tendinosis and asymptomatic tendons. Understanding and being able to measure quantitatively the process of tendon degeneration and subsequent tearing may help clinicians to better predict at-risk groups and to stratify treatment options. III.

  9. Quantitative restoration the Gulf of Mexico continental margins based on a newly-derived, basin-wide, crustal thickness map

    Science.gov (United States)

    Nguyen, L. C.; Mann, P.

    2016-12-01

    For decades, one of the main difficulties for understanding the tectonic evolution of the Gulf of Mexico (GOM) is quantifying the amount of crustal thinning of its deeply-buried and salt-covered continental margins formed during the Triassic-Jurassic rifting. In this study, we present a new crustal thickness map for the entire GOM and its surrounding areas based on integration of: 1) depth to basement compilation of previous seismic refraction and well data; and 2) regional estimation of Moho depths from 3D gravity inversion. Gravity modeling of salt thickness and Moho depth provide new constraints on crustal thickness in areas where refraction and well data are not available from both the US and Mexican GOM. Our derived crustal thickness map shows a zone of stretched continental crust with an average thickness of 20 km extending 700 km from the Ouachita foldbelt to the Sigsbee escarpment and in a 200-km-wide zone along the north and NW edge of the Yucatan block. To fully reconstruct the GOM to its pre-rift stage, we first close the late Jurassic oceanic part of the deep GOM using the traces of oceanic transform faults mapped from satellite gravity data. We then use our crustal thickness map to restore the thinned continental crust of the conjugate margins. Restoring the Yucatan block in a NW-SE direction produces the optimal, closed-fit model which supports a two-phase, GOM opening concept with early asymmetrical rifting across a broader, more extended, North American lower plate ( 250 km) in the northern, US GOM and a narrower, less extended, Yucatan upper plate ( 100 km) in the southern, Mexican GOM. Our full-fit reconstruction shows a single, post-rift Louann-Campeche salt-filled sag basin and re-aligned Paleozoic magnetic trends between the Yucatan block and Florida.

  10. Quantitative analysis of disc degeneration using axial T2 mapping in a percutaneous annular puncture model in rabbits

    Energy Technology Data Exchange (ETDEWEB)

    Chai, Jee Won; Kim, Su Jin [Dept. of Radiology, SMG-SNU Boramae Medical Center, Seoul (Korea, Republic of); Kang, Heung Sik; Lee, Joon Woo [Dept. of Radiology, Seoul National University Bundang Hospital, Seongnam (Korea, Republic of); Hong, Sung Hwan [Dept. of Radiology, Seoul National University Hospital, Seoul (Korea, Republic of)

    2016-02-15

    To evaluate T2 relaxation time change using axial T2 mapping in a rabbit degenerated disc model and determine the most correlated variable with histologic score among T2 relaxation time, disc height index, and Pfirrmann grade. Degenerated disc model was made in 4 lumbar discs of 11 rabbits (n = 44) by percutaneous annular puncture with various severities of an injury. Lumbar spine lateral radiograph, MR T2 sagittal scan and MR axial T2 mapping were obtained at baseline and 2 weeks and 4 weeks after the injury in 7 rabbits and at baseline and 2 weeks, 4 weeks, and 6 weeks after the injury in 4 rabbits. Generalized estimating equations were used for a longitudinal analysis of changes in T2 relaxation time in degenerated disc model. T2 relaxation time, disc height index and Pfirrmann grade were correlated with the histologic scoring of disc degeneration using Spearman's rho test. There was a significant difference in T2 relaxation time between uninjured and injured discs after annular puncture. Progressive decrease in T2 relaxation time was observed in injured discs throughout the study period. Lower T2 relaxation time was observed in the more severely injured discs. T2 relaxation time showed the strongest inverse correlation with the histologic score among the variables investigated (r = -0.811, p < 0.001). T2 relaxation time measured with axial T2 mapping in degenerated discs is a potential method to assess disc degeneration.

  11. Quantitative in vivo MRI evaluation of lumbar facet joints and intervertebral discs using axial T2 mapping

    Energy Technology Data Exchange (ETDEWEB)

    Stelzeneder, David; Messner, Alina; Scheurecker, Georg; Goed, Sabine; Friedrich, Klaus M.; Trattnig, Siegfried [Medical University of Vienna, Department of Radiology, MR Centre-High Field MR, Vienna (Austria); Vlychou, Marianna [Medical University of Vienna, Department of Radiology, MR Centre-High Field MR, Vienna (Austria); University Hospital of Larissa, Department of Radiology, Larissa (Greece); Welsch, Goetz H. [Medical University of Vienna, Department of Radiology, MR Centre-High Field MR, Vienna (Austria); University of Erlangen, Department of Trauma Surgery, Erlangen (Germany); Pieber, Karin; Pflueger, Verena [Medical University of Vienna, Department of Physical Medicine and Rehabilitation, Vienna (Austria)

    2011-11-15

    To assess the feasibility of T2 mapping of lumbar facet joints and intervertebral discs in a single imaging slab and to compare the findings with morphological grading. Sixty lumbar spine segments from 10 low back pain patients and 5 healthy volunteers were examined by axial T2 mapping and morphological MRI at 3.0 Tesla. Regions of interest were drawn on a single slice for the facet joints and the intervertebral discs (nucleus pulposus, anterior and posterior annulus fibrosus). The Weishaupt grading was used for facet joints and the Pfirrmann score was used for morphological disc grading (''normal'' vs. ''abnormal'' discs). The inter-rater agreement was excellent for the facet joint T2 evaluation (r = 0.85), but poor for the morphological Weishaupt grading (kappa = 0.15). The preliminary results show similar facet joint T2 values in segments with normal and abnormal Pfirrmann scores. There was no difference in mean T2 values between facet joints in different Weishaupt grading groups. Facet joint T2 values showed a weak correlation with T2 values of the posterior annulus (r = 0.32) This study demonstrates the feasibility of a combined T2 mapping approach for the facet joints and intervertebral discs using a single axial slab. (orig.)

  12. Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.)

    Indian Academy of Sciences (India)

    Reza Mohammadi; Merlyn S. Mendioro; Genaleen Q. Diaz; Glenn B. Gregorio; Rakesh K. Singh

    2013-12-01

    Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6–8 dS m-1) after the active tillering stage to identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD >3, out of which 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423–RM174), 4 (RM551–RM518) and 6 (RM20224–RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.

  13. Genetic map construction and quantitative trait locus (QTL detection of growth-related traits in Litopenaeus vannamei for selective breeding applications.

    Directory of Open Access Journals (Sweden)

    Farafidy Andriantahina

    Full Text Available Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL have been regarded as useful for marker-assisted selection (MAS in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP and simple sequence repeats (SSR markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW, total length (TL and partial carapace length (PCL, two QTLs for body length (BL, one QTL for first abdominal segment depth (FASD, third abdominal segment depth (TASD and first abdominal segment width (FASW, which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei .

  14. Mapping Quantitative Trait Loci Associated with Aluminum Toxin Tolerance in NJRIKY Recombinant Inbred Line Population of Soybean(Glycine max)

    Institute of Scientific and Technical Information of China (English)

    Bo Qi; Paul Korir; Tuanjie Zhao; Deyue Yu; Shouyi Chen; Junyi Gai

    2008-01-01

    To investigate the genetic mechanism of AI-tolerance in soybean,a recombinant inbred line population (RIL) with 184 F2:7:11 lines derived from the cross of Kefeng No.1 x Nannong 1138-2 (AI-tolerant x AI-sensitive) were tested in pot experimentwith sand culture medium in net room in Nanjing.Four traits,i.e.plant height,number of leaves,shoot dry weight and root dry weight at seedling stage,were evaluated and used to calculate the average membership index (FAi) as the indicator of AI-tolerance.The composite interval mapping (ClM) under WinQTL Cartographer v.2.5 detected five QTLs (i.e.qFAiol,qFAi-2,qFAi-3,qFAi-4 and qFAi-5),explaining 5.20%-9.07% of the total phenotypic variation individually.While with the multiple interval mapping (MIM) of the same software,five QTLs (qFAi-1,qFAi-5,qFAi-6,qFAi-7,and qFAi-8) explaining 5.7%-24.60% of the total phenotypic variation individually were mapped.Here qFAi-1 and qFAi-5 were detected by both CIM and MIM with the locations in a same flanking marker region,GMKF046-GMKF080 on B1 and satt278-sat_95 on L,respectively.While qFAi-2 under CIM and qFAi-6 under MIM both on D1b2 were located in neighboring regions with their confidence intervals overlapped and might be the same locus.Segregation analysis under major gene plus polygene inheritance model showed that Al-tolerance was controlled by two major genes (h2mg =33.05%) plus polygenes (h2pg=52.73%).Both QTL mapping and segregation analysis confirmed two QTLs responsible for Al-tolerance with relatively low heritability,and there might be a third QTL,confounded with the polygenes in segregation analysis.

  15. A comparison of phase imaging and quantitative susceptibility mapping in the imaging of multiple sclerosis lesions at ultrahigh field

    OpenAIRE

    Cronin, Matthew John; Wharton, Samuel; Al-Radaideh, Ali; Constantinescu, Chris; Evangelou, Nikos; Bowtell, Richard W.; Gowland, Penny A.

    2016-01-01

    Objective\\ud \\ud The aim of this study was to compare the use of high-resolution phase and QSM images acquired at ultra-high field in the investigation of multiple sclerosis (MS) lesions with peripheral rings, and to discuss their usefulness for drawing inferences about underlying tissue composition.\\ud \\ud Materials and methods\\ud \\ud Thirty-nine Subjects were scanned at 7 T, using 3D T2*-weighted and T1-weighted sequences. Phase images were then unwrapped and filtered, and quantitative susc...

  16. Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

    Directory of Open Access Journals (Sweden)

    Sehgal Deepmala

    2012-01-01

    Full Text Available Abstract Background Identification of genes underlying drought tolerance (DT quantitative trait loci (QTLs will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL. Results Seventy five single nucleotide polymorphism (SNP and conserved intron spanning primer (CISP markers were developed from available expressed sequence tags (ESTs using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions. Conclusions We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene

  17. 地图的定性和定量分析%Qualitative and Quantitative Analysis of Map

    Institute of Scientific and Technical Information of China (English)

    王劲峰

    2009-01-01

    空间数据可以通过意念制图、图形分析、图谱分析、空间统计等处理发现挖掘得到新的信息.意念地图(mental map)通过空间变换将真实地理对象在欧几里德空间上的分布绘制成人们意念感知中的地图.图形分析(geometric analysis)是基于空间数据的几何形状度量或几何操作进行推断的方法,常用的有缓冲区(buffer)、叠加(overlay)、邻近度(proximity)等操作,几何重心、几何形状等度量、两图案比对等算法等.图谱(summary mapping)系通过非数据分析的办法,对大量图案的观察、归纳和物理机制推断,将杂乱的信息去粗取精、去伪存真、高度抽象和浓缩,得到抽象和简化,但反映地学过程本质的地图.

  18. Ecosystem services - from assessements of estimations to quantitative, validated, high-resolution, continental-scale mapping via airborne LIDAR

    Science.gov (United States)

    Zlinszky, András; Pfeifer, Norbert

    2016-04-01

    "Ecosystem services" defined vaguely as "nature's benefits to people" are a trending concept in ecology and conservation. Quantifying and mapping these services is a longtime demand of both ecosystems science and environmental policy. The current state of the art is to use existing maps of land cover, and assign certain average ecosystem service values to their unit areas. This approach has some major weaknesses: the concept of "ecosystem services", the input land cover maps and the value indicators. Such assessments often aim at valueing services in terms of human currency as a basis for decision-making, although this approach remains contested. Land cover maps used for ecosystem service assessments (typically the CORINE land cover product) are generated from continental-scale satellite imagery, with resolution in the range of hundreds of meters. In some rare cases, airborne sensors are used, with higher resolution but less covered area. Typically, general land cover classes are used instead of categories defined specifically for the purpose of ecosystem service assessment. The value indicators are developed for and tested on small study sites, but widely applied and adapted to other sites far away (a process called benefit transfer) where local information may not be available. Upscaling is always problematic since such measurements investigate areas much smaller than the output map unit. Nevertheless, remote sensing is still expected to play a major role in conceptualization and assessment of ecosystem services. We propose that an improvement of several orders of magnitude in resolution and accuracy is possible through the application of airborne LIDAR, a measurement technique now routinely used for collection of countrywide three-dimensional datasets with typically sub-meter resolution. However, this requires a clear definition of the concept of ecosystem services and the variables in focus: remote sensing can measure variables closely related to "ecosystem

  19. Fine mapping and candidate gene prediction of a pleiotropic quantitative trait locus for yield-related trait in Zea mays.

    Directory of Open Access Journals (Sweden)

    Ruixiang Liu

    Full Text Available The yield of maize grain is a highly complex quantitative trait that is controlled by multiple quantitative trait loci (QTLs with small effects, and is frequently influenced by multiple genetic and environmental factors. Thus, it is challenging to clone a QTL for grain yield in the maize genome. Previously, we identified a major QTL, qKNPR6, for kernel number per row (KNPR across multiple environments, and developed two nearly isogenic lines, SL57-6 and Ye478, which differ only in the allelic constitution at the short segment harboring the QTL. Recently, qKNPR6 was re-evaluated in segregating populations derived from SL57-6×Ye478, and was narrowed down to a 2.8 cM interval, which explained 56.3% of the phenotypic variance of KNPR in 201 F(2∶3 families. The QTL simultaneously affected ear length, kernel weight and grain yield. Furthermore, a large F(2 population with more than 12,800 plants, 191 recombinant chromosomes and 10 overlapping recombinant lines placed qKNPR6 into a 0.91 cM interval corresponding to 198Kb of the B73 reference genome. In this region, six genes with expressed sequence tag (EST evidence were annotated. The expression pattern and DNA diversity of the six genes were assayed in Ye478 and SL57-6. The possible candidate gene and the pathway involved in inflorescence development were discussed.

  20. Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti

    Energy Technology Data Exchange (ETDEWEB)

    Severson, D.W.; Thathy, V.; Mori, A. [Univ. of Wisconsin, Madison, WI (United States)] [and others

    1995-04-01

    Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F{sub 2} populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs [2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI], is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filaria nematode Brugia malayi and the yellow fever virus. 35 refs., 2 figs., 3 tabs.

  1. Autoradiographic distribution of /sup 125/I-galanin binding sites in the rat central nervous system

    Energy Technology Data Exchange (ETDEWEB)

    Skofitsch, G.; Sills, M.A.; Jacobowitz, D.M.

    1986-11-01

    Galanin (GAL) binding sites in coronal sections of the rat brain were demonstrated using autoradiographic methods. Scatchard analysis of /sup 125/I-GAL binding to slide-mounted tissue sections revealed saturable binding to a single class of receptors with a Kd of approximately 0.2 nM. /sup 125/I-GAL binding sites were demonstrated throughout the rat central nervous system. Dense binding was observed in the following areas: prefrontal cortex, the anterior nuclei of the olfactory bulb, several nuclei of the amygdaloid complex, the dorsal septal area, dorsal bed nucleus of the stria terminalis, the ventral pallidum, the internal medullary laminae of the thalamus, medial pretectal nucleus, nucleus of the medial optic tract, borderline area of the caudal spinal trigeminal nucleus adjacent to the spinal trigeminal tract, the substantia gelatinosa and the superficial layers of the dorsal spinal cord. Moderate binding was observed in the piriform, periamygdaloid, entorhinal, insular cortex and the subiculum, the nucleus accumbens, medial forebrain bundle, anterior hypothalamic, ventromedial, dorsal premamillary, lateral and periventricular thalamic nuclei, the subzona incerta, Forel's field H1 and H2, periventricular gray matter, medial and superficial gray strata of the superior colliculus, dorsal parts of the central gray, peripeduncular area, the interpeduncular nucleus, substantia nigra zona compacta, ventral tegmental area, the dorsal and ventral parabrachial and parvocellular reticular nuclei. The preponderance of GAL-binding in somatosensory as well as in limbic areas suggests a possible involvement of GAL in a variety of brain functions.

  2. Ligand autoradiographical quantification of histamine H3 receptor in human dementia with Lewy bodies.

    Science.gov (United States)

    Lethbridge, Natasha L; Chazot, Paul L

    2016-11-01

    Dementia with Lewy bodies (DLB) is a serious age-dependent human neurodegenerative disease, with multiple debilitating symptoms, including dementia, psychosis and significant motor deficits, but with little or no effective treatments. This comparative ligand autoradiographical study has quantified histamine H3 receptors (H3R) in a series of major cortical and basal ganglia structures in human DLB and Alzheimer's (AD) post-mortem cases using the highly selective radioligand, [(3)H] GSK189254. In the main, the levels of H3 receptor were largely preserved in DLB cases when compared with aged-matched controls. However, we provide new evidence showing variable levels in the globus pallidus, and, moreover, raised levels of Pallidum H3 correlated with positive psychotic symptoms, in particular delusions and visual hallucinations, but not symptoms associated with depression. Furthermore, no correlation was detected for H3 receptor levels to MMSE or IUPRS symptom severity. This study suggests that H3R antagonists have scope for treating the psychotic symptomologies in DLB and other human brain disorders.

  3. ELECTRON MICROSCOPIC AUTORADIOGRAPHIC STUDY ON SUBCELLULAR LOCALIZATION OF FISSION PRODUCT 147Pm IN TISSUE CELLS

    Institute of Scientific and Technical Information of China (English)

    朱寿彭; 汪源长

    1994-01-01

    The early risk of internal contaminated accumualtion of 147Pm is in blood cells and endothelial cells,especially in red blood cells.Then 147Pm is selectively deposited in ultrastructure of liver cells,such as in nucleus,nucleolus,rough endoplasmic reticulum,mitochondria and microbodies,Dense tracks also appear in mitochondria and lysosome of pedal cells within renal corpuscle,and so dose in nucleus as well as in mitochondria and microbodies of epicyte of kidney near-convoluted tubule.With the prolongation of observing time,147Pm is selectively and steadily depostied in subcellular level of organic ocmponent for bone.Substantial amount of 147Pm is taken up into the nuclear fraction of osteoclasts and osteoblasts.Particularly,in organelles 147Pm is mainly accumulated in rough endoplasmic reticulum and in mitochondria.Autoradiographic tracks especially localize in combined point between Golgi complex and transitive vesicle of rough endoplasmic reticulum.In addition,numerous 147Pm deposited in collagenous fibre within interstitial of bone cells is hardly excreted.

  4. A study on measurement of the regional cerebral blood flow using autoradiographic method in moyamoya disease

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, Tomohiro; Kiya, Katsuzo; Yuki, Kiyoshi; Kawamoto, Hitoshi; Mizoue, Tatsuya; Kiura, Yoshihiro; Uozumi, Tohru [Hiroshima Prefectural Hospital (Japan); Ikawa, Fusao

    1997-11-01

    Development of Autoradiographic method (ARG) has provided measurement of cerebral blood flow in moyamoya disease. We evaluate a cerebral vasodilatory capacity (CVC) for moyamoya disease using ARG method. We used 5 patients with moyamoya disease as a candidate for measurement of the cerebral blood flow (CBF) who admitted to Hiroshima Prefectural Hospital during the past one year. There were 3 patients in an adult age and 2 patients in a young age. We tried to measure the regional CBF (rCBF) using ARG method which was a easy way to estimate the rCBF on SPECT. The CVC was calculated from the difference of the rCBF between resting SPECT and Diamox-loading SPECT. Results were as follows; Reactivity of cerebral vessels to CO{sub 2} loading and CVC weakened in moyamoya disease. The rCBF and CVC in the territories of anterior and middle cerebral arteries reduced in comparison with those in the area supplied by the posterior cerebral artery. The CVC at the treated side with surgical reconstruction recovered somewhat in an adult type. From these results, measurement of CBF using ARG method seems to be useful for evaluation of the CVC in moyamoya disease. (author)

  5. Cluster analysis of quantitative parametric maps from DCE-MRI: application in evaluating heterogeneity of tumor response to antiangiogenic treatment.

    Science.gov (United States)

    Longo, Dario Livio; Dastrù, Walter; Consolino, Lorena; Espak, Miklos; Arigoni, Maddalena; Cavallo, Federica; Aime, Silvio

    2015-07-01

    The objective of this study was to compare a clustering approach to conventional analysis methods for assessing changes in pharmacokinetic parameters obtained from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) during antiangiogenic treatment in a breast cancer model. BALB/c mice bearing established transplantable her2+ tumors were treated with a DNA-based antiangiogenic vaccine or with an empty plasmid (untreated group). DCE-MRI was carried out by administering a dose of 0.05 mmol/kg of Gadocoletic acid trisodium salt, a Gd-based blood pool contrast agent (CA) at 1T. Changes in pharmacokinetic estimates (K(trans) and vp) in a nine-day interval were compared between treated and untreated groups on a voxel-by-voxel analysis. The tumor response to therapy was assessed by a clustering approach and compared with conventional summary statistics, with sub-regions analysis and with histogram analysis. Both the K(trans) and vp estimates, following blood-pool CA injection, showed marked and spatial heterogeneous changes with antiangiogenic treatment. Averaged values for the whole tumor region, as well as from the rim/core sub-regions analysis were unable to assess the antiangiogenic response. Histogram analysis resulted in significant changes only in the vp estimates (pclustering approach depicted marked changes in both the K(trans) and vp estimates, with significant spatial heterogeneity in vp maps in response to treatment (pclustered in three or four sub-regions. This study demonstrated the value of cluster analysis applied to pharmacokinetic DCE-MRI parametric maps for assessing tumor response to antiangiogenic therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Quantitative trait loci map for growth and morphometric traits using a channel catfish x blue catfish interspecific hybrid system.

    Science.gov (United States)

    Hutson, A M; Liu, Z; Kucuktas, H; Umali-Maceina, G; Su, B; Dunham, R A

    2014-05-01

    Head length, head depth, head width, body depth, body width, caudal depth, and caudal width and total length and BW were measured for 71 backcross full sibs between the interspecific backcross F1 (female channel catfish [Ictalurus punctatus] × male blue catfish [Ictalurus furcatus]) female × blue catfish male. Body measurements were corrected for both size and the relationship between relative body shape and size, which is critical but usually ignored in fish research. Amplified fragment length polymorphism analysis was used for construction of a QTL map with 44 linkage groups. Eleven of 44 linkage groups had at least 1 significant QTL (P ≤ 0.05) and 11 of 44 at P = 0.10. Linkage group 19 was unique as it had multiple QTL for every trait measured, except for caudal width for which no QTL was identified on any linkage group. Approximately half of the markers measured were associated with positive effects (increase in size) on the traits and half had negative effects (decrease in size). Linkage groups 5, 9, 18, 20, 39, and 40 were significant for multiple traits and always had a trait negative effect. Total length is represented on the map by the most linkage groups and the most markers. The linkage relationships found among BW, total length, and the 7 morphometric traits indicated that multiple trait marker-assisted selection to simultaneously increase BW body depth, body width, and caudal depth while decreasing the head traits with the goal to increase body weight and carcass yield would be very difficult. Multiple genetic enhancement approaches would likely be needed to simultaneously improve BW and body conformation.

  7. Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels

    DEFF Research Database (Denmark)

    Olsen, Jesper V; Nielsen, Peter Aa; Andersen, Jens R

    2007-01-01

    of recently developed methods for isolation of membrane proteins from 10-20 mg brain tissue [Nielsen, P.Aa., Olsen, J.V., Podtelejnokov, A.V., Andersen, J.R., Mann, M., Wisniewski, J.R., 2005. Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 4, 402--408] and the Hys......Analysis of the brain proteome and studying brain diseases through clinical biopsies and animal disease models require methods of quantitative proteomics that are sensitive and allow identification and quantification of low abundant membrane proteins from minute amount of tissue. Taking advantage......Tag-quantification method [Olsen, J.V., Andersen, J.R., Nielsen, P.Aa., Nielsen, M.L., Figeys, D., Mann, M., Wisniewski, J.R., 2004. HysTag---A novel proteomic qualification tool applied to differential analysis of membrane proteins from distinct areas of mouse brain. Mol. Cell. Proteomics 3, 82--92] we performed...

  8. Quantitative x-ray magnetic circular dichroism mapping with high spatial resolution full-field magnetic transmission soft x-ray spectro-microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, MacCallum J. [Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Physics Department, University of California, Berkeley, California 94720 (United States); Agostino, Christopher J. [Physics Department, University of California, Berkeley, California 94720 (United States); National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); N' Diaye, Alpha T. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Chen, Gong [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Im, Mi-Young [Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873 (Korea, Republic of); Fischer, Peter, E-mail: PJFischer@lbl.gov [Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Physics Department, University of California, Santa Cruz, California 94056 (United States)

    2015-05-07

    The spectroscopic analysis of X-ray magnetic circular dichroism (XMCD), which serves as strong and element-specific magnetic contrast in full-field magnetic transmission soft x-ray microscopy, is shown to provide information on the local distribution of spin (S) and orbital (L) magnetic moments down to a spatial resolution of 25 nm limited by the x-ray optics used in the x-ray microscope. The spatially resolved L/S ratio observed in a multilayered (Co 0.3 nm/Pt 0.5 nm) × 30 thin film exhibiting a strong perpendicular magnetic anisotropy decreases significantly in the vicinity of domain walls, indicating a non-uniform spin configuration in the vertical profile of a domain wall across the thin film. Quantitative XMCD mapping with x-ray spectro-microscopy will become an important characterization tool for systems with topological or engineered magnetization inhomogeneities.

  9. Quantitative trait loci mapping of pubescence density and flowering time of insect-resistant soybean (Glycine max L. Merr.

    Directory of Open Access Journals (Sweden)

    Kunihiko Komatsu

    2007-01-01

    Full Text Available Analysis of antibiosis resistance to common cutworm (Spodoptera litura Fabricius in soybean (Glycine max (L. Merr. has progressed significantly, but the immediate cause remains unknown. We performed quantitative trait loci (QTL analysis of pubescence density and plant development stage because these factors are assumed to be the immediate cause of resistance to cutworm. The QTLs for pubescence appeared to be identical to the previously detected the Pd1 and Ps loci controlling pubescence density. We found no candidate loci for flowering time QTLs, although one could be identical to the gene governing the long-juvenile trait or to the E6 loci controlling maturity. None of the QTLs overlapped with the QTLs for antibiosis resistance.

  10. Quantitative assessment of hepatic function: modified look-locker inversion recovery (MOLLI) sequence for T1 mapping on Gd-EOB-DTPA-enhanced liver MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jeong Hee [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Lee, Jeong Min; Han, Joon Koo; Choi, Byung Ihn [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Seoul National University College of Medicine, Institute of Radiation Medicine, Jongno-gu, Seoul (Korea, Republic of); Paek, Munyoung [Siemens Healthcare, Seoul (Korea, Republic of)

    2016-06-15

    To determine whether multislice T1 mapping of the liver using a modified look-locker inversion recovery (MOLLI) sequence on gadoxetic acid-enhanced magnetic resonance imaging (MRI) can be used as a quantitative tool to estimate liver function and predict the presence of oesophageal or gastric varices. Phantoms filled with gadoxetic acid were scanned three times using MOLLI sequence to test repeatability. Patients with chronic liver disease or liver cirrhosis who underwent gadoxetic acid-enhanced liver MRI including MOLLI sequence at 3 T were included (n = 343). Pre- and postcontrast T1 relaxation times of the liver (T1liver), changes between pre- and postcontrast T1liver (ΔT1liver), and adjusted postcontrast T1liver (postcontrast T1liver-T1spleen/T1spleen) were compared among Child-Pugh classes. In 62 patients who underwent endoscopy, all T1 parameters and spleen sizes were correlated with varices. Phantom study showed excellent repeatability of MOLLI sequence. As Child-Pugh scores increased, pre- and postcontrast T1liver were significantly prolonged (P < 0.001), and ΔT1liver and adjusted postcontrast T1liver decreased (P< 0.001). Adjusted postcontrast T1liver and spleen size were independently associated with varices (R{sup 2} = 0.29, P < 0.001). T1 mapping of the liver using MOLLI sequence on gadoxetic acid-enhanced MRI demonstrated potential in quantitatively estimating liver function, and adjusted postcontrast T1liver was significantly associated with varices. (orig.)

  11. Development of a Genomic Resource and Quantitative Trait Loci Mapping of Male Calling Traits in the Lesser Wax Moth, Achroia grisella.

    Directory of Open Access Journals (Sweden)

    Jennifer M Gleason

    Full Text Available In the study of sexual selection among insects, the Lesser Waxmoth, Achroia grisella (Lepidoptera: Pyralidae, has been one of the more intensively studied species over the past 20 years. Studies have focused on how the male calling song functions in pair formation and on the quantitative genetics of male song characters and female preference for the song. Recent QTL studies have attempted to elucidate the genetic architecture of male song and female preference traits using AFLP markers. We continued these QTL studies using SNP markers derived from an EST library that allowed us to measure both DNA sequence variation and map loci with respect to the lepidopteran genome. We report that the level of sequence variation within A. grisella is typical among other Lepidoptera that have been examined, and that comparison with the Bombyx mori genome shows that macrosynteny is conserved. Our QTL map shows that a QTL for a male song trait, pulse-pair rate, is situated on the Z chromosome, a prediction for sexually selected traits in Lepidoptera. Our findings will be useful for future studies of genetic architecture of this model species and may help identify the genetics associated with the evolution of its novel acoustic communication.

  12. Quantitative Susceptibility Mapping-Based Microscopy of Magnetic Resonance Venography (QSM-mMRV for In Vivo Morphologically and Functionally Assessing Cerebromicrovasculature in Rat Stroke Model.

    Directory of Open Access Journals (Sweden)

    Meng-Chi Hsieh

    Full Text Available Abnormal cerebral oxygenation and vessel structure is a crucial feature of stroke. An imaging method with structural and functional information is necessary for diagnosis of stroke. This study applies QSM-mMRV (quantitative susceptibility mapping-based microscopic magnetic resonance venography for noninvasively detecting small cerebral venous vessels in rat stroke model. First, susceptibility mapping is optimized and calculated from magnetic resonance (MR phase images of a rat brain. Subsequently, QSM-mMRV is used to simultaneously provide information on microvascular architecture and venous oxygen saturation (SvO2, both of which can be used to evaluate the physiological and functional characteristics of microvascular changes for longitudinally monitoring and therapeutically evaluating a disease model. Morphologically, the quantification of vessel sizes using QSM-mMRV was 30% smaller than that of susceptibility-weighted imaging (SWI, which eliminated the overestimation of conventional SWI. Functionally, QSM-mMRV estimated an average SvO2 ranging from 73% to 85% for healthy rats. Finally, we also applied QSM to monitor the revascularization of post-stroke vessels from 3 to 10 days after reperfusion. QSM estimations of SvO2 were comparable to those calculated using the pulse oximeter standard metric. We conclude that QSM-mMRV is useful for longitudinally monitoring blood oxygen and might become clinically useful for assessing cerebrovascular diseases.

  13. Quantitative Susceptibility Mapping-Based Microscopy of Magnetic Resonance Venography (QSM-mMRV) for In Vivo Morphologically and Functionally Assessing Cerebromicrovasculature in Rat Stroke Model.

    Science.gov (United States)

    Hsieh, Meng-Chi; Tsai, Ching-Yi; Liao, Min-Chiao; Yang, Jenq-Lin; Su, Chia-Hao; Chen, Jyh-Horng

    2016-01-01

    Abnormal cerebral oxygenation and vessel structure is a crucial feature of stroke. An imaging method with structural and functional information is necessary for diagnosis of stroke. This study applies QSM-mMRV (quantitative susceptibility mapping-based microscopic magnetic resonance venography) for noninvasively detecting small cerebral venous vessels in rat stroke model. First, susceptibility mapping is optimized and calculated from magnetic resonance (MR) phase images of a rat brain. Subsequently, QSM-mMRV is used to simultaneously provide information on microvascular architecture and venous oxygen saturation (SvO2), both of which can be used to evaluate the physiological and functional characteristics of microvascular changes for longitudinally monitoring and therapeutically evaluating a disease model. Morphologically, the quantification of vessel sizes using QSM-mMRV was 30% smaller than that of susceptibility-weighted imaging (SWI), which eliminated the overestimation of conventional SWI. Functionally, QSM-mMRV estimated an average SvO2 ranging from 73% to 85% for healthy rats. Finally, we also applied QSM to monitor the revascularization of post-stroke vessels from 3 to 10 days after reperfusion. QSM estimations of SvO2 were comparable to those calculated using the pulse oximeter standard metric. We conclude that QSM-mMRV is useful for longitudinally monitoring blood oxygen and might become clinically useful for assessing cerebrovascular diseases.

  14. Mapping quantitative trait loci (QTL in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2009-10-01

    Full Text Available Abstract An (Awassi × Merino × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P P http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

  15. Expression Quantitative Trait Locus Mapping Studies in Mid-secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes.

    Directory of Open Access Journals (Sweden)

    Courtney K Burrows

    2016-07-01

    Full Text Available Fertility traits in humans are heritable, however, little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals, particularly women. To address this gap in knowledge, we performed an unbiased genome-wide expression quantitative trait locus (eQTL mapping study to identify common regulatory (expression single nucleotide polymorphisms (eSNPs in mid-secretory endometrium. We identified 423 cis-eQTLs for 132 genes that were significant at a false discovery rate (FDR of 1%. After pruning for strong LD (r2 >0.95, we tested for associations between eSNPs and fecundability (the ability to get pregnant, measured as the length of the interval to pregnancy, in 117 women. Two eSNPs were associated with fecundability at a FDR of 5%; both were in the HLA region and were eQTLs for the TAP2 gene (P = 1.3x10-4 and the HLA-F gene (P = 4.0x10-4, respectively. The effects of these SNPs on fecundability were replicated in an independent sample. The two eSNPs reside within or near regulatory elements in decidualized human endometrial stromal cells. Our study integrating eQTL mapping in a primary tissue with association studies of a related phenotype revealed novel genes and associated alleles with independent effects on fecundability, and identified a central role for two HLA region genes in human implantation success.

  16. VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

    Energy Technology Data Exchange (ETDEWEB)

    Orlić, Ivica; Mekterović, Darko [Department of Physics, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka (Croatia); Mekterović, Igor [Faculty of Electrical Engineering and Computing, University of Zagreb (Croatia); Ivošević, Tatjana [Faculty of Engineering, University of Rijeka, Vukovarska 58, HR-51000 Rijeka (Croatia)

    2015-11-15

    VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster–Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By “running” a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

  17. VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

    Science.gov (United States)

    Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

    2015-11-01

    VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

  18. Mapping and validation of quantitative trait loci for resistance to Cercospora zeae-maydis infection in tropical maize (Zea mays L.).

    Science.gov (United States)

    Pozar, Gilberto; Butruille, David; Silva, Heyder Diniz; McCuddin, Zoe Patterson; Penna, Julio Cesar Viglioni

    2009-02-01

    Breeding for resistance to gray leaf spot, caused by Cercospora zeae-maydis (Cz) is paramount for many maize environments, in particular under warm and humid growing conditions. In this study, we mapped and characterized quantitative trait loci (QTL) involved in the resistance of maize against Cz. We confirmed the impact of the QTL on disease severity using near-isogenic lines (NILs), and estimated their effects on three major agronomic traits using their respective near isogenic hybrids (NIHs), which we obtained by crossing the NILs with an inbred from a complementary heterotic pool. We further validated three of the four QTL that were mapped using the Multiple Interval Mapping approach and showed LOD values>2.5. NILs genotype included all combinations between favorable alleles of the two QTL located in chromosome 1 (Q1 in bin 1.05 and Q2 in bin 1.07), and the allele in chromosome 3 (Q3 in bin 3.07). Each of the three QTL separately significantly reduced the severity of Cz. However, we found an unfavorable epistatic interaction between Q1 and Q2: presence of the favorable allele at one of the QTL allele effectively nullified the effect of the favorable allele at the other. In contrast, the interaction between Q2 and Q3 was additive, promoting the reduction of the severity to a greater extent than the sum of their individual effects. When evaluating the NIH we found significant individual effects for Q1 and Q3 on gray leaf spot severity, for Q2 on stalk lodging and grain yield, and for Q3 on grain moisture and stalk lodging. We detected significant epitasis between Q1 and Q2 for grain moisture and between Q1 and Q3 for stalk lodging. These results suggest that the combination of QTL impacts the effectiveness of marker-assisted selection procedures in commercial product development programs.

  19. A Field-Portable Membrane Introduction Mass Spectrometer for Real-time Quantitation and Spatial Mapping of Atmospheric and Aqueous Contaminants

    Science.gov (United States)

    Bell, Ryan J.; Davey, Nicholas G.; Martinsen, Morten; Collin-Hansen, Christian; Krogh, Erik T.; Gill, Christopher G.

    2015-02-01

    Environmental concentrations of volatile and semivolatile organic compounds (VOC/SVOCs) can vary dramatically in time and space under the influence of environmental conditions. In an industrial setting, multiple point and diffuse sources can contribute to fugitive emissions. Assessments and monitoring programs using periodic grab sampling provide limited information, often with delay times of days or weeks. We report the development and use of a novel, portable membrane introduction mass spectrometry (MIMS) system capable of resolving and quantifying VOC and SVOCs with high spatial and temporal resolution, in the field, in real-time. An electron impact ionization cylindrical ion trap mass spectrometer modified with a capillary hollow fiber polydimethylsiloxane membrane interface was used for continuous air and water sampling. Tandem mass spectrometry and selected ion monitoring scans performed in series allowed for the quantitation of target analytes, and full scan mode was used to survey for unexpected analytes. Predeployment and in-field external calibrations were combined with a continuously infused internal standard to enable real-time quantitation and monitor instrument performance. The system was operated in a moving vehicle with internet-linked data processing and storage. Software development to integrate MIMS and relevant meta-data for visualization and geospatial presentation in Google Earth is presented. Continuous quantitation enables the capture of transient events that may be missed or under-represented by traditional grab sampling strategies. Real-time geospatial maps of chemical concentration enable adaptive sampling and in-field decision support. Sample datasets presented in this work were collected in Northern Alberta in 2010-2012.

  20. A field-portable membrane introduction mass spectrometer for real-time quantitation and spatial mapping of atmospheric and aqueous contaminants.

    Science.gov (United States)

    Bell, Ryan J; Davey, Nicholas G; Martinsen, Morten; Collin-Hansen, Christian; Krogh, Erik T; Gill, Christopher G

    2015-02-01

    Environmental concentrations of volatile and semivolatile organic compounds (VOC/SVOCs) can vary dramatically in time and space under the influence of environmental conditions. In an industrial setting, multiple point and diffuse sources can contribute to fugitive emissions. Assessments and monitoring programs using periodic grab sampling provide limited information, often with delay times of days or weeks. We report the development and use of a novel, portable membrane introduction mass spectrometry (MIMS) system capable of resolving and quantifying VOC and SVOCs with high spatial and temporal resolution, in the field, in real-time. An electron impact ionization cylindrical ion trap mass spectrometer modified with a capillary hollow fiber polydimethylsiloxane membrane interface was used for continuous air and water sampling. Tandem mass spectrometry and selected ion monitoring scans performed in series allowed for the quantitation of target analytes, and full scan mode was used to survey for unexpected analytes. Predeployment and in-field external calibrations were combined with a continuously infused internal standard to enable real-time quantitation and monitor instrument performance. The system was operated in a moving vehicle with internet-linked data processing and storage. Software development to integrate MIMS and relevant meta-data for visualization and geospatial presentation in Google Earth is presented. Continuous quantitation enables the capture of transient events that may be missed or under-represented by traditional grab sampling strategies. Real-time geospatial maps of chemical concentration enable adaptive sampling and in-field decision support. Sample datasets presented in this work were collected in Northern Alberta in 2010-2012.

  1. Stability of R2* and quantitative susceptibility mapping of the brain tissue in a large scale multi-center study

    Science.gov (United States)

    Wang, Rongpin; Xie, Guangyou; Zhai, Maoxiong; Zhang, Zhongping; Wu, Bing; Zheng, Dandan; Hong, Nan; Jiang, Tao; Wen, Baohong; Cheng, Jingliang

    2017-01-01

    Multi-center studies are advantageous for enrolling participants of varying pathological and demographical conditions, and especially in neurological studies. Hence stability of the obtained quantitative R2* and susceptibility in multicenter studies is a key issue for their widespread applications. In this work, the stabilities of simultaneously obtained R2* and susceptibility are investigated and compared across 10 sites that are equipped with the same scanner and receiver coil, the same post-processing process was used to achieve consistent experiment setup. Two healthy adult volunteers (one male and female) participated in this study. High intraclass correlation coefficient was obtained for both susceptibility (0.94) and R2* (0.96). The coefficients of variance for all measurements obtained were smaller than 0.1, the largest variations of measurements in all the chosen ROIs fall within ±20% from the median value. Higher level of stability was obtained in R2* as compared to susceptibility at 1 mm resolution (P < 0.05) and at 1.5 mm (P < 0.01). PMID:28349957

  2. Quantitatively analyzing dielectrical properties of resins and mapping permittivity variations in CFRP with high-frequency eddy current device technology

    Science.gov (United States)

    Gäbler, Simone; Heuer, Henning; Heinrich, Gert; Kupke, Richard

    2015-03-01

    Eddy current testing is well-established for non-destructive characterization of electrical conductive materials. The development of high-frequency eddy current technology (with frequency ranges up to 100 MHz) made it even possible to extend the classical fields of application towards less conductive materials like CFRP. Maxwell's equations and recent research show that the use of high-frequency eddy current technology is also suitable for non-conductive materials. In that case the change of complex impedance of the probing coil contains information on sample permittivity. This paper shows that even a quantitative measurement of complex permittivity with high-frequency eddy current device technology is possible using an appropriate calibration. Measurement accuracy is comparable to commercial capacitive dielectric analyzers. If the sample material is electrically conductive, both, permittivity and conductivity influence the complex impedance measured with high-frequency eddy current devices. Depending on the measurement setup and the sheet resistance of the sample a parallel characterization of both parameters is possible on isotropic multi-layer materials. On CFRP the permittivity measurement is much more complex due to the capacitive effects between the carbon rovings. However, first results show that at least the local permittivity variations (like those caused by thermal damages) are detectable.

  3. Quantitative full-colour transmitted light microscopy and dyes for concentration mapping and measurement of diffusion coefficients in microfluidic architectures.

    Science.gov (United States)

    Werts, Martinus H V; Raimbault, Vincent; Texier-Picard, Rozenn; Poizat, Rémi; Français, Olivier; Griscom, Laurent; Navarro, Julien R G

    2012-02-21

    A simple and versatile methodology has been developed for the simultaneous measurement of multiple concentration profiles of colourants in transparent microfluidic systems, using a conventional transmitted light microscope, a digital colour (RGB) camera and numerical image processing combined with multicomponent analysis. Rigorous application of the Beer-Lambert law would require monochromatic probe conditions, but in spite of the broad spectral bandwidths of the three colour channels of the camera, a linear relation between the measured optical density and dye concentration is established under certain conditions. An optimised collection of dye solutions for the quantitative optical microscopic characterisation of microfluidic devices is proposed. Using the methodology for optical concentration measurement we then implement and validate a simplified and robust method for the microfluidic measurement of diffusion coefficients using an H-filter architecture. It consists of measuring the ratio of the concentrations of the two output channels of the H-filter. It enables facile determination of the diffusion coefficient, even for non-fluorescent molecules and nanoparticles, and is compatible with non-optical detection of the analyte.

  4. Genome-wide quantitative trait locus mapping identifies multiple major loci for brittle rachis and threshability in Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao.

    Directory of Open Access Journals (Sweden)

    Yun-Feng Jiang

    Full Text Available Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao is a semi-wild hexaploid wheat resource that is only naturally distributed in the Qinghai-Tibet Plateau. Brittle rachis and hard threshing are two important characters of Tibetan semi-wild wheat. A whole-genome linkage map of T. aestivum ssp. tibetanum was constructed using a recombinant inbred line population (Q1028×ZM9023 with 186 lines, 564 diversity array technology markers, and 117 simple sequence repeat markers. Phenotypic data on brittle rachis and threshability, as two quantitative traits, were evaluated on the basis of the number of average spike rachis fragments per spike and percent threshability in 2012 and 2013, respectively. Quantitative trait locus (QTL mapping performed using inclusive composite interval mapping analysis clearly identified four QTLs for brittle rachis and three QTLs for threshability. However, three loci on 2DS, 2DL, and 5AL showed pleiotropism for brittle rachis and threshability; they respectively explained 5.3%, 18.6%, and 18.6% of phenotypic variation for brittle rachis and 17.4%, 13.2%, and 35.2% of phenotypic variation for threshability. A locus on 3DS showed an independent effect on brittle rachis, which explained 38.7% of the phenotypic variation. The loci on 2DS and 3DS probably represented the effect of Tg and Br1, respectively. The locus on 5AL was in very close proximity to the Q gene, but was different from the predicted q in Tibetan semi-wild wheat. To our knowledge, the locus on 2DL has never been reported in common wheat but was prominent in T. aestivum ssp. tibetanum accession Q1028. It remarkably interacted with the locus on 5AL to affect brittle rachis. Several major loci for brittle rachis and threshability were identified in Tibetan semi-wild wheat, improving the understanding of these two characters and suggesting the occurrence of special evolution in Tibetan semi-wild wheat.

  5. Prognostic Significance of Remote Myocardium Alterations Assessed by Quantitative Noncontrast T1 Mapping in ST-Segment Elevation Myocardial Infarction.

    Science.gov (United States)

    Reinstadler, Sebastian J; Stiermaier, Thomas; Liebetrau, Johanna; Fuernau, Georg; Eitel, Charlotte; de Waha, Suzanne; Desch, Steffen; Reil, Jan-Christian; Pöss, Janine; Metzler, Bernhard; Lücke, Christian; Gutberlet, Matthias; Schuler, Gerhard; Thiele, Holger; Eitel, Ingo

    2017-06-09

    This study assessed the prognostic significance of remote zone native T1 alterations for the prediction of clinical events in a population with ST-segment elevation myocardial infarction (STEMI) who were treated by primary percutaneous coronary intervention (PPCI) and compared it with conventional markers of infarct severity. The exact role and incremental prognostic relevance of remote myocardium native T1 mapping alterations assessed by cardiac magnetic resonance (CMR) after STEMI remains unclear. We included 255 consecutive patients with STEMI who were reperfused within 12 h after symptom onset. CMR core laboratory analysis was performed to assess left ventricular (LV) function, standard infarct characteristics, and native T1 values of the remote, noninfarcted myocardium. The primary endpoint was a composite of death, reinfarction, and new congestive heart failure within 6 months (major adverse cardiac events [MACE]). Patients with increased remote zone native T1 values (>1,129 ms) had significantly larger infarcts (p = 0.012), less myocardial salvage (p = 0.002), and more pronounced LV dysfunction (p = 0.011). In multivariable analysis, remote zone native T1 was independently associated with MACE after adjusting for clinical risk factors (p = 0.001) or other CMR variables (p = 0.007). In C-statistics, native T1 of remote myocardium provided incremental prognostic information beyond clinical risk factors, LV ejection fraction, and other markers of infarct severity (all p infarct size, and myocardial salvage index) led to net reclassification improvement of 0.82 (95% confidence interval: 0.46 to 1.17; p Myocardial Damage in STEMI [LIPSIA-COND]; NCT02158468). Copyright © 2017 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  6. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

    Directory of Open Access Journals (Sweden)

    Wenchao Zhang

    2016-05-01

    Full Text Available The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS, for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.

  7. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

    Science.gov (United States)

    Zhang, Wenchao; Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X

    2016-05-01

    The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS), for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.

  8. Expansion of the Knockdown Resistance Frequency Map for Human Head Lice (Phthiraptera: Pediculidae) in the United States Using Quantitative Sequencing.

    Science.gov (United States)

    Gellatly, Kyle J; Krim, Sarah; Palenchar, Daniel J; Shepherd, Katie; Yoon, Kyong Sup; Rhodes, Christopher J; Lee, Si Hyeock; Marshall Clark, J

    2016-05-01

    Pediculosis is a prevalent parasitic infestation of humans, which is increasing due, in part, to the selection of lice resistant to either the pyrethrins or pyrethroid insecticides by the knockdown resistance (kdr) mechanism. To determine the extent and magnitude of the kdr-type mutations responsible for this resistance, lice were collected from 138 collection sites in 48 U.S. states from 22 July 2013 to 11 May 2015 and analyzed by quantitative sequencing. Previously published data were used for comparisons of the changes in the frequency of the kdr-type mutations over time. Mean percent resistance allele frequency (mean % RAF) values across the three mutation loci were determined from each collection site. The overall mean % RAF (±SD) for all analyzed lice was 98.3 ± 10%. 132/138 sites (95.6%) had a mean % RAF of 100%, five sites (3.7%) had intermediate values, and only a single site had no mutations (0.0%). Forty-two states (88%) had a mean % RAF of 100%. The frequencies of kdr-type mutations did not differ regardless of the human population size that the lice were collected from, indicating a uniformly high level of resistant alleles. The loss of efficacy of the Nix formulation (Prestige Brand, Tarrytown, NY) from 1998 to 2013 was correlated to the increase in kdr-type mutations. These data provide a plausible reason for the decrease in the effectiveness of permethrin in the Nix formulation, which is the parallel increase of kdr-type mutations in lice over time. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America.

  9. Quantitative autoradiographic determination of binding sites for a peripheral benzodiazepine ligand ((/sup 3/H)PK 11195) in human iris

    Energy Technology Data Exchange (ETDEWEB)

    Valtier, D.; Malgouris, C.; Uzan, A.

    1987-01-01

    Specific binding sites of peripheral-type benzodiazepines were investigated in human iris/ciliary body (8 eyes). Examination of color-coded prints and densitometric quantification of autoradiograms were performed on slides (20 ..mu..m) labelled with (/sup 3/H)PK 11195 (1 nM) at 25 deg C. Nonspecific binding was determined with PK 11211 (5 ..mu..M) or Ro 5-4864 (5 ..mu..M). Binding sites were present on all the slides, with equivalent density in the 3 regions of the preparation (ciliary body, iris and pupil margin). The numbers of binding sites in ciliary body, iris, and pupil margin, respectively were: 42.7 +- 0.2, 30.1 +- 0.5 and 37.4 +- 0.4 femtomol/mg protein. Labelling on the pupil margin seemed to coincide with the iris sphincter muscle. The presence of peripheral benzodiazepine binding sites in iris muscular tissue, and particularly in the pupil margin, suggests that the iris preparation may be a valuable tool to detect putative physiological effects of peripheral benzodiazepines on muscular motility.

  10. Validation of MRI-based 3D digital atlas registration with histological and autoradiographic volumes: an anatomofunctional transgenic mouse brain imaging study.

    Science.gov (United States)

    Lebenberg, J; Hérard, A-S; Dubois, A; Dauguet, J; Frouin, V; Dhenain, M; Hantraye, P; Delzescaux, T

    2010-07-01

    Murine models are commonly used in neuroscience to improve our knowledge of disease processes and to test drug effects. To accurately study neuroanatomy and brain function in small animals, histological staining and ex vivo autoradiography remain the gold standards to date. These analyses are classically performed by manually tracing regions of interest, which is time-consuming. For this reason, only a few 2D tissue sections are usually processed, resulting in a loss of information. We therefore proposed to match a 3D digital atlas with previously 3D-reconstructed post mortem data to automatically evaluate morphology and function in mouse brain structures. We used a freely available MRI-based 3D digital atlas derived from C57Bl/6J mouse brain scans (9.4T). The histological and autoradiographic volumes used were obtained from a preliminary study in APP(SL)/PS1(M146L) transgenic mice, models of Alzheimer's disease, and their control littermates (PS1(M146L)). We first deformed the original 3D MR images to match our experimental volumes. We then applied deformation parameters to warp the 3D digital atlas to match the data to be studied. The reliability of our method was qualitatively and quantitatively assessed by comparing atlas-based and manual segmentations in 3D. Our approach yields faster and more robust results than standard methods in the investigation of post mortem mouse data sets at the level of brain structures. It also constitutes an original method for the validation of an MRI-based atlas using histology and autoradiography as anatomical and functional references, respectively.

  11. Quantitative mapping of precursory seismic quiescence before the 1989, M 7.1off-Sanriku earthquake, Japan

    Directory of Open Access Journals (Sweden)

    N. Umino

    1999-06-01

    Full Text Available The first main shock of the off-Sanriku earthquake sequence (02/11/89, M 7.1; 18/07/92, M 6.9; 28/12/94, M 7.5 was preceded by a precursory seismic quiescence lasting 2.5 ± 1 year and up to this main shock. The detailed properties of this quiescence were mapped as a function of time and space by a gridding technique using the ZMAP computer code, and the statistical significance was estimated by generating a synthetic catalog based on the microearthquake catalog of Tohoku University, which was the data set used. The statistically most significant expression of this precursory quiescence has a probability of 0.1% to have occurred at random and was located in the eastern part of the 1989 aftershock area, at a point to which the 1994 aftershocks extended also. If we define the dimensions of the quiescence anomaly by a vertical cylinder with the depth of the entire seismogenic layer, centered at the point of most significant quiescence and showing a rate decrease of 75%, then we find its radius is 25 ± 9 km. If we allow other shapes, such as the simplified aftershock volume of 1989, or other simple geometric figures, to define the rate decrease we find dimensions of 80 by 80 km. The characteristics of the quiescence anomaly do not depend strongly on the choice of free parameters within the following ranges: 100 ? number of events ? 400, 2.0 ? Mmin £ 3.0, 1 ? time window ? 3 years. With our method, a thorough analysis of the period before the 1994 main shock is not possible because of the interference of the extended aftershock sequence of 1989. Nevertheless, we identified a quiescence of nearly zero earthquakes located near the center of the 1994 aftershock area that lasted for one year up to that main shock. However, this quiescence period ranked only 46th in significance, behind other quiescences of equal duration and similar dimensions distributed in time and space through the data set. Because of the ubiquitous existence of periods of near

  12. Autoradiographic visualization of muscarinic receptor subtypes in human and guinea pig lung

    Energy Technology Data Exchange (ETDEWEB)

    Mak, J.C.; Barnes, P.J. (National Heart and Lung Institute, London (England))

    1990-06-01

    Muscarinic receptor subtypes have been localized in human and guinea pig lung sections by an autoradiographic technique, using (3H)(-)quinuclidinyl benzilate (( 3H)QNB) and selective muscarinic antagonists. (3H)QNB was incubated with tissue sections for 90 min at 25 degrees C, and nonspecific binding was determined by incubating adjacent serial sections in the presence of 1 microM atropine. Binding to lung sections had the characterization expected for muscarinic receptors. Autoradiography revealed that muscarinic receptors were widely distributed in human lung, with dense labeling over submucosal glands and airway ganglia, and moderate labeling over nerves in intrapulmonary bronchi and of airway smooth muscle of large and small airways. In addition, alveolar walls were uniformly labeled. In guinea pig lung, labeling of airway smooth muscle was similar, but in contrast to human airways, epithelium was labeled but alveolar walls were not. The muscarinic receptors of human airway smooth muscle from large to small airways were entirely of the M3-subtype, whereas in guinea pig airway smooth muscle, the majority were the M3-subtype with a very small population of the M2-subtype present. In human bronchial submucosal glands, M1- and M3-subtypes appeared to coexist in the proportions of 36 and 64%, respectively. In human alveolar walls the muscarinic receptors were entirely of the M1-subtype, which is absent from the guinea pig lung. No M2-receptors were demonstrated in human lung. The localization of M1-receptors was confirmed by direct labeling with (3H)pirenzepine. With the exception of the alveolar walls in human lung, the localization of muscarinic receptor subtypes on structures in the lung is consistent with known functional studies.

  13. Ultrastructural and autoradiographic studies of the role of nucleolar vacuoles in soybean root meristem.

    Directory of Open Access Journals (Sweden)

    Dariusz Stepiński

    2004-03-01

    Full Text Available Ultrastructural and autoradiographic studies of nucleoli in soybean root meristematic cells in seedlings: (1 grown for 3 days at 25 degrees C (control, (2 grown for three days at 25 degrees C and for 4 days at 10 degrees C, and (3 grown as in (2 and recovered for 1 day at 25 degrees C were carried out. Control nucleoli had dense structure and a few small nucleolar vacuoles. Chilled plant nucleoli had less dense structure and no vacuoles. Nucleoli of plants recovered at 25 degrees C had big nucleolar vacuoles. In autoradiograms of squashed preparations, the labeling of nucleoli and cytoplasm after 20-min incubation in 3H-uridine was 5- and 6-fold stronger, respectively, in control than in chilled roots. Following recovery, the labeling of nucleoli and cytoplasm was much stronger than after chilling or even than in control roots. After 80-min postincubation in non-radioactive medium, average labeling of particular areas of cells was the highest in recovered plants which indicated intensification of rRNA synthesis, maturation and transport into cytoplasm resulting from the resumption of optimal conditions which was correlated with the appearance of big nucleolar vacuoles. In autoradiograms of semi-thin sections from roots of seedlings chilled for 4 days then recovered and incubated for 20 min in 3H-uridine, practically only extravacuolar parts of nucleoli were labeled. After 80-min postincubation, the labeling of nucleolar vacuoles was observed. Thus, during postincubation the labeled molecules were translocated from the nucleolar periphery into nucleolar vacuoles in cells where intensive transport of these molecules to the cytoplasm takes place. On the basis of these results, a hypothesis has been put forward that nucleolar vacuoles may be involved in the intensification of pre-ribosome transport outside nucleolus.

  14. Memory consolidation and amnesia modify 5-HT6 receptors expression in rat brain: an autoradiographic study.

    Science.gov (United States)

    Meneses, A; Manuel-Apolinar, L; Castillo, C; Castillo, E

    2007-03-12

    Traditionally, the search for memory circuits has been centered on examinations of amnesic and AD patients, cerebral lesions and, neuroimaging. A complementary alternative might be the use of autoradiography with radioligands. Indeed, ex vivo autoradiographic studies offer the advantage to detect functionally active receptors altered by pharmacological tools and memory formation. Hence, herein the 5-HT(6) receptor antagonist SB-399885 and the amnesic drugs scopolamine or dizocilpine were used to manipulate memory consolidation and 5-HT(6) receptors expression was determined by using [(3)H]-SB-258585. Thus, memory consolidation was impaired in scopolamine and dizocilpine treated groups relative to control vehicle but improved it in SB-399885-treated animals. SB-399885 improved memory consolidation seems to be associated with decreased 5-HT(6) receptors expression in 15 out 17 brain areas. Scopolamine or dizocilpine decreased 5-HT(6) receptors expression in nine different brain areas and increased it in CA3 hippocampus or other eight areas, respectively. In brain areas thought to be in charge of procedural memory such basal ganglia (i.e., nucleus accumbens, caudate putamen, and fundus striate) data showed that relative to control animals amnesic groups showed diminished (scopolamine) or augmented (dizocilpine) 5-HT(6) receptor expression. SB-399885 showing improved memory displayed an intermediate expression in these same brain regions. A similar intermediate expression occurs with regard to amygdala, septum, and some cortical areas in charge of explicit memory storage. However, relative to control group amnesic and SB-399885 rats in the hippocampus, region where explicit memory is formed, showed a complex 5-HT(6) receptors expression. In conclusion, these results indicate neural circuits underlying the effects of 5-HT(6) receptor antagonists in autoshaping task and offer some general clues about cognitive processes in general.

  15. Mitochondrial DNA synthesis studied autoradiographically in various cell types in vivo

    Directory of Open Access Journals (Sweden)

    Korr H.

    1998-01-01

    Full Text Available It is generally accepted that mitochondria are able to proliferate even in postmitotic cells due to their natural turnover and also to satisfy increased cell energy requirements. However, no detailed studies are available, particularly with respect to specific cell types. Since [3H]-thymidine is incorporated not only into nuclear (n DNA but also into the DNA of cytoplasmic mitochondria, an autoradiographic approach was developed at the light microscopy level in order to study basic questions of mitochondrial (mt proliferation in organs of rodents in situ via the cytoplasmic incorporation of [3H]-thymidine injected into the animals 1 h before sacrifice. Experiments carried out on mice after X-irradiation showed that cytoplasmic labeling was not due to a process such as unscheduled nuclear DNA synthesis (nUDS. Furthermore, half-lives of mitochondria between 8-23 days were deduced specifically in relation to cell types. The phase of mtDNA synthesis was about 75 min. Finally, mt proliferation was measured in brain cells of mice as a function of age. While all neurons showed a decreasing extent of mtDNA synthesis during old age, nUDS decreased only in distinct cell types of the cortex and hippocampus. We conclude that the leading theories explaining the phenomenon of aging are closely related, i.e., aging is due to a decreasing capacity of nDNA repair, which leads to unrepaired nDNA damage, or to an accumulation of mitochondria with damaged mtDNA, which leads to a deficit of cellular energy production

  16. Autoradiographic localization of /sup 3/H-digoxin binding by neural cells in the medulla

    Energy Technology Data Exchange (ETDEWEB)

    Traurig, H.H.; Bhagat, A.; Bass, N.H.

    1985-01-01

    The purpose of this investigation was to localize binding sites for the cardiac glycoside digoxin in the medulla of the rat in vivo. Adult male Sprague-Dawley rats were injected (IV) with /sup 3/H-digoxin and killed 30 minutes later. Autoradiographs of medullas showed evidence of /sup 3/H-digoxin binding to small- and medium-sized neural cells in the regions of the nucleus solitarius, dorsal motor nucleus of the vagus, area postrema, and in the zone between the area postrema and the underlying neuropil. However, the parasympathetic preganglionic neurons of the dorsal motor nucleus were not labeled. The /sup 3/H-digoxin-labeled cells in the medulla were located mainly in the commissural and medial portions of nucleus solitarius at the level of the area postrema. Animals injected with unlabeled digoxin followed by /sup 3/H-digoxin showed reduced binding of radioactivity. The small- and medium-sized neurons of the caudal portions of the nucleus solitarius are internuncial in position with respect to cardiovascular afferents of the glossopharyngeal and vagus nerves and sympathetic and parasympathetic cardiovascular efferent neurons of the medulla. The results of this study suggest that these /sup 3/H-digoxin-labeled cells, presumably neurons of nucleus solitarius, may possess high affinity binding sites for digoxin. Further, the area postrema, which lacks a blood-brain barrier, may provide a portal of entry for /sup 3/H-digoxin into regions of the medulla known to contain neurons that play a role in the regulation of cardiac rhythm.

  17. Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

    Science.gov (United States)

    Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

    2015-08-18

    Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16

  18. Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

    Science.gov (United States)

    Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

    2015-09-01

    Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells.

  19. Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC‐MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes

    Science.gov (United States)

    Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi

    2015-01-01

    Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel‐cutting, and quantitative LC‐MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an “overlap score,” (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 “overlap factors,” (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. PMID:26031785

  20. Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity.

    Science.gov (United States)

    Sajuthi, Satria P; Sharma, Neeraj K; Chou, Jeff W; Palmer, Nicholette D; McWilliams, David R; Beal, John; Comeau, Mary E; Ma, Lijun; Calles-Escandon, Jorge; Demons, Jamehl; Rogers, Samantha; Cherry, Kristina; Menon, Lata; Kouba, Ethel; Davis, Donna; Burris, Marcie; Byerly, Sara J; Ng, Maggie C Y; Maruthur, Nisa M; Patel, Sanjay R; Bielak, Lawrence F; Lange, Leslie A; Guo, Xiuqing; Sale, Michèle M; Chan, Kei Hang K; Monda, Keri L; Chen, Gary K; Taylor, Kira; Palmer, Cameron; Edwards, Todd L; North, Kari E; Haiman, Christopher A; Bowden, Donald W; Freedman, Barry I; Langefeld, Carl D; Das, Swapan K

    2016-08-01

    Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet, published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes, were evaluated by mining GWAS datasets. eQTL analysis identified 1971 and 2078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2 were identified in both tissues. 62.1 % of top cis-eSNPs were within ±50 kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu ) and identified genetically regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes.

  1. Evaluation of intervertebral disc regeneration with implantation of bone marrow mesenchymal stem cells (BMSCs) using quantitative T2 mapping: a study in rabbits.

    Science.gov (United States)

    Cai, Feng; Wu, Xiao-Tao; Xie, Xin-Hui; Wang, Feng; Hong, Xin; Zhuang, Su-Yang; Zhu, Lei; Rui, Yun-Feng; Shi, Rui

    2015-01-01

    The aim of the study was to investigate the curative effects of transplantation of bone marrow mesenchymal stem cells (BMSCs) on intervertebral disc regeneration and to investigate the feasibility of the quantitative T2 mapping method for evaluating repair of the nucleus pulposus after implantation of BMSCs. Forty-eight New Zealand white rabbits were used to establish the lumber disc degenerative model by stabbing the annulus fibrosus and then randomly divided into four groups, i.e. two weeks afterwards, BMSCs or phosphate-buffered saline (PBS) were transplanted into degenerative discs (BMSCs group and PBS group), while the operated rabbits without implantation of BMSCs or PBS served as the sham group and the rabbits without operation were used as the control group. At weeks two, six and ten after operation, the T2 values and disc height indices (DHI) were calculated by magnetic resonance imaging (MRI 3.0 T), and the gene expressions of type II collagen (COL2) and aggrecan (ACAN) in degenerative discs were evaluated by real-time reverse transcription polymerase chain reaction (RT-PCR). T2 values for the nucleus pulposus were correlated with ACAN or COL2 expression by regression analysis. Cell clusters, disorganised fibres, interlamellar glycosaminoglycan (GAG) matrix and vascularisation were observed in lumber degenerative discs. BMSCs could be found to survive in intervertebral discs and differentiate into nucleus pulposus-like cells expressing COL2 and ACAN. The gene expression of COL2 and ACAN increased during ten weeks after transplantation as well as the T2 signal intensity and T2 value. The DHI in the BMSCs group decreased more slowly than that in PBS and sham groups. The T2 value correlated significantly with the gene expression of ACAN and COL2 in the nucleus pulposus. Transplantation of BMSCs was able to promote the regeneration of degenerative discs. Quantitative and non-invasive T2 mapping could be used to evaluate the regeneration of the nucleus

  2. Quantitative assessment of the supraspinatus tendon on MRI using T2/T2* mapping and shear-wave ultrasound elastography: a pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Krepkin, Konstantin; Adler, Ronald S.; Gyftopoulos, Soterios [NYU Langone Medical Center/Hospital for Joint Diseases, Department of Radiology, New York, NY (United States); Bruno, Mary; Raya, Jose G. [NYU Langone Medical Center, Center for Biomedical Imaging, Department of Radiology, New York, NY (United States)

    2017-02-15

    To determine whether there is an association between T2/T2* mapping and supraspinatus tendon mechanical properties as assessed by shear-wave ultrasound elastography (SWE). This HIPAA-compliant prospective pilot study received approval from our hospital's institutional review board. Eight patients (3 males/5 females; age range 44-72 years) and nine shoulders underwent conventional shoulder MRI, T2/T2* mapping on a 3-T scanner, and SWE. Two musculoskeletal radiologists reviewed the MRI examinations in consensus for evidence of supraspinatus tendon pathology, with tear size measured for full-thickness tears. T2/T2* values and ultrasound shear-wave velocities (SWV) were calculated in three corresponding equidistant regions of interest (ROIs) within the insertional 1-2 cm of the supraspinatus tendon (medial, middle, lateral). Pearson correlation coefficients between T2/T2* values and SWV, as well as among T2, T2*, SWV and tear size, were calculated. There was a significant negative correlation between T2* and SWV in the lateral ROI (r = -0.86, p = 0.013) and overall mean ROI (r = -0.90, p = 0.006). There was significant positive correlation between T2 and measures of tear size in the lateral and mean ROIs (r range 0.71-0.77, p range 0.016-0.034). There was significant negative correlation between SWV and tear size in the middle and mean ROIs (r range -0.79-0.68, p range 0.011-0.046). Our pilot study demonstrated a potential relationship between T2* values and shear wave velocity values in the supraspinatus tendon, a finding that could lead to an improved, more quantitative evaluation of the rotator cuff tendons. (orig.)

  3. Quantitative assessment of the supraspinatus tendon on MRI using T2/T2* mapping and shear-wave ultrasound elastography: a pilot study.

    Science.gov (United States)

    Krepkin, Konstantin; Bruno, Mary; Raya, José G; Adler, Ronald S; Gyftopoulos, Soterios

    2017-02-01

    To determine whether there is an association between T2/T2* mapping and supraspinatus tendon mechanical properties as assessed by shear-wave ultrasound elastography (SWE). This HIPAA-compliant prospective pilot study received approval from our hospital's institutional review board. Eight patients (3 males/5 females; age range 44-72 years) and nine shoulders underwent conventional shoulder MRI, T2/T2* mapping on a 3-T scanner, and SWE. Two musculoskeletal radiologists reviewed the MRI examinations in consensus for evidence of supraspinatus tendon pathology, with tear size measured for full-thickness tears. T2/T2* values and ultrasound shear-wave velocities (SWV) were calculated in three corresponding equidistant regions of interest (ROIs) within the insertional 1-2 cm of the supraspinatus tendon (medial, middle, lateral). Pearson correlation coefficients between T2/T2* values and SWV, as well as among T2, T2*, SWV and tear size, were calculated. There was a significant negative correlation between T2* and SWV in the lateral ROI (r = -0.86, p = 0.013) and overall mean ROI (r = -0.90, p = 0.006). There was significant positive correlation between T2 and measures of tear size in the lateral and mean ROIs (r range 0.71-0.77, p range 0.016-0.034). There was significant negative correlation between SWV and tear size in the middle and mean ROIs (r range -0.79--0.68, p range 0.011-0.046). Our pilot study demonstrated a potential relationship between T2* values and shear wave velocity values in the supraspinatus tendon, a finding that could lead to an improved, more quantitative evaluation of the rotator cuff tendons.

  4. Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice

    Science.gov (United States)

    Adachi, Shunsuke; Yoshikawa, Kazuaki; Yamanouchi, Utako; Tanabata, Takanari; Sun, Jian; Ookawa, Taiichiro; Yamamoto, Toshio; Sage, Rowan F.; Hirasawa, Tadashi; Yonemaru, Junichi

    2017-01-01

    Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops. PMID:28197156

  5. Increased brain iron deposition is a risk factor for brain atrophy in patients with haemodialysis: a combined study of quantitative susceptibility mapping and whole brain volume analysis.

    Science.gov (United States)

    Chai, Chao; Zhang, Mengjie; Long, Miaomiao; Chu, Zhiqiang; Wang, Tong; Wang, Lijun; Guo, Yu; Yan, Shuo; Haacke, E Mark; Shen, Wen; Xia, Shuang

    2015-08-01

    To explore the correlation between increased brain iron deposition and brain atrophy in patients with haemodialysis and their correlation with clinical biomarkers and neuropsychological test. Forty two patients with haemodialysis and forty one age- and gender-matched healthy controls were recruited in this prospective study. 3D whole brain high resolution T1WI and susceptibility weighted imaging were scanned on a 3 T MRI system. The brain volume was analyzed using voxel-based morphometry (VBM) in patients and to compare with that of healthy controls. Quantitative susceptibility mapping was used to measure and compare the susceptibility of different structures between patients and healthy controls. Correlation analysis was used to investigate the relationship between the brain volume, iron deposition and neuropsychological scores. Stepwise multiple regression analysis was used to explore the effect of clinical biomarkers on the brain volumes in patients. Compared with healthy controls, patients with haemodialysis showed decreased volume of bilateral putamen and left insular lobe (All P putamen, substantia nigra, red nucleus and dentate nucleus were significantly higher (All P putamen (P putamen (P < 0.05). Our study indicated increased brain iron deposition and dialysis duration was risk factors for brain atrophy in patients with haemodialysis. The decreased gray matter volume of the left insular lobe was correlated with neurocognitive impairment.

  6. Mapping of quantitative trait locus (QTLs that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica×Setaria viridis.

    Directory of Open Access Journals (Sweden)

    Lufeng Qie

    Full Text Available Drought tolerance is an important breeding target for enhancing the yields of grain crop species in arid and semi-arid regions of the world. Two species of Setaria, domesticated foxtail millet (S. italica and its wild ancestor green foxtail (S. viridis are becoming widely adopted as models for functional genomics studies in the Panicoid grasses. In this study, the genomic regions controlling germination and early seedling drought tolerance in Setaria were identified using 190 F7 lines derived from a cross between Yugu1, a S. italica cultivar developed in China, and a wild S. viridis genotype collected from Uzbekistan. Quantitative trait loci were identified which contribute to a number of traits including promptness index, radical root length, coleoptile length and lateral root number at germinating stage and seedling survival rate was characterized by the ability of desiccated seedlings to revive after rehydration. A genetic map with 128 SSR markers which spans 1293.9 cM with an average of 14 markers per linkage group of the 9 linkage groups was constructed. A total of eighteen QTLs were detected which included nine that explained over 10% of the phenotypic variance for a given trait. Both the wild green foxtail genotype and the foxtail millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtail millet breeding.

  7. Fine-mapping quantitative trait loci affecting murine external ear tissue regeneration in the LG/J by SM/J advanced intercross line.

    Science.gov (United States)

    Cheverud, J M; Lawson, H A; Bouckaert, K; Kossenkov, A V; Showe, L C; Cort, L; Blankenhorn, E P; Bedelbaeva, K; Gourevitch, D; Zhang, Y; Heber-Katz, E

    2014-05-01

    External ear hole closure in LG/J mice represents a model of regenerative response. It is accompanied by the formation of a blastema-like structure and the re-growth of multiple tissues, including cartilage. The ability to regenerate tissue is heritable. An F34 advanced intercross line of mice (Wustl:LG,SM-G34) was generated to identify genomic loci involved in ear hole closure over a 30-day healing period. We mapped 19 quantitative trait loci (QTL) for ear hole closure. Individual gene effects are relatively small (0.08 mm), and most loci have co-dominant effects with phenotypically intermediate heterozygotes. QTL support regions were limited to a median size of 2 Mb containing a median of 19 genes. Positional candidate genes were evaluated using differential transcript expression between LG/J and SM/J healing tissue, function analysis and bioinformatic analysis of single-nucleotide polymorphisms in and around positional candidate genes of interest. Analysis of the set of 34 positional candidate genes and those displaying expression differences revealed over-representation of genes involved in cell cycle regulation/DNA damage, cell migration and adhesion, developmentally related genes and metabolism. This indicates that the healing phenotype in LG/J mice involves multiple physiological mechanisms.

  8. Volume perfusion CT (VPCT) for the differential diagnosis of patients with suspected cerebral vasospasm: Qualitative and quantitative analysis of 3D parameter maps

    Energy Technology Data Exchange (ETDEWEB)

    Dolatowski, K., E-mail: karoline.dolatowski@gmail.com [Department of Neuroradiology, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Malinova, V., E-mail: vesna.malinova@gmail.com [Department of Neurosurgery, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Frölich, A.M.J., E-mail: a.froelich@gmail.com [Department of Neuroradiology, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Schramm, R., E-mail: ramona.schramm@med.uni-goettingen.de [Department of Neuroradiology, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Haberland, U., E-mail: ulrike.haberland@siemens.com [Siemens AG, Healthcare Sector, Computed Tomography, H IM CR R and D PA SC, Siemensstr. 1, 91301 Forchheim (Germany); Klotz, E., E-mail: ernst.klotz@siemens.com [Siemens AG, Healthcare Sector, Computed Tomography, H IM CR R and D PA SC, Siemensstr. 1, 91301 Forchheim (Germany); Mielke, D., E-mail: dorothee.wachter@med.uni-goettingen.de [Department of Neurosurgery, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Knauth, M., E-mail: michael.knauth@med.uni-goettingen.de [Department of Neuroradiology, University Medicine Göttingen, Robert-Koch-Str. 40, 37075 Göttingen (Germany); Schramm, P., E-mail: Peter.Schramm@uksh.de [Department of Neuroradiology, UKSH University hospital Schleswig-Holstein Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck (Germany)

    2014-10-15

    Object: Cerebral vasospasm (CV) following subarachnoid hemorrhage (SAH) implies high risk for secondary ischemia. It requires early diagnosis to start treatment on time. We aimed to assess the utility of “whole brain” VPCT for detecting localization and characteristics of arterial vasospasm. Methods: 23 patients received a non-enhanced CT, VPCT and CTA of the brain. The distribution of ischemic lesions was analyzed on 3D-perfusion-parameter-maps of CBF, CBV, MTT, TTS, TTP, and TTD. CT-angiographic axial and coronal maximum-intensity-projections were reconstructed to determine arterial vasospasm. CT-data was compared to DSA, if performed additionally. Volume-of-interest placement was used to obtain quantitative mean VPCT values. Results: 82% patients (n = 19) had focal cerebral hypoperfusion. 100% sensitivity and 100% specificity was found for TTS (median 1.9 s), MTT (median 5.9 s) and TTD (median 7.6 s). CBV showed no significant differences. In 78% (n = 18) focal vessel aberrations could be detected either on CTA or DSA or on both. Conclusion: VPCT is a non-invasive method with the ability to detect focal perfusion deficits almost in the whole brain. While DSA remains to be the gold standard for detection of CV, VPCT has the potential to improve noninvasive diagnosis and treatment decisions.

  9. Quantitative trait mapping reveals a regulatory axis involving peroxisome proliferator-activated receptors, PRDM16, transforming growth factor-β2 and FLT3 in hematopoiesis.

    Science.gov (United States)

    Avagyan, Serine; Aguilo, Francesca; Kamezaki, Kenjiro; Snoeck, Hans-Willem

    2011-12-01

    Hematopoiesis is the process whereby BM HSCs renew to maintain their number or to differentiate into committed progenitors to generate all blood cells. One approach to gain mechanistic insight into this complex process is the investigation of quantitative genetic variation in hematopoietic function among inbred mouse strains. We previously showed that TGF-β2 is a genetically determined positive regulator of hematopoiesis. In the presence of unknown nonprotein serum factors TGF-β2, but not TGF-β1 or -β3, enhances progenitor proliferation in vitro, an effect that is subject to mouse strain-dependent variation mapping to a locus on chr.4, Tb2r1. TGF-β2-deficient mice show hematopoietic defects, demonstrating the physiologic role of this cytokine. Here, we show that TGF-β2 specifically and predominantly cell autonomously enhances signaling by FLT3 in vitro and in vivo. A coding polymorphism in Prdm16 (PR-domain-containing 16) underlies Tb2r1 and differentially regulates transcriptional activity of peroxisome proliferator-activated receptor-γ (PPARγ), identifying lipid PPAR ligands as the serum factors required for regulation of FLT3 signaling by TGF-β2. We furthermore show that PPARγ agonists play a FLT3-dependent role in stress responses of progenitor cells. These observations identify a novel regulatory axis that includes PPARs, Prdm16, and TGF-β2 in hematopoiesis.

  10. T2 mapping and quantitative analysis of the porcine patellar osteoarthritis model in vitro by collagenase%胶原酶消化猪髌软骨模型T2 mapping 成像与定量分析

    Institute of Scientific and Technical Information of China (English)

    杨朝湘; 王伟; Queenie Chan; 陈玲; 梁文; 全显跃

    2015-01-01

    Objective To investigate the ability of T2 mapping in early detection of the change of cartilage collagen by quantitative analysis.Methods 20 porcine patellae were randomly assigned into 4 groups,3 treated groups and 1 control group.The samples of 3 treated groups were respectively immersed in PBS with 100 mg/100 mL,1 50 mg/100 mL and 200 mg/100 mL typeⅡ collagenase for 4 h,whereas control group samples in PBS for 4 h.T2 relaxation times of superficial,deep and full layers of cartilage and mean densi-ty after Van Gieson stain were measured.The correlation of T2 relaxation times and mean density were statistically analyzed.Results Gross pathology showed all articular cartilages maintained intact after treatment.T2 relaxation times of superficial and full layers and mean density increased significantly in any treated group in comparison with control group(P 0.05).Pearson correlation analysis showed a close correlation(r=-0.837)between T2 relaxation times of full layers and mean density.Conclusion T2 map-ping can adequately detect the change of cartilage collagen in the early stage of osteoarthritis,and shows a good clinical application prospect.%目的:定量分析 T2 mapping 技术检测早期关节软骨退变中胶原含量变化的能力,并探讨其机制和意义。方法20个家猪髌骨随机分为4组,分别经浓度100 mg/100 mL、150 mg/100 mL、200 mg/100 mL 的Ⅱ型胶原酶(酶处理组)和无酶 PBS 缓冲液(对照组)处理。处理后髌骨行 MR T2 WI 和 T2 mapping 成像。分别测定髌关节软骨浅深2层和全层的 T2值。采用 Van Gieson染色法对软骨标本进行染色,并测定各组软骨染色后的平均光密度,分析软骨 T2值与平均光密度之间的关系。结果大体病理示各组髌骨软骨与处理前相比,软骨表面均无明显变化。统计学分析表明,各处理组与对照组比较,在软骨浅层与全层 T2值以及软骨平均光密度值上均有明显差异(P 0.05)

  11. Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar: comparing survival analysis with analysis on affected/resistant data

    Directory of Open Access Journals (Sweden)

    Lien Sigbjørn

    2007-08-01

    Full Text Available Abstract Background Infectious Salmon Anaemia (ISA is a viral disease affecting farmed Atlantic salmon (Salmo salar worldwide. The identification of Quantitative Trait Loci (QTL affecting resistance to the disease could improve our understanding of the genetics underlying the trait and provide a means for Marker-Assisted Selection. We previously performed a genome scan on commercial Atlantic salmon families challenge tested for ISA resistance, identifying several putative QTL. In the present study, we set out to validate the strongest of these QTL in a larger family material coming from the same challenge test, and to determine the position of the QTL by interval mapping. We also wanted to explore different ways of performing QTL analysis within a survival analysis framework (i.e. using time-to-event data, and to compare results using survival analysis with results from analysis on the dichotomous trait 'affected/resistant'. Results The QTL, located on Atlantic salmon linkage group 8 (following SALMAP notation, was confirmed in the new data set. Its most likely position was at a marker cluster containing markers BHMS130, BHMS170 and BHMS553. Significant segregation distortion was observed in the same region, but was shown to be unrelated to the QTL. A maximum likelihood procedure for identifying QTL, based on the Cox proportional hazard model, was developed. QTL mapping was also done using the Haley-Knott method (affected/resistant data, and within a variance-component framework (affected/resistant data and time-to-event data. In all cases, analysis using affected/resistant data gave stronger evidence for a QTL than did analysis using time-to-event data. Conclusion A QTL for resistance to Infectious Salmon Anaemia in Atlantic salmon was validated in this study, and its more precise location on linkage group eight was determined. The QTL explained 6% of the phenotypic variation in resistance to the disease. The linkage group also displayed

  12. Investigation on positive correlation of increased brain iron deposition with cognitive impairment in Alzheimer disease by using quantitative MR R2' mapping.

    Science.gov (United States)

    Qin, Yuanyuan; Zhu, Wenzhen; Zhan, Chuanjia; Zhao, Lingyun; Wang, Jianzhi; Tian, Qing; Wang, Wei

    2011-08-01

    Brain iron deposition has been proposed to play an important role in the pathophysiology of Alzheimer disease (AD). The aim of this study was to investigate the correlation of brain iron accumulation with the severity of cognitive impairment in patients with AD by using quantitative MR relaxation rate R2' measurements. Fifteen patients with AD, 15 age- and sex-matched healthy controls, and 30 healthy volunteers underwent 1.5T MR multi-echo T2 mapping and T2* mapping for the measurement of transverse relaxation rate R2' (R2'=R2*-R2). We statistically analyzed the R2' and iron concentrations of bilateral hippocampus (HP), parietal cortex (PC), frontal white matter (FWM), putamen (PU), caudate nucleus (CN), thalamus (TH), red nucleus (RN), substantia nigra (SN), and dentate nucleus (DN) of the cerebellum for the correlation with the severity of dementia. Two-tailed t-test, Student-Newman-Keuls test (ANOVA) and linear correlation test were used for statistical analysis. In 30 healthy volunteers, the R2' values of bilateral SN, RN, PU, CN, globus pallidus (GP), TH, and FWM were measured. The correlation with the postmortem iron concentration in normal adults was analyzed in order to establish a formula on the relationship between regional R2' and brain iron concentration. The iron concentration of regions of interest (ROI) in AD patients and controls was calculated by this formula and its correlation with the severity of AD was analyzed. Regional R2' was positively correlated with regional brain iron concentration in normal adults (r=0.977, PIron concentrations in bilateral HP, PC, PU, CN, and DN of patients with AD were significantly higher than those of the controls (Piron concentrations, especially in parietal cortex and hippocampus at the early stage of AD, were positively correlated with the severity of patients' cognitive impairment (Piron concentrations were, the more severe the cognitive impairment was. Regional R2' and iron concentration in parietal cortex and

  13. Quantitative evaluation of CT-perfusion map as indicator of tumor response to transarterial chemoembolization and radiofrequency ablation in HCC patients

    Energy Technology Data Exchange (ETDEWEB)

    Ippolito, Davide, E-mail: davide.atena@tiscalinet.it [School of Medicine, University of Milano-Bicocca, Via Pergolesi 33, 20900 Monza, MB (Italy); Department of Diagnostic Radiology, H. S. Gerardo Monza, Via Pergolesi 33, 20900 Monza, MB (Italy); Fior, Davide; Bonaffini, Pietro Andrea; Capraro, Cristina [School of Medicine, University of Milano-Bicocca, Via Pergolesi 33, 20900 Monza, MB (Italy); Department of Diagnostic Radiology, H. S. Gerardo Monza, Via Pergolesi 33, 20900 Monza, MB (Italy); Leni, Davide; Corso, Rocco [Department of Interventional Radiology, H. S. Gerardo Monza, Via Pergolesi 33, 20900 Monza, MB (Italy); Sironi, Sandro [School of Medicine, University of Milano-Bicocca, Via Pergolesi 33, 20900 Monza, MB (Italy); Department of Diagnostic Radiology, H. S. Gerardo Monza, Via Pergolesi 33, 20900 Monza, MB (Italy)

    2014-09-15

    Highlights: • We examine perfusion values in two different categories of treated HCC patients. • Perfusion parameters are not influenced by TACE or RFA treatments. • CT-p represents a non-invasive diagnostic technique able to assess treatment response. - Abstract: Purpose: To assess if radiofrequency ablation (RFA) and transarterial chemoembolization (TACE) may influence the evaluation of perfusion parameters obtained with CT-perfusion (CT-p) in HCC treated patients. Materials and methods: Thirty-three consecutive cirrhotic patients with biopsy-proven diagnosis of HCC lesions and candidates to TACE or RFA were included. The CT-p study of hepatic parenchyma and of treated lesions was performed about 1 month after treatment on 16 multidetector CT after injection of 50 mL of non ionic contrast agent (350 mg I/mL) at a flow rate of 6 mL/s acquiring 40 dynamic scans. A dedicated perfusion software which generated a quantitative map of arterial and portal perfusion by means of colour scale was employed.The following perfusion parameters were assessed before and after RFA or TACE treatment: hepatic perfusion (HP), arterial perfusion (AP), blood volume (BV), time to peak (TTP), hepatic perfusion index (HPI). Results: A complete treatment was obtained in 16 cases and incomplete treatment in the 17 remaining cases. The perfusion data of completely treated lesions were: HP 10.2 ± 6.3; AP 10.4 ± 7; BV 4.05 ± 4.8; TTP 38.9 ± 4.2; HPI 9.9 ± 9.2, whereas in partially treated lesions were: HP 43.2 ± 15.1 mL/s/100 g; AP 38.7 ± 8.8 mL/min; BV 20.7 ± 9.5 mL/100 mg; TTP 24 ± 3.7 s; HPI 61.7 ± 7.5%. In adjacent cirrhotic parenchyma, the parameters of all evaluated patients were: HP 13.2 ± 4; AP 12.3 ± 3.4; BV 11.8 ± 2.8; TTP 43.9 ± 2.9; and HPI 17.1 ± 9.8. A significant difference (P < 0.001) was found for all parameters between residual viable tumor tissue (P < 0.001) compared to successfully treated lesion due to the presence of residual arterial vascular

  14. A novel radioligand for glycine transporter 1: characterization and use in autoradiographic and in vivo brain occupancy studies

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Zhizhen [Imaging, Merck Research Laboratories, West Point, PA 19486 (United States)], E-mail: zhizhen_zeng@merck.com; O' Brien, Julie A. [Sleep and Psychiatric Disorders, Merck Research Laboratories, West Point, PA 19486 (United States); Lemaire, Wei [Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486 (United States); O' Malley, Stacey S.; Miller, Patricia J. [Imaging, Merck Research Laboratories, West Point, PA 19486 (United States); Zhao Zhijian [Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486 (United States); Wallace, Michael A. [Drug Metabolism, Merck Research Laboratories, Rahway, NJ 07065 (United States); Raab, Conrad [Drug Metabolism, Merck Research Laboratories, West Point, PA 19486 (United States); Lindsley, Craig W. [Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486 (United States); Departments of Pharmacology and Chemistry, Vanderbilt University, Nashville, TN 37232 (United States); Sur, Cyrille; Williams, David L. [Imaging, Merck Research Laboratories, West Point, PA 19486 (United States)

    2008-04-15

    Introduction: In an effort to develop agents to test the NMDA hypofunction hypothesis of schizophrenia, benchmark compounds from a program to discover potent, selective, competitive glycine transporter 1 (GlyT1) inhibitors were radiolabeled in order to further study the detailed pharmacology of these inhibitors and the distribution of GlyT1 in brain. We here report the in vitro characterization of [{sup 35}S](S)-2-amino-4-chloro-N-(1-(4-phenyl-1-(propylsulfonyl)piperidin-4-yl) ethyl)benzamide ([{sup 35}S]ACPPB), a radiotracer developed from a potent and selective non-sarcosine-derived GlyT1 inhibitor, its use in autoradiographic studies to localize (S)-2-amino-6-chloro-N-(1-(4-phenyl-1-(propylsulfonyl)piperidin-4-yl)ethyl) benzamide (ACPPB) binding sites in rat and rhesus brain and for in vivo occupancy assays of competitive GlyT1 inhibitors. Methods: Functional potencies of unlabeled compounds were characterized by [{sup 14}C]glycine uptake into JAR (human placental choriocarcinoma) cells and synaptosomes. Radioligand binding studies were performed with tissue homogenates. Autoradiographic studies were performed on tissue slices. Results: ACPPB is a potent (K{sub d}=1.9 nM), selective, GlyT1 inhibitor that, when radiolabeled with [{sup 35}S], is a well-behaved radioligand with low nondisplaceable binding. Autoradiographic studies of rat and rhesus brain slices with this ligand showed that specific binding sites were plentiful and nonhomogeneously distributed, with high levels of binding in the brainstem, cerebellar white matter, thalamus, cortical white matter and spinal cord gray matter. In vivo studies demonstrate displaceable binding of [{sup 35}S]ACPPB in rat brain tissues following iv administration of this radioligand. Conclusions: This is the first report of detailed anatomical localization of GlyT1 using direct radioligand binding, and the first demonstration that an in vivo occupancy assay is feasible, suggesting that it may also be feasible to develop

  15. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq).

    Science.gov (United States)

    Yu, Hui; You, Xinxin; Li, Jia; Liu, Hankui; Meng, Zining; Xiao, Ling; Zhang, Haifa; Lin, Hao-Ran; Zhang, Yong; Shi, Qiong

    2016-04-06

    Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish.

  16. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq

    Directory of Open Access Journals (Sweden)

    Hui Yu

    2016-04-01

    Full Text Available Mapping of quantitative trait loci (QTL is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms by double digest restriction site associated DNA sequencing (ddRADseq, and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1 including three (tert, ftz-f1 and notch1 that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS efforts to improve growth-related traits in this economically important fish.

  17. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation

    Directory of Open Access Journals (Sweden)

    Brockmann Knut

    2009-03-01

    Full Text Available Abstract Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR. The aim of the study was to evaluate a quantitative PCR (qPCR protocol established by Boehm et al. (2004 in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8% with 20 subtelomeric imbalances were identified. Six of the aberrations (2% were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases or the aberration were be detected in the patient and an equally affected parent (1 case. The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%. Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.

  18. Genetic mapping of semi-polar metabolites in pepper fruits (Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci.

    Science.gov (United States)

    Wahyuni, Yuni; Stahl-Hermes, Vanessa; Ballester, Ana-Rosa; de Vos, Ric C H; Voorrips, Roeland E; Maharijaya, Awang; Molthoff, Jos; Zamora, Marcela Viquez; Sudarmonowati, Enny; Arisi, Ana Carolina Maisonnave; Bino, Raoul J; Bovy, Arnaud G

    2014-01-01

    Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental accessions were selected based on their variation in fruit morphological characteristics and fruit content of some target phytonutrients. Clear segregation of fruit colour and fruit metabolite profiles was observed in the F2 population. The F2 plants formed three clusters based on their metabolite profiles. Of the total of 542 metabolites, 52 could be annotated, including a range of flavonoids, such as flavone C-glycosides, flavonol O-glycosides and naringenin chalcone, as well as several phenylpropanoids, a capsaicin analogue, fatty acid derivatives and amino acid derivatives. Interval mapping revealed 279 mQTLs in total. Two mQTL hotspots were found on chromosome 9. These two chromosomal regions regulated the relative levels of 35 and 103 metabolites, respectively. Analysis also revealed an mQTL for a capsaicin analogue, located on chromosome 7. Confirmation of flavonoid mQTLs using a set of six flavonoid candidate gene markers and their corresponding expression data (expression QTLs) indicated the Ca-MYB12 transcription factor gene on chromosome 1 and the gene encoding flavone synthase (FS-2) on chromosome 6 as likely causative genes determining the variation in naringenin chalcone and flavone C-glycosides, respectively, in this population. The combination of large-scale metabolite profiling and QTL analysis provided valuable insight into the genomic regions and genes important for the production of (secondary) metabolites in pepper fruit. This will impact breeding strategies aimed at optimising the content of specific metabolites in pepper fruit.

  19. Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions.

    Science.gov (United States)

    Gu, Junfei; Yin, Xinyou; Struik, Paul C; Stomph, Tjeerd Jan; Wang, Huaqi

    2012-01-01

    Photosynthesis is fundamental to biomass production, but sensitive to drought. To understand the genetics of leaf photosynthesis, especially under drought, upland rice cv. Haogelao, lowland rice cv. Shennong265, and 94 of their introgression lines (ILs) were studied at flowering and grain filling under drought and well-watered field conditions. Gas exchange and chlorophyll fluorescence measurements were conducted to evaluate eight photosynthetic traits. Since these traits are very sensitive to fluctuations in microclimate during measurements under field conditions, observations were adjusted for microclimatic differences through both a statistical covariant model and a physiological approach. Both approaches identified leaf-to-air vapour pressure difference as the variable influencing the traits most. Using the simple sequence repeat (SSR) linkage map for the IL population, 1-3 quantitative trait loci (QTLs) were detected per trait-stage-treatment combination, which explained between 7.0% and 30.4% of the phenotypic variance of each trait. The clustered QTLs near marker RM410 (the interval from 57.3 cM to 68.4 cM on chromosome 9) were consistent over both development stages and both drought and well-watered conditions. This QTL consistency was verified by a greenhouse experiment under a controlled environment. The alleles from the upland rice at this interval had positive effects on net photosynthetic rate, stomatal conductance, transpiration rate, quantum yield of photosystem II (PSII), and the maximum efficiency of light-adapted open PSII. However, the allele of another main QTL from upland rice was associated with increased drought sensitivity of photosynthesis. These results could potentially be used in breeding programmes through marker-assisted selection to improve drought tolerance and photosynthesis simultaneously.

  20. Genome-scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus).

    Science.gov (United States)

    Esmailizadeh, A K

    2014-12-01

    The objective of this study was to locate quantitative trait loci (QTL) causing variation in birth weight and age of puberty of doe kids in a population of Rayini cashmere goats. Four hundred and thirty kids from five half-sib families were genotyped for 116 microsatellite markers located on the caprine autosomes. The traits recorded were birth weight of the male and female kids, body weight at puberty, average daily gain from birth to age of puberty and age at puberty of the doe kids. QTL analysis was conducted using the least squares interval mapping approach. Linkage analysis indicated significant QTL for birth weight on Capra hircus chromosomes (CHI) 4, 5, 6, 18 and 21. Five QTL located on CHI 5, 14 and 29 were associated with age at puberty. Across-family analysis revealed evidence for overlapping QTL affecting birth weight (78 cM), body weight at puberty (72 cM), average daily gain from birth to age of puberty (72 cM) and age at puberty (76 cM) on CHI 5 and overlapping QTL controlling body weight at puberty and age at puberty on CHI 14 at 18-19 cM. The proportion of the phenotypic variance explained by the detected QTL ranged between 7.9% and 14.4%. Confirming some of the previously reported results for birth weight and growth QTL in goats, this study identified more QTL for these traits and is the first report of QTL for onset of puberty in doe kids.

  1. Directional and quantitative phosphorylation networks

    DEFF Research Database (Denmark)

    Jørgensen, Claus; Linding, Rune

    2008-01-01

    for unravelling phosphorylation-mediated cellular interaction networks. In particular, we will discuss how the combination of new quantitative mass-spectrometric technologies and computational algorithms together are enhancing mapping of these largely uncharted dynamic networks. By combining quantitative...

  2. Genetic mapping and quantitative trait loci analysis for disease resistance using F2 and F5 generation-based genetic maps derived from 'Tifrunner' x'GT-C20' in peanut

    Science.gov (United States)

    One mapping population derived from Tifrunner × GT-C20 has shown great potential in developing a high dense genetic map and identification of QTLs for important disease resistance, Tomato spotted wilt virus (TSWV) and leaf spot (LS). Both F2 and F5 generation-based genetic maps were constructed prev...

  3. Autoradiographic Distribution and Applied Pharmacological Characteristics of Dextromethorphan and Related Antitissue/Anticonvulsant Drugs and Novel Analogs.

    Science.gov (United States)

    1994-10-01

    4.4 4 Cerebellum: Purkinje cell layer 64.0 ± 10.5 4 granular cell layer 46.1 ± 7.5 4 molecular cell layer 23.4 ± 1.1 4 TABLE 2: Autoradiographical...43.0 ± 7.4 5 granular cell layer 23.0 ± 7.3 5 molecular cell layer 14.0 ± 4.4 5 j cu 4) A k- , -.- ’ A 1 *9 ,𔃻 I A .. ’, * 3A .. . .A *4...nucleus solitary tract 36.8 ± 7.1 5 reticular nucleus 36.6 ± 7.6 5 Cerebellum: Purkinje cell layer 48.6 ± 10.3 5 granular cell layer 28.6 ± 7.8 5 molecular

  4. Autoradiographic localization of target cells for 1. cap alpha. , 25-dihydroxyvitamin D/sub 3/ in bones from fetal rats

    Energy Technology Data Exchange (ETDEWEB)

    Narbaitz, R.; Stumpf, W.E.; Sar, M.; Huang, S.; DeLuca, H.F.

    1983-01-01

    Thaw-mount autoradiographic studies after injection of /sup 3/H-1,25-D/sub 3/ were conducted on 18- and 20-day-old rat fetuses. In maxillary bones, ribs, and tibia, nuclear concentration of radioactivity was found in osteoprogenitor cells and osteoblasts. Osteocytes and chondrocytes in epiphyseal plates were either unlabeled or weakly labeled. In competition experiments, nuclear concentration of radioactivity was blocked by the injection of a high dose of nonradioactive 1,25-D/sub 3/ prior to the administration of the labeled hormone, but not by a similar dose of nonradioactive 25-D/sub 3/. The results are interpreted as indicating that osteoprogenitor cells and osteoblasts are target cells for the direct action of 1,25-D/sub 3/ on fetal bone.

  5. Preparation of (125)I-ricin suitable as a probe for the autoradiographic localization of toxin binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Doebler, J.A.; Mayer, T.W.; Traub, R.K.; Broomfield, C.A.; Calamaio, C.A.

    1993-05-13

    The long term objectives of this research are to identify cellular binding sites for ricin and examine its organ distribution in mice following aerosol inhalation exposure. Preliminary studies relating to the synthesis and evaluation of (125 I)-ricin as an autoradiographic probe have been conducted. Non-radioactive (I)-ricin prepared using the Iodogen method was found to be non-toxic both in vivo and in vitro. Lactose was then added to the Iodogen reaction medium to block galactose-binding site associated tyrosines in an attempt to retain toxicity. However, this did not prevent iodination-induced loss of biological potency. We then switched to the lactoperoxidase method of iodination, which yielded an (I)-ricin preparation with toxicity comparable to that of native toxin.

  6. Dissociation of glucose tracer uptake and glucose transporter distribution in the regionally ischaemic isolated rat heart: application of a new autoradiographic technique

    Energy Technology Data Exchange (ETDEWEB)

    Southworth, Richard; Medina, Rodolfo A.; Garlick, Pamela B. [Department of Radiological Sciences, Guy' s, King' s and St Thomas' School of Medicine, Guy' s Campus, London, SE1 9RT (United Kingdom); Dearling, Jason L.J.; Flynn, Aiden A.; Pedley, Barbara R. [Cancer Research UK Targeting and Imaging Group, Academic Department of Oncology, University College London, Royal Free Campus, London, NW3 2PF (United Kingdom)

    2002-10-01

    Fluorine-18 fluoro-2-deoxyglucose ({sup 18}FDG) and carbon-14 2-deoxyglucose ({sup 14}C-2-DG) are both widely used tracers of myocardial glucose uptake and phosphorylation. We have recently shown, using positron emission tomography (PET) and nuclear magnetic resonance, that ischaemia-reperfusion (I-R) causes differential changes in their uptake. We describe here the novel application of an autoradiographic technique allowing the investigation of this phenomenon at high resolution, using tracer concentrations of both analogues in the dual-perfused isolated rat heart. We also investigate the importance of glucose transporter (GLUT 1 and GLUT 4) distribution in governing the observed phosphorylated analogue accumulation. Hearts (n=5) were perfused with Krebs buffer for 40 min, made regionally zero-flow ischaemic for 40 min and reperfused for 60 min with Krebs containing tracer {sup 18}FDG (200 MBq) and tracer {sup 14}C-2-DG (0.37 MBq). Hearts were then frozen and five sections (10 {mu}m) were cut per heart, fixed and exposed on phosphor storage plates for 18 h (for {sup 18}FDG) and then for a further 9 days (for {sup 14}C-2-DG). Quantitative digital images of tracer accumulation were obtained using a phosphor plate reader. The protocol was repeated in a second group of hearts and GLUT 1 and GLUT 4 distribution analysed. Post-ischaemic accumulation of {sup 18}FDG-6-P was inhibited by 38.2%{+-}1.7% and {sup 14}C-DG-6-P by 19.0%{+-}2.2%, compared with control (P<0.05). After placing seven ''lines of interrogation'' across each heart section and analysing the phosphorylated tracer accumulation along them, a transmural gradient of both tracers was observed; this was highest at the endocardium and lowest at the epicardium. GLUT 4 translocated to the sarcolemma in the ischaemic/reperfused region (from 24%{+-}3% to 59%{+-}5%), while there was no cellular redistribution of GLUT 1. We conclude that since decreased phosphorylated tracer accumulation occurs

  7. Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1 and Data-Independent (MS2 Acquisitions

    Directory of Open Access Journals (Sweden)

    Jason M. Held

    2013-01-01

    Full Text Available The receptor tyrosine kinase ErbB2 is a breast cancer biomarker whose posttranslational modifications (PTMs are a key indicator of its activation. Quantifying the expression and PTMs of biomarkers such as ErbB2 by selected reaction monitoring (SRM mass spectrometry has several limitations, including minimal coverage and extensive assay development time. Therefore, we assessed the utility of two high resolution, full scan mass spectrometry approaches, MS1 Filtering and SWATH MS2, for targeted ErbB2 proteomics. Endogenous ErbB2 immunoprecipitated from SK-BR-3 cells was in-gel digested with trypsin, chymotrypsin, Asp-N, or trypsin plus Asp-N in triplicate. Data-dependent acquisition with an AB SCIEX TripleTOF 5600 and MS1 Filtering data processing was used to assess peptide and PTM coverage as well as the reproducibility of enzyme digestion. Data-independent acquisition (SWATH was also performed for MS2 quantitation. MS1 Filtering and SWATH MS2 allow quantitation of all detected analytes after acquisition, enabling the use of multiple proteases for quantitative assessment of target proteins. Combining high resolution proteomics with multiprotease digestion enabled quantitative mapping of ErbB2 with excellent reproducibility, improved amino acid sequence and PTM coverage, and decreased assay development time compared to typical SRM assays. These results demonstrate that high resolution quantitative proteomic approaches are an effective tool for targeted biomarker quantitation.

  8. Autoradiographic localization of substance P receptors in the rat and bovine spinal cord and the rat and cat spinal trigeminal nucleus pars caudalis and the effects of neonatal capsaicin

    Energy Technology Data Exchange (ETDEWEB)

    Mantyh, P.W.; Hunt, S.P. (Medical Research Council Centre, Cambridge (UK). Medical School, MRC Neurochemical Pharmacology Unit)

    1985-04-22

    Substance P (SP) is a putative neurotransmitter in the central nervous system. In the present report the authors have used autoradiographic receptor binding techniques to investigate the distribution of SP receptor binding sites in the rat and bovine spinal cord and in the rat and cat spinal trigeminal nucleus pars caudalis. Although some quantitative differences were evident, all species appeared to have a similar distribution of SP receptor binding sites in both the spinal cord and in the spinal trigeminal nucleus pars caudalis. In the spinal cord the heaviest concentration of SP receptors is located in lamina X, while moderate to heavy concentrations were found in laminae I, II and V-IX. Very low concentrations of SP receptors were present in laminae III and IV. Examination of the cat and rat spinal trigeminal nucleus pars caudalis revealed a moderate density of SP receptor binding sites in laminae I and II, very low concentrations in laminae III and IV, and low to moderate concentrations in lamina V. Rats treated neonatally with capsaicin showed a small (11%) but significant (P < 0.02) increase in the levels of SP receptor binding sites in laminae I and II of the cervical and lumbar spinal cord while in all other laminae the levels remained unchanged.

  9. Autoradiographic studies on mucilage synthesis in Chara vulgaris antheridium with the use of {sup 3}H-fucose in total darkness and light

    Energy Technology Data Exchange (ETDEWEB)

    Gosek, A. [Lodz Univ. (Poland)

    1996-12-31

    Autoradiographic studies with {sup 3}H-fucose have shown that this precursor of polysaccharide compounds is incorporated into manubria and antheridial mucilage of Chara vulgaris both in the light and in the darkness. The dynamic of this process is lower in total darkness. The decrease in overall labelling of antheridium (manubria an mucilage) reflects secondary metabolic changes both in proliferative phase and in spermiogenesis. The pulse (2 and 5 min) incubations with the isotope confirm the intensive mucilage translocation which at later developmental stages is more dynamic than at earlier ones. It can explain previously observed decrease in manubria radioactivity at later stages after long (40 min) incubation, because PAS-positive polysaccharide synthesis is simultaneous with their fast translocation to the antheridial space. The present and previous autoradiographic and cytophotometric data taken altogether confirm the assumption about a nutritive role of mucilage filling Chara antheridium during the process of spermatogenesis. (author). 19 refs, 7 figs.

  10. Quantitative multi-element mapping of ancient glass using a simple and robust LA-ICP-MS rastering procedure in combination with image analysis.

    Science.gov (United States)

    Selih, Vid S; van Elteren, Johannes T

    2011-08-01

    The surface of two glass artefacts in mosaic style, probably fragments of conglomerate glass bowls dating back two millennia, was investigated by laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS). By rastering with the laser beam over a selected area of the surface of the glass artefacts, elemental oxide maps were generated. Quantification of the elemental oxides in the maps was achieved using a so-called sum normalization procedure, summating the elements-54 in total-as their oxides to 100% (w/w), without using an internal standard and applying only one external standard (NIST SRM glass 610). This results in a robust mapping procedure which automatically corrects for drift and defocusing issues. Sum normalization was applied to each pixel in the map separately and required a custom source code to process all the data in the tens of thousands of pixels to generate the elemental oxide concentration maps. The digital element maps generated upon rastering of the two glass artefacts are very compelling and are an excellent entry point to gain detailed insight into their fabrication and provenance using image analysis software for retrieval of localized elemental oxide concentrations and correlations.

  11. Voxel-based statistical analysis of cerebral glucose metabolism in the rat cortical deafness model by 3D reconstruction of brain from autoradiographic images

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Sung; Park, Kwang Suk [Seoul National University College of Medicine, Department of Nuclear Medicine, 28 Yungun-Dong, Chongno-Ku, Seoul (Korea); Seoul National University College of Medicine, Department of Biomedical Engineering, Seoul (Korea); Ahn, Soon-Hyun; Oh, Seung Ha; Kim, Chong Sun; Chung, June-Key; Lee, Myung Chul [Seoul National University College of Medicine, Department of Otolaryngology, Head and Neck Surgery, Seoul (Korea); Lee, Dong Soo; Jeong, Jae Min [Seoul National University College of Medicine, Department of Nuclear Medicine, 28 Yungun-Dong, Chongno-Ku, Seoul (Korea)

    2005-06-01

    Animal models of cortical deafness are essential for investigation of the cerebral glucose metabolism in congenital or prelingual deafness. Autoradiographic imaging is mainly used to assess the cerebral glucose metabolism in rodents. In this study, procedures for the 3D voxel-based statistical analysis of autoradiographic data were established to enable investigations of the within-modal and cross-modal plasticity through entire areas of the brain of sensory-deprived animals without lumping together heterogeneous subregions within each brain structure into a large region of interest. Thirteen 2-[1-{sup 14}C]-deoxy-D-glucose autoradiographic images were acquired from six deaf and seven age-matched normal rats (age 6-10 weeks). The deafness was induced by surgical ablation. For the 3D voxel-based statistical analysis, brain slices were extracted semiautomatically from the autoradiographic images, which contained the coronal sections of the brain, and were stacked into 3D volume data. Using principal axes matching and mutual information maximization algorithms, the adjacent coronal sections were co-registered using a rigid body transformation, and all sections were realigned to the first section. A study-specific template was composed and the realigned images were spatially normalized onto the template. Following count normalization, voxel-wise t tests were performed to reveal the areas with significant differences in cerebral glucose metabolism between the deaf and the control rats. Continuous and clear edges were detected in each image after registration between the coronal sections, and the internal and external landmarks extracted from the spatially normalized images were well matched, demonstrating the reliability of the spatial processing procedures. Voxel-wise t tests showed that the glucose metabolism in the bilateral auditory cortices of the deaf rats was significantly (P<0.001) lower than that in the controls. There was no significantly reduced metabolism in

  12. Effect of root conditioning on periodontal wound healing with and without guided tissue regeneration: a pilot study. II. Autoradiographic evaluation.

    Science.gov (United States)

    Sammons, P R; Wang, H L; Chiego, D J; Castelli, W A; Smith, B A

    1994-02-01

    This investigation deals with the proliferation and migration of the progenitor cells during the healing of closed periodontal wounds. Periodontal surgical defects affecting the bone and dentin were created in four mongrel dogs. The defects were treated with topical applications of citric acid, tetracycline, or sterile water with and without the placement of nonresorbable membranes. The dogs were killed at 1, 3, 7, and 21 days after surgery. One hour before they were killed, they were intravenously injected with tritiated thymidine. Tissues were processed and routinely prepared for autoradiographic studies. Labeled cells were counted at the apical, coronal, and central areas of the defects. Results suggested that the citric acid and tetracycline treatments inhibited cellular proliferation at the initial time periods of 1 and 3 days. At 7 and 21 days, differences between citric acid and tetracycline treatments were minimal, and neither showed any advantage over the application of sterile water. The placement of the nonresorbable membrane demonstrated a trend of increased labeling at 21 days for all three treatments.

  13. Specificity of indium-111 granulocyte scanning and fecal excretion measurement in inflammatory bowel disease--an autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Keshavarzian, A.; Price, Y.E.; Peters, A.M.; Lavender, J.P.; Wright, N.A.; Hodgson, H.J.

    1985-12-01

    The validity of /sup 111/In granulocyte scanning and fecal excretion measurement, as a reflection of loss of cells into the gastrointestinal tract, was studied using an autoradiographic technique in 11 patients in whom /sup 111/In granulocyte scan and colonoscopy were carried out simultaneously. /sup 111/In granulocytes were injected 1.5-4 hr prior to colonoscopy, and intraluminal fluid, mucosal brushings, and colonic biopsies were collected during the colonoscopy. In two patients with no histological evidence of inflammatory bowel disease, and four patients with clinically and histologically inactive inflammatory bowel disease, no /sup 111/Indium was detected in fluid, brushing, or biopsies. In five patients with active disease, 85% of the /sup 111/In activity in colonic fluid was precipitated by low-speed centrifugation. Autoradiography confirmed that the label remained attached to whole granulocytes in colonic fluid and mucosal brushings. Studies on biopsies, at intervals up to 4 1/2 hr following labeled granulocyte injection, demonstrated labeled polymorphonuclear neutrophils (PMNs) on the inflamed epithelial surface, with occasional cells in crypt abscesses by 110 min. We conclude that the techniques of /sup 111/In granulocyte scanning and fecal counting in patients with IBD are specifically measuring cell loss; labeled PMNs are capable of migrating through the gastrointestinal mucosa, in active disease, within 2 hr of administration.

  14. Effect of morphine on /sup 3/H-thymidine incorporation in the subependyma of the rat: an autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Miller, C.R.; O' Steen, W.K.; Deadwyler, S.A.

    1982-06-20

    Following morphine treatment, an autoradiographic study investigated the uptake of /sup 3/H-thymidine by the subependymal cells in the rat brain. /sup 3/H-thymidine was administered subcutaneously to adult, male Sprague-Dawley rats 30 minutes after saline or morphine (19 mg/kg) injection. The animals were sacrified 1 hour after /sup 3/H-thymidine administration. In some experiments the opioid antagonist, naloxone, was given alone 45 minutes before /sup 3/H-thymidine or 125 minutes before morphine treatment. Three areas of the subependyma were evaluated in terms of the percentage labeled cells and number of grains per nucleus, and a dorsal-to-ventral gradiant was described. Morphine treatment significantly increased the number of /sup 3/H-thymidine labeled subependymal cells and number of grains/nucleus within labeled cells. Examination of the distribution of grains/nucleus showed that morphine-treated animals had significantly more cells labeled with 30 or more grains than did saline-injected controls. Prior administration of naloxone blocked the increased /sup 3/H-thymidine uptake in morphine-treated animals but had no significant influence on cell proliferation when administered alone. The data are discussed in terms of morphine's possible dual influence on mechanisms which enhance cell transition from G to S phase and/or which accelerate DNA synthesis once these cells have entered the S phase of cell replication.

  15. 地图个性化认知适合度的眼动试验评估%Quantitative Evaluation of Personalized Cognition Suitability on Maps by Eye Movement Experi ment

    Institute of Scientific and Technical Information of China (English)

    郑束蕾; 陈毓芬; 杨春雷; 王双; 王成舜

    2015-01-01

    Map personalized cognition is an important question in map design and map usability evaluation.In this paper,different electronic map on computer screen was designed to match designated user.During this process,eye movement experiment and quantitative evaluating methods were conducted to explore the different cognition effect and personalized cognition suitability.At first,four simplified types of map prototypes were produced with some similarity,which supported personalized cognition suitability evaluation and eye movement experiment after.Then an eye movement experiment in subjects who belonged to the designated user class was conducted by eye tracker Tobii X120.The indexes such as time to first fixation,first fixation duration and time to first mouse click in AOI around aim point were recorded by the eye tracker automatically.In the following,multivariate statistical analysis methods were used to obtain the significant results,including the descriptive statistical analysis,the analysis of variance and the simple effect inspection.Furthermore,the visualized heat maps of users’eye movement paths were generated and overlaid at the same time.The quantitative analysis results in eye movement experiment show there are significant difference in the eye movement and mouse action indexes between each map, which explain the different cognition susceptibility,attention and information processing speed in deep brain thinking level.And the personalized cognition suitability on map comes from the age,gender,hobby, even the familiarity degree to handle map.So,eventually,some cognitive psychology theories are referred to.Personalized cognition characters of map user are emphasized by this research to improve map design quality and spatial information transmission efficiency.%地图个性化认知是地图设计与地图可用性研究中的重要问题。本文以二维电子地图为例,针对不同样式地图原型对特定用户的认知适合度问题进行研

  16. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Science.gov (United States)

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  17. Genetic mapping of semi-polar metabolites in pepper fruits (Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci

    NARCIS (Netherlands)

    Wahyuni, Y.; Stahl-Hermes, V.; Ballester, A.R.; Vos, de C.H.; Voorrips, R.E.; Maharijaya, A.; Molthoff, J.W.; Víquez Zamora, A.M.; Sudarmonowati, E.; Arisi, A.C.M.; Bino, R.J.; Bovy, A.G.

    2014-01-01

    Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental

  18. Genetic mapping of semi-polar metabolites in pepper fruits (Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci

    NARCIS (Netherlands)

    Wahyuni, Y.; Stahl-Hermes, V.; Ballester, A.R.; Vos, de C.H.; Voorrips, R.E.; Maharijaya, A.; Molthoff, J.W.; Víquez Zamora, A.M.; Sudarmonowati, E.; Arisi, A.C.M.; Bino, R.J.; Bovy, A.G.

    2014-01-01

    Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental access

  19. Quantitative temperature-depending mapping of mechanical properties of bitumen at the nanoscale using the AFM operated with PeakForce TappingTM mode

    NARCIS (Netherlands)

    Fischer, H.R.; Stadler, H.; Erina, N.

    2013-01-01

    The mechanical properties of bitumen, such as elasticity/Young's modulus, stickiness/adhesion, hardness and energy loss, and sample deformation were acquired quantitatively and simultaneously with the topology at the microscale, discriminating clearly two separate phases within the bitumen. Temperat

  20. A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides.

    Science.gov (United States)

    Branham, Sandra E; Levi, Amnon; Farnham, Mark W; Patrick Wechter, W

    2017-02-01

    A major QTL for resistance to Fusarium oxysporum f. sp. niveum race 2 was mapped to a narrow 1.2 Mb interval using a high-density GBS-SNP linkage map, the first map of Citrullus lanatus var. citroides. Fusarium wilt, a fungal disease caused by Fusarium oxysporum f. sp. niveum (Fon), devastates watermelon crop production worldwide. Several races, which are differentiated by host range, of the pathogen exist. Resistance to Fon race 2, a particularly virulent strain prevalent in the United States, does not exist in edible cultivars of the sweet cultivated watermelon Citrullus lanatus var. lanatus (Cll) and has been well described in a few plant introductions of the wild subspecies of watermelon, C. lanatus var. citroides (Clc). Clc provides a vital source of genetic diversity, as well as resistance to numerous diseases. Unfortunately, both genetic diversity and disease resistance are lacking in Cll due to the narrow genetic base. Despite the importance of Clc to continued watermelon improvement, intra-variety genetic studies are lacking. Here, we present the first Clc genetic linkage map, generated with 2495 single nucleotide polymorphisms developed through genotyping-by-sequencing, and use it to identify quantitative trait loci associated with Fon race 2 resistance. Multiple QTL mapping in a Clc F2:3 population (N = 173) identified one major and four minor QTL. The major QTL explained 43% of the variation in Fon race 2 resistance and was delimited to a 1.2-Mb interval on chromosome 9, a region spanning 44 genes.

  1. Nondestructive quantitative mapping of impurities and point defects in thin films: Ga and V{sub Zn} in ZnO:Ga

    Energy Technology Data Exchange (ETDEWEB)

    Look, David C., E-mail: david.look@wright.edu [Semiconductor Research Center, Wright State University, 3640 Colonel Glenn Hwy., Dayton, Ohio 45435 (United States); Wyle, 2601 Mission Point Blvd., Dayton, Ohio 45431 (United States); Air Force Research Laboratory Sensors Directorate, 2241 Avionics Circle, Wright-Patterson AFB, Ohio 45433 (United States); Leedy, Kevin D.; Agresta, Donald L. [Air Force Research Laboratory Sensors Directorate, 2241 Avionics Circle, Wright-Patterson AFB, Ohio 45433 (United States)

    2014-06-16

    Ga-doped ZnO (GZO) films grown by pulsed-laser deposition on quartz and other lattice-mismatched substrates can routinely attain resistivities of 2 × 10{sup −4} Ω·cm and thus compete with Sn-doped In{sub 2}O{sub 3} (ITO) in large-area transparent-electrode applications. Nondestructive, high-resolution (1-mm) maps of thickness d, concentration n, and mobility μ on such films can be obtained automatically from commercial spectroscopic ellipsometers. From n and μ, degenerate-electron scattering theory yields donor N{sub D} and acceptor N{sub A} concentrations at each point. Finally, N{sub D} and N{sub A} can be identified as [Ga] and [V{sub Zn}], respectively, demonstrating high-density mapping of impurities and point defects in a semiconductor thin film.

  2. Mapping quantitative trait loci controlling high Fe and Zn density in self and open pollinated grains of pearl millet [Pennisetum glaucum (L. R. Br.

    Directory of Open Access Journals (Sweden)

    Sushil Kumar

    2016-11-01

    Full Text Available Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world’s poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain [Fe] and [Zn] using replicated samples of 106 pearl millet RILs (F6 derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn concentration using atomic absorption spectrophotometer. Grain mineral concentrations ranged from 28.4-124.0 ppm for Fe and 28.7-119.8 ppm for Zn. Similarly,grain Fe and Zn in open pollinated seeds ranged between 22.4-77.4 and 21.9-73.7 ppm, respectively. Mapping with 305 (96 SSRs; 208 DArT markers detected seven linkage groups covering 1749 cM (Haldane with an average intermarker distance of 5.73 cM. On the basis of two environment phenotypic data, two co-localized QTLs for Fe and Zn density on LG 3 were identified by composite interval mapping (CIM. Fe QTL explained 19% phenotypic variation, whereas the Zn QTL explained 36% phenotypic variation. Likewise for open pollinated seeds, the QTL analysis led to identification of two QTLs for grain Fe density on LG 3 and 5, and two QTLs for grain Zn density on LG 3 and 7. The total phenotypic variance for Fe and Zn QTLs in open pollinated seeds was 16% and 42%, respectively. Analysis of QTL × QTL and QTL × QTL× environment interactions indicated no major epistasis.

  3. Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of Catharanthus roseus

    Indian Academy of Sciences (India)

    Vishakha Sharma; Swati Chaudhary; Suchi Srivastava; Richa Pandey; Sushil Kumar

    2011-04-01

    Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.

  4. Autoradiographic studies and experiments on partial synchronization of human tumors, especially mammary carcinomas, in vitro and in vivo following xenotransplantation to NU/NU mice

    Energy Technology Data Exchange (ETDEWEB)

    Nord, D.

    1980-08-20

    Human mammary carcinomas were evaluated radiographically in vitro in the native state. Penetration depths up to 552 ..mu..m into the tissue were reached by the incubating medium. The labelling indices for the 3H-thymidine autoradiography lay between 1.5 and 19.3 percent. A correlation of the autoradiographic labelling indices with the findings of a simultaneously performed in vitro sensitivity test against cytostatics could not be proved. There seems to be a relation between the histomorphological tumour image and the proliferation behaviour expressed by the autoradiographic labelling index. Human mammary carcinomas were cultivated as xeno-transplant on thymus-aplastic NU/NU mice in parallel to this investigation. These heterotransplants show a remarkable correlation to the proliferation behaviour of the directly examined human tumours, after an autoradiographic in-vivo-labelling, with index values between 1.5 and 23.8 percent. This parallelism in the biological behaviour represents a further proof for the usefulness of the oncological test model of the NU/NU mouse as a carrier for human carcinomas. The application of this pre-therapeutical test model followed by determination of the synchronization behaviour of three human malignomas after xeno-transplantation onto NU/NU mice. For all three tumous an individual synchronization behaviour could be determined. Therapy attempts followed with cyclophosphomide or ionizing radiation by using the optimal cell-cycle therapy. Therefore an improvement of the therapeutical success by means of pre-therapeutical synchronization of human tumours can be reached in particular cases.

  5. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2010-09-01

    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  6. GnRH receptors in human granulosa cells: Anatomical localization and characterization by autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Latouche, J.; Crumeyrolle-Arias, M.; Jordan, D.; Kopp, N.; Augendre-Ferrante, B.; Cedard, L.; Haour, F. (Institut Pasteur, Paris (France))

    1989-09-01

    The presence of receptors for GnRH in human ovary has been investigated by quantitative autoradiography. Simultaneous visualization and characterization of specific receptors on frozen sections were obtained on six pairs of human ovaries. Among them only one exhibited a large preovulatory follicle. This dominant follicle exhibited a specific and high affinity binding capacity for {sup 125}I-GnRHa exclusively localized on the granulosa cell layer. Analysis of saturation curve indicates a Kd value of 0.22 nM and Bmax of 9.6 fmol/mg protein. In contrast LH-hCG binding sites were present in all antral follicles. These data demonstrate for the first time the presence of high affinity GnRH receptors in human granulosa cells at a late stage of follicular maturation.

  7. Autoradiographic analysis of tritiated imipramine binding in the human brain post mortem: effects of suicide

    Energy Technology Data Exchange (ETDEWEB)

    Gross-Isseroff, R.; Israeli, M.; Biegon, A.

    1989-03-01

    In vitro quantitative autoradiography of high-affinity tritiated imipramine binding sites was performed on brains of 12 suicide victims and 12 matched controls. Region-specific differences in imipramine binding were found between the two groups. Thus, the pyramidal and molecular layers of the cornu ammoni hippocampal fields and the hilus of the dentate gyrus exhibited 80%, 60%, and 90% increases in binding in the suicide group, respectively. The postcentral cortical gyrus, insular cortex, and claustrum had 45%, 28%, and 75% decreases in binding in the suicide group, respectively. No difference in imipramine binding was observed in prefrontal cortical regions, in the basal ganglia, and in mesencephalic nuclei. No sex and postmortem delay effects on imipramine binding were found. Imipramine binding was positively correlated with age, the effect of age being most pronounced in portions of the basal ganglia and temporal cortex.

  8. Quantitative assessment of the infarct size with the unfolded map method of sup 201 Tl myocardial SPECT in patient with acute myocardial infarction

    Energy Technology Data Exchange (ETDEWEB)

    Kubota, Masahiro (Sapporo Medical Coll. (Japan))

    1992-03-01

    The unfolded map method of {sup 201}Tl single photon emission computed tomography (SPECT) was evaluated as to the ability to quantify and the clinical reliability in estimation of infarct size. The following results were obtained from basic experiments using a thoracic phantom. The defect area estimated by the unfolded map method was well correlated with the real defect area, in spite of overestimation of the defect area, when the defect area was determined by an isocount method (below 80% of maximum count) (y=1.941 + 2.292x, r=0.971). The defect volume estimated by short-axis images of {sup 201}Tl SPECT was closely correlated with real defect volume in spite of overestimation of defect volume (y=0.762 + 2.156x, r=0.982). When the defect area was estimated by division of the defect volume by the mean myocardial compartment thickness, it was closely correlated with real defect area (y=0.946 + 1.232x, r=0.990). When the volume was calculated from the summation of voxels in the regions districted by isocount threshold level at each section of the {sup 99m}Tc SPECT, the optimal isocount threshold level (percentage to maximum count) was 55%. Then, the clinical reliability of the unfolded map method as infarct sizing was evaluated in 26 patients with acute myocardial infarction by comparing it with enzymatic method, Bull's eye method, and {sup 99m}Tc pyrophosphate (PYP) SPECT method. In 14 first attack patients without right ventricular infarction, infarct area (IA) of the unfolded map method correlated most closely with the accumulated creatine kinase MB isoenzyme release (CK-MBr) (r=0.897), compared with the extent score (ES) (r=0.853) and the severity score (SS) (r=0.871) of Bull's eye method and the infarct volume (IV) (r=0.595) of {sup 99m}Tc PYP SPECT. In conclusion, although the unfolded map method of {sup 201}Tl SPECT has the tendency for overestimating infarct size, it is accurate and clinically reliable in estimating infarct size. (author).

  9. Differential light microscopic autoradiographic localization of muscarinic cholinergic receptors in the brainstem and spinal cord of the rat using (/sup 3/H)pirenzepine

    Energy Technology Data Exchange (ETDEWEB)

    Yamamura, H.I.; Deshmukh, P.; Roeske, W.R. (Arizona Univ., Tucson (USA). Health Sciences Center); Wamsley, J.K. (Utah Univ., Salt Lake City (USA). Medical Center)

    1983-07-15

    Recently, the authors demonstrated that radiolabelled pirenzepine ((/sup 3/H)PZ) bound to a high affinity population of muscarinic binding sites in the rat cerebral cortex, hippocampus, and corpus striatum. However, in the heart, cerebellum and ileum they found little or no (/sup 3/H)PZ binding. These data suggest that (/sup 3/H)PZ labels a subpopulation of muscarinic receptors. The present study examines the light microscopic autoradiographic localization of 3-(/sup 3/H)quinuclidinyl benzilate, (-)(/sup 3/H)QNB, an antagonist which labels muscarinic receptors with equal affinity and compares its localization to (/sup 3/H)PZ in the rat brainstem and spinal cord.

  10. Calcium in pollen-pistil interaction in `Petunia hybrida Hor`. Pt. 1. Localization of Ca{sup 2+} ions in mature pollen grain using pyroantimonate and autoradiographic methods

    Energy Technology Data Exchange (ETDEWEB)

    Bednarska, E.; Butowt, R. [Uniwersytet Mikolaja Kopernika, Torun (Poland)

    1994-12-31

    The localization of Ca{sup 2+} in the mature pollen grain and the flow of these ions the somatic tissues of the anther to the pollen grains has been studied using pyroantimonate and autoradiographic methods. In the pollen grain, Ca{sup 2+} ions have been localized in the sporoderm in the cytoplasmic vesicles of probably dictyosomal origin. Calcium ions were transported into the sporoderm together with the compounds of degenerating tapetum. The material of degenerating tapetum forms pollen coat surrounding the mature pollen grains. (author). 18 refs, 9 figs.

  11. Mapeamento de locos de características quantitativas nos cromossomos 5, 7 e 8 de suínos Mapping of quantitative trait loci mapping in chromosomes 5, 7 and 8 of swines

    Directory of Open Access Journals (Sweden)

    Katiene Régia Silva Sousa

    2011-01-01

    Full Text Available Objetivou-se mapear QTL nos cromossomos 5, 7 e 8 e associá-los a características de carcaça, cortes de carcaça, qualidade de carne, desempenho e órgãos internos de suínos. Uma progênie F2 de 614 animais foi produzida do cruzamento de dois varrões da raça naturalizada brasileira Piau e 18 fêmeas comerciais (Landrace x Large White x Pietrain. A população foi genotipada para 14 marcadores microssatélites cobrindo os cromossomos 5, 7 e 8. Em seguida, foi construído o mapa de ligação para cada cromossomo. As análises de associação foram feitas usando o mapeamento de intervalo por regressão para detecção de QTL. Para características de carcaça e cortes de carcaça, foram mapeados 20 QTL nos três cromossomos, enquanto, para características de qualidade de carne, foram encontrados apenas três QTL nos cromossomos 7 e 8. Entre eles, QTL significativos a 5% no genoma foram encontrados para menor espessura de toucinho na região acima da última vértebra lombar, na linha dorsolombar no cromossomo 5; e para comprimento total do intestino delgado, peso da banha-rama e luminosidade no cromossomo 8. Para comprimento de carcaça pelo método brasileiro e comprimento de carcaça pelo método americano, QTL significativos a 1% no genoma foram encontrados no cromossomo 7. Os resultados encontrados facilitarão estudos futuros, como o mapeamento fino e a identificação de genes que controlam a composição corporal e a qualidade de carne e que poderão ser incorporados em programas de seleção assistida por marcadores para acelerar o melhoramento genético de populações de suínos, além de ajudar no melhor entendimento da fisiologia das características de produção de suínos.The aim of this experiment was to map QTL in chromosomes 5, 7 and 8 and to associate them to carcass traits, carcass cuts, meat quality, performance and internal organs of swines. An F2 offspring with 614 animals was produced from the matting of two Brazilian

  12. 3.0 T MR imaging of the ankle: Axial traction for morphological cartilage evaluation, quantitative T2 mapping and cartilage diffusion imaging—A preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Jungmann, Pia M., E-mail: pia.jungmann@tum.de [Department of Radiology, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Baum, Thomas, E-mail: thomas.baum@tum.de [Department of Radiology, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Schaeffeler, Christoph, E-mail: schaeffeler@me.com [Department of Radiology, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Musculoskeletal Imaging, Kantonsspital Graubuenden, Loestrasse 170, CH-7000 Chur (Switzerland); Sauerschnig, Martin, E-mail: martin.sauerschnig@mri.tum.de [Department of Trauma Surgery, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Department of Orthopaedic Sports Medicine, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Brucker, Peter U., E-mail: peter.brucker@lrz.tu-muenchen.de [Department of Orthopaedic Sports Medicine, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Mann, Alexander, E-mail: abmann@onlinemed.de [Department of Radiology, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Department of Orthopaedic Sports Medicine, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Ganter, Carl, E-mail: cganter@tum.de [Department of Radiology, Klinikum rechts der Isar, Technische Universitaet Muenchen, Ismaninger Strasse 22, 81675 Munich (Germany); Bieri, Oliver, E-mail: oliver.bieri@unibas.ch [Division of Radiological Physics, Department of Radiology, University of Basel Hospital, Petersgraben 4, 4031 Basel (Switzerland); and others

    2015-08-15

    Highlights: • Axial traction is applicable during high resolution MR imaging of the ankle. • Axial traction during MR imaging oft the ankle improves cartilage surface delineation of the individual tibial and talar cartilage layer for better morphological evaluation without the need of intraarticular contrast agent application. • Coronal T1-weighted MR images with a driven equilibrium pulse performed best. • Axial traction during MR imaging of the ankle facilitates compartment discrimination for segmentation purposes resulting in better reproducibility. - Abstract: Purpose: To determine the impact of axial traction during high resolution 3.0 T MR imaging of the ankle on morphological assessment of articular cartilage and quantitative cartilage imaging parameters. Materials and Methods: MR images of n = 25 asymptomatic ankles were acquired with and without axial traction (6 kg). Coronal and sagittal T1-weighted (w) turbo spin echo (TSE) sequences with a driven equilibrium pulse and sagittal fat-saturated intermediate-w (IMfs) TSE sequences were acquired for morphological evaluation on a four-point scale (1 = best, 4 = worst). For quantitative assessment of cartilage degradation segmentation was performed on 2D multislice-multiecho (MSME) SE T2, steady-state free-precession (SSFP; n = 8) T2 and SSFP diffusion-weighted imaging (DWI; n = 8) images. Wilcoxon-tests and paired t-tests were used for statistical analysis. Results: With axial traction, joint space width increased significantly and delineation of cartilage surfaces was rated superior (P < 0.05). Cartilage surfaces were best visualized on coronal T1-w images (P < 0.05). Differences for cartilage matrix evaluation were smaller. Subchondral bone evaluation, motion artifacts and image quality were not significantly different between the acquisition methods (P > 0.05). T2 values were lower at the tibia than at the talus (P < 0.001). Reproducibility was better for images with axial traction. Conclusion

  13. Three-dimensional autoradiographic localization of quench-corrected glycine receptor specific activity in the mouse brain using sup 3 H-strychnine as the ligand

    Energy Technology Data Exchange (ETDEWEB)

    White, W.F.; O' Gorman, S.; Roe, A.W. (Harvard Medical School, Boston, MA (USA))

    1990-03-01

    The autoradiographic analysis of neurotransmitter receptor distribution is a powerful technique that provides extensive information on the localization of neurotransmitter systems. Computer methodologies are described for the analysis of autoradiographic material which include quench correction, 3-dimensional display, and quantification based on anatomical boundaries determined from the tissue sections. These methodologies are applied to the problem of the distribution of glycine receptors measured by 3H-strychnine binding in the mouse CNS. The most distinctive feature of this distribution is its marked caudorostral gradient. The highest densities of binding sites within this gradient were seen in somatic motor and sensory areas; high densities of binding were seen in branchial efferent and special sensory areas. Moderate levels were seen in nuclei related to visceral function. Densities within the reticular formation paralleled the overall gradient with high to moderate levels of binding. The colliculi had low and the diencephalon had very low levels of binding. No binding was seen in the cerebellum or the telencephalon with the exception of the amygdala, which had very low levels of specific binding. This distribution of glycine receptors correlates well with the known functional distribution of glycine synaptic function. These data are illustrated in 3 dimensions and discussed in terms of the significance of the analysis techniques on this type of data as well as the functional significance of the distribution of glycine receptors.

  14. Methods in laboratory investigation. Autoradiographic demonstration of the specific binding and nuclear localization of 3H-dexamethasone in adult mouse lung.

    Science.gov (United States)

    Beer, D G; Cunha, G R; Malkinson, A M

    1983-12-01

    This report describes the first autoradiographic demonstration of specific nuclear localization of 3H-dexamethasone in different cell types of the lung. Adult mouse lung tissue was incubated in vitro for 90 minutes with 17 nM 3H-dexamethasone in the presence or absence of various nonradioactive steroids. After extensive washing to remove any nonspecifically bound ligand, the specimens were processed for autoradiography using the thaw-mount method. In the absence of competing steroids, silver grains were localized in the nuclei of alveolar type II cells, bronchiolar and arteriolar smooth muscle cells, fibroblasts, and endothelial cells of the pulmonary vasculature. No significant nuclear concentration of label was observed in the bronchiolar epithelium, however. The specificity of 3H-dexamethasone labeling was demonstrated by incubating 17 nM 3H-dexamethasone with a 600-fold excess of either unlabeled dexamethasone, estrogen, dihydrotestosterone, or progesterone. These autoradiographic binding and steroid competition studies were confirmed by quantifying with liquid scintillation counting the specific 3H-dexamethasone binding in nuclear and cytosolic fractions prepared from lung tissues that had undergone identical incubation and washing procedures as those for autoradiography. These results demonstrate that many cell types in adult lung are targets for glucocorticoids and may respond to physiologic concentrations of this hormone.

  15. Detection of degenerative cartilage disease: comparison of high-resolution morphological MR and quantitative T2 mapping at 3.0 Tesla.

    Science.gov (United States)

    Apprich, S; Welsch, G H; Mamisch, T C; Szomolanyi, P; Mayerhoefer, M; Pinker, K; Trattnig, S

    2010-09-01

    The aim of the study was to investigate the association of T2 relaxation times of the knee with early degenerative cartilage changes. Furthermore the impact of unloading the knee on T2 values was evaluated. Forty-three patients with knee pain and an ICRS (International Cartilage Repair Society) cartilage defect grade Morphological cartilage grading was based on high-resolution proton-density (PD), turbo-spin-echo (TSE) and three-dimensional (3D) isotropic True fast imaging with steady-state precession (FISP) images of slices covering the cartilage layer above the posterior horn of the meniscus. T2 maps were calculated from a multi-echo, spin-echo (MESE) sequence, performed at the beginning and at the end of the scan (time interval 40 min). Influence of cartilage defect grading on deep, superficial, and global T2 values as well as on T2 values for zonal variation was assessed using analysis of variance (ANOVA) and Spearman rank correlation test. Differences among both T2 measurements were compared using paired t-test. Global and superficial T2 values significantly increased with cartilage defect grade regardless of the time elapsed from unloading (global T2: ICRS grade 0, 38.9 and 40.1 ms; grade 1, 41.2 and 44.5 ms; grade 2, 47.7 and 53.4 ms; P=0.041 and 0.008) with stronger correlation for second T2 measurement. In contrast there were no significant differences among grades in the zonal variation at any time. Significant differences for T2 values between the two subsequent measurements were consistently found. T2 mapping might be a sensitive method for the detection of early cartilage degeneration. From our results we would recommend to measure T2 after unloading. Copyright 2010. Published by Elsevier Ltd.

  16. Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower ( Helianthus annuus L.).

    Science.gov (United States)

    Mokrani, L; Gentzbittel, L; Azanza, F; Fitamant, L; Al-Chaarani, G; Sarrafi, A

    2002-12-01

    Crosses were made between two inbred lines of sunflower. Parents and 118 F(3) families were planted in the field in a randomized complete block design in two replications. Genetic control for some agronomical traits: grain weight by plant (GWP), 1,000-grain weight (TGW), percentage of oil in grain (POG) and sowing to flowering date (STF) was investigated in F(3) families and their parents. Genetic variability was observed among the 118 F(3) families for all the traits studied. Genetic gain was obtained when the best F(3) family, or the mean of 10% of the selected families was compared with the best parent for GWP, TWG and POG. Heritability was 0.23 for GWP, 0.55 for TGW, 0.57 for POG and 0.32 for STF. A set of 244 F(3) families from the same cross, including the above 118 mentioned families and their two parents, were screened with 276 AFLP and microsatellite markers and a linkage map was constructed based on 170 markers. Two putative QTLs for the GWP trait ( gmp), one QTL for TGW ( tgw), six QTLs for POG ( pog) and two for STF ( stf) were detected. The percentage of phenotypic variance explained by each QTL ranged from 2.6% to 70.9%. The percentage of total phenotypic variance explained was 50.7% for GWP, 5.4% for TGW, 90.4% for POG and 89.3% for STF. Although these regions need to be more-precisely mapped, the information obtained should help in marker-assisted selection.

  17. Genetic map construction and quantitative trait loci (QTL) mapping for nitrogen use efficiency and its relationship with productivity and quality of the biennial crop Belgian endive (Cichorium intybus L.).

    Science.gov (United States)

    Cassan, Laurent; Moreau, Laurence; Segouin, Samuel; Bellamy, Annick; Falque, Mathieu; Limami, Anis M

    2010-10-15

    A genetic study of the biennial crop Belgian endive (Cichorium intybus) was carried out to examine the effect of nitrogen nutrition during the vegetative phase in the control of the productivity and quality of the chicon (etiolated bud), a crop that grows during the second phase of development (forcing process). A population of 302 recombinant inbred lines (RIL) was obtained from the cross between contrasting lines "NS1" and "NR2". A genetic map was constructed and QTLs of several physiological and agronomical traits were mapped under two levels of nitrogen fertilization during the vegetative phase (N- and N+). The agronomical traits showed high broad sense heritability, whereas the physiological traits were characterized by low broad sense heritability. Nitrogen reserves mobilization during the forcing process was negatively correlated with nitrogen reserves content of the tuberized root and common QTLs were detected for these traits. The chicon productivity and quality were not correlated, but showed one common QTL. This study revealed that chicon productivity and quality were genetically associated with nitrogen reserves mobilization that exerts opposite effects on both traits. Chicon productivity was positively correlated with N reserves mobilization under N- and N+ and a common QTL with the same additive effects was detected for both traits. Chicon quality was negatively correlated with N reserves mobilization under N- and N+ and a common QTL with opposite additive effects was detected for both traits. These results lead to the conclusion that N reserves mobilization is a more effective trait than N reserves content in predicting chicon productivity and quality. Finally, this study revealed agronomical and physiological QTLs utilizable by breeders via marker-assisted selection to aid the optimization of chicon quality under adapted N fertilization.

  18. Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses

    Directory of Open Access Journals (Sweden)

    Bartenschlager Heinz

    2010-07-01

    Full Text Available Abstract Background QTL affecting fat deposition related performance traits have been considered in several studies and mapped on numerous porcine chromosomes. However, activity of specific enzymes, protein content and cell structure in fat tissue probably depend on a smaller number of genes than traits related to fat content in carcass. Thus, in this work traits related to metabolic and cytological features of back fat tissue and fat related performance traits were investigated in a genome-wide QTL analysis. QTL similarities and differences were examined between three F2 crosses, and between male and female animals. Methods A total of 966 F2 animals originating from crosses between Meishan (M, Pietrain (P and European wild boar (W were analysed for traits related to fat performance (11, enzymatic activity (9 and number and volume of fat cells (20. Per cross, 216 (M × P, 169 (W × P and 195 (W × M genome-wide distributed marker loci were genotyped. QTL mapping was performed separately for each cross in steps of 1 cM and steps were reduced when the distance between loci was shorter. The additive and dominant components of QTL positions were detected stepwise by using a multiple position model. Results A total of 147 genome-wid