Shielding from space radiations

NASA Technical Reports Server (NTRS)

Chang, C. Ken; Badavi, Forooz F.; Tripathi, Ram K.

1993-01-01

This Progress Report covering the period of December 1, 1992 to June 1, 1993 presents the development of an analytical solution to the heavy ion transport equation in terms of Green's function formalism. The mathematical development results are recasted into a highly efficient computer code for space applications. The efficiency of this algorithm is accomplished by a nonperturbative technique of extending the Green's function over the solution domain. The code may also be applied to accelerator boundary conditions to allow code validation in laboratory experiments. Results from the isotopic version of the code with 59 isotopes present for a single layer target material, for the case of an iron beam projectile at 600 MeV/nucleon in water is presented. A listing of the single layer isotopic version of the code is included.

Effect of Isotope Mass in Simulations of JET H-mode Discharges

NASA Astrophysics Data System (ADS)

Snyder, S. E.; Onjun, T.; Kritz, A. H.; Bateman, G.; Parail, V.

2004-11-01

In JET type-I ELMy H-mode discharges, it is found that the height of the pressure pedestal increases and the frequency of the ELMs decreases with increasing isotope mass. These experimentally observed trends are obtained in these simulations only if the pedestal width increases with isotope mass. Simulations are carried out using the JETTO integrated modeling code with a dynamic model for the H-mode pedestal and the ELMs.(T. Onjun et al, Phys. Plasmas 11 (2004) 1469 and 3006.) The HELENA and MISHKA stability codes are applied to calibrate the stability criteria used to trigger ELM crashes in the JETTO code and to explore possible access to second stability in the pedestal. In the simulations, transport in the pedestal is given by the ion thermal neoclassical diffusivity, which increases with isotope mass. Consequently, as the isotope mass is increased, the pressure gradient and the bootstrap current in the pedestal rebuild more slowly after each ELM crash. Several models are explored in which the pedestal width increases with isotope mass.

Rb-Sr isotopic studies of postorogenic granites from the eastern Arabian Shield, Kingdom of Saudi Arabia

USGS Publications Warehouse

Stuckless, J.S.; Futa, Kiyoto

1987-01-01

Available data indicate that postorogenic granites tend to be older in the southern part of the Arabian Shield. This suggests that plutonism started in the south and progressed to the north. Initial 87Sr/86Sr values also form a regional pattern. These ratios tend to be higher in the eastern part of the Arabian Shield, and suggest one source of continental affinity to the east and one of oceanic affinity to the west. The distribution of initial strontium isotope ratios does not clearly discriminate between the various models for Shield evolution; however, a sedimentary source region of mixed end members seems more compatible with the data pattern than models based on discrete boundaries between unrelated accreted blocks.

Identification of candidate angiogenic inhibitors processed by matrix metalloproteinase 2 (MMP-2) in cell-based proteomic screens: disruption of vascular endothelial growth factor (VEGF)/heparin affin regulatory peptide (pleiotrophin) and VEGF/Connective tissue growth factor angiogenic inhibitory complexes by MMP-2 proteolysis.

PubMed

Dean, Richard A; Butler, Georgina S; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R; Courty, José; Overall, Christopher M

2007-12-01

Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2-/- mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2-/- cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis.

Identification of Candidate Angiogenic Inhibitors Processed by Matrix Metalloproteinase 2 (MMP-2) in Cell-Based Proteomic Screens: Disruption of Vascular Endothelial Growth Factor (VEGF)/Heparin Affin Regulatory Peptide (Pleiotrophin) and VEGF/Connective Tissue Growth Factor Angiogenic Inhibitory Complexes by MMP-2 Proteolysis▿ †

PubMed Central

Dean, Richard A.; Butler, Georgina S.; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R.; Courty, José; Overall, Christopher M.

2007-01-01

Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2−/− mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2−/− cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis. PMID:17908800

Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

NASA Astrophysics Data System (ADS)

Wichard, Thomas; Deicke, Michael; Frieder Mohr, Jan; Klein, Martin

2017-04-01

Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals. We present a targeted analysis of low-molecular-weight organic ligands based on fast UHPLC-ESI-MS measurements. Replacement of, for example, natural iron or molybdenum with isotopically pure 54Fe/58Fe (ratio 1:1) or 95Mo/98Mo (ratio 1:1) causes easily detectable unique isotopic signatures in the mass spectra of potential metal-complexing ligands. This can be achieved under laboratory conditions not only in growth media, but also by spiking directly aqueous samples or solid-phase extracts. Importantly, as the relative affinity of the metallophores for e.g., Mo or Fe is dependent on the pH, all experiments needs to be conducted under pH-controlled conditions. The improved ionization efficiency of some metal complexes helps to enhance the signal-to-noise ratio compared to the free ligand at the same chromatographic conditions. The methodology does not necessarily depend on HR-ESI-MS measurements (e.g., Q-Exactive Orbitrap) and can be applied to any mass spectrometer. With MICP, two birds can be killed with one stone: (i) the identification of metallophores (e.g., siderophores, molybdophores) for metal uptake by any organism and (ii) organic ligands which solely work as metal buffer in dissolved organic matter (DOM). We currently address following two main research lines: First, DOM has often been used as a proxy for bio-productivity in terms of a carbon source; however, the specific impact of DOM as a "metal buffer" for biological processes is still under-investigated. Upon the administration of individual isotopes or isotopic pairs, for example, 54Fe/58Fe, 63Cu/65Cu, 66Zn/68Zn, or 95Mo/98Mo and subsequent measurements by mass spectrometry, organic ligands can be identified that contribute potentially to the regulation of bioavailability and toxicity of metals in the water column. Secondly, metal acquisition by ligand exchange processes is vital for macroalgae-bacteria interactions. Both alga and bacteria contribute to the "soup of organic ligands" which potentially increases the bioavailability of metals due to various ligand exchanges with DOM. In particular, we will outline the analytical process resulting in the identification of ligands in the chemosphere of the marine macroalga Ulva (Chlorophyta) and its associated bacteria. In summary, the identification of metal organic ligands in natural samples will pave the way for understanding the organic ligand-mediated metal acquisition shuttled from DOM to alga. (References: Wichard T. (2016) Front. Mar. Sci. 3:131; Deicke M., Mohr J.M., Wichard T. (2014) Analyst, 139, 6096-6099)

Quantitative interaction proteomics using mass spectrometry.

PubMed

Wepf, Alexander; Glatter, Timo; Schmidt, Alexander; Aebersold, Ruedi; Gstaiger, Matthias

2009-03-01

We present a mass spectrometry-based strategy for the absolute quantification of protein complex components isolated through affinity purification. We quantified bait proteins via isotope-labeled reference peptides corresponding to an affinity tag sequence and prey proteins by label-free correlational quantification using the precursor ion signal intensities of proteotypic peptides generated in reciprocal purifications. We used this method to quantitatively analyze interaction stoichiometries in the human protein phosphatase 2A network.

Stable isotope reactive transport modeling in water-rock interactions during CO2 injection

NASA Astrophysics Data System (ADS)

Hidalgo, Juan J.; Lagneau, Vincent; Agrinier, Pierre

2010-05-01

Stable isotopes can be of great usefulness in the characterization and monitoring of CO2 sequestration sites. Stable isotopes can be used to track the migration of the CO2 plume and identify leakage sources. Moreover, they provide unique information about the chemical reactions that take place on the CO2-water-rock system. However, there is a lack of appropriate tools that help modelers to incorporate stable isotope information into the flow and transport models used in CO2 sequestration problems. In this work, we present a numerical tool for modeling the transport of stable isotopes in groundwater reactive systems. The code is an extension of the groundwater single-phase flow and reactive transport code HYTEC [2]. HYTEC's transport module was modified to include element isotopes as separate species. This way, it is able to track isotope composition of the system by computing the mixing between the background water and the injected solution accounting for the dependency of diffusion on the isotope mass. The chemical module and database have been expanded to included isotopic exchange with minerals and the isotope fractionation associated with chemical reactions and mineral dissolution or precipitation. The performance of the code is illustrated through a series of column synthetic models. The code is also used to model the aqueous phase CO2 injection test carried out at the Lamont-Doherty Earth Observatory site (Palisades, New York, USA) [1]. References [1] N. Assayag, J. Matter, M. Ader, D. Goldberg, and P. Agrinier. Water-rock interactions during a CO2 injection field-test: Implications on host rock dissolution and alteration effects. Chemical Geology, 265(1-2):227-235, July 2009. [2] Jan van der Lee, Laurent De Windt, Vincent Lagneau, and Patrick Goblet. Module-oriented modeling of reactive transport with HYTEC. Computers & Geosciences, 29(3):265-275, April 2003.

Water Isotopes in the GISS GCM: History, Applications and Potential

NASA Astrophysics Data System (ADS)

Schmidt, G. A.; LeGrande, A. N.; Field, R. D.; Nusbaumer, J. M.

2017-12-01

Water isotopes have been incorporated in the GISS GCMs since the pioneering work of Jean Jouzel in the 1980s. Since 2005, this functionality has been maintained within the master branch of the development code and has been usable (and used) in all subsequent versions. This has allowed a wide variety of applications, across multiple time-scales and interests, to be tackled coherently. Water isotope tracers have been used to debug the atmospheric model code, tune parameterisations of moist processes, assess the isotopic fingerprints of multiple climate drivers, produce forward models for remotely sensed isotope products, and validate paleo-climate interpretations from the last millennium to the Eocene. We will present an overview of recent results involving isotope tracers, including improvements in models for the isotopic fractionation processes themselves, and demonstrate the potential for using these tracers and models more systematically in paleo-climate reconstructions and investigations of the modern hydrological cycle.

Comparison of deterministic and stochastic approaches for isotopic concentration and decay heat uncertainty quantification on elementary fission pulse

NASA Astrophysics Data System (ADS)

Lahaye, S.; Huynh, T. D.; Tsilanizara, A.

2016-03-01

Uncertainty quantification of interest outputs in nuclear fuel cycle is an important issue for nuclear safety, from nuclear facilities to long term deposits. Most of those outputs are functions of the isotopic vector density which is estimated by fuel cycle codes, such as DARWIN/PEPIN2, MENDEL, ORIGEN or FISPACT. CEA code systems DARWIN/PEPIN2 and MENDEL propagate by two different methods the uncertainty from nuclear data inputs to isotopic concentrations and decay heat. This paper shows comparisons between those two codes on a Uranium-235 thermal fission pulse. Effects of nuclear data evaluation's choice (ENDF/B-VII.1, JEFF-3.1.1 and JENDL-2011) is inspected in this paper. All results show good agreement between both codes and methods, ensuring the reliability of both approaches for a given evaluation.

Determination of the NPP Kr\\vsko spent fuel decay heat

NASA Astrophysics Data System (ADS)

Kromar, Marjan; Kurinčič, Bojan

2017-07-01

Nuclear fuel is designed to support fission process in a reactor core. Some of the isotopes, formed during the fission, decay and produce decay heat and radiation. Accurate knowledge of the nuclide inventory producing decay heat is important after reactor shut down, during the fuel storage and subsequent reprocessing or disposal. In this paper possibility to calculate the fuel isotopic composition and determination of the fuel decay heat with the Serpent code is investigated. Serpent is a well-known Monte Carlo code used primarily for the calculation of the neutron transport in a reactor. It has been validated for the burn-up calculations. In the calculation of the fuel decay heat different set of isotopes is important than in the neutron transport case. Comparison with the Origen code is performed to verify that the Serpent is taking into account all isotopes important to assess the fuel decay heat. After the code validation, a sensitivity study is carried out. Influence of several factors such as enrichment, fuel temperature, moderator temperature (density), soluble boron concentration, average power, burnable absorbers, and burnup is analyzed.

Tectonic affinities of the accreted basalts in southern Taiwan

NASA Astrophysics Data System (ADS)

Chen, Hsin-Yu; Yang, Huai-Jen; Liu, Yung-Hsin; Huang, Kuo-Fang; Takazawa, Eiichi

2018-06-01

Tectonic affinities of accreted basalts provide constraints on mass transport in convergent boundaries, improving our understandings on the evolution of regional geology. In this study, nineteen accreted basalts from the southernmost tip of Taiwan Island, which is on the convergent boundary between the Eurasian and Philippine Sea Plates, were analyzed for element concentrations as well as Sr, Nd, Hf, and Pb isotope ratios to investigate their tectonic affinities. All the samples contain > 3% LOI, reflecting post-magmatic alteration. LOI and Nb variation diagrams together with comparisons to oceanic basalt compositions indicated that the concentrations of most major elements and Rb, Sr, and Ba were modified by post-magmatic processes to varying extents, while P2O5, REE and HFSE remained immobile. Although some samples show Pb loss, most samples have Pb concentrations not affected by post-magmatic processes. Isotope ratios of Pb, Nd and Hf, generally reflect the mantle source characteristics. The εNd-εHf relationship and trace element abundance ratios indicated that the LREE-depleted samples were mostly scraped off the subducting South China Sea floor, reflecting the volumetric dominance of N-MORB on ocean floors. The overriding Philippine Sea Plate contributed both N-MORB and E-MORB to the accretionary prism. The tectonic affinities of the LREE-enriched samples, however, could not be unambiguously determined for the large geochemical variability of OIB from both subducting and overlying slabs. Based on our results, it is proposed that the tectonic affinity of the basalts in an accretionary prism can indicate the subduction polarity of the associated convergent boundary, providing a constraint for regional geology evolution.

Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster

PubMed Central

Menger, Katja E.; James, Andrew M.; Cochemé, Helena M.; Harbour, Michael E.; Chouchani, Edward T.; Ding, Shujing; Fearnley, Ian M.; Partridge, Linda; Murphy, Michael P.

2015-01-01

Summary Altering the redox state of cysteine residues on protein surfaces is an important response to environmental challenges. Although aging and fasting alter many redox processes, the role of cysteine residues is uncertain. To address this, we used a redox proteomic technique, oxidative isotope-coded affinity tags (OxICAT), to assess cysteine-residue redox changes in Drosophila melanogaster during aging and fasting. This approach enabled us to simultaneously identify and quantify the redox state of several hundred cysteine residues in vivo. Cysteine residues within young flies had a bimodal distribution with peaks at ∼10% and ∼85% reversibly oxidized. Surprisingly, these cysteine residues did not become more oxidized with age. In contrast, 24 hr of fasting dramatically oxidized cysteine residues that were reduced under fed conditions while also reducing cysteine residues that were initially oxidized. We conclude that fasting, but not aging, dramatically alters cysteine-residue redox status in D. melanogaster. PMID:26095360

Exploiting Diffusion Barrier and Chemical Affinity of Metal-Organic Frameworks for Efficient Hydrogen Isotope Separation.

PubMed

Kim, Jin Yeong; Balderas-Xicohténcatl, Rafael; Zhang, Linda; Kang, Sung Gu; Hirscher, Michael; Oh, Hyunchul; Moon, Hoi Ri

2017-10-25

Deuterium plays a pivotal role in industrial and scientific research, and is irreplaceable for various applications such as isotope tracing, neutron moderation, and neutron scattering. In addition, deuterium is a key energy source for fusion reactions. Thus, the isolation of deuterium from a physico-chemically almost identical isotopic mixture is a seminal challenge in modern separation technology. However, current commercial approaches suffer from extremely low separation efficiency (i.e., cryogenic distillation, selectivity of 1.5 at 24 K), requiring a cost-effective and large-scale separation technique. Herein, we report a highly effective hydrogen isotope separation system based on metal-organic frameworks (MOFs) having the highest reported separation factor as high as ∼26 at 77 K by maximizing synergistic effects of the chemical affinity quantum sieving (CAQS) and kinetic quantum sieving (KQS). For this purpose, the MOF-74 system having high hydrogen adsorption enthalpies due to strong open metal sites is chosen for CAQS functionality, and imidazole molecules (IM) are employed to the system for enhancing the KQS effect. To the best of our knowledge, this work is not only the first attempt to implement two quantum sieving effects, KQS and CAQS, in one system, but also provides experimental validation of the utility of this system for practical industrial usage by isolating high-purity D 2 through direct selective separation studies using 1:1 D 2 /H 2 mixtures.

Laser photodetachment of radioactive 128 I -

DOE PAGES

Rothe, Sebastian; Sundberg, Julia; Welander, Jakob; ...

2017-08-31

The first experimental investigation of the electron affinity (EA) of a radioactive isotope has been conducted at the CERN-ISOLDE radioactive ion beam facility. The EA of the radioactive iodine isotope 128I ($t$ 1/2 = 25 min) was determined to be 3.059 052(38) eV. The experiment was conducted using the newly developed Gothenburg ANion Detector for Affinity measurements by Laser PHotodetachment (GANDALPH) apparatus, connected to a CERN-ISOLDE experimental beamline. 128I was produced in fission induced by 1.4 GeV protons striking a thorium/tantalum foil target and then extracted as singly charged negative ions at a beam energy of 20 keV. Laser photodetachmentmore » of the fast ion beam was performed in a collinear geometry inside the GANDALPH chamber. Neutral atoms produced in the photodetachment process were detected by allowing them to impinge on a glass surface, creating secondary electrons which were then detected using a channel electron multiplier. The photon energy of the laser was tuned across the threshold of the photodetachment process and the detachment threshold data were fitted to a Wigner law function in order to extract the EA. In conclusion, this first successful demonstration of photodetachment at an isotope separator on line facility opens up the opportunity for future studies of the fundamental properties of negatively charged radioactive isotopes such as the EA of astatine and polonium.« less

Comprehensive analytical methodology to determine hydrocarbons in marine waters using extraction disks coupled to glass fiber filters and compound-specific isotope analyses.

PubMed

Ternon, Eva; Tolosa, Imma

2015-07-24

Solid-phase extraction of both aliphatic (AHs) and aromatic polycyclic hydrocarbons (PAHs) from seawater samples was evaluated using a GFF filter stacked upon an octadecyl bonded silica (C18) disk. Stable-isotope measurements were developed on hydrocarbons extracted from both GFF and C18-disks in order to characterize the source of hydrocarbons. A clear partition of hydrocarbon compounds between the dissolved and the particulate phase was highlighted. PAHs showed a higher affinity with the dissolved phase (recoveries efficiency of 48-71%) whereas AHs presented strong affinity with the particulate phase (up to 76% of extraction efficiency). Medium volumes of seawater samples were tested and no breakthrough was observed for a 5L sample. Isotopic fractionation was investigated within all analytical steps but none was evidenced. This method has been applied to harbor seawater samples and very low AH and PAH concentrations were achieved. Due to the low concentration levels of hydrocarbons in the samples, the source of hydrocarbons was determined by molecular indices rather than isotopic measurements and a pyrolytic origin was evidenced. The aliphatic profile also revealed the presence of long-chain linear alkylbenzenes (LABs). The methodology presented here would better fit to polluted coastal environments affected by recent oil spills. Copyright © 2015 Elsevier B.V. All rights reserved.

A porewater - based stable isotope approach for the investigation of subsurface hydrological processes

NASA Astrophysics Data System (ADS)

Garvelmann, J.; Külls, C.; Weiler, M.

2011-10-01

Predicting and understanding subsurface flowpaths is still a crucial issue in hydrological research. We present an experimental approach to reveal present and past subsurface flowpaths of water in the unsaturated and saturated zone. Two hillslopes in a humid moutainous catchment have been investigated. The H2O(liquid) - H2O(vapor) equilibration laser spectroscopy method was used to obtain high resolution δ2H vertical depth profiles of porewater at various points along a fall line of a pasture hillslope in the southern Black Forest, Germany. The Porewater Stable Isotope Profile (PSIP) approach was developed to use the integrated information of several vertical depth profiles of deuterium along two transects at the hillslopes. Different shapes of depth profiles were observed in relation to hillslope position. The statistical variability (inter-quartile range and standard deviation) of each profile was used to characterize different types of depth profiles. The profiles upslope or with a weak affinity for saturation as indicated by a low topographic wetness index preserve the isotopic input signal by precipitation with a distinct seasonal variability. These observations indicate mainly vertical movement of soil water in the upper part of the hillslope before sampling. The profiles downslope or at locations with a strong affinity for saturation do not show a similar seasonal isotopic signal. The input signal is erased in the foothills and a large proportion of pore water samples are close to the isotopic values of δ2H in stream water during base flow. Near the stream indications for efficient mixing of water from lateral subsurface flow paths with vertical percolation are found.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hervey, IV, William Judson; Khalsa-Moyers, Gurusahai K; Lankford, Patricia K

Protein enrichments of engineered, affinity-tagged (or bait ) fusion proteins with interaction partners are often laden with background, non-specific proteins, due to interactions that occur in vitro as an artifact of the technique. Furthermore, the in vivo expression of the bait protein may itself affect physiology or metabolism. In this study, intrinsic affinity purification challenges were investigated in a model protein complex, DNA-dependent RNA polymerase (RNAP), encompassing chromosome- and plasmid-encoding strategies for bait proteins in two different microbial species: Escherichia coli and Rhodopseudomonas palustris. Isotope ratio measurements of bait protein expression strains relative to native, wild-type strains were performed bymore » liquid chromatography tandem mass spectrometry (LC-MS-MS) to assess bait protein expression strategies in each species. Authentic interacting proteins of RNAP were successfully discerned from artifactual co-isolating proteins by the isotopic differentiation of interactions as random or targeted (I-DIRT) method (A. J. Tackett et al. J. Proteome Res. 2005, 4 (5), 1752-1756). To investigate broader effects of bait protein production in the bacteria, we compared proteomes from strains harboring a plasmid that encodes an affinity-tagged subunit (RpoA) of the RNAP complex with the corresponding wild-type strains using stable isotope metabolic labeling. The ratio of RpoA abundance in plasmid strains versus wild type was 0.8 for R. palustris and 1.7 for E. coli. While most other proteins showed no appreciable difference, proteins significantly increased in abundance in plasmid-encoded bait-expressing strains of both species included the plasmid encoded antibiotic resistance protein, GenR and proteins involved in amino acid biosynthesis. Together, these local, complex-specific and more global, whole proteome isotopic abundance ratio measurements provided a tool for evaluating both in vivo and in vitro effects of plasmid-encoding strategies for bait protein expression. This approach has the potential for enabling discovery of protein-protein interactions among the growing number of sequenced microbial species without the need for development of chromosomal insertion systems.« less

Improvement of Modeling HTGR Neutron Physics by Uncertainty Analysis with the Use of Cross-Section Covariance Information

NASA Astrophysics Data System (ADS)

Boyarinov, V. F.; Grol, A. V.; Fomichenko, P. A.; Ternovykh, M. Yu

2017-01-01

This work is aimed at improvement of HTGR neutron physics design calculations by application of uncertainty analysis with the use of cross-section covariance information. Methodology and codes for preparation of multigroup libraries of covariance information for individual isotopes from the basic 44-group library of SCALE-6 code system were developed. A 69-group library of covariance information in a special format for main isotopes and elements typical for high temperature gas cooled reactors (HTGR) was generated. This library can be used for estimation of uncertainties, associated with nuclear data, in analysis of HTGR neutron physics with design codes. As an example, calculations of one-group cross-section uncertainties for fission and capture reactions for main isotopes of the MHTGR-350 benchmark, as well as uncertainties of the multiplication factor (k∞) for the MHTGR-350 fuel compact cell model and fuel block model were performed. These uncertainties were estimated by the developed technology with the use of WIMS-D code and modules of SCALE-6 code system, namely, by TSUNAMI, KENO-VI and SAMS. Eight most important reactions on isotopes for MHTGR-350 benchmark were identified, namely: 10B(capt), 238U(n,γ), ν5, 235U(n,γ), 238U(el), natC(el), 235U(fiss)-235U(n,γ), 235U(fiss).

Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-10-25

The analysis of the qualitative and quantitative changes of metabolites in body fluids and tissues yields valuable information for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-(tandem) mass spectrometry [LC/ESI-MS(/MS)] has been widely used for these purposes due to the high separation capability of LC, broad coverage of ESI for various compounds and high specificity of MS(/MS). However, there are still two major problems to be solved regarding the biological sample analysis; lack of sensitivity and limited availability of stable isotope-labeled analogues (internal standards, ISs) for most metabolites. Stable isotope-coded derivatization (ICD) can be the answer for these problems. By the ICD, different isotope-coded moieties are introduced to the metabolites and one of the resulting derivatives can serve as the IS, which minimize the matrix effects. Furthermore, the derivatization can improve the ESI efficiency, fragmentation property in the MS/MS and chromatographic behavior of the metabolites, which lead to a high sensitivity and specificity in the various detection modes. Based on this background, this article reviews the recently-reported isotope-coded ESI-enhancing derivatization (ICEED) reagents, which are key components for the ICD-based LC/MS(/MS) studies, and their applications to the detection, identification, quantification and profiling of metabolites in human and animal samples. The LC/MS(/MS) using the ICEED reagents is the powerful method especially for the differential analysis (relative quantification) of metabolites in two comparative samples, simultaneous quantification of multiple metabolites whose stable isotope-labeled ISs are not available, and submetabolome profiling. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Fractionation of Fe isotopes by soil microbes and organic acids

USGS Publications Warehouse

Brantley, Susan L.; Liermann, Laura; Bullen, Thomas D.

2001-01-01

Small natural variations in Fe isotopes have been attributed to biological cycling. However, without understanding the mechanism of fractionation, it is impossible to interpret such variations. Here we show that the δ56Fe of Fe dissolved from a silicate soil mineral by siderophore-producing bacteria is as much as 0.8% lighter than bulk Fe in the mineral. A smaller isotopic shift is observed for Fe released abiotically by two chelates, and the magnitude of the shift increases with affinity of the ligand for Fe, consistent with a kinetic isotope effect during hydrolysis of Fe at the mineral surface. Fe dissolved abiotically without chelates shows no isotopic shift. The δ56Fe of the exchange fraction on soil grains is also lighter by ~0.6%-1% than Fe from both hornblende and iron oxyhydroxides. The kinetic isotope effect is therefore preserved in open systems such as soils. when recorded in the rock record, Fe isotopic fractionation could document Fe transport by organic molecules or by microbes where such entities were present in the geologic past.

Profiling global kinome signatures of the radioresistant MCF-7/C6 breast cancer cells using MRM-based targeted proteomics.

PubMed

Guo, Lei; Xiao, Yongsheng; Fan, Ming; Li, Jian Jian; Wang, Yinsheng

2015-01-02

Ionizing radiation is widely used in cancer therapy; however, cancer cells often develop radioresistance, which compromises the efficacy of cancer radiation therapy. Quantitative assessment of the alteration of the entire kinome in radioresistant cancer cells relative to their radiosensitive counterparts may provide important knowledge to define the mechanism(s) underlying tumor adaptive radioresistance and uncover novel target(s) for effective prevention and treatment of tumor radioresistance. By employing a scheduled multiple-reaction monitoring analysis in conjunction with isotope-coded ATP affinity probes, we assessed the global kinome of radioresistant MCF-7/C6 cells and their parental MCF-7 human breast cancer cells. We rigorously quantified 120 kinases, of which (1)/3 exhibited significant differences in expression levels or ATP binding affinities. Several kinases involved in cell cycle progression and DNA damage response were found to be overexpressed or hyperactivated, including checkpoint kinase 1 (CHK1), cyclin-dependent kinases 1 and 2 (CDK1 and CDK2), and the catalytic subunit of DNA-dependent protein kinase. The elevated expression of CHK1, CDK1, and CDK2 in MCF-7/C6 cells was further validated by Western blot analysis. Thus, the altered kinome profile of radioresistant MCF-7/C6 cells suggests the involvement of kinases on cell cycle progression and DNA repair in tumor adaptive radioresistance. The unique kinome profiling results also afforded potential effective targets for resensitizing radioresistant cancer cells and counteracting deleterious effects of ionizing radiation exposure.

A porewater-based stable isotope approach for the investigation of subsurface hydrological processes

NASA Astrophysics Data System (ADS)

Garvelmann, J.; Külls, C.; Weiler, M.

2012-02-01

Predicting and understanding subsurface flowpaths is still a crucial issue in hydrological research. We present an experimental approach to reveal present and past subsurface flowpaths of water in the unsaturated and saturated zone. Two hillslopes in a humid mountainous catchment have been investigated. The H2O(liquid) - H2O(vapor) equilibration laser spectroscopy method was used to obtain high resolution δ2H vertical depth profiles of pore water at various points along two fall lines of a pasture hillslope in the southern Black Forest, Germany. The Porewater-based Stable Isotope Profile (PSIP) approach was developed to use the integrated information of several vertical depth profiles of deuterium along transects at the hillslope. Different shapes of depth profiles were observed in relation to hillslope position. The statistical variability (inter-quartile range and standard deviation) of each profile was used to characterize different types of depth profiles. The profiles upslope or with a weak affinity for saturation as indicated by a low topographic wetness index preserve the isotopic input signal by precipitation with a distinct seasonal variability. These observations indicate mainly vertical movement of soil water in the upper part of the hillslope before sampling. The profiles downslope or at locations with a strong affinity for saturation do not show a similar seasonal isotopic signal. The input signal is erased in the foothills and a large proportion of pore water samples are close to the isotopic values of δ2H in streamwater during base flow conditions indicating the importance of the groundwater component in the catchment. Near the stream indications for efficient mixing of water from lateral subsurface flow paths with vertical percolation are found.

Unravelling biocultural population structure in 4th/3rd century BC Monterenzio Vecchio (Bologna, Italy) through a comparative analysis of strontium isotopes, non-metric dental evidence, and funerary practices.

PubMed

Sorrentino, Rita; Bortolini, Eugenio; Lugli, Federico; Mancuso, Giuseppe; Buti, Laura; Oxilia, Gregorio; Vazzana, Antonino; Figus, Carla; Serrangeli, Maria Cristina; Margherita, Cristiana; Penzo, Annachiara; Gruppioni, Giorgio; Gottarelli, Antonio; Jochum, Klaus Peter; Belcastro, Maria Giovanna; Cipriani, Anna; Feeney, Robin N M; Benazzi, Stefano

2018-01-01

The 4th century BC marks the main entrance of Celtic populations in northern Italy. Their arrival has been suggested based on the presence of Celtic customs in Etruscan mortuary contexts, yet up to now few bioarchaeological data have been examined to support or reject the arrival of these newcomers. Here we use strontium isotopes, non-metric dental traits and funerary patterns to unravel the biocultural structure of the necropolis of Monterenzio Vecchio (Bologna, Italy). Subsamples of our total sample of 38 individuals were analyzed based on different criteria characterizing the following analyses: 1) strontium isotope analysis to investigate migratory patterns and provenance; 2) non-metric dental traits to establish biological relationships between Monterenzio Vecchio, 13 Italian Iron age necropolises and three continental and non-continental Celtic necropolises; 3) grave goods which were statistically explored to detect possible patterns of cultural variability. The strontium isotopes results indicate the presence of local and non-local individuals, with some revealing patterns of mobility. The dental morphology reveals an affinity between Monterenzio Vecchio and Iron Age Italian samples. However, when the Monterenzio Vecchio sample is separated by isotopic results into locals and non-locals, the latter share affinity with the sample of non-continental Celts from Yorkshire (UK). Moreover, systematic analyses demonstrate that ethnic background does not retain measurable impact on the distribution of funerary elements. Our results confirm the migration of Celtic populations in Monterenzio as archaeologically hypothesized on the basis of the grave goods, followed by a high degree of cultural admixture between exogenous and endogenous traits. This contribution shows that combining different methods offers a more comprehensive perspective for the exploration of biocultural processes in past and present populations.

Nd, Pb, Sr, and O isotopic characterization of Saudi Arabian Shield terranes

USGS Publications Warehouse

Stoeser, D.B.; Frost, C.D.

2006-01-01

New Nd, Sr and O isotopic data for granitoid rocks of the Saudi Arabian Shield are presented together with published Nd, Pb, Sr and O isotopic data and all available geologic and geochronologic information to re-evaluate the terranes defined for the Saudi Arabian part of the Arabian-Nubian Shield. Three groups of terranes are identified: 1) the western arc terranes, 2) the eastern arc terranes, and 3) the Khida terrane. The Khida terrane is the only terrane composed of pre-Neoproterozoic continental crust. The western arc terranes are of oceanic arc affinity, and have the least radiogenic Pb and Sr and most radiogenic Nd isotopic compositions and some of the lowest ??18O values of any rocks of the Saudi Arabian Shield. Although some previous studies have characterized the eastern arc terranes as of continental affinity, this study shows that they too are composed of Neoproterozoic oceanic arcs, although their sources have slightly elevated 208Pb/204Pb, Nd, Sri, and ??18O values compared to the western arc terranes. These data suggest that either the isotopic composition of the mantle source for the western arc terranes is more depleted than that of the eastern arc terranes or the eastern arc terranes have been mixed with a small amount of cratonic source material, or both. We further elaborate on the Hulayfah-Ad Dafinah fault zone as a major boundary within the Saudi Arabian portion of the East African Orogen. With further study, its northern extension may be shown to pass through what has been defined as the Hail terrane, and its southern extension appears to lie under cover east of the Tathlith-Malahah terrane and extend into Yemen. It may represent the collision zone between East and West Gondwana, and at the very least it is an important suture between groups of arc terranes of contrasting isotopic composition caught between two converging continents.

Isotopic Dependence of GCR Fluence behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.; Saganti, Premkumar; Kim, Myung-Hee Y.; Cleghorn, Timothy; Zeitlin, Cary; Tripathi, Ram K.

2006-01-01

In this paper we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR), nuclear fragmentation cross-sections, and isotopic-grid on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. For the nuclear interaction data-base and transport solution, we use the quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, respectively. The QMSFRG model is shown to accurately describe existing fragmentation data including proper description of the odd-even effects as function of the iso-spin dependence on the projectile nucleus. The principle finding of this study is that large errors (+/-100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotopic-grid (approx.170 ions) to ones that use a reduced isotopic-grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (<+/-20%) occur in the elemental-fluence spectra. Because a complete isotopic-grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

Burnup calculations and chemical analysis of irradiated fuel samples studied in LWR-PROTEUS phase II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimm, P.; Guenther-Leopold, I.; Berger, H. D.

2006-07-01

The isotopic compositions of 5 UO{sub 2} samples irradiated in a Swiss PWR power plant, which were investigated in the LWR-PROTEUS Phase II programme, were calculated using the CASMO-4 and BOXER assembly codes. The burnups of the samples range from 50 to 90 MWd/kg. The results for a large number of actinide and fission product nuclides were compared to those of chemical analyses performed using a combination of chromatographic separation and mass spectrometry. A good agreement of calculated and measured concentrations is found for many of the nuclides investigated with both codes. The concentrations of the Pu isotopes are mostlymore » predicted within {+-}10%, the two codes giving quite different results, except for {sup 242}Pu. Relatively significant deviations are found for some isotopes of Cs and Sm, and large discrepancies are observed for Eu and Gd. The overall quality of the predictions by the two codes is comparable, and the deviations from the experimental data do not generally increase with burnup. (authors)« less

Drop-out phagemid vector for switching from phage displayed affinity reagents to expression formats.

PubMed

Pershad, Kritika; Sullivan, Mark A; Kay, Brian K

2011-05-15

Affinity reagents that are generated by phage display are typically subcloned into an expression vector for further biochemical characterization. This insert transfer process is time consuming and laborious especially if many inserts are to be subcloned. To simplify the transfer process, we have constructed a "drop-out" phagemid vector that can be rapidly converted to an expression vector by a simple restriction enzyme digestion with MfeI (to "drop-out" the gene III coding sequence), which generates alkaline phosphatase (AP) fusions of the affinity reagents on religation. Subsequently, restriction digestion with AscI drops out the AP coding region and religation generates affinity reagents with a C-terminal six-histidine tag. To validate the usefulness of this vector, four different human single chain Fragments of variable regions (scFv) were tested, three of which show specific binding to three zebrafish (Danio rerio) proteins, namely suppression of tumorigenicity 13, recoverin, and Ppib and the fourth binds to human Lactoferrin protein. For each of the constructs tested, the gene III and AP drop-out efficiency was between 90% and 100%. This vector is especially useful in speeding up the downstream screening of affinity reagents and bypassing the time-consuming subcloning experiments. Copyright © 2011 Elsevier Inc. All rights reserved.

High-spin level structure and Ground-state phase transition in the odd-mass 103-109Rh isotopes in the framework of exactly solvable sdg interacting boson-fermion model

NASA Astrophysics Data System (ADS)

Ghapanvari, M.; Ghorashi, A. H.; Ranjbar, Z.; Jafarizadeh, M. A.

2018-03-01

In this article, the negative-parity states in the odd-mass 103 - 109Rh isotopes in terms of the sd and sdg interacting-boson fermion models were studied. The transitional interacting boson-fermion model Hamiltonians in sd and sdg-IBFM versions based on affine SU (1 , 1) Lie Algebra were employed to describe the evolution from the spherical to deformed gamma unstable shapes along with the chain of Rh isotopes. In this method, sdg-IBFM Hamiltonian, which is a three level pairing Hamiltonian was determined easily via the exactly solvable method. Some observables of the shape phase transitions such as energy levels, the two neutron separation energies, signature splitting of the γ-vibrational band, the α-decay and double β--decay energies were calculated and examined for these isotopes. The present calculation correctly reproduces the spherical to gamma-soft phase transition in the Rh isotopes. Some comparisons were made with sd-IBFM.

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates.

PubMed

Butler, Georgina S; Dean, Richard A; Smith, Derek; Overall, Christopher M

2009-01-01

The modification of cell surface proteins by plasma membrane and soluble proteases is important for physiological and pathological processes. Methods to identify shed and soluble substrates are crucial to further define the substrate repertoire, termed the substrate degradome, of individual proteases. Identifying protease substrates is essential to elucidate protease function and involvement in different homeostatic and disease pathways. This characterisation is also crucial for drug target identification and validation, which would then allow the rational design of specific targeted inhibitors for therapeutic intervention. We describe two methods for identifying and quantifying shed cell surface protease targets in cultured cells utilising Isotope-Coded Affinity Tags (ICAT) and Isobaric Tags for Relative and Absolute Quantification (iTRAQ). As a model system to develop these techniques, we chose a cell-membrane expressed matrix metalloproteinase, MMP-14, but the concepts can be applied to proteases of other classes. By over-expression, or conversely inhibition, of a particular protease with careful selection of control conditions (e.g. vector or inactive protease) and differential labelling, shed proteins can be identified and quantified by mass spectrometry (MS), MS/MS fragmentation and database searching.

Quantitative proteomic analysis of human breast epithelial cells with differential telomere length

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Li-Rong; Chan, King C.; Tahara, Hidetoshi

Telomeres play important functional roles in cell proliferation, cell cycle regulation, and genetic stability, in which telomere length is critical. In this study, quantitative proteome comparisons for the human breast epithelial cells with short and long telomeres (184-hTERT{sub L} vs. 184-hTERT{sub S} and 90P-hTERT{sub L} vs. 90P-hTERT{sub S}), resulting from transfection of the human telomerase reverse transcriptase (hTERT) gene, were performed using cleavable isotope-coded affinity tags. More than 2000 proteins were quantified in each comparative experiment, with approximately 77% of the proteins identified in both analyses. In the cells with long telomeres, significant and consistent alterations were observed in metabolismmore » (amino acid, nucleotide, and lipid metabolism), genetic information transmission (transcription and translation regulation, spliceosome and ribosome complexes), and cell signaling. Interestingly, the DNA excision repair pathway is enhanced, while integrin and its ligands are downregulated in the cells with long telomeres. These results may provide valuable information related to telomere functions.« less

Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled High-Resolution Gamma Spectrometry Systems Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreyer, Jonathan G.; Wang, Tzu-Fang; Vo, Duc T.

Under a 2006 agreement between the Department of Energy (DOE) of the United States of America and the Institut de Radioprotection et de Sûreté Nucléaire (IRSN) of France, the National Nuclear Security Administration (NNSA) within DOE and IRSN initiated a collaboration to improve isotopic identification and analysis of nuclear material [i.e., plutonium (Pu) and uranium (U)]. The specific aim of the collaborative project was to develop new versions of two types of isotopic identification and analysis software: (1) the fixed-energy response-function analysis for multiple energies (FRAM) codes and (2) multi-group analysis (MGA) codes. The project is entitled Action Sheet 4more » – Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled, High-Resolution Gamma Spectrometry Systems (Action Sheet 4). FRAM and MGA/U235HI are software codes used to analyze isotopic ratios of U and Pu. FRAM is an application that uses parameter sets for the analysis of U or Pu. MGA and U235HI are two separate applications that analyze Pu or U, respectively. They have traditionally been used by safeguards practitioners to analyze gamma spectra acquired with high-resolution gamma spectrometry (HRGS) systems that are cooled by liquid nitrogen. However, it was discovered that these analysis programs were not as accurate when used on spectra acquired with a newer generation of more portable, electrically cooled HRGS (ECHRGS) systems. In response to this need, DOE/NNSA and IRSN collaborated to update the FRAM and U235HI codes to improve their performance with newer ECHRGS systems. Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) performed this work for DOE/NNSA.« less

Study of phase transition of even and odd nuclei based on q-deforme SU(1,1) algebraic model

NASA Astrophysics Data System (ADS)

Jafarizadeh, M. A.; Amiri, N.; Fouladi, N.; Ghapanvari, M.; Ranjbar, Z.

2018-04-01

The q-deformed Hamiltonian for the SO (6) ↔ U (5) transitional case in s, d interaction boson model (IBM) can be constructed by using affine SUq (1 , 1) Lie algebra in the both IBM-1 and 2 versions and IBFM. In this research paper, we have studied the energy spectra of 120-128Xe isotopes and 123-131Xe isotopes and B(E2) transition probabilities of 120-128Xe isotopes in the shape phase transition region between the spherical and gamma unstable deformed shapes of the theory of quantum deformation. The theoretical results agree with the experimental data fairly well. It is shown that the q-deformed SO (6) ↔ U (5) transitional dynamical symmetry remains after deformation.

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

PubMed

Gonçalves, Cristina P; Mohallem, José R

2004-11-15

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

PubMed Central

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

Using Tidal Fluctuation-Induced Dynamics of Radium Isotopes (224Ra, 223Ra, and 228Ra) to Trace the Hydrodynamics and Geochemical Reactions in a Coastal Groundwater Mixing Zone

NASA Astrophysics Data System (ADS)

Liu, Yi; Jiao, Jiu Jimmy; Liang, Wenzhao; Luo, Xin

2018-04-01

The reactive transport of radium isotopes (224Ra, 223Ra, and 228Ra) in coastal groundwater mixing zones (CGMZs) is sensitive to shifts of redox conditions and geochemical reactions induced by tidal fluctuation. This study presents a spatial distribution and temporal variation of radium isotopes in the CGMZ for the first time. Results show that the activity of radium isotopes in the upper saline plume (USP) is comparatively low due to a short residence time and mixing loss induced by the infiltration of low radium seawater whereas the activity of radium isotopes in the salt wedge (SW) is comparatively high due to a long residence time in the aquifer. The spatial distribution of radium isotopes is determined by the partitioning of radium isotopes, groundwater residence time, and relative ingrowth rates of radium isotopes. In addition, the variation of radium isotopes in the USP lags slightly (˜0 h) whereas the fluctuation of radium isotopes in the SW lags significantly (˜12 h) behind sea level oscillation. Tidal fluctuation affects the partitioning of radium isotopes through controlling seawater infiltration and subsequently influences the dynamics of radium isotopes in the USP. Concurrently, seawater infiltration significantly affects geochemical processes such as the production of nutrients and total alkalinity. Therefore, radium dynamics in the USP have implications for these geochemical processes. The variation of radium isotopes in the USP also has potential implications for transformation of trace metals such as iron and manganese because of the close affinity of radium isotopes to manganese and iron oxides.

Inhibition of ethylene synthesis reduces salt-tolerance in tomato wild relative species Solanum chilense.

PubMed

Gharbi, Emna; Martínez, Juan-Pablo; Benahmed, Hela; Lepoint, Gilles; Vanpee, Brigitte; Quinet, Muriel; Lutts, Stanley

2017-03-01

Exposure to salinity induces a burst in ethylene synthesis in the wild tomato halophyte plant species Solanum chilense. In order to gain information on the role of ethylene in salt adaptation, plants of Solanum chilense (accession LA4107) and of cultivated glycophyte Solanum lycopersicum (cv. Ailsa Craig) were cultivated for 7days in nutrient solution containing 0 or 125mM NaCl in the presence or absence of the inhibitor of ethylene synthesis (aminovinylglycine (AVG) 2μM). Salt-induced ethylene synthesis in S. chilense occurred concomitantly with an increase in stomatal conductance, an efficient osmotic adjustment and the maintenance of carbon isotope discrimination value (Δ 13 C). In contrast, in S. lycopersicum, salt stress decreased stomatal conductance and Δ 13 C values while osmotic potential remained higher than in S. chilense. Inhibition of stress-induced ethylene synthesis by AVG decreased stomatal conductance and Δ 13 C in S. chilense and compromised osmotic adjustment. Solanum chilense behaved as an includer and accumulated high amounts of Na in the shoot but remained able to maintain K nutrition in the presence of NaCl. This species however did not stimulate the expression of genes coding for high-affinity K transport but genes coding for ethylene responsive factor ERF5 and JREF1 were constitutively more expressed in S. chilense than in S. lycopersicum. It is concluded that ethylene plays a key role in salt tolerance of S. chilense. Copyright © 2016. Published by Elsevier GmbH.

Isotopic composition analysis and age dating of uranium samples by high resolution gamma ray spectrometry

NASA Astrophysics Data System (ADS)

Apostol, A. I.; Pantelica, A.; Sima, O.; Fugaru, V.

2016-09-01

Non-destructive methods were applied to determine the isotopic composition and the time elapsed since last chemical purification of nine uranium samples. The applied methods are based on measuring gamma and X radiations of uranium samples by high resolution low energy gamma spectrometric system with planar high purity germanium detector and low background gamma spectrometric system with coaxial high purity germanium detector. The ;Multigroup γ-ray Analysis Method for Uranium; (MGAU) code was used for the precise determination of samples' isotopic composition. The age of the samples was determined from the isotopic ratio 214Bi/234U. This ratio was calculated from the analyzed spectra of each uranium sample, using relative detection efficiency. Special attention is paid to the coincidence summing corrections that have to be taken into account when performing this type of analysis. In addition, an alternative approach for the age determination using full energy peak efficiencies obtained by Monte Carlo simulations with the GESPECOR code is described.

Simulation of multi-photon emission isotopes using time-resolved SimSET multiple photon history generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiang, Chih-Chieh; Lin, Hsin-Hon; Lin, Chang-Shiun

Abstract-Multiple-photon emitters, such as In-111 or Se-75, have enormous potential in the field of nuclear medicine imaging. For example, Se-75 can be used to investigate the bile acid malabsorption and measure the bile acid pool loss. The simulation system for emission tomography (SimSET) is a well-known Monte Carlo simulation (MCS) code in nuclear medicine for its high computational efficiency. However, current SimSET cannot simulate these isotopes due to the lack of modeling of complex decay scheme and the time-dependent decay process. To extend the versatility of SimSET for simulation of those multi-photon emission isotopes, a time-resolved multiple photon history generatormore » based on SimSET codes is developed in present study. For developing the time-resolved SimSET (trSimSET) with radionuclide decay process, the new MCS model introduce new features, including decay time information and photon time-of-flight information, into this new code. The half-life of energy states were tabulated from the Evaluated Nuclear Structure Data File (ENSDF) database. The MCS results indicate that the overall percent difference is less than 8.5% for all simulation trials as compared to GATE. To sum up, we demonstrated that time-resolved SimSET multiple photon history generator can have comparable accuracy with GATE and keeping better computational efficiency. The new MCS code is very useful to study the multi-photon imaging of novel isotopes that needs the simulation of lifetime and the time-of-fight measurements. (authors)« less

Nuclear Forensics and Radiochemistry: Reaction Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rundberg, Robert S.

In the intense neutron flux of a nuclear explosion the production of isotopes may occur through successive neutron induced reactions. The pathway to these isotopes illustrates both the complexity of the problem and the need for high quality nuclear data. The growth and decay of radioactive isotopes can follow a similarly complex network. The Bateman equation will be described and modified to apply to the transmutation of isotopes in a high flux reactor. A alternative model of growth and decay, the GD code, that can be applied to fission products will also be described.

Cross sections and differential spectra for reactions of 2-20 MeV neutrons of /sup 27/Al

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blann, M.; Komoto, T.T.

1988-01-01

This report summarizes product yields, secondary n,p and ..cap alpha.. spectra, and ..gamma..-ray spectra calculated for incident neutrons of 2-20 MeV on /sup 27/Al targets. Results are all from the code ALICE, using the version ALISO which does weighting of results for targets which are a mix of isotopes. Where natural isotopic targets are involved, yields and n,p,..cap alpha.. spectra will be reported weighted over isotopic yields. Gamma-ray spectra, however, will be reported for the most abundant isotope.

High-Affinity Recombinant Antibody Fragments (Fabs) Can Be Applied in Peptide Enrichment Immuno-MRM Assays

PubMed Central

2015-01-01

High-affinity antibodies binding to linear peptides in solution are a prerequisite for performing immuno-MRM, an emerging technology for protein quantitation with high precision and specificity using peptide immunoaffinity enrichment coupled to stable isotope dilution and targeted mass spectrometry. Recombinant antibodies can be generated from appropriate libraries in high-throughput in an automated laboratory and thus may offer advantages over conventional monoclonal antibodies. However, recombinant antibodies are typically obtained as fragments (Fab or scFv) expressed from E. coli, and it is not known whether these antibody formats are compatible with the established protocols and whether the affinities necessary for immunocapture of small linear peptides can be achieved with this technology. Hence, we performed a feasibility study to ask: (a) whether it is feasible to isolate high-affinity Fabs to small linear antigens and (b) whether it is feasible to incorporate antibody fragments into robust, quantitative immuno-MRM assays. We describe successful isolation of high-affinity Fab fragments against short (tryptic) peptides from a human combinatorial Fab library. We analytically characterize three immuno-MRM assays using recombinant Fabs, full-length IgGs constructed from these Fabs, or traditional monoclonals. We show that the antibody fragments show similar performance compared with traditional mouse- or rabbit-derived monoclonal antibodies. The data establish feasibility of isolating and incorporating high-affinity Fabs into peptide immuno-MRM assays. PMID:24568200

High-affinity recombinant antibody fragments (Fabs) can be applied in peptide enrichment immuno-MRM assays.

PubMed

Whiteaker, Jeffrey R; Zhao, Lei; Frisch, Christian; Ylera, Francisco; Harth, Stefan; Knappik, Achim; Paulovich, Amanda G

2014-04-04

High-affinity antibodies binding to linear peptides in solution are a prerequisite for performing immuno-MRM, an emerging technology for protein quantitation with high precision and specificity using peptide immunoaffinity enrichment coupled to stable isotope dilution and targeted mass spectrometry. Recombinant antibodies can be generated from appropriate libraries in high-throughput in an automated laboratory and thus may offer advantages over conventional monoclonal antibodies. However, recombinant antibodies are typically obtained as fragments (Fab or scFv) expressed from E. coli, and it is not known whether these antibody formats are compatible with the established protocols and whether the affinities necessary for immunocapture of small linear peptides can be achieved with this technology. Hence, we performed a feasibility study to ask: (a) whether it is feasible to isolate high-affinity Fabs to small linear antigens and (b) whether it is feasible to incorporate antibody fragments into robust, quantitative immuno-MRM assays. We describe successful isolation of high-affinity Fab fragments against short (tryptic) peptides from a human combinatorial Fab library. We analytically characterize three immuno-MRM assays using recombinant Fabs, full-length IgGs constructed from these Fabs, or traditional monoclonals. We show that the antibody fragments show similar performance compared with traditional mouse- or rabbit-derived monoclonal antibodies. The data establish feasibility of isolating and incorporating high-affinity Fabs into peptide immuno-MRM assays.

A guide for the laboratory information management system (LIMS) for light stable isotopes--Versions 7 and 8

USGS Publications Warehouse

Coplen, Tyler B.

2000-01-01

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program, the Laboratory Information Management System (LIMS) for Light Stable Isotopes, is presented herein. Major benefits of this system include (i) a dramatic improvement in quality assurance, (ii) an increase in laboratory efficiency, (iii) a reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) a decrease in errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for laboratories. LIMS for Light Stable Isotopes is available for both Microsoft Office 97 Professional and Microsoft Office 2000 Professional as versions 7 and 8, respectively. Both source code (mdb file) and precompiled executable files (mde) are available. Numerous improvements have been made for continuous flow isotopic analysis in this version (specifically 7.13 for Microsoft Access 97 and 8.13 for Microsoft Access 2000). It is much easier to import isotopic results from Finnigan ISODAT worksheets, even worksheets on which corrections for amount of sample (linearity corrections) have been added. The capability to determine blank corrections using isotope mass balance from analyses of elemental analyzer samples has been added. It is now possible to calculate and apply drift corrections to isotopic data based on the time of day of analysis. Whereas Finnigan ISODAT software is confined to using only a single peak for calculating delta values, LIMS now enables one to use the mean of two or more reference injections during a continuous flow analysis to calculate delta values. This is useful with Finnigan?s GasBench II online sample preparation system. Concentrations of carbon, nitrogen, and sulfur can be calculated based one or more isotopic reference materials analyzed with a group of samples. Both sample data and isotopic analysis data can now be exported to Excel files. A calculator for determining the amount of sample needed for isotopic analysis based on a previous amount of sample and continuous flow area is now an integral part of LIMS for Light Stable Isotopes. LIMS for Light Stable Isotopes can now assign an error code to Finnigan elemental analyzer analyses in which one of the electrometers has saturated due to analysis of too much sample material, giving rise to incorrect isotopic abundances. Information on downloading this report and downloading code and databases is provided at the Internet addresses: http://water.usgs.gov/software/geochemical.html or http://www.geogr.uni-jena.de/software/geochemical.html in the Eastern Hemisphere.

Identification of midgut proteins that are differentially expressed in trypanosome-susceptible and normal tsetse flies (Glossina morsitans morsitans).

PubMed

Haddow, J D; Haines, L R; Gooding, R H; Olafson, R W; Pearson, T W

2005-05-01

Molecules in the midgut of tsetse flies (Diptera: Glossinidiae) are thought to play important roles in the life cycle of African trypanosomes by influencing initial parasite establishment and subsequent differentiation events that ultimately lead to maturation of mammal-infective trypanosomes. The molecular composition of the tsetse midgut is, therefore, of critical importance to disease transmission by these medically important vectors. In this study we compared protein expression profiles of midguts of the salmon mutant and wild type Glossina morsitans morsitans Westwood that display marked differences in their susceptibility to infection by African trypanosomes. Isotope coded affinity tag (ICAT) technology was used to identify 207 proteins including 17 that were up regulated and nine that were down regulated in the salmon mutants. Several of the up regulated molecules were previously described as tsetse midgut or salivary gland proteins. Of particular interest was the up regulation in the salmon flies of tsetse midgut EP protein, a recently described molecule with lectin-like activity that was also found to be induced in tsetse by bacterial challenge. The up regulation of the EP protein in midguts of salmon mutants was confirmed by two-dimensional gel electrophoresis and tandem mass spectrometry.

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

DOEpatents

Goodman, Mark M.; Faraj, Bahjat

1999-01-01

Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

DOEpatents

Goodman, M.M.; Faraj, B.

1999-07-06

Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

Mineralogical, geochemical and isotopic characteristics of alkaline mafic igneous rocks from Punta delle Pietre Nere (Gargano, Southern Italy)

NASA Astrophysics Data System (ADS)

Mazzeo, F. C.; Arienzo, I.; Aulinas, M.; Casalini, M.; Di Renzo, V.; D'Antonio, M.

2018-05-01

The Punta delle Pietre Nere (Gargano, Southern Italy) igneous body is constituted by gabbroic and syenitic rocks with lamprophyric affinity of different age (58 and 62 Ma, respectively). The chemical composition of the minerals clearly indicates that there is no genetic relationship between the two lithotypes, in agreement with their significant age difference. The chemical (trace elements) and Sr-Nd-Pb-isotopic composition of these rocks highlights an "anorogenic" geochemical affinity derived from mixed DMM-HIMU-EM mantle reservoirs, similarly to other Paleogene-Oligocene magmatic provinces in the Circum-Mediterranean Area. In past literature, these features were interpreted as evidences for enriched asthenospheric mantle plume upwelling from deep regions beneath the Western Europe. Here we suggest that the HIMU-like composition of Punta delle Pietre Nere rocks is related to a lithospheric mantle source bearing amphibole-rich veins, resulting from crystallization of melts within the amphibole stability field in presence of H2O, as shown by several experimental works. Our results suggests partial melting at 70-90 km depth, which corresponds to the spinel-garnet transition (2.5-3.5 GPa) close to the amphibole stability limit ( 90-110 km and 2.5-3.5 GPa).

Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

PubMed

Guo, Guangyu; Li, Ning

2011-07-01

In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

A preliminary assessment on the use of biochar as a soil additive for reducing soil-to-plant uptake of cesium isotopes in radioactively contaminated environments

DOE PAGES

Hamilton, Terry F.; Martinelli, Roger E.; Kehl, Steven R.; ...

2015-10-19

A series of K d tracer batch experiments were conducted in this paper to assess the absorptive-desorption properties of Biochar as a potential agent to selectively sequester labile soil Cs or otherwise help reduce the uptake of Cs isotopes into plants. A parallel experiment was conducted for strontium. Fine-grained fractionated Woodlands tree Biochar was found to have a relatively high affinity for Cs ions (K d > 100) relative to coral soil (K d < 10) collected from the Marshall Islands. The Biochar material also contains an abundance of K (and Mg). Finally, these findings support a hypothesis that themore » addition of Biochar as a soil amendment may provide a simple yet effective method for reducing soil-to-plant transfer of Cs isotopes in contaminated environments.« less

Factors influencing the rate of non-enzymatic activation of carboxylic and amino acids by ATP

NASA Technical Reports Server (NTRS)

Mullins, D. W., Jr.; Lacey, J. C., Jr.

1981-01-01

The nonenzymatic formation of adenylate anhydrides of carboxylic and amino acids is discussed as a necessary step in the origin of the genetic code and protein biosynthesis. Results of studies are presented which have shown the rate of activation to depend on the pKa of the carboxyl group, the pH of the medium, temperature, the divalent metal ion catalyst, salt concentration, and the nature of the amino acid. In particular, it was found that of the various amino acids investigated, phenylalanine had the greatest affinity for the adenine derivatives adenosine and ATP. Results thus indicate that selective affinities between amino acids and nucleotides were important during prebiotic chemical evolution, and may have played a major role in the origin of protein synthesis and genetic coding.

Update and evaluation of decay data for spent nuclear fuel analyses

NASA Astrophysics Data System (ADS)

Simeonov, Teodosi; Wemple, Charles

2017-09-01

Studsvik's approach to spent nuclear fuel analyses combines isotopic concentrations and multi-group cross-sections, calculated by the CASMO5 or HELIOS2 lattice transport codes, with core irradiation history data from the SIMULATE5 reactor core simulator and tabulated isotopic decay data. These data sources are used and processed by the code SNF to predict spent nuclear fuel characteristics. Recent advances in the generation procedure for the SNF decay data are presented. The SNF decay data includes basic data, such as decay constants, atomic masses and nuclide transmutation chains; radiation emission spectra for photons from radioactive decay, alpha-n reactions, bremsstrahlung, and spontaneous fission, electrons and alpha particles from radioactive decay, and neutrons from radioactive decay, spontaneous fission, and alpha-n reactions; decay heat production; and electro-atomic interaction data for bremsstrahlung production. These data are compiled from fundamental (ENDF, ENSDF, TENDL) and processed (ESTAR) sources for nearly 3700 nuclides. A rigorous evaluation procedure of internal consistency checks and comparisons to measurements and benchmarks, and code-to-code verifications is performed at the individual isotope level and using integral characteristics on a fuel assembly level (e.g., decay heat, radioactivity, neutron and gamma sources). Significant challenges are presented by the scope and complexity of the data processing, a dearth of relevant detailed measurements, and reliance on theoretical models for some data.

Image authentication using distributed source coding.

PubMed

Lin, Yao-Chung; Varodayan, David; Girod, Bernd

2012-01-01

We present a novel approach using distributed source coding for image authentication. The key idea is to provide a Slepian-Wolf encoded quantized image projection as authentication data. This version can be correctly decoded with the help of an authentic image as side information. Distributed source coding provides the desired robustness against legitimate variations while detecting illegitimate modification. The decoder incorporating expectation maximization algorithms can authenticate images which have undergone contrast, brightness, and affine warping adjustments. Our authentication system also offers tampering localization by using the sum-product algorithm.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Physics of the Isotopic Dependence of Galactic Cosmic Ray Fluence Behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Saganti, Premkumar B.; Hu, Xiao-Dong; Kim, Myung-Hee Y.; Cleghorn, Timothy F.; Wilson, John W.; Tripathi, Ram K.; Zeitlin, Cary J.

2003-01-01

For over 25 years, NASA has supported the development of space radiation transport models for shielding applications. The NASA space radiation transport model now predicts dose and dose equivalent in Earth and Mars orbit to an accuracy of plus or minus 20%. However, because larger errors may occur in particle fluence predictions, there is interest in further assessments and improvements in NASA's space radiation transport model. In this paper, we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR) and the isotopic dependence of nuclear fragmentation cross-sections on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. Using NASA's quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, we study the effect of the isotopic dependence of the primary GCR composition and secondary nuclei on shielding calculations. The QMSFRG is shown to accurately describe the iso-spin dependence of nuclear fragmentation. The principal finding of this study is that large errors (plus or minus 100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotope grid (approximately 170 ions) to ones that use a reduced isotope grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (less than 20%) occur in the elemental-fluence spectra. Because a complete isotope grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.

PubMed

Lee, Tai-Sung; Hu, Yuan; Sherborne, Brad; Guo, Zhuyan; York, Darrin M

2017-07-11

We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.

Isotopic perspectives on the western Himalayan syntaxis

NASA Astrophysics Data System (ADS)

Argles, T. W.; Foster, G. L.; Whittington, A. G.; George, M. T.

2003-04-01

The western syntaxis has been characterised as a structural and metamorphic anomaly within the Himalaya, resulting from extreme Neogene exhumation and associated partial melting. However, an integration of detailed fieldwork with whole-rock isotopic data indicates that all the major tectonic units observed along the arc of the orogen also occur in the syntaxis. Most of the rocks exposed by the extreme exhumation have very different characteristics to their correlatives in the rest of the Himalayan mountain belt, because they represent very different crustal levels. The generally higher metamorphic grade of most syntaxial units obscures their affinities, while high strain throughout the syntaxis also conspires to mask the major tectonic faults that form boundaries to the units in the rest of the orogen. The Lesser Himalayan affinity of the gneissic core of the Nanga Parbat massif has been revealed previously using Nd isotopes. This study confirms the distinction between Lesser (E(Nd) = -20 to -29) and High (E(Nd) = -12 to -19) Himalayan rocks, but further subdivides those units with a High Himalayan Nd signature using Sr isotopic data. Some low-grade schists within the syntaxis have a relatively low 87Sr/86Sr ratio (<0.720) that distinguishes them from the High Himalayan rocks, and suggests they are metamorphic equivalents of the Tethyan sediments exposed in the main Himalayan orogen. The tectonic contact between the Lesser and High Himalayan units in the central Himalaya is the Main Central Thrust, a zone characterised by inverted metamorphism and high strain, but in the uniformly high-strain syntaxis this thrust is difficult to locate except by isotopic signatures. Extensive thermobarometric studies in the syntaxis, however, show two things. The first is the varying intensity of Neogene metamorphic overprint, whose strength is closely related to the degree of deformation (and rheology). The second is a zone of distinctly lower temperature mineral assemblages related to extensional (top-to-the-north) fabrics that straddles the boundary between the High Himalayan gneisses and the Tethyan metasediments. This extensional zone occupies the same structural position in the syntaxis as the South Tibetan Detachment System does in the central Himalaya.

Origin of the DUPAL anomaly in mantle xenoliths of Patagonia (Argentina) and geodynamic consequences

NASA Astrophysics Data System (ADS)

Mazzucchelli, Maurizio; Cipriani, Anna; Hémond, Christophe; Zanetti, Alberto; Bertotto, Gustavo Walter; Cingolani, Carlos Alberto

2016-04-01

The sub-continental lithospheric mantle of South America has been known for some time to carry the DUPAL isotope anomaly as seen in volcanics from the Paraná volcanic province. However, this has not allowed discriminating whether the DUPAL anomaly is a primary feature of the mantle source or acquired during the upwelling and emplacement of the primary magmas. We discovered mantle xenoliths from the Tres Lagos location in Patagonia that carry evidence of percolation by metasomatic melts that imparted the DUPAL isotope anomaly signature. We discuss a model that requires four isotope components (LCC, EM2, HIMU and DM) to account for the Sr, Nd and Pb isotope variability of our samples. We propose that upwelling of hot astenosphere during the Miocene could have triggered the melting of the LCC and EM2 components carrying the DUPAL anomaly, previously entrained in the subcontinental mantle by subduction. These ascending melts would have then metasomatised the local SCLM characterised by DMM and HIMU geochemical affinity generating the hybrid DUPAL-bearing mantle sampled by the Tres Lagos xenoliths.

Carbon isotopic composition of individual Precambrian microfossils

NASA Technical Reports Server (NTRS)

House, C. H.; Schopf, J. W.; McKeegan, K. D.; Coath, C. D.; Harrison, T. M.; Stetter, K. O.

2000-01-01

Ion microprobe measurements of carbon isotope ratios were made in 30 specimens representing six fossil genera of microorganisms petrified in stromatolitic chert from the approximately 850 Ma Bitter Springs Formation, Australia, and the approximately 2100 Ma Gunflint Formation, Canada. The delta 13C(PDB) values from individual microfossils of the Bitter Springs Formation ranged from -21.3 +/- 1.7% to -31.9 +/- 1.2% and the delta 13C(PDB) values from microfossils of the Gunflint Formation ranged from -32.4 +/- 0.7% to -45.4 +/- 1.2%. With the exception of two highly 13C-depleted Gunflint microfossils, the results generally yield values consistent with carbon fixation via either the Calvin cycle or the acetyl-CoA pathway. However, the isotopic results are not consistent with the degree of fractionation expected from either the 3-hydroxypropionate cycle or the reductive tricarboxylic acid cycle, suggesting that the microfossils studied did not use either of these pathways for carbon fixation. The morphologies of the microfossils suggest an affinity to the cyanobacteria, and our carbon isotopic data are consistent with this assignment.

Tracking the rise of eukaryotes to ecological dominance with zinc isotopes.

PubMed

Isson, Terry T; Love, Gordon D; Dupont, Christopher L; Reinhard, Christopher T; Zumberge, Alex J; Asael, Dan; Gueguen, Bleuenn; McCrow, John; Gill, Ben C; Owens, Jeremy; Rainbird, Robert H; Rooney, Alan D; Zhao, Ming-Yu; Stueeken, Eva E; Konhauser, Kurt O; John, Seth G; Lyons, Timothy W; Planavsky, Noah J

2018-06-05

The biogeochemical cycling of zinc (Zn) is intimately coupled with organic carbon in the ocean. Based on an extensive new sedimentary Zn isotope record across Earth's history, we provide evidence for a fundamental shift in the marine Zn cycle ~800 million years ago. We discuss a wide range of potential drivers for this transition and propose that, within available constraints, a restructuring of marine ecosystems is the most parsimonious explanation for this shift. Using a global isotope mass balance approach, we show that a change in the organic Zn/C ratio is required to account for observed Zn isotope trends through time. Given the higher affinity of eukaryotes for Zn relative to prokaryotes, we suggest that a shift toward a more eukaryote-rich ecosystem could have provided a means of more efficiently sequestering organic-derived Zn. Despite the much earlier appearance of eukaryotes in the microfossil record (~1700 to 1600 million years ago), our data suggest a delayed rise to ecological prominence during the Neoproterozoic, consistent with the currently accepted organic biomarker records. © 2018 John Wiley & Sons Ltd.

Automated determination of the stable carbon isotopic composition (δ13C) of total dissolved inorganic carbon (DIC) and total nonpurgeable dissolved organic carbon (DOC) in aqueous samples: RSIL lab codes 1851 and 1852

USGS Publications Warehouse

Révész, Kinga M.; Doctor, Daniel H.

2014-01-01

The purposes of the Reston Stable Isotope Laboratory (RSIL) lab codes 1851 and 1852 are to determine the total carbon mass and the ratio of the stable isotopes of carbon (δ13C) for total dissolved inorganic carbon (DIC, lab code 1851) and total nonpurgeable dissolved organic carbon (DOC, lab code 1852) in aqueous samples. The analysis procedure is automated according to a method that utilizes a total carbon analyzer as a peripheral sample preparation device for analysis of carbon dioxide (CO2) gas by a continuous-flow isotope ratio mass spectrometer (CF-IRMS). The carbon analyzer produces CO2 and determines the carbon mass in parts per million (ppm) of DIC and DOC in each sample separately, and the CF-IRMS determines the carbon isotope ratio of the produced CO2. This configuration provides a fully automated analysis of total carbon mass and δ13C with no operator intervention, additional sample preparation, or other manual analysis. To determine the DIC, the carbon analyzer transfers a specified sample volume to a heated (70 °C) reaction vessel with a preprogrammed volume of 10% phosphoric acid (H3PO4), which allows the carbonate and bicarbonate species in the sample to dissociate to CO2. The CO2 from the reacted sample is subsequently purged with a flow of helium gas that sweeps the CO2 through an infrared CO2 detector and quantifies the CO2. The CO2 is then carried through a high-temperature (650 °C) scrubber reactor, a series of water traps, and ultimately to the inlet of the mass spectrometer. For the analysis of total dissolved organic carbon, the carbon analyzer performs a second step on the sample in the heated reaction vessel during which a preprogrammed volume of sodium persulfate (Na2S2O8) is added, and the hydroxyl radicals oxidize the organics to CO2. Samples containing 2 ppm to 30,000 ppm of carbon are analyzed. The precision of the carbon isotope analysis is within 0.3 per mill for DIC, and within 0.5 per mill for DOC.

Affinity-aware checkpoint restart

DOE PAGES

Saini, Ajay; Rezaei, Arash; Mueller, Frank; ...

2014-12-08

Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core mapsmore » and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.« less

Affinity-aware checkpoint restart

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saini, Ajay; Rezaei, Arash; Mueller, Frank

Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core mapsmore » and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.« less

Automatic Data Traffic Control on DSM Architecture

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Jin, Hao-Qiang; Yan, Jerry; Kwak, Dochan (Technical Monitor)

2000-01-01

We study data traffic on distributed shared memory machines and conclude that data placement and grouping improve performance of scientific codes. We present several methods which user can employ to improve data traffic in his code. We report on implementation of a tool which detects the code fragments causing data congestions and advises user on improvements of data routing in these fragments. The capabilities of the tool include deduction of data alignment and affinity from the source code; detection of the code constructs having abnormally high cache or TLB misses; generation of data placement constructs. We demonstrate the capabilities of the tool on experiments with NAS parallel benchmarks and with a simple computational fluid dynamics application ARC3D.

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2018-01-15

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in parallel tiled code implementing Nussinov's RNA folding. Experimental results, received on modern Intel multi-core processors, demonstrate that this code outperforms known closely related implementations when the length of RNA strands is bigger than 2500.

Re-evaluation of Spent Nuclear Fuel Assay Data for the Three Mile Island Unit 1 Reactor and Application to Code Validation

DOE PAGES

Gauld, Ian C.; Giaquinto, J. M.; Delashmitt, J. S.; ...

2016-01-01

Destructive radiochemical assay measurements of spent nuclear fuel rod segments from an assembly irradiated in the Three Mile Island unit 1 (TMI-1) pressurized water reactor have been performed at Oak Ridge National Laboratory (ORNL). Assay data are reported for five samples from two fuel rods of the same assembly. The TMI-1 assembly was a 15 X 15 design with an initial enrichment of 4.013 wt% 235U, and the measured samples achieved burnups between 45.5 and 54.5 gigawatt days per metric ton of initial uranium (GWd/t). Measurements were performed mainly using inductively coupled plasma mass spectrometry after elemental separation via highmore » performance liquid chromatography. High precision measurements were achieved using isotope dilution techniques for many of the lanthanides, uranium, and plutonium isotopes. Measurements are reported for more than 50 different isotopes and 16 elements. One of the two TMI-1 fuel rods measured in this work had been measured previously by Argonne National Laboratory (ANL), and these data have been widely used to support code and nuclear data validation. Recently, ORNL provided an important opportunity to independently cross check results against previous measurements performed at ANL. The measured nuclide concentrations are used to validate burnup calculations using the SCALE nuclear systems modeling and simulation code suite. These results show that the new measurements provide reliable benchmark data for computer code validation.« less

Determination of the delta(2H/1H)of Water: RSIL Lab Code 1574

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler B.

2008-01-01

Reston Stable Isotope Laboratory (RSIL) lab code 1574 describes a method used to determine the relative hydrogen isotope-ratio delta(2H,1H), abbreviated hereafter as d2H of water. The d2H measurement of water also is a component of the National Water Quality Laboratory (NWQL) schedules 1142 and 1172. The water is collected unfiltered in a 60-mL glass bottle and capped with a Polyseal cap. In the laboratory, the water sample is equilibrated with gaseous hydrogen using a platinum catalyst (Horita, 1988; Horita and others, 1989; Coplen and others, 1991). The reaction for the exchange of one hydrogen atom is shown in equation 1.

Evidence of isotopic fractionation of natural uranium in cultured human cells

NASA Astrophysics Data System (ADS)

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

Evidence of isotopic fractionation of natural uranium in cultured human cells

PubMed Central

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-01-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes. PMID:27872304

Evidence of isotopic fractionation of natural uranium in cultured human cells.

PubMed

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-06

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235 U isotope with regard to 238 U. Efforts were made to develop and then validate a procedure for highly accurate n( 238 U)/n( 235 U) determinations in microsamples of cells. We found that intracellular U is enriched in 235 U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO 2 2+ ) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, Terry F.; Martinelli, Roger E.; Kehl, Steven R.

A series of K d tracer batch experiments were conducted in this paper to assess the absorptive-desorption properties of Biochar as a potential agent to selectively sequester labile soil Cs or otherwise help reduce the uptake of Cs isotopes into plants. A parallel experiment was conducted for strontium. Fine-grained fractionated Woodlands tree Biochar was found to have a relatively high affinity for Cs ions (K d > 100) relative to coral soil (K d < 10) collected from the Marshall Islands. The Biochar material also contains an abundance of K (and Mg). Finally, these findings support a hypothesis that themore » addition of Biochar as a soil amendment may provide a simple yet effective method for reducing soil-to-plant transfer of Cs isotopes in contaminated environments.« less

Northwest Africa 8159: An approximately 2.3 Billion Year Old Martian Olivine-Bearing Augite Basalt

NASA Technical Reports Server (NTRS)

Simon, J. I.; Peters, T. J.; Tappa, M. J.; Agee, C. B.

2014-01-01

Based on petrology, mineralogy, and bulk composition, the new NWA 8159 martian meteorite is distinct from all known samples from Mars. In particular, the augite compositional trends are unique, but most similar to those of nakhite intercumulus. Whether NWA 8159 represents a new lithology or is related to a known meteorite group remains to be determined. Sr and Nd isotopic analyses will allow comparison of source characteristics with SNC and other new ungrouped meteorites (e.g., NWA 7635). Here we report initial Rb-Sr and Sm-Nd isotopic results for NWA 8159 with the objective to determine its formation age and to potentially identify similarities and potential source affinities with other martian rocks.

Le complexe annulaire d'âge Oligocène de l'Achkal (hoggar Central, Sud Algérie) : témoin de la transition au Cénozoïque entre les magmatismes tholéitique et alcalin. Évidences par les isotopes du Sr, Nd et Pb

NASA Astrophysics Data System (ADS)

Maza, Mustapha; Briqueu, Louis; Dautria, Jean-Marie; Bosch, Delphine

1998-08-01

The Achkal Oligocene ring complex cross-cuts the Upper Eocene tholeiitic traps located on the top of the Hoggar swell. The plutonic rocks range from tholeiitic gabbros to alkali essexites, monzonites and syenites, whereas the volcanites are restricted to late peralkaline rhyolites. The affinity change linked to the large isotopic heterogeneities (from EM1 to HIMU) suggests that the parental magmas are issued from two distinct mantle sources, first lithospheric then deeper. The Achkal has recorded the magmatic evolution of the Hoggar hot spot, between Eocene and Miocene.

h5-HT1B receptor-mediated constitutive Gαi3-protein activation in stably transfected Chinese hamster ovary cells: an antibody capture assay reveals protean efficacy of 5-HT

PubMed Central

Newman-Tancredi, Adrian; Cussac, Didier; Marini, Laetitia; Touzard, Manuelle; Millan, Mark J

2003-01-01

Serotonin 5-HT1B receptors couple to G-proteins of the Gi/o family. However, their activation of specific G-protein subtypes is poorly characterised. Using an innovative antibody capture/guanosine-5′-0-(3-[35S]thio)-triphosphate ([35S]GTPγS) binding strategy, we characterised Gαi3 subunit activation by h5-HT1B receptors stably expressed in Chinese hamster ovary (CHO) cells. The agonists, 5-HT, alniditan and BMS181,101, stimulated Gαi3, whereas methiothepin and SB224,289 behaved as inverse agonists. The selective 5-HT1B receptor ligand, S18127, modestly stimulated Gαi3 and reversed the actions of both 5-HT and methiothepin. S18127 (1 μM) also produced parallel, dextral shifts of the 5-HT and methiothepin isotherms. Isotopic dilution experiments ([35S]GTPγS versus GTPγS) revealed high-affinity [35S]GTPγS binding to Gαi3 subunits in the absence of receptor ligands indicating constitutive activity. High-affinity [35S]GTPγS binding was increased 2.8-fold by 5-HT with an increase in the affinity of GTPγS for Gαi3 subunits. In contrast, methiothepin halved the number of high-affinity binding sites and decreased their affinity. h5-HT1B receptor-mediated Gαi3 subunit activation was dependent on the concentration of NaCl. At 300 mM, 5-HT stimulated [35S]GTPγS binding, basal Gαi3 activation was low and methiothepin was inactive. In contrast, at 10 mM NaCl, basal activity was enhanced and the inverse agonist activity of methiothepin was accentuated. Under these conditions, 5-HT decreased Gαi3 activation. In conclusion, at h5-HT1B receptors expressed in CHO cells: (i) inverse agonist induced inhibition of Gαi3, and its reversal by S18127, reveals constitutive activation of this Gα subunit; (ii) constitutive Gαi3 activation can be quantified by isotopic dilution [35S]GTPγS binding and (iii) decreasing NaCl concentrations enhances Gαi3 activation and leads to protean agonist properties of 5-HT: that is a switch to inhibition of Gαi3. PMID:12684263

h5-HT(1B) receptor-mediated constitutive Galphai3-protein activation in stably transfected Chinese hamster ovary cells: an antibody capture assay reveals protean efficacy of 5-HT.

PubMed

Newman-Tancredi, Adrian; Cussac, Didier; Marini, Laetitia; Touzard, Manuelle; Millan, Mark J

2003-03-01

1. Serotonin 5-HT(1B) receptors couple to G-proteins of the Gi/o family. However, their activation of specific G-protein subtypes is poorly characterised. Using an innovative antibody capture/guanosine-5'-0-(3-[(35)S]thio)-triphosphate ([(35)S]GTPgammaS) binding strategy, we characterised Galpha(i3) subunit activation by h5-HT(1B) receptors stably expressed in Chinese hamster ovary (CHO) cells. 2. The agonists, 5-HT, alniditan and BMS181,101, stimulated Galpha(i3), whereas methiothepin and SB224,289 behaved as inverse agonists. The selective 5-HT(1B) receptor ligand, S18127, modestly stimulated Galpha(i3) and reversed the actions of both 5-HT and methiothepin. S18127 (1 micro M) also produced parallel, dextral shifts of the 5-HT and methiothepin isotherms. 3. Isotopic dilution experiments ([(35)S]GTPgammaS versus GTPgammaS) revealed high-affinity [(35)S]GTPgammaS binding to Galpha(i3) subunits in the absence of receptor ligands indicating constitutive activity. High-affinity [(35)S]GTPgammaS binding was increased 2.8-fold by 5-HT with an increase in the affinity of GTPgammaS for Galpha(i3) subunits. In contrast, methiothepin halved the number of high-affinity binding sites and decreased their affinity. 4. h5-HT(1B) receptor-mediated Galpha(i3) subunit activation was dependent on the concentration of NaCl. At 300 mM, 5-HT stimulated [(35)S]GTPgammaS binding, basal Galpha(i3) activation was low and methiothepin was inactive. In contrast, at 10 mM NaCl, basal activity was enhanced and the inverse agonist activity of methiothepin was accentuated. Under these conditions, 5-HT decreased Galpha(i3) activation. 5. In conclusion, at h5-HT(1B) receptors expressed in CHO cells: (i) inverse agonist induced inhibition of Galpha(i3), and its reversal by S18127, reveals constitutive activation of this Galpha subunit; (ii) constitutive Galpha(i3) activation can be quantified by isotopic dilution [(35)S]GTPgammaS binding and (iii) decreasing NaCl concentrations enhances Galpha(i3) activation and leads to protean agonist properties of 5-HT: that is a switch to inhibition of Galpha(i3).

NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans*

PubMed Central

Rhoads, Timothy W.; Prasad, Aman; Kwiecien, Nicholas W.; Merrill, Anna E.; Zawack, Kelson; Westphall, Michael S.; Schroeder, Frank C.; Kimble, Judith; Coon, Joshua J.

2015-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress. PMID:26392051

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV

NASA Astrophysics Data System (ADS)

Duchemin, C.; Guertin, A.; Haddad, F.; Michel, N.; Métivier, V.

2015-02-01

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV.

PubMed

Duchemin, C; Guertin, A; Haddad, F; Michel, N; Métivier, V

2015-02-07

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

The optimal code searching method with an improved criterion of coded exposure for remote sensing image restoration

NASA Astrophysics Data System (ADS)

He, Lirong; Cui, Guangmang; Feng, Huajun; Xu, Zhihai; Li, Qi; Chen, Yueting

2015-03-01

Coded exposure photography makes the motion de-blurring a well-posed problem. The integration pattern of light is modulated using the method of coded exposure by opening and closing the shutter within the exposure time, changing the traditional shutter frequency spectrum into a wider frequency band in order to preserve more image information in frequency domain. The searching method of optimal code is significant for coded exposure. In this paper, an improved criterion of the optimal code searching is proposed by analyzing relationship between code length and the number of ones in the code, considering the noise effect on code selection with the affine noise model. Then the optimal code is obtained utilizing the method of genetic searching algorithm based on the proposed selection criterion. Experimental results show that the time consuming of searching optimal code decreases with the presented method. The restoration image is obtained with better subjective experience and superior objective evaluation values.

Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RAχFC): A Visual Basic computer code for calculating trace element and isotope variations of open-system magmatic systems

NASA Astrophysics Data System (ADS)

Bohrson, Wendy A.; Spera, Frank J.

2007-11-01

Volcanic and plutonic rocks provide abundant evidence for complex processes that occur in magma storage and transport systems. The fingerprint of these processes, which include fractional crystallization, assimilation, and magma recharge, is captured in petrologic and geochemical characteristics of suites of cogenetic rocks. Quantitatively evaluating the relative contributions of each process requires integration of mass, species, and energy constraints, applied in a self-consistent way. The energy-constrained model Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RaχFC) tracks the trace element and isotopic evolution of a magmatic system (melt + solids) undergoing simultaneous fractional crystallization, recharge, and assimilation. Mass, thermal, and compositional (trace element and isotope) output is provided for melt in the magma body, cumulates, enclaves, and anatectic (i.e., country rock) melt. Theory of the EC computational method has been presented by Spera and Bohrson (2001, 2002, 2004), and applications to natural systems have been elucidated by Bohrson and Spera (2001, 2003) and Fowler et al. (2004). The purpose of this contribution is to make the final version of the EC-RAχFC computer code available and to provide instructions for code implementation, description of input and output parameters, and estimates of typical values for some input parameters. A brief discussion highlights measures by which the user may evaluate the quality of the output and also provides some guidelines for implementing nonlinear productivity functions. The EC-RAχFC computer code is written in Visual Basic, the programming language of Excel. The code therefore launches in Excel and is compatible with both PC and MAC platforms. The code is available on the authors' Web sites http://magma.geol.ucsb.edu/and http://www.geology.cwu.edu/ecrafc) as well as in the auxiliary material.

Geochemical and oxygen isotope perspective of a new R chondrite Dhofar 1671: Affinity with ordinary chondrites

NASA Astrophysics Data System (ADS)

Ali, Arshad; Nasir, Sobhi J.; Jabeen, Iffat; Al Rawas, Ahmed; Banerjee, Neil R.; Osinski, Gordon R.

2017-09-01

Dhofar 1671 is a relatively new meteorite that previous studies suggest belongs to the Rumuruti chondrite class. Major and REE compositions are generally in agreement with average values of the R chondrites (RCs). Moderately volatile elements such as Se and Zn abundances are lower than the R chondrite values that are similar to those in ordinary chondrites (OCs). Porphyritic olivine pyroxene (POP), radial pyroxene (RP), and barred olivine (BO) chondrules are embedded in a proportionately equal volume of matrix, one of the characteristic features of RCs. Microprobe analyses demonstrate compositional zoning in chondrule and matrix olivines showing Fa-poor interior and Fa-rich outer zones. Precise oxygen isotope data for chondrules and matrix obtained by laser-assisted fluorination show a genetic isotopic relationship between OCs and RCs. On the basis of our data, we propose a strong affinity between these groups and suggest that OC chondrule precursors could have interacted with a 17O-rich matrix to form RC chondrules (i.e., ∆17O shifts from 1‰ to 3‰). These interactions could have occurred at the same time as "exotic" clasts in brecciated samples formed such as NWA 10214 (LL3-6), Parnallee (LL3), PCA91241 (R3.8-6), and Dhofar 1671 (R3.6). We also infer that the source of the oxidation and 17O enrichment is the matrix, which may have been enriched in 17O-rich water. The abundance of matrix in RCs relative to OCs, ensured that these rocks would be apparently more oxidized and appreciably 17O-enriched. In situ analysis of Dhofar 1671 is recommended to further strengthen the link between OCs and RCs.

Multiplexed Affinity-Based Separation of Proteins and Cells Using Inertial Microfluidics.

PubMed

Sarkar, Aniruddh; Hou, Han Wei; Mahan, Alison E; Han, Jongyoon; Alter, Galit

2016-03-30

Isolation of low abundance proteins or rare cells from complex mixtures, such as blood, is required for many diagnostic, therapeutic and research applications. Current affinity-based protein or cell separation methods use binary 'bind-elute' separations and are inefficient when applied to the isolation of multiple low-abundance proteins or cell types. We present a method for rapid and multiplexed, yet inexpensive, affinity-based isolation of both proteins and cells, using a size-coded mixture of multiple affinity-capture microbeads and an inertial microfluidic particle sorter device. In a single binding step, different targets-cells or proteins-bind to beads of different sizes, which are then sorted by flowing them through a spiral microfluidic channel. This technique performs continuous-flow, high throughput affinity-separation of milligram-scale protein samples or millions of cells in minutes after binding. We demonstrate the simultaneous isolation of multiple antibodies from serum and multiple cell types from peripheral blood mononuclear cells or whole blood. We use the technique to isolate low abundance antibodies specific to different HIV antigens and rare HIV-specific cells from blood obtained from HIV+ patients.

PolyCheck: Dynamic Verification of Iteration Space Transformations on Affine Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Wenlei; Krishnamoorthy, Sriram; Pouchet, Louis-noel

2016-01-11

High-level compiler transformations, especially loop transformations, are widely recognized as critical optimizations to restructure programs to improve data locality and expose parallelism. Guaranteeing the correctness of program transformations is essential, and to date three main approaches have been developed: proof of equivalence of affine programs, matching the execution traces of programs, and checking bit-by-bit equivalence of the outputs of the programs. Each technique suffers from limitations in either the kind of transformations supported, space complexity, or the sensitivity to the testing dataset. In this paper, we take a novel approach addressing all three limitations to provide an automatic bug checkermore » to verify any iteration reordering transformations on affine programs, including non-affine transformations, with space consumption proportional to the original program data, and robust to arbitrary datasets of a given size. We achieve this by exploiting the structure of affine program control- and data-flow to generate at compile-time lightweight checker code to be executed within the transformed program. Experimental results assess the correctness and effectiveness of our method, and its increased coverage over previous approaches.« less

Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative ProteomicsW⃞

PubMed Central

Majeran, Wojciech; Cai, Yang; Sun, Qi; van Wijk, Klaas J.

2005-01-01

Chloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway. PMID:16243905

Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

PubMed

Pesavento, James J; Bullock, Courtney R; LeDuc, Richard D; Mizzen, Craig A; Kelleher, Neil L

2008-05-30

Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10(4) using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.

An Isotopic Exchange Kinetic Model to Assess the Speciation of Metal Available Pool in Soil: The Case of Nickel.

PubMed

Zelano, I O; Sivry, Y; Quantin, C; Gélabert, A; Maury, A; Phalyvong, K; Benedetti, M F

2016-12-06

In this study an innovative approach is proposed to predict the relative contribution of each mineral phase to the total metal availability in soils, which, in other words, could be called the available metal fractionation. Through the use of isotopic exchange kinetics (IEK) performed on typical Ni bearing phases (i.e., two types of serpentines, chlorite, smectite, goethite, and hematite) the isotopic exchange and metal-solid interaction processes are connected, considering both the thermodynamic and kinetic aspects. Results of Ni IEK experiments on mineral phases are fitted with a pseudo-first order kinetic model. For each Ni bearing phase, this allows to (i) determine the number and size of exchangeable pools (E Ni(i) ), (ii) assess their corresponding kinetic constants (k (i) ), and (iii) discuss the mechanism of Ni isotopic exchange at mineral surfaces. It is shown that all the phases investigated, with the only exception of hematite, present at least two distinct reactive pools with significantly different k (i) values. Results suggest also that metal involved in outer-sphere complexes would display isotopic exchange between 100 and 1000 times faster than metal involved in inner-sphere complexes, and that the presence of high and low affinity sites may influence the rate of isotopic exchange up to 1 order of magnitude. Moreover, the method developed represents a tool to predict and estimate Ni mobility and availability in natural soil samples on the basis of soil mineral composition, providing information barely obtained with other techniques.

Petrogenesis and tectonic implications of Triassic mafic complexes with MORB/OIB affinities from the western Garzê-Litang ophiolitic mélange, central Tibetan Plateau

NASA Astrophysics Data System (ADS)

Liu, Bin; Ma, Chang-Qian; Guo, Yu-Heng; Xiong, Fu-Hao; Guo, Pan; Zhang, Xin

2016-09-01

Although numerous Paleo-Tethyan ophiolites with mid-oceanic ridge basalts (MORB) and/or oceanic-island basalt (OIB) affinities have been reported in the central Tibetan Plateau (CTP), the origin and tectonic nature of these ophiolites are not well understood. The petrogenesis, mantle sources and geodynamic setting of the mafic rocks from these ophiolites are unclear, which is the main reason for this uncertainty. In this paper, we present new geochronological, mineralogical and Sr-Nd isotopic data for the Chayong and Xiewu mafic complexes in the western Garzê-Litang suture zone (GLS), a typical Paleo-Tethyan suture crossing the CTP. Zircon LA-ICP-MS U-Pb ages of 234 ± 3 Ma and 236 ± 2 Ma can be interpreted as formation times of the Chayong and Xiewu mafic complexes, respectively. The basalts and gabbros of the Chayong complex exhibit enriched MORB (E-MORB) compositional affinities except for a weak depletion of Nb, Ta and Ti relative to the primitive mantle, whereas the basalts and gabbros of the Xiewu complex display distinct E-MORB and OIB affinities. The geochemical features suggest a probable fractionation of olivine ± clinopyroxene ± plagioclase as well as insignificant crustal contamination. The geochemical and Sr-Nd isotopic data reveal that the Chayong mafic rocks may have been derived from depleted MORB-type mantle metasomatized by crustal components and Xiewu mafic rocks from enriched lithospheric mantle metasomatized by OIB-like components. The ratios of Zn/Fet, La/Yb and Sm/Yb indicate that these mafic melts were produced by the partial melting of garnet + minor spinel-bearing peridotite or spinel ± minor garnet-bearing peridotite. We propose that back-arc basin spreading associated with OIB/seamount recycling had occurred in the western GLS at least since the Middle Triassic times, and the decompression melting of the depleted MORB-type asthenosphere mantle and partial melting of sub-continental lithosphere were metasomatized by plume-related melts, such as OIB s, which led to the generation of the Chayong and Xiewu mafic melts.

Evaluation of a metalloporphyrin (THPPMnCl) for necrosis-affinity in rat models of necrosis.

PubMed

Li, Yue; Liu, Xuejiao; Zhang, Dongjian; Lou, Bin; Peng, Fei; Wang, Xiaoning; Shan, Xin; Jiang, Cuihua; Gao, Meng; Sun, Ziping; Ni, Yicheng; Huang, Dejian; Zhang, Jian

2015-12-01

The combination of an (13I)I-labeled necrosis-targeting agent (NTA) with a vascular disrupting agent is a novel and potentially powerful technique for tumor necrosis treatment (TNT). The purpose of this study was to evaluate a NTA candidate, THPPMnCl, using (131)I isotope for tracing its biodistribution and necrosis affinity. (131)I-THPPMnCl was intravenously injected in rat models with liver, muscle, and tumor necrosis and myocardial infarction (MI), followed by investigations with macroscopic autoradiography, triphenyltetrazolium chloride (TTC) histochemical staining, fluorescence microscopy and H&E stained histology for up to 9 days. (131)I-THPPMnCl displayed a long-term affinity for all types of necrosis and accumulation in the mononuclear phagocytic system especially in the liver. Autoradiograms and TTC staining showed a good targetability of (131)I-THPPMnCl for MI. These findings indicate the potential of THPPMnCl for non-invasive imaging assessment of necrosis, such as in MI. However, (13I)I-THPPMnCl is unlikely suitable for TNT due to its long-term retention in normal tissues.

Photolabeling of Tonoplast from Sugar Beet Cell Suspensions by [3H]5-(N-Methyl-N-Isobutyl)-Amiloride, an Inhibitor of the Vacuolar Na+/H+ Antiport 1

PubMed Central

Barkla, Bronwyn J.; Charuk, Jeffrey H. M.; Cragoe, Edward J.; Blumwald, Eduardo

1990-01-01

The effects of 5-(N-methyl-N-isobutyl)-amiloride (MIA), an amiloride analog, was tested on the Na+/H+ antiport activity of intact vacuoles and tonoplast vesicles isolated from sugar beet (Beta vulgaris L.) cell suspension cultures. MIA inhibited Na+/H+ exchange in a competitive manner with a Ki of 2.5 and 5.9 micromolar for ΔpH-dependent 22Na+ influx in tonoplast vesicles and Na+-dependent H+ efflux in intact vacuoles, respectively. Scatchard analysis of the binding of [3H]MIA to tonoplast membranes revealed a high affinity binding component with a Kd of 1.3 micromolar. The close relationship between the dissociation constant value obtained and the constants of inhibition for MIA obtained by fluorescence quenching and isotope exchange suggests that the high affinity component represents a class of sites associated with the tonoplast Na+/H+ antiport. Photolabeling of the tonoplast with [3H]MIA revealed two sets of polypeptides with a different affinity to amiloride and its analog. Images Figure 7 PMID:16667602

Photolabeling of tonoplast from sugar beet cell suspensions by [h]5-(N-methyl-N-isobutyl)-amiloride, an inhibitor of the vacuolar na/h antiport.

PubMed

Barkla, B J; Charuk, J H; Cragoe, E J; Blumwald, E

1990-07-01

The effects of 5-(N-methyl-N-isobutyl)-amiloride (MIA), an amiloride analog, was tested on the Na(+)/H(+) antiport activity of intact vacuoles and tonoplast vesicles isolated from sugar beet (Beta vulgaris L.) cell suspension cultures. MIA inhibited Na(+)/H(+) exchange in a competitive manner with a K(i) of 2.5 and 5.9 micromolar for DeltapH-dependent (22)Na(+) influx in tonoplast vesicles and Na(+)-dependent H(+) efflux in intact vacuoles, respectively. Scatchard analysis of the binding of [(3)H]MIA to tonoplast membranes revealed a high affinity binding component with a K(d) of 1.3 micromolar. The close relationship between the dissociation constant value obtained and the constants of inhibition for MIA obtained by fluorescence quenching and isotope exchange suggests that the high affinity component represents a class of sites associated with the tonoplast Na(+)/H(+) antiport. Photolabeling of the tonoplast with [(3)H]MIA revealed two sets of polypeptides with a different affinity to amiloride and its analog.

Measurement of radon and xenon binding to a cryptophane molecular host

PubMed Central

Jacobson, David R.; Khan, Najat S.; Collé, Ronald; Fitzgerald, Ryan; Laureano-Pérez, Lizbeth; Bai, Yubin; Dmochowski, Ivan J.

2011-01-01

Xenon and radon have many similar properties, a difference being that all 35 isotopes of radon (195Rn–229Rn) are radioactive. Radon is a pervasive indoor air pollutant believed to cause significant incidence of lung cancer in many geographic regions, yet radon affinity for a discrete molecular species has never been determined. By comparison, the chemistry of xenon has been widely studied and applied in science and technology. Here, both noble gases were found to bind with exceptional affinity to tris-(triazole ethylamine) cryptophane, a previously unsynthesized water-soluble organic host molecule. The cryptophane–xenon association constant, Ka = 42,000 ± 2,000 M-1 at 293 K, was determined by isothermal titration calorimetry. This value represents the highest measured xenon affinity for a host molecule. The partitioning of radon between air and aqueous cryptophane solutions of varying concentration was determined radiometrically to give the cryptophane–radon association constant Ka = 49,000 ± 12,000 M-1 at 293 K. PMID:21690357

Isotopic anomalies from neutron reactions during explosive carbon burning

NASA Technical Reports Server (NTRS)

Lee, T.; Schramm, D. N.; Wefel, J. P.; Blake, J. B.

1978-01-01

The possibility that the newly discovered correlated isotopic anomalies for heavy elements in the Allende meteorite were synthesized in the secondary neutron capture episode during the explosive carbon burning, the possible source of the O-16 and Al-26 anomalies, is examined. Explosive carbon burning calculations under typical conditions were first performed to generate time profiles of temperature, density, and free particle concentrations. These quantities were inputted into a general neutron capture code which calculates the resulting isotopic pattern from exposing the preexisting heavy seed nuclei to these free particles during the explosive carbon burning conditions. The interpretation avoids the problem of the Sr isotopic data and may resolve the conflict between the time scales inferred from 1-129, Pu-244, and Al-26.

Energy spectra and E2 transition rates of 124—130Ba

NASA Astrophysics Data System (ADS)

Sabri, H.; Seidi, M.

2016-10-01

In this paper, we have studied the energy spectra and B(E2) values of 124—130Ba isotopes in the shape phase transition region between the spherical and gamma unstable deformed shapes. We have used a transitional interacting Boson model (IBM), Hamiltonian which is based on affine SU(1,1) Lie algebra in the both IBM-1 and 2 versions and also the Catastrophe theory in combination with a coherent state formalism to generate energy surfaces and determine the exact values of control parameters. Our results for control parameters suggest a combination of U(5) and SO(6) dynamical symmetries in this isotopic chain. Also, the theoretical predictions can be rather well reproduce the experimental counterparts, when the control parameter is approached to the SO(6) limit.

ICT: isotope correction toolbox.

PubMed

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Glycan reductive isotope labeling for quantitative glycomics.

PubMed

Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

2009-04-15

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

GLYCAN REDUCTIVE ISOTOPE LABELING (GRIL) FOR QUANTITATIVE GLYCOMICS

PubMed Central

Xia, Baoyun; Feasley, Christa L.; Sachdev, Goverdhan P.; Smith, David F.; Cummings, Richard D.

2009-01-01

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed Glycan Reductive Isotope Labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [12C6]-aniline and [13C6]-aniline. These dual-labeled aniline-tagged glycans can be recovered by reversed-phase chromatography and quantified based on UV-absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins using this method. This technique allows for linear, relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of Glycomics. PMID:19454239

Specific DNA binding of the two chicken Deformed family homeodomain proteins, Chox-1.4 and Chox-a.

PubMed Central

Sasaki, H; Yokoyama, E; Kuroiwa, A

1990-01-01

The cDNA clones encoding two chicken Deformed (Dfd) family homeobox containing genes Chox-1.4 and Chox-a were isolated. Comparison of their amino acid sequences with another chicken Dfd family homeodomain protein and with those of mouse homologues revealed that strong homologies are located in the amino terminal regions and around the homeodomains. Although homologies in other regions were relatively low, some short conserved sequences were also identified. E. coli-made full length proteins were purified and used for the production of specific antibodies and for DNA binding studies. The binding profiles of these proteins to the 5'-leader and 5'-upstream sequences of Chox-1.4 and Chox-a coding regions were analyzed by immunoprecipitation and DNase I footprint assays. These two Chox proteins bound to the same sites in the 5'-flanking sequences of their coding regions with various affinities and their binding affinities to each site were nearly the same. The consensus sequences of the high and low affinity binding sites were TAATGA(C/G) and CTAATTTT, respectively. A clustered binding site was identified in the 5'-upstream of the Chox-a gene, suggesting that this clustered binding site works as a cis-regulatory element for auto- and/or cross-regulation of Chox-a gene expression. Images PMID:1970866

Testing isotopic labeling with [¹³C₆]glucose as a method of advanced glycation sites identification.

PubMed

Kielmas, Martyna; Kijewska, Monika; Stefanowicz, Piotr; Szewczuk, Zbigniew

2012-12-01

The Maillard reaction occurring between reducing sugars and reactive amino groups of biomolecules leads to the formation of a heterogeneous mixture of compounds: early, intermediate, and advanced glycation end products (AGEs). These compounds could be markers of certain diseases and of the premature aging process. Detection of Amadori products can be performed by various methods, including MS/MS techniques and affinity chromatography on immobilized boronic acid. However, the diversity of the structures of AGEs makes detection of these compounds more difficult. The aim of this study was to test a new method of AGE identification based on isotope (13)C labeling. The model protein (hen egg lysozyme) was modified with an equimolar mixture of [(12)C(6)]glucose and [(13)C(6)]glucose and then subjected to reduction of the disulfide bridges followed by tryptic hydrolysis. The digest obtained was analyzed by LC-MS. The glycation products were identified on the basis of characteristic isotopic patterns resulting from the use of isotopically labeled glucose. This method allowed identification of 38 early Maillard reaction products and five different structures of the end glycation products. This isotopic labeling technique combined with LC-MS is a sensitive method for identification of advanced glycation end products even if their chemical structure is unknown. Copyright © 2012 Elsevier Inc. All rights reserved.

An extended version of the SERPENT-2 code to investigate fuel burn-up and core material evolution of the Molten Salt Fast Reactor

NASA Astrophysics Data System (ADS)

Aufiero, M.; Cammi, A.; Fiorina, C.; Leppänen, J.; Luzzi, L.; Ricotti, M. E.

2013-10-01

In this work, the Monte Carlo burn-up code SERPENT-2 has been extended and employed to study the material isotopic evolution of the Molten Salt Fast Reactor (MSFR). This promising GEN-IV nuclear reactor concept features peculiar characteristics such as the on-line fuel reprocessing, which prevents the use of commonly available burn-up codes. Besides, the presence of circulating nuclear fuel and radioactive streams from the core to the reprocessing plant requires a precise knowledge of the fuel isotopic composition during the plant operation. The developed extension of SERPENT-2 directly takes into account the effects of on-line fuel reprocessing on burn-up calculations and features a reactivity control algorithm. It is here assessed against a dedicated version of the deterministic ERANOS-based EQL3D procedure (PSI-Switzerland) and adopted to analyze the MSFR fuel salt isotopic evolution. Particular attention is devoted to study the effects of reprocessing time constants and efficiencies on the conversion ratio and the molar concentration of elements relevant for solubility issues (e.g., trivalent actinides and lanthanides). Quantities of interest for fuel handling and safety issues are investigated, including decay heat and activities of hazardous isotopes (neutron and high energy gamma emitters) in the core and in the reprocessing stream. The radiotoxicity generation is also analyzed for the MSFR nominal conditions. The production of helium and the depletion in tungsten content due to nuclear reactions are calculated for the nickel-based alloy selected as reactor structural material of the MSFR. These preliminary evaluations can be helpful in studying the radiation damage of both the primary salt container and the axial reflectors.

Rates for neutron-capture reactions on tungsten isotopes in iron meteorites. [Abstract only

NASA Technical Reports Server (NTRS)

Masarik, J.; Reedy, R. C.

1994-01-01

High-precision W isotopic analyses by Harper and Jacobsen indicate the W-182/W-183 ratio in the Toluca iron meteorite is shifted by -(3.0 +/- 0.9) x 10(exp -4) relative to a terrestrial standard. Possible causes of this shift are neutron-capture reactions on W during Toluca's approximately 600-Ma exposure to cosmic ray particles or radiogenic growth of W-182 from 9-Ma Hf-182 in the silicate portion of the Earth after removal of W to the Earth's core. Calculations for the rates of neutron-capture reactions on W isotopes were done to study the first possibility. The LAHET Code System (LCS) which consists of the Los Alamos High Energy Transport (LAHET) code and the Monte Carlo N-Particle(MCNP) transport code was used to numerically simulate the irradiation of the Toluca iron meteorite by galactic-cosmic-ray (GCR) particles and to calculate the rates of W(n, gamma) reactions. Toluca was modeled as a 3.9-m-radius sphere with the composition of a typical IA iron meteorite. The incident GCR protons and their interactions were modeled with LAHET, which also handled the interactions of neutrons with energies above 20 MeV. The rates for the capture of neutrons by W-182, W-183, and W-186 were calculated using the detailed library of (n, gamma) cross sections in MCNP. For this study of the possible effect of W(n, gamma) reactions on W isotope systematics, we consider the peak rates. The calculated maximum change in the normalized W-182/W-183 ratio due to neutron-capture reactions cannot account for more than 25% of the mass 182 deficit observed in Toluca W.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gauld, Ian C.; Giaquinto, J. M.; Delashmitt, J. S.

Destructive radiochemical assay measurements of spent nuclear fuel rod segments from an assembly irradiated in the Three Mile Island unit 1 (TMI-1) pressurized water reactor have been performed at Oak Ridge National Laboratory (ORNL). Assay data are reported for five samples from two fuel rods of the same assembly. The TMI-1 assembly was a 15 X 15 design with an initial enrichment of 4.013 wt% 235U, and the measured samples achieved burnups between 45.5 and 54.5 gigawatt days per metric ton of initial uranium (GWd/t). Measurements were performed mainly using inductively coupled plasma mass spectrometry after elemental separation via highmore » performance liquid chromatography. High precision measurements were achieved using isotope dilution techniques for many of the lanthanides, uranium, and plutonium isotopes. Measurements are reported for more than 50 different isotopes and 16 elements. One of the two TMI-1 fuel rods measured in this work had been measured previously by Argonne National Laboratory (ANL), and these data have been widely used to support code and nuclear data validation. Recently, ORNL provided an important opportunity to independently cross check results against previous measurements performed at ANL. The measured nuclide concentrations are used to validate burnup calculations using the SCALE nuclear systems modeling and simulation code suite. These results show that the new measurements provide reliable benchmark data for computer code validation.« less

COMPLETE DETERMINATION OF POLARIZATION FOR A HIGH-ENERGY DEUTERON BEAM (thesis)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Button, J

1959-05-01

please delete the no. 17076<>13:017077The P/sub 1/ multigroup code was written for the IBM-704 in order to determine the accuracy of the few- group diffusion scheme with various imposed conditions and also to provide an alternate computational method when this scheme fails to be sufficiently accurate. The code solves for the spatially dependent multigroup flux, taking into account such nuclear phenomena is slowing down of neutrons resulting from elastic and inelastic scattering, the removal of neutrons resulting from epithermal capture and fission resonances, and the regeneration of fist neutrons resulting from fissioning which may occur in any of as manymore » as 80 fast multigroups or in the one thermal group. The code will accept as input a physical description of the reactor (that is: slab, cylindrical, or spherical geometry, number of points and regions, composition description group dependent boundary condition, transverse buckling, and mesh sizes) and a prepared library of nuclear properties of all the isotopes in each composition. The code will produce as output multigroup fluxes, currents, and isotopic slowing-down densities, in addition to pointwise and regionwise few-group macroscopic cross sections. (auth)« less

Secondary neutrons as the main source of neutron-rich fission products in the bombardment of a thick U target by 1 GeV protons

NASA Astrophysics Data System (ADS)

Barzakh, A. E.; Lhersonneau, G.; Batist, L. Kh.; Fedorov, D. V.; Ivanov, V. S.; Mezilev, K. A.; Molkanov, P. L.; Moroz, F. V.; Orlov, S. Yu.; Panteleev, V. N.; Volkov, Yu. M.; Alyakrinskiy, O.; Barbui, M.; Stroe, L.; Tecchio, L. B.

2011-05-01

The diffusion-effusion model has been used to analyse the release and yields of Fr and Cs isotopes from uranium carbide targets of very different thicknesses (6.3 and 148 g/cm2) bombarded by a 1 GeV proton beam. Release curves of several isotopes of the same element and production efficiency versus decay half-life are well fitted with the same set of parameters. Comparison of efficiencies for neutron-rich and neutron-deficient Cs isotopes enables separation of the contributions from the primary ( p + 238U) and secondary (n + 238U) reactions to the production of neutron-rich Cs isotopes. A rather simple calculation of the neutron contribution describes these data fairly well. The FLUKA code describes the primary and secondary-reaction contributions to the Cs isotopes production efficiencies for different targets quite well.

Integral nuclear data validation using experimental spent nuclear fuel compositions

DOE PAGES

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco; ...

2017-07-19

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

Integral nuclear data validation using experimental spent nuclear fuel compositions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

A new approach for deciphering between single and multiple accumulation events using intra-tooth isotopic variations: Application to the Middle Pleistocene bone bed of Schöningen 13 II-4.

PubMed

Julien, Marie-Anne; Rivals, Florent; Serangeli, Jordi; Bocherens, Hervé; Conard, Nicholas J

2015-12-01

It is often difficult to differentiate between archaeological bonebeds formed by one event such as a mass kill of a single herd, and those formed by multiple events that occurred over a longer period of time. The application of high temporal resolution studies such as intra-tooth isotopic profiles on archaeological mammal cohorts offers new possibilities for exploring this issue, allowing investigators to decipher between single and multiple accumulation events. We examined (18)O and (13)C isotopic variations from the enamel carbonate of 23 horse third molars from the Middle Pleistocene archaeological site of Schöningen. We employed a new approach to investigate processes of fossil accumulation that uses both bulk and intra-tooth isotopic variations and takes into account animal behavior, age at death and dental development to test the degree of isotopic affinity of animals from the same fossil assemblage. Oxygen and carbon isotope bulk values indicate that the horses from Schöningen 13 II-4 experienced relatively similar climatic and dietary regimes. Inter-individual differences of the bulk values of the horses sampled in the current study present nevertheless inter-individual variability similar to individuals from multi-layered localities. In addition, the intra-tooth isotopic variation of specimens of the same age at death seems to indicate that the studied cohort corresponds to a mix of individuals that recorded both similar and different isotopic histories. Finally, the conditions recorded in the isotopic signal shortly before death (i.e., for teeth not fully mineralized) varied between sampled individuals, suggesting possible differences in the seasonality of death. Considering those results, we discuss the possibility that the horses from Schöningen 13 II-4 correspond to an accumulation of different death events. Copyright © 2015 Elsevier Ltd. All rights reserved.

Vitamin D3 Analogues with Low Vitamin D Receptor Binding Affinity Regulate Chondrocyte Proliferation, Proteoglycan Synthesis, and Protein Kinase C Activity

DTIC Science & Technology

1997-07-11

REPORT DOCUMENTATION PAGE Form ApprovedOMB No. 0704-0188 Public reporting burden for this collection of information is estimated to average 1 hour...DISTRIBUTION CODE 13. ABSTRACT (Maximum 200 words) 14. SUBJECT TERMS 15. NUMBER OF PAGES 50 16. PRICE CODE 17. SECURITY CLASSIFICATION 18. SECURITY...CLASSIFICATION 19. SECURITY CLASSIFICATION 20. LIMITATION OF ABSTRACT OF REPORT OF THIS PAGE OF ABSTRACT Standard Form 298(Rev. 2-89) (EG) Prescribed byANSI

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand–protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency

PubMed Central

Delius, Judith; Frank, Oliver

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein–polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein–ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate “anti-astringent” protein binding antagonist, on the polyphenol–protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives. PMID:28886151

Plutonium isotopes offer an alternative approach to establishing chronological profiles in coarse sediments

NASA Astrophysics Data System (ADS)

Pondell, C.; Kuehl, S. A.; Canuel, E. A.

2016-12-01

There are several methodologies used to determine chronologies for sediments deposited within the past 100 years, including 210Pb and 137Cs radioisotopes and organic and inorganic contaminants. These techniques are quite effective in fine sediments, which generally have a high affinity for metals and organic compounds. However, the application of these chronological tools becomes limited in systems where coarse sediments accumulate. Englebright Lake is an impoundment in northern California where sediment accumulation is characterized by a combination of fine and coarse sediments. This combination of sediment grain size complicated chronological analysis using the more traditional 137Cs chronological approach. This study established a chronology of these sediments using 239+240Pu isotopes. While most of the 249+240Pu activity was measured in the fine grain size fraction (<63 microns), up to 25% of the plutonium activity was detected in the coarse size fractions of sediments from Englebright Lake. Profiles of 239+240Pu were similar to available 137Cs profiles, verifying the application of plutonium isotopes for determining sediment chronologies and expanding the established geochronology for Englebright Lake sediments. This study of sediment accumulation in Englebright Lake demonstrates the application of plutonium isotopes in establishing chronologies in coarse sediments and highlights the potential for plutonium to offer new insights into patterns of coarse sediment accumulation.

Isotopic Effects in Nuclear Fragmentation and GCR Transport Problems

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.

2002-01-01

Improving the accuracy of the galactic cosmic ray (GCR) environment and transport models is an important goal in preparing for studies of the projected risks and the efficiency of potential mitigations methods for space exploration. In this paper we consider the effects of the isotopic composition of the primary cosmic rays and the isotopic dependence of nuclear fragmentation cross sections on GCR transport models. Measurements are used to describe the isotopic composition of the GCR including their modulation throughout the solar cycle. The quantum multiple-scattering approach to nuclear fragmentation (QMSFRG) is used as the data base generator in order to accurately describe the odd-even effect in fragment production. Using the Badhwar and O'Neill GCR model, the QMSFRG model and the HZETRN transport code, the effects of the isotopic dependence of the primary GCR composition and on fragment production for transport problems is described for a complete GCR isotopic-grid. The principle finding of this study is that large errors ( 100%) will occur in the mass-flux spectra when comparing the complete isotopic-grid (141 ions) to a reduced isotopic-grid (59 ions), however less significant errors 30%) occur in the elemental-flux spectra. Because the full isotopic-grid is readily handled on small computer work-stations, it is recommended that they be used for future GCR studies.

Background Perchlorate Source Identification Technical Guidance

DTIC Science & Technology

2013-12-01

Sciences Branch (Code 71752) of the Advanced Systems and Applied Sciences Division (Code 71700), Space and Naval Warfare Systems Center (SSC Pacific), San...Head Advanced Systems & Applied Sciences Division iii EXECUTIVE SUMMARY The objective of this document is to outline the approach, tools, and...Helium HMX Octahydro-1,3,5,7-Tetranitro-1,3,5,7- Tetrazocine IR Installation Restoration IRIS Integrated Risk Information System IR-MS Isotope-Ratio

Measurement of Ligand–Target Residence Times by 1H Relaxation Dispersion NMR Spectroscopy

PubMed Central

2016-01-01

A ligand-observed 1H NMR relaxation experiment is introduced for measuring the binding kinetics of low-molecular-weight compounds to their biomolecular targets. We show that this approach, which does not require any isotope labeling, is applicable to ligand–target systems involving proteins and nucleic acids of variable molecular size. The experiment is particularly useful for the systematic investigation of low affinity molecules with residence times in the micro- to millisecond time regime. PMID:27933946

Antarctic Meteorite Newsletter, Volume 29, Number 1

NASA Technical Reports Server (NTRS)

Satterwhite, Cecilia (Editor); Righter, Kevin (Editor)

2006-01-01

This newsletter contains classifications for 597 new meteorites from the 2003 and 2004 ANtarctic Search for METeorites (ANSMET) seasons. They include samples from the Cumulus Hills, Dominion Range, Grosvenor Mountains, LaPaz Icefield, MacAlpine Hills, and the Miller Range. Macroscopic and petrographic descriptions are given for 25 of the new meteorites: 1 acapulcoite/Iodranite, 1 howardite, 1 diogenite, 2 eucrites, 1 enstatite chondrite, four L3 and two H3 chondrites, 2 CM, 3 CK and 1 CV chondrites, three R chondrites, and four impact melt breccias (with affinities for H and L). Likely the most interesting sample announced in this newsletter is LAP04840, with affinity to R chondrites. This meteorite contains approximately 15% horneblende, and has mineral compositional ranges and oxygen isotopic values similar to those of R chondrites. The presence of an apparently hydrous phase in this petrologic grade 6 chondrite is very unusual, and should be of great interest to many meteoriticists.

co2amp: A software program for modeling the dynamics of ultrashort pulses in optical systems with CO 2 amplifiers

DOE PAGES

Polyanskiy, Mikhail N.

2015-01-01

We describe a computer code for simulating the amplification of ultrashort mid-infrared laser pulses in CO 2 amplifiers and their propagation through arbitrary optical systems. This code is based on a comprehensive model that includes an accurate consideration of the CO 2 active medium and a physical optics propagation algorithm, and takes into account the interaction of the laser pulse with the material of the optical elements. Finally, the application of the code for optimizing an isotopic regenerative amplifier is described.

Plant proteome analysis: a 2006 update.

PubMed

Jorrín, Jesús V; Maldonado, Ana M; Castillejo, Ma Angeles

2007-08-01

This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.

Latest Pleistocene crustal cannibalization at Baekdusan (Changbaishan) as traced by oxygen isotopes of zircon from the Millennium Eruption

NASA Astrophysics Data System (ADS)

Cheong, Albert Chang-sik; Sohn, Young Kwan; Jeong, Youn-Joong; Jo, Hui Je; Park, Kye-Hun; Lee, Youn Soo; Li, Xian-Hua

2017-07-01

The silicic volcanism of Baekdusan (Changbaishan), which is on the border between North Korea and China, was initiated in the Late Pleistocene and culminated in the 10th century with a powerful (volcanic explosivity index = 7) commendite-trachyte eruption commonly referred to as the "Millennium Eruption." This study presents oxygen isotope data of zircon in trachydacitic pumices ejected during the Millennium Eruption, together with whole-rock geochemical and Sr-Nd-Pb isotopic data that manifest once again the A-type and EM1 affinities of the Millennium Eruption magma. The zircon crystals, dated by previous studies at ca. 12-9 ka, show a moderate inter-grain variation in δ18O from 3.69‰ to 5.03‰. These values are consistently lower than the normal mantle range, and interpreted to have resulted from the digestion of meteoric-hydrothermally altered intracaldera rocks in the shallow magma chamber beneath Baekdusan just prior to the crystallization of the zircons, rather than from derivation from low-δ18O sources deep in the mantle. The whole-rock geochemical/isotopic considerations suggest that the magma mainly self-cannibalized the earlier erupted volcanic carapace around the magma chamber. This study highlights the usefulness of zircon oxygen isotopes for characterizing past volcanic activity that has now been commonly eroded away and implies that the generation of Yellowstone-type low-δ18O magma is not a rare phenomenon in large-volume silicic eruptions.

HRB-22 preirradiation thermal analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acharya, R.; Sawa, K.

1995-05-01

This report describes the preirradiation thermal analysis of the HRB-22 capsule designed for irradiation in the removable beryllium (RB) position of the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). CACA-2 a heavy isotope and fission product concentration calculational code for experimental irradiation capsules was used to determine time dependent fission power for the fuel compacts. The Heat Engineering and Transfer in Nine Geometries (HEATING) computer code, version 7.2, was used to solve the steady-state heat conduction problem. The diameters of the graphite fuel body that contains the compacts and the primary pressure vessel were selected suchmore » that the requirements of running the compacts at an average temperature of < 1,250 C and not exceeding a maximum fuel temperature of 1,350 C was met throughout the four cycles of irradiation.« less

Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR

PubMed Central

Chung, Wai Keen; Freed, Alexander S.; Holstein, Melissa A.; McCallum, Scott A.; Cramer, Steven M.

2010-01-01

NMR titration experiments with labeled human ubiquitin were employed in concert with chromatographic data obtained with a library of ubiquitin mutants to study the nature of protein adsorption in multimodal (MM) chromatography. The elution order of the mutants on the MM resin was significantly different from that obtained by ion-exchange chromatography. Further, the chromatographic results with the protein library indicated that mutations in a defined region induced greater changes in protein affinity to the solid support. Chemical shift mapping and determination of dissociation constants from NMR titration experiments with the MM ligand and isotopically enriched ubiquitin were used to determine and rank the relative binding affinities of interaction sites on the protein surface. The results with NMR confirmed that the protein possessed a distinct preferred binding region for the MM ligand in agreement with the chromatographic results. Finally, coarse-grained ligand docking simulations were employed to study the modes of interaction between the MM ligand and ubiquitin. The use of NMR titration experiments in concert with chromatographic data obtained with protein libraries represents a previously undescribed approach for elucidating the structural basis of protein binding affinity in MM chromatographic systems. PMID:20837551

Earth Processes: Reading the Isotopic Code

NASA Astrophysics Data System (ADS)

Basu, Asish; Hart, Stan

Publication of this monograph will coincide, to a precision of a few per mil, with the centenary of Henri Becquerel's discovery of "radiations actives" (C. R. Acad. Sci., Feb. 24, 1896). In 1896 the Earth was only 40 million years old according to Lord Kelvin. Eleven years later, Boltwood had pushed the Earth's age past 2000 million years, based on the first U/Pb chemical dating results. In exciting progression came discovery of isotopes by J. J. Thomson in 1912, invention of the mass spectrometer by Dempster (1918) and Aston (1919), the first measurement of the isotopic composition of Pb (Aston, 1927) and the final approach, using Pb-Pb isotopic dating, to the correct age of the Earth: close—2.9 Ga (Gerling, 1942), closer—3.0 Ga (Holmes, 1949) and closest—4.50 Ga (Patterson, Tilton and Inghram, 1953).

Planned Monolayer Assemblies by Adsorption

DTIC Science & Technology

1988-09-01

RESEARCH OFFICE OF TBE U.S. ARMY Xcndn, Engan aONRAcM NUMBE DAJA45-84-C-0055 acntractor: The Weizmn InstituteAttn: Ms. N. Guter Office of Research ...ORGANIZATION The Weizmann Inst’,a#. of (if appficable) European Research office ScienceUSARDSG-UK) Sk. ADDRESS (Wiy State, and ZIP Code) 7b. ADDRESS (City...State. and ZIP Code) Department of Isotope Research Box 65 76100 Rehoyot FPO NY 09510-1500 IsraelJ

Biosensors and Bio-Bar Code Assays Based on Biofunctionalized Magnetic Microbeads

PubMed Central

Jaffrezic-Renault, Nicole; Martelet, Claude; Chevolot, Yann; Cloarec, Jean-Pierre

2007-01-01

This review paper reports the applications of magnetic microbeads in biosensors and bio-bar code assays. Affinity biosensors are presented through different types of transducing systems: electrochemical, piezo electric or magnetic ones, applied to immunodetection and genodetection. Enzymatic biosensors are based on biofunctionalization through magnetic microbeads of a transducer, more often amperometric, potentiometric or conductimetric. The bio-bar code assays relie on a sandwich structure based on specific biological interaction of a magnetic microbead and a nanoparticle with a defined biological molecule. The magnetic particle allows the separation of the reacted target molecules from unreacted ones. The nanoparticles aim at the amplification and the detection of the target molecule. The bio-bar code assays allow the detection at very low concentration of biological molecules, similar to PCR sensitivity.

Quantitative proteomic analysis of CMS-related changes in Honglian CMS rice anther.

PubMed

Sun, Qingping; Hu, Chaofeng; Hu, Jun; Li, Shaoqing; Zhu, Yingguo

2009-10-01

Honglian (HL) cytoplasmic male sterility (CMS) is one of the rice CMS types and has been widely used in hybrid rice production in China. The CMS line (Yuetai A, YTA) has a Yuetai B (maintainer line, YTB) nuclear genome, but has a rearranged mitochondrial (mt) genome consisting of Yuetai B. The fertility of hybrid (HL-6) was restored by restorer gene in nuclear genome of restorer line (9311). We used isotope-code affinity tag (ICAT) technology to perform the protein profiling of uninucleate stage rice anther and identify the CMS-HL related proteins. Two separate ICAT analyses were performed in this study: (1) anthers from YTA versus anthers from YTB, and (2) anthers from YTA versus anthers from HL-6. Based on the two analyses, a total of 97 unique proteins were identified and quantified in uninucleate stage rice anther under the error rate of less than 10%, of which eight proteins showed abundance changes of at least twofold between YTA and YTB. Triosephosphate isomerase, fructokinase II, DNA-binding protein GBP16 and ribosomal protein L3B were over-expressed in YTB, while oligopeptide transporter, floral organ regulator 1, kinase and S-adenosyl-L: -methionine synthetase were over-expressed in YTA. Reduction of the proteins associated with energy production and lesser ATP equivalents detected in CMS anther indicated that the low level of energy production played an important role in inducing CMS-HL.

Thiol-based Redox Proteins in Brassica napus Guard Cell Abscisic Acid and Methyl Jasmonate Signaling

PubMed Central

Zhu, Mengmeng; Zhu, Ning; Song, Wen-yuan; Harmon, Alice C.; Assmann, Sarah M.; Chen, Sixue

2014-01-01

SUMMARY Reversibly oxidized cysteine sulfhydryl groups serve as redox sensors or targets of redox sensing that are important in different physiological processes. Little is known, however, about redox sensitive proteins in guard cells and how they function in stomatal signaling. In this study, Brassica napus guard cell proteins altered by redox in response to abscisic acid (ABA) or methyl jasmonate (MeJA) were identified by complementary proteomics approaches, saturation differential in-gel electrophoresis (DIGE) and isotope-coded affinity tag (ICAT). In total, 65 and 118 potential redox responsive proteins were identified in ABA and MeJA treated guard cells, respectively. All the proteins contain at least one cysteine, and over half of them are predicted to form intra-molecular disulfide bonds. Most of the proteins fall into the functional groups of energy, stress and defense, and metabolism. Based on the peptide sequences identified by mass spectrometry, 30 proteins were common to ABA and MeJA treated samples. A total of 44 cysteines was mapped in all the identified proteins, and their levels of redox sensitivity were quantified. Two of the proteins, a SNRK2 kinase and an isopropylmalate dehydrogenase were confirmed to be redox regulated and involved in stomatal movement. This study creates an inventory of potential redox switches, and highlights a protein redox regulatory mechanism in guard cell ABA and MeJA signal transduction. PMID:24580573

Low-complexity piecewise-affine virtual sensors: theory and design

NASA Astrophysics Data System (ADS)

Rubagotti, Matteo; Poggi, Tomaso; Oliveri, Alberto; Pascucci, Carlo Alberto; Bemporad, Alberto; Storace, Marco

2014-03-01

This paper is focused on the theoretical development and the hardware implementation of low-complexity piecewise-affine direct virtual sensors for the estimation of unmeasured variables of interest of nonlinear systems. The direct virtual sensor is designed directly from measured inputs and outputs of the system and does not require a dynamical model. The proposed approach allows one to design estimators which mitigate the effect of the so-called 'curse of dimensionality' of simplicial piecewise-affine functions, and can be therefore applied to relatively high-order systems, enjoying convergence and optimality properties. An automatic toolchain is also presented to generate the VHDL code describing the digital circuit implementing the virtual sensor, starting from the set of measured input and output data. The proposed methodology is applied to generate an FPGA implementation of the virtual sensor for the estimation of vehicle lateral velocity, using a hardware-in-the-loop setting.

Random mutagenesis of BoNT/E Hc nanobody to construct a secondary phage-display library.

PubMed

Shahi, B; Mousavi Gargari, S L; Rasooli, I; Rajabi Bazl, M; Hoseinpoor, R

2014-08-01

To construct secondary mutant phage-display library of recombinant single variable domain (VHH) against botulinum neurotoxin E by error-prone PCR. The gene coding for specific VHH derived from the camel immunized with binding domain of botulinum neurotoxin E (BoNT/E) was amplified by error-prone PCR. Several biopanning rounds were used to screen the phage-displaying BoNT/E Hc nanobodies. The final nanobody, SHMR4, with increased affinity recognized BoNT/E toxin with no cross-reactivity with other antigens especially with related BoNT toxins. The constructed nanobody could be a suitable candidate for VHH-based biosensor production to detect the Clostridium botulinum type E. Diagnosis and treatment of botulinum neurotoxins are important. Generation of high-affinity antibodies based on the construction of secondary libraries using affinity maturation step leads to the development of reagents for precise diagnosis and therapy. © 2014 The Society for Applied Microbiology.

Vibrationally averaged post Born-Oppenheimer isotopic dipole moment calculations approaching spectroscopic accuracy.

PubMed

Arapiraca, A F C; Jonsson, Dan; Mohallem, J R

2011-12-28

We report an upgrade of the Dalton code to include post Born-Oppenheimer nuclear mass corrections in the calculations of (ro-)vibrational averages of molecular properties. These corrections are necessary to achieve an accuracy of 10(-4) debye in the calculations of isotopic dipole moments. Calculations on the self-consistent field level present this accuracy, while numerical instabilities compromise correlated calculations. Applications to HD, ethane, and ethylene isotopologues are implemented, all of them approaching the experimental values.

Thermal Neutron Capture onto the Stable Tungsten Isotopes

NASA Astrophysics Data System (ADS)

Hurst, A. M.; Firestone, R. B.; Sleaford, B. W.; Summers, N. C.; Revay, Zs.; Szentmiklósi, L.; Belgya, T.; Basunia, M. S.; Capote, R.; Choi, H.; Dashdorj, D.; Escher, J.; Krticka, M.; Nichols, A.

2012-02-01

Thermal neutron-capture measurements of the stable tungsten isotopes have been carried out using the guided thermal-neutron beam at the Budapest Reactor. Prompt singles spectra were collected and analyzed using the HYPERMET γ-ray analysis software package for the compound tungsten systems 183W, 184W, and 187W, prepared from isotopically-enriched samples of 182W, 183W, and 186W, respectively. These new data provide both confirmation and new insights into the decay schemes and structure of the tungsten isotopes reported in the Evaluated Gamma-ray Activation File based upon previous elemental analysis. The experimental data have also been compared to Monte Carlo simulations of γ-ray emission following the thermal neutron-capture process using the statistical-decay code DICEBOX. Together, the experimental cross sections and modeledfeeding contribution from the quasi continuum, have been used to determine the total radiative thermal neutron-capture cross sections for the tungsten isotopes and provide improved decay-scheme information for the structural- and neutron-data libraries.

CLONING AND CHARACTERIZATION OF CDNA ENCODING GIARDIA LAMBLIA d-GIARDIN

USDA-ARS?s Scientific Manuscript database

A cDNA coding for d-giardin was cloned from Giardia lamblia trophozoites in order to localize the protein and study its function in mediating surface attachment. Recombinant d-giardin antigen was produced in Escherichia coli as a poly-histidine fusion protein and was purified by affinity chromatogr...

pH-regulated formation of side products in the reductive amination approach for differential labeling of peptides in relative quantitative experiments.

PubMed

Levi Mortera, Stefano; Dioni, Ilaria; Greco, Viviana; Neri, Cristina; Rovero, Paolo; Urbani, Andrea

2014-05-01

Among the most common stable-isotope labeling strategies, the reaction of formaldehyde with peptides in the presence of NaCNBH₃ features many attractive aspects that are conducive to its employment in quantitation experiments in proteomics. Reductive amination, with formaldehyde and d(2)-formaldehyde, is reported to be a fast, easy, and specific reaction, undoubtedly inexpensive if compared with commercially available kits for differential isotope coding. Acetaldehyde and d(4)-acetaldehyde could be employed as well without a substantial increase in terms of cost, and should provide a wider spacing between the differentially tagged peptides in the mass spectrum. Nevertheless, only a single paper reports about a diethylation approach for quantitation. We undertook a systematic analytical investigation on the reductive amination of some standard peptides pointing out the occasional occurrence of side reactions in dependence of pH or reagents order of addition, particularly observing the formation of cyclic adducts ascribable to rearrangements involving the generated Schiff-base and all the nucleophilic sites of its chemical environment. We also tried to evaluate how much this side-products amount may impair isotope coded relative quantitation.

Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.

PubMed

Duss, Olivier; Michel, Erich; Diarra dit Konté, Nana; Schubert, Mario; Allain, Frédéric H-T

2014-04-01

The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.

Affinity of C-Reactive Protein toward FcγRI Is Strongly Enhanced by the γ-Chain

PubMed Central

Röcker, Carlheinz; Manolov, Dimitar E.; Kuzmenkina, Elza V.; Tron, Kyrylo; Slatosch, Holger; Torzewski, Jan; Nienhaus, G. Ulrich

2007-01-01

C-reactive protein (CRP), the prototype human acute phase protein, is widely regarded as a key player in cardiovascular disease, but the identity of its cellular receptor is still under debate. By using ultrasensitive confocal imaging analysis, we have studied CRP binding to transfected COS-7 cells expressing the high-affinity IgG receptor FcγRI. Here we show that CRP binds to FcγRI on intact cells, with a kd of 10 ± 3 μmol/L. Transfection of COS-7 cells with a plasmid coding for both FcγRI and its functional counterpart, the γ-chain, markedly increases CRP affinity to FcγRI, resulting in a kd of 0.35 ± 0.10 μmol/L. The affinity increase results from an ∼30-fold enhanced association rate coefficient. The pronounced enhancement of affinity by the γ-chain suggests its crucial involvement in the CRP receptor interaction, possibly by mediating interactions between the transmembrane moieties of the receptors. Dissociation of CRP from the cell surfaces cannot be detected throughout the time course of several hours and is thus extremely slow. Considering the pentameric structure of CRP, this result indicates that multivalent binding and receptor clustering are crucially involved in the interaction of CRP with nucleated cells. PMID:17255341

Oxygen isotopic composition of chondritic interplanetary dust particles: A genetic link between carbonaceous chondrites and comets

NASA Astrophysics Data System (ADS)

Aléon, J.; Engrand, C.; Leshin, L. A.; McKeegan, K. D.

2009-08-01

Oxygen isotopes were measured in four chondritic hydrated interplanetary dust particles (IDPs) and five chondritic anhydrous IDPs including two GEMS-rich particles (Glass embedded with metal and sulfides) by a combination of high precision and high lateral resolution ion microprobe techniques. All IDPs have isotopic compositions tightly clustered around that of solar system planetary materials. Hydrated IDPs have mass-fractionated oxygen isotopic compositions similar to those of CI and CM carbonaceous chondrites, consistent with hydration of initially anhydrous protosolar dust. Anhydrous IDPs have small 16O excesses and depletions similar to those of carbonaceous chondrites, the largest 16O variations being hosted by the two GEMS-rich IDPs. Coarse-grained forsteritic olivine and enstatite in anhydrous IDPs are isotopically similar to their counterparts in comet Wild 2 and in chondrules suggesting a high temperature inner solar system origin. The small variations in the 16O content of GEMS-rich IDPs suggest that most GEMS either do not preserve a record of interstellar processes or the initial interstellar dust is not 16O-rich as expected by self-shielding models, although a larger dataset is required to verify these conclusions. Together with other chemical and mineralogical indicators, O isotopes show that the parent-bodies of carbonaceous chondrites, of chondritic IDPs, of most Antarctic micrometeorites, and comet Wild 2 belong to a single family of objects of carbonaceous chondrite chemical affinity as distinct from ordinary, enstatite, K- and R-chondrites. Comparison with astronomical observations thus suggests a chemical continuum of objects including main belt and outer solar system asteroids such as C-type, P-type and D-type asteroids, Trojans and Centaurs as well as short-period comets and other Kuiper Belt Objects.

Mapping the local protein interactome of the NuA3 histone acetyltransferase

PubMed Central

Smart, Sherri K; Mackintosh, Samuel G; Edmondson, Ricky D; Taverna, Sean D; Tackett, Alan J

2009-01-01

Protein–protein interactions modulate cellular functions ranging from the activity of enzymes to signal transduction cascades. A technology termed transient isotopic differentiation of interactions as random or targeted (transient I-DIRT) is described for the identification of stable and transient protein–protein interactions in vivo. The procedure combines mild in vivo chemical cross-linking and non-stringent affinity purification to isolate low abundance chromatin-associated protein complexes. Using isotopic labeling and mass spectrometric readout, purified proteins are categorized with respect to the protein ‘bait’ as stable, transient, or contaminant. Here we characterize the local interactome of the chromatin-associated NuA3 histone lysine-acetyltransferase protein complex. We describe transient associations with the yFACT nucleosome assembly complex, RSC chromatin remodeling complex and a nucleosome assembly protein. These novel, physical associations with yFACT, RSC, and Nap1 provide insight into the mechanism of NuA3-associated transcription and chromatin regulation. PMID:19621382

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Botta, F; Di Dia, A; Pedroli, G

The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernel (DPK),more » quantifying the energy deposition all around a point isotropic source, is often the one.Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10–3 MeV) and for beta emitting isotopes commonly used for therapy (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, and 188Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8·RCSDA and 0.9·RCSDA for monoenergetic electrons (RCSDA being the continuous slowing down approximation range) and within 0.8·X90 and 0.9·X90 for isotopes (X90 being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9·RCSDA and 0.9·X90 for electrons and isotopes, respectively.Results: Concerning monoenergetic electrons, within 0.8·RCSDA (where 90%–97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in water, 8.3% in bone). The discrepancies between fluka and the other codes are of the same order of magnitude than those observed when comparing the other codes among them, which can be referred to the different simulation algorithms. When considering the beta spectra, discrepancies notably reduce: within 0.9·X90, fluka and penelope differ for less than 1% in water and less than 2% in bone with any of the isotopes here considered. Complete data of fluka DPKs are given as Supplementary Material as a tool to perform dosimetry by analytical point kernel convolution.Conclusions: fluka provides reliable results when transporting electrons in the low energy range, proving to be an adequate tool for nuclear medicine dosimetry.« less

Determination of the δ15N of total nitrogen in solids; RSIL lab code 2893

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 2893 is to determine the δ(15N/14N), abbreviated as δ15N , of total nitrogen in solid samples. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total nitrogen in a solid sample into N2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines relative difference in the isotope-amount ratios of stable nitrogen isotopes (15N/14N)of the product N2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated reaction tube that contains an oxidant, where the combustion takes place in a helium atmosphere containing an excess of oxygen gas. Combustion products are transported by a helium carrier through a reduction tube to remove excess oxygen and convert all nitrous oxides into N2 and through a drying tube to remove water. The gas-phase products, mainly CO2 and N2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which also is used to inject N2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector, two wide cups with a narrow cup in the middle, capable of measuring mass/charge (m/z) 28, 29, 30, simultaneously. The ion beams from N2 are as follows: m/z 28 = N2 = 14N14N; m/z 29 = N2 = 14N15N primarily; m/z 30 = NO = 14N16O primarily, which is a sign of contamination or incomplete reduction.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Spent fuel pool storage calculations using the ISOCRIT burnup credit tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kucukboyaci, Vefa; Marshall, William BJ J

2012-01-01

In order to conservatively apply burnup credit in spent fuel pool criticality safety analyses, Westinghouse has developed a software tool, ISOCRIT, for generating depletion isotopics. This tool is used to create isotopics data based on specific reactor input parameters, such as design basis assembly type; bounding power/burnup profiles; reactor specific moderator temperature profiles; pellet percent theoretical density; burnable absorbers, axial blanket regions, and bounding ppm boron concentration. ISOCRIT generates burnup dependent isotopics using PARAGON; Westinghouse's state-of-the-art and licensed lattice physics code. Generation of isotopics and passing the data to the subsequent 3D KENO calculations are performed in an automated fashion,more » thus reducing the chance for human error. Furthermore, ISOCRIT provides the means for responding to any customer request regarding re-analysis due to changed parameters (e.g., power uprate, exit temperature changes, etc.) with a quick turnaround.« less

The stable isotope composition of nitrogen and carbon and elemental contents in modern and fossil seabird guano from Northern Chile - Marine sources and diagenetic effects.

PubMed

Lucassen, Friedrich; Pritzkow, Wolfgang; Rosner, Martin; Sepúlveda, Fernando; Vásquez, Paulina; Wilke, Hans; Kasemann, Simone A

2017-01-01

Seabird excrements (guano) have been preserved in the arid climate of Northern Chile since at least the Pliocene. The deposits of marine organic material in coastal areas potentially open a window into the present and past composition of the coastal ocean and its food web. We use the stable isotope composition of nitrogen and carbon as well as element contents to compare the principal prey of the birds, the Peruvian anchovy, with the composition of modern guano. We also investigate the impact of diagenetic changes on the isotopic composition and elemental contents of the pure ornithogenic sediments, starting with modern stratified deposits and extending to fossil guano. Where possible, 14C systematics is used for age information. The nitrogen and carbon isotopic composition of the marine prey (Peruvian anchovy) of the birds is complex as it shows strong systematic variations with latitude. The detailed study of a modern profile that represents a few years of guano deposition up to present reveals systematic changes in nitrogen and carbon isotopic composition towards heavier values that increase with age, i.e. depth. Only the uppermost, youngest layers of modern guano show compositional affinity to the prey of the birds. In the profile, the simultaneous loss of nitrogen and carbon occurs by degassing, and non-volatile elements like phosphorous and calcium are passively enriched in the residual guano. Fossil guano deposits are very low in nitrogen and low in carbon contents, and show very heavy nitrogen isotopic compositions. One result of the study is that the use of guano for tracing nitrogen and carbon isotopic and elemental composition in the marine food web of the birds is restricted to fresh material. Despite systematic changes during diagenesis, there is little promise to retrieve reliable values of marine nitrogen and carbon signatures from older guano. However, the changes in isotopic composition from primary marine nitrogen isotopic signatures towards very heavy values generate a compositionally unique material. These compositions trace the presence of guano in natural ecosystems and its use as fertilizer in present and past agriculture.

The stable isotope composition of nitrogen and carbon and elemental contents in modern and fossil seabird guano from Northern Chile – Marine sources and diagenetic effects

PubMed Central

Pritzkow, Wolfgang; Rosner, Martin; Sepúlveda, Fernando; Vásquez, Paulina; Wilke, Hans; Kasemann, Simone A.

2017-01-01

Seabird excrements (guano) have been preserved in the arid climate of Northern Chile since at least the Pliocene. The deposits of marine organic material in coastal areas potentially open a window into the present and past composition of the coastal ocean and its food web. We use the stable isotope composition of nitrogen and carbon as well as element contents to compare the principal prey of the birds, the Peruvian anchovy, with the composition of modern guano. We also investigate the impact of diagenetic changes on the isotopic composition and elemental contents of the pure ornithogenic sediments, starting with modern stratified deposits and extending to fossil guano. Where possible, 14C systematics is used for age information. The nitrogen and carbon isotopic composition of the marine prey (Peruvian anchovy) of the birds is complex as it shows strong systematic variations with latitude. The detailed study of a modern profile that represents a few years of guano deposition up to present reveals systematic changes in nitrogen and carbon isotopic composition towards heavier values that increase with age, i.e. depth. Only the uppermost, youngest layers of modern guano show compositional affinity to the prey of the birds. In the profile, the simultaneous loss of nitrogen and carbon occurs by degassing, and non-volatile elements like phosphorous and calcium are passively enriched in the residual guano. Fossil guano deposits are very low in nitrogen and low in carbon contents, and show very heavy nitrogen isotopic compositions. One result of the study is that the use of guano for tracing nitrogen and carbon isotopic and elemental composition in the marine food web of the birds is restricted to fresh material. Despite systematic changes during diagenesis, there is little promise to retrieve reliable values of marine nitrogen and carbon signatures from older guano. However, the changes in isotopic composition from primary marine nitrogen isotopic signatures towards very heavy values generate a compositionally unique material. These compositions trace the presence of guano in natural ecosystems and its use as fertilizer in present and past agriculture. PMID:28594902

O and H Isotope Ratios of Syenite Blocks in the El Abrigo Ignimbrite, Tenerife, Canary Islands: A Hydrothermal Fingerprint for Assimilation

NASA Astrophysics Data System (ADS)

Larson, P. B.; Nichols, H. J.; Wolff, J. A.; Marti, J.

2001-12-01

As part of an ongoing project investigating assimilation in ocean island magmas, we are measuring stable isotope ratios of hydrothermally altered lithic fragments in phonolitic pyroclastic deposits from Tenerife, Canary Islands. Nepheline syenite blocks occur in the 0.196 Ma El Abrigo ignimbrite of the Diego Hernandez Formation (DHF). The DHF is the most recent of at least three caldera-forming magmatic cycles on Tenerife. The blocks are fragments of evolved plutons that are chemically similar to phonolites but extend to more strongly differentiated compositions. Distinct major and trace element concentrations suggest that the blocks derive from two intrusions, here referred to as A and B. The B syenites have chemical affinities with the El Abrigo phonolite, and some blocks contain small pockets of residual glass, suggesting that the B pluton may have been coeval with the El Abrigo magma. O isotope ratios of the B syenites lie within the range 4.8 to 7.0 per mil. The B samples are mostly fresh, and their higher O isotope ratios are near pristine magmatic values. Lower values occur in rocks with mild hydrothermal mineralogic alteration, and their values reflect limited high-temperature water-rock isotope exchange. O isotope ratios for A blocks are lower (0.1 to 6.3 per mil, most less than 2.0 per mil), and some samples show extensive mineral alteration. Near-ubiquitous alteration among the A samples, distinct major and trace element compositions, and lack of glass show that this syenite was older than, and unrelated to, the El Abrigo magma. Syenite D/H ratios range from -90 to -120 per mil. O vs H isotope relations indicate that an 18O-depleted meteoric water was the most important reservoir for the high-temperature hydrothermal fluid. Assimilation of altered syenite should provide a distinct stable isotope fingerprint that would be inherited by the product magma. DHF phonolites yield O ratios in the range 5.5 to 7.0 per mil, which may be this fingerprint. Assimilation of variably altered syenites, with accompanying fractionation, is a viable mechanism for producing this stable isotope variability in the magmas.

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses-Isotopic Composition Predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radulescu, Georgeta; Gauld, Ian C; Ilas, Germina

2011-01-01

The expanded use of burnup credit in the United States (U.S.) for storage and transport casks, particularly in the acceptance of credit for fission products, has been constrained by the availability of experimental fission product data to support code validation. The U.S. Nuclear Regulatory Commission (NRC) staff has noted that the rationale for restricting the Interim Staff Guidance on burnup credit for storage and transportation casks (ISG-8) to actinide-only is based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address themore » issues of burnup credit criticality validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the isotopic composition (depletion) validation approach and resulting observations and recommendations. Validation of the criticality calculations is addressed in a companion paper at this conference. For isotopic composition validation, the approach is to determine burnup-dependent bias and uncertainty in the effective neutron multiplication factor (keff) due to bias and uncertainty in isotopic predictions, via comparisons of isotopic composition predictions (calculated) and measured isotopic compositions from destructive radiochemical assay utilizing as much assay data as is available, and a best-estimate Monte Carlo based method. This paper (1) provides a detailed description of the burnup credit isotopic validation approach and its technical bases, (2) describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models to demonstrate its usage and applicability, (3) provides reference bias and uncertainty results based on a quality-assurance-controlled prerelease version of the Scale 6.1 code package and the ENDF/B-VII nuclear cross section data.« less

Treatment of isomers in nucleosynthesis codes

NASA Astrophysics Data System (ADS)

Reifarth, René; Fiebiger, Stefan; Göbel, Kathrin; Heftrich, Tanja; Kausch, Tanja; Köppchen, Christoph; Kurtulgil, Deniz; Langer, Christoph; Thomas, Benedikt; Weigand, Mario

2018-03-01

The decay properties of long-lived excited states (isomers) can have a significant impact on the destruction channels of isotopes under stellar conditions. In sufficiently hot environments, the population of isomers can be altered via thermal excitation or de-excitation. If the corresponding lifetimes are of the same order of magnitude as the typical time scales of the environment, the isomers have to be treated explicitly. We present a general approach to the treatment of isomers in stellar nucleosynthesis codes and discuss a few illustrative examples. The corresponding code is available online at http://exp-astro.de/isomers/.

Coordinated In Situ Analyses of Organic Nanoglobules in the Sutter's Mill Meteorite

NASA Technical Reports Server (NTRS)

Nakamura--Messenger, K.; Messenger, S.; Keller, L. P.; Clemett, S. J.; Nguyen, A. N.; Gibson, E. K.

2013-01-01

The Sutter s Mill meteorite is a newly fallen carbonaceous chondrite that was collected and curated quickly after its fall [1]. Preliminary petrographic and isotopic investigations suggest affinities to the CM2 carbonaceous chondrites. The primitive nature of this meteorite and its rapid recovery provide an opportunity to investigate primordial solar system organic matter in a unique new sample. Organic matter in primitive meteorites and chondritic porous interplanetary dust particles (CP IDPs) is commonly enriched in D/H and N-15/N-14 relative to terrestrial values [2-4]. These anomalies are ascribed to the partial preservation of presolar cold molecular cloud material [2]. Some meteorites and IDPs contain gm-size inclusions with extreme H and N isotopic anomalies [3-5], possibly due to preserved primordial organic grains. The abundance and isotopic composition of C in Sutter's Mill were found to be similar to the Tagish Lake meteorite [6]. In the Tagish Lake meteorite, the principle carriers of large H and N isotopic anomalies are sub-micron hollow organic spherules known as organic nanoglobules [7]. Organic nanoglobules are commonly distributed among primitive meteorites [8, 9] and cometary samples [10]. Here we report in-situ analyses of organic nano-globules in the Sutter's Mill meteorite using UV fluorescence imaging, Fourier-transform infrared spectroscopy (FTIR), scanning transmission electron microscopy (STEM), NanoSIMS, and ultrafast two-step laser mass spectrometry (ultra-L2MS).

New Hafnium Isotope and Trace Element Constraints on the Role of a Plume in Genesis of the Eastern Snake River Plain Basalts, Idaho

NASA Astrophysics Data System (ADS)

Taylor, R. D.; Reid, M. R.; Blichert-Toft, J.

2009-12-01

Bimodal volcanism associated with the eastern Snake River Plain (ESRP)-Yellowstone Plateau province has persisted since approximately 16 Ma. A time-transgressive track of rhyolitic eruptions which young progressively to the east and parallel the motion of the North American plate are overlain by younger basalts with no age progression. Interpretations for the origin of these basalts range from a thermo-chemical mantle plume to incipient melting of the shallow upper mantle, and remain controversial. The enigmatic ESRP basalts are characterized by high 3He/4He, diagnostic of a plume source, but also by lithophile radiogenic isotope signatures that are more enriched than expected for plume-derived OIBs. These features could possibly be caused by isotopic decoupling associated with shallow melting of a hybridized upper mantle, or derivation from an atypical mantle plume, or both by way of mixing. New Hf isotope and trace element data further constrain potential sources for the ESRP basalts. Their Hf isotopic signatures (ɛHf = +0.1 to -5.8) are moderately enriched and consistently fall above or in the upper part of the field of OIBs, with similar Nd isotope signatures (ɛNd = -2.0 to -5.8), indicating a source with high time-integrated Lu/Hf compared with Sm/Nd. The isotopic compositions of the basalts lie between those of Archean SCML and a more depleted end-member source, suggestive of contributions from at least two sources. The grouping of isotopic characteristics is compact compared to other regional volcanism, implying that the hybridization process is highly reproducible within the ESRP. Minor localized differences in isotopic composition may signify local variations in the relative proportions of the end-members. Trace element patterns also support genesis of the ESRP basalts from an enriched source. Our data detect evidence of deeper contributions derived from the garnet-stability field, and a greater affinity of the trace element signatures to plume sources than to sources in the mantle lithosphere. The Hf isotope and trace element characteristics of the ESRP basalts thus support a model of derivation from a deep mantle plume with additional melt contributions and isotopic overprinting from SCML.

Contrasting Cu-Au and Sn-W Granite Metallogeny through the Zircon Geochemical and Isotopic Record

NASA Astrophysics Data System (ADS)

Gardiner, Nicholas; Hawkesworth, Chris; Robb, Laurence; Whitehouse, Martin; Roberts, Nick; Kirkland, Chris

2017-04-01

Magmatic genesis and evolution - mediated by geodynamic setting - exert a primary control on the propensity of granites to be metal fertile. A revolution in our understanding of these petrogenetic processes has been made through a range of mineral-based tools, most notably the common accessory mineral zircon. There is consequently considerable interest in whether the geochemical and isotopic compositions of zircon can be applied to metallogenic problems. The paired magmatic belts of Myanmar have broadly contrasting metallogenic affinities (Sn-W versus Cu-Au), and are interpreted to have formed on the accretionary margin of the subducting Neo-Tethys Ocean. They therefore present the opportunity to geochemically compare and contrast the zircon compositions in two end-member types of granite-hosted mineral deposits generated in collisional settings. We present an integrated zircon isotope (U-Pb, Lu-Hf, O) and trace element dataset that fingerprint: (a) source; (b) redox conditions; and (c) degree of fractionation. These variables all impact on magma fertility, and our key question to address is whether they can be reliably traced and calibrated within the Myanmar zircon record. Granitoid-hosted zircons from the I-type copper arc have juvenile ɛHf (+7 to +12) and mantle-like δ18O (5.3 ‰), whereas zircons from the S-type tin belt have low ɛHf (-7 to -13) and heavier δ18O (6.2-7.7 ‰). Plotting Hf versus U/Yb reaffirms that the tin belt magmas contain greater crustal contributions than the copper arc rocks. Links between whole rock Rb/Sr and zircon Eu/Eu* highlights that the latter can be used to monitor magma fractionation in systems that crystallize plagioclase (low Sr/Y). Ce/Ce* and Eu/Eu* in zircon are thus sensitive to redox and fractionation respectively, and can be used to evaluate the sensitivity of zircons to the metallogenic affinity of their host rocks. Tin contents that exceed the solubility limit are required in order to make a magmatic-hydrothermal deposit, and empirical observations suggest that this threshold may be marked by zircon Eu/Eu* values of ca. < 0.08. The isotope and trace element signatures of both magmatic and detrital zircons can be developed into a useful exploration tool.

Long-Lived Mantle Plumes Sample Multiple Deep Mantle Geochemical Domains: The Example of the Hawaiian-Emperor Chain

NASA Astrophysics Data System (ADS)

Harrison, L.; Weis, D.

2017-12-01

Oceanic island basalts provide the opportunity for the geochemist to study the deep mantle source removed from continental sources of contamination and, for long-lived systems, the evolution of mantle sources with time. In the case of the Hawaiian-Emperor (HE) chain, formation by a long-lived (>81 Myr), deeply-sourced mantle plume allows for insight into plume dynamics and deep mantle geochemistry. The geochemical record of the entire chain is now complete with analysis of Pb-Hf-Nd-Sr isotopes and elemental compositions of the Northwest Hawaiian Ridge (NWHR), which consists of 51 volcanoes spanning 42 Ma between the bend in the chain and the Hawaiian Islands. This segment of the chain previously represented a significant data gap where Hawaiian plume geochemistry changed markedly, along with magmatic flux: only Kea compositions have been observed on Emperor seamounts (>50 Ma), whereas the Hawaiian Islands (<6 Ma) present both Kea and Loa compositions. A database of 700 Hawaiian Island shield basalts Pb-Hf-Nd-Sr isotopic compositions were compiled to construct a logistical regression model of Loa or Kea affinity that sorts data into a dichotomous category and provides insight into the relationship between independent variables. We use this model to predict whether newly analyzed NWHR samples are Loa or Kea composition based on their Pb-Sr-Nd-Hf isotopic compositions. The logistical regression model is significantly better at prediciting Loa or Kea affinity than the constant only model (χ2=263.3, df=4, p<0.0001), with Pb and Sr isotopes providing the most predicitive power. Daikakuji, West Nihoa, Nihoa, and Mokumanamana erupt Loa-type lavas, suggesting that the Loa source is sampled ephemerally during the NWHR and increases in presence and volume towards the younger section of the NWHR (younger than Midway 20-25 Ma). These results complete the picture of Hawaiian mantle plume geochemistry and geodynamics for 81 Myr, and show that the Hawaiian mantle plume has transitioned from a dominately Kea source during the Emperor seamounts and older NWHR to an increasingly enriched Loa source from the mid NWHR to Hawaiian Islands. We propose this is due to Hawaiian mantle plume drift through different lower mantle geohemical domains.

EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations: Theoretical manual, user`s guide, and related documentation (Version 7.0); Part 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolery, T.J.

1992-09-14

EQ3NR is an aqueous solution speciation-solubility modeling code. It is part of the EQ3/6 software package for geochemical modeling. It computes the thermodynamic state of an aqueous solution by determining the distribution of chemical species, including simple ions, ion pairs, and complexes, using standard state thermodynamic data and various equations which describe the thermodynamic activity coefficients of these species. The input to the code describes the aqueous solution in terms of analytical data, including total (analytical) concentrations of dissolved components and such other parameters as the pH, pHCl, Eh, pe, and oxygen fugacity. The input may also include a desiredmore » electrical balancing adjustment and various constraints which impose equilibrium with special pure minerals, solid solution end-member components (of specified mole fractions), and gases (of specified fugacities). The code evaluates the degree of disequilibrium in terms of the saturation index (SI = 1og Q/K) and the thermodynamic affinity (A = {minus}2.303 RT log Q/K) for various reactions, such as mineral dissolution or oxidation-reduction in the aqueous solution itself. Individual values of Eh, pe, oxygen fugacity, and Ah (redox affinity) are computed for aqueous redox couples. Equilibrium fugacities are computed for gas species. The code is highly flexible in dealing with various parameters as either model inputs or outputs. The user can specify modification or substitution of equilibrium constants at run time by using options on the input file.« less

Boron isotopes at the catchment scale, a new potential tool to infer critical zone processes.

NASA Astrophysics Data System (ADS)

Gaillardet, J.; Noireaux, J.; Braun, J. J.; Riotte, J.; Louvat, P.; Bouchez, J.; Lemarchand, D.; Muddu, S.; Mohan Kumar, M.; Candaudap, F.

2017-12-01

Boron is a mid-mass element that has two isotopes, 10B and 11B. These isotopes are largely fractioned by a number of chemical, biological and physical processes. Boron as a great affinity for clays and is useful for life, making it a double tracer of critical zone processes. This study focuses on the Mule Hole Critical Zone Observatory in South India. This is part of the French Research Infrastructure OZCAR and has benefited from the fruitful Indo-French collaboration (Indo-French Cell for Water Sciences) for more that 15 years. Boron and its isotopes were measured in the different compartment of the CZ in Mule Hole, vegetation, atmosphere, throughfall, soil, soil water, river water and compared to the behavior of other elements. The well constrained hydrology in Mule Hole allowed us to calculate the main fluxes affecting boron in the Critical Zone and came to the first order conclusion that the recycling of boron by vegetation is by far the most important flux within the system, reaching 15-20 times the catchment outlet flux. From an isotopic point of view, the total range of variation is measured between -3 ‰ and 77‰, with a bedrock value at 10‰ in classical delta unit, making boron a well suited tracer for constraining CZ processes. The flux of boron most enriched in heavy boron is the throughfall, showing the importance of biological processes in controlling the boron isotopic composition of the stream. Boron in soils in depleted in the heavy isotope but is enriched in boron compared to the bedrock, a surprising situation that we interpret as the legacy of a previous stage of transient weathering. These results indicate a strong decoupling between the behaviors of boron at the surface of the CZ and at depth.

Thallium isotope variations in an ore-bearing continental igneous setting: Collahuasi Formation, northern Chile

NASA Astrophysics Data System (ADS)

Baker, R. G. A.; Rehkämper, M.; Ihlenfeld, C.; Oates, C. J.; Coggon, R.

2010-08-01

Thallium is a highly incompatible element and a large fraction of the bulk silicate Earth Tl budget is, therefore, expected to reside in the continental crust. Nonetheless, the Tl isotope systematics of continental rocks are essentially unexplored at present. Here, we present new Tl isotope composition and concentration data for a suite of 36 intrusive and extrusive igneous rocks from the vicinity of porphyry Cu deposits in the Collahuasi Formation of the Central Andes in northern Chile. The igneous lithologies of the rocks are variably affected by the hydrothermal alteration that accompanied the formation of the Cu deposits. The samples display Tl concentrations that vary by more than an order of magnitude, from 0.1 to 3.2 μg/g, whilst ɛ 205Tl ranges between -5.1 and +0.1 (ɛ 205Tl is the deviation of the 205Tl/ 203Tl isotope ratio of a sample from a standard in parts per 10 4). These variations are primarily thought to be a consequence of hydrothermal alteration processes, including metasomatic transport of Tl, and formation/breakdown of Tl-bearing minerals, which are associated with small but significant Tl isotope effects. The Tl abundances show excellent correlations with both K and Rb concentrations but no co-variation with Cu. This demonstrates that Tl displays only limited chalcophile affinity in the continental crust of the Collahuasi Formation, but behaves as a lithophile element with a distribution that is primarily governed by partitioning of Tl + into K +-bearing phases. Collahuasi samples with propylitic alteration features, which are derived from the marginal parts of the hydrothermal systems, have, on average, slightly lighter Tl isotope compositions than rocks from the more central sericitic and argillic alteration zones. This small but statistically significant difference most likely reflects preferential retention of isotopically heavy Tl in alteration phases, such as white micas and clays, which formed during sericitic and argillic alteration.

Constitutive expression of a putative high-affinity nitrate transporter in Nicotiana plumbaginifolia: evidence for post-transcriptional regulation by a reduced nitrogen source.

PubMed

Fraisier, V; Gojon, A; Tillard, P; Daniel-Vedele, F

2000-08-01

The NpNRT2.1 gene encodes a putative inducible component of the high-affinity nitrate (NO3-) uptake system in Nicotiana plumbaginifolia. Here we report functional and physiological analyses of transgenic plants expressing the NpNRT2.1 coding sequence fused to the CaMV 35S or rolD promoters. Irrespective of the level of NO3- supplied, NO3- contents were found to be remarkably similar in wild-type and transgenic plants. Under specific conditions (growth on 10 mM NO3-), the steady-state NpNRT2. 1 mRNA level resulting from the deregulated transgene expression was accompanied by an increase in 15NO3- influx measured in the low concentration range. This demonstrates for the first time that the NRT2.1 sequence codes a limiting element of the inducible high-affinity transport system. Both 15NO3- influx and mRNA levels decreased in the wild type after exposure to ammonium, in agreement with previous results from many species. Surprisingly, however, influx was also markedly decreased in transgenic plants, despite stable levels of transgene expression in independent transformants after ammonium addition. We conclude that the conditions associated with the supply of a reduced nitrogen source such as ammonium, or with the generation of a further downstream metabolite, probably exert a repressive effect on NO3- influx at both transcriptional and post-transcriptional levels.

Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone.

PubMed

Sić, Siniša; Maier, Norbert M; Rizzi, Andreas M

2016-09-07

The potential and benefits of isotope-coded labeling in the context of MS-based glycan profiling are evaluated focusing on the analysis of O-glycans. For this purpose, a derivatization strategy using d0/d5-1-phenyl-3-methyl-5-pyrazolone (PMP) is employed, allowing O-glycan release and derivatization to be achieved in one single step. The paper demonstrates that this release and derivatization reaction can be carried out also in-gel with only marginal loss in sensitivity compared to in-solution derivatization. Such an effective in-gel reaction allows one to extend this release/labeling method also to glycoprotein/glycoform samples pre-separated by gel-electrophoresis without the need of extracting the proteins/digested peptides from the gel. With highly O-glycosylated proteins (e.g. mucins) LODs in the range of 0.4 μg glycoprotein (100 fmol) loaded onto the electrophoresis gel can be attained, with minor glycosylated proteins (like IgAs, FVII, FIX) the LODs were in the range of 80-100 μg (250 pmol-1.5 nmol) glycoprotein loaded onto the gel. As second aspect, the potential of isotope coded labeling as internal standardization strategy for the reliable determination of quantitative glycan profiles via MALDI-MS is investigated. Towards this goal, a number of established and emerging MALDI matrices were tested for PMP-glycan quantitation, and their performance is compared with that of ESI-based measurements. The crystalline matrix 2,6-dihydroxyacetophenone (DHAP) and the ionic liquid matrix N,N-diisopropyl-ethyl-ammonium 2,4,6-trihydroxyacetophenone (DIEA-THAP) showed potential for MALDI-based quantitation of PMP-labeled O-glycans. We also provide a comprehensive overview on the performance of MS-based glycan quantitation approaches by comparing sensitivity, LOD, accuracy and repeatability data obtained with RP-HPLC-ESI-MS, stand-alone nano-ESI-MS with a spray-nozzle chip, and MALDI-MS. Finally, the suitability of the isotope-coded PMP labeling strategy for O-glycan profiling of biological important proteins is demonstrated by comparative analysis of IgA immunoglobulins and two coagulation factors. Copyright © 2016 Elsevier B.V. All rights reserved.

VEGF-Iron Oxide Conjugate for Dual MR and PET Imaging of Breast Cancer Angiogenesis

DTIC Science & Technology

2007-09-01

with both VEGF121 and PET isotope 64Cu (t1/2 = 12.7 h) and test the dual probe in vitro. Aim 2: To test the PET and mMRI efficacy of the dual...iron oxide nanoparticles conjugated with macrocyclic chelating agent DOTA for 64Cu -labeling and cyclic RGD peptide for integrin alpha(v)beta(3...radionuclide 64Cu without loss of receptor affinity and functional activity of the protein. 64Cu -VEGF is also able to delineate small tumors that are

Carbon-13 Isotopic Abundance and Concentration of Atmospheric Methane for Background Air in the Southern and Northern Hemispheres from 1978 to 1989 (NDP-049)

DOE Data Explorer

Stevens, C. M. [Chemical Technology Division, Argonne National Laboratory, Argonne, Illinois (USA)

2012-01-01

This data package presents atmospheric CH4 concentration and 13C isotopic abundance data derived from air samples collected over the period 1978-1989 at globally distributed clean-air sites. The data set comprises 201 records, 166 from the Northern Hemisphere and 35 from the Southern Hemisphere. The air samples were collected mostly in rural or marine locations remote from large sources of CH4 and are considered representative of tropospheric background conditions. The air samples were processed by isolation of CH4 from air and conversion to CO2 for isotopic analysis by isotope ratio mass spectrometry. These data represent one of the earliest records of 13C isotopic yy!measurements for atmospheric methane and have been used to refine estimates of CH4 emissions, calculate annual growth rates of emissions from changing sources, and provide evidence for changes in the rate of atmospheric removal of CH4. The data records consist of sample collection date; number of samples combined for analysis; sampling location; analysis date; CH4 concentration; 13C isotopic abundance; and flag codes to indicate outliers, repeated analyses, and other information.

Nuclear Fuel Depletion Analysis Using Matlab Software

NASA Astrophysics Data System (ADS)

Faghihi, F.; Nematollahi, M. R.

Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the 239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.

Large-scale shell-model calculations for 32-39P isotopes

NASA Astrophysics Data System (ADS)

Srivastava, P. C.; Hirsch, J. G.; Ermamatov, M. J.; Kota, V. K. B.

2012-10-01

In this work, the structure of 32-39P isotopes is described in the framework of stateof-the-art large-scale shell-model calculations, employing the code ANTOINE with three modern effective interactions: SDPF-U, SDPF-NR and the extended pairing plus quadrupole-quadrupoletype forces with inclusion of monopole interaction (EPQQM). Protons are restricted to fill the sd shell, while neutrons are active in the sd - pf valence space. Results for positive and negative level energies and electromagnetic observables are compared with the available experimental data.

ORNL Resolved Resonance Covariance Generation for ENDF/B-VII.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leal, Luiz C.; Guber, Klaus H.; Wiarda, Dorothea

2012-12-01

Resonance-parameter covariance matrix (RPCM) evaluations in the resolved resonance regionwere done at the Oak Ridge National Laboratory (ORNL) for the chromium isotopes, titanium isotopes, 19F, 58Ni, 60Ni, 35Cl, 37Cl, 39K, 41K, 55Mn, 233U, 235U, 238U, and 239Pu using the computer code SAMMY. The retroactive approach of the code SAMMY was used to generate the RPCMs for 233U. For 235U, the approach used for covariance generation was similar to the retroactive approach with the distinction that real experimental data were used as opposed to data generated from the resonance parameters. RPCMs for 238U and 239Pu were generated together with the resonancemore » parameter evaluations. The RPCMs were then converted in the ENDF format using the FILE32 representation. Alternatively, for computer storage reasons, the FILE32 was converted in the FILE33 cross section covariance matrix (CSCM). Both representations were processed using the computer code PUFF-IV. This paper describes the procedures used to generate the RPCM and CSCM in the resonance region for ENDF/B-VII.1. The impact of data uncertainty in nuclear reactor benchmark calculations is also presented.« less

Complexes of DOTA-bisphosphonate conjugates: probes for determination of adsorption capacity and affinity constants of hydroxyapatite.

PubMed

Vitha, Tomas; Kubícek, Vojtech; Hermann, Petr; Kolar, Zvonimir I; Wolterbeek, Hubert Th; Peters, Joop A; Lukes, Ivan

2008-03-04

The adsorption on hydroxyapatite of three conjugates of a bisphosphonate and a macrocycle having C1, C2, and C3 spacers and their terbium complexes was studied by the radiotracer method using 160Tb as the label. The radiotracer-containing complex of the conjugate with the C3 spacer was used as a probe for the determination of the adsorption parameters of other bisphosphonates that lack a DOTA unit. A physicochemical model describing the competitive adsorption was successfully applied in the fitting of the obtained data. The maximum adsorption capacity of bisphosphonates containing bulky substituents is determined mainly by their size. For bisphosphonates having no DOTA moiety, the maximum adsorption capacity is determined by the electrostatic repulsion between negatively charged bisphosphonate groups. Compounds with a hydroxy or amino group attached to the alpha-carbon atom show higher affinities. Macrocyclic compounds containing a short spacer between the different bisphosphonic acid groups and the macrocyclic unit exhibit high affinities, indicating a synergic effect of the bisphosphonic and the macrocyclic groups during adsorption. The competition method described uses a well-characterized complex and allows a simple evaluation of the adsorption behavior of bisphosphonates. The application of the macrocycle-bisphosphonate conjugates allows easy radiolabeling via complexation of a suitable metal isotope.

77 FR 37446 - Advisory Committee on the Medical Uses of Isotopes: Meeting Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-21

...; and (6) update on domestic production of molybdenum-99. The regular meeting agenda is subject to..., Advisory Committee Management Officer. [FR Doc. 2012-15173 Filed 6-20-12; 8:45 am] BILLING CODE 7590-01-P ...

Benchmarking of neutron production of heavy-ion transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase.

PubMed

Michael, Claudia; Rizzi, Andreas M

2015-02-27

Glycan reductive isotope labeling (GRIL) using (12)C6-/(13)C6-aniline as labeling reagent is reported with the aim of quantitative N-glycan fingerprinting. Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. The main benefit of using stable isotope-coding in the context of comparative glycomics lies in the improved accuracy and precision of the quantitative analysis in combined samples and in the potential of correcting for structure-dependent incomplete enzymatic release of oligosaccharides when comparing identical target proteins. The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. It is shown that the developed method is capable of determining relative amounts of N-glycans (including isomers) comparing two samples in one single HPLC-MS run. The analytical potential and usefulness of GRIL in combination with PGC-ESI-TOF-MS is demonstrated comparing glycosylation in human monoclonal antibodies produced in Chinese hamster ovary cells (CHO) and hybridoma cell lines. Copyright © 2015 Elsevier B.V. All rights reserved.

Statistical uncertainty analysis applied to the DRAGONv4 code lattice calculations and based on JENDL-4 covariance data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez-Solis, A.; Demaziere, C.; Ekberg, C.

2012-07-01

In this paper, multi-group microscopic cross-section uncertainty is propagated through the DRAGON (Version 4) lattice code, in order to perform uncertainty analysis on k{infinity} and 2-group homogenized macroscopic cross-sections predictions. A statistical methodology is employed for such purposes, where cross-sections of certain isotopes of various elements belonging to the 172 groups DRAGLIB library format, are considered as normal random variables. This library is based on JENDL-4 data, because JENDL-4 contains the largest amount of isotopic covariance matrixes among the different major nuclear data libraries. The aim is to propagate multi-group nuclide uncertainty by running the DRAGONv4 code 500 times, andmore » to assess the output uncertainty of a test case corresponding to a 17 x 17 PWR fuel assembly segment without poison. The chosen sampling strategy for the current study is Latin Hypercube Sampling (LHS). The quasi-random LHS allows a much better coverage of the input uncertainties than simple random sampling (SRS) because it densely stratifies across the range of each input probability distribution. Output uncertainty assessment is based on the tolerance limits concept, where the sample formed by the code calculations infers to cover 95% of the output population with at least a 95% of confidence. This analysis is the first attempt to propagate parameter uncertainties of modern multi-group libraries, which are used to feed advanced lattice codes that perform state of the art resonant self-shielding calculations such as DRAGONv4. (authors)« less

EASY-II Renaissance: n, p, d, α, γ-induced Inventory Code System

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Eastwood, J. W.; Morgan, J. G.

2014-04-01

The European Activation SYstem has been re-engineered and re-written in modern programming languages so as to answer today's and tomorrow's needs in terms of activation, transmutation, depletion, decay and processing of radioactive materials. The new FISPACT-II inventory code development project has allowed us to embed many more features in terms of energy range: up to GeV; incident particles: alpha, gamma, proton, deuteron and neutron; and neutron physics: self-shielding effects, temperature dependence and covariance, so as to cover all anticipated application needs: nuclear fission and fusion, accelerator physics, isotope production, stockpile and fuel cycle stewardship, materials characterization and life, and storage cycle management. In parallel, the maturity of modern, truly general purpose libraries encompassing thousands of target isotopes such as TENDL-2012, the evolution of the ENDF-6 format and the capabilities of the latest generation of processing codes PREPRO, NJOY and CALENDF have allowed the activation code to be fed with more robust, complete and appropriate data: cross sections with covariance, probability tables in the resonance ranges, kerma, dpa, gas and radionuclide production and 24 decay types. All such data for the five most important incident particles (n, p, d, α, γ), are placed in evaluated data files up to an incident energy of 200 MeV. The resulting code system, EASY-II is designed as a functional replacement for the previous European Activation System, EASY-2010. It includes many new features and enhancements, but also benefits already from the feedback from extensive validation and verification activities performed with its predecessor.

Iron and silicon isotope behaviour accompanying weathering in Icelandic soils, and the implications for iron export from peatlands

NASA Astrophysics Data System (ADS)

Opfergelt, S.; Williams, H. M.; Cornelis, J. T.; Guicharnaud, R. A.; Georg, R. B.; Siebert, C.; Gislason, S. R.; Halliday, A. N.; Burton, K. W.

2017-11-01

Incipient warming of peatlands at high latitudes is expected to modify soil drainage and hence the redox conditions, which has implications for Fe export from soils. This study uses Fe isotopes to assess the processes controlling Fe export in a range of Icelandic soils including peat soils derived from the same parent basalt, where Fe isotope variations principally reflect differences in weathering and drainage. In poorly weathered, well-drained soils (non-peat soils), the limited Fe isotope fractionation in soil solutions relative to the bulk soil (Δ57Fesolution-soil = -0.11 ± 0.12‰) is attributed to proton-promoted mineral dissolution. In the more weathered poorly drained soils (peat soils), the soil solutions are usually lighter than the bulk soil (Δ57Fesolution-soil = -0.41 ± 0.32‰), which indicates that Fe has been mobilised by reductive mineral dissolution and/or ligand-controlled dissolution. The results highlight the presence of Fe-organic complexes in solution in anoxic conditions. An additional constraint on soil weathering is provided by Si isotopes. The Si isotope composition of the soil solutions relative to the soil (Δ30Sisolution-soil = 0.92 ± 0.26‰) generally reflects the incorporation of light Si isotopes in secondary aluminosilicates. Under anoxic conditions in peat soils, the largest Si isotope fractionation in soil solutions relative to the bulk soil is observed (Δ30Sisolution-soil = 1.63 ± 0.40‰) and attributed to the cumulative contribution of secondary clay minerals and amorphous silica precipitation. Si supersaturation in solution with respect to amorphous silica is reached upon freezing when Al availability to form aluminosilicates is limited by the affinity of Al for metal-organic complexes. Therefore, the precipitation of amorphous silica in peat soils indirectly supports the formation of metal-organic complexes in poorly drained soils. These observations highlight that in a scenario of decreasing soil drainage with warming high latitude peatlands, Fe export from soils as Fe-organic complexes will increase, which in turn has implications for Fe transport in rivers, and ultimately the delivery of Fe to the oceans.

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Botta, F.; Mairani, A.; Battistoni, G.

Purpose: The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernelmore » (DPK), quantifying the energy deposition all around a point isotropic source, is often the one. Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10{sup -3} MeV) and for beta emitting isotopes commonly used for therapy ({sup 89}Sr, {sup 90}Y, {sup 131}I, {sup 153}Sm, {sup 177}Lu, {sup 186}Re, and {sup 188}Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8{center_dot}R{sub CSDA} and 0.9{center_dot}R{sub CSDA} for monoenergetic electrons (R{sub CSDA} being the continuous slowing down approximation range) and within 0.8{center_dot}X{sub 90} and 0.9{center_dot}X{sub 90} for isotopes (X{sub 90} being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9{center_dot}R{sub CSDA} and 0.9{center_dot}X{sub 90} for electrons and isotopes, respectively. Results: Concerning monoenergetic electrons, within 0.8{center_dot}R{sub CSDA} (where 90%-97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in water, 8.3% in bone). The discrepancies between fluka and the other codes are of the same order of magnitude than those observed when comparing the other codes among them, which can be referred to the different simulation algorithms. When considering the beta spectra, discrepancies notably reduce: within 0.9{center_dot}X{sub 90}, fluka and penelope differ for less than 1% in water and less than 2% in bone with any of the isotopes here considered. Complete data of fluka DPKs are given as Supplementary Material as a tool to perform dosimetry by analytical point kernel convolution. Conclusions: fluka provides reliable results when transporting electrons in the low energy range, proving to be an adequate tool for nuclear medicine dosimetry.« less

Reactive Fluid Flow and Applications to Diagenesis, Mineral Deposits, and Crustal Rocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rye, Danny M.; Bolton, Edward W.

2002-11-04

The objective is to initiate new: modeling of coupled fluid flow and chemical reactions of geologic environments; experimental and theoretical studies of water-rock reactions; collection and interpretation of stable isotopic and geochemical field data at many spatial scales of systems involving fluid flow and reaction in environments ranging from soils to metamorphic rocks. Theoretical modeling of coupled fluid flow and chemical reactions, involving kinetics, has been employed to understand the differences between equilibrium, steady-state, and non-steady-state behavior of the chemical evolution of open fluid-rock systems. The numerical codes developed in this project treat multi-component, finite-rate reactions combined with advective andmore » dispersive transport in multi-dimensions. The codes incorporate heat, mass, and isotopic transfer in both porous and fractured media. Experimental work has obtained the kinetic rate laws of pertinent silicate-water reactions and the rates of Sr release during chemical weathering. Ab-initio quantum mechanical techniques have been applied to obtain the kinetics and mechanisms of silicate surface reactions and isotopic exchange between water and dissolved species. Geochemical field-based studies were carried out on the Wepawaug metamorphic schist, on the Irish base-metal sediment-hosted ore system, in the Dalradian metamorphic complex in Scotland, and on weathering in the Columbia River flood basalts. The geochemical and isotopic field data, and the experimental and theoretical rate data, were used as constraints on the numerical models and to determine the length and time scales relevant to each of the field areas.« less

Application of Strep-Tactin XT for affinity purification of Twin-Strep-tagged CB2, a G protein-coupled cannabinoid receptor

PubMed Central

Yeliseev, Alexei; Zoubak, Lioudmila; Schmidt, Thomas G.M.

2017-01-01

Human cannabinoid receptor CB2 belongs to the class A of G protein-coupled receptor (GPCR). High resolution structural studies of CB2 require milligram quantities of purified, structurally intact protein. Here we describe an efficient protocol for purification of this protein using the Twin-Strep-tag/Strep-Tactin XT system. To improve the affinity of interaction of the recombinant CB2 with the resin, the double repeat of the Strep-tag was attached either to the N- or C-terminus of CB2 via a short linker. The CB2 was isolated at high purity from dilute solutions containing high concentrations of detergents, glycerol and salts, by capturing onto the Strep-Tactin XT resin, and was eluted from the resin under mild conditions upon addition of biotin. Surface plasmon resonance studies performed demonstrate the high affinity of interaction between the Twin-Strep-tag fused to the CB2 and Strep-Tactin XT with an estimated Kd in the low nanomolar range. The affinity of binding did not vary significantly in response to the position of the tag at either N- or C-termini of the fusion. The variation in the length of the linker between the double repeats of the Strep-tag from 6 to 12 amino acid residues did not significantly affect the binding. The novel purification protocol reported here enables efficient isolation of a recombinant GPCR expressed at low titers in host cells. This procedure is suitable for preparation of milligram quantities of stable isotope-labelled receptor for high-resolution NMR studies. PMID:27867058

Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling1[C][W

PubMed Central

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg

2012-01-01

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study.

PubMed

Han, Wen-Ge; Sandala, Gregory M; Giammona, Debra Ann; Bashford, Donald; Noodleman, Louis

2011-11-14

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.

A versatile expression vector for the growth and amplification of unmodified phage display polypeptides.

PubMed

Winton, Alexander J; Baptiste, Janae L; Allen, Mark A

2018-09-01

Proteins and polypeptides represent nature's most complex and versatile polymer. They provide complicated shapes, diverse chemical functionalities, and tightly regulated and controlled sizes. Several disease states are related to the misfolding or overproduction of polypeptides and yet polypeptides are present in several therapeutic molecules. In addition to biological roles; short chain polypeptides have been shown to interact with and drive the bio-inspired synthesis or modification of inorganic materials. This paper outlines the development of a versatile cloning vector which allows for the expression of a short polypeptide by controlling the incorporation of a desired DNA coding insert. As a demonstration of the efficacy of the expression system, a solid binding polypeptide identified from M13 phage display was expressed and purified. The solid binding polypeptide was expressed as a soluble 6xHis-SUMO tagged construct. Expression was performed in E. coli using auto-induction followed by Ni-NTA affinity chromatography and ULP1 protease cleavage. Methodology demonstrates the production of greater than 8 mg of purified polypeptide per liter of E. coli culture. Isotopic labeling of the peptide is also demonstrated. The versatility of the designed cloning vector, use of the 6xHis-SUMO solubility partner, bacterial expression in auto-inducing media and the purification methodology make this expressionun vector a readily scalable and user-friendly system for the creation of desired peptide domains. Copyright © 2018. Published by Elsevier Inc.

Functional study of miR-27a in human hepatic stellate cells by proteomic analysis: comprehensive view and a role in myogenic tans-differentiation.

PubMed

Ji, Yuhua; Zhang, Jinsheng; Wang, Wenwen; Ji, Juling

2014-01-01

We previous reported that miR-27a regulates lipid metabolism and cell proliferation during hepatic stellate cells (HSCs) activation. To further explore the biological function and underlying mechanisms of miR-27a in HSCs, global protein expression affected by overexpression of miR-27a in HSCs was analyzed by a cleavable isotope-coded affinity tags (cICAT) based comparative proteomic approach. In the present study, 1267 non-redundant proteins were identified with unique accession numbers (score ≥1.3, i.e. confidence ≥95%), among which 1171 were quantified and 149 proteins (12.72%) were differentially expressed with a differential expression ratio of 1.5. We found that up-regulated proteins by miR-27a mainly participate in cell proliferation and myogenesis, while down-regulated proteins were the key enzymes involved in de novo lipid synthesis. The expression of a group of six miR-27a regulated proteins was validated and the function of one miR-27a regulated protein was further validated. The results not only delineated the underlying mechanism of miR-27a in modulating fat metabolism and cell proliferation, but also revealed a novel role of miR-27a in promoting myogenic tans-differentiation during HSCs activation. This study also exemplified proteomics strategy as a powerful tool for the functional study of miRNA.

Thiol-based redox proteins in abscisic acid and methyl jasmonate signaling in Brassica napus guard cells.

PubMed

Zhu, Mengmeng; Zhu, Ning; Song, Wen-yuan; Harmon, Alice C; Assmann, Sarah M; Chen, Sixue

2014-05-01

Reversibly oxidized cysteine sulfhydryl groups serve as redox sensors or targets of redox sensing that are important in various physiological processes. However, little is known about redox-sensitive proteins in guard cells and how they function in stomatal signaling. In this study, Brassica napus guard-cell proteins altered by redox in response to abscisic acid (ABA) or methyl jasmonate (MeJA) were identified by complementary proteomics approaches, saturation differential in-gel electrophoresis and isotope-coded affinity tagging. In total, 65 and 118 potential redox-responsive proteins were identified in ABA- and MeJA-treated guard cells, respectively. All the proteins contain at least one cysteine, and over half of them are predicted to form intra-molecular disulfide bonds. Most of the proteins fall into the functional groups of 'energy', 'stress and defense' and 'metabolism'. Based on the peptide sequences identified by mass spectrometry, 30 proteins were common to ABA- and MeJA-treated samples. A total of 44 cysteines were mapped in the identified proteins, and their levels of redox sensitivity were quantified. Two of the proteins, a sucrose non-fermenting 1-related protein kinase and an isopropylmalate dehydrogenase, were confirmed to be redox-regulated and involved in stomatal movement. This study creates an inventory of potential redox switches, and highlights a protein redox regulatory mechanism in ABA and MeJA signal transduction in guard cells. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*

PubMed Central

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

Evaluating the provenance of Permian-Triassic and Palaeocene-Eocene ash beds by high precision U-Pb and Lu-Hf isotopic analyses of zircons: linking local sedimentary records to global events

NASA Astrophysics Data System (ADS)

Eivind Augland, Lars; Jones, Morgan; Planke, Sverre; Svensen, Henrik; Tegner, Christian

2016-04-01

Zircons are a powerful tool in geochronology and isotope geochemistry, as their affinity for U and Hf in the crystal structure and the low initial Pb and Lu allow for precise and accurate dating by U-Pb ID-TIMS and precise and accurate determination of initial Hf isotopic composition by solution MC-ICP-MS analysis. The U-Pb analyses provide accurate chronostratigraphic controls on the sedimentary successions and absolute age frames for the biotic evolution across geological boundaries. Moreover, the analyses of Lu-Hf by solution MC-ICP-MS after Hf-purification column chemistry provide a powerful and robust fingerprinting tool to test the provenance of individual ash beds. Here we focus on ash beds from Permian-Triassic and Palaeocene successions in Svalbard and from the Palaeocene-Eocene Thermal Maximum (PETM) in Fur, Denmark. Used in combination with whole rock geochemistry from the ash layers and the available geochemical and isotopic data from potential source volcanoes, these data are used to evaluate the provenance of the Permian-Triassic and Palaeocene ashes preserved in Svalbard and PETM ashes in Denmark. If explosive eruptions from volcanic centres such as the Siberian Traps and the North Atlantic Igneous Province (NAIP) can be traced to distal basins as ash layers, they provide robust tests of hypotheses of global synchronicity of environmental changes and biotic crises. In addition, the potential correlation of ash layers with source volcanoes will aid in constraining the extent of explosive volcanism in the respective volcanic centres. The new integrated data sets will also contribute to establish new reference sections for the study of these boundary events when combined with stable isotope data and biostratigraphy.

Steroid isotopic standards for gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS).

PubMed

Zhang, Ying; Tobias, Herbert J; Brenna, J Thomas

2009-03-01

Carbon isotope ratio (CIR) analysis of urinary steroids using gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS) is a recognized test to detect illicit doping with synthetic testosterone. There are currently no universally used steroid isotopic standards (SIS). We adapted a protocol to prepare isotopically uniform steroids for use as a calibrant in GCC-IRMS that can be analyzed under the same conditions as used for steroids extracted from urine. Two separate SIS containing a mixture of steroids were created and coded CU/USADA 33-1 and CU/USADA 34-1, containing acetates and native steroids, respectively. CU/USADA 33-1 contains 5alpha-androstan-3beta-ol acetate (5alpha-A-AC), 5alpha-androstan-3alpha-ol-17-one acetate (androsterone acetate, A-AC), 5beta-androstan-3alpha-ol-11, 17-dione acetate (11-ketoetiocholanolone acetate, 11k-AC) and 5alpha-cholestane (Cne). CU/USADA 34-1 contains 5beta-androstan-3alpha-ol-17-one (etiocholanolone, E), 5alpha-androstan-3alpha-ol-17-one (androsterone, A), and 5beta-pregnane-3alpha, 20alpha-diol (5betaP). Each mixture was prepared and dispensed into a set of about 100 ampoules using a protocol carefully designed to minimize isotopic fractionation and contamination. A natural gas reference material, NIST RM 8559, traceable to the international standard Vienna PeeDee Belemnite (VPDB) was used to calibrate the SIS. Absolute delta(13)C(VPDB) and Deltadelta(13)C(VPDB) values from randomly selected ampoules from both SIS indicate uniformity of steroid isotopic composition within measurement reproducibility, SD(delta(13)C)<0.2 per thousand. This procedure for creation of isotopic steroid mixtures results in consistent standards with isotope ratios traceable to the relevant international reference material.

Total and Compound Formation Cross Sections for Americium Nuclei: Recommendations for Coupled-Channels Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escher, J. E.

Calculations for total cross sections and compound-nucleus (CN) formation cross sections for americium isotopes are described, for use in the 2017 NA-22 evaluation effort. The code ECIS 2006 was used in conjunction with Frank Dietrich's wrapper `runtemplate'.

Adjoint-Based Sensitivity and Uncertainty Analysis for Density and Composition: A User’s Guide

DOE PAGES

Favorite, Jeffrey A.; Perko, Zoltan; Kiedrowski, Brian C.; ...

2017-03-01

The ability to perform sensitivity analyses using adjoint-based first-order sensitivity theory has existed for decades. This paper provides guidance on how adjoint sensitivity methods can be used to predict the effect of material density and composition uncertainties in critical experiments, including when these uncertain parameters are correlated or constrained. Two widely used Monte Carlo codes, MCNP6 (Ref. 2) and SCALE 6.2 (Ref. 3), are both capable of computing isotopic density sensitivities in continuous energy and angle. Additionally, Perkó et al. have shown how individual isotope density sensitivities, easily computed using adjoint methods, can be combined to compute constrained first-order sensitivitiesmore » that may be used in the uncertainty analysis. This paper provides details on how the codes are used to compute first-order sensitivities and how the sensitivities are used in an uncertainty analysis. Constrained first-order sensitivities are computed in a simple example problem.« less

Determination of the δ34S of Total Sulfur in Solids: RSIL Lab Code 1800

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler B.

2006-01-01

The purpose of Reston Stable Isotope Laboratory Lab (RSIL) Code 1800 is to determine the δ(34S/32S), abbreviated as δ34S, of total sulfur in a solid sample. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total sulfur in a solid sample into SO2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the relative difference in stable sulfur isotope-amount ratio (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in tin capsules and loaded into a Costech Zero-Blank Autosampler on the EA. Under computer control, samples are dropped into a heated tube reaction tube that combines both the oxidation and the reduction reactions. The combustion takes place in a He atmosphere that contains an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a He carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph (GC). The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Thermo-Finnigan ConFlo II interface, which also is used to inject SO2 reference gas and He for sample dilution. The IRMS is a Thermo-Finnigan DeltaPlus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; and m/z 66 = SO2 = 34S16O16O primarily.

Odorant Screening and Quantitation of Thiols in Carmenere Red Wine by Gas Chromatography-Olfactometry and Stable Isotope Dilution Assays.

PubMed

Pavez, Carolina; Agosin, Eduardo; Steinhaus, Martin

2016-05-04

The sensory impact of thiols in Vitis vinifera 'Carmenere' red wines was evaluated. For this purpose, aroma extract dilution analysis was applied to the thiols isolated from a Carmenere red wine by affinity chromatography with a mercurated agarose gel. Results revealed the presence of four odorants, identified as 2-furanylmethanethiol, 3-sulfanylhexyl acetate, 3-sulfanyl-1-hexanol, and 2-methyl-3-sulfanyl-1-butanol, with the latter being described here for the first time in Carmenere red wines. Quantitation of the four thiols in the Carmenere wine screened by aroma extract dilution analysis and in three additional Carmenere wines by stable isotope dilution assays resulted in concentrations above the respective orthonasal odor detection threshold values. Triangle tests applied to wine model solutions with and without the addition of the four thiols showed significant differences, thus suggesting that the compounds do have the potential to influence the overall aroma of red wine.

"Live" (stained) benthic foraminiferal living depths, stable isotopes, and taxonomy offshore South Georgia, Southern Ocean: implications for calcification depths

NASA Astrophysics Data System (ADS)

Dejardin, Rowan; Kender, Sev; Allen, Claire S.; Leng, Melanie J.; Swann, George E. A.; Peck, Victoria L.

2018-01-01

It is widely held that benthic foraminifera exhibit species-specific calcification depth preferences, with their tests recording sediment pore water chemistry at that depth (i.e. stable isotope and trace metal compositions). This assumed depth-habitat-specific pore water chemistry relationship has been used to reconstruct various palaeoenvironmental parameters, such as bottom water oxygenation. However, many deep-water foraminiferal studies show wide intra-species variation in sediment living depth but relatively narrow intra-species variation in stable isotope composition. To investigate this depth-habitat-stable-isotope relationship on the shelf, we analysed depth distribution and stable isotopes of living (Rose Bengal stained) benthic foraminifera from two box cores collected on the South Georgia shelf (ranging from 250 to 300 m water depth). We provide a comprehensive taxonomic analysis of the benthic fauna, comprising 79 taxonomic groupings. The fauna shows close affinities with shelf assemblages from around Antarctica. We find live specimens of a number of calcareous species from a range of depths in the sediment column. Stable isotope ratios (δ13C and δ18O) were measured on stained specimens of three species, Astrononion echolsi, Cassidulinoides porrectus, and Buccella sp. 1, at 1 cm depth intervals within the downcore sediment sequences. In agreement with studies in deep-water settings, we find no significant intra-species variability in either δ13Cforam or δ18Oforam with sediment living depth on the South Georgia shelf. Our findings add to the growing evidence that infaunal benthic foraminiferal species calcify at a fixed depth. Given the wide range of depths at which we find living, infaunal species, we speculate that they may actually calcify predominantly at the sediment-seawater interface, where carbonate ion concentration and organic carbon availability is at a maximum.

The origin of Neoproterozoic Cap Carbonates: a view from Mg and Sr Isotopes

NASA Astrophysics Data System (ADS)

Liu, C.; Raub, T. D.; Evans, D. A.; Wang, Z.

2010-12-01

Neoproterozoic cap carbonates are suggested to document Earth’s transition from a ‘snowball earth’ to an ‘extreme greenhouse’ environment. Geochemistry of these rocks is essential for its paleo-environment reconstruction, and Mg and Sr isotopes can help to understand its origin and constrain geochemical evolution of the contemporary ocean. In this study, we studied Mg and Sr isotope composition of 18 cap dolostone samples from Nuccaleena formation carbonate and one from the the mixed siliciclastic transition at its base at Elatina Creek in Adelaide Geosyncline of South Australia. We established a step-leaching procedure using ammonium acetate, various concentrations of acetic acid, and HCl on four of these cap carbonate samples to untangle the isotopic signatures of its various constituent phases. 87Sr/86Sr values of the leachates in each sample decrease continuously as leaching process proceeds and sometimes rebound as silicates are dissolved. The lowest leachate 87Sr/86Sr values, down to 0.7084, are lower than the reported dolostone(~0.7096) but still higher than those of limestones overlying the dolostone in other basins(~0.7079), indicating an input of increasing level of weathering to the ocean over the course of cap-carbonate precipitation. In contrast, δ26MgDSM3 variation with progressing leaching steps exhibits a wave pattern (variation up to 0.4~0.5‰) during the leaching processes, due to different chemical affinity of Mg in various mineral phases. More importantly, Mg isotope composition of the portion that is associated with stratigraphically low, minimum Sr isotope composition is similar to those of contemporary corals (or inorganic aragonite precipitation), but up to ca. 0.6 per mil lower than stratigraphically-higher values, suggesting a warmer weather and/or more significant silicate weathering than contemporary Earth’s climate, and a transition from physical weathering to chemical weather during deglaciation.

Coordinated in Situ Analyses of Organic Nanoglobules in the Sutter's Mill Meteorite

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Messenger, S.; Keller, L. P.; Clemett, S. J.; Nguyen, A. N.; Gibson, E. K.

2013-01-01

The Sutter's Mill meteorite is a newly fallen carbonaceous chondrite that was collected and curated quickly after its fall. Preliminary petrographic and isotopic investigations suggest affinities to the CM2 carbonaceous chondrites. The primitive nature of this meteorite and its rapid recovery provide an opportunity to investigate primordial solar system organic matter in a unique new sample. Here we report in-situ analyses of organic nanoglobules in the Sutter's Mill meteorite using UV fluorescence imaging, Fourier-transform infrared spectroscopy (FTIR), scanning transmission electron microscopy (STEM), NanoSIMS, and ultrafast two-step laser mass spectrometry (ultra-L2MS).

"Taconic" arc magmatism in the central Brooks Range, Alaska: New U-Pb zircon geochronology and Hf isotopic data from the lower Paleozoic Apoon assemblage of the Doonerak fenster

NASA Astrophysics Data System (ADS)

Strauss, J. V.; Hoiland, C. W.; Ward, W.; Johnson, B.; McClelland, W.

2015-12-01

The Doonerak fenster in the central Brooks Range, AK, exposes an important package of early Paleozoic volcanic and sedimentary rocks called the Apoon assemblage, which are generally interpreted as para-autochthonous basement to the Mesozoic-Cenozoic Brookian fold-thrust belt. Recognition in the 1970's of a major pre-Mississippian unconformity within the window led to correlations between Doonerak and the North Slope (sub-) terrane of the Arctic Alaska Chukotka microplate (AACM); however, the presence of arc-affinity volcanism and the apparent lack of pre-Mississippian deformation in the Apoon assemblage makes this link tenuous and complicates Paleozoic tectonic reconstructions of the AACM. Previous age constraints on the Apoon assemblage are limited to a handful of Middle Cambrian-Silurian paleontological collections and five K-Ar and 40Ar/39Ar hornblende ages from mafic dikes ranging from ~380-520 Ma. We conducted U-Pb geochronologic and Hf isotopic analyses on igneous and sedimentary zircon from the Apoon assemblage to test Paleozoic links with the North Slope and to assess the tectonic and paleogeographic setting of the Doonerak region. U-Pb analyses on detrital zircon from Apoon rocks yield a spectrum of unimodal and polymodal age populations, including prominent age groups of ca. 420-490, 960-1250, 1380­-1500, 1750-1945, and 2650-2830 Ma. Hf isotopic data from the ca. 410-490 Ma age population are generally juvenile (~7-10 ɛHf), implying a distinct lack of crustal assimilation during Ordovician-Silurian Doonerak arc magmatism despite its proximity to a cratonic source terrane as indicated by an abundance of Archean and Proterozoic zircon in the interbedded siliciclastic strata. These data are in stark contrast to geochronological data from the non-Laurentian portions of the AACM, highlighting a prominent tectonic boundary between Laurentian- and Baltic-affinity rocks at the Doonerak window and implying a link to "Taconic"-age arc magmatism documented along the NE Laurentian margin.

Expansion and diversification of high-latitude radiolarian assemblages in the late Eocene linked to a cooling event in the southwest Pacific

NASA Astrophysics Data System (ADS)

Pascher, K. M.; Hollis, C. J.; Bohaty, S. M.; Cortese, G.; McKay, R. M.; Seebeck, H.; Suzuki, N.; Chiba, K.

2015-12-01

The long-term cooling trend from middle to late Eocene was punctuated by several large-scale climate perturbations that culminated in a shift to "icehouse" climates at the Eocene-Oligocene transition. We present radiolarian micro-fossil assemblage and foraminiferal oxygen and carbon stable isotope data from Deep Sea Drilling Project (DSDP) sites 277, 280, 281, and 283 and Ocean Drilling Project (ODP) Site 1172 to identify significant oceanographic changes in the southwest Pacific through this climate transition (~ 40-30 Ma). We find that the Middle Eocene Climatic Optimum at ~ 40 Ma, which is truncated but identified by a negative shift in foraminiferal δ18O values at Site 277, is associated with a small increase in radiolarian taxa with low-latitude affinities (5 % of total fauna). In the early late Eocene at ~ 37 Ma, a positive oxygen isotope shift at Site 277 is correlated with the Priabonian Oxygen Isotope Maximum (PrOM). Radiolarian abundance, diversity, and preservation increase within this cooling event at Site 277 at the same time as diatom abundance. A negative δ18O excursion above the PrOM is correlated with a late Eocene warming event (~ 36.4 Ma). Radiolarian abundance and diversity decline within this event and taxa with low-latitude affinities reappear. Apart from this short-lived warming event, the PrOM and latest Eocene radiolarian assemblages are characterised by abundant high-latitude taxa. High-latitude taxa are also abundant during the late Eocene and early Oligocene (~ 38-30 Ma) at DSDP sites 280, 281, 283 and 1172 and are associated with very high diatom abundance. We therefore infer a northward expansion of high-latitude radiolarian taxa onto the Campbell Plateau in the latest Eocene. In the early Oligocene there is an overall decrease in radiolarian abundance and diversity at Site 277, and diatoms are scarce. These data indicate that, once the Antarctic Circumpolar Current was established in the early Oligocene (~ 30 Ma), a frontal system similar to present day developed, with nutrient-depleted Subantarctic waters bathing the area around DSDP Site 277, resulting in a more restricted siliceous plankton assemblage.

Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N6-Methyladenine in Human Cells.

PubMed

Liu, Baodong; Liu, Xiaoling; Lai, Weiyi; Wang, Hailin

2017-06-06

DNA N 6 -methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [ 15 N 5 ]-2'-deoxyadenosine ([ 15 N 5 ]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [ 15 N 5 ]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15 N, and further utilizes the purine salvage pathway to generate mainly both [ 15 N 4 ]-dA and [ 15 N 4 ]-2'-deoxyguanosine ([ 15 N 4 ]-dG) in mammalian genomes. However, [ 15 N 5 ]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [ 15 N 4 ]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

In Vitro Evolution and Affinity-Maturation with Coliphage Qβ Display

PubMed Central

Skamel, Claudia; Aller, Stephen G.; Bopda Waffo, Alain

2014-01-01

The Escherichia coli bacteriophage, Qβ (Coliphage Qβ), offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV). DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb) SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets. PMID:25393763

Shell-model-based deformation analysis of light cadmium isotopes

NASA Astrophysics Data System (ADS)

Schmidt, T.; Heyde, K. L. G.; Blazhev, A.; Jolie, J.

2017-07-01

Large-scale shell-model calculations for the even-even cadmium isotopes 98Cd-108Cd have been performed with the antoine code in the π (2 p1 /2;1 g9 /2) ν (2 d5 /2;3 s1 /2;2 d3 /2;1 g7 /2;1 h11 /2) model space without further truncation. Known experimental energy levels and B (E 2 ) values could be well reproduced. Taking these calculations as a starting ground we analyze the deformation parameters predicted for the Cd isotopes as a function of neutron number N and spin J using the methods of model independent invariants introduced by Kumar [Phys. Rev. Lett. 28, 249 (1972), 10.1103/PhysRevLett.28.249] and Cline [Annu. Rev. Nucl. Part. Sci. 36, 683 (1986), 10.1146/annurev.ns.36.120186.003343].

Oxygen transport by hemoglobin.

PubMed

Mairbäurl, Heimo; Weber, Roy E

2012-04-01

Hemoglobin (Hb) constitutes a vital link between ambient O2 availability and aerobic metabolism by transporting oxygen (O2) from the respiratory surfaces of the lungs or gills to the O2-consuming tissues. The amount of O2 available to tissues depends on the blood-perfusion rate, as well as the arterio-venous difference in blood O2 contents, which is determined by the respective loading and unloading O2 tensions and Hb-O2-affinity. Short-term adjustments in tissue oxygen delivery in response to decreased O2 supply or increased O2 demand (under exercise, hypoxia at high altitude, cardiovascular disease, and ischemia) are mediated by metabolically induced changes in the red cell levels of allosteric effectors such as protons (H(+)), carbon dioxide (CO2), organic phosphates, and chloride (Cl(-)) that modulate Hb-O2 affinity. The long-term, genetically coded adaptations in oxygen transport encountered in animals that permanently are subjected to low environmental O2 tensions commonly result from changes in the molecular structure of Hb, notably amino acid exchanges that alter Hb's intrinsic O2 affinity or its sensitivity to allosteric effectors. Structure-function studies of animal Hbs and human Hb mutants illustrate the different strategies for adjusting Hb-O2 affinity and optimizing tissue oxygen supply. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012.

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE PAGES

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.; ...

2017-08-02

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments.

PubMed

Cannataro, Mario; Cuda, Giovanni; Gaspari, Marco; Greco, Sergio; Tradigo, Giuseppe; Veltri, Pierangelo

2007-07-15

Isotope-coded affinity tags (ICAT) is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS). The method allows the identification and relative quantification of proteins present in two samples and consists of the following phases. First, cysteine residues are either labeled using the ICAT Light or ICAT Heavy reagent (having identical chemical properties but different masses). Then, after whole sample digestion, the labeled peptides are captured selectively using the biotin tag contained in both ICAT reagents. Finally, the simplified peptide mixture is analyzed by nanoscale liquid chromatography-tandem mass spectrometry (LC-MS/MS). Nevertheless, the ICAT LC-MS/MS method still suffers from insufficient sample-to-sample reproducibility on peptide identification. In particular, the number and the type of peptides identified in different experiments can vary considerably and, thus, the statistical (comparative) analysis of sample sets is very challenging. Low information overlap at the peptide and, consequently, at the protein level, is very detrimental in situations where the number of samples to be analyzed is high. We designed a method for improving the data processing and peptide identification in sample sets subjected to ICAT labeling and LC-MS/MS analysis, based on cross validating MS/MS results. Such a method has been implemented in a tool, called EIPeptiDi, which boosts the ICAT data analysis software improving peptide identification throughout the input data set. Heavy/Light (H/L) pairs quantified but not identified by the MS/MS routine, are assigned to peptide sequences identified in other samples, by using similarity criteria based on chromatographic retention time and Heavy/Light mass attributes. EIPeptiDi significantly improves the number of identified peptides per sample, proving that the proposed method has a considerable impact on the protein identification process and, consequently, on the amount of potentially critical information in clinical studies. The EIPeptiDi tool is available at http://bioingegneria.unicz.it/~veltri/projects/eipeptidi/ with a demo data set. EIPeptiDi significantly increases the number of peptides identified and quantified in analyzed samples, thus reducing the number of unassigned H/L pairs and allowing a better comparative analysis of sample data sets.

Preservation and detection of microstructural and taxonomic correlations in the carbon isotopic compositions of individual Precambrian microfossils

NASA Astrophysics Data System (ADS)

Williford, Kenneth H.; Ushikubo, Takayuki; Schopf, J. William; Lepot, Kevin; Kitajima, Kouki; Valley, John W.

2013-03-01

Here we present techniques for, and new data from, in situ carbon isotope (δ13C) analysis of Precambrian permineralized microscopic fossils with a reproducibility of 1-2‰ using secondary ion mass spectrometry (SIMS). Individual microfossils, selected for their excellent preservation, were analyzed in petrographic thin sections of stromatolitic cherts from the Proterozoic Gunflint (˜1880 Ma), Bitter Springs (˜830 Ma), Min'yar (˜740 Ma), and Chichkan (˜775 Ma) Formations. The range of δ13C values (-34.6‰ to -22.1‰ VPDB) among the 46 individuals analyzed falls within that expected for photoautotrophic carbon fixation by ribulose bisphosphate carboxylase (RuBisCO), consistent with morphology-based taxonomic assignments for these specimens. Microfossils classified as cyanobacteria from the Gunflint, Bitter Springs, and Min'yar Formations (for which published carbonate carbon isotope data can be used to estimate the δ13C of the original dissolved inorganic carbon substrate) exhibit a consistent ˜19‰ total fractionation (δ13C of dissolved inorganic carbon - δ13C of biomass) similar to that observed in living cyanobacteria, over a wide range of δ13Ccarb values (-2.9‰ to 3.4‰). In stromatolitic chert of the Min'yar Formation, morphologically diverse microfossils preserved in a ˜1 mm2 part of a microbial mat exhibit systematic isotopic differences among and within taxa that correlate with their morphologically inferred biological affinities and suggest that isotopic signatures of their original biosynthetic processes (e.g., lipid and peptidoglycan synthesis) are preserved. Isotopic offsets consistent with the different RuBisCO-based fractionations typical of cyanobacteria and photosynthetic eukaryotes are documented by the differing δ13C values of a colonial cyanobacterium (-22.6 ± 0.5‰) and a phytoplanktonic protistan acritarch (-28.9 ± 1.0‰) situated <1 cm apart in the stromatolitic Chichkan chert. These findings show for the first time the possibility of using in situ isotopic microanalysis of fossil microbial mats and ancient sediments in order to distinguish metabolic fingerprints within complex microbial ecosystems and consortia.

Gamma-ray spectroscopy: The diffuse galactic glow

NASA Technical Reports Server (NTRS)

Hartmann, Dieter H.

1991-01-01

The goal of this project is the development of a numerical code that provides statistical models of the sky distribution of gamma-ray lines due to the production of radioactive isotopes by ongoing Galactic nucleosynthesis. We are particularly interested in quasi-steady emission from novae, supernovae, and stellar winds, but continuum radiation and transient sources must also be considered. We have made significant progress during the first half period of this project and expect the timely completion of a code that can be applied to Oriented Scintillation Spectrometer Experiment (OSSE) Galactic plane survey data.

Extending the half-life of a fab fragment through generation of a humanized anti-human serum albumin Fv domain: An investigation into the correlation between affinity and serum half-life.

PubMed

Adams, Ralph; Griffin, Laura; Compson, Joanne E; Jairaj, Mark; Baker, Terry; Ceska, Tom; West, Shauna; Zaccheo, Oliver; Davé, Emma; Lawson, Alastair Dg; Humphreys, David P; Heywood, Sam

2016-10-01

We generated an anti-albumin antibody, CA645, to link its Fv domain to an antigen-binding fragment (Fab), thereby extending the serum half-life of the Fab. CA645 was demonstrated to bind human, cynomolgus, and mouse serum albumin with similar affinity (1-7 nM), and to bind human serum albumin (HSA) when it is in complex with common known ligands. Importantly for half-life extension, CA645 binds HSA with similar affinity within the physiologically relevant range of pH 5.0 - pH 7.4, and does not have a deleterious effect on the binding of HSA to neonatal Fc receptor (FcRn). A crystal structure of humanized CA645 Fab in complex with HSA was solved and showed that CA645 Fab binds to domain II of HSA. Superimposition with the crystal structure of FcRn bound to HSA confirmed that CA645 does not block HSA binding to FcRn. In mice, the serum half-life of humanized CA645 Fab is 84.2 h. This is a significant extension in comparison with < 1 h for a non-HSA binding CA645 Fab variant. The Fab-HSA structure was used to design a series of mutants with reduced affinity to investigate the correlation between the affinity for albumin and serum half-life. Reduction in the affinity for MSA by 144-fold from 2.2 nM to 316 nM had no effect on serum half-life. Strikingly, despite a reduction in affinity to 62 µM, an extension in serum half-life of 26.4 h was still obtained. CA645 Fab and the CA645 Fab-HSA complex have been deposited in the Protein Data Bank (PDB) with accession codes, 5FUZ and 5FUO, respectively.

Light water detritiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fedorchenko, O.A.; Aleksee, I.A.; Bondarenko, S.D.

2015-03-15

Hundreds of thousands of tons of tritiated light water have been accumulating from the enterprises of nuclear fuel cycles around the world. The Dual-Temperature Water-Hydrogen (DTWH) process looks like the only practical alternative to Combined Electrolysis and Catalytic Exchange (CECE). In DTWH power-consuming lower reflux device (electrolytic cell) is replaced by a so-called 'hot tower' (LPCE column operating at conditions which ensure relatively small value of elementary separation factor α(hot)). In the upper, cold tower, the tritium transfers from hydrogen to water while in the lower, hot tower - in the opposite direction - from water to hydrogen. The DTWHmore » process is much more complicated compared to CECE; it must be thoroughly computed and strictly controlled by an automatic control system. The use of a simulation code for DTWH is absolutely important. The simulation code EVIO-5 deals with 3 flows inside a column (hydrogen gas, water vapour and liquid water) and 2 simultaneous isotope exchange sub-processes (counter-current phase exchange and co-current catalytic exchange). EVIO-5 takes into account the strong dependence of process performance on given conditions (temperature and pressure). It calculates steady-state isotope concentration profiles considering a full set of reversible exchange reactions between different isotope modifications of water and hydrogen (12 molecular species). So the code can be used for simulation of LPCE column operation for detritiation of hydrogen and water feed, which contains H and D not only at low concentrations but above 10 at.% also. EVIO-5 code is used to model a Tritium Removal Facility with a throughput capacity of about 400 m{sup 3}/day. Simulation results show that a huge amount of wet-proofed catalyst is required (about 6000 m{sup 3}), mainly (90%) in the first stage. One reason for these large expenses (apart from a big scale of the problem itself) is the relatively high tritium separation factor in the hot tower. The introduction of some quantity of deuterium into the gaseous flow before the hot tower lowers the tritium separation factor in that column. One possible variant of deuterium introduction to the hot tower of the first stage was modelled. The decontamination capacity increases by a 2.5 factor.« less

Fossil wood from the upper Miocene Mpesida Beds at Cheparain (Baringo District, Kenya): Botanical affinities and palaeoenvironmental implications

NASA Astrophysics Data System (ADS)

De Franceschi, Dario; Bamford, Marion; Pickford, Martin; Senut, Brigitte

2016-03-01

Seven wood samples from a petrified forest, in situ in ash flow deposits at Cheparain in the Tugen Hills (Kenya) in the Mpesida Beds, were discovered and studied. The age of the Mpesida Formation is estimated to be about 6.3 Ma on the basis of radio-isotope age determinations on the volcanic deposits, which overlie and underlie the sedimentary levels. The wood samples are mineralized with obvious sectors of differential mineralization, and different degrees of silica impregnation. All samples show heteroxylous structures corresponding to angiosperm dicotyledon trees. One sample consists in a half cylinder showing a well preserved mineralized structure of heteroxylous wood and probably corresponds to a fragment of root. This wood, with solitary (or in radial group) vessels, heterocellular multiseriate rays, paratracheal parenchyma in wide bands, and partly storied fusiform cells, clearly shows affinities with the genus Erythrina (Fabaceae). A slightly compressed branch, partly disturbed by injuries and highly mineralized shows solitary (or in short radial group) vessels, the rays uni-(bi) seriate are heterocellular, and the apotracheal parenchyma is in thin tangential bands. The closest affinities are with the genus Spirostachys (Euphorbiaceae). The other structures are poorly preserved (highly mineralized) and precise botanical affinities cannot be accessed. But the growth rings are distinct or diversely marked and the samples show semi-ring porous structures. They exhibit two different patterns. The growth rings reveal the presence of seasonal climate, and numerous injuries, a disturbance of the vegetation by animals and/or strong climatic events. Erythrina and Spirostachys are present in the extant vegetation of the Tana River Valley, in Kenya, which could represent a modern analogue for the vegetation of the Mpesida Beds prior to the major uplift of the Tugen Hills at the end of the Miocene.

Computer codes for checking, plotting and processing of neutron cross-section covariance data and their application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sartori, E.; Roussin, R.W.

This paper presents a brief review of computer codes concerned with checking, plotting, processing and using of covariances of neutron cross-section data. It concentrates on those available from the computer code information centers of the United States and the OECD/Nuclear Energy Agency. Emphasis will be placed also on codes using covariances for specific applications such as uncertainty analysis, data adjustment and data consistency analysis. Recent evaluations contain neutron cross section covariance information for all isotopes of major importance for technological applications of nuclear energy. It is therefore important that the available software tools needed for taking advantage of this informationmore » are widely known as hey permit the determination of better safety margins and allow the optimization of more economic, I designs of nuclear energy systems.« less

The effects of magnesium on potassium transport in ferret red cells.

PubMed Central

Flatman, P W

1988-01-01

1. The magnesium dependence of net and isotopic (using 86Rb as tracer) potassium transport was measured in fed ferret red cells. Bumetanide (0.1 mM) was used to dissect total flux into two components: bumetanide sensitive and bumetanide resistant. 2. Increasing the external magnesium concentration from zero (added) to 2 mM stimulated bumetanide-sensitive uptake by 16% but inhibited the bumetanide-resistant component by about 20%. 3. Ionophore A23187 was used to control internal magnesium concentration. A23187 was usually present in the cells during measurement of isotopic fluxes but was washed away before measurement of net fluxes. The magnesium-buffering characteristics of fed ferret red cells were assessed during these experiments. The cytoplasm acts as a high-capacity, low-affinity magnesium buffer over most of the range. Some high-affinity binding was seen in the presence of A23187 and 2 mM-EDTA. 4. A23187 itself slightly inhibits bumetanide-sensitive potassium transport. 5. Bumetanide-sensitive potassium transport is strongly dependent on the concentration of internal ionized magnesium. Transport is 35% maximal at 10(-7) M and increases up to the maximal rate at 1.3 mM. Further increase in ionized magnesium concentration to 3.5 mM has no additional effect. The curve relating activity to magnesium concentration is steepest at the physiological magnesium concentration. The effects of changing magnesium concentration are fully reversible. 6. Reduction of internal ionized magnesium concentration to 10(-7) M with A23187 and EDTA approximately doubles bumetanide-resistant potassium transport. 7. Bumetanide-sensitive fluxes occur via the sodium-potassium-chloride co-transport system under the conditions used. Results described in this paper thus suggest that internal magnesium may be an important physiological controller of sodium-potassium-chloride co-transport activity. PMID:3137332

XDATA

DTIC Science & Technology

2017-05-01

Parallelizing PINT The main focus of our research into the parallelization of the PINT algorithm has been to find appropriately scalable matrix math algorithms...leading eigenvector of the adjacency matrix of the pairwise affinity graph. We reviewed the matrix math implementation currently being used in PINT and...the new versions support a feature called matrix.distributed, which is some level of support for distributed matrix math ; however our code is not

Single step purification of recombinant proteins using the metal ion-inducible autocleavage (MIIA) domain as linker for tag removal.

PubMed

Ibe, Susan; Schirrmeister, Jana; Zehner, Susanne

2015-08-20

For fast and easy purification, proteins are typically fused with an affinity tag, which often needs to be removed after purification. Here, we present a method for the removal of the affinity tag from the target protein in a single step protocol. The protein VIC_001052 of the coral pathogen Vibrio coralliilyticus ATCC BAA-450 contains a metal ion-inducible autocatalytic cleavage (MIIA) domain. Its coding sequence was inserted into an expression vector for the production of recombinant fusion proteins. Following, the target proteins MalE and mCherry were produced as MIIA-Strep fusion proteins in Escherichia coli. The target proteins could be separated from the MIIA-Strep part simply by the addition of calcium or manganese(II) ions within minutes. The cleavage is not affected in the pH range from 5.0 to 9.0 or at low temperatures (6°C). Autocleavage was also observed with immobilized protein on an affinity column. The protein yield was similar to that achieved with a conventional purification protocol. Copyright © 2015 Elsevier B.V. All rights reserved.

Isotope and mixture effects on neoclassical transport in the pedestal

NASA Astrophysics Data System (ADS)

Pusztai, Istvan; Buller, Stefan; Omotani, John T.; Newton, Sarah L.

2017-10-01

The isotope mass scaling of the energy confinement time in tokamak plasmas differs from gyro-Bohm estimates, with implications for the extrapolation from current experiments to D-T reactors. Differences in mass scaling in L-mode and various H-mode regimes suggest that the isotope effect may originate from the pedestal. In the pedestal, sharp gradients render local diffusive estimates invalid, and global effects due to orbit-width scale profile variations have to be taken into account. We calculate neoclassical cross-field fluxes from a radially global drift-kinetic equation using the PERFECT code, to study isotope composition effects in density pedestals. The relative reduction to the peak heat flux due to global effects as a function of the density scale length is found to saturate at an isotope-dependent value that is larger for heavier ions. We also consider D-T and H-D mixtures with a focus on isotope separation. The ability to reproduce the mixture results via single-species simulations with artificial ``DT'' and ``HD'' species has been considered. These computationally convenient single ion simulations give a good estimate of the total ion heat flux in corresponding mixtures. Funding received from the International Career Grant of Vetenskapsradet (VR) (330-2014-6313) with Marie Sklodowska Curie Actions, Cofund, Project INCA 600398, and Framework Grant for Strategic Energy Research of VR (2014-5392).

SFCOMPO 2.0 - A relational database of spent fuel isotopic measurements, reactor operational histories, and design data

NASA Astrophysics Data System (ADS)

Michel-Sendis, Franco; Martinez-González, Jesus; Gauld, Ian

2017-09-01

SFCOMPO-2.0 is a database of experimental isotopic concentrations measured in destructive radiochemical analysis of spent nuclear fuel (SNF) samples. The database includes corresponding design description of the fuel rods and assemblies, relevant operating conditions and characteristics of the host reactors necessary for modelling and simulation. Aimed at establishing a thorough, reliable, and publicly available resource for code and data validation of safety-related applications, SFCOMPO-2.0 is developed and maintained by the OECD Nuclear Energy Agency (NEA). The SFCOMPO-2.0 database is a Java application which is downloadable from the NEA website.

Sea surface salinity of the Eocene Arctic Azolla event using innovative isotope modeling

NASA Astrophysics Data System (ADS)

Speelman, E. N.; Sewall, J. O.; Noone, D.; Huber, M.; Sinninghe Damste, J. S.; Reichart, G. J.

2009-04-01

With the realization that the Eocene Arctic Ocean was covered with enormous quantities of the free floating freshwater fern Azolla, new questions regarding Eocene conditions facilitating these blooms arose. Our present research focuses on constraining the actual salinity of, and water sources for, the Eocene Arctic basin through the application of stable water isotope tracers. Precipitation pathways potentially strongly affect the final isotopic composition of water entering the Arctic Basin. Therefore we use the Community Atmosphere Model (CAM3), developed by NCAR, combined with a recently developed integrated isotope tracer code to reconstruct the isotopic composition of global Eocene precipitation and run-off patterns. We further addressed the sensitivity of the modeled hydrological cycle to changes in boundary conditions, such as pCO2, sea surface temperatures (SSTs) and sea ice formation. In this way it is possible to assess the effect of uncertainties in proxy estimates of these parameters. Overall, results of all runs with Eocene boundary conditions, including Eocene topography, bathymetry, vegetation patterns, TEX86 derived SSTs and pCO2 estimates, show the presence of an intensified hydrological cycle with precipitation exceeding evaporation in the Arctic region. Enriched, precipitation weighted, isotopic values of around -120‰ are reported for the Arctic region. Combining new results obtained from compound specific isotope analyses (δD) on terrestrially derived n-alkanes extracted from Eocene sediments, and model outcomes make it possible to verify climate reconstructions for the middle Eocene Arctic. Furthermore, recently, characteristic long-chain mid-chain ω20 hydroxy wax constituents of Azolla were found in ACEX sediments. δD values of these C32 - C36 diols provide insight into the isotopic composition of the Eocene Arctic surface water. As the isotopic signature of the runoff entering the Arctic is modelled, and the final isotopic composition of the surface waters can be deduced from the isotopic composition of the diols, we can calculate the degree of mixing between freshwater (isotopically light) and seawater (isotopically heavy) in the surface waters. This way we quantify Eocene Arctic surface water salinity, which in turn will shed light on the degree of (seasonal) mixing and stratification.

Projectile fragmentation of 40,48Ca and isotopic scaling in a transport approach

NASA Astrophysics Data System (ADS)

Mikhailova, T. I.; Erdemchimeg, B.; Artukh, A. G.; Di Toro, M.; Wolter, H. H.

2016-07-01

We investigate theoretically projectile fragmentation in reactions of 40,48Ca on 9Be and 181Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculation exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the 40,48Ca pair. The symmetry energy determined in this way depends on these structure effects.

Projectile fragmentation of {sup 40,48}Ca and isotopic scaling in a transport approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhailova, T. I., E-mail: tmikh@jinr.ru; Erdemchimeg, B.; Artukh, A. G.

2016-07-15

We investigate theoretically projectile fragmentation in reactions of {sup 40,48}Ca on {sup 9}Be and {sup 181}Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculationmore » exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the {sup 40,48}Ca pair. The symmetry energy determined in this way depends on these structure effects.« less

Interlinked Test Results for Fusion Fuel Processing and Blanket Tritium Recovery Systems Using Cryogenic Molecular Sieve Bed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamanishi, Toshihiko; Hayashi, Takumi; Kawamura, Yoshinori

2005-07-15

A simulated fuel processing (cryogenic distillation columns and a palladium diffuser) and CMSB (cryogenic molecular sieve bed) systems were linked together, and were operated. The validity of the CMSB was discussed through this experiment as an integrated system for the recovery of blanket tritium. A gas stream of hydrogen isotopes and He was supplied to the CMSB as the He sweep gas in blanket of a fusion reactor. After the breakthrough of tritium was observed, regeneration of the CMSB was carried out by evacuating and heating. The hydrogen isotopes were finally recovered by the diffuser. At first, only He gasmore » was sent by the evacuating. The hydrogen isotopes gas was then rapidly released by the heating. The system worked well against the above drastic change of conditions. The amount of hydrogen isotopes gas finally recovered by the diffuser was in good agreement with that adsorbed by the CMSB. The dynamic behaviors (breakthrough and regeneration) of the system were explained well by a set of basic codes.« less

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

PubMed

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-03-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Sequestration by IFIT1 Impairs Translation of 2′O-unmethylated Capped RNA

PubMed Central

Lacerda, Livia; Benda, Christian; Holze, Cathleen; Eberl, Christian H.; Mann, Angelika; Kindler, Eveline; Gil-Cruz, Cristina; Ziebuhr, John; Thiel, Volker; Pichlmair, Andreas

2013-01-01

Viruses that generate capped RNA lacking 2′O methylation on the first ribose are severely affected by the antiviral activity of Type I interferons. We used proteome-wide affinity purification coupled to mass spectrometry to identify human and mouse proteins specifically binding to capped RNA with different methylation states. This analysis, complemented with functional validation experiments, revealed that IFIT1 is the sole interferon-induced protein displaying higher affinity for unmethylated than for methylated capped RNA. IFIT1 tethers a species-specific protein complex consisting of other IFITs to RNA. Pulsed stable isotope labelling with amino acids in cell culture coupled to mass spectrometry as well as in vitro competition assays indicate that IFIT1 sequesters 2′O-unmethylated capped RNA and thereby impairs binding of eukaryotic translation initiation factors to 2′O-unmethylated RNA template, which results in inhibition of translation. The specificity of IFIT1 for 2′O-unmethylated RNA serves as potent antiviral mechanism against viruses lacking 2′O-methyltransferase activity and at the same time allows unperturbed progression of the antiviral program in infected cells. PMID:24098121

Visual communications and image processing '92; Proceedings of the Meeting, Boston, MA, Nov. 18-20, 1992

NASA Astrophysics Data System (ADS)

Maragos, Petros

The topics discussed at the conference include hierarchical image coding, motion analysis, feature extraction and image restoration, video coding, and morphological and related nonlinear filtering. Attention is also given to vector quantization, morphological image processing, fractals and wavelets, architectures for image and video processing, image segmentation, biomedical image processing, and model-based analysis. Papers are presented on affine models for motion and shape recovery, filters for directly detecting surface orientation in an image, tracking of unresolved targets in infrared imagery using a projection-based method, adaptive-neighborhood image processing, and regularized multichannel restoration of color images using cross-validation. (For individual items see A93-20945 to A93-20951)

Digital Isotope Coding to Trace the Growth Process of Individual Single-Walled Carbon Nanotubes.

PubMed

Otsuka, Keigo; Yamamoto, Shun; Inoue, Taiki; Koyano, Bunsho; Ukai, Hiroyuki; Yoshikawa, Ryo; Xiang, Rong; Chiashi, Shohei; Maruyama, Shigeo

2018-04-24

Single-walled carbon nanotubes (SWCNTs) are attracting increasing attention as an ideal material for high-performance electronics through the preparation of arrays of purely semiconducting SWCNTs. Despite significant progress in the controlled synthesis of SWCNTs, their growth mechanism remains unclear due to difficulties in analyzing the time-resolved growth of individual SWCNTs under practical growth conditions. Here we present a method for tracing the diverse growth profiles of individual SWCNTs by embedding digitally coded isotope labels. Raman mapping showed that, after various incubation times, SWCNTs elongated monotonically until their abrupt termination. Ex situ analysis offered an opportunity to capture rare chirality changes along the SWCNTs, which resulted in sudden acceleration/deceleration of the growth rate. Dependence on growth parameters, such as temperature and carbon concentration, was also traced along individual SWCNTs, which could provide clues to chirality control. Systematic growth studies with a variety of catalysts and conditions, which combine the presented method with other characterization techniques, will lead to further understanding and control of chirality, length, and density of SWCNTs.

Thermo-hydrological and chemical (THC) modeling to support Field Test Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stauffer, Philip H.; Jordan, Amy B.; Harp, Dylan Robert

This report summarizes ongoing efforts to simulate coupled thermal-hydrological-chemical (THC) processes occurring within a hypothetical high-level waste (HLW) repository in bedded salt. The report includes work completed since the last project deliverable, “Coupled model for heat and water transport in a high level waste repository in salt”, a Level 2 milestone submitted to DOE in September 2013 (Stauffer et al., 2013). Since the last deliverable, there have been code updates to improve the integration of the salt module with the pre-existing code and development of quality assurance (QA) tests of constitutive functions and precipitation/dissolution reactions. Simulations of bench-scale experiments, bothmore » historical and currently in the planning stages have been performed. Additional simulations have also been performed on the drift-scale model that incorporate new processes, such as an evaporation function to estimate water vapor removal from the crushed salt backfill and isotopic fractionation of water isotopes. Finally, a draft of a journal paper on the importance of clay dehydration on water availability is included as Appendix I.« less

Determination of the δ34S of low-concentration sulfate in water; RSIL lab code 1949

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1949 is to determine the δ(34S/32S), abbreviated as δ34S, of dissolved sulfate having a concentration less than 20 milligrams per liter. Dissolved sulfate is collected on an anion-exchange resin in the field, eluted in the laboratory with 3 M KCl, and precipitated with BaCl2 at pH 3 to 4 as BaSO4. The precipitated BaSO4 is filtered and dried before introduction into an elemental analyzer (EA) Carlo Erba NC 2500. The EA is used to convert sulfur in a BaSO4 solid sample into SO2 gas, and the EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines differences in the isotope-amount ratios of stable sulfur isotopes (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated reaction tube that combines the oxidation and reduction reactions. The combustion takes place in a helium atmosphere containing an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a helium carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which is also used to inject SO2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; m/z 66 = SO2 = 34S16O16O primarily.

Nuclear data uncertainty propagation by the XSUSA method in the HELIOS2 lattice code

NASA Astrophysics Data System (ADS)

Wemple, Charles; Zwermann, Winfried

2017-09-01

Uncertainty quantification has been extensively applied to nuclear criticality analyses for many years and has recently begun to be applied to depletion calculations. However, regulatory bodies worldwide are trending toward requiring such analyses for reactor fuel cycle calculations, which also requires uncertainty propagation for isotopics and nuclear reaction rates. XSUSA is a proven methodology for cross section uncertainty propagation based on random sampling of the nuclear data according to covariance data in multi-group representation; HELIOS2 is a lattice code widely used for commercial and research reactor fuel cycle calculations. This work describes a technique to automatically propagate the nuclear data uncertainties via the XSUSA approach through fuel lattice calculations in HELIOS2. Application of the XSUSA methodology in HELIOS2 presented some unusual challenges because of the highly-processed multi-group cross section data used in commercial lattice codes. Currently, uncertainties based on the SCALE 6.1 covariance data file are being used, but the implementation can be adapted to other covariance data in multi-group structure. Pin-cell and assembly depletion calculations, based on models described in the UAM-LWR Phase I and II benchmarks, are performed and uncertainties in multiplication factor, reaction rates, isotope concentrations, and delayed-neutron data are calculated. With this extension, it will be possible for HELIOS2 users to propagate nuclear data uncertainties directly from the microscopic cross sections to subsequent core simulations.

Modeling nuclear field shift isotope fractionation in crystals

NASA Astrophysics Data System (ADS)

Schauble, E. A.

2013-12-01

In this study nuclear field shift fractionations in solids (and chemically similar liquids) are estimated using calibrated density functional theory calculations. The nuclear field shift effect is a potential driver of mass independent isotope fractionation(1,2), especially for elements with high atomic number such as Hg, Tl and U. This effect is caused by the different shapes and volumes of isotopic nuclei, and their interactions with electronic structures and energies. Nuclear field shift isotope fractionations can be estimated with first principles methods, but the calculations are computationally difficult, limiting most theoretical studies so far to small gas-phase molecules and molecular clusters. Many natural materials of interest are more complex, and it is important to develop ways to estimate field shift effects that can be applied to minerals, solutions, in biomolecules, and at mineral-solution interfaces. Plane-wave density functional theory, in combination with the projector augmented wave method (DFT-PAW), is much more readily adapted to complex materials than the relativistic all-electron calculations that have been the focus of most previous studies. DFT-PAW is a particularly effective tool for studying crystals with periodic boundary conditions, and may also be incorporated into molecular dynamics simulations of solutions and other disordered phases. Initial calibrations of DFT-PAW calculations against high-level all-electron models of field shift fractionation suggest that there may be broad applicability of this method to a variety of elements and types of materials. In addition, the close relationship between the isomer shift of Mössbauer spectroscopy and the nuclear field shift isotope effect makes it possible, at least in principle, to estimate the volume component of field shift fractionations in some species that are too complex even for DFT-PAW models, so long as there is a Mössbauer isotope for the element of interest. Initial results will be presented for calculations of liquid-vapor fractionation of cadmium and mercury, which indicate an affinity for heavy isotopes in the liquid phase. In the case of mercury the results match well with recent experiments. Mössbauer-calibrated fractionation factors will also be presented for tin and platinum species. Platinum isotope behaviour in metals appears to particularly interesting, with very distinct isotope partitioning behaviour for iron-rich alloys, relative to pure platinum metal. References: 1) Bigeleisen, J. (1996) J. Am. Chem. Soc. 118, 3676-3680. 2) Nomura, M., Higuchi, N., Fujii, Y. (1996) J. Am. Chem. Soc. 118, 9127-9130.

Affinity approaches in RNAi-based therapeutics purification.

PubMed

Pereira, Patrícia; Queiroz, João A; Figueiras, Ana; Sousa, Fani

2016-05-15

The recent investigation on RNA interference (RNAi) related mechanisms and applications led to an increased awareness of the importance of RNA in biology. Nowadays, RNAi-based technology has emerged as a potentially powerful tool for silencing gene expression, being exploited to develop new therapeutics for treating a vast number of human disease conditions, as it is expected that this technology can be translated onto clinical applications in a near future. This approach makes use of a large number of small (namely short interfering RNAs, microRNAs and PIWI-interacting RNAs) and long non-coding RNAs (ncRNAs), which are likely to have a crucial role as the next generation therapeutics. The commercial and biomedical interest in these RNAi-based therapy applications have fostered the need to develop innovative procedures to easily and efficiently purify RNA, aiming to obtain the final product with high purity degree, good quality and biological activity. Recently, affinity chromatography has been applied to ncRNAs purification, in view of the high specificity. Therefore, this article intends to review the biogenesis pathways of regulatory ncRNAs and also to discuss the most significant and recent developments as well as applications of affinity chromatography in the challenging task of purifying ncRNAs. In addition, the importance of affinity chromatography in ncRNAs purification is addressed and prospects for what is forthcoming are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Status Report on NEAMS PROTEUS/ORIGEN Integration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wieselquist, William A

2016-02-18

The US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program has contributed significantly to the development of the PROTEUS neutron transport code at Argonne National Laboratory and to the Oak Ridge Isotope Generation and Depletion Code (ORIGEN) depletion/decay code at Oak Ridge National Laboratory. PROTEUS’s key capability is the efficient and scalable (up to hundreds of thousands of cores) neutron transport solver on general, unstructured, three-dimensional finite-element-type meshes. The scalability and mesh generality enable the transfer of neutron and power distributions to other codes in the NEAMS toolkit for advanced multiphysics analysis. Recently, ORIGEN has received considerablemore » modernization to provide the high-performance depletion/decay capability within the NEAMS toolkit. This work presents a description of the initial integration of ORIGEN in PROTEUS, mainly performed during FY 2015, with minor updates in FY 2016.« less

One improved LSB steganography algorithm

NASA Astrophysics Data System (ADS)

Song, Bing; Zhang, Zhi-hong

2013-03-01

It is easy to be detected by X2 and RS steganalysis with high accuracy that using LSB algorithm to hide information in digital image. We started by selecting information embedded location and modifying the information embedded method, combined with sub-affine transformation and matrix coding method, improved the LSB algorithm and a new LSB algorithm was proposed. Experimental results show that the improved one can resist the X2 and RS steganalysis effectively.

Age, geochemical and Sr Nd Pb isotopic constraints for mantle source characteristics and petrogenesis of Teru Volcanics, Northern Kohistan Terrane, Pakistan

NASA Astrophysics Data System (ADS)

Khan, S. D.; Stern, R. J.; Manton, M. I.; Copeland, P.; Kimura, J. I.; Khan, M. A.

2004-11-01

This paper presents new geochemical and geochronology data for the Teru Volcanic Formation (previously known as the Shamran Volcanics) exposed west of Gilgit in the Kohistan terrane of the Pakistani Himalayas. The Teru Volcanic Formation ranges from basalt through andesite to rhyolite and has subalkaline and midalkaline affinities. Trace-element compositions and isotopic characteristics suggest these magmas were formed in a subduction zone setting; isotopic studies also support this conclusion. It is suggested that these lavas originated from a depleted mantle source, which experienced contamination by variable subduction components. Model mixing calculations using 87Sr/ 86Sr and 143Nd/ 144Nd data suggest that addition of 0.2-0.6% of Indus margin sediments and/or 2-4% of fluids derived from Indus margin sediment can generate the compositional variation of the Teru Volcanic Formation. Two samples from the Teru Volcanic Formation yielded 40Ar/ 39Ar ages of 43.8+0.5 and 32.5+0.4 Ma. These ages make the volcanic rocks of the Teru Volcanic Formation the youngest reported in the Kohistan terrane. These volcanic rocks unconformably overly the Shunji Pluton, which has a 65 Ma Rb-Sr whole-rock isochron age. The results of this research suggest that subduction-related volcanism was active until 33 Ma in the India-Asia collision zone.

Effect of quantum nuclear motion on hydrogen bonding

NASA Astrophysics Data System (ADS)

McKenzie, Ross H.; Bekker, Christiaan; Athokpam, Bijyalaxmi; Ramesh, Sai G.

2014-05-01

This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H⋯O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4 - 3.0 Å, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends.

Redox regulation of mitochondrial proteins and proteomes by cysteine thiol switches.

PubMed

Nietzel, Thomas; Mostertz, Jörg; Hochgräfe, Falko; Schwarzländer, Markus

2017-03-01

Mitochondria are hotspots of cellular redox biochemistry. Respiration as a defining mitochondrial function is made up of a series of electron transfers that are ultimately coupled to maintaining the proton motive force, ATP production and cellular energy supply. The individual reaction steps involved require tight control and flexible regulation to maintain energy and redox balance in the cell under fluctuating demands. Redox regulation by thiol switching has been a long-standing candidate mechanism to support rapid adjustment of mitochondrial protein function at the posttranslational level. Here we review recent advances in our understanding of cysteine thiol switches in the mitochondrial proteome with a focus on their operation in vivo. We assess the conceptual basis for thiol switching in mitochondria and discuss to what extent insights gained from in vitro studies may be valid in vivo, considering thermodynamic, kinetic and structural constraints. We compare functional proteomic approaches that have been used to assess mitochondrial protein thiol switches, including thioredoxin trapping, redox difference gel electrophoresis (redoxDIGE), isotope-coded affinity tag (OxICAT) and iodoacetyl tandem mass tag (iodoTMT) labelling strategies. We discuss conditions that may favour active thiol switching in mitochondrial proteomes in vivo, and appraise recent advances in dissecting their impact using combinations of in vivo redox sensing and quantitative redox proteomics. Finally we focus on four central facets of mitochondrial biology, aging, carbon metabolism, energy coupling and electron transport, exemplifying the current emergence of a mechanistic understanding of mitochondrial regulation by thiol switching in living plants and animals. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Sm-Nd isotopic data from Archean metavolcanic rocks at Holenarsipur, South India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drury, S.A.; Van Calsteren, P.C.; Reeves-Smith, G.J.

1987-11-01

Results of a Sm-Nd isotopic analysis of Archean metavolcanics in the Holenarsipur greenstone belt, Karnataka, South India, give a whole-rock isochron age of 2.62 Ga for lightly deformed metabasaltic amphibolites in the northern part of the belt. This is within error of the age of high-grade metamorphism and crustal thickening which affected areas further to the south during the late Archean. Together with the geochemical affinities of these and other metavolcanics in Karnataka, and results of regional structural analysis, this unexpected age supports a model relating volcanism and crustal thickening to northward subduction and crustal accretion during the late Archean.more » Data from basic and ultrabasic metavolcanics from the more strongly deformed and higher-grade southern arm of the Holenarsipur belt do not permit an age greater than 3.0 Ga. Previously, these rocks were regarded as part of an older supracrustal sequence that predated the local 3.0 to 3.3 Ga gneissic complex. The new dates therefore considerably simplify attempts at accounting for greenstone evolution in South India.« less

40Ar/ 39Ar age and oxygen isotope temperature of the Centinela Formation, southwestern Argentina: An Eocene age for crustacean-rich "Patagonian" beds

NASA Astrophysics Data System (ADS)

Casadío, Silvio; Feldmann, Rodney M.; Foland, Kenneth A.

2000-05-01

The presence of a prominent volcanic ash enclosed within sediments of the Centinela Formation, southwestern Argentina, permits establishment of an 40Ar/ 39Ar age of approximately 46 Ma for these rocks. Oxygen isotopic analysis of shell material from the oyster Crassostrea? hatcheriOrtmann, 1897, suggests seasonal fluctuation of temperature from about 15°C to about 21°C. In concordance with this, a diverse crustacean fauna, including nine families within the order Decapoda and one within Isopoda, bears strong affinities with temperate and subtropical faunas of the Atlantic Ocean basin and documents the southernmost extension of low latitude oceanographic influence on this region during the Paleogene. Establishment of an Eocene age for the rocks in the Centinela Formation provides the first definitive documentation of rocks of that age in the region of Calafate, permits correlation of these rocks with Eocene strata southward to the vicinity of Río Turbio, and suggests that these rocks, assigned to the Patagonian sequence, may be substantially older than those in eastern Argentina.

Neodymium, strontium, and oxygen isotopic variations in the crust of the western United States: Origin of Proterozoic continental crust and tectonic implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, V.C.

1989-01-01

Initial Nd isotopic ratios of crystalline rocks from an area of about 1.5 {times} 10{sup 6} km{sup 2} of the western United States have been determined in order to map Precambrian age province boundaries and thus document the growth and modification of the North American continent in the Proterozoic. Three age provinces have been delineated. It is demonstrated that large regions of Early Proterozoic continental crust were formed with anomalous isotopic compositions ({sup 143}Nd/{sup 144}Nd ratios lower than Early Proterozoic depleted-mantle). The variations in the initial {epsilon}{sub Nd} and {delta}{sup 18}O values correlate with each other, and correspond to themore » previously determined Nd isotopic provinces. The Pelona, Rand, Chocolate Mountain and Orocopia Schists are represented by 15 lithologically and structurally similar schist bodies exposed along the San Andreas and Garlock faults in southern California. The grayschists have measured {epsilon}{sub Nd} values from -1.7 to -11.7 with depleted-mantle model ages of 0.9 to 1.7 Ga. The Nd isotopic compositions can be modeled as variable mixtures of Early Proterozoic continental crust with a Mesozoic are component. The measured {sup 87}Sr/{sup 86}Sr ratios are from 0.7087 to 0.7129 and reflect the presence of an old continental source. Independent of age, the high initial {epsilon}{sub Nd} values ({sup +}9 {plus minus} 1.5) are consistent with derivation at an oceanic spreading center, either at a MORB or in a back-arc basin environment. The presence of both Early Proterozoic continental detritus and a younger sedimentary component in the grayschist protolith, and the MORB affinity of the metabasalts are compatible with formation of the protoliths of the Pelona and related schists in a Mesozoic basin adjacent to the southwestern United States continental margin.« less

Carboniferous continental arc in the Hegenshan accretionary belt: Constrains from plutonic complex in central Inner Mongolia

NASA Astrophysics Data System (ADS)

Wei, Ruihua; Gao, Yongfeng; Xu, Shengchuan; Santosh, M.; Xin, Houtian; Zhang, Zhenmin; Li, Weilong; Liu, Yafang

2018-05-01

The architecture and tectonic evolution of the Hegenshan accretionary belt in the Central Asian Orogenic Belt (CAOB) remains debated. Here we present an integrated study of zircon U-Pb isotopic ages, whole rock major-trace elements, and Sr-Nd-Pb isotopic data from the Hegenshan volcanic-plutonic belt in central Inner Mongolia. Field observations and zircon U-Pb ages allow us to divide the intrusive complex into an early phase at 329-306 Ma and a late phase at 304 to 299 Ma. The intrusive bodies belong to two magma series: calc-alkaline rocks with I-type affinity and A-type granites. The early intrusions are composed of granodiorite, monzogranite and porphyritic granite, and the late calc-alkaline intrusions include gabbro though diorite to granodiorite. The calc-alkaline intrusive rocks exhibit a well-defined compositional trend from gabbro to granite, reflecting continuous fractional crystallization. These rocks show obvious enrichment in LILEs and LREEs and relative depletion of HFSEs, typical of subduction-related magma. They also exhibit isotopic characteristics of mantle-derived magmas such as low initial 87Sr/86Sr (0.7029-0.7053), positive ɛNd(t) values (0.06-4.76) and low radiogenic Pb isotopic compositions ((206Pb/204Pb)I = 17.907-19.198, (207Pb/204Pb)I = 15.474-15.555, (208Pb/204Pb)I = 37.408-38.893). The marked consistency in geochemical and isotopic compositions between the intrusive rocks and the coeval Baoligaomiao volcanic rocks define a Carboniferous continental arc. Together with available regional data, we infer that this east-west trending continental arc was generated by northward subduction of the Hegenshan ocean during Carboniferous. The late alkali-feldspar granites and the high-Si rhyolites of the Baoligaomiao volcanic succession show similar geochemical compositions with high SiO2 and variable total alkali contents, and low TiO2, MgO and CaO. These rocks are characterized by unusually low Sr and Ba, and high abundances of Zr, Th, Nb, HREEs and Y, comparable to the features of typical A2-type granites including their high ratios of FeOT/MgO, Ga/Al and Y/Nb. Our study suggests that the A-type granite was derived from a distinct magma source rather than through fractional crystallization of the coeval calc-alkaline magmas. Their Nd-Pb isotopic compositions are similar to those of calc-alkaline arc rocks and are compatible with partial melting of pre-existing juvenile basaltic crust in the continental arc. Notably, the widespread eruptions of A2-type rhyolitic magmas (305.3 Ma-303.4 Ma) following a short period of magmatic quiescence was temporally and spatially associated with bimodal magmatism with mantle-derived gabbro-diorites and A-type granites (304.3 Ma-299.03 Ma) in the pre-existing arc volcanic-plutonic belt (329 Ma-306 Ma). Such a marked change in the magma affinity likely indicates subducted slab break-off resulting in a change of the regional stress field to an extensional setting within the Carboniferous continental arc that runs E-W for few thousands of kilometers. Thus, the onset of the late magmatism (305-299 Ma) likely represents the maximum age for the cessation of the northward subduction in the Hegenshan ophiolite-arc-accretion belt.

Evidence for collective expansion in light-particle emission following Au+Au collisions at 100, 150 and 250 A·MeV

NASA Astrophysics Data System (ADS)

Poggi, G.; Pasquali, G.; Bini, M.; Maurenzig, P.; Olmi, A.; Taccetti, N.; Alard, J. P.; Amouroux, V.; Basrak, Z.; Bastid, N.; Belayev, I. M.; Berger, L.; Blaich, Th.; Boussange, S.; Buta, A.; Čaplar, R.; Cerruti, C.; Cindro, N.; Coffin, J. P.; Donà, R.; Dupieux, P.; Dželalija, M.; Erö, J.; Fan, Z. G.; Fintz, P.; Fodor, Z.; Fraysse, L.; Freifelder, R.; Frolov, S.; Gobbi, A.; Grigorian, Y.; Guillaume, G.; Herrmann, N.; Hildenbrand, K. D.; Hölbling, S.; Houari, A.; Jeong, S. C.; Jundt, F.; Kecskemeti, J.; Koncz, P.; Korchagin, Y.; Kotte, R.; Krämer, M.; Kuhn, C.; Ibnouzahir, M.; Legrand, I.; Lebedev, A.; Maguire, C.; Manko, V.; Mgebrishvili, G.; Mösner, J.; Moisa, D.; Montarou, G.; Montbel, I.; Morel, P.; Neubert, W.; Pelte, D.; Petrovici, M.; Rami, F.; Ramillien, V.; Reisdorf, W.; Sadchikov, A.; Schüll, D.; Seres, Z.; Sikora, B.; Simion, V.; Smolyankin, S.; Sodan, U.; The, K.; Tezkratt, R.; Trzaska, M.; Vasiliev, M. A.; Wagner, P.; Wessels, J. P.; Wienold, T.; Wilhelmi, Z.; Wohlfarth, D.; Zhilin, A. V.; Danielewicz, P.; FOPI Collaboration

1995-02-01

Light-particle emission from Au+Au collisions has been studied in the bombarding-energy range 100-250 A·MeV, using ΔE- ER telescopes in coincidence with the FOPI detector in its phase I configuration. Center-of-mass energy spectra have been measured for Z = 1,2 isotopes emitted in central collisions at CM polar angles between 60° and 90°. Evidence for a collective expansion is reported, on the basis of the mean kinetic energies of hydrogen isotopes. Comparison is presented with statistical calculations (WIX code). For CM kinetic energy spectra, fair agreement is found between data and a recently developed transport model.

Evaluation of excitation functions of proton and deuteron induced reactions on enriched tellurium isotopes with special relevance to the production of iodine-124.

PubMed

Aslam, M N; Sudár, S; Hussain, M; Malik, A A; Shah, H A; Qaim, S M

2010-09-01

Cross-section data for the production of medically important radionuclide (124)I via five proton and deuteron induced reactions on enriched tellurium isotopes were evaluated. The nuclear model codes, STAPRE, EMPIRE and TALYS, were used for consistency checks of the experimental data. Recommended excitation functions were derived using a well-defined statistical procedure. Therefrom integral yields were calculated. The various production routes of (124)I were compared. Presently the (124)Te(p,n)(124)I reaction is the method of choice; however, the (125)Te(p,2n)(124)I reaction also appears to have great potential.

Integrated modelling of enhanced in situ biodenitrification in a fractured aquifer: biogeochemistry and isotope geochemistry

NASA Astrophysics Data System (ADS)

Rodríguez-Escales, Paula; Folch, Albert; van Breukelen, Boris M.; Vidal-Gavilan, Georgina; Soler, Albert

2014-05-01

Enhanced in-situ biodenitrification is a feasible technology to recovery groundwater polluted by nitrates and achieves drinking water standards. Under optimum conditions, nitrate is reduced by autochthonous bacteria trough different reactions until arrive to harmless dinitrogen gas. Isotopic fractionation monitoring in field applications allows knowing the exact degree and the real scope of this technology. Using the Rayleigh equation the change in the isotope ratio of the nitrate molecule (δ15N-NO3-, δ18O-NO3-) is related to the fraction of molecules remaining as a result of biodenitrification. However, Rayleigh application at field scale is sometimes limited due to other processes involved during groundwater flow such as dispersion or adsorption and geological media heterogeneities that interferes in concentration values. Then, include isotope fractionation processes in reactive transport models is a useful tool to interpret and predict data from in-situ biodenitrification. We developed a reactive transport model of enhanced in situ application at field scale in a fractured aquifer that considers biogeochemical processes as well as isotope fractionation to enable better monitoring and management of this technology. Processes considered were: microbiological- exogenous and endogenous nitrate and sulfate respiration coupled with microbial growth and decay, geochemical reactions (precipitation of calcite) and isotopic fractionation (δ15N-NO3-; δ18O- NO3- and carbon isotope network). The 2-D simulations at field scale were developed using PHAST code. Modeling of nitrate isotope geochemistry has allowed determining the extent of biodenitrification in model domain. We have quantified which is the importance in decreasing of nitrate concentrations due to biodegradation (percentage of biodegradation, 'B%') and due to dilution process (percentage of dilution, 'D%'). On the other hand, the stable carbon isotope geochemistry has been modeled. We have considered the isotopic carbon fractionation of different carbon species involved in enhanced biodenitrification: external organic carbon, biomass, inorganic carbon (in different forms) and calcite. The inclusion of carbon isotopes in the model, which are involved in both direct (oxidation of organic carbon) and indirect (carbonate mineral interaction) processes of enhanced biodenitrification, improves the evaluation of the overall model consistency due to the central role of carbon in the reaction network.

YNOGK: A New Public Code for Calculating Null Geodesics in the Kerr Spacetime

NASA Astrophysics Data System (ADS)

Yang, Xiaolin; Wang, Jiancheng

2013-07-01

Following the work of Dexter & Agol, we present a new public code for the fast calculation of null geodesics in the Kerr spacetime. Using Weierstrass's and Jacobi's elliptic functions, we express all coordinates and affine parameters as analytical and numerical functions of a parameter p, which is an integral value along the geodesic. This is the main difference between our code and previous similar ones. The advantage of this treatment is that the information about the turning points does not need to be specified in advance by the user, and many applications such as imaging, the calculation of line profiles, and the observer-emitter problem, become root-finding problems. All elliptic integrations are computed by Carlson's elliptic integral method as in Dexter & Agol, which guarantees the fast computational speed of our code. The formulae to compute the constants of motion given by Cunningham & Bardeen have been extended, which allow one to readily handle situations in which the emitter or the observer has an arbitrary distance from, and motion state with respect to, the central compact object. The validation of the code has been extensively tested through applications to toy problems from the literature. The source FORTRAN code is freely available for download on our Web site http://www1.ynao.ac.cn/~yangxl/yxl.html.

Dynamics of Zn in an urban wetland soil-plant system: Coupling isotopic and EXAFS approaches

NASA Astrophysics Data System (ADS)

Aucour, Anne-Marie; Bedell, Jean-Philippe; Queyron, Marine; Magnin, Valérie; Testemale, Denis; Sarret, Géraldine

2015-07-01

Plants play a key role in the stabilization of metals in contaminated environments. Studies have been performed on Zn uptake and storage mechanisms, mainly for Zn hyperaccumulating plants, though less is known about Zn stabilization in the rhizosphere of non-accumulating plants. This study was focused on the dynamics of Zn in a whole soil-litter-plant system and the processes controlling Zn mobilization and stabilization. The site studied was an infiltration basin receiving urban stormwater, in which Phalaris arundinacea (reed canary grass) developed spontaneously. A combination of chemical extractions (CaCl2, DTPA), EXAFS spectroscopy and Zn stable isotope measurements was applied for the water inlet, soil, plant organs and decaying biomass. Zn speciation changed from the water inlet to the soil. In the soil, Zn was present as Zn-layered double hydroxide (Zn-LDH), tetrahedral and octahedral sorbed Zn species. The formation of Zn-LDH participates in Zn stabilization. Tetrahedral Zn species, which were partly DTPA exchangeable, were enriched in heavy isotopes, whereas octahedral Zn (Zn-LDH and sorbed species) were enriched in light isotopes. Based on a linear model between δ66Zn and Zn speciation, δ66Zn for pure tetrahedral and octahedral end-members were estimated at ca. 0.33‰ and 0.04‰, respectively. In the plant, a mixture of octahedral Zn (attributed to aqueous Zn-organic acid complexes present in the symplasm), and tetrahedral Zn (attributed to apoplasmic Zn-cell wall complexes) was observed in all organs. Large enrichment in light isotopes from the soil to the plant Δ66Zn (of ca. -0.6‰) was observed. The stem was enriched in light isotopes versus roots and, to a lesser extent, versus leaves. The results suggest that Zn was taken up via a low-affinity transport system and that Zn was sequestrated in the stem symplasm after transit through leaves. Finally, intense Zn exchanges were observed between the decaying biomass and the soil, with the sorption of heavy Zn from the soil to cell wall remains and release of light Zn to the soil. Overall, this study provides a complete overview of Zn cycling in an urban wetland soil-plant system, and describes several changes in Zn speciation with Zn isotopic fractionation processes in a complex system.

Analysis of reaction cross-section production in neutron induced fission reactions on uranium isotope using computer code COMPLET.

PubMed

Asres, Yihunie Hibstie; Mathuthu, Manny; Birhane, Marelgn Derso

2018-04-22

This study provides current evidence about cross-section production processes in the theoretical and experimental results of neutron induced reaction of uranium isotope on projectile energy range of 1-100 MeV in order to improve the reliability of nuclear stimulation. In such fission reactions of 235 U within nuclear reactors, much amount of energy would be released as a product that able to satisfy the needs of energy to the world wide without polluting processes as compared to other sources. The main objective of this work is to transform a related knowledge in the neutron-induced fission reactions on 235 U through describing, analyzing and interpreting the theoretical results of the cross sections obtained from computer code COMPLET by comparing with the experimental data obtained from EXFOR. The cross section value of 235 U(n,2n) 234 U, 235 U(n,3n) 233 U, 235 U(n,γ) 236 U, 235 U(n,f) are obtained using computer code COMPLET and the corresponding experimental values were browsed by EXFOR, IAEA. The theoretical results are compared with the experimental data taken from EXFOR Data Bank. Computer code COMPLET has been used for the analysis with the same set of input parameters and the graphs were plotted by the help of spreadsheet & Origin-8 software. The quantification of uncertainties stemming from both experimental data and computer code calculation plays a significant role in the final evaluated results. The calculated results for total cross sections were compared with the experimental data taken from EXFOR in the literature, and good agreement was found between the experimental and theoretical data. This comparison of the calculated data was analyzed and interpreted with tabulation and graphical descriptions, and the results were briefly discussed within the text of this research work. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Isotopic, geochemical, and temporal characterization of Proterozoic basement rocks in the Quitovac region, northwestern Sonora, Mexico: Implications for the reconstruction of the southwestern margin of Laurentia

USGS Publications Warehouse

Iriondo, A.; Premo, W.R.; Martínez-Torres, Luis M.; Budahn, J.R.; Atkinson, William W.; Siems, D.F.; Guaras-Gonzalez, B.

2004-01-01

A detailed geochemical characterization of 19 representative Proterozoic basement rocks in the Quitovac region in northwestern Sonora, Mexico, has identified two distinct Paleoproterozoic basement blocks that coincide spatially with the previously proposed Caborca and "North America" blocks. New U-Pb zircon geochronology revises their age ranges, the Caborca (1.78-1.69 Ga) and "North America" (1.71-1.66 Ga) blocks at Quitovac, and precludes a simple age differentiation between them. In addition, Grenvillian-age granitoids (ca. 1.1 Ga), spatially associated with the Caborca block have been identified at Quitovac. Nd isotopes and major- and trace-element geochemistry support the distinction of these Paleoproterozoic blocks. Granitoids of the "North America" block are characterized by depleted ??Nd values (3.4-3.9) and younger Nd model ages (1800-1740 Ma) and have lower K2O, Y, Rb, Ba, Th, REE, and Fe/Mg values than coeval rocks of the Caborca block. The Caborca block granitoids are likewise characterized by slightly less depleted ??Nd (0.6-2.6) and older Nd model ages (2070-1880 Ma). Despite the subtle differences, granitoids from both the Caborca and "North America" blocks exhibit island arc-like affinities. We propose that the Proterozoic basement rocks from the Quitovac region are an extension of the Proterozoic crustal provinces in the southwestern United States. Specifically, rocks of the Caborca block exhibit an affinity to rocks of either the Yavapai province or the Mojave-Yavapai transition zone, whereas rocks of the "North America" block have signatures similar to those of the Mazatzal province or possibly the Yavapai province of Arizona. The new isotopic ages and geochemical data do not support the existence of the Late Jurassic Mojave-Sonora megashear at Quitovac, as originally proposed. However, the Quitovac region accounts only for a small fraction of the Proterozoic basement in Sonora, so these findings do not eliminate the possibility of a megashear elsewhere in northern Sonora. Our new data create the possibility of alternative hypotheses for the distribution of Paleoproterozoic crustal provinces in southwestern North America that affect reconstructions of the original southwestern margin of Laurentia, and reduce uncertainties in the configuration, timing, and existence of the Proterozoic supercontinent, Rodinia.

AFRRI Reports, Second Quarter 1994

DTIC Science & Technology

1994-08-01

the antrum wete immediately placed in sterile 0.9% NaCl, kept on ice, coded, and then prepared for culture, smears, and urease assay by homogeniza...high urease specific activity (>1 |J.mol- min-1 ■ mg protein-1) plus high-affinity substrate binding (Mi- chaelis constant [K^\\ < 1 mmol/L),27 in at...031, respectively), and the characteristic bacterial growth with high-activity product.on of a urease with tight substrate binding " was found in

Pharmacoproteomics of a metalloproteinase hydroxamate inhibitor in breast cancer cells: dynamics of membrane type 1 matrix metalloproteinase-mediated membrane protein shedding.

PubMed

Butler, Georgina S; Dean, Richard A; Tam, Eric M; Overall, Christopher M

2008-08-01

Broad-spectrum matrix metalloproteinase (MMP) inhibitors (MMPI) were unsuccessful in cancer clinical trials, partly due to side effects resulting from limited knowledge of the full repertoire of MMP substrates, termed the substrate degradome, and hence the in vivo functions of MMPs. To gain further insight into the degradome of MMP-14 (membrane type 1 MMP) an MMPI, prinomastat (drug code AG3340), was used to reduce proteolytic processing and ectodomain shedding in human MDA-MB-231 breast cancer cells transfected with MMP-14. We report a quantitative proteomic evaluation of the targets and effects of the inhibitor in this cell-based system. Proteins in cell-conditioned medium (the secretome) and membrane fractions with levels that were modulated by the MMPI were identified by isotope-coded affinity tag (ICAT) labeling and tandem mass spectrometry. Comparisons of the expression of MMP-14 with that of a vector control resulted in increased MMP-14/vector ICAT ratios for many proteins in conditioned medium, indicating MMP-14-mediated ectodomain shedding. Following MMPI treatment, the MMPI/vehicle ICAT ratio was reversed, suggesting that MMP-14-mediated shedding of these proteins was blocked by the inhibitor. The reduction in shedding or the release of substrates from pericellular sites in the presence of the MMPI was frequently accompanied by the accumulation of the protein in the plasma membrane, as indicated by high MMPI/vehicle ICAT ratios. Considered together, this is a strong predictor of biologically relevant substrates cleaved in the cellular context that led to the identification of many undescribed MMP-14 substrates, 20 of which we validated biochemically, including DJ-1, galectin-1, Hsp90alpha, pentraxin 3, progranulin, Cyr61, peptidyl-prolyl cis-trans isomerase A, and dickkopf-1. Other proteins with altered levels, such as Kunitz-type protease inhibitor 1 and beta-2-microglobulin, were not substrates in biochemical assays, suggesting an indirect affect of the MMPI, which might be important in drug development as biomarkers or, in preclinical phases, to predict systemic drug actions and adverse side effects. Hence, this approach describes the dynamic pattern of cell membrane ectodomain shedding and its perturbation upon metalloproteinase drug treatment.

Cost Function Network-based Design of Protein-Protein Interactions: predicting changes in binding affinity.

PubMed

Viricel, Clément; de Givry, Simon; Schiex, Thomas; Barbe, Sophie

2018-02-20

Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces. Using guaranteed Cost Function Network algorithms, Rosetta energy functions and Dunbrack's rotamer library, we developed and assessed EasyE and JayZ, two methods for binding affinity estimation that ignore or include conformational entropic contributions on a large benchmark of binding affinity experimental measures. If both approaches outperform most established tools, we observe that side-chain conformational entropy brings little or no improvement on most systems but becomes crucial in some rare cases. as open-source Python/C ++ code at sourcesup.renater.fr/projects/easy-jayz. thomas.schiex@inra.fr and sophie.barbe@insa-toulouse.fr. Supplementary data are available at Bioinformatics online.

Molecular Cloning, Biochemical Characterization, and Antitumor Properties of a Novel L-Asparaginase from Synechococcus elongatus PCC6803.

PubMed

Kebeish, R; El-Sayed, A; Fahmy, H; Abdel-Ghany, A

2016-10-01

L-asparaginase (EC 3.5.1.1), which catalyzes the deamidation of L-asparagine to L-aspartic acid and ammonia, has been widely used as a key therapeutic tool in the treatment of tumors. The current commercially available L-asparaginases, produced from bacteria, have signs of toxicity and hypersensitivity reactions during the course of tumor therapy. Therefore, searching for L-asparaginases with unique biochemical properties and fewer adverse effects was the objective of this work. In this study, cyanobacterial strain Synechococcus elongatus PCC6803 was found as a novel source of L-asparaginase. The L-asparaginase gene coding sequence (gi:939195038) was cloned and expressed in E. coli BL21(DE3), and the recombinant protein (Se.ASPII) was purified by affinity chromatography. The enzyme has high affinity towards L-asparagine and shows very weak affinity towards L-glutamine. The enzymatic properties of the recombinant enzyme were investigated, and the kinetic parameters (K m , V max ) were measured. The pH and temperature dependence profiles of the novel enzyme were analyzed. The work was extended to measure the antitumor properties of the novel enzyme against different human tumor cell lines.

Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity.

PubMed

Marini, Simone; Nazzicari, Nelson; Biscarini, Filippo; Wang, Guang-Zhong

2017-06-15

Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations. We developed Dscam1 Web Server to quickly predict Dscam1 self- and hetero- binding affinity for batches of Dscam1 isomers. The server can help the study of Dscam1 affinity and help researchers navigate through the tens of millions of possible isomer combinations to isolate the strong-binding ones. Dscam1 Web Server is freely available at: http://bioinformatics.tecnoparco.org/Dscam1-webserver . Web server code is available at https://gitlab.com/ne1s0n/Dscam1-binding . simone.marini@unipv.it or guangzhong.wang@picb.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS.

PubMed

Baars, Oliver; Morel, François M M; Perlman, David H

2014-11-18

Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).

The impact of nuclear mass models on r-process nucleosynthesis network calculations

NASA Astrophysics Data System (ADS)

Vaughan, Kelly

2002-10-01

An insight into understanding various nucleosynthesis processes is via modelling of the process with network calculations. My project focus is r-process network calculations where the r-process is nucleosynthesis via rapid neutron capture thought to take place in high entropy supernova bubbles. One of the main uncertainties of the simulations is the Nuclear Physics input. My project investigates the role that nuclear masses play in the resulting abundances. The code tecode, involves rapid (n,γ) capture reactions in competition with photodisintegration and β decay onto seed nuclei. In order to fully analyze the effects of nuclear mass models on the relative isotopic abundances, calculations were done from the network code, keeping the initial environmental parameters constant throughout. The supernova model investigated by Qian et al (1996) in which two r-processes, of high and low frequency with seed nucleus ^90Se and of fixed luminosity (fracL_ν_e(0)r_7(0)^2 ˜= 8.77), contribute to the nucleosynthesis of the heavier elements. These two r-processes, however, do not contribute equally to the total abundance observed. The total isotopic abundance produced from both events was therefore calculated using equation refabund. Y(H+L) = fracY(H)+fY(L)f+1 <~belabund where Y(H) denotes the relative isotopic abundance produced in the high frequency event, Y(L) corresponds to the low freqeuncy event and f is the ratio of high event matter to low event matter produced. Having established reliable, fixed parameters, the network code was run using data files containing parameters such as the mass excess, neutron separation energy, β decay rates and neutron capture rates based around three different nuclear mass models. The mass models tested are the HFBCS model (Hartree-Fock BCS) derived from first principles, the ETFSI-Q model (Extended Thomas-Fermi with Strutinsky Integral including shell Quenching) known for its particular successes in the replication of Solar System abundances, and the P-Scheme Model tePscheme. The aims of this research is to test the applicability of the P-Scheme in relation to the other mass models to the r-process network calculations. 02 Pscheme Aprahamian,A., Gadala-Maria,A. & Cuka,N. 1996, Revista Mexicana de Fisica,42,1 code Surman,R. & Engel,J. 1998, Phys.Rev. C,54,4 thebibliography

Determination of the delta(18O/16O)of Water: RSIL Lab Code 489

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler

2008-01-01

The purpose of the technique described by the Reston Stable Isotope Laboratory (RSIL) lab code 489 is to present a method to determine the delta(180/160), abbreviated as delta-180, of water. This delta-18O measurement of water also is a component of National Water Quality Laboratory (NWQL in USGS) schedules 1142 and 1172. Water samples are loaded into glass sample containers on a vacuum manifold to equilibrate gaseous CO2 at constant temperature (25 deg C) with water samples. After loading water samples on the vacuum manifold, air is evacuated through capillary to avoid evaporation, and CO2 is added. The samples are shaken to increase the equilibration rate of water and CO2. When isotopic equilibrium has been attained, an aliquot of CO2 is extracted sequentially from each sample container, separated from water vapor by means of a dry ice trap, and introduced into a dual-inlet isotope-ratio mass spectrometer (DI-IRMS) for determination of the delta-18O value. There is oxygen isotopic fractionation between water and CO2, but it is constant at constant temperature. The DI-IRMS is a DuPont double-focusing mass spectrometer. It has a double collector. One ion beam passes through a slit in a forward collector and is collected in the rear collector. The other ion beams are collected in the front collector. The instrument is capable of measuring mass/charge (m/z) 44 and 45 or 44 and 46 by changing the ion-accelerating voltage under computer control. The ion beams from these m/z values are as follows: m/z 44=CO2=12C16O16O, m/z 45=CO2=13C16O16O primarily, and m/z 46 = CO2=12C16O18O primarily. The data acquisition and control software calculates delta-18O values.

RNA therapeutics: RNAi and antisense mechanisms and clinical applications.

PubMed

Chery, Jessica

2016-07-01

RNA therapeutics refers to the use of oligonucleotides to target primarily ribonucleic acids (RNA) for therapeutic efforts or in research studies to elucidate functions of genes. Oligonucleotides are distinct from other pharmacological modalities, such as small molecules and antibodies that target mainly proteins, due to their mechanisms of action and chemical properties. Nucleic acids come in two forms: deoxyribonucleic acids (DNA) and ribonucleic acids (RNA). Although DNA is more stable, RNA offers more structural variety ranging from messenger RNA (mRNA) that codes for protein to non-coding RNAs, microRNA (miRNA), transfer RNA (tRNA), short interfering RNAs (siRNAs), ribosomal RNA (rRNA), and long-noncoding RNAs (lncRNAs). As our understanding of the wide variety of RNAs deepens, researchers have sought to target RNA since >80% of the genome is estimated to be transcribed. These transcripts include non-coding RNAs such as miRNAs and siRNAs that function in gene regulation by playing key roles in the transfer of genetic information from DNA to protein, the final product of the central dogma in biology 1 . Currently there are two main approaches used to target RNA: double stranded RNA-mediated interference (RNAi) and antisense oligonucleotides (ASO). Both approaches are currently in clinical trials for targeting of RNAs involved in various diseases, such as cancer and neurodegeneration. In fact, ASOs targeting spinal muscular atrophy and amyotrophic lateral sclerosis have shown positive results in clinical trials 2 . Advantages of ASOs include higher affinity due to the development of chemical modifications that increase affinity, selectivity while decreasing toxicity due to off-target effects. This review will highlight the major therapeutic approaches of RNA medicine currently being applied with a focus on RNAi and ASOs.

Minerals as mantle fingerprints: Sr-Nd-Pb-Hf in clinopyroxene and He in olivine distinguish an unusual ancient mantle lithosphere beneath the East African Rift System

NASA Astrophysics Data System (ADS)

Nelson, W. R.; Shirey, S. B.; Graham, D. W.

2011-12-01

The East African Rift System is a complex region that holds keys to understanding the fundamental geodynamics of continental break-up. In this region, the volcanic record preserves over 30 Myrs of geochemical variability associated with the interplay between shallow and deep asthenospheric sources, continental lithospheric mantle, and continental crust. One fundamental question that is still subject to debate concerns the relationship between the lithospheric mantle and the voluminous flood basalt province that erupted at ~30 Ma in Ethiopia and Yemen. Whole-rock Re-Os isotopic data demonstrate the high-Ti (HT2) flood basalts (187Os/188Ost = 0.1247-0.1329) and peridotite xenoliths (187Os/188Ost = 0.1235-0.1377) from NW Ethiopia have similar isotopic compositions. However, Sr-Nd-Pb-Hf isotopic signatures from peridotite clinopyroxene grains are different from those of the flood basalts. The peridotite clinopyroxene separates bear isotopic affinities to anciently depleted mantle (87Sr/86Sr = 0.7019-0.7029; ɛNd = 12.6-18.5; ɛHf = 13.8-27.6) - more depleted than the MORB source - rather than to the OIB-like 30 Ma flood basalts (87Sr/86Sr ~ 0.704; ɛNd = 4.7-6.7; ɛHf = 12.1-13.5). Peridotite clinopyroxenes display two groups of 206Pb/204Pb compositions: the higher 206Pb/204Pb group (18.7-19.3) is compositionally similar to the flood basalts (206Pb/204Pb = 18.97-19.02) whereas the lower 206Pb/204Pb group (17.1-17.9) overlaps with depleted mantle. This suggests that the Pb isotope systematics in some of the peridotites have been metasomatically perturbed. Helium isotopes were analyzed by crushing olivine separated from the peridotites and the flood basalts. Olivine in the peridotites has low He concentrations (0.78-4.7 ncc/g) and low 3He/4He (4.6-6.6 RA), demonstrating that they cannot be the petrogenetic precursor to the high 3He/4He (>12 RA) flood basalts. Notably, these peridotites have 3He/4He signatures consistent with a lithospheric mantle source. Therefore, although the flood basalts and lithospheric mantle bear some isotopic similarities, the basalts were not derived from this portion of the lithospheric mantle, nor are the peridotites crystalline cumulates derived from asthenosphere -derived magmas. The isotopic variations in these peridotites demonstrate that the Afro-Arabian lithosphere contains anciently depleted mantle, created during or prior to the late Proterozoic Pan-African orogeny.

Mechanistic insights into a hydrate contribution to the Paleocene-Eocene carbon cycle perturbation from coupled thermohydraulic simulations

NASA Astrophysics Data System (ADS)

Minshull, T. A.; Marín-Moreno, H.; Armstrong McKay, D. I.; Wilson, P. A.

2016-08-01

During the Paleocene-Eocene Thermal Maximum (PETM), the carbon isotopic signature (δ13C) of surface carbon-bearing phases decreased abruptly by at least 2.5 to 3.0‰. This carbon isotope excursion (CIE) has been attributed to widespread methane hydrate dissociation in response to rapid ocean warming. We ran a thermohydraulic modeling code to simulate hydrate dissociation due to ocean warming for various PETM scenarios. Our results show that hydrate dissociation in response to such warming can be rapid but suggest that methane release to the ocean is modest and delayed by hundreds to thousands of years after the onset of dissociation, limiting the potential for positive feedback from emission-induced warming. In all of our simulations at least half of the dissociated hydrate methane remains beneath the seabed, suggesting that the pre-PETM hydrate inventory needed to account for all of the CIE is at least double that required for isotopic mass balance.

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Electron Scattering from MERCURY-198 and Mercury -204.

NASA Astrophysics Data System (ADS)

Laksanaboonsong, Jarungsaeng

This experiment is the first electron scattering study on mercury isotopes. Electron scattering from ^{198}Hg and ^{204 }Hg has been performed at the NIKHEF-K Medium Energy Accelerator. Measured cross sections cover an effective momentum transfer range from 0.4 to 2.9 fm^ {-1}. Elastic cross sections were determined for scattering from both isotopes. Cross section for inelastic excitations in ^{198}Hg below 3 MeV were also determined. Measured cross sections were fit using DWBA phase shift codes to determine coefficients for Fourier-Bessel expansions of ground state and transition charge densities. Differences between the ground state charge densities of the two isotopes reveal the effect of the polarization of the proton core in response to the addition of neutrons. Spin and parity of several excited states of ^{198}Hg were determined. Extracted transition densities of these states show their predominantly collective nature. Charge densities for members of the ground state rotational band were compared with axially symmetric Hartree-Fock and geometrical model predictions.

Rovibrational bound states of SO2 isotopologues. II: Total angular momentum J = 11-20

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Poirier, Bill

2015-11-01

In a two-part series, the rovibrational bound states of SO2 are investigated in comprehensive detail, for all four stable sulfur isotopes 32-34,36S. All low-lying rovibrational energy levels-both permutation-symmetry-allowed and not allowed-are computed, for all values of total angular momentum in the range J = 0-20. The calculations have carried out using the ScalIT suite of parallel codes. The present study (Paper II) examines the J = 11-20 rovibrational levels, providing symmetry and rovibrational labels for every computed state, relying on a new lambda-doublet splitting technique to make completely unambiguous assignments. Isotope shifts are analyzed, as is the validity of ;J-shifting; as a predictor of rotational fine structure. Among other ramifications, this work will facilitate understanding of mass-independent fractionation of sulfur isotopes (S-MIF) observed in the Archean rock record-particularly as this may have arisen from self shielding. S-MIF, in turn is highly relevant in the broader context of understanding the ;oxygen revolution;.

Rovibrational bound states of SO2 isotopologues. I: Total angular momentum J = 0-10

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Ellis, Joseph; Poirier, Bill

2015-04-01

Isotopic variation of the rovibrational bound states of SO2 for the four stable sulfur isotopes 32-34,36S is investigated in comprehensive detail. In a two-part series, we compute the low-lying energy levels for all values of total angular momentum in the range J = 0-20. All rovibrational levels are computed, to an extremely high level of numerical convergence. The calculations have been carried out using the ScalIT suite of parallel codes. The present study (Paper I) examines the J = 0-10 rovibrational levels, providing unambiguous symmetry and rovibrational label assignments for each computed state. The calculated vibrational energy levels exhibit very good agreement with previously reported experimental and theoretical data. Rovibrational energy levels, calculated without any Coriolis approximations, are reported here for the first time. Among other potential ramifications, this data will facilitate understanding of the origin of mass-independent fractionation of sulfur isotopes in the Archean rock record-of great relevance for understanding the "oxygen revolution".

Paleobotany of Livingston Island: The first report of a Cretaceous fossil flora from Hannah Point

USGS Publications Warehouse

Leppe, M.; Michea, W.; Muñoz, C.; Palma-Heldt, S.; Fernandoy, F.

2007-01-01

This is the first report of a fossil flora from Hannah Point, Livingston Island, South Shetland Islands, Antarctica. The fossiliferous content of an outcrop, located between two igneous rock units of Cretaceous age are mainly composed of leaf imprints and some fossil trunks. The leaf assemblage consists of 18 taxa of Pteridophyta, Pinophyta and one angiosperm. The plant assemblage can be compared to other Early Cretaceous floras from the South Shetland Islands, but several taxa have an evidently Late Cretaceous affinity. A Coniacian-Santonian age is the most probable age for the outcrops, supported by previous K/Ar isotopic studies of the basalts over and underlying the fossiliferous sequence

PCP METHODOLOGY FOR DETERMINING DOSE RATES FOR SMALL GRAM QUANTITIES IN SHIPPING PACKAGINGS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nathan, S.

The Small Gram Quantity (SGQ) concept is based on the understanding that small amounts of hazardous materials, in this case radioactive materials, are significantly less hazardous than large amounts of the same materials. This study describes a methodology designed to estimate an SGQ for several neutron and gamma emitting isotopes that can be shipped in a package compliant with 10 CFR Part 71 external radiation level limits regulations. These regulations require packaging for the shipment of radioactive materials perform, under both normal and accident conditions, the essential functions of material containment, subcriticality, and maintain external radiation levels within regulatory limits.more » 10 CFR 71.33(b)(1)(2)&(3) state radioactive and fissile materials must be identified and their maximum quantity, chemical and physical forms be included in an application. Furthermore, the U.S. Federal Regulations require application contain an evaluation demonstrating the package (i.e., the packaging and its contents) satisfies the external radiation standards for all packages (10 CFR 71.31(2), 71.35(a), & 71.47). By placing the contents in a He leak-tight containment vessel, and limiting the mass to ensure subcriticality, the first two essential functions are readily met. Some isotopes emit sufficiently strong photon radiation that small amounts of material can yield a large external dose rate. Quantifying of the dose rate for a proposed content is a challenging issue for the SGQ approach. It is essential to quantify external radiation levels from several common gamma and neutron sources that can be safely placed in a specific packaging, to ensure compliance with federal regulations. The Packaging Certification Program (PCP) Methodology for Determining Dose Rate for Small Gram Quantities in Shipping Packagings described in this report provides bounding mass limits for a set of proposed SGQ isotopes. Methodology calculations were performed to estimate external radiation levels for the 9977 shipping package using the MCNP radiation transport code to develop a set of response multipliers (Green's functions) for 'dose per particle' for each neutron and photon spectral group. The source spectrum for each isotope generated using the ORIGEN-S and RASTA computer codes was folded with the response multipliers to generate the dose rate per gram of each isotope in the 9977 shipping package and its associated shielded containers. The maximum amount of a single isotope that could be shipped within the regulatory limits contained in 10 CFR 71.47 for dose rate at the surface of the package is determined. If a package contains a mixture of isotopes, the acceptability for shipment can be determined by a sum of fractions approach. Furthermore, the results of this analysis can be easily extended to additional radioisotopes by simply evaluating the neutron and/or photon spectra of those isotopes and folding the spectral data with the Green's functions provided.« less

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Transformations based on continuous piecewise-affine velocity fields

DOE PAGES

Freifeld, Oren; Hauberg, Soren; Batmanghelich, Kayhan; ...

2017-01-11

Here, we propose novel finite-dimensional spaces of well-behaved Rn → Rn transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume preservation and/or boundary conditions), and supports convenient modeling choices such as smoothing priors and coarse-to-fine analysis. Importantly, the proposed approach, partly due to its rapid likelihood evaluations and partly due to its other properties, facilitates tractable inference over rich transformation spaces, including using Markov-Chain Monte-Carlo methods. Its applications include, but are not limited to: monotonic regression (more generally, optimization overmore » monotonic functions); modeling cumulative distribution functions or histograms; time-warping; image warping; image registration; real-time diffeomorphic image editing; data augmentation for image classifiers. Our GPU-based code is publicly available.« less

Transformations Based on Continuous Piecewise-Affine Velocity Fields

PubMed Central

Freifeld, Oren; Hauberg, Søren; Batmanghelich, Kayhan; Fisher, Jonn W.

2018-01-01

We propose novel finite-dimensional spaces of well-behaved ℝn → ℝn transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume preservation and/or boundary conditions), and supports convenient modeling choices such as smoothing priors and coarse-to-fine analysis. Importantly, the proposed approach, partly due to its rapid likelihood evaluations and partly due to its other properties, facilitates tractable inference over rich transformation spaces, including using Markov-Chain Monte-Carlo methods. Its applications include, but are not limited to: monotonic regression (more generally, optimization over monotonic functions); modeling cumulative distribution functions or histograms; time-warping; image warping; image registration; real-time diffeomorphic image editing; data augmentation for image classifiers. Our GPU-based code is publicly available. PMID:28092517

Reactive transport modeling of Li isotope fractionation

NASA Astrophysics Data System (ADS)

Wanner, C.; Sonnenthal, E. L.

2013-12-01

The fractionation of Li isotopes has been used as a proxy for interaction processes between silicate rocks and any kind of fluids. In particular, Li isotope measurements are powerful because Li is almost exclusively found in silicate minerals. Moreover, the two stable Li isotopes, 6Li and 7Li, differ by 17% in mass introducing a large mass dependent isotope fractionation even at high temperature. Typical applications include Li isotope measurements along soil profiles and of river waters to track silicate weathering patterns and Li isotope measurements of geothermal wells and springs to assess water-rock interaction processes in geothermal systems. For this contribution we present a novel reactive transport modeling approach for the simulation of Li isotope fractionation using the code TOUGHREACT [1]. It is based on a 6Li-7Li solid solution approach similar to the one recently described for simulating Cr isotope fractionation [2]. Model applications include the simulation of granite weathering along a 1D flow path as well as the simulation of a column experiment related to an enhanced geothermal system. Results show that measured δ7Li values are mainly controlled by (i) the degree of interaction between Li bearing primary silicate mineral phases (e.g., micas, feldspars) and the corresponding fluid, (ii) the Li isotope fractionation factor during precipitation of secondary mineral phases (e.g., clays), (iii) the Li concentration in primary and secondary Li bearing mineral phases and (iv) the proportion of dissolved Li that adsorbs to negatively charged surfaces (e.g., clays, Fe/Al-hydroxides). To date, most of these parameters are not very well constrained. Reactive transport modeling thus currently has to rely on many assumptions. Nevertheless, such models are powerful because they are the only viable option if individual contributions of all potential processes on the resulting (i.e., measured) Li isotopic ratio have to be quantitatively assessed. Accordingly, we suggest performing more experimental work in conjunction with reactive transport modeling to better understand Li isotope fractionation processes and to obtain a better understanding of water rock interaction processes, eventually. [1] Xu, T., Spycher, N., Sonnenthal, E. L., Zhang, G., Zheng, L., Pruess, K. (2011), Comput. Geosci. 37, 763-774. [2] Wanner, C., Sonnenthal, E. L. (2013), Chem. Geol. 337, 88-98.

Evaluation of different multidimensional LC-MS/MS pipelines for iTRAQ-based proteomic analysis of potato tubers in response to cold storage

USDA-ARS?s Scientific Manuscript database

Cold-induced sweetening in potato tubers is a costly problem for food industry. To systematically identify the proteins associated with this process, we employed a comparative proteomics approach using isobaric, stable isotope coded labels to compare the proteomes of potato tubers after 0 and 5 mont...

Simulation of HEAO 3 Background

DTIC Science & Technology

2007-01-01

i i o iipp i i o iinn VdE A NaEEf VdE A NaEEfprod ji ji j R where i is a stable isotope in volume V, ai is its fractional abundance, i the...National Nuclear Data Center (NNDC), Brookhaven National Laboratory, Brookhaven, NY. [10] W. Nelson et al., ”The EGS4 code system ”, SLAC-Report-265

Multiple tag labeling method for DNA sequencing

DOEpatents

Mathies, Richard A.; Huang, Xiaohua C.; Quesada, Mark A.

1995-01-01

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

RADSOURCE. Volume 1, Part 1, A scaling factor prediction computer program technical manual and code validation: Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vance, J.N.; Holderness, J.H.; James, D.W.

1992-12-01

Waste stream scaling factors based on sampling programs are vulnerable to one or more of the following factors: sample representativeness, analytic accuracy, and measurement sensitivity. As an alternative to sample analyses or as a verification of the sampling results, this project proposes the use of the RADSOURCE code, which accounts for the release of fuel-source radionuclides. Once the release rates of these nuclides from fuel are known, the code develops scaling factors for waste streams based on easily measured Cobalt-60 (Co-60) and Cesium-137 (Cs-137). The project team developed mathematical models to account for the appearance rate of 10CFR61 radionuclides inmore » reactor coolant. They based these models on the chemistry and nuclear physics of the radionuclides involved. Next, they incorporated the models into a computer code that calculates plant waste stream scaling factors based on reactor coolant gamma- isotopic data. Finally, the team performed special sampling at 17 reactors to validate the models in the RADSOURCE code.« less

Knockout and fragmentation reactions using a broad range of tin isotopes

NASA Astrophysics Data System (ADS)

Rodríguez-Sánchez, J. L.; Benlliure, J.; Bertulani, C. A.; Vargas, J.; Ayyad, Y.; Alvarez-Pol, H.; Atkinson, J.; Aumann, T.; Beceiro-Novo, S.; Boretzky, K.; Caamaño, M.; Casarejos, E.; Cortina-Gil, D.; Díaz-Cortes, J.; Fernández, P. Díaz; Estrade, A.; Geissel, H.; Kelić-Heil, A.; Litvinov, Yu. A.; Mostazo, M.; Paradela, C.; Pérez-Loureiro, D.; Pietri, S.; Prochazka, A.; Takechi, M.; Weick, H.; Winfield, J. S.

2017-09-01

Production cross sections of residual nuclei obtained by knockout and fragmentation reactions of different tin isotopes accelerated at 1 A GeV have been measured with the fragment separator (FRS) at GSI, Darmstadt. The new measurements are used to investigate the neutron-excess dependence of the neutron- and proton-knockout cross sections. These cross sections are compared to Glauber model calculations coupled to a nuclear de-excitation code in order to investigate the role of the remnant excitations. This bench marking shows an overestimation of the cross sections for the removal of deeply bound nucleons. A phenomenological increase in the excitation energy induced in the remnants produced in these cases allows us to reproduce the measured cross sections.

A high burnup model developed for the DIONISIO code

NASA Astrophysics Data System (ADS)

Soba, A.; Denis, A.; Romero, L.; Villarino, E.; Sardella, F.

2013-02-01

A group of subroutines, designed to extend the application range of the fuel performance code DIONISIO to high burn up, has recently been included in the code. The new calculation tools, which are tuned for UO2 fuels in LWR conditions, predict the radial distribution of power density, burnup, and concentration of diverse nuclides within the pellet. The balance equations of all the isotopes involved in the fission process are solved in a simplified manner, and the one-group effective cross sections of all of them are obtained as functions of the radial position in the pellet, burnup, and enrichment in 235U. In this work, the subroutines are described and the results of the simulations performed with DIONISIO are presented. The good agreement with the data provided in the FUMEX II/III NEA data bank can be easily recognized.

Carrier-mediated γ-aminobutyric acid transport across the basolateral membrane of human intestinal Caco-2 cell monolayers.

PubMed

Nielsen, Carsten Uhd; Carstensen, Mette; Brodin, Birger

2012-06-01

The aim of the present study was to investigate the transport of γ-aminobutyric acid (GABA) across the basolateral membrane of intestinal cells. The proton-coupled amino acid transporter, hPAT1, mediates the influx of GABA and GABA mimetic drug substances such as vigabatrin and gaboxadol and the anticancer prodrug δ-aminolevulinic acid across the apical membrane of small intestinal enterocytes. Little is however known about the basolateral transport of these substances. We investigated basolateral transport of GABA in mature Caco-2 cell monolayers using isotope studies. Here we report that, at least two transporters seem to be involved in the basolateral transport of GABA. The basolateral uptake consisted of a high-affinity system with a K(m) of 290 μM and V(max) of 75 pmol cm(-2) min(-1) and a low affinity system with a K(m) of approximately 64 mM and V(max) of 1.6 nmol cm(-2) min(-1). The high-affinity transporter is Na(+) and Cl(-) dependent. The substrate specificity of the high-affinity transporter was further studied and Gly-Sar, Leucine, gaboxadol, sarcosine, lysine, betaine, 5-hydroxythryptophan, proline and glycine reduced the GABA uptake to approximately 44-70% of the GABA uptake in the absence of inhibitor. Other substances such as β-alanine, GABA, 5-aminovaleric acid, taurine and δ-aminolevulinic acid reduced the basolateral GABA uptake to 6-25% of the uptake in the absence of inhibitor. Our results indicate that the distance between the charged amino- and acid-groups is particular important for inhibition of basolateral GABA uptake. Thus, there seems to be a partial substrate overlap between the basolateral GABA transporter and hPAT1, which may prove important for understanding drug interactions at the level of intestinal transport. Copyright © 2012 Elsevier B.V. All rights reserved.

European Science Notes (ESN) Information Bulletin. Reports on Current European/Middle Eastern Science,

DTIC Science & Technology

1987-12-01

mRNA), lular viruses within a few hours in dif- and Sl-analysis showed that anti-IgM and ferent body fluids and may be used for phorbol esters...suppressed mRNA coding for general virus diagnosis. the secreted form of IgM, showing that Thiophilic adsorption for the puri- these additives affect...constructs were and can be an alternative method to pro- utilized containing the prokaryotic CAT - tein A affinity chromatography, especial- gene

Recognition of Double Stranded RNA by Guanidine-Modified Peptide Nucleic Acids (GPNA)

PubMed Central

Gupta, Pankaj; Muse, Oluwatoyosi; Rozners, Eriks

2011-01-01

Double helical RNA has become an attractive target for molecular recognition because many non-coding RNAs play important roles in control of gene expression. Recently, we discovered that short peptide nucleic acids (PNA) bind strongly and sequence selectively to a homopurine tract of double helical RNA via triple helix formation. Herein we tested if the molecular recognition of RNA can be enhanced by α-guanidine modification of PNA. Our study was motivated by the discovery of Ly and co-workers that the guanidine modification greatly enhances the cellular delivery of PNA. Isothermal titration calorimetry showed that the guanidine-modified PNA (GPNA) had reduced affinity and sequence selectivity for triple helical recognition of RNA. The data suggested that in contrast to unmodified PNA, which formed a 1:1 PNA-RNA triple helix, GPNA preferred a 2:1 GPNA-RNA triplex-invasion complex. Nevertheless, promising results were obtained for recognition of biologically relevant double helical RNA. Consistent with enhanced strand invasion ability, GPNA derived from D-arginine recognized the transactivation response element (TAR) of HIV-1 with high affinity and sequence selectivity, presumably via Watson-Crick duplex formation. On the other hand, strong and sequence selective triple helices were formed by unmodified and nucelobase-modified PNAs and the purine rich strand of bacterial A-site. These results suggest that appropriate chemical modifications of PNA may enhance molecular recognition of complex non-coding RNAs. PMID:22146072

Determination of the δ34S of sulfate in water; RSIL lab code 1951

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1951 is to determine the δ(34S/32S), abbreviated as δ34S, of dissolved sulfate. Dissolved sulfate is collected in the field and precipitated with BaCl2 at pH 3 to 4 as BaSO4 in the laboratory. However, the dissolved organic sulfur (DOS) is oxidized to SO2, and the carbonate is acidified to CO2. Both are degassed from the water sample before the sulfate is precipitated. The precipitated BaSO4 is filtered and dried before introduction into an elemental analyzer (EA) Carlo Erba NC 2500. The EA is used to convert sulfur in a BaSO4 solid sample into SO2 gas, and the EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the differences in the isotope-amount ratios of stable sulfur isotopes (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated tube reaction tube that combines the oxidation and reduction reactions. The combustion takes place in a helium atmosphere containing an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a helium carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which also is used to inject SO2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; m/z 66 = SO2 = 34S16O16O primarily.

Preparation of stable isotope-labeled peripheral cannabinoid receptor CB2 by bacterial fermentation

PubMed Central

Berger, Christian; Ho, Jenny T.C.; Kimura, Tomohiro; Hess, Sonja; Gawrisch, Klaus; Yeliseev, Alexei

2010-01-01

We developed a bacterial fermentation protocol for production of a stable isotope-labeled cannabinoid receptor CB2 for subsequent structural studies of this protein by nuclear magnetic resonance spectroscopy. The human peripheral cannabinoid receptor was expressed in Escherichia coli as a fusion with maltose binding protein and two affinity tags. The fermentation was performed in defined media comprised of mineral salts, glucose and 15N2-L-tryptophan to afford incorporation of the labeled amino acid into the protein. Medium, growth and expression conditions were optimized so that the fermentation process produced about 2 mg of purified, labeled CB2 per liter of culture medium. By performing a mass spectroscopic characterization of the purified CB2, we determined that one of the two 15N atoms in tryptophan was incorporated into the recombinant protein. NMR analysis of 15N chemical shifts strongly suggests that the 15N atoms are located in Trp-indole rings. Importantly, analysis of the peptides derived from the CNBr cleavage of the purified protein confirmed a minimum of 95% incorporation of the labeled tryptophan into the CB2 sequence. The labeled CB2, purified and reconstituted into liposomes at a protein-to-lipid molar ratio of 1:500, was functional as confirmed by activation of cognate G proteins in an in vitro coupled assay. To our knowledge, this is the first reported production of a biologically active, stable isotope-labeled G protein-coupled receptor by bacterial fermentation. PMID:20044006

Development of Parallel Computing Framework to Enhance Radiation Transport Code Capabilities for Rare Isotope Beam Facility Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostin, Mikhail; Mokhov, Nikolai; Niita, Koji

A parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. It is intended to be used with older radiation transport codes implemented in Fortran77, Fortran 90 or C. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was developed and tested in conjunction with the MARS15 code. It is possible to use it with other codes such as PHITS, FLUKA andmore » MCNP after certain adjustments. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility can be used in single process calculations as well as in the parallel regime. The framework corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

Identification of low-abundance cancer biomarker candidate TIMP1 from serum with lectin fractionation and peptide affinity enrichment by ultrahigh-resolution mass spectrometry.

PubMed

Ahn, Yeong Hee; Kim, Kwang Hoe; Shin, Park Min; Ji, Eun Sun; Kim, Hoguen; Yoo, Jong Shin

2012-02-07

As investigating a proteolytic target peptide originating from the tissue inhibitor of metalloproteinase 1 (TIMP1) known to be aberrantly glycosylated in patients with colorectal cancer (CRC), we first confirmed that TIMP1 is to be a CRC biomarker candidate in human serum. For this, we utilized matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) showing ultrahigh-resolution and high mass accuracy. This investigation used phytohemagglutinin-L(4) (L-PHA) lectin, which shows binding affinity to the β-1,6-N-acetylglucosamine moiety of N-linked glycan on a protein, to compare fractionated aberrant protein glycoforms from both noncancerous control and CRC serum. Each lectin-captured fraction containing aberrant glycoforms of TIMP1 was digested by trypsin, resulting in the tryptic target peptide, representative of the serum glycoprotein TIMP1. The resulting target peptide was enriched using a stable isotope standard and capture by the antipeptide antibody (SISCAPA) technique and analyzed by a 15 T MALDI FTICR mass spectrometer with high mass accuracy (Δ < 0.5 ppm to the theoretical mass value of the target peptide). Since exact measurement of multiplex isotopic peaks of the target peptide could be accomplished by virtue of high mass resolution (Rs > 400,000), robust identification of the target peptide is only achievable with 15 T FTICR MS. Also, MALDI data obtained in this study showed that the L-PHA-captured glycoforms of TIMP1 were measured in the pooled CRC serum with about 5 times higher abundance than that in the noncancerous serum, and were further proved by MRM mass analysis. These results confirm that TIMP1 in human serum is a potent CRC biomarker candidate, demonstrating that ultrahigh-resolution MS can be a powerful tool toward identifying and verifying potential protein biomarker candidates. © 2011 American Chemical Society

The relationship between CK and CV chondrites

NASA Astrophysics Data System (ADS)

Greenwood, R. C.; Franchi, I. A.; Kearsley, A. T.; Alard, O.

2010-03-01

CK chondrites are highly oxidized meteorites containing abundant magnetite and trace amounts of Fe,Ni metal. Although the group is predominately composed of equilibrated meteorites (types 4-6), in recent years a significant number of new samples have been classified as being either CK3 or CK3-anomalous. These unequilibrated CKs often display a close affinity with members of the CV oxidized subgroup. CKs and CVs (oxidized subgroup) may therefore form a continuum and by implication could be derived from a single common parent body. To investigate the relationship between these two groups a detailed study of the oxygen isotope composition, opaque mineralogy and major and trace element geochemistry of a suite of CV and CK chondrites has been undertaken. The results of oxygen isotope analysis confirm the close affinity between CV and CK chondrites, while excluding the possibility of a linkage between the CO and CK groups. Magnetites in both CV and CK chondrites show significant compositional similarities, but high Ti contents are a diagnostic feature of the latter group. The results of major and trace element analysis demonstrate that both CV and CK chondrites show overlapping variation. Supporting evidence for a single common source for both groups comes from their similar cosmic-ray exposure age distributions. Recent reflectance spectral analysis is consistent with both the CVs and CKs being derived from Eos family asteroids, which are believed to have formed by the catastrophic disruption of a single large asteroid. Thus, a range of evidence appears to be consistent with CV and CK chondrites representing samples from a single thermally stratified parent body. In view of the close similarity between CV and CK chondrites some modification of the present classification scheme may be warranted, possibly involving integration of the two groups. One means of achieving this would be to reassigned CK chondrites to a subgroup of the oxidized CVs. It is recognized that a full evaluation of this proposal may require further study of the still poorly understood CK3 chondrites.

Automatic Data Distribution for CFD Applications on Structured Grids

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Yan, Jerry

2000-01-01

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAFT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAFT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly.

PubMed

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-02-27

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Automatic Data Distribution for CFD Applications on Structured Grids

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Yan, Jerry

1999-01-01

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAPT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAPT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

RNA-protein interactions in an unstructured context.

PubMed

Zagrovic, Bojan; Bartonek, Lukas; Polyansky, Anton A

2018-05-31

Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA-protein interactions in general. © 2018 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Ethanol Attenuates Histiotrophic Nutrition Pathways and Alters the Intracellular Redox Environment and Thiol Proteome during Rat Organogenesis

PubMed Central

Jilek, Joseph L.; Sant, Karilyn E.; Cho, Katherine H.; Reed, Matthew S.; Pohl, Jan; Hansen, Jason M.; Harris, Craig

2015-01-01

Ethanol (EtOH) is a reactive oxygen-generating teratogen involved in the etiology of structural and functional developmental defects. Embryonic nutrition, redox environment, and changes in the thiol proteome following EtOH exposures (1.56.0 mg/ml) were studied in rat whole embryo culture. Glutathione (GSH) and cysteine (Cys) concentrations with their respective intracellular redox potentials (Eh) were determined using high-performance liquid chromatography. EtOH reduced GSH and Cys concentrations in embryo (EMB) and visceral yolk sac (VYS) tissues, and also in yolk sac and amniotic fluids. These changes produced greater oxidation as indicated by increasingly positive Eh values. EtOH reduced histiotrophic nutrition pathway activities as measured by the clearance of fluorescin isothiocyanate (FITC)-albumin from culture media. A significant decrease in total FITC clearance was observed at all concentrations, reaching approximately 50% at the highest dose. EtOH-induced changes to the thiol proteome were measured in EMBs and VYSs using isotope-coded affinity tags. Decreased concentrations for specific proteins from cytoskeletal dynamics and endocytosis pathways (α-actinin, α-tubulin, cubilin, and actin-related protein 2); nuclear translocation (Ran and RanBP1); and maintenance of receptor-mediated endocytosis (cubilin) were observed. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis also identified a decrease in ribosomal proteins in both EMB and VYS. Results show that EtOH interferes with nutrient uptake to reduce availability of amino acids and micronutrients required by the conceptus. Intracellular antioxidants such as GSH and Cys are depleted following EtOH and Eh values increase. Thiol proteome analysis in the EMB and VYS show selectively altered actin/cytoskeleton, endocytosis, ribosome biogenesis and function, nuclear transport, and stress-related responses. PMID:26185205

A Targeted Quantitative Proteomics Strategy for Global Kinome Profiling of Cancer Cells and Tissues*

PubMed Central

Xiao, Yongsheng; Guo, Lei; Wang, Yinsheng

2014-01-01

Kinases are among the most intensively pursued enzyme superfamilies as targets for anti-cancer drugs. Large data sets on inhibitor potency and selectivity for more than 400 human kinases became available recently, offering the opportunity to design rationally novel kinase-based anti-cancer therapies. However, the expression levels and activities of kinases are highly heterogeneous among different types of cancer and even among different stages of the same cancer. The lack of effective strategy for profiling the global kinome hampers the development of kinase-targeted cancer chemotherapy. Here, we introduced a novel global kinome profiling method, based on our recently developed isotope-coded ATP-affinity probe and a targeted proteomic method using multiple-reaction monitoring (MRM), for assessing simultaneously the expression of more than 300 kinases in human cells and tissues. This MRM-based assay displayed much better sensitivity, reproducibility, and accuracy than the discovery-based shotgun proteomic method. Approximately 250 kinases could be routinely detected in the lysate of a single cell line. Additionally, the incorporation of iRT into MRM kinome library rendered our MRM kinome assay easily transferrable across different instrument platforms and laboratories. We further employed this approach for profiling kinase expression in two melanoma cell lines, which revealed substantial kinome reprogramming during cancer progression and demonstrated an excellent correlation between the anti-proliferative effects of kinase inhibitors and the expression levels of their target kinases. Therefore, this facile and accurate kinome profiling assay, together with the kinome-inhibitor interaction map, could provide invaluable knowledge to predict the effectiveness of kinase inhibitor drugs and offer the opportunity for individualized cancer chemotherapy. PMID:24520089

Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of cd toxicity.

PubMed

Go, Young-Mi; Roede, James R; Orr, Michael; Liang, Yongliang; Jones, Dean P

2014-05-01

Cadmium (Cd) exposure contributes to human diseases affecting liver, kidney, lung, and other organ systems, but mechanisms underlying the pleotropic nature of these toxicities are poorly understood. Cd accumulates in humans from dietary, environmental (including cigarette smoke), and occupational sources, and has a twenty-year biologic half-life. Our previous mouse and cell studies showed that environmental low-dose Cd exposure altered protein redox states resulting in stimulation of inflammatory signaling and disruption of the actin cytoskeleton system, suggesting that Cd could impact multiple mechanisms of disease. In the current study, we investigated the effects of acute Cd exposure on the redox proteome and metabolome of mouse liver mitochondria to gain insight into associated toxicological mechanisms and functions. We analyzed redox states of liver mitochondrial proteins by redox proteomics using isotope coded affinity tag (ICAT) combined mass spectrometry. Redox ICAT identified 2687 cysteine-containing peptides (peptidyl Cys) of which 1667 peptidyl Cys (657 proteins) were detected in both control and Cd-exposed samples. Of these, 46% (1247 peptidyl Cys, 547 proteins) were oxidized by Cd more than 1.5-fold relative to controls. Bioinformatics analysis using MetaCore software showed that Cd affected 86 pathways, including 24 Cys in proteins functioning in branched chain amino acid (BCAA) and 14 Cys in proteins functioning in fatty acid (acylcarnitine/carnitine) metabolism. Consistently, high-resolution metabolomics data showed that Cd treatment altered levels of BCAA and carnitine metabolites. Together, these results show that mitochondrial protein redox and metabolites are targets in Cd-induced hepatotoxicity. The results further indicate that redox proteomics and metabolomics can be used in an integrated systems approach to investigate complex disease mechanisms.

Selenocysteine in proteins-properties and biotechnological use.

PubMed

Johansson, Linda; Gafvelin, Guro; Arnér, Elias S J

2005-10-30

Selenocysteine (Sec), the 21st amino acid, exists naturally in all kingdoms of life as the defining entity of selenoproteins. Sec is a cysteine (Cys) residue analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group in Cys. The selenium atom gives Sec quite different properties from Cys. The most obvious difference is the lower pK(a) of Sec, and Sec is also a stronger nucleophile than Cys. Proteins naturally containing Sec are often enzymes, employing the reactivity of the Sec residue during the catalytic cycle and therefore Sec is normally essential for their catalytic efficiencies. Other unique features of Sec, not shared by any of the other 20 common amino acids, derive from the atomic weight and chemical properties of selenium and the particular occurrence and properties of its stable and radioactive isotopes. Sec is, moreover, incorporated into proteins by an expansion of the genetic code as the translation of selenoproteins involves the decoding of a UGA codon, otherwise being a termination codon. In this review, we will describe the different unique properties of Sec and we will discuss the prerequisites for selenoprotein production as well as the possible use of Sec introduction into proteins for biotechnological applications. These include residue-specific radiolabeling with gamma or positron emitters, the use of Sec as a reactive handle for electophilic probes introducing fluorescence or other peptide conjugates, as the basis for affinity purification of recombinant proteins, the trapping of folding intermediates, improved phasing in X-ray crystallography, introduction of 77Se for NMR spectroscopy, or, finally, the analysis or tailoring of enzymatic reactions involving thiol or oxidoreductase (redox) selenolate chemistry.

Determination of the δ2H and δ18O of soil water and water in plant matter; RSIL lab code 1700

USGS Publications Warehouse

Revesz, Kinga M.; Buck, Bryan; Coplen, Tyler B.

2012-01-01

The purpose of the Reston Stable Isotope Laboratory lab code 1700 is to determine the δ2H/1H), abbreviated as δ2H, and the δ18O/16O), abbreviated as δ18O, of soil water and water in plant matter. This method is based on the observation that water and toluene form an azeotropic mixture at 84.1 °C. This temperature is substantially lower than the boiling points of water (100 °C) and toluene (110 °C), but water and toluene are immiscible at ambient temperature. The water content of a soil or plant is determined by weighing, drying, and reweighing a small amount of sample. Sufficient sample to collect 3 to 5 milliliters of water after distillation is loaded into a distillation flask. Sufficient toluene is added so that the sample is immersed throughout the entire distillation to minimize evaporation of water, which would affect the δ2H and δ18O values. The mixture of sample and toluene is heated in a flask to its boiling point (84.1 °C) so that water from the sample and toluene can distill together into a specially designed collection funnel. The temperature of 84.1 °C is maintained until the water has been quantitatively transferred to the collection funnel, at which time the temperature is raised to the boiling point of the remaining component (toluene, 110 °C). The collection funnel is maintained at ambient temperature so that the sample water and toluene can be separated physically. After separation, the sample water is purified by addition of paraffin wax to the container with the sample water, capping the container, and heating to approximately 60 °C to melt the wax. Trace amounts of toluene will dissolve in the wax, purifying the sample water for isotopic analysis. The isotopic composition of the purified water is then determined by equilibration with gaseous hydrogen or carbon dioxide, followed by dual-inlet isotope-ratio mass spectrometry. Because laser-absorption spectrometry is sensitive to organic compounds, such as trace toluene remaining in water samples, water samples should be analyzed for isotopic composition only by mass spectrometry and not by laser-absorption spectrometry.

Initial Results: An Ultra-Low-Background Germanium Crystal Array

DTIC Science & Technology

2010-09-01

data (focused on γ -γ coincidence signatures) (Smith et al., 2004) and the Multi- Isotope Coincidence Analysis code (MICA) (Warren et al., 2006). The...The follow-on “CASCADES” project aims to develop a multicoincidence data- analysis package and make robust fission-product demonstration measurements...sensitivity. This effort is focused on improving gamma analysis capabilities for nuclear detonation detection (NDD) applications, e.g., nuclear treaty

Prise en compte d'un couplage fin neutronique-thermique dans les calculs d'assemblage pour les reacteurs a eau pressurisee

NASA Astrophysics Data System (ADS)

Greiner, Nathan

Core simulations for Pressurized Water Reactors (PWR) is insured by a set of computer codes which allows, under certain assumptions, to approximate the physical quantities of interest, such as the effective multiplication factor or the power or temperature distributions. The neutronics calculation scheme relies on three great steps : -- the production of an isotopic cross-sections library ; -- the production of a reactor database through the lattice calculation ; -- the full-core calculation. In the lattice calculation, in which Boltzmann's transport equation is solved over an assembly geometry, the temperature distribution is uniform and constant during irradiation. This represents a set of approximations since, on the one hand, the temperature distribution in the assembly is not uniform (strong temperature gradients in the fuel pins, discrepancies between the fuel pins) and on the other hand, irradiation causes the thermal properties of the pins to change, which modifies the temperature distribution. Our work aims at implementing and introducing a neutronics-thermomechanics coupling into the lattice calculation to finely discretize the temperature distribution and to study its effects. To perform the study, CEA (Commissariat a l'Energie Atomique et aux Energies Alternatives) lattice code APOLLO2 was used for neutronics and EDF (Electricite De France) code C3THER was used for the thermal calculations. We show very small effects of the pin-scaled coupling when comparing the use of a temperature profile with the use of an uniform temperature over UOX-type and MOX-type fuels. We next investigate the thermal feedback using an assembly-scaled coupling taking into account the presence of large water gaps on an UOX-type assembly at burnup 0. We show the very small impact on the calculation of the hot spot factor. Finally, the coupling is introduced into the isotopic depletion calculation and we show that reactivity and isotopic number densities deviations remain small albeit not negligible for UOX-type and MOX-type assemblies. The specific behavior of gadolinium-stuffed fuel pins in an UO2Gd2O 3-type assembly is highlighted.

Magmatism and fenitization in the Cretaceous potassium-alkaline-carbonatitic complex of Ipanema São Paulo State, Brazil

NASA Astrophysics Data System (ADS)

Guarino, Vincenza; Azzone, Rogério Guitarrari; Brotzu, Pietro; de Barros Gomes, Celso; Melluso, Leone; Morbidelli, Lucio; Ruberti, Excelso; Tassinari, Colombo Celso Gaeta; Brilli, Mauro

2012-01-01

The Ipanema alkaline-carbonatitic complex is part of the Meso-Cenozoic alkaline magmatism located within the southeastern part of the Brazilian Platform. Drill-core and field sampling have indicated the occurrence of glimmerites, with subordinate shonkinites (mela-syenites), clinopyroxene-bearing glimmerites, diorites and syenites. The glimmerites are cross-cut by lamprophyric dykes and calciocarbonatites. Fenitization has deeply affected the country rocks, originating dioritic and syenitic rocks. The Ipanema rocks show a distinct potassic affinity. The initial Sr-Nd- isotopic composition of the Ipanema rocks (87Sr/86Sr = 0.70661-0.70754 and 143Nd/144Nd = 0.51169-0.51181) is similar to that of tholeiitic and potassium-rich-alkaline rocks of the Eastern Paraguay. Stable isotope data for the Ipanema calciocarbonatite suggest interaction with fluids at temperatures typical of hydrothermal stages, as hypothesized for other carbonatite complexes from southeastern Brazil. The chemical differences between the lamprophyre, glimmerites, carbonatites, apatitites and magnetitites, and the absence of marked REE enrichment in the evolved lithologies, all indicate that fractional crystallization and accumulus of liquidus phases in a magma reservoir, likely coupled with liquid immiscibility processes, may have played an important role in the genesis of the Ipanema rocks.

Geochronology and petrogenesis of the western highlands alkali suite: Radiogenic isotopic evidence from Apollo 14

NASA Astrophysics Data System (ADS)

Snyder, Gregory A.; Taylor, Lawrence A.; Halliday, Alex N.

1993-03-01

Several rocks of alkalic affinity, from the western highlands of the Moon, have been analyzed for their Nd and Sr isotopic compositions. One sample yields a Sm-Nd mineral isochron of 4110 = 41 Ma. This age, in conjunction with U-Pb zircon ages on two other alkalic rocks from the Apollo 14 landing site suggests a distinct western highlands 'event' which was approximately 100 Ma in duration. Since the last dregs of the lunar magma ocean likely crystallized prior to 4.3 Ga, this alkalic 'event' may have included the re-melting of evolved plutons or the remobilization of urKREEP trapped liquid from upper mantle cumulates. Alkalic lithologies such as granites and felsites have been known from the Moon since the earliest days of the Apollo lunar sample returns. However, not until 1977 were alkali-rich rocks recognized from typical highlands suites such as ferroan anorthosites (FAN) and norites and Mg-suite rocks. In the intervening years, several other alkali suite samples have been discovered and characterized, mostly through labor-intesive breccia pull-apart studies of clasts and analyses of coarse-fine fractions of soils. We will speculate on the origins of this suite of lunar highlands rocks.

Geochronology and petrogenesis of the western highlands alkali suite: Radiogenic isotopic evidence from Apollo 14

NASA Technical Reports Server (NTRS)

Snyder, Gregory A.; Taylor, Lawrence A.; Halliday, Alex N.

1993-01-01

Several rocks of alkalic affinity, from the western highlands of the Moon, have been analyzed for their Nd and Sr isotopic compositions. One sample yields a Sm-Nd mineral isochron of 4110 = 41 Ma. This age, in conjunction with U-Pb zircon ages on two other alkalic rocks from the Apollo 14 landing site suggests a distinct western highlands 'event' which was approximately 100 Ma in duration. Since the last dregs of the lunar magma ocean likely crystallized prior to 4.3 Ga, this alkalic 'event' may have included the re-melting of evolved plutons or the remobilization of urKREEP trapped liquid from upper mantle cumulates. Alkalic lithologies such as granites and felsites have been known from the Moon since the earliest days of the Apollo lunar sample returns. However, not until 1977 were alkali-rich rocks recognized from typical highlands suites such as ferroan anorthosites (FAN) and norites and Mg-suite rocks. In the intervening years, several other alkali suite samples have been discovered and characterized, mostly through labor-intesive breccia pull-apart studies of clasts and analyses of coarse-fine fractions of soils. We will speculate on the origins of this suite of lunar highlands rocks.

A new fast-cycling system for AMS at ANU

NASA Astrophysics Data System (ADS)

De Cesare, M.; Fifield, L. K.; Weisser, D. C.; Tsifakis, D.; Cooper, A.; Lobanov, N. R.; Tunningley, T. B.; Tims, S. G.; Wallner, A.

2015-10-01

In order to perform higher precision measurements, an upgrade of the ANU accelerator is underway. Fast switching times on the low-energy side, with maximum settling times of 30 ms, are achieved by holding the injector magnet field constant while changing the energy of the different isotopes by changing the pre-acceleration voltage after the ion source. Because ions of the different isotopes then have different energies before injection, it is necessary to adjust the strength and steering of the electrostatic quadrupole lens that focusses the beam before entry into the accelerator. First tests of the low-energy system will be reported. At the high energy end, a larger vacuum box in the analyzing magnet has been designed, manufactured and installed to allow the transport of differences in mass as large as 10% at constant terminal voltage. For the cases where more than one isotope must be transported to the detector an additional refinement is necessary. If the accelerator voltage is to be kept constant, then the trajectories of the different isotopes around both the analyzing and switching magnets must be modified. This will be achieved using bounced electrostatic steerers before and after the magnets. Simulations have been performed with the ion optic code COSY Infinity to determine the optimal positions and sizes of these steerers.

Fragment emission from the mass-symmetric reactions 58Fe,58Ni +58Fe,58Ni at Ebeam=30 MeV/nucleon

NASA Astrophysics Data System (ADS)

Ramakrishnan, E.; Johnston, H.; Gimeno-Nogues, F.; Rowland, D. J.; Laforest, R.; Lui, Y.-W.; Ferro, S.; Vasal, S.; Yennello, S. J.

1998-04-01

The mass-symmetric reactions 58Fe,58Ni +58Fe,58Ni were studied at a beam energy of Ebeam=30 MeV/nucleon in order to investigate the isospin dependence of fragment emission. Ratios of inclusive yields of isotopic fragments from hydrogen through nitrogen were extracted as a function of laboratory angle. A moving source analysis of the data indicates that at laboratory angles around 40° the yield of intermediate mass fragments (IMF's) beyond Z=3 is predominantly from a midrapidity source. The angular dependence of the relative yields of isotopes beyond Z=3 indicates that the IMF's at more central angles originate from a source which is more neutron deficient than the source responsible for fragments emitted at forward angles. The charge distributions and kinetic energy spectra of the IMF's at various laboratory angles were well reproduced by calculations employing a quantum molecular-dynamics code followed by a statistical multifragmentation model for generating fragments. The calculations indicate that the measured IMF's originate mainly from a single source. The isotopic composition of the emitted fragments is, however, not reproduced by the same calculation. The measured isotopic and isobaric ratios indicate an emitting source that is more neutron rich in comparison to the source predicted by model calculations.

Disk mass determination through CO isotopologues

NASA Astrophysics Data System (ADS)

Miotello, Anna; Kama, Mihkel; van Dishoeck, Ewine

2015-08-01

One of the key properties for understanding how disks evolve to planetary systems is their overall mass, combined with their surface density distribution. So far, virtually all disk mass determinations are based on observations of the millimeter continuum dust emission.To derive the total gas + dust disk mass from these data involves however several big assumptions. The alternative method is to directly derive the gas mass through the detection of carbon monoxide (CO) and its less abundant isotopologues. CO chemistry is well studied and easily implemented in chemical models, provided that isotope-selective processes are properly accounted for.CO isotope-selective photodissociation was implemented for the first time in a full physical-chemical code in Miotello et al. (2014). The main result is that if isotope-selective effects are not considered in the data analysis, disk masses can be underestimated by an order of magnitude or more. For example, the mass discrepancy found for the renowned TW Hya disk may be explained or at least mitigated by this implementation. In this poster, we present new results for a large grid of disk models. We derive mass correction factors for different disk, stellar and grain properties in order to account for isotope-selective effects in analyzing ALMA data of CO isotopologues (Miotello et al., in prep.).

IsoWeb: A Bayesian Isotope Mixing Model for Diet Analysis of the Whole Food Web

PubMed Central

Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

2012-01-01

Quantitative description of food webs provides fundamental information for the understanding of population, community, and ecosystem dynamics. Recently, stable isotope mixing models have been widely used to quantify dietary proportions of different food resources to a focal consumer. Here we propose a novel mixing model (IsoWeb) that estimates diet proportions of all consumers in a food web based on stable isotope information. IsoWeb requires a topological description of a food web, and stable isotope signatures of all consumers and resources in the web. A merit of IsoWeb is that it takes into account variation in trophic enrichment factors among different consumer-resource links. Sensitivity analysis using realistic hypothetical food webs suggests that IsoWeb is applicable to a wide variety of food webs differing in the number of species, connectance, sample size, and data variability. Sensitivity analysis based on real topological webs showed that IsoWeb can allow for a certain level of topological uncertainty in target food webs, including erroneously assuming false links, omission of existent links and species, and trophic aggregation into trophospecies. Moreover, using an illustrative application to a real food web, we demonstrated that IsoWeb can compare the plausibility of different candidate topologies for a focal web. These results suggest that IsoWeb provides a powerful tool to analyze food-web structure from stable isotope data. We provide R and BUGS codes to aid efficient applications of IsoWeb. PMID:22848427

Novel Codon Insert in HIV Type 1 Clade B Reverse Transcriptase Associated with Low-Level Viremia During Antiretroviral Therapy

PubMed Central

Gianella, Sara; Vazquez, Homero; Ignacio, Caroline; Zweig, Adam C.; Richman, Douglas D.; Smith, Davey M.

2014-01-01

Abstract We investigated the pol genotype in two phylogenetically and epidemiologically linked partners, who were both experiencing persistent low-level viremia during antiretroviral therapy. In one partner we identified a new residue insertion between codon 248 and 249 of the HIV-1 RNA reverse transcriptase (RT) coding region (HXB2 numbering). We then investigated the potential impact of identified mutations in RT and antiretroviral binding affinity using a novel computational approach. PMID:24020934

Nuclear Resonance Fluorescence for Materials Assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quiter, Brian; Ludewigt, Bernhard; Mozin, Vladimir

This paper discusses the use of nuclear resonance fluorescence (NRF) techniques for the isotopic and quantitative assaying of radioactive material. Potential applications include age-dating of an unknown radioactive source, pre- and post-detonation nuclear forensics, and safeguards for nuclear fuel cycles Examples of age-dating a strong radioactive source and assaying a spent fuel pin are discussed. The modeling work has ben performed with the Monte Carlo radiation transport computer code MCNPX, and the capability to simulate NRF has bee added to the code. Discussed are the limitations in MCNPX's photon transport physics for accurately describing photon scattering processes that are importantmore » contributions to the background and impact the applicability of the NRF assay technique.« less

Preliminary investigation of parasitic radioisotope production using the LANL IPF secondary neutron flux

NASA Astrophysics Data System (ADS)

Engle, J. W.; Kelsey, C. T.; Bach, H.; Ballard, B. D.; Fassbender, M. E.; John, K. D.; Birnbaum, E. R.; Nortier, F. M.

2012-12-01

In order to ascertain the potential for radioisotope production and material science studies using the Isotope Production Facility at Los Alamos National Lab, a two-pronged investigation has been initiated. The Monte Carlo for Neutral Particles eXtended (MCNPX) code has been used in conjunction with the CINDER 90 burnup code to predict neutron flux energy distributions as a result of routine irradiations and to estimate yields of radioisotopes of interest for hypothetical irradiation conditions. A threshold foil activation experiment is planned to study the neutron flux using measured yields of radioisotopes, quantified by HPGe gamma spectroscopy, from representative nuclear reactions with known thresholds up to 50 MeV.

Evaluation of Production Cross Sections of Li, Be, B in CR

NASA Technical Reports Server (NTRS)

Moskalenko, I. V.; Mashnik, S. G.

2003-01-01

Accurate evaluation of the production cross section of light elements is important for models of cosmic ray (CR) propagation, galactic chemical evolution, and cosmological studies. However, the experimental spallation cross section data are scarce and often unavailable to CR community while semi-empirical systematics are frequently wrong by a significant factor. Running sophisticated nuclear codes is not an option of choice for everyone either. We use the Los Alamos versions of the Quark-Gluon String Model code LAQGSM and the improved Cascade-Exciton Model code CEM2k together with all available data from Los Alamos Nuclear Laboratory (LANL) nuclear database to produce evaluated production cross sections of isotopes of Li, Be, and B suitable for astrophysical applications. The LAQGSM and CEM2k models have been shown to reproduce well nuclear reactions and hadronic data in the range 0.01-800 GeV/nucleon.

CEM2k and LAQGSM Codes as Event-Generators for Space Radiation Shield and Cosmic Rays Propagation Applications

NASA Technical Reports Server (NTRS)

Mashnik, S. G.; Gudima, K. K.; Sierk, A. J.; Moskalenko, I. V.

2002-01-01

Space radiation shield applications and studies of cosmic ray propagation in the Galaxy require reliable cross sections to calculate spectra of secondary particles and yields of the isotopes produced in nuclear reactions induced both by particles and nuclei at energies from threshold to hundreds of GeV per nucleon. Since the data often exist in a very limited energy range or sometimes not at all, the only way to obtain an estimate of the production cross sections is to use theoretical models and codes. Recently, we have developed improved versions of the Cascade-Exciton Model (CEM) of nuclear reactions: the codes CEM97 and CEM2k for description of particle-nucleus reactions at energies up to about 5 GeV. In addition, we have developed a LANL version of the Quark-Gluon String Model (LAQGSM) to describe reactions induced both by particles and nuclei at energies up to hundreds of GeVhucleon. We have tested and benchmarked the CEM and LAQGSM codes against a large variety of experimental data and have compared their results with predictions by other currently available models and codes. Our benchmarks show that CEM and LAQGSM codes have predictive powers no worse than other currently used codes and describe many reactions better than other codes; therefore both our codes can be used as reliable event-generators for space radiation shield and cosmic ray propagation applications. The CEM2k code is being incorporated into the transport code MCNPX (and several other transport codes), and we plan to incorporate LAQGSM into MCNPX in the near future. Here, we present the current status of the CEM2k and LAQGSM codes, and show results and applications to studies of cosmic ray propagation in the Galaxy.

Construction of armored RNA containing long-size chimeric RNA by increasing the number and affinity of the pac site in exogenous rna and sequence coding coat protein of the MS2 bacteriophage.

PubMed

Wei, Baojun; Wei, Yuxiang; Zhang, Kuo; Yang, Changmei; Wang, Jing; Xu, Ruihuan; Zhan, Sien; Lin, Guigao; Wang, Wei; Liu, Min; Wang, Lunan; Zhang, Rui; Li, Jinming

2008-01-01

To construct a one-plasmid expression system of the armored RNA containing long chimeric RNA by increasing the number and affinity of the pac site. The plasmid pET-MS2-pac was constructed with one C-variant pac site, and then the plasmid pM-CR-2C containing 1,891-bp chimeric sequences and two C-variant pac sites was produced. Meanwhile, three plasmids (pM-CR-C, pM-CR-2W and pM-CR-W) were obtained as parallel controls with a different number and affinity of the pac site. Finally, the armored RNA was expressed and purified. The armored RNA with 1,891 bases target RNA was expressed successfully by the one-plasmid expression system with two C-variant pac sites, while for one pac site, no matter whether the affinity was changed or not, only the 1,200 bases target RNA was packaged. It was also found that the C-variant pac site could increase the expression efficiency of the armored RNA. The armored RNA with 1,891-bp exogenous RNA in our study showed the characterization of ribonuclease resistance and stability at different time points and temperature conditions. The armored RNA with 1,891 bases exogenous RNA was constructed and the expression system can be used as a platform for preparation of the armored RNA containing long RNA sequences. Copyright 2008 S. Karger AG, Basel.

Characterizing cosmochemical materials with genetic affinities to the Earth: Genetic and chronological diversity within the IAB iron meteorite complex

NASA Astrophysics Data System (ADS)

Worsham, Emily A.; Bermingham, Katherine R.; Walker, Richard J.

2017-06-01

The IAB iron meteorite complex consists of a main group (MG) and five chemical subgroups (sLL, sLM, sLH, sHL, and sHH). Here, mass-independent Mo and radiogenic 182W isotope compositions are reported for IAB complex meteorites to evaluate the genetics and chronology, respectively, of the MG and subgroups. Osmium isotopes are used to correct for cosmic ray exposure effects on isotopes of Mo and W. The MG and three subgroups (i.e., sLL, sLM, and sLH), characterized by low Au abundances, have the same Mo isotopic compositions within analytical uncertainty, consistent with a common genetic origin. These meteorites, together with winonaites, are the only cosmochemical materials yet identified with Mo isotopic compositions that are identical to Earth. The Mo isotopic compositions of two subgroups characterized by higher Au abundances (sHL and sHH) are identical to one another within uncertainty, but differ from the low Au subgroups, indicating derivation from genetically distinct materials. The MG has a 182W, post calcium-aluminum inclusion (CAI) formation model age of 3.4 ± 0.7 Ma. One of the low Au subgroups (sLM) is ∼1.7 Ma younger, whereas the high Au subgroups are ∼1.5-3 Ma older. The new Mo-W data, coupled with chemical data, indicate that the MG and the low Au subgroups formed in different impact-generated melts, some of which evidently formed on a chemically disparate, but genetically identical parent body. The high Au subgroups likely formed via core-formation processes on separate, internally-heated parent bodies from other IAB subgroups. The IAB complex meteorites fall on a linear trend defined by 94Mo/96Mo vs. 95Mo/96Mo, along with most other iron meteorite groups. Variation along this line was caused by mixing between at least two nebular components. One component was likely a pure s-process enriched nucleosynthetic carrier, and the other a homogenized nebular component. Sombrerete, currently classified as an sHL iron, has a Mo isotopic composition that is distinct from all IAB complex meteorites analyzed here. Along with group IVB iron meteorites and some ungrouped iron meteorites, it falls on a separate line from other meteorites which may reflect addition of an r-process-enriched component, and it should no longer be classified as a IAB iron.

On the Numerical Analysis of Decay Rate Enhancement in Metallic Environment

NASA Astrophysics Data System (ADS)

Mehedinteanu, S.

2007-10-01

Motivated on the very recent experiments to determine the acceleration of the alpha decay of meta-stable radionuclides in metallic environment some work has been done to strengthten the importance in the process of electrons screening in metals. Thus, by combining the Gamow decay theory with electrostatic screening in Debye-Hückel approximation (jellium model) a formula for ``the shift'' in screening energy which enters in the decay enhancement factor expression that copes well with these experiments has been derived. It was established that to simulate the poly-atoms system containing decaying isotopes in QM&MD codes calculations, and to include ``the screening energy shift'' of protons, decay alpha, beta+ particles due to all surrounding interacting effects, it is sufficiently only to substitute the code ruly pseudo-potential input for hydrogen-like atoms (including alpha) by a screened Coulomb potential as from the well-known Gamow alpha decay theory. For demonstration is used the QM&MD code package which usually performs density-functional theory (DFT) total-energy calculations for materials ranging from insulators to transition metals. This package employs first-principles pseudo-potentials and a plane-wave basis-set, and it was used to do a special calculus for some metal environments (Pd) where protons-deuterons are implanted or when it is alloyed with a radionuclide-like isotopes (174Hf72), the results compare well with the existing experiments on the decay enhancement. These works give further arguments for a cheap solution to remove the transuranic waste (involving all alpha-decay) of used-up rods of fission reactors in a time period of a few years.

Cross-sections of residual nuclei from deuteron irradiation of thin thorium target at energy 7 GeV

NASA Astrophysics Data System (ADS)

Vespalec, Radek; Adam, Jindrich; Baldin, Anton Alexandrovich; Khushvaktov, Jurabek; Solnyshkin, Alexander Alexandrovich; Tsoupko-Sitnikov, Vsevolod Mikhailovich; Tyutyunikov, Sergey Ivanovich; Vrzalova, Jitka; Zavorka, Lukas; Zeman, Miroslav

2017-09-01

The residual nuclei yields are of great importance for the estimation of basic radiation-technology characteristics (like a total target activity, production of long-lived nuclides etc.) of accelerator driven systems planned for transmutation of spent nuclear fuel and for a design of radioisotopes production facilities. Experimental data are also essential for validation of nuclear codes describing various stages of a spallation reaction. Therefore, the main aim of this work is to add new experimental data in energy region of relativistic deuterons, as similar data are missing in nuclear databases. The sample made of thin natural thorium foil was irradiated at JINR Nuclotron accelerator with a deuteron beam of the total kinetic energy 7 GeV. Integral number of deuterons was determined with the use of aluminum activation detectors. Products of deuteron induced spallation reaction were qualified and quantified by means of gamma-ray spectroscopy method. Several important spectroscopic corrections were applied to obtain results of high accuracy. Experimental cumulative and independent cross-sections were determined for more than 80 isotopes including meta-stable isomers. The total uncertainty of results rarely exceeded 9%. Experimental results were compared with MCNP6.1 Monte-Carlo code predictions. Generally, experimental and calculated cross-sections are in a reasonably good agreement, with the exception of a few light isotopes in a fragmentation region, where the calculations are highly under-estimated. Measured data will be useful for future development of high-energy nuclear codes. After completion, final data will be added into the EXFOR database.

Preface to highly siderophile element constraints on Earth and planetary processes

NASA Astrophysics Data System (ADS)

Riches, Amy J. V.

2017-11-01

The geochemical properties of the highly siderophile elements (HSEs; Os, Ir, Ru, Rh, Pt, Pd, Re and Au) - being strongly iron-loving, but also chalcophile (i.e., having an affinity for sulphide), and generally occurring at ultra trace levels in silicate rocks, their weathered products, and oceanic waters - mean that this suite of elements and their isotopic compositions are useful in tracing a wide variety of processes. Thus, the HSEs are useful probes with which to tackle major research questions pertinent to past and present day change at a variety of scales and in a range of Earth and other-worldly environments by constraining reservoir compositions, chemical drivers, and the timing of key events and/or transformation rates.

Geant4 Modifications for Accurate Fission Simulations

NASA Astrophysics Data System (ADS)

Tan, Jiawei; Bendahan, Joseph

Monte Carlo is one of the methods to simulate the generation and transport of radiation through matter. The most widely used radiation simulation codes are MCNP and Geant4. The simulation of fission production and transport by MCNP has been thoroughly benchmarked. There is an increasing number of users that prefer using Geant4 due to the flexibility of adding features. However, it has been found that Geant4 does not have the proper fission-production cross sections and does not produce the correct fission products. To achieve accurate results for studies in fissionable material applications, Geant4 was modified to correct these inaccuracies and to add new capabilities. The fission model developed by the Lawrence Livermore National Laboratory was integrated into the neutron-fission modeling package. The photofission simulation capability was enabled using the same neutron-fission library under the assumption that nuclei fission in the same way, independent of the excitation source. The modified fission code provides the correct multiplicity of prompt neutrons and gamma rays, and produces delayed gamma rays and neutrons with time and energy dependencies that are consistent with ENDF/B-VII. The delayed neutrons are now directly produced by a custom package that bypasses the fragment cascade model. The modifications were made for U-235, U-238 and Pu-239 isotopes; however, the new framework allows adding new isotopes easily. The SLAC nuclear data library is used for simulation of isotopes with an atomic number above 92 because it is not available in Geant4. Results of the modified Geant4.10.1 package of neutron-fission and photofission for prompt and delayed radiation are compared with ENDFB-VII and with results produced with the original package.

Bruyères-le-Châtel Neutron Evaluations of Actinides with the TALYS Code: The Fission Channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romain, P., E-mail: pascal.romain@cea.fr; Morillon, B.; Duarte, H.

For several years, various neutron evaluations of plutonium and uranium isotopes have been performed at Bruyères-le-Châtel (BRC), from 1 keV up to 30 MeV. Since only nuclear reaction models have been used to produce these evaluations, our approach was named the “Full Model” approach. Total, shape elastic and direct inelastic cross sections were obtained from the coupled channels model using a dispersive optical potential developed for actinides, with a large enough coupling scheme including the lowest octupolar band. All other cross sections were calculated using the Hauser-Feshbach theory (TALYS code) with a pre-equilibrium component above 8–10 MeV. In this paper,more » we focus our attention on the fission channel. More precisely, we will present the BRC contribution to fission modeling and the philosophy adopted in our “Full Model” approach. Performing evaluations with the “Full Model” approach implies the optimization of a large number of model parameters. With increasing neutron incident energy, many residual nuclei produced by nucleon emission also lead to fission. All available experimental data assigned to various fission mechanisms of the same nucleus were used to determine fission barrier parameters. For uranium isotopes, triple-humped fission barriers were required in order to reproduce accurately variations of the experimental fission cross sections. Our BRC fission modeling has shown that the effects of the class II or class III states located in the wells of the fission barrier sometimes provide an anti-resonant transmission rather than a resonant one. Consistent evaluations were produced for a large series of U and Pu isotopes. Resulting files were tested against integral data.« less

Sensitive determination of thiols in wine samples by a stable isotope-coded derivatization reagent d0/d4-acridone-10-ethyl-N-maleimide coupled with high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry analysis.

PubMed

Lv, Zhengxian; You, Jinmao; Lu, Shuaimin; Sun, Weidi; Ji, Zhongyin; Sun, Zhiwei; Song, Cuihua; Chen, Guang; Li, Guoliang; Hu, Na; Zhou, Wu; Suo, Yourui

2017-03-31

As the key aroma compounds, varietal thiols are the crucial odorants responsible for the flavor of wines. Quantitative analysis of thiols can provide crucial information for the aroma profiles of different wine styles. In this study, a rapid and sensitive method for the simultaneous determination of six thiols in wine using d 0 /d 4 -acridone-10-ethyl-N-maleimide (d 0 /d 4 -AENM) as stable isotope-coded derivatization reagent (SICD) by high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) has been developed. Quantification of thiols was performed by using d 4 -AENM labeled thiols as the internal standards (IS), followed by stable isotope dilution HPLC-ESI-MS/MS analysis. The AENM derivatization combined with multiple reactions monitoring (MRM) not only allowed trace analysis of thiols due to the extremely high sensitivity, but also efficiently corrected the matrix effects during HPLC-MS/MS and the fluctuation in MS/MS signal intensity due to instrument. The obtained internal standard calibration curves for six thiols were linear over the range of 25-10,000pmol/L (R 2 ≥0.9961). Detection limits (LODs) for most of analytes were below 6.3pmol/L. The proposed method was successfully applied for the simultaneous determination of six kinds of thiols in wine samples with precisions ≤3.5% and recoveries ≥78.1%. In conclusion, the developed method is expected to be a promising tool for detection of trace thiols in wine and also in other complex matrix. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a pair of differential H/D isotope-coded derivatization reagents d(0)/d(3)-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine and its application for determination of aldehydes in selected aquatic products by liquid chromatography-tandem mass spectrometry.

PubMed

Sun, Zhiwei; Wang, Xiaoxiang; Cai, Yiping; Fu, Junqing; You, Jinmao

2014-03-01

A new pair of derivatization reagents, d0-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine (d0-MPIA) and d3-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine (d3-MPIA) have been designed and synthesized. It was successfully used to label aliphatic aldehydes and the aldehyde derivatives were analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The new isotope-coded reagents could easily label aldehydes under acidic conditions in the presence of NaCNBH3. The target derivatives exhibited intense [M+H](+) and regular product ions with electrospray ionization source in positive mode. The d0/d3-MPIA-aldehydes were monitored by the transitions of [M+H](+)→m/z 322 and [M+H](+)→m/z 165, and the obtained detection limits were in the range of 0.18-15.9 pg/mL at signal to noise ratio of 3. The global isotope internal standard technology was employed for quantification analysis with d3-MPIA-aldehyde as internal standard for corresponding d0-MPIA-aldehyde. Excellent linear responses for relative quantification were observed in the range of 1/10-10/1 with coefficients >0.998. The developed method has been applied to the quantification of aliphatic aldehydes in selected aquatic products with RSD<3.6% and recoveries >85.2%. © 2013 Elsevier B.V. All rights reserved.

A source-depleted Early Jurassic granitic pluton from South China: Implication to the Mesozoic juvenile accretion of the South China crust

NASA Astrophysics Data System (ADS)

Zhou, Zuo-Min; Ma, Chang-Qian; Wang, Lian-Xun; Chen, Shu-Guang; Xie, Cai-Fu; Li, Yong; Liu, Wei

2018-02-01

Source-depleted granites were rarely reported in South China. Hereby we identified such a granitic pluton, the Tiandong pluton, at Northeastern Guangdong province in Southeastern (SE) China. Whole-rock Sr-Nd and zircon Hf isotopes of the Tiandong granites both revealed obviously depleted source signatures, with initial isotopic values of initial 87Sr/86Sr = 0.7032-0.7040, εNd(t) = 1.1-1.5, and εHf(t) = 6-13, respectively. Zircon U-Pb dating implied the granite was intruded in Early Jurassic (188 Ma). The dominant minerals of the Tiandong granite consist of K-feldspar, plagioclase, quartz and biotite, with accessory mineral assemblage of apatite + zircon + magnetite. Based on the mineralogy and the depleted isotopic signature, the granites chemically show I-type affinity such as low Zr + Nb + Ce + Y (131.6 to 212.2), 104 × Ga/Al (2.12-2.27), A/CNK values < 1.1 (0.97-1.03), corundum molecule < 1 (0-0.55) and extremely low P2O5 contents (0.05 wt%). The one-stage and two-stage depleted mantle Nd model ages (TDM = 0.89 to 0.84 Ga, T2DM = 0.88 to 0.85 Ga) are consistent. TDM(Hf) values of 0.31-0.63 Ga are also indistinguishable from T2DM(Hf) values of 0.35-0.75 Ga. The Nd and Hf isotopic compositions confirm that the Tiandong granites are juvenile crustal accretion but decoupled Nd-Hf isotopic systems. The juvenile crust is likely to originate from a mixed source of the primary asthenospheric mantle and the subordinate EMII. Combined with early studies of adjacent rocks, we propose that the early Jurassic ( 200-175 Ma) magmatism as evidenced by the Tiandong granites might be driven by upwelling of asthenosphere and subsequent underplating of mafic melts in an intra-plate extensional setting as a response to far-field stress during early stage subduction of the paleo-pacific plate.

Petrogenesis of Late Jurassic granodiorites from Gutian, Fujian Province, South China: Implications for multiple magma sources and origin of porphyry Cu-Mo mineralization

NASA Astrophysics Data System (ADS)

Li, Bin; Jiang, Shao-Yong; Lu, An-Huai; Lai, Jian-Qing; Zhao, Kui-Dong; Yang, Tao

2016-11-01

The Gutian porphyry Cu-Mo deposit is a newly proved porphyry copper deposit in the coastal South China associated with granodioritic porphyries. In this study, zircon U-Pb ages and Hf isotope data, as well as geochemical and Sr-Nd-Pb-Re-Os isotopic compositions, are reported for these intrusions and minerals. Both zircon U-Pb and molybdenite Re-Os dating suggest that the Gutian granodiorite porphyries and related mineralization formed at 160 Ma. The Gutian granodiorites show a low-Mg adakitic geochemical affinity, with relatively high K2O but low Cr and Ni contents. These rocks have initial (87Sr/86Sr)i ratios of 0.7085 to 0.7097, negative εNd(t) values (- 12.5 to - 7.8), (206Pb/204Pb)t ratios of 18.048 to 18.241, (207Pb/204Pb)t ratios of 15.609 to 15.628, and (208Pb/204Pb)t ratios of 38.494 to 38.667. Zircons from the granodiorites have negative εHf(t) values of - 15.7 to - 8.5, which are close to those of Cathaysia crust-derived melts. Geochemical and Sr-Nd-Pb-Hf isotopic compositions suggest that they may be derived from Late Jurassic thickened juvenile lower crust. These lower crustal magma sources may not only contain pre-Proterozoic basement rocks, but also involve Triassic and Middle-Late Jurassic arc magmas within the lower crust, which were likely derived from an enriched mantle source associated with paleo-Pacific Plate subduction from the Middle to Late Jurassic. The Gutian ore-related granodiorites represent a new example for significant contributions of ancient subduction melts and enriched mantle-derived sources for porphyry-type magmatism and Cu-Mo mineralization, which occurred in response to an arc regime during the Middle to Late Jurassic in South China. Supplemental Table S2. Hf isotopic compositions of zircons from the studied rocks from the Gutian porphyry deposit in South China. Supplemental Table S3. Statistics for zircon U-Pb ages and Hf isotope compositions from Gutian granodiorites in South China Supplemental Table S4. Major element (wt.%) and trace element (ppm) concentrations of Gutian intrusions in Fujian Province, South China. Supplemental Table S5. Sr and Nd isotopic compositions of the studied rocks from the Gutian porphyry deposit in Fujian Province, South China. Supplemental Table S6. Pb isotopic compositions of the studied rocks from the Gutian porphyry deposit in South China. Supplemental Table S7. Re-Os isotopic compositions of molybdenite from the Gutian porphyry deposit in South China.

Validation of Heavy Ion Transport Capabilities in PHITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronningen, Reginald M.

The performance of the Monte Carlo code system PHITS is validated for heavy ion transport capabilities by performing simulations and comparing results against experimental data from heavy ion reactions of benchmark quality. These data are from measurements of secondary neutron production cross sections in reactions of Xe at 400 MeV/u with lithium and lead targets, measurements of neutrons outside of thick concrete and iron shields, and measurements of isotope yields produced in the fragmentation of a 140 MeV/u 48Ca beam on a beryllium target and on a tantalum target. A practical example that tests magnetic field capabilities is shown formore » a simulated 48Ca beam at 500 MeV/u striking a lithium target to produce the rare isotope 44Si, with ion transport through a fragmentation-reaction magnetic pre-separator. The results of this study show that PHITS performs reliably for the simulation of radiation fields that is necessary for designing safe, reliable and cost effective future high-powered heavy-ion accelerators in rare isotope beam facilities.« less

Automated collection and processing of environmental samples

DOEpatents

Troyer, Gary L.; McNeece, Susan G.; Brayton, Darryl D.; Panesar, Amardip K.

1997-01-01

For monitoring an environmental parameter such as the level of nuclear radiation, at distributed sites, bar coded sample collectors are deployed and their codes are read using a portable data entry unit that also records the time of deployment. The time and collector identity are cross referenced in memory in the portable unit. Similarly, when later recovering the collector for testing, the code is again read and the time of collection is stored as indexed to the sample collector, or to a further bar code, for example as provided on a container for the sample. The identity of the operator can also be encoded and stored. After deploying and/or recovering the sample collectors, the data is transmitted to a base processor. The samples are tested, preferably using a test unit coupled to the base processor, and again the time is recorded. The base processor computes the level of radiation at the site during exposure of the sample collector, using the detected radiation level of the sample, the delay between recovery and testing, the duration of exposure and the half life of the isotopes collected. In one embodiment, an identity code and a site code are optically read by an image grabber coupled to the portable data entry unit.

Structure of neutron-rich nuclei around the N = 50 shell-gap closure

NASA Astrophysics Data System (ADS)

Faul, T.; Duchêne, G.; Thomas, J.-C.; Nowacki, F.; Huyse, M.; Van Duppen, P.

2010-04-01

The structure of neutron-rich nuclei in the vicinity of 78Ni have been investigated via the β-decay of 71,73,75Cu isotopes (ISOLDE, CERN). Experimental results have been compared with shell-model calculations performed with the ANTOINE code using a large (2p3/21f5/22p1/21g9/2) valence space and a 56/28Ni28 core.

Comparison of short-lived medical isotopes activation by laser thin target induced protons and conventional cyclotron proton beams

NASA Astrophysics Data System (ADS)

Murray, Joseph; Dudnikova, Galina; Liu, Tung-Chang; Papadopoulos, Dennis; Sagdeev, Roald; Su, J. J.; UMD MicroPET Team

2014-10-01

Production diagnostic or therapeutic nuclear medicines are either by nuclear reactors or by ion accelerators. In general, diagnostic nuclear radioisotopes have a very short half-life varying from tens of minutes for PET tracers and few hours for SPECT tracers. Thus supplies of PET and SPECT radiotracers are limited by regional production facilities. For example 18F-fluorodeoxyglucose (FDG) is the most desired tracer for positron emission tomography because its 110 minutes half-life is sufficient long for transport from production facilities to nearby users. From nuclear activation to completing image taking must be done within 4 hours. Decentralized production of diagnostic radioisotopes will be idea to make high specific activity radiotracers available to researches and clinicians. 11 C, 13 N, 15 O and 18 F can be produced in the energy range from 10-20 MeV by protons. Protons of energies up to tens of MeV generated by intense laser interacting with hydrogen containing targets have been demonstrated by many groups in the past decade. We use 2D PIC code for proton acceleration, Geant4 Monte Carlo code for nuclei activation to compare the yields and specific activities of short-lived isotopes produced by cyclotron proton beams and laser driven protons.

Isotope-coded, iodoacetamide-based reagent to determine individual cysteine pKa values by MALDI-TOF mass spectrometry

PubMed Central

Nelson, Kimberly J.; Day, Amanda E.; Zeng, Bubing B.; King, S. Bruce; Poole, Leslie B.

2008-01-01

Cysteine reactivity in enzymes is imparted to a large extent by the stabilization of the deprotonated form of the reduced cysteine (i.e. the thiolate) within the active site. While this is likely to be an important chemical attribute of many thiol-based enzymes including cysteine-dependent peroxidases (peroxiredoxins) and proteases, only relatively few pKa values have been determined experimentally. Presented here is a new technique for determining the pKa value of cysteine residues through quantitative mass spectrometry following chemical modification with an iodoacetamide-based reagent over a range of pH buffers. This isotope-coded reagent, N-phenyl iodoacetamide (iodoacetanilide), is readily prepared in deuterated (d5) and protiated (d0) versions and is more reactive toward free cysteine than is iodoacetamide. Using this approach, the pKa values for the two cysteine residues in Escherichia coli thioredoxin were determined to be 6.5 and > 10, in good agreement with previous reports using chemical modification approaches. This technique allows the pKa of specific cysteine residues to be determined in a clear, fast, and simple manner and, because cysteine residues on separate tryptic peptides are measured separately, is not complicated by the presence of multiple cysteines within the protein of interest. PMID:18162165

Efficient mRNA-Based Genetic Engineering of Human NK Cells with High-Affinity CD16 and CCR7 Augments Rituximab-Induced ADCC against Lymphoma and Targets NK Cell Migration toward the Lymph Node-Associated Chemokine CCL19.

PubMed

Carlsten, Mattias; Levy, Emily; Karambelkar, Amrita; Li, Linhong; Reger, Robert; Berg, Maria; Peshwa, Madhusudan V; Childs, Richard W

2016-01-01

For more than a decade, investigators have pursued methods to genetically engineer natural killer (NK) cells for use in clinical therapy against cancer. Despite considerable advances in viral transduction of hematopoietic stem cells and T cells, transduction efficiencies for NK cells have remained disappointingly low. Here, we show that NK cells can be genetically reprogramed efficiently using a cGMP-compliant mRNA electroporation method that induces rapid and reproducible transgene expression in nearly all transfected cells, without negatively influencing their viability, phenotype, and cytotoxic function. To study its potential therapeutic application, we used this approach to improve key aspects involved in efficient lymphoma targeting by adoptively infused ex vivo-expanded NK cells. Electroporation of NK cells with mRNA coding for the chemokine receptor CCR7 significantly promoted migration toward the lymph node-associated chemokine CCL19. Further, introduction of mRNA coding for the high-affinity antibody-binding receptor CD16 (CD16-158V) substantially augmented NK cell cytotoxicity against rituximab-coated lymphoma cells. Based on these data, we conclude that this approach can be utilized to genetically modify multiple modalities of NK cells in a highly efficient manner with the potential to improve multiple facets of their in vivo tumor targeting, thus, opening a new arena for the development of more efficacious adoptive NK cell-based cancer immunotherapies.

RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3′-Tail of the Long Non-coding RNA BC200 (BCYRN1)*

PubMed Central

Booy, Evan P.; McRae, Ewan K. S.; Howard, Ryan; Deo, Soumya R.; Ariyo, Emmanuel O.; Dzananovic, Edis; Meier, Markus; Stetefeld, Jörg; McKenna, Sean A.

2016-01-01

RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3′-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3′-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences. PMID:26740632

Uranium-Lead Zircon Ages and Sr, Nd, and Pb Isotope Geochemistry of Selected Plutonic Rocks from Western Idaho

USGS Publications Warehouse

Unruh, Daniel M.; Lund, Karen; Kuntz, Mel A.; Snee, Lawrence W.

2008-01-01

Across the Salmon River suture in western Idaho, where allochthonous Permian to Cretaceous oceanic rocks are juxtaposed against Proterozoic North American rocks, a wide variety of plutonic rocks are exposed. Available data indicate much variation in composition, source, and structural state of these plutons. The plutonic rocks were long described as the western border zone of the Cretaceous Idaho batholith but limited pre-existing age data indicate more complicated origins. Because the affinity and age of the plutonic rocks cannot be reliably determined from field relations, TIMS U-Pb dating in conjunction with Sr, Nd, and Pb isotopic studies of selected plutons across the suture in western Idaho were undertaken. The data indicate three general groups of plutons including (1) those that intruded the island arc terranes during the Triassic and Jurassic, those that intruded near the western edge of oceanic rocks along the suture in the Early Cretaceous, and the plutons of the Idaho batholith that intruded Proterozoic North American rocks in the Late Cretaceous. Plutons that intruded Proterozoic North American rocks commonly include xenocrystic zircons and in several cases, ages could not be determined. The least radiogenic Sr and most radiogenic Nd are found among the Blue Mountains superterrane island arc samples. Suture-zone plutons have isotopic characteristics that span the range between Idaho batholith and island arc samples but mostly follow island arc signatures. Plutons of the Idaho batholith have the most radiogenic initial Pb and Sr ratios and the least radiogenic Nd of the samples analyzed.

A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

PubMed

Cassaignau, Anaïs M E; Launay, Hélène M M; Karyadi, Maria-Evangelia; Wang, Xiaolin; Waudby, Christopher A; Deckert, Annika; Robertson, Amy L; Christodoulou, John; Cabrita, Lisa D

2016-08-01

During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome.

An interactive code (NETPATH) for modeling NET geochemical reactions along a flow PATH, version 2.0

USGS Publications Warehouse

Plummer, Niel; Prestemon, Eric C.; Parkhurst, David L.

1994-01-01

NETPATH is an interactive Fortran 77 computer program used to interpret net geochemical mass-balance reactions between an initial and final water along a hydrologic flow path. Alternatively, NETPATH computes the mixing proportions of two to five initial waters and net geochemical reactions that can account for the observed composition of a final water. The program utilizes previously defined chemical and isotopic data for waters from a hydrochemical system. For a set of mineral and (or) gas phases hypothesized to be the reactive phases in the system, NETPATH calculates the mass transfers in every possible combination of the selected phases that accounts for the observed changes in the selected chemical and (or) isotopic compositions observed along the flow path. The calculations are of use in interpreting geochemical reactions, mixing proportions, evaporation and (or) dilution of waters, and mineral mass transfer in the chemical and isotopic evolution of natural and environmental waters. Rayleigh distillation calculations are applied to each mass-balance model that satisfies the constraints to predict carbon, sulfur, nitrogen, and strontium isotopic compositions at the end point, including radiocarbon dating. DB is an interactive Fortran 77 computer program used to enter analytical data into NETPATH, and calculate the distribution of species in aqueous solution. This report describes the types of problems that can be solved, the methods used to solve problems, and the features available in the program to facilitate these solutions. Examples are presented to demonstrate most of the applications and features of NETPATH. The codes DB and NETPATH can be executed in the UNIX or DOS1 environment. This report replaces U.S. Geological Survey Water-Resources Investigations Report 91-4078, by Plummer and others, which described the original release of NETPATH, version 1.0 (dated December, 1991), and documents revisions and enhancements that are included in version 2.0. 1 The use of trade, brand or product names in this report is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.

Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis.

PubMed

Giménez, Estela; Balmaña, Meritxell; Figueras, Joan; Fort, Esther; de Bolós, Carme; Sanz-Nebot, Victòria; Peracaula, Rosa; Rizzi, Andreas

2015-03-25

In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and μZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a candidate structure worth to be corroborated by an extended study including more clinical cases; especially those with chronic pancreatitis and initial stages of pancreatic cancer. Importantly, the results demonstrate that the presented methodology combining an enrichment of a target protein by IAC with isotope coded relative quantitation of N-glycans can be successfully used for targeted glycomics studies. The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers. Copyright © 2015 Elsevier B.V. All rights reserved.

Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly

PubMed Central

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-01-01

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code “NANO” and reversible exchange of uppercase letter “I” with lowercase “i”. The yields of the conjugations are high (> 90%) and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates. PMID:23373425

Europium-labeled epidermal growth factor and neurotensin: novel probes for receptor-binding studies.

PubMed

Mazor, Ohad; Hillairet de Boisferon, Marc; Lombet, Alain; Gruaz-Guyon, Anne; Gayer, Batya; Skrzydelsky, Delphine; Kohen, Fortune; Forgez, Patricia; Scherz, Avigdor; Rostene, William; Salomon, Yoram

2002-02-01

We investigated the possibility of labeling two biologically active peptides, epidermal growth factor (EGF) and neurotensin (NT), with europium (Eu)-diethylenetriaminepentaacetic acid. More specifically, we tested them as probes in studying receptor binding using time-resolved fluorescence of Eu3+. The relatively simple synthesis yields ligands with acceptable binding characteristics similar to isotopically labeled derivatives. The binding affinity (Kd) of labeled Eu-EGF to human A431 epidermal carcinoid cells was 3.6 +/- 1.2 nM, similar to the reported Kd values of EGF, whereas the Kd of Eu-NT to human HT29 colon cancer cells (7.4 +/- 0.5 nM) or to Chinese hamster ovary (CHO) cells transfected with the high-affinity NT receptor (CHO-NT1) were about 10-fold higher than the Kd values of NT. The bioactivity of the Eu-labeled EGF as determined by stimulation of cultured murine D1 hematopoietic cell proliferation was nearly the same as that obtained with native EGF. The maximal stimulation of Ca2+ influx with NT and Eu-NT in CHO-NT1 cells was similar, but the respective K0.5 values were 20 pM and 1 nM, corresponding to differences in the binding affinities previously described. The results of these studies indicate that Eu labeling of peptide hormones and growth factor molecules ranging from 10(3) to 10(5) Da can be conveniently accomplished. Importantly, the Eu-labeled products are stable for approximately 2 years and are completely safe for laboratory use compared to the biohazardous radioligands. Thus, Eu-labeled peptides present an attractive alternative for commonly used radiolabeled ligands in biological studies in general and in receptor assays in particular.

Helium isotope, C/3He, and Ba-Nb-Ti signatures in the northern Lau Basin: Distinguishing arc, back-arc, and hotspot affinities

NASA Astrophysics Data System (ADS)

Lupton, John; Rubin, Ken H.; Arculus, Richard; Lilley, Marvin; Butterfield, David; Resing, Joseph; Baker, Edward; Embley, Robert

2015-04-01

The northern Lau Basin hosts a complicated pattern of volcanism, including Tofua Arc volcanoes, several back-arc spreading centers, and individual "rear-arc" volcanoes not associated with these structures. Elevated 3He/4He ratios in lavas of the NW Lau Spreading Center suggest the influence of a mantle plume, possibly from Samoa. We show that lavas from mid-ocean ridges, volcanic arcs, and hotspots occupy distinct, nonoverlapping fields in a 3He/4He versus C/3He plot. Applied to the northern Lau Basin, this approach shows that most of Lau back-arc spreading systems have mid-ocean ridge 3He/4He-C/3He characteristics, except the NW Lau spreading center, which has 3He/4He-C/3He similar to "high 3He" hotspots such as Loihi, Kilauea, and Yellowstone, but with slightly lower C/3He. Niua seamount, on the northern extension of the Tofua Arc, falls squarely in the arc field. All the NE Lau rear-arc volcanoes, including the recently erupting West Mata, also have arc-like 3He/4He-C/3He characteristics. Ba-Nb-Ti contents of the lavas, which are more traditional trace element indicators of mantle source enrichment, depletion, and subduction input, likewise indicate arc and hot spot influences in the lavas of the northern Lau Basin, but in a more ambiguous fashion because of a complex prior history. This verifies that 3He/4He-C/3He systematics are useful for differentiating between mid-ocean ridge, arc, and hotspot affinities in submarine volcanic systems, that all three of these affinities are expressed in the northern Lau Basin, and provides additional support for the Samoan plume influence in the region.

Determination of the δ15N and δ13C of total nitrogen and carbon in solids; RSIL lab code 1832

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplan, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1832 is to determine the δ(15N/14N), abbreviated as δ15N, and the δ(13C/12C), abbreviated as δ13C, of total nitrogen and carbon in a solid sample. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total nitrogen and carbon in a solid sample into N2 and CO2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the relative difference in stable nitrogen isotope-amount ratio (15N/14N) of the product N2 gas and the relative difference in stable carbon isotope-amount ratio (13C/12C) of the product CO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in tin capsules and loaded into a Costech Zero Blank Autosampler on the EA. Under computer control, samples then are dropped into a heated reaction tube that contains an oxidant, where combustion takes place in a helium atmosphere containing an excess of oxygen gas. Combustion products are transported by a helium carrier through a reduction furnace to remove excess oxygen and to convert all nitrous oxides into N2 and through a drying tube to remove water. The gas-phase products, mainly CO2 and N2, are separated by a gas chromatograph. The gas is then introduced into the IRMS through a Finnigan MAT (now Thermo Scientific) ConFlo II interface. The Finnigan MAT ConFlo II interface is used for introducing not only sample into the IRMS but also N2 and CO2 reference gases and helium for sample dilution. The flash combustion is quantitative; no isotopic fractionation is involved. The IRMS is a Thermo Scientific Delta V CF-IRMS. It has a universal triple collector, two wide cups with a narrow cup in the middle; it is capable of measuring mass/charge (m/z) 28, 29, 30 or with a magnet current change 44, 45, 46, simultaneously. The ion beams from these m/z values are as follows: m/z 28 = N2 = 14N/14N; m/z 29 = N2 = 14N/15N primarily; m/z 30 = NO = 14N/16O primarily, which is a sign of contamination or incomplete reduction; m/z 44 = CO2 = 12C16O16O; m/z 45 = CO2 = 13C16O16O primarily; and m/z 46 = CO2 = 12C16O18O primarily.

Petrogenesis of the reversely-zoned Turtle pluton, southeastern California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, C.M.

1989-01-01

Few plutons with a reversed geometry of a felsic rim and mafic core have been described in the geologic literature. The Turtle pluton of S.E. California is an intrusion composed of a granitic rim and granodioritic core and common microgranitoid enclaves. Field observations, mineral textures and chemistries, major and trace element geochemistry, and isotopic variability support a petrogenetic model of in situ, concomitant, magma mixing and fractional crystallization of rhyolitic magma progressively mixed with an increasing volume of andesitic magma, all without chemical contribution from entrained basaltic enclaves. Hornblende geobarometry indicates the Turtle pluton crystallized at about 3.5 kb. Amore » crystallization sequence of biotite before hornblende (and lack of pyroxenes) suggests the initial granitic magma contained less than 4 wt% H{sub 2}O at temperatures less than 780C. U-Pb, Pb-Pb, Rb-Sr and oxygen isotope studies indicate the terrane intruded by the Turtle pluton is 1.8 Ga, that the Turtle pluton crystallized at 130 Ma, that the Target Granite and garnet aplites are about 100 Ma, and that these intrusions were derived from different sources. Models based on isotopic data suggest the rhyolitic end member magma of the Turtle pluton was derived from mafic igneous rocks, and was not derived from sampled Proterozoic country rocks. Similarity of common Sr and Pb isotopic ratios of these rocks to other Mesozoic intrusions in the Colorado River Region suggest the Turtle pluton and Target Granite have affinities like rocks to the east, including the Whipple Mountains and plutons of western Arizona. P-T-t history of the southern Turtle Mountains implies uplift well into the upper crust by Late Cretaceous time so that the heating and deformation events of the Late Cretaceous and Tertiary observed in flanking ranges did not affect the study area.« less

Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine

NASA Astrophysics Data System (ADS)

Sappati, Subrahmanyam; Hassanali, Ali; Gebauer, Ralph; Ghosh, Prasenjit

2016-11-01

Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak.

Benchmarking Heavy Ion Transport Codes FLUKA, HETC-HEDS MARS15, MCNPX, and PHITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronningen, Reginald Martin; Remec, Igor; Heilbronn, Lawrence H.

Powerful accelerators such as spallation neutron sources, muon-collider/neutrino facilities, and rare isotope beam facilities must be designed with the consideration that they handle the beam power reliably and safely, and they must be optimized to yield maximum performance relative to their design requirements. The simulation codes used for design purposes must produce reliable results. If not, component and facility designs can become costly, have limited lifetime and usefulness, and could even be unsafe. The objective of this proposal is to assess the performance of the currently available codes PHITS, FLUKA, MARS15, MCNPX, and HETC-HEDS that could be used for designmore » simulations involving heavy ion transport. We plan to access their performance by performing simulations and comparing results against experimental data of benchmark quality. Quantitative knowledge of the biases and the uncertainties of the simulations is essential as this potentially impacts the safe, reliable and cost effective design of any future radioactive ion beam facility. Further benchmarking of heavy-ion transport codes was one of the actions recommended in the Report of the 2003 RIA R&D Workshop".« less

Improvements of MCOR: A Monte Carlo depletion code system for fuel assembly reference calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tippayakul, C.; Ivanov, K.; Misu, S.

2006-07-01

This paper presents the improvements of MCOR, a Monte Carlo depletion code system for fuel assembly reference calculations. The improvements of MCOR were initiated by the cooperation between the Penn State Univ. and AREVA NP to enhance the original Penn State Univ. MCOR version in order to be used as a new Monte Carlo depletion analysis tool. Essentially, a new depletion module using KORIGEN is utilized to replace the existing ORIGEN-S depletion module in MCOR. Furthermore, the online burnup cross section generation by the Monte Carlo calculation is implemented in the improved version instead of using the burnup cross sectionmore » library pre-generated by a transport code. Other code features have also been added to make the new MCOR version easier to use. This paper, in addition, presents the result comparisons of the original and the improved MCOR versions against CASMO-4 and OCTOPUS. It was observed in the comparisons that there were quite significant improvements of the results in terms of k{sub inf}, fission rate distributions and isotopic contents. (authors)« less

Nuclear Resonance Fluorescence for Materials Assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quiter, Brian J.; Ludewigt, Bernhard; Mozin, Vladimir

This paper discusses the use of nuclear resonance fluorescence (NRF) techniques for the isotopic and quantitative assaying of radioactive material. Potential applications include age-dating of an unknown radioactive source, pre- and post-detonation nuclear forensics, and safeguards for nuclear fuel cycles Examples of age-dating a strong radioactive source and assaying a spent fuel pin are discussed. The modeling work has ben performed with the Monte Carlo radiation transport computer code MCNPX, and the capability to simulate NRF has bee added to the code. Discussed are the limitations in MCNPX?s photon transport physics for accurately describing photon scattering processes that are importantmore » contributions to the background and impact the applicability of the NRF assay technique.« less

Automated Installation Verification of COMSOL via LiveLink for MATLAB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crowell, Michael W

Verifying that a local software installation performs as the developer intends is a potentially time-consuming but necessary step for nuclear safety-related codes. Automating this process not only saves time, but can increase reliability and scope of verification compared to ‘hand’ comparisons. While COMSOL does not include automatic installation verification as many commercial codes do, it does provide tools such as LiveLink™ for MATLAB® and the COMSOL API for use with Java® through which the user can automate the process. Here we present a successful automated verification example of a local COMSOL 5.0 installation for nuclear safety-related calculations at the Oakmore » Ridge National Laboratory’s High Flux Isotope Reactor (HFIR).« less

Role of (n,2n) reactions in transmutation of long-lived fission products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Apse, V. A.; Kulikov, G. G., E-mail: ggkulikov@mephi.ru; Kulikov, E. G.

2016-12-15

The conditions under which (n,γ) and (n,2n) reactions can help or hinder each other in neutron transmutation of long-lived fission products (LLFPs) are considered. Isotopic and elemental transmutation for the main long-lived fission products, {sup 79}Se, {sup 93}Zr, {sup 99}Tc, {sup 107}Pd, {sup 126}Sn, {sup 129}I, and {sup 135}Cs, are considered. The effect of (n,2n) reactions on the equilibrium amount of nuclei of the transmuted isotope and the neutron consumption required for the isotope processing is estimated. The aim of the study is to estimate the influence of (n,2n) reactions on efficiency of neutron LLFP transmutation. The code TIME26 andmore » the libraries of evaluated nuclear data ABBN-93, JEF-PC, and JANIS system are applied. The following results are obtained: (1) The effect of (n,2n) reactions on the minimum number of neutrons required for transmutation and the equilibrium amount of LLFP nuclei is estimated. (2) It is demonstrated that, for three LLFP isotopes ({sup 126}Sn, {sup 129}I, and {sup 135}Cs), (n,γ) and (n,2n) reactions are partners facilitating neutron transmutation. The strongest effect of (n,2n) reaction is found for {sup 126}Sn transmutation (reduction of the neutron consumption by 49% and the equilibrium amount of nuclei by 19%).« less

The Clemson University, University Research Initiative Program in Discrete Mathematics and Computational Analysis

DTIC Science & Technology

1990-03-01

Assmus, E. F., and J. D. Key, "Affine and projective planes", to appear in Discrete Math (Special Coding Theory Issue). 5. Assumus, E. F. and J. D...S. Locke, ’The subchromatic number of a graph", Discrete Math . 74 (1989)33-49. 24. Hedetniemi, S. T., and T. V. Wimer, "K-terminal recursive families...34Designs and geometries with Cayley", submitted to Journal of Symbolic Computation. 34. Key, J. D., "Regular sets in geometries", Annals of Discrete Math . 37

Development of a patient-specific dosimetry estimation system in nuclear medicine examination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, H. H.; Dong, S. L.; Yang, H. J.

2011-07-01

The purpose of this study is to develop a patient-specific dosimetry estimation system in nuclear medicine examination using a SimSET-based Monte Carlo code. We added a dose deposition routine to store the deposited energy of the photons during their flights in SimSET and developed a user-friendly interface for reading PET and CT images. Dose calculated on ORNL phantom was used to validate the accuracy of this system. The S values for {sup 99m}Tc, {sup 18}F and {sup 131}I obtained by the system were compared to those from the MCNP4C code and OLINDA. The ratios of S values computed by thismore » system to those obtained with OLINDA for various organs were ranged from 0.93 to 1.18, which are comparable to that obtained from MCNP4C code (0.94 to 1.20). The average ratios of S value were 0.99{+-}0.04, 1.03{+-}0.05, and 1.00{+-}0.07 for isotopes {sup 131}I, {sup 18}F, and {sup 99m}Tc, respectively. The simulation time of SimSET was two times faster than MCNP4C's for various isotopes. A 3D dose calculation was also performed on a patient data set with PET/CT examination using this system. Results from the patient data showed that the estimated S values using this system differed slightly from those of OLINDA for ORNL phantom. In conclusion, this system can generate patient-specific dose distribution and display the isodose curves on top of the anatomic structure through a friendly graphic user interface. It may also provide a useful tool to establish an appropriate dose-reduction strategy to patients in nuclear medicine environments. (authors)« less

Pharmacoproteomics of a Metalloproteinase Hydroxamate Inhibitor in Breast Cancer Cells: Dynamics of Membrane Type 1 Matrix Metalloproteinase-Mediated Membrane Protein Shedding ▿ ‡

PubMed Central

Butler, Georgina S.; Dean, Richard A.; Tam, Eric M.; Overall, Christopher M.

2008-01-01

Broad-spectrum matrix metalloproteinase (MMP) inhibitors (MMPI) were unsuccessful in cancer clinical trials, partly due to side effects resulting from limited knowledge of the full repertoire of MMP substrates, termed the substrate degradome, and hence the in vivo functions of MMPs. To gain further insight into the degradome of MMP-14 (membrane type 1 MMP) an MMPI, prinomastat (drug code AG3340), was used to reduce proteolytic processing and ectodomain shedding in human MDA-MB-231 breast cancer cells transfected with MMP-14. We report a quantitative proteomic evaluation of the targets and effects of the inhibitor in this cell-based system. Proteins in cell-conditioned medium (the secretome) and membrane fractions with levels that were modulated by the MMPI were identified by isotope-coded affinity tag (ICAT) labeling and tandem mass spectrometry. Comparisons of the expression of MMP-14 with that of a vector control resulted in increased MMP-14/vector ICAT ratios for many proteins in conditioned medium, indicating MMP-14-mediated ectodomain shedding. Following MMPI treatment, the MMPI/vehicle ICAT ratio was reversed, suggesting that MMP-14-mediated shedding of these proteins was blocked by the inhibitor. The reduction in shedding or the release of substrates from pericellular sites in the presence of the MMPI was frequently accompanied by the accumulation of the protein in the plasma membrane, as indicated by high MMPI/vehicle ICAT ratios. Considered together, this is a strong predictor of biologically relevant substrates cleaved in the cellular context that led to the identification of many undescribed MMP-14 substrates, 20 of which we validated biochemically, including DJ-1, galectin-1, Hsp90α, pentraxin 3, progranulin, Cyr61, peptidyl-prolyl cis-trans isomerase A, and dickkopf-1. Other proteins with altered levels, such as Kunitz-type protease inhibitor 1 and beta-2-microglobulin, were not substrates in biochemical assays, suggesting an indirect affect of the MMPI, which might be important in drug development as biomarkers or, in preclinical phases, to predict systemic drug actions and adverse side effects. Hence, this approach describes the dynamic pattern of cell membrane ectodomain shedding and its perturbation upon metalloproteinase drug treatment. PMID:18505826

Competitive sorption of atenolol, trimetoprim, carbamazepine and sulfamethoxazole in three soil types

NASA Astrophysics Data System (ADS)

Kočárek, Martin; Kodešová, Radka; Klement, Aleš; Golovko, Oksana; Fér, Miroslav; Nikodem, Antonín; Vondráčková, Lenka; Jakšík, Ondřej; Grabic, Roman

2016-04-01

Transport of human and veterinary pharmaceuticals in soils and consequent ground-water contamination are influenced by many factors, including compound sorption on soil particles and dissipation. Batch sorption experiment for 9 soils (3 soil types with 3 (Greyic Phaeozem on loess), 4 (Haplic Luvisol on loess) and 2 (Haplic Cambisol on gneiss) horizons) and mixture of 4 pharmaceuticals (atenolol, trimetoprim, carbamazepine and sulfamethoxazole) was performed to study competitive sorption of compounds in each soil sample. Sorption affinities and dissipation half-lives of all compounds in topsoils were previously studied by Kodešová et al. (2015 and 2016). Ten grams of dry soil was placed directly into the plastic centrifuge tubes and 20 ml of solution of a known pharmaceutical concentration was added. The same concentrations (0.5, 1, 2.5, 5 and 10 mg/l) were used for all compounds. Three replicates of each concentration were applied for each soil. Tube was shaken for 24 h using the shaking apparatus at 20 C. After shaking, the analyzed soil suspension was centrifuged for 10 min at 6,000 rotations per minute. The actual initial and final equilibrium pharmaceutical concentrations were measured using two-dimensional liquid chromatography-tandem mass spectrometry LC/LC-MS/MS using isotope dilution and internal standard methods. The pharmaceutical concentration adsorbed on soil particles was calculated using the initial and final (i.e. after incubation) pharmaceutical concentrations. The Freundlich equations were used to fit data points of the measured adsorption isotherms. In the case of carbamazepine (neutral form) and sulfamethoxazole (partly negatively charged) sorption affinity of compounds decrease with soil depth. On the other hand in the case of atenolol and trimethoprim (both positively charged) compound sorption affinity was not depth dependent. Data obtained for top soils were compared with sorption affinities for single compounds published by (Kodešová et al., 2015). While sorption affinities of atenolol, trimethoprim and carbamazepine due to compound competition decrease, sorption affinity of sulfamethoxazole increased. Pearson product moment correlation coefficient and p-value were used to evaluate relationships between sorption coefficients and soil properties. Kodešová, R., Grabic, R., Kočárek, M., Klement, A., Golovko, O., Fér, M., Nikodem, A., Jakšík, O. (2015a): Pharmaceuticals' sorptions relative to properties of thirteen different soils. Science of the Total Environment, 511, 435-443. Kodešová, R., Kočárek, M., Klement, A., Golovko, O., Koba, O., Fér, M., Nikodem, A., Vondráčková, L., Jakšík, O., Grabic, R. (2016): An analysis of the dissipation of pharmaceuticals under thirteen different soil conditions. Science of the Total Environment, 544, 369-381.

Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe

PubMed Central

Yong, Hoi-Sen; Song, Sze-Looi; Lim, Phaik-Eem; Chan, Kok-Gan; Chow, Wan-Loo; Eamsobhana, Praphathip

2015-01-01

The whole mitochondrial genome of the pest fruit fly Bactrocera arecae was obtained from next-generation sequencing of genomic DNA. It had a total length of 15,900 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The control region (952 bp) was flanked by rrnS and trnI genes. The start codons included 6 ATG, 3 ATT and 1 each of ATA, ATC, GTG and TCG. Eight TAA, two TAG, one incomplete TA and two incomplete T stop codons were represented in the protein-coding genes. The cloverleaf structure for trnS1 lacked the D-loop, and that of trnN and trnF lacked the TΨC-loop. Molecular phylogeny based on 13 protein-coding genes was concordant with 37 mitochondrial genes, with B. arecae having closest genetic affinity to B. tryoni. The subgenus Bactrocera of Dacini tribe and the Dacinae subfamily (Dacini and Ceratitidini tribes) were monophyletic. The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general. PMID:26472633

Quartz crystal microbalance detection of DNA single-base mutation based on monobase-coded cadmium tellurium nanoprobe.

PubMed

Zhang, Yuqin; Lin, Fanbo; Zhang, Youyu; Li, Haitao; Zeng, Yue; Tang, Hao; Yao, Shouzhuo

2011-01-01

A new method for the detection of point mutation in DNA based on the monobase-coded cadmium tellurium nanoprobes and the quartz crystal microbalance (QCM) technique was reported. A point mutation (single-base, adenine, thymine, cytosine, and guanine, namely, A, T, C and G, mutation in DNA strand, respectively) DNA QCM sensor was fabricated by immobilizing single-base mutation DNA modified magnetic beads onto the electrode surface with an external magnetic field near the electrode. The DNA-modified magnetic beads were obtained from the biotin-avidin affinity reaction of biotinylated DNA and streptavidin-functionalized core/shell Fe(3)O(4)/Au magnetic nanoparticles, followed by a DNA hybridization reaction. Single-base coded CdTe nanoprobes (A-CdTe, T-CdTe, C-CdTe and G-CdTe, respectively) were used as the detection probes. The mutation site in DNA was distinguished by detecting the decreases of the resonance frequency of the piezoelectric quartz crystal when the coded nanoprobe was added to the test system. This proposed detection strategy for point mutation in DNA is proved to be sensitive, simple, repeatable and low-cost, consequently, it has a great potential for single nucleotide polymorphism (SNP) detection. 2011 © The Japan Society for Analytical Chemistry

Cultivation-Independent Detection of Autotrophic Hydrogen-Oxidizing Bacteria by DNA Stable-Isotope Probing ▿

PubMed Central

Pumphrey, Graham M.; Ranchou-Peyruse, Anthony; Spain, Jim C.

2011-01-01

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of 13CO2 was H2 dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from 13C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H2 concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation. PMID:21622787

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing.

PubMed

Pumphrey, Graham M; Ranchou-Peyruse, Anthony; Spain, Jim C

2011-07-01

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

The Khida terrane - Geology of Paleoproterozoic rocks in the Muhayil area, eastern Arabian Shield, Saudi Arabia

USGS Publications Warehouse

Stoeser, D.B.; Whitehouse, M.J.; Stacey, J.S.

2001-01-01

The bulk of the Arabian Shield of Saudi Arabia is underlain by Neoproterozoic terranes of oceanic affinity that were accreted during Pan-African time (about 680- 640Ma). Geologicalmappingandisotopicinvestigations during the 1980’s,however, provided the first evidence for Paleoproterozoic continental crust within the east- central part of the shield in Saudi Arabia. These studies delineated an older basement domain, herein referred to as the Khida terrane (Fig. l), which is defined as that part of the southern Afif composite terrane underlain by Paleoproterozoicto Archean continental crust (Stoeser and Stacey, 1988). The isotopic and geochronologic work to support our current studies within the Khida terrane are discussed in a companion abstract (Whitehouse et al., this volume). The regional geology and geochronology of the region has been summarized in detail by Johnson (1996). The current study is based on the continued use of samples previously collected in the Khida area by the authors and others as well as new field work conducted by us in 1999. This work further defines the occurrence of late Paleoproterozoic rocks at Jabal Muhayil, which is located at the eastern margin of the exposed terrane (Fig. 1). Our isotopic work is at an early stage and this abstract partly relates geologic problems that remain to be resolved. 

Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy

PubMed Central

Hagen, Sven; Baumann, Tobias; Wagner, Hanna J.; Morath, Volker; Kaufmann, Beate; Fischer, Adrian; Bergmann, Stefan; Schindler, Patrick; Arndt, Katja M.; Müller, Kristian M.

2014-01-01

The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT). PMID:24457557

emcee: The MCMC Hammer

NASA Astrophysics Data System (ADS)

Foreman-Mackey, Daniel; Hogg, David W.; Lang, Dustin; Goodman, Jonathan

2013-03-01

We introduce a stable, well tested Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) proposed by Goodman & Weare (2010). The code is open source and has already been used in several published projects in the astrophysics literature. The algorithm behind emcee has several advantages over traditional MCMC sampling methods and it has excellent performance as measured by the autocorrelation time (or function calls per independent sample). One major advantage of the algorithm is that it requires hand-tuning of only 1 or 2 parameters compared to ˜N2 for a traditional algorithm in an N-dimensional parameter space. In this document, we describe the algorithm and the details of our implementation. Exploiting the parallelism of the ensemble method, emcee permits any user to take advantage of multiple CPU cores without extra effort. The code is available online at http://dan.iel.fm/emcee under the GNU General Public License v2.

Selection of the simplest RNA that binds isoleucine

PubMed Central

LOZUPONE, CATHERINE; CHANGAYIL, SHANKAR; MAJERFELD, IRENE; YARUS, MICHAEL

2003-01-01

We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA–amino acid binding structures. PMID:14561881

Identification of NH4+-regulated genes of Herbaspirillum seropedicae by random insertional mutagenesis.

PubMed

Schwab, Stefan; Ramos, Humberto J; Souza, Emanuel M; Pedrosa, Fábio O; Yates, Marshall G; Chubatsu, Leda S; Rigo, Liu U

2007-05-01

Random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. Using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. These include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter AmtB, and uptake systems for alternative nitrogen sources; nine genes coding for proteins responsible for restoring intracellular ammonium levels through enzymatic reactions, such as nitrogenase, amidase, and arginase; and a third group includes metabolic switch genes, coding for sensor kinases or transcription regulation factors, whose role in metabolism was previously unknown. Also, four genes identified were of unknown function. This paper describes their involvement in response to ammonium limitation. The results provide a preliminary profile of the metabolic response of Herbaspirillum seropedicae to ammonium stress.

Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells.

PubMed

Autour, Alexis; C Y Jeng, Sunny; D Cawte, Adam; Abdolahzadeh, Amir; Galli, Angela; Panchapakesan, Shanker S S; Rueda, David; Ryckelynck, Michael; Unrau, Peter J

2018-02-13

Despite having many key roles in cellular biology, directly imaging biologically important RNAs has been hindered by a lack of fluorescent tools equivalent to the fluorescent proteins available to study cellular proteins. Ideal RNA labelling systems must preserve biological function, have photophysical properties similar to existing fluorescent proteins, and be compatible with established live and fixed cell protein labelling strategies. Here, we report a microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers. Two of these are as bright or brighter than enhanced GFP when bound to TO1-Biotin. Furthermore, we show that the new Mangos can accurately image the subcellular localization of three small non-coding RNAs (5S, U6, and a box C/D scaRNA) in fixed and live mammalian cells. These new aptamers have many potential applications to study RNA function and dynamics both in vitro and in mammalian cells.

Generation of syntectonic calc-alkaline, magnesian granites through remelting of pre-tectonic igneous sources - U-Pb zircon ages and Sr, Nd and Pb isotope data from the Donkerhoek granite (southern Damara orogen, Namibia)

NASA Astrophysics Data System (ADS)

Schwark, L.; Jung, S.; Hauff, F.; Garbe-Schönberg, D.; Berndt, J.

2018-06-01

The 541 ± 4 Ma-old magnesian, weakly peraluminous, calc-alkalic Donkerhoek Onanis granite is part of the ca. 6000 km2 large Donkerhoek batholith in the Southern Zone of the Damara orogen of Namibia. Linear major and trace element variations and decreasing MgO, FeO, Al2O3, CaO, K2O, Na2O, Ba and Sr concentrations with increasing SiO2 indicate that this part of the batholith represent a coherent mass and underwent fractional crystallization processes. The Donkerhoek Onanis granites are isotopically evolved (initial εNd: -4.7 to -12.3, initial 87Sr/86Sr: 0.7099-0.7157) with moderately radiogenic Pb isotope ratios (206Pb/204Pb: 17.26-18.22; 207Pb/204Pb: 15.59-15.67; 208Pb/204Pb: 37.60-38.06). Beside heterogeneities imparted by the sources, an evaluation of LREE fractionation and Nd isotope data suggests that AFC processes also modified some samples. Based on the chemical and isotope data, the Donkerhoek Onanis granites cannot be derived by partial melting of Al- and Fe-rich metasedimentary rocks of the Kuiseb formation in which they intruded. Instead, melting of meta-igneous crustal sources with Proterozoic crustal residence ages is more likely. Three igneous to meta-igneous rock suites from the area (Matchless amphibolites, Proterozoic mafic to felsic gneisses from the southern Kalahari craton basement, syn-tectonic Salem granodiorites to granites) are potential sources. An evaluation of chemical and isotope data suggests that remelting of early syn-orogenic Salem-type granites is the most likely process which would also explain the existence of ca. 563 ± 4 Ma-old zircon in the Donkerhoek Onanis granites. Comparison of the Donkerhoek Onanis granites with experimentally derived melt compositions from an intermediate igneous parent indicates temperatures between 800 and 850 °C. It is suggested that the Pan-African igneous activity in this part of the Damara Belt was a moderate-temperature intra-crustal event. Although there are some compositional similarities with juvenile granites generated in subduction zones, unradiogenic Pb isotope ratios and moderately radiogenic Sr and unradiogenic Nd isotopes suggest that reprocessed crustal rocks are more likely sources. Previously obtained high δ18O values of the Donkerhoek Onanis granites ranging from 11.8 to 13.6‰, covering the range of δ18O values obtained on Salem-type granites from the area (12.5-13.3‰) confirm this view. In contrast to igneous processes along active continental margins that produce juvenile batholiths with calc-alkaline affinities, this igneous event was not a major crust-forming episode and the Donkerhoek Onanis granites represent reprocessed crustal material.

Kinetics of Fe Release from Organic Ligand Complexes: Implications for Fe Isotopes?

NASA Astrophysics Data System (ADS)

Nuester, J.; Liermann, L. J.; Brantley, S. L.

2006-12-01

Although iron is the fourth most abundant element in the earth's surface, its bioavailability is limited by its natural tendency to form insoluble iron (oxyhydr)oxides in terrestrial and marine environments. Paradoxically, iron is an essential nutrient for virtually all living cells, so in order to survive, organisms must develop mechanisms to solubilize iron. To acquire iron, organisms synthesize and release iron-specific chelators called siderophores. These siderophores facilitate the transformation of insoluble crystal-bound iron to organically ligand-bound dissolved iron. The reverse process whereby ferric iron is released from siderophores resulting in the precipitation of iron (oxyhydr)oxides or complexation by other iron chelators is an important but not well studied process in the B-horizon of soils. Fe mobility is documented in soils where Fe is often extracted at the top and precipitated at depth. Both the concentration and isotopic signature of Fe varies with depth due to dissolution, precipitation, sorption, and biological processes. Our study is focused on measurement of isotopic fractionation during this reverse process. In a first approach to understand iron liberation form organic ligands, we mimic this process using a reductive mechanism. We use acetohydroxamic acid (aha), EDTA and desferrioxamine B (DFMB) as test ligands to investigate iron release by sodium ascorbate at varying pH. Our first kinetic measurements showed significant differences in iron release depending on pH and stability of the iron complex. Within one hour all iron is released from aha with a small pH effect in the pH range between 4 and 6. In contrast, the pH has a major influence on the iron release from EDTA and DFMB. Depending on pH, total iron is released from EDTA within 24 hours, while only an incomplete iron release from DFMB could be observed within two weeks. These strong kinetic differences in iron release as a consequence of iron reduction are expected to result in significant iron isotope effects, and we are testing for these effects. For example, we expect to see enrichment of light isotopes in the early released fractions as iron is reduced (like effects observed by Wiederhold et al. (2006) for ligand-controlled and reductive dissolution of goethite). Such kinetic isotope effects should be particularly strong for iron release from siderophores with high Fe affinities like DFMB (log ß_(Fe(III)) = 30.60). We are also investigating other mechanisms to liberate iron from organic ligands including a pathway with extracellular iron reductases.

The enigmatic ichnofossil Tisoa siphonalis and widespread authigenic seep carbonate formation during the Late Pliensbachian in southern France

NASA Astrophysics Data System (ADS)

van de Schootbrugge, B.; Harazim, D.; Sorichter, K.; Oschmann, W.; Fiebig, J.; Püttmann, W.; Peinl, M.; Zanella, F.; Teichert, B. M. A.; Hoffmann, J.; Stadnitskaia, A.; Rosenthal, Y.

2010-10-01

Tubular carbonate concretions of up to 1 m in length and perpendicular to bedding, occur abundantly in the Upper Pliensbachian (upper Amaltheus margaritatus Zone, Gibbosus Subzone) in outcrops (Fontaneilles section) in the vicinity of Rivière-sûr-Tarn, southern France. Stable isotope analyses of these concretions show negative δ13C values that decrease from the rim to the center from -18.8‰ to -25.7‰ (V-PDB), but normal marine δ18O values (-1.8‰). Carbon isotope analyses of Late Pliensbachian bulk carbonate (matrix) samples from the Fontaneilles section show clearly decreasing C-isotope values across the A. margaritatus Zone, from +1‰ to -3‰ (V-PDB). Isotope analyses of coeval belemnite rostra do not document such a negative C-isotope trend with values remaining stable around +2‰ (V-PDB). Computer tomographic (CT) scanning of the tubular concretions show multiple canals that are lined or filled entirely with pyrite. Previously, the formation of these concretions with one, two, or more central tubes, has been ascribed to the activity of an enigmatic organism, possibly with annelid or arthropod affinities, known asTisoa siphonalis. Our results suggest tisoan structures are abiogenic. Based on our geochemical analyses and sedimentological observations we suggest that these concretions formed as a combination of the anaerobic oxidation of methane (AOM) and sulfate reduction within the sediment. Fluids rich in methane and/or hydrocarbons likely altered local bulk rock carbon isotope records, but did not affect the global carbon cycle. Interestingly, Tisoa siphonalis has been described from many locations in the Grands Causses Basin in southern France, and from northern France and Luxemburg, always occurring at the same stratigraphic level. Upper Pliensbachian authigenic carbonates thus possibly cover an area of many thousand square kilometers. Greatly reduced sedimentation rates are needed to explain the stabilization of the sulfate-methane transition zone in the sedimentary column in order for the tubular concretions to form. Late Pliensbachian cooling, reducing run-off, and/or the influx of colder water and more vigorous circulation could be responsible for a halt in sedimentation. At the same time (thermogenic) methane may have destabilized during a major phase of Late Pliensbachian sea level fall. As such Tisoa siphonalis is more than a geological curiosity, and its further study could prove pivotal in understanding Early Jurassic paleoenvironmental change.

The enigmatic ichnofossil Tisoa siphonalis and widespread authigenic seep carbonate formation during the Late Pliensbachian in southern France

NASA Astrophysics Data System (ADS)

van de Schootbrugge, B.; Harazim, D.; Sorichter, K.; Oschmann, W.; Fiebig, J.; Püttmann, W.; Peinl, M.; Zanella, F.; Teichert, B.; Hoffmann, J.; Stadnitskaia, A.; Rosenthal, Y.

2010-06-01

Tubular carbonate concretions of up to 1 m in length and perpendicular to bedding, occur abundantly in the Upper Pliensbachian (upper Amaltheus margaritatus Zone, Gibbosus Subzone) in outcrops (Fontaneilles section) in the vicinity of Rivière-sûr-Tarn, southern France. Stable isotope analyses of these concretions show negative &delta13C values that decrease from the rim to the center from -18.8‰ to -25.7‰ (V-PDB), but normal marine δ18O values (-1.8‰). Carbon isotope analyses of Late Pliensbachian bulk carbonate (matrix) samples from the Fontaneilles section show clearly decreasing C-isotope values across the A. margaritatus Zone, from +1‰ to -3‰ (V-PDB). Isotope analyses of coeval belemnite rostra do not document such a negative C-isotope trend with values remaining stable around +2‰ (V-PDB). Computer tomographic (CT) scanning of the tubular concretions show multiple canals that are lined or filled entirely with pyrite. Previously, the formation of these concretions with one, two, or more central tubes, has been ascribed to the activity of an enigmatic organism, possibly with annelid or arthropod affinities, known as Tisoa siphonalis. Our results suggest tisoan structures are abiogenic. Based on our geochemical analyses and sedimentological observations we suggest that these concretions formed as a combination of the anaerobic oxidation of methane (AOM) and sulfate reduction within the sediment. Fluids rich in methane and/or hydrocarbons likely altered local bulk rock carbon isotope records, but did not affect the global carbon cycle. Interestingly, Tisoa siphonalis has been described from many locations in the Grands Causses Basin in southern France, and from northern France and Luxemburg, always occurring at the same stratigraphic level. Upper Pliensbachian authigenic carbonates thus possibly cover an area of many thousand square kilometers. Greatly reduced sedimentation rates are needed to explain the stabilization of the sulfate-methane transition zone in the sedimentary column in order for the tubular concretions to form. Late Pliensbachian cooling, reducing run-off, and/or the influx of colder water and more vigorous circulation could be responsible for a halt in sedimentation. At the same time (thermogenic) methane may have destabilized during a major phase of Late Pliensbachian sea level fall. As such Tisoa siphonalis is more than a geological curiosity, and its further study could prove pivotal in understanding Early Jurassic paleoenvironmental change.

The organic inventory of primitive meteorites

NASA Astrophysics Data System (ADS)

Martins, Zita

Carbonaceous meteorites are primitive samples that provide crucial information about the solar system genesis and evolution. This class of meteorites has also a rich organic inventory, which may have contributed the first prebiotic building blocks of life to the early Earth. We have studied the soluble organic inventory of several CR and CM meteorites, using high performance liquid chromatography with UV fluorescence detection (HPLC-FD), gas chromatography-mass spectrometry (GC-MS) and gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Our target organic molecules include amino acids, nucleobases and polycyclic aromatic hydrocarbons (PAHs), among others. CR chondrites contain the highest amino acids concentration ever detected in a meteorite. The degree of aqueous alteration amongst this class of meteorites seems to be responsible for the amino acid distribution. Pioneering compound-specific carbon isotope measurements of nucleobases present in carbonaceous chondrites show that these compounds have a non-terrestrial origin. This suggests that components of the ge-netic code may have had a crucial role in life's origin. Investigating the abundances, distribution and isotopic composition of organic molecules in primitive meteorites significantly improves our knowledge of the chemistry of the early solar system, and the resources available for the first living organisms on Earth.

SRNL Development of Recovery Processes for Mark-18A Heavy Actinide Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allender, Jeffrey S.; Bridges, Nicholas J.; Loftin, Bradley M.

2015-07-14

Savannah River National Laboratory (SRNL) and Oak Ridge National Laboratory (ORNL) are developing plans for the recovery of rare and unique isotopes contained within heavy-actinide target assemblies, specifically the Mark-18A. Mark-18A assemblies were irradiated in Savannah River Site (SRS) reactors in the 1970s under extremely high neutron-flux conditions and produced, virtually, the world's supply of plutonium-244, an isotope of key importance to high-precision actinide measurement and other scientific and nonproliferation uses; and curium highly enriched in heavy isotopes (e.g., curium-246 and curium-248). In 2015 and 2016, SRNL is pursuing tasks that would reduce program risk and budget requirements, including furthermore » characterization of unprocessed targets; engineering studies for the use of the SRNL Shielded Cells Facility (SCF) for recovery; and development of onsite and offsite shipping methods including a replacement for the heavy (70 ton) cask previously used for onsite transfer of irradiated items at SRS. A status update is provided for the characterization, including modeling using the Monte Carlo N-Particle Transport Code (MCNP); direct non-destructive assay measurements; and cask design.« less

Isotopic Ratios of Carbon and Oxygen in Titan’s CO using ALMA

NASA Astrophysics Data System (ADS)

Serigano, Joseph; Nixon, C. A.; Cordiner, M. A.; Irwin, P. G. J.; Teanby, N. A.; Charnley, S. B.; Lindberg, J. E.

2016-04-01

We report interferometric observations of carbon monoxide (CO) and its isotopologues in Titan’s atmosphere using the Atacama Large Millimeter/submillimeter Array (ALMA). The following transitions were detected: CO (J = 1-0, 2-1, 3-2, 6-5), 13CO (J = 2-1, 3-2, 6-5), C18O (J = 2-1, 3-2), and C17O (J = 3-2). Molecular abundances and the vertical atmospheric temperature profile were derived by modeling the observed emission line profiles using NEMESIS, a line-by-line radiative transfer code. We present the first spectroscopic detection of 17O in the outer solar system with C17O detected at >8σ confidence. The abundance of CO was determined to be 49.6 +/- 1.8 ppm, assumed to be constant with altitude, with isotopic ratios 12C/13C = 89.9 +/- 3.4, 16O/18O = 486 +/- 22, and 16O/17O = 2917 +/- 359. The measurements of 12C/13C and 16O/18O ratios are the most precise values obtained in Titan’s atmospheric CO to date. Our results are in good agreement with previous studies and suggest no significant deviations from standard terrestrial isotopic ratios.

Isotopic Ratios of Carbon and Oxygen in Titan's CO Using Alma

NASA Technical Reports Server (NTRS)

Serigano, Joseph; Nixon, C. A.; Cordiner, M. A.; Irwin, P. G. J.; Teanby, N. A.; Charnley, S. B.; Lindberg, J. E.

2016-01-01

We report interferometric observations of carbon monoxide (CO) and its isotopologues in Titan's atmosphere using the Atacama Large Millimeter/submillimeter Array (ALMA). The following transitions were detected: CO (J = 1-0, 2-1, 3-2, 6-5), C-13 O (J = 2-1, 3-2, 6-5), C-18 O (J = 2-1, 3-2), and C-17 O (J = 3-2). Molecular abundances and the vertical atmospheric temperature profile were derived by modeling the observed emission line profiles using NEMESIS, a line-by-line radiative transfer code. We present the first spectroscopic detection of O-17 in the outer solar system with C-17 O detected at greater than 8 sigma confidence. The abundance of CO was determined to be 49.6 +/- 1.8 ppm, assumed to be constant with altitude, with isotopic ratios C-12/C-13 = 89.9 +/- 3.4, O-16/O-18 = 486 +/- 22, and O-16/O-17 = 2917 +/- 359. The measurements of C-12/C-13 and O-16/O-18 ratios are the most precise values obtained in Titan's atmospheric CO to date. Our results are in good agreement with previous studies and suggest no significant deviations from standard terrestrial isotopic ratios.

The RIB production target for the SPES project

NASA Astrophysics Data System (ADS)

Monetti, Alberto; Andrighetto, Alberto; Petrovich, Carlo; Manzolaro, Mattia; Corradetti, Stefano; Scarpa, Daniele; Rossetto, Francesco; Martinez Dominguez, Fernando; Vasquez, Jesus; Rossignoli, Massimo; Calderolla, Michele; Silingardi, Roberto; Mozzi, Aldo; Borgna, Francesca; Vivian, Gianluca; Boratto, Enrico; Ballan, Michele; Prete, Gianfranco; Meneghetti, Giovanni

2015-10-01

Facilities making use of the Isotope Separator On-Line (ISOL) method for the production of Radioactive Ion Beams (RIB) attract interest because they can be used for nuclear structure and reaction studies, astrophysics research and interdisciplinary applications. The ISOL technique is based on the fast release of the nuclear reaction products from the chosen target material together with their ionization into short-lived nuclei beams. Within this context, the SPES (Selective Production of Exotic Species) facility is now under construction in Italy at INFN-LNL (Istituto Nazionale di Fisica Nucleare — Laboratori Nazionali di Legnaro). The SPES facility will produce RIBs mainly from n-rich isotopes obtained by a 40 MeV cyclotron proton beam (200 μA) directly impinging on a uranium carbide multi-foil fission target. The aim of this work is to describe and update, from a comprehensive point of view, the most important results obtained by the analysis of the on-line behavior of the SPES production target assembly. In particular an improved target configuration has been studied by comparing different codes and physics models: the thermal analyses and the isotope production are re-evaluated. Then some consequent radioprotection aspects, which are essential for the installation and operation of the facility, are presented.

KAOS/LIB-V: A library of nuclear response functions generated by KAOS-V code from ENDF/B-V and other data files

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farawila, Y.; Gohar, Y.; Maynard, C.

1989-04-01

KAOS/LIB-V: A library of processed nuclear responses for neutronics analyses of nuclear systems has been generated. The library was prepared using the KAOS-V code and nuclear data from ENDF/B-V. The library includes kerma (kinetic energy released in materials) factors and other nuclear response functions for all materials presently of interest in fusion and fission applications for 43 nonfissionable and 15 fissionable isotopes and elements. The nuclear response functions include gas production and tritium-breeding functions, and all important reaction cross sections. KAOS/LIB-V employs the VITAMIN-E weighting function and energy group structure of 174 neutron groups. Auxiliary nuclear data bases, e.g., themore » Japanese evaluated nuclear data library JENDL-2 were used as a source of isotopic cross sections when these data are not provided in ENDF/B-V files for a natural element. These are needed mainly to estimate average quantities such as effective Q-values for the natural element. This analysis of local energy deposition was instrumental in detecting and understanding energy balance deficiencies and other problems in the ENDF/B-V data. Pertinent information about the library and a graphical display of the main nuclear response functions for all materials in the library are given. 35 refs.« less

Chondritic Earth: comparisons, guidelines and status

NASA Astrophysics Data System (ADS)

McDonough, W. F.

2014-12-01

The chemical and isotopic composition of the Earth is rationally understood within the context of the chondritic reference frame, without recourse to hidden reservoirs, collision erosion, or strict interpretation of an enstatite chondrite model. Challenges to interpreting the array of recent and disparate chemical and isotopic observations from meteorites need to be understood as rich data harvests that inform us of the compositional heterogeneity in the early solar system. Our ability to resolve small, significant compositional differences between chondrite families provide critical insights into integrated compositional signatures at differing annuli distances from the Sun (i.e., 1-6 AU). Rigorous evaluation of chondritic models for planets requires treatment of both statistical and systematic uncertainties - to date these efforts are uncommonly practiced. Planetary olivine to pyroxene ratio reflects fO2 and temperature potentials in the nebular, given possible ISM compositional conditions; thus this ratio is a non-unique parameter of terrestrial bodies. Consequently the Mg/Si value of a planet (ie., olivine to pyroxene ratio) is a free variable; there is no singular chondritic Mg/Si value. For the Earth, there is an absence of physical and chemical evidence requiring a major element, chemical distinction between the upper and lower mantle, within uncertainties. Early Earth differentiation likely occurred, but there is an absence of chemical and isotopic evidence of its imprint. Chondrites, peridotites, komatiites, and basalts (ancient and modern) reveal a coherent picture of a chondritic compositional Earth, with compositionally affinities to enstatite chondrites. At present results from geoneutrino studies non-uniquely support these conclusions. Future experiments can provide true transformative insights into the Earth's thermal budget, define compositional BSE models, and will restrict discussions on Earth dynamics and its thermal evolution.

Noble gas isotopes and halogens in volatile-rich inclusions in diamonds

NASA Technical Reports Server (NTRS)

Burgess, Raymond; Turner, Grenville

1994-01-01

Application of the (40)Ar-(39)Ar method and noble gas studies to diamonds has increased our understanding of their age relationships to the host kimberlite or lamproite, and of the source and composition of volatile-rich fluids in the upper mantle. The properties of diamond (inert, high mechanical strength and low gas diffusivities) means they are especially useful samples for studying gases trapped deep within the earth (less than 150 km) as they are unlikely to have undergone loss or exchange of entrapped material since formation. Volatile-rich fluids (H2O-CO2) are important agents for metasomatic processes in the upper mantle, and the noble gases and halogens preferentially partition into this phase leading to a strong geochemical coherence between these groups of elements. The abundances of the halogens in the major reservoirs of the Earth shows a marked progression from chlorine, concentrated in the oceans, through to iodine which, through its affinity to organic material, is concentrated mainly in sediments. Abundances in the upper mantle are low. This is particularly true for iodine which is of special interest in view of its potential significance as an indicator of sediment recycling and by way of its link to (129)Xe amomalies in the mantle through the low extinct isotope (129)I. Extensions of the (40)Ar-(39)Ar technique enable measurements of halogens and other elements (K, Ca, Ba, U) by production of noble gas isotopes from these species during neutron irradiation. Samples analyzed in this way include 15 coated stones from an unknown source in Zaire, 3 boarts from the Jwaneng and 1 boart from the Orapa kimberlites, both in Botswana.

Disturbances in the Isotopic Record of Asuka 881394

NASA Technical Reports Server (NTRS)

Nyquist, L. E.; Bogard, D. D.

2011-01-01

Asuka 881394 is a unique achondrite with a granulitic texture, very calcic approximately An(sub 98) plagioclase, and pigeonite that has not inverted to orthopyroxene. First thought to be a eucrite, recent Oisotopic studies show it has a closer affinity to angrites . Initial isotopic studies provided evidence for now extinct A-26, Mn-53, and Sm-146. A recent study confirmed an early chronology with an absolute Pb-207 - Pb-206 age of 4566.5 +/- 0.2 Ma, a new measurement of the Al-Mg formation interval as 3.7 +/- 0.1 Ma since Al-26/Al-27 = approximately 4.63 x 10(exp -5) for the E60 CAI, and a Mn-Cr formation interval of -6.0 +/- 0.2 Ma relative to LEW86010 ("LEW"). Absolute ages relative to age anchors presented by were 4563.4 +/- 0.2 Ma by Al- Mg and 4564.6 +/- 0.5 Ma by Mn-Cr. These ages are in good, but not perfect, agreement with the Pb-207 - Pb-206 age. Perhaps the most direct comparison of the early chronology of A881394 as determined by various workers is provided by reported Al-26/Al-27 values of 1.18 +/- 0.14, 1.28 +/- 0.07, and 2.1 +/- 0.4 x 10(exp -6). Analyses of mineral separates by TIMS and MC-ICPMS6] agree well, but the higher value obtained by in situ SIMS analysis is significant in light of the slight inconsistency between absolute ages inferred from the short-lived chronometers and the Pb-207 - Pb-206 age. We examine the possibility that inconsistencies in the earliest fine-scale chronology of Asuka 881394 may be related to isotopic "disturbances" observed in Ar-39 - Ar-40, Rb-97 - Sr-87, and Sm-147 - Nd-143 chronometers.

Early Cretaceous gabbroic complex from Yinan, Shandong Province: petrogenesis and mantle domains beneath the North China Craton

NASA Astrophysics Data System (ADS)

Xu, Yi-Gang; Ma, Jin-Long; Huang, Xiao-Long; Iizuka, Yoshiyuki; Chung, Sun-Lin; Wang, Yan-Bin; Wu, Xiang-Yang

2004-12-01

Sensitive high resolution ion microprobe (SHRIMP) zircon U Pb ages, geochemical and Sr-Nd-Pb isotopic data are reported for the gabbroic complex from Yinan (Shandong Province) with the aims of characterizing the nature of the Mesozoic mantle beneath the North China Craton. The Yinan gabbros contain alkali feldspar and biotite, and are characterized by moderate Mg#, high SiO2, low FeO and TiO2 contents and a strong enrichment of light rare earth elements [(La/Yb)n=11 50], but no Eu anomaly. They have low Nb/La (0.07 0.29), radiogenic 87Sr/86Sr (0.710) and unradiogenic ɛNd(t) (-15 to -13). These “crustal fingerprints” cannot be attributed to crustal contamination, given the lack of correlation between isotopic ratios and differentiation indices and the unreasonably high proportion of crustal contaminant (>20%) required in modeling. Instead, compositional similarities to contemporaneous basalts from nearby regions imply that the Yinan gabbros were not significantly affected by crystal cumulation. Isotopic data available for the Mesozoic mafic magmas reveal two distinct mantle domains beneath Shandong. While the EM1-like domain (with low 87Sr/86Sr) is confined to western Shandong, the mantle beneath eastern Shandong is dominated by EM2-type (with high 87Sr/86Sr) affinities. This aerial distinction suggests that the EM2-like signature of the Yinan gabbros may have been inherited from westerly-subducted Yangtze crust during the Triassic North China-South China collision. Emplacement of the Yinan gabbros (127 Ma) is likely affiliated with the widespread and protracted extension during the late Mesozoic in this region.

DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics.

PubMed

Naylor, Bradley C; Porter, Michael T; Wilson, Elise; Herring, Adam; Lofthouse, Spencer; Hannemann, Austin; Piccolo, Stephen R; Rockwood, Alan L; Price, John C

2017-05-15

Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don't access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement. This method utilizes both isotope distribution and changes in neutromer spacing, which benefits the analysis of both concentration and turnover. We have developed a data analysis tool, DeuteRater, to measure protein turnover from metabolic D 2 O labeling. DeuteRater uses theoretical predictions for label-dependent change in isotope abundance and inter-peak (neutromer) spacing within the isotope envelope to calculate protein turnover rate. We have also used these metrics to evaluate the accuracy and precision of peptide measurements and thereby determined the optimal data acquisition parameters of different instruments, as well as the effect of data processing steps. We show that these combined measurements can be used to remove noise and increase confidence in the protein turnover measurement for each protein. Source code and ReadMe for Python 2 and 3 versions of DeuteRater are available at https://github.com/JC-Price/DeuteRater . Data is at https://chorusproject.org/pages/index.html project number 1147. Critical Intermediate calculation files provided as Tables S3 and S4. Software has only been tested on Windows machines. jcprice@chem.byu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Caractérisation pétrologique et géochimique du magmatisme ubendien du secteur de Pepa-Lubumba, sur le plateau des Marungu (Nord-Est du Shaba, Zaire). Signification géodynamique dans l'évolution de la chaîne ubendienne

NASA Astrophysics Data System (ADS)

Kabengele, M.; Lubala, R. T.; Cabanis, B.

Volcanic and plutonic rocks of Pepa-Lubumba area in the Marungu plateau (Zaire) are mainly represented by intermediate and acid members which contain low abundances in TiO 2 (0.3 - 1.3 wt%). All these rocks exhibit a high-K calc-alkaline affinity and belong to a calc-alkaline continental-margin series. The large proportion of frequently zoned (normal and reverse zoning) plagioclase, the presence of hydrous phases (tschermakitic and Mg-hornblende, Mg-biotite), the early crystallization of FeTi oxides indicate crystallization under high water pressure conditions, consistent with a calc-alkaline affinity. High abundances in K, Rb, Sr and Ba; lack of correlation between Rb and Ba, low values of Rb/Zr (0.5 - 0.9) in granitoids, high contents of LREE and HFSE (Th/Ta : 6 - 14), are characteristic of "Andinotype" magmas. A whole rock RbSr isochron gives an emplacement age for granitoids of 1861 ± 28 Ma (MSWD : 0.82), Sr initial ratio of 0.7026 and epsilon Sr i of + 4.7. PbPb isotopes systematics for the same rocks give the following ratio ranges : 206Pb/ 204Pb : 17.26 - 20.10; 207Pb/ 204Pb 15.52 - 15.85, 208Pb/ 204Pb : 37.2 - 41.80. The low Sr initial ratio indicates an upper mantle source; while the PBPb isotope ratios suggest that the mantellic liquids have been contaminated by crustal material en route to the upper levels. In the regional geologic context, this magmatism forms a part of an important plutovolcanic Ubendian (Early Proterozoic) complex which crops out in Western Tanzania, North-Eastern Zambia and Marungu plateau (Zaire) and contains two magmatic cycles which define a spatial and temporal zonation suggesting a geodynamic evolution model for the Ubendian belt comprising subduction-obduction-collision processes. This latter episode has been relayed by a relaxation phase marked by emplacement of a third tholeiitic basic plutonic cycle.

Light elements burning reaction rates at stellar temperatures as deduced by the Trojan Horse measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamia, L.; Spitaleri, C.; La Cognata, M.

2015-02-24

Experimental nuclear astrophysics aims at determining the reaction rates for astrophysically relevant reactions at their Gamow energies. For charged-particle induced reactions, the access to these energies is usually hindered, in direct measurements, by the presence of the Coulomb barrier between the interacting particles or by electron screening effects, which make hard the determination of the bare-nucleus S(E)-factor of interest for astrophysical codes. The use of the Trojan Horse Method (THM) appears as one of the most suitable tools for investigating nuclear processes of interest for astrophysics. Here, in view of the recent TH measurements, the main destruction channels for deuteriummore » ({sup 2}H), for the two lithium {sup 6,7}Li isotopes, for the {sup 9}Be and the one for the two boron {sup 10,11}B isotopes will be discussed.« less

Numerical study of the effects of physical parameters on the dynamic fuel retention in tungsten materials

NASA Astrophysics Data System (ADS)

Sang, Chaofeng; Sun, Jizhong; Bonnin, Xavier; Dai, Shuyu; Hu, Wanpeng; Wang, Dezhen

2014-12-01

Effects of different possible values of physical parameters on the fuel retention in tungsten (W) materials are studied in this work since W is considered as the primary plasma-facing surface material and fuel retention is a critical issue for next-step fusion devices. The upgraded Hydrogen Isotope Inventory Processes Code is used to conduct the study. First, the inventories of hydrogen isotopes (HI) inside W with different possible values of diffusivities and recombination rate coefficients are studied; then the influences of uncertainties in diffusivity, trap concentration, and recombination rate on the effective diffusion are also analyzed. Finally, an illustration of effective diffusion on the permeation and inventory is given. The enhancements of HI permeation flux and inventory in bulk W due to the presence of a carbide WxC layer on the PFS are explained.

Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes

NASA Astrophysics Data System (ADS)

André, T.; Morini, F.; Karamitros, M.; Delorme, R.; Le Loirec, C.; Campos, L.; Champion, C.; Groetz, J.-E.; Fromm, M.; Bordage, M.-C.; Perrot, Y.; Barberet, Ph.; Bernal, M. A.; Brown, J. M. C.; Deleuze, M. S.; Francis, Z.; Ivanchenko, V.; Mascialino, B.; Zacharatou, C.; Bardiès, M.; Incerti, S.

2014-01-01

Monte Carlo simulations of S-values have been carried out with the Geant4-DNA extension of the Geant4 toolkit. The S-values have been simulated for monoenergetic electrons with energies ranging from 0.1 keV up to 20 keV, in liquid water spheres (for four radii, chosen between 10 nm and 1 μm), and for electrons emitted by five isotopes of iodine (131, 132, 133, 134 and 135), in liquid water spheres of varying radius (from 15 μm up to 250 μm). The results have been compared to those obtained from other Monte Carlo codes and from other published data. The use of the Kolmogorov-Smirnov test has allowed confirming the statistical compatibility of all simulation results.

The puzzle of the CNO isotope ratios in asymptotic giant branch carbon stars

NASA Astrophysics Data System (ADS)

Abia, C.; Hedrosa, R. P.; Domínguez, I.; Straniero, O.

2017-03-01

Context. The abundance ratios of the main isotopes of carbon, nitrogen and oxygen are modified by the CNO-cycle in the stellar interiors. When the different dredge-up events mix the burning material with the envelope, valuable information on the nucleosynthesis and mixing processes can be extracted by measuring these isotope ratios. Aims: Previous determinations of the oxygen isotopic ratios in asymptotic giant branch (AGB) carbon stars were at odds with the existing theoretical predictions. We aim to redetermine the oxygen ratios in these stars using new spectral analysis tools and further develop discussions on the carbon and nitrogen isotopic ratios in order to elucidate this problem. Methods: Oxygen isotopic ratios were derived from spectra in the K-band in a sample of galactic AGB carbon stars of different spectral types and near solar metallicity. Synthetic spectra calculated in local thermodynamic equillibrium (LTE) with spherical carbon-rich atmosphere models and updated molecular line lists were used. The CNO isotope ratios derived in a homogeneous way, were compared with theoretical predictions for low-mass (1.5-3 M⊙) AGB stars computed with the FUNS code assuming extra mixing both during the RGB and AGB phases. Results: For most of the stars the 16O/17O/18O ratios derived are in good agreement with theoretical predictions confirming that, for AGB stars, are established using the values reached after the first dredge-up (FDU) according to the initial stellar mass. This fact, as far as the oxygen isotopic ratios are concerned, leaves little space for the operation of any extra mixing mechanism during the AGB phase. Nevertheless, for a few stars with large 16O/17O/18O, the operation of such a mechanism might be required, although their observed 12C/13C and 14N/15N ratios would be difficult to reconcile within this scenario. Furthermore, J-type stars tend to have lower 16O/17O ratios than the normal carbon stars, as already indicated in previous studies. Excluding these peculiar stars, AGB carbon stars occupy the same region as pre-solar type I oxide grains in a 17O/16O vs. 18O/16O diagram, showing little spread. This reinforces the idea that these grains were probably formed in low-mass stars during the previous O-rich phases.

Eruptive history of Mount Katmai, Alaska

USGS Publications Warehouse

Hildreth, Edward; Fierstein, Judith

2012-01-01

Compositionally, products of Mount Katmai represent an ordinary medium-K arc array, both tholeiitic and calcalkaline, that extends from 51.6% to 72.3% SiO2. Values of 87Sr/86Sr range from 0.70335 to 0.70372, correlating loosely with fractionation indices. The 5–6 km3 of continuously zoned andesite-dacite magma (58%–68% SiO2) that erupted at Novarupta in 1912 was withdrawn from beneath Mount Katmai and bears close compositional affinity with products of that edifice, not with pre-1912 products of the adjacent Trident cluster. Evidence is presented that the 7–8 km3 of high-silica rhyolite (77% SiO2) released in 1912 is unlikely to have been stored under Novarupta or Trident. Pre-eruptive contiguity with the andesite-dacite reservoir is suggested by (1) eruption of ∼3 km3 of rhyolite magma first, followed by mutual mingling in fluctuating proportions; (2) thermal and redox continuity of the whole zoned sequence despite the wide compositional gap; (3) Nd, Sr, O isotopic, and rare earth element (REE) affinities of the whole array; (4) compositional continuity of the nearly aphyric rhyolite with the glass (melt) phase of the phenocryst-rich dacite; and (5) phase-equilibrium experiments that indicate similar shallow pre-eruptive storage depths (3–6 km) for rhyolite, dacite, and andesite.

Methods for determining the genetic affinity of microorganisms and viruses

NASA Technical Reports Server (NTRS)

Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)

2012-01-01

Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

The Practical Application of Aqueous Geochemistry in Mapping Groundwater Flow Systems in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Bursey, G.; Seok, E.; Gale, J. E.

2017-12-01

Flow to underground mines and open pits takes place through an interconnected network of regular joints/fractures and intermediate to large scale structural features such as faults and fracture zones. Large scale features can serve either as high permeability pathways or as barriers to flow, depending on the internal characteristics of the structure. Predicting long term water quality in barrier-well systems and long-term mine water inflows over a mine life, as a mine expands, requires the use of a 3D numerical flow and transport code. The code is used to integrate the physical geometry of the fractured-rock mass with porosity, permeability, hydraulic heads, storativity and recharge data and construct a model of the flow system. Once that model has been calibrated using hydraulic head and permeability/inflow data, aqueous geochemical and isotopic data provide useful tools for validating flow-system properties, when one is able to recognize and account for the non-ideal or imperfect aspects of the sampling methods used in different mining environments. If groundwater samples are collected from discrete depths within open boreholes, water in those boreholes have the opportunity to move up or down in response to the forces that drive groundwater flow, whether they be hydraulic gradients, gas pressures, or density differences associated with variations in salinity. The use of Br/Cl ratios, for example, can be used to determine if there is active flow into, or out of, the boreholes through open discontinuities in the rock mass (i.e., short-circuiting). Natural groundwater quality can also be affected to varying degrees by mixing with drilling fluids. The combined use of inorganic chemistry and stable isotopes can be used effectively to identify dilution signals and map the dilution patterns through a range of fresh, brackish and saline water types. The stable isotopes of oxygen and hydrogen are nearly ideal natural tracers of water, but situations occur when deep groundwater samples can plot to the left of the meteoric water line as a result of isotopic exchange between meteoric water and silicate rock in near-surface environments at low temperatures. These and other examples are considered in the practical application of aqueous geochemistry in helping to map flow systems in fractured-rock systems.

pre-Mesozoic evolution of the basement of the Catalan Coastal Ranges: implications from geochemical and Sm-Nd isotope data of the Palaeozoic succession of the Collserola Range

NASA Astrophysics Data System (ADS)

Vilà, Miquel; Pin, Christian

2016-04-01

In the whole of the Western Europe and neighbouring areas numerous studies have addressed the provenance of pre-Mesozoic sedimentary rocks and the Palaeozoic geodynamic evolution using the Sm-Nd systematics. However, at present, there are still large areas of the Variscan mountain chain without systematic determinations of their whole - rock Sm-Nd isotope signatures. This is the case of the Palaeozoic blocks of the Catalan Coastal Ranges (NE Iberia). In the context of the Variscan belt many authors interpret the Palaeozoic basement of the Catalan Coastal Ranges as part of the southern foreland basin of the mountain belt. The pre-Mesozoic rocks in the Catalan Coastal Ranges exhibit important stratigraphical affinities with those outcropping in the Eastern Pyrenees, Montagne Noire, Sardinia and Iberian Range. Paleogeographic reconstructions predict that the Catalan Coastal Ranges were located in a transitional area between the northern branch of the Ibero-Armorican arc and the core of the arc. The Collserola Range, located in the metropolitan area of Barcelona, includes a representative Palaeozoic stratigraphic section, from Cambro-Ordovician to Carboniferous, of the central part of the Catalan Coastal Ranges. In this presentation we present an up-to-date review of the stratigraphy and structure of the Palaeozoic of the Collserola Range, and provide geochemical and Sm-Nd isotope data to constrain the Pre-Mesozoic crustal evolution of this sector of the Variscan belt. Geochemical compositions indicate that the Palaeozoic siliciclastic rocks of the Collserola Range were fed by a relative mature heterogeneous source of sediment, comprising from quartz-rich sediments to intermediate igneous rocks. The siliciclastic rocks of the Collserola Range show great geochemical affinity with the turbidites of passive margins. The Sm-Nd signature of the siliciclastic rocks is compatible with those of the Palaeozoic and Late Proterozoic fine grained siliciclastic rocks of the neighbouring terrains of SW Europe. There is a small decrease of the ɛNdT with decreasing age of sedimentation, from the Cambro-Ordovician to the Carboniferous, suggesting an increase of the amount of more 'juvenile' material. The presence of small volumes of alkaline basaltic rocks provides evidence for the input of juvenile material in the Early Palaeozoic basin and suggests that an extensional tectonic regime prevailed during the Cambro-Ordovician sedimentation. From a geodynamic point of view, overall, the analysis of the data evokes that the Palaeozoic rocks of the Catalan Coastal Ranges were part of the Northern Gondwana passive margin before the closure of the Rheic Ocean and the subsequent Variscan orogeny.

Identification of human antibody fragment clones specific for tetanus toxoid in a bacteriophage. lambda. immunoexpression library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mullinax, R.L.; Gross, E.A.; Amberg, J.R.

1990-10-01

The authors have applied a molecular biology approach to the identification of human monoclonal antibodies. Human peripheral blood lymphocyte mRNA was converted to cDNA and a select subset was amplified by the polymerase chain reaction. These products, containing coding sequences for numerous immunoglobulin heavy- and {kappa} light-chain variable and constant region domains, were inserted into modified bacteriophase {lambda} expression vectors and introduced into Escherichia coli by infection to yield a combinatorial immunoexpression library. Clones with binding activity to tetanus toxoid were identified by filter hybridization with radiolabeled antigen and appeared at a frequency of 0.2{percent} in the library. These humanmore » antigen binding fragments, consisting of a heavy-chain fragment covalently linked to a light chain, displayed high affinity of binding to tetanus toxoid with equilibrium constants in the nanomolar range but did not cross-react with other proteins tested. They estimate that this human immunoexpression library contains 20,000 clones with high affinity and specificity to our chosen antigen.« less

CaFE: a tool for binding affinity prediction using end-point free energy methods.

PubMed

Liu, Hui; Hou, Tingjun

2016-07-15

Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. tingjunhou@zju.edu.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effect on magnetic properties of germanium encapsulated C60 fullerene

NASA Astrophysics Data System (ADS)

Umran, Nibras Mossa; Kumar, Ranjan

2013-02-01

Structural and electronic properties of Gen(n = 1-4) doped C60 fullerene are investigated with ab initio density functional theory calculations by using an efficient computer code, known as SIESTA. The pseudopotentials are constructed using a Trouiller-Martins scheme, to describe the interaction of valence electrons with the atomic cores. In endohedral doped embedding of more germanium atoms complexes we have seen that complexes are stable and thereafter cage break down. We have also investigated that binding energy, electronic affinity increases and magnetic moment oscillating behavior as the number of semiconductor atoms in C60 fullerene goes on increasing.

The southern route "out of Africa": evidence for an early expansion of modern humans into Arabia.

PubMed

Armitage, Simon J; Jasim, Sabah A; Marks, Anthony E; Parker, Adrian G; Usik, Vitaly I; Uerpmann, Hans-Peter

2011-01-28

The timing of the dispersal of anatomically modern humans (AMH) out of Africa is a fundamental question in human evolutionary studies. Existing data suggest a rapid coastal exodus via the Indian Ocean rim around 60,000 years ago. We present evidence from Jebel Faya, United Arab Emirates, demonstrating human presence in eastern Arabia during the last interglacial. The tool kit found at Jebel Faya has affinities to the late Middle Stone Age in northeast Africa, indicating that technological innovation was not necessary to facilitate migration into Arabia. Instead, we propose that low eustatic sea level and increased rainfall during the transition between marine isotope stages 6 and 5 allowed humans to populate Arabia. This evidence implies that AMH may have been present in South Asia before the Toba eruption.

Finite mixture models for the computation of isotope ratios in mixed isotopic samples

NASA Astrophysics Data System (ADS)

Koffler, Daniel; Laaha, Gregor; Leisch, Friedrich; Kappel, Stefanie; Prohaska, Thomas

2013-04-01

Finite mixture models have been used for more than 100 years, but have seen a real boost in popularity over the last two decades due to the tremendous increase in available computing power. The areas of application of mixture models range from biology and medicine to physics, economics and marketing. These models can be applied to data where observations originate from various groups and where group affiliations are not known, as is the case for multiple isotope ratios present in mixed isotopic samples. Recently, the potential of finite mixture models for the computation of 235U/238U isotope ratios from transient signals measured in individual (sub-)µm-sized particles by laser ablation - multi-collector - inductively coupled plasma mass spectrometry (LA-MC-ICPMS) was demonstrated by Kappel et al. [1]. The particles, which were deposited on the same substrate, were certified with respect to their isotopic compositions. Here, we focus on the statistical model and its application to isotope data in ecogeochemistry. Commonly applied evaluation approaches for mixed isotopic samples are time-consuming and are dependent on the judgement of the analyst. Thus, isotopic compositions may be overlooked due to the presence of more dominant constituents. Evaluation using finite mixture models can be accomplished unsupervised and automatically. The models try to fit several linear models (regression lines) to subgroups of data taking the respective slope as estimation for the isotope ratio. The finite mixture models are parameterised by: • The number of different ratios. • Number of points belonging to each ratio-group. • The ratios (i.e. slopes) of each group. Fitting of the parameters is done by maximising the log-likelihood function using an iterative expectation-maximisation (EM) algorithm. In each iteration step, groups of size smaller than a control parameter are dropped; thereby the number of different ratios is determined. The analyst only influences some control parameters of the algorithm, i.e. the maximum count of ratios, the minimum relative group-size of data points belonging to each ratio has to be defined. Computation of the models can be done with statistical software. In this study Leisch and Grün's flexmix package [2] for the statistical open-source software R was applied. A code example is available in the electronic supplementary material of Kappel et al. [1]. In order to demonstrate the usefulness of finite mixture models in fields dealing with the computation of multiple isotope ratios in mixed samples, a transparent example based on simulated data is presented and problems regarding small group-sizes are illustrated. In addition, the application of finite mixture models to isotope ratio data measured in uranium oxide particles is shown. The results indicate that finite mixture models perform well in computing isotope ratios relative to traditional estimation procedures and can be recommended for more objective and straightforward calculation of isotope ratios in geochemistry than it is current practice. [1] S. Kappel, S. Boulyga, L. Dorta, D. Günther, B. Hattendorf, D. Koffler, G. Laaha, F. Leisch and T. Prohaska: Evaluation Strategies for Isotope Ratio Measurements of Single Particles by LA-MC-ICPMS, Analytical and Bioanalytical Chemistry, 2013, accepted for publication on 2012-12-18 (doi: 10.1007/s00216-012-6674-3) [2] B. Grün and F. Leisch: Fitting finite mixtures of generalized linear regressions in R. Computational Statistics & Data Analysis, 51(11), 5247-5252, 2007. (doi:10.1016/j.csda.2006.08.014)

Evaluation of Pharmacokinetic Models for the Disposition of Lead (Pb) in Humans, in Support of Application to Occupational Exposure Limit Derivation

DTIC Science & Technology

2015-11-09

as biokinetic or physiologically-based pharmacokinetic (PBPK) models, can readily incorporate multiple routes of exposure (e.g., baseline dietary ...1998) and in the code provided as a supplement to O’Flaherty (2000), as noted above. An aspect of the O’Flaherty model that contrasts to the... dietary Pb; a stable Pb isotope was substituted for some of the dietary Pb for limited periods. Tracer Pb concentrations were measured in blood

Neutronics Assessments for a RIA Fragmentation Line Beam Dump Concept

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boles, J L; Reyes, S; Ahle, L E

Heavy ion and radiation transport calculations are in progress for conceptual beam dump designs for the fragmentation line of the proposed Rare Isotope Accelerator (RIA). Using the computer code PHITS, a preliminary design of a motor-driven rotating wheel beam dump and adjacent downstream multipole has been modeled. Selected results of these calculations are given, including neutron and proton flux in the wheel, absorbed dose and displacements per atom in the hub materials, and heating from prompt radiation and from decay heat in the multipole.

Evaluation of fusion-evaporation cross-section calculations

NASA Astrophysics Data System (ADS)

Blank, B.; Canchel, G.; Seis, F.; Delahaye, P.

2018-02-01

Calculated fusion-evaporation cross sections from five different codes are compared to experimental data. The present comparison extents over a large range of nuclei and isotopic chains to investigate the evolution of experimental and calculated cross sections. All models more or less overestimate the experimental cross sections. We found reasonable agreement by using the geometrical average of the five model calculations and dividing the average by a factor of 11.2. More refined analyses are made for example for the 100Sn region.

Body Composition in Military or Military Eligible Women.

DTIC Science & Technology

1998-02-01

aqueous exchange of hydrogen, isotopic fractionation. All values will be converted to kilograms using the constant 0.009934. This method has a day to...into a microtube for storage. Samples will be coded to protect subject identity and shipped to the U.S. Department of Agriculture Western Human...weighing will be conducted in a rectangular (7 feet long x 4 feet wide x 5 feet deep), glass-fronted tank of heated water (35°C/96°F) . The swimsuit

A novel lectin from Agrocybe aegerita shows high binding selectivity for terminal N-acetylglucosamine

PubMed Central

Jiang, Shuai; Chen, Yijie; Wang, Man; Yin, Yalin; Pan, Yongfu; Gu, Bianli; Yu, Guojun; Li, Yamu; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2012-01-01

A novel lectin was isolated from the mushroom Agrocybe aegerita (designated AAL-2) by affinity chromatography with GlcNAc (N-acetylglucosamine)-coupled Sepharose 6B after ammonium sulfate precipitation. The AAL-2 coding sequence (1224 bp) was identified by performing a homologous search of the five tryptic peptides identified by MS against the translated transcriptome of A. aegerita. The molecular mass of AAL-2 was calculated to be 43.175 kDa from MS, which was consistent with the data calculated from the amino acid sequence. To analyse the carbohydrate-binding properties of AAL-2, a glycan array composed of 465 glycan candidates was employed, and the result showed that AAL-2 bound with high selectivity to terminal non-reducing GlcNAc residues, and further analysis revealed that AAL-2 bound to terminal non-reducing GlcNAc residues with higher affinity than previously well-known GlcNAc-binding lectins such as WGA (wheatgerm agglutinin) and GSL-II (Griffonia simplicifolia lectin-II). ITC (isothermal titration calorimetry) showed further that GlcNAc bound to AAL-2 in a sequential manner with moderate affinity. In the present study, we also evaluated the anti-tumour activity of AAL-2. The results showed that AAL-2 could bind to the surface of hepatoma cells, leading to induced cell apoptosis in vitro. Furthermore, AAL-2 exerted an anti-hepatoma effect via inhibition of tumour growth and prolongation of survival time of tumour-bearing mice in vivo. PMID:22268569

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets.

PubMed

Nelson, Christopher S; Fuller, Chris K; Fordyce, Polly M; Greninger, Alexander L; Li, Hao; DeRisi, Joseph L

2013-07-01

The transcription factor forkhead box P2 (FOXP2) is believed to be important in the evolution of human speech. A mutation in its DNA-binding domain causes severe speech impairment. Humans have acquired two coding changes relative to the conserved mammalian sequence. Despite intense interest in FOXP2, it has remained an open question whether the human protein's DNA-binding specificity and chromatin localization are conserved. Previous in vitro and ChIP-chip studies have provided conflicting consensus sequences for the FOXP2-binding site. Using MITOMI 2.0 microfluidic affinity assays, we describe the binding site of FOXP2 and its affinity profile in base-specific detail for all substitutions of the strongest binding site. We find that human and chimp FOXP2 have similar binding sites that are distinct from previously suggested consensus binding sites. Additionally, through analysis of FOXP2 ChIP-seq data from cultured neurons, we find strong overrepresentation of a motif that matches our in vitro results and identifies a set of genes with FOXP2 binding sites. The FOXP2-binding sites tend to be conserved, yet we identified 38 instances of evolutionarily novel sites in humans. Combined, these data present a comprehensive portrait of FOXP2's-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved.

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets

PubMed Central

Nelson, Christopher S.; Fuller, Chris K.; Fordyce, Polly M.; Greninger, Alexander L.; Li, Hao; DeRisi, Joseph L.

2013-01-01

The transcription factor forkhead box P2 (FOXP2) is believed to be important in the evolution of human speech. A mutation in its DNA-binding domain causes severe speech impairment. Humans have acquired two coding changes relative to the conserved mammalian sequence. Despite intense interest in FOXP2, it has remained an open question whether the human protein’s DNA-binding specificity and chromatin localization are conserved. Previous in vitro and ChIP-chip studies have provided conflicting consensus sequences for the FOXP2-binding site. Using MITOMI 2.0 microfluidic affinity assays, we describe the binding site of FOXP2 and its affinity profile in base-specific detail for all substitutions of the strongest binding site. We find that human and chimp FOXP2 have similar binding sites that are distinct from previously suggested consensus binding sites. Additionally, through analysis of FOXP2 ChIP-seq data from cultured neurons, we find strong overrepresentation of a motif that matches our in vitro results and identifies a set of genes with FOXP2 binding sites. The FOXP2-binding sites tend to be conserved, yet we identified 38 instances of evolutionarily novel sites in humans. Combined, these data present a comprehensive portrait of FOXP2’s-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved. PMID:23625967

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

PubMed Central

Garcia Lopez, Sebastian; Kim, Philip M.

2014-01-01

Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

A mirror code for protein-cholesterol interactions in the two leaflets of biological membranes

NASA Astrophysics Data System (ADS)

Fantini, Jacques; di Scala, Coralie; Evans, Luke S.; Williamson, Philip T. F.; Barrantes, Francisco J.

2016-02-01

Cholesterol controls the activity of a wide range of membrane receptors through specific interactions and identifying cholesterol recognition motifs is therefore critical for understanding signaling receptor function. The membrane-spanning domains of the paradigm neurotransmitter receptor for acetylcholine (AChR) display a series of cholesterol consensus domains (referred to as “CARC”). Here we use a combination of molecular modeling, lipid monolayer/mutational approaches and NMR spectroscopy to study the binding of cholesterol to a synthetic CARC peptide. The CARC-cholesterol interaction is of high affinity, lipid-specific, concentration-dependent, and sensitive to single-point mutations. The CARC motif is generally located in the outer membrane leaflet and its reverse sequence CRAC in the inner one. Their simultaneous presence within the same transmembrane domain obeys a “mirror code” controlling protein-cholesterol interactions in the outer and inner membrane leaflets. Deciphering this code enabled us to elaborate guidelines for the detection of cholesterol-binding motifs in any membrane protein. Several representative examples of neurotransmitter receptors and ABC transporters with the dual CARC/CRAC motifs are presented. The biological significance and potential clinical applications of the mirror code are discussed.

Development of tools and techniques for momentum compression of fast rare isotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

David J. Morrissey; Bradley M. Sherrill; Oleg Tarasov

2010-11-21

As part of our past research and development work, we have created and developed the LISE++ simulation code [Tar04, Tar08]. The LISE++ package was significantly extended with the addition of a Monte Carlo option that includes an option for calculating ion trajectories using a Taylor-series expansion up to fifth order, and implementation of the MOTER Monte Carlo code [Kow87] for ray tracing of the ions into the suite of LISE++ codes. The MOTER code was rewritten from FORTRAN into C++ and transported to the MS-Windows operating system. Extensive work went into the creation of a user-friendly interface for the code.more » An example of the graphical user interface created for the MOTER code is shown in the left panel of Figure 1 and the results of a typical calculation for the trajectories of particles that pass through the A1900 fragment separator are shown in the right panel. The MOTER code is presently included as part of the LISE++ package for downloading without restriction by the worldwide community. The LISE++ was extensively developed and generalized to apply to any projectile fragment separator during the early phase of this grant. In addition to the inclusion of the MOTER code, other important additions to the LISE++ code made during FY08/FY09 are listed. The LISE++ is distributed over the web (http://groups.nscl.msu.edu/lise ) and is available without charge to anyone by anonymous download, thus, the number of individual users is not recorded. The number of 'hits' on the servers that provide the LISE++ code is shown in Figure 3 for the last eight calendar years (left panel) along with the country from the IP address (right panel). The data show an increase in web-activity with the release of the new version of the program during the grant period and a worldwide impact. An important part of the proposed work carried out during FY07, FY08 and FY09 by a graduate student in the MSU Physics program was to benchmark the codes by comparison of detailed measurements to the LISE++ predictions. A large data set was obtained for fission fragments from the reaction of 238U ions at 81 MeV/u in a 92 mg/cm2 beryllium target with the A1900 projectile fragment separator. The data were analyzed and form the bulk of a Ph.D. dissertation that is nearing completion. The rich data set provides a number of benchmarks for the improved LISE++ code and only a few examples can be shown here. The primary information obtained from the measurements is the yield of the products as a function of mass, charge and momentum. Examples of the momentum distributions of individually identified fragments can be seen in Figures 2 and 4 along with comparisons to the predicted distributions. The agreement is remarkably good and indicates the general validity of the model of the nuclear reactions producing these fragments and of the higher order transmission calculations in the LISE++ code. The momentum distributions were integrated to provide the cross sections for the individual isotopes. As shown in Figure 5, there is good agreement with the model predictions although the observed cross sections are a factor of five or so higher in this case. Other comparisons of measured production cross sections from abrasion-fission reactions have been published by our group working at the NSCL during this period [Fol09] and through our collaboration with Japanese researchers working at RIKEN with the BigRIPS separator [Ohn08, Ohn10]. The agreement of the model predictions with the data obtained with two different fragment separators is very good and indicates the usefulness of the new LISE++ code.« less

Permian arc-back-arc basin development along the Ailaoshan tectonic zone: Geochemical, isotopic and geochronological evidence from the Mojiang volcanic rocks, Southwest China

NASA Astrophysics Data System (ADS)

Fan, Weiming; Wang, Yuejun; Zhang, Aimei; Zhang, Feifei; Zhang, Yuzhi

2010-10-01

This paper presents a set of new SHRIMP zircon U-Pb geochronological, elemental and Sr-Nd-Pb isotopic data for the Wusu and Yaxuanqiao basaltic rocks (the Mojiang area) along the Ailaoshan tectonic zone. The Wusu basaltic sequence is dominated by SiO 2-poor, MgO- and TiO 2-rich basalts with a major mineral assemblage of plagioclase + clinopyroxene. These rocks gave a SHRIMP zircon U-Pb age of 287 ± 5 Ma (MSWD = 0.58). In contrast, the Yaxuanqiao basaltic sequence is predominantly composed of high-Al basaltic andesite, which gave a SHRIMP zircon U-Pb age of 265 ± 7 Ma (MSWD = 0.34). The analyzed samples for both sequences exhibit significant enrichment in LILEs and depletion in HFSEs with (Nb/La)n of 0.38-0.81, similar to arc-like volcanics. They have positive ɛNd(t) values (+ 3.52 to + 5.54). In comparison with MORB-derived magmatic rocks, the Wusu basalts are more enriched in LILEs and REEs, and the Yaxuanqiao samples are more enriched in LILEs but variably depleted in Ti, Y and HREE. The Wusu samples show high Pb isotopic ratios, similar to the Tethyan basalts, whereas the Yaxuanqiao samples plot in the field of the global pelagic sediments. The geochemical and Sr-Nd-Pb isotopic characteristics suggest that the Wusu basalts originated from a MORB-like source metasomatised by slab-derived fluids, while the Yaxuanqiao rocks have a fluid-modified MORB source with the input of subducted sediments. The geochemical affinity to both MORB- and arc-like sources, together with other geological observations, appears to support the development of a Permian arc-back-arc basin along the Ailaoshan-Song Ma tectonic zone in response to the northward subduction of the Paleotethys main Ocean. The final closure of the arc-back-arc basin took place in the uppermost Triassic due to the diachronous amalgamation between the Yangtze and Simao-Indochina Blocks.

Petrogenesis of the middle Jurassic appinite and coeval granitoids in the Eastern Hebei area of North China Craton

NASA Astrophysics Data System (ADS)

Fan, Wenbo; Jiang, Neng; Xu, Xiyang; Hu, Jun; Zong, Keqing

2017-05-01

An integrated study of zircon U-Pb ages and Hf-O isotopic compositions, whole rock elemental and Sr-Nd isotope geochemistry was conducted on three lithologically diverse middle Jurassic plutons from the Eastern Hebei area of the North China Craton (NCC), in order to reveal both their petrogenesis and possible tectonic affinity. The three plutons have consistent magmatic zircon U-Pb ages from 167 ± 1 Ma to 173 ± 1 Ma. The Nianziyu pluton has typical characteristics of appinite with low SiO2 (43.7-52.6%), high Ca, Mg, Fe and H2O contents. It possesses subduction-related trace element patterns, enriched Nd-Hf isotopic signatures as well as elevated zircon δ18O values (6.2-7.2‰), arguing for an enriched mantle source metasomatized by fluids related to subduction. The Shuihutong monzogranites have high silica (SiO2 = 75.4-75.9%) and alkali contents, low Ca contents and striking negative Ba, Sr and Eu anomalies. Samples from the pluton have more evolved Nd-Hf isotopic values and are considered to be most likely derived from anatexis of ancient lower continental crust. Hybridization between mantle- and ancient lower crust-derived magmas is proposed for the mafic microgranular enclave-bearing Baijiadian granitoids, which are characterized by variable εNd (t) and εHf(t) values. Integrated with the regional geologic history, we suggest that the formation of the three middle Jurassic plutons were related to the subduction of the Paleo-Pacific ocean plate beneath the NCC. Their petrogenetic differences reflect complex magmatic processes in subduction settings involving melting of multiple sources, possible partly facilitated by fluid metasomatism and water-rich magma injection, accompanied with various degrees of magma mixing. The appearance of middle Jurassic appinitic rocks leads us to propose that the NCC destruction and lithosphere thinning were facilitated and controlled by the weakening of the lithospheric mantle after hydration because of the subduction of the paleo-Pacific ocean plate. The lower crust of the craton was also reactivated at the same time due to the subduction.

Evolution of the lithospheric mantle beneath Mt. Baekdu (Changbaishan)

NASA Astrophysics Data System (ADS)

Choi, S. H.; Park, K.; Cho, M.; Lee, D. C.

2017-12-01

Major and trace element compositions of minerals as well as Sr-Nd-Hf isotopic compositions of clinopyroxenes from spinel peridotite xenoliths entrained in Late Cenozoic trachybasalt from Mt. Baekdu (Changbaishan) were used to elucidate lithospheric mantle formation and evolution in the eastern North China Craton (NCC). The analyzed peridotites were mainly spinel lherzolites with rare harzburgites. They consisted of olivine, enstatite, diopside and spinel. Plots of the Cr# in spinel against the Mg# in coexisting olivine or spinel suggested an affinity with abyssal peridotites. Comparisons of Cr# and TiO2 in spinel were also compatible with an abyssal peridotite-like composition; however, harzburgites were slightly enriched in TiO2 because of the reaction with MORB-like melt. Temperatures estimated using two-pyroxene thermometry ranged from 750 to 1,010°C, reflecting their lithospheric mantle origin. The REE patterns in clinopyroxenes of the peridotites varied from LREE-depleted to spoon shaped to LREE-enriched, reflecting secondary overprinting effects of metasomatic melts or fluids on the residues from primordial melting. The calculated trace element pattern of metasomatic melt equilibrated with clinopyroxene in Mt. Baekdu peridotite showed strong enrichment in LILEs, Th and U together with slight fractionation in HREEs and considerable depletion in Nb and Ti. The Sr-Nd-Hf isotopic compositions of clinopyroxenes separated from the peridotites varied from more depleted than present-day MORB to bulk Earth values. However, some clinopyroxene showed a decoupling between Nd and Sr isotopes, deviating from the mantle array with a high 87Sr/86Sr ratio. This sample also showed a significant Nd-Hf isotope decoupling lying well above the mantle array. The Lu-Hf and Sm-Nd model ages of residual clinopyroxenes yielded Early Proterozoic to Phanerozoic ages. No signature of Archean cratonic mantle was present. Therefore, Mt. Baekdu peridotite is residual lithospheric mantle that has undergone variable degrees of diachronous melt extraction and infiltration metasomatism involving subduction-related, fluid-bearing silicate melts. The predominance of Phanerozoic Hf model ages indicates that the lherzolites represent lithospheric mantle fragments newly accreted underneath the eastern NCC.

Fuel Performance Experiments and Modeling: Fission Gas Bubble Nucleation and Growth in Alloy Nuclear Fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDeavitt, Sean; Shao, Lin; Tsvetkov, Pavel

2014-04-07

Advanced fast reactor systems being developed under the DOE's Advanced Fuel Cycle Initiative are designed to destroy TRU isotopes generated in existing and future nuclear energy systems. Over the past 40 years, multiple experiments and demonstrations have been completed using U-Zr, U-Pu-Zr, U-Mo and other metal alloys. As a result, multiple empirical and semi-empirical relationships have been established to develop empirical performance modeling codes. Many mechanistic questions about fission as mobility, bubble coalescience, and gas release have been answered through industrial experience, research, and empirical understanding. The advent of modern computational materials science, however, opens new doors of development suchmore » that physics-based multi-scale models may be developed to enable a new generation of predictive fuel performance codes that are not limited by empiricism.« less

Features of MCNP6 Relevant to Medical Radiation Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, H. Grady III; Goorley, John T.

2012-08-29

MCNP (Monte Carlo N-Particle) is a general-purpose Monte Carlo code for simulating the transport of neutrons, photons, electrons, positrons, and more recently other fundamental particles and heavy ions. Over many years MCNP has found a wide range of applications in many different fields, including medical radiation physics. In this presentation we will describe and illustrate a number of significant recently-developed features in the current version of the code, MCNP6, having particular utility for medical physics. Among these are major extensions of the ability to simulate large, complex geometries, improvement in memory requirements and speed for large lattices, introduction of mesh-basedmore » isotopic reaction tallies, advances in radiography simulation, expanded variance-reduction capabilities, especially for pulse-height tallies, and a large number of enhancements in photon/electron transport.« less

A large column analog experiment of stable isotope variations during reactive transport: I. A comprehensive model of sulfur cycling and δ34S fractionation

NASA Astrophysics Data System (ADS)

Druhan, Jennifer L.; Steefel, Carl I.; Conrad, Mark E.; DePaolo, Donald J.

2014-01-01

This study demonstrates a mechanistic incorporation of the stable isotopes of sulfur within the CrunchFlow reactive transport code to model the range of microbially-mediated redox processes affecting kinetic isotope fractionation. Previous numerical models of microbially mediated sulfate reduction using Monod-type rate expressions have lacked rigorous coupling of individual sulfur isotopologue rates, with the result that they cannot accurately simulate sulfur isotope fractionation over a wide range of substrate concentrations using a constant fractionation factor. Here, we derive a modified version of the dual-Monod or Michaelis-Menten formulation (Maggi and Riley, 2009, 2010) that successfully captures the behavior of the 32S and 34S isotopes over a broad range from high sulfate and organic carbon availability to substrate limitation using a constant fractionation factor. The new model developments are used to simulate a large-scale column study designed to replicate field scale conditions of an organic carbon (acetate) amended biostimulation experiment at the Old Rifle site in western Colorado. Results demonstrate an initial period of iron reduction that transitions to sulfate reduction, in agreement with field-scale behavior observed at the Old Rifle site. At the height of sulfate reduction, effluent sulfate concentrations decreased to 0.5 mM from an influent value of 8.8 mM over the 100 cm flow path, and thus were enriched in sulfate δ34S from 6.3‰ to 39.5‰. The reactive transport model accurately reproduced the measured enrichment in δ34S of both the reactant (sulfate) and product (sulfide) species of the reduction reaction using a single fractionation factor of 0.987 obtained independently from field-scale measurements. The model also accurately simulated the accumulation and δ34S signature of solid phase elemental sulfur over the duration of the experiment, providing a new tool to predict the isotopic signatures associated with reduced mineral pools. To our knowledge, this is the first rigorous treatment of sulfur isotope fractionation subject to Monod kinetics in a mechanistic reactive transport model that considers the isotopic spatial distribution of both dissolved and solid phase sulfur species during microbially-mediated sulfate reduction. describe the design and results of the large-scale column experiment; demonstrate incorporation of the stable isotopes of sulfur in a dual-Monod kinetic expression such that fractionation is accurately modeled at both high and low substrate availability; verify accurate simulation of the chemical and isotopic gradients in reactant and product sulfur species using a kinetic fractionation factor obtained from field-scale analysis (Druhan et al., 2012); utilize the model to predict the final δ34S values of secondary sulfur minerals accumulated in the sediment over the course of the experiment. The development of rigorous isotope-specific Monod-type rate expressions are presented here in application to sulfur cycling during amended biostimulation, but are readily applicable to a variety of stable isotope systems associated with both steady state and transient biogenic redox environments. In other words, the association of this model with a uranium remediation experiment does not limit its applicability to more general redox systems. Furthermore, the ability of this model treatment to predict the isotopic composition of secondary minerals accumulated as a result of fractionating processes (item 4) offers an important means of interpreting solid phase isotopic compositions and tracking long-term stability of precipitates.

Impact of Chronic Alcohol Ingestion on Cardiac Muscle Protein Expression

PubMed Central

Fogle, Rachel L.; Lynch, Christopher J.; Palopoli, Mary; Deiter, Gina; Stanley, Bruce A.; Vary, Thomas C.

2014-01-01

Background Chronic alcohol abuse contributes not only to an increased risk of health-related complications, but also to a premature mortality in adults. Myocardial dysfunction, including the development of a syndrome referred to as alcoholic cardiomyopathy, appears to be a major contributing factor. One mechanism to account for the pathogenesis of alcoholic cardiomyopathy involves alterations in protein expression secondary to an inhibition of protein synthesis. However, the full extent to which myocardial proteins are affected by chronic alcohol consumption remains unresolved. Methods The purpose of this study was to examine the effect of chronic alcohol consumption on the expression of cardiac proteins. Male rats were maintained for 16 weeks on a 40% ethanol-containing diet in which alcohol was provided both in drinking water and agar blocks. Control animals were pair-fed to consume the same caloric intake. Heart homogenates from control- and ethanol-fed rats were labeled with the cleavable isotope coded affinity tags (ICAT™). Following the reaction with the ICAT™ reagent, we applied one-dimensional gel electrophoresis with in-gel trypsin digestion of proteins and subsequent MALDI-TOF-TOF mass spectrometric techniques for identification of peptides. Differences in the expression of cardiac proteins from control- and ethanol-fed rats were determined by mass spectrometry approaches. Results Initial proteomic analysis identified and quantified hundreds of cardiac proteins. Major decreases in the expression of specific myocardial proteins were observed. Proteins were grouped depending on their contribution to multiple activities of cardiac function and metabolism, including mitochondrial-, glycolytic-, myofibrillar-, membrane-associated, and plasma proteins. Another group contained identified proteins that could not be properly categorized under the aforementioned classification system. Conclusions Based on the changes in proteins, we speculate modulation of cardiac muscle protein expression represents a fundamental alteration induced by chronic alcohol consumption, consistent with changes in myocardial wall thickness measured under the same conditions. PMID:20477769

Synthesis and radiolabeling of a somatostatin analog for multimodal imaging

NASA Astrophysics Data System (ADS)

Edwards, W. Barry; Liang, Kexian; Xu, Baogang; Anderson, Carolyn J.; Achilefu, Samuel

2006-02-01

A new multimodal imaging agent for imaging the somatostatin receptor has been synthesized and evaluated in vitro and in vivo. A somatostatin analog, conjugated to both 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaceticacid (DOTA) and cypate (BS-296), was synthesized entirely on the solid phase (Fmoc) and purified by RP-HPLC. DOTA was added as a ligand for radiometals such as 64Cu or 177Lu for either radio-imaging or radiotherapy respectively. Cytate, a cypatesomatostatin analog conjugate, has previously demonstrated the ability to visualize somatostatin receptor rich tumor xenografts and natural organs by optical imaging techniques. BS-296 exhibited low nanomolar inhibitory capacity toward the binding of radiolabeled somatostatin analogs in cell membranes enriched in the somatostatin receptor, demonstrating the high affinity of this multimodal imaging peptide and indicating its potential as a molecular imaging agent. 64Cu, an isotope for diagnostic imaging and radiotherapy, was selected as the isotope for radiolabeling BS-296. BS-296 was radiolabeled with 64Cu in high specific activity (200 μCi/μg) in 90% radiochemical yield. Addition of 2,5-dihydroxybenzoic acid (gentisic acid) prevented radiolysis of the sample, allowing for study of the 64Cu -BS-296 the day following radiolabeling. Furthermore, inclusion of DMSO at a level of 20% was found not to interfere with radiolabeling yields and prevented the adherence of 64Cu -BS-296 to the walls of the reaction vessel.

Synthesis and preliminary biological evaluations of fluorescent or 149Promethium labeled Trastuzumab-polyethylenimine

DOE PAGES

Fitzsimmons, Jonathan; Nayak, Tapan; Cutler, Cathy; ...

2015-12-30

Radioimmunotherapy utilize a targeting antibody coupled to a therapeutic isotope to target and treat a tumor or disease. In this study we examine the synthesis and cell binding of a polymer scaffold containing a radiotherapeutic isotope and a targeting antibody. Methods: The multistep synthesis of a fluorescent or 149Promethium-labeled Trastuzumab-polyethyleneimine (PEI), Trastuzumab, or PEI is described. In vitro uptake, internalization and/or the binding affinity to the Her2/neu expressing human breast adenocarcinoma SKBr3 cells was investigated with the labeled compounds. Fluorescent-labeled Trastuzumab-PEI was internalized more into cells at 2 and 18 h than fluorescent-labeled Trastuzumab or PEI. The fluorescent-labeled Trastuzumab wasmore » concentrated on the cell surface at 2 and 18 h and the labeled PEI had minimal uptake. DOTA-PEI was prepared and contained an average of 16 chelates per PEI; the compound was radio-labeled with 149Promethium and conjugated to Trastuzumab. The purified 149Pm-DOTA-PEI-Trastuzumab had a radiochemical purity of 96.7% and a specific activity of 0.118 TBq/g. The compound demonstrated a dissociation constant for the Her2/neu receptor of 20.30 ± 6.91 nM. In conclusion, the results indicate the DOTA-PEI-Trastuzumab compound has potential as a targeted therapeutic carrier, and future in vivo studies should be performed.« less

On the potential of laser driven isotope generation at ELI-NP for positron emission tomography

NASA Astrophysics Data System (ADS)

Cucoanes, A. S.; Balabanski, D. L.; Canova, F.; Cuong, P.; Negoita, F.; Puicea, F.; Tanaka, K. A.

2017-05-01

The huge progress made in the laser driven ion acceleration had open the possibility of using ions generated in high power laser interactions with solid targets for the production of medical isotopes. Indeed, lasers could provide several key features with respect to the traditional method where the target activation is produced by particle beams delivered by cyclotrons. The price and the dimensions of high power lasers are on a descendant slope and the quality of the produced ion beams is continuously increasing. However, in order to compete with cyclotrons, the average proton current intensity has to be increased for example by increasing the frequency of the laser pulses. In our contribution, we review the general ideas of the laser-based radioisotope production and we present our analysis on the potential of the medical isotope generation at ELI-NP with a focus on 18F. We use estimations of the proton beam parameters and a code implemented in Geant4 for computing the yield of the main production channel taking into account the experimental conditions available soon at ELI-NP. The obtained results are compatible with previous studies and will be verified by experiments foreseen at the future ELI-NP facility, under construction now in Magurele, Romania.

Find Pairs: The Module for Protein Quantification of the PeakQuant Software Suite

PubMed Central

Eisenacher, Martin; Kohl, Michael; Wiese, Sebastian; Hebeler, Romano; Meyer, Helmut E.

2012-01-01

Abstract Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data. For demonstrating the high applicability of FindPairs, we focused on the quantitative analysis of proteome data acquired in 14N/15N labeling experiments. We further provide a comprehensive overview of the features of the FindPairs software, and compare these with existing quantification packages. The software presented here supports a wide range of proteomics applications, allowing one to quantitatively assess data derived from different stable isotope labeling approaches, such as 14N/15N labeling, SILAC, and iTRAQ. The software is publicly available at http://www.medizinisches-proteom-center.de/software and free for academic use. PMID:22909347

Calculated differential and double differential cross section of DT neutron induced reactions on natural chromium (Cr)

NASA Astrophysics Data System (ADS)

Rajput, Mayank; Vala, Sudhirsinh; Srinivasan, R.; Abhangi, M.; Subhash, P. V.; Pandey, B.; Rao, C. V. S.; Bora, D.

2018-01-01

Chromium is an important alloying element of stainless steel (SS) and SS is the main constituent of structural material proposed for fusion reactors. Energy and double differential cross section data will be required to estimate nuclear responses in the materials used in fusion reactors. There are no experimental data of energy and double differential cross section, available for neutron induced reactions on natural chromium at 14 MeV neutron energy. In this study, energy and double differential cross section data of (n,p) and (n,α) reactions for all the stable isotopes of chromium have been estimated, using appropriate nuclear models in TALYS code. The cross section data of stable isotopes are later converted into the energy and double differential cross section data of natural Cr using the isotopic abundance. The contribution from compound, pre-equilibrium and direct nuclear reaction to total reaction have also been calculated for 52,50Cr(n,p) and 52Cr(n,α). The calculation of energy differential cross section shows that most of emitted protons and alpha particles are of 3 and 8 MeV respectively. The calculated data is compared with the data from EXFOR data library and is found to be in good agreement.

Pre-clinical evaluation of eight DOTA coupled gastrin-releasing peptide receptor (GRP-R) ligands for in vivo targeting of receptor-expressing tumors.

PubMed

Accardo, Antonella; Galli, Filippo; Mansi, Rosalba; Del Pozzo, Luigi; Aurilio, Michela; Morisco, Anna; Ringhieri, Paola; Signore, Alberto; Morelli, Giancarlo; Aloj, Luigi

2016-12-01

Overexpression of the gastrin-releasing peptide receptor (GRP-R) has been documented in several human neoplasms such as breast, prostate, and ovarian cancer. There is growing interest in developing radiolabeled peptide-based ligands toward these receptors for the purpose of in vivo imaging and radionuclide therapy of GRP-R-overexpressing tumors. A number of different peptide sequences, isotopes, and labeling methods have been proposed for this purpose. The aim of this work is to perform a direct side-by-side comparison of different GRP-R binding peptides utilizing a single labeling strategy to identify the most suitable peptide sequence. Solid-phase synthesis of eight derivatives (BN1-8) designed based on literature analysis was carried out. Peptides were coupled to the DOTA chelator through a PEG4 spacer at the N-terminus. Derivatives were characterized for serum stability, binding affinity on PC-3 human prostate cancer cells, biodistribution in tumor-bearing mice, and gamma camera imaging at 1, 6, and 24 h after injection. Serum stability was quite variable among the different compounds with half-lives ranging from 16 to 400 min at 37 °C. All compounds tested showed K d values in the nanomolar range with the exception of BN3 that showed no binding. Biodistribution and imaging studies carried out for compounds BN1, BN4, BN7, and BN8 showed targeting of the GRP-R-positive tumors and the pancreas. The BN8 compound (DOTA-PEG-DPhe-Gln-Trp-Ala-Val-NMeGly-His-Sta-Leu-NH2) showed high affinity, the longest serum stability, and the highest target-to-background ratios in biodistribution and imaging experiments among the compounds tested. Our results indicate that the NMeGly for Gly substitution and the Sta-Leu substitution at the C-terminus confer high serum stability while maintaining high receptor affinity, resulting in biodistribution properties that outperform those of the other peptides.

Role of Secondary Transporters and Phosphotransferase Systems in Glucose Transport by Oenococcus oeni ▿

PubMed Central

Kim, Ok Bin; Richter, Hanno; Zaunmüller, Tanja; Graf, Sabrina; Unden, Gottfried

2011-01-01

Glucose uptake by the heterofermentative lactic acid bacterium Oenococcus oeni B1 was studied at the physiological and gene expression levels. Glucose- or fructose-grown bacteria catalyzed uptake of [14C]glucose over a pH range from pH 4 to 9, with maxima at pHs 5.5 and 7. Uptake occurred in two-step kinetics in a high- and low-affinity reaction. The high-affinity uptake followed Michaelis-Menten kinetics and required energization. It accumulated the radioactivity of glucose by a factor of 55 within the bacteria. A large portion (about 80%) of the uptake of glucose was inhibited by protonophores and ionophores. Uptake of the glucose at neutral pH was not sensitive to degradation of the proton potential, Δp. Expression of the genes OEOE_0819 and OEOE_1574 (here referred to as 0819 and 1574), coding for secondary transporters, was induced by glucose as identified by quantitative real-time (RT)-PCR. The genes 1574 and 0819 were able to complement growth of a Bacillus subtilis hexose transport-deficient mutant on glucose but not on fructose. The genes 1574 and 0819 therefore encode secondary transporters for glucose, and the transports are presumably Δp dependent. O. oeni codes, in addition, for a phosphotransferase transport system (PTS) (gene OEOE_0464 [0464] for the permease) with similarity to the fructose- and mannose-specific PTS of lactic acid bacteria. Quantitative RT-PCR showed induction of the gene 0464 by glucose and by fructose. The data suggest that the PTS is responsible for Δp-independent hexose transport at neutral pH and for the residual Δp-independent transport of hexoses at acidic pH. PMID:22020640

External Guide Sequences Targeting the aac(6′)-Ib mRNA Induce Inhibition of Amikacin Resistance▿

PubMed Central

Bistué, Alfonso J. C. Soler; Ha, Hongphuc; Sarno, Renee; Don, Michelle; Zorreguieta, Angeles; Tolmasky, Marcelo E.

2007-01-01

The dissemination of AAC(6′)-I-type acetyltransferases have rendered amikacin and other aminoglycosides all but useless in some parts of the world. Antisense technologies could be an alternative to extend the life of these antibiotics. External guide sequences are short antisense oligoribonucleotides that induce RNase P-mediated cleavage of a target RNA by forming a precursor tRNA-like complex. Thirteen-nucleotide external guide sequences complementary to locations within five regions accessible for interaction with antisense oligonucleotides in the mRNA that encodes AAC(6′)-Ib were analyzed. While small variations in the location targeted by different external guide sequences resulted in big changes in efficiency of binding to native aac(6′)-Ib mRNA, most of them induced high levels of RNase P-mediated cleavage in vitro. Recombinant plasmids coding for selected external guide sequences were introduced into Escherichia coli harboring aac(6′)-Ib, and the transformant strains were tested to determine their resistance to amikacin. The two external guide sequences that showed the strongest binding efficiency to the mRNA in vitro, EGSC3 and EGSA2, interfered with expression of the resistance phenotype at different degrees. Growth curve experiments showed that E. coli cells harboring a plasmid coding for EGSC3, the external guide sequence with the highest mRNA binding affinity in vitro, did not grow for at least 300 min in the presence of 15 μg of amikacin/ml. EGSA2, which had a lower mRNA-binding affinity in vitro than EGSC3, inhibited the expression of amikacin resistance at a lesser level; growth of E. coli harboring a plasmid coding for EGSA2, in the presence of 15 μg of amikacin/ml was undetectable for 200 min but reached an optical density at 600 nm of 0.5 after 5 h of incubation. Our results indicate that the use of external guide sequences could be a viable strategy to preserve the efficacy of amikacin. PMID:17387154

Oceanization of the lithospheric mantle: the study case of the spinel peridotites from Monte Maggiore (Corsica, France).

NASA Astrophysics Data System (ADS)

Piccardo, G. B.

2009-04-01

The Monte Maggiore peridotite body, cropping out within the Alpine Corsica metamorphic belt, is an ophiolite massif derived from the more internal setting of the Jurassic Ligurian Tethys basin. It is mostly composed by spinel and plagioclase peridotites that are cut by MORB gabbroic dykes. The spinel peridotites, similarly to other ophiolitic peridotites from the Internal Ligurides, have been considered, on the basis of their low abundance of fusible components, low Si and high Mg contents, as refractory residua after MORB-type partial melting related to the formation of the Jurassic basin (e.g. Rampone et al., 1997). Recent studies (e.g. Müntener & Piccardo 2003; Rampone et al. 2008) have evidenced that these depleted spinel peridotites show diffuse melt-rock interaction micro-textures and contrasting bulk vs. mineral chemistry features which cannot be simply reconciled with partial melting. Accordingly, these peridotites have been recognized as reactive peridotites, formed by interaction of pristine peridotites with melts percolating by porous flow. Geochemical data have evidenced the depleted MORB signature of the percolating melts. Recent field studies at Monte Maggiore (Piccardo, 2007; Piccardo & Guarnieri, 2009), have revealed: 1) the presence and local abundance of pyroxenite-bearing, cpx-rich spinel lherzolites and 2) the replacement relationships of the reactive peridotites on the pyroxenite-bearing lherzolite rock-types. The pyroxenite-veined spinel lherzolites record a composite history of subsolidus evolution under lithospheric P-T conditions, thus indicating their provenance from the sub-continental lithospheric mantle. Accordingly, the pristine sub-continental mantle protoliths were infiltrated by MORB melts and transformed by melt-rock interaction to reactive spinel peridotites and refertilized by melt impregnation to plagioclase-enriched peridotites. Available isotopic data on the Mt. Maggiore spinel and plagioclase peridotites and gabbroic rocks (Rampone, 2004; Rampone et al., 2008; 2009) provide reliable geochronological informations (i.e. Sm-Nd cpx-plg-wr isochron ages and Sm-Nd model ages) and evidence that the whole mafic and ultramafic rocks show an overall Sm/Nd isotopic homogeneity. Cpx-plg-wr data from gabbroic dykes define internal isochrones yielding Jurassic ages (162+/-10 Ma and 159+/-15 Ma, respectively). The plg-cpx(-wr) isochrons for impregnated plagioclase peridotites yields age of 155+/-6 Ma. The initial ɛNd values (8.9-9.7) are indicative of a MORB affinity. Calculated DM model ages for both spinel and plagioclase peridotites point to a Late Jurassic age (150 Ma). Isotope ratios of cpx from spinel and plagioclase peridotites conform to the linear array defined by overall gabbroic rocks. The isotopic evidence from the melt-percolated, reactive and impregnated peridotites indicates that the pristine lithospheric mantle protoliths were isotopically homogenized by the melt-rock interaction during percolation/impregnation processes which erased any pre-existing isotopic signature. Moreover, the overall Sm/Nd isotopic homogeneity indicates that the asthenospheric mantle sources of the infiltrating melts were isotopically homogeneous. Accordingly, it is plausible that percolation and intrusion were operated by similar and coeval Late Jurassic MORB-type melts. In conclusion, petrologic and isotopic data allow to recognize that the extending sub-continental lithospheric mantle was infiltrated by Late Jurassic MORB melts, formed by asthenospheric decompression-induced partial melting during continental extension and rifting. Melt-peridotite interaction modified the compositional features of the lithospheric mantle and caused its isotopic resetting. Accordingly, the sub-continental lithospheric mantle underwent an "oceanization" process (i.e. isotope resetting to "oceanic" MORB signatures) during Late Jurassic times operated by asthenospheric MORB melts. Depending on the melt composition, the lithospheric level and the mode of melt-rock interaction, fertile peridotites from the sub-continental lithospheric mantle were transformed, concomitantly, to depleted spinel peridotites and refertilized plagioclase peridotites.

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

Preliminary Assessment of the Impact on Reactor Vessel dpa Rates Due to Installation of a Proposed Low Enriched Uranium (LEU) Core in the High Flux Isotope Reactor (HFIR)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Charles R.

2015-10-01

An assessment of the impact on the High Flux Isotope Reactor (HFIR) reactor vessel (RV) displacements-per-atom (dpa) rates due to operations with the proposed low enriched uranium (LEU) core described by Ilas and Primm has been performed and is presented herein. The analyses documented herein support the conclusion that conversion of HFIR to low-enriched uranium (LEU) core operations using the LEU core design of Ilas and Primm will have no negative impact on HFIR RV dpa rates. Since its inception, HFIR has been operated with highly enriched uranium (HEU) cores. As part of an effort sponsored by the National Nuclearmore » Security Administration (NNSA), conversion to LEU cores is being considered for future HFIR operations. The HFIR LEU configurations analyzed are consistent with the LEU core models used by Ilas and Primm and the HEU balance-of-plant models used by Risner and Blakeman in the latest analyses performed to support the HFIR materials surveillance program. The Risner and Blakeman analyses, as well as the studies documented herein, are the first to apply the hybrid transport methods available in the Automated Variance reduction Generator (ADVANTG) code to HFIR RV dpa rate calculations. These calculations have been performed on the Oak Ridge National Laboratory (ORNL) Institutional Cluster (OIC) with version 1.60 of the Monte Carlo N-Particle 5 (MCNP5) computer code.« less

Hardening neutron spectrum for advanced actinide transmutation experiments in the ATR.

PubMed

Chang, G S; Ambrosek, R G

2005-01-01

The most effective method for transmuting long-lived isotopes contained in spent nuclear fuel into shorter-lived fission products is in a fast neutron spectrum reactor. In the absence of a fast test reactor in the United States, initial irradiation testing of candidate fuels can be performed in a thermal test reactor that has been modified to produce a test region with a hardened neutron spectrum. Such a test facility, with a spectrum similar but somewhat softer than that of the liquid-metal fast breeder reactor (LMFBR), has been constructed in the INEEL's Advanced Test Reactor (ATR). The radial fission power distribution of the actinide fuel pin, which is an important parameter in fission gas release modelling, needs to be accurately predicted and the hardened neutron spectrum in the ATR and the LMFBR fast neutron spectrum is compared. The comparison analyses in this study are performed using MCWO, a well-developed tool that couples the Monte Carlo transport code MCNP with the isotope depletion and build-up code ORIGEN-2. MCWO analysis yields time-dependent and neutron-spectrum-dependent minor actinide and Pu concentrations and detailed radial fission power profile calculations for a typical fast reactor (LMFBR) neutron spectrum and the hardened neutron spectrum test region in the ATR. The MCWO-calculated results indicate that the cadmium basket used in the advanced fuel test assembly in the ATR can effectively depress the linear heat generation rate in the experimental fuels and harden the neutron spectrum in the test region.

Determination of the δ13C of dissolved inorganic carbon in water; RSIL lab code 1710

USGS Publications Warehouse

Singleton, Glenda L.; Revesz, Kinga; Coplen, Tyler B.

2012-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1710 is to present a method to determine the δ13C of dissolved inorganic carbon (DIC) of water. The DIC of water is precipitated using ammoniacal strontium chloride (SrCl2) solution to form strontium carbonate (SrCO3). The δ13C is analyzed by reacting SrCO3 with 100-percent phosphoric acid (H3PO4) to liberate carbon quantitatively as carbon dioxide (CO2), which is collected, purified by vacuum sublimation, and analyzed by dual inlet isotope-ratio mass spectrometry (DI-IRMS). The DI-IRMS is a DuPont double-focusing mass spectrometer. One ion beam passes through a slit in a forward collector and is collected in the rear collector. The other measurable ion beams are collected in the front collector. By changing the ion-accelerating voltage under computer control, the instrument is capable of measuring mass/charge (m/z) 45 or 46 in the rear collector and m/z 44 and 46 or 44 and 45, respectively, in the front collector. The ion beams from these m/z values are as follows: m/z 44 = CO2 = 12C16O16O, m/z 45 = CO2 = 13C16O16O primarily, and m/z 46 = CO2 = 12C16O18O primarily. The data acquisition and control software calculates δ13C values.

Modelling of the Gadolinium Fuel Test IFA-681 using the BISON Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pastore, Giovanni; Hales, Jason Dean; Novascone, Stephen Rhead

2016-05-01

In this work, application of Idaho National Laboratory’s fuel performance code BISON to modelling of fuel rods from the Halden IFA-681 gadolinium fuel test is presented. First, an overview is given of BISON models, focusing on UO2/UO2-Gd2O3 fuel and Zircaloy cladding. Then, BISON analyses of selected fuel rods from the IFA-681 test are performed. For the first time in a BISON application to integral fuel rod simulations, the analysis is informed by detailed neutronics calculations in order to accurately capture the radial power profile throughout the fuel, which is strongly affected by the complex evolution of absorber Gd isotopes. Inmore » particular, radial power profiles calculated at IFE–Halden Reactor Project with the HELIOS code are used. The work has been carried out in the frame of the collaboration between Idaho National Laboratory and Halden Reactor Project. Some slide have been added as an Appendix to present the newly developed PolyPole-1 algorithm for modeling of intra-granular fission gas release.« less

Characterization of an AtCCX5 gene from Arabidopsis thaliana that involves in high-affinity K{sup +} uptake and Na{sup +} transport in yeast

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xinxin; Zhang, Min; Takano, Tetsuo

Highlights: {yields} The AtCCX5 protein coding a putative cation calcium exchanger was characterized. {yields} AtCCX5 expressed in yeast was localized in the plasma membrane and nuclear periphery. {yields} AtCCX5 protein did not show the same transport properties as the CAXs. {yields} AtCCX5 protein involves in mediating high-affinity K{sup +} uptake in yeast. {yields} AtCCX5 protein also involves in Na{sup +} transport in yeast. -- Abstract: The gene for a putative cation calcium exchanger (CCX) from Arabidopsis thaliana, AtCCX5, was cloned and its function was analyzed in yeast. Green fluorescent protein-tagged AtCCX5 expressed in yeast was localized in the plasma membranemore » and nuclear periphery. The yeast transformants expressing AtCCX5 were created and their growth in the presence of various cations (K{sup +}, Na{sup +}, Ca{sup 2+}, Mg{sup 2+}, Fe{sup 2+}, Cu{sup 2+}, Co{sup 2+}, Cd{sup 2+}, Mn{sup 2+}, Ba{sup 2+}, Ni{sup 2+}, Zn{sup 2+}, and Li{sup +}) were analyzed. AtCCX5 expression was found to affect the response to K{sup +} and Na{sup +} in yeast. The AtCCX5 transformant also showed a little better growth to Zn{sup 2+}. The yeast mutant 9.3 expressing AtCCX5 restored growth of the mutant on medium with low K{sup +} (0.5 mM), and also suppressed its Na{sup +} sensitivity. Ion uptake experiments showed that AtCCX5 mediated relatively high-affinity K{sup +} uptake and was also involved in Na{sup +} transport in yeast. Taken together, these findings suggest that the AtCCX5 is a novel transport protein involves in mediating high-affinity K{sup +} uptake and Na{sup +} transport in yeast.« less

Application of Strep-Tactin XT for affinity purification of Twin-Strep-tagged CB2, a G protein-coupled cannabinoid receptor.

PubMed

Yeliseev, Alexei; Zoubak, Lioudmila; Schmidt, Thomas G M

2017-03-01

Human cannabinoid receptor CB 2 belongs to the class A of G protein-coupled receptor (GPCR). CB 2 is predominantly expressed in membranes of cells of immune origin and is implicated in regulation of metabolic pathways of inflammation, neurodegenerative disorders and pain sensing. High resolution structural studies of CB 2 require milligram quantities of purified, structurally intact protein. While we previously reported on the methodology for expression of the recombinant CB 2 and its stabilization in a functional state, here we describe an efficient protocol for purification of this protein using the Twin-Strep-tag/Strep-Tactin XT system. To improve the affinity of interaction of the recombinant CB 2 with the resin, the double repeat of the Strep-tag (a sequence of eight amino acids WSHPQFEK), named the Twin-Strep-tag was attached either to the N- or C-terminus of CB 2 via a short linker, and the recombinant protein was expressed in cytoplasmic membranes of E. coli as a fusion with the N-terminal maltose binding protein (MBP). The CB 2 was isolated at high purity from dilute solutions containing high concentrations of detergents, glycerol and salts, by capturing onto the Strep-Tactin XT resin, and was eluted from the resin under mild conditions upon addition of biotin. Surface plasmon resonance studies performed on the purified protein demonstrate the high affinity of interaction between the Twin-Strep-tag fused to the CB 2 and Strep-Tactin XT with an estimated Kd in the low nanomolar range. The affinity of binding did not vary significantly in response to the position of the tag at either N- or C-termini of the fusion. The binding capacity of the resin was several-fold higher for the tag located at the N-terminus of the protein as opposed to the C-terminus- or middle of the fusion. The variation in the length of the linker between the double repeats of the Strep-tag from 6 to 12 amino acid residues did not significantly affect the binding. The novel purification protocol reported here enables efficient isolation of a recombinant GPCR expressed at low titers in host cells. This procedure is suitable for preparation of milligram quantities of stable isotope-labelled receptor for high-resolution NMR studies. Published by Elsevier Inc.

Equilibrium cycle pin by pin transport depletion calculations with DeCART

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kochunas, B.; Downar, T.; Taiwo, T.

As the Advanced Fuel Cycle Initiative (AFCI) program has matured it has become more important to utilize more advanced simulation methods. The work reported here was performed as part of the AFCI fellowship program to develop and demonstrate the capability of performing high fidelity equilibrium cycle calculations. As part of the work here, a new multi-cycle analysis capability was implemented in the DeCART code which included modifying the depletion modules to perform nuclide decay calculations, implementing an assembly shuffling pattern description, and modifying iteration schemes. During the work, stability issues were uncovered with respect to converging simultaneously the neutron flux,more » isotopics, and fluid density and temperature distributions in 3-D. Relaxation factors were implemented which considerably improved the stability of the convergence. To demonstrate the capability two core designs were utilized, a reference UOX core and a CORAIL core. Full core equilibrium cycle calculations were performed on both cores and the discharge isotopics were compared. From this comparison it was noted that the improved modeling capability was not drastically different in its prediction of the discharge isotopics when compared to 2-D single assembly or 2-D core models. For fissile isotopes such as U-235, Pu-239, and Pu-241 the relative differences were 1.91%, 1.88%, and 0.59%), respectively. While this difference may not seem large it translates to mass differences on the order of tens of grams per assembly, which may be significant for the purposes of accounting of special nuclear material. (authors)« less

Precise U and Pu isotope ratio measurements in nuclear samples by hyphenating capillary electrophoresis and MC-ICPMS.

PubMed

Martelat, Benoit; Isnard, Helene; Vio, Laurent; Dupuis, Erwan; Cornet, Terence; Nonell, Anthony; Chartier, Frederic

2018-06-22

Precise isotopic and elemental characterization of spent nuclear fuel is a major concern for the validation of the neutronic calculation codes and waste management strategy in the nuclear industry. Generally, the elements of interest, particularly U and Pu which are the two major elements present in spent fuel, are purified by ion exchange or extractant resins before off-line measurements by thermal ionization mass spectrometry. The aim of the present work was to develop a new analytical approach based on capillary electrophoresis (CE) hyphenated to a multicollector inductively coupled plasma mass spectrometer (MC-ICPMS) for online isotope ratio measurements. An electrophoretic separation protocol of U, Pu and the fraction containing fission products and minor actinides (Am and Cm) was developed using acetic acid as the electrolyte and complexing agent. The instrumentation for CE was designed to be used in a glove box and a laboratory-built interface was developed for hyphenation with MC-ICPMS. The separation was realized with only a few nL of a solution of spent nuclear fuel and the reproducibilities obtained on the U and Pu isotope ratios were on the order of a few ‰ which is comparable to those obtained by thermal ionization mass spectrometer (TIMS). This innovative protocol allowed a tremendous reduction of the analyte masses from μg to ng and also a drastic reduction of the liquid waste production from mL to μL. In addition, the time of analysis was shorted by at least a factor three. All of these improved parameters are of major interest for nuclear applications.

Direct Identification of On-Bead Peptides Using Surface-Enhanced Raman Spectroscopic Barcoding System for High-Throughput Bioanalysis

PubMed Central

Kang, Homan; Jeong, Sinyoung; Koh, Yul; Geun Cha, Myeong; Yang, Jin-Kyoung; Kyeong, San; Kim, Jaehi; Kwak, Seon-Yeong; Chang, Hye-Jin; Lee, Hyunmi; Jeong, Cheolhwan; Kim, Jong-Ho; Jun, Bong-Hyun; Kim, Yong-Kweon; Hong Jeong, Dae; Lee, Yoon-Sik

2015-01-01

Recently, preparation and screening of compound libraries remain one of the most challenging tasks in drug discovery, biomarker detection, and biomolecular profiling processes. So far, several distinct encoding/decoding methods such as chemical encoding, graphical encoding, and optical encoding have been reported to identify those libraries. In this paper, a simple and efficient surface-enhanced Raman spectroscopic (SERS) barcoding method using highly sensitive SERS nanoparticles (SERS ID) is presented. The 44 kinds of SERS IDs were able to generate simple codes and could possibly generate more than one million kinds of codes by incorporating combinations of different SERS IDs. The barcoding method exhibited high stability and reliability under bioassay conditions. The SERS ID encoding based screening platform can identify the peptide ligand on the bead and also quantify its binding affinity for specific protein. We believe that our SERS barcoding technology is a promising method in the screening of one-bead-one-compound (OBOC) libraries for drug discovery. PMID:26017924

Direct identification of on-bead peptides using surface-enhanced Raman spectroscopic barcoding system for high-throughput bioanalysis.

PubMed

Kang, Homan; Jeong, Sinyoung; Koh, Yul; Geun Cha, Myeong; Yang, Jin-Kyoung; Kyeong, San; Kim, Jaehi; Kwak, Seon-Yeong; Chang, Hye-Jin; Lee, Hyunmi; Jeong, Cheolhwan; Kim, Jong-Ho; Jun, Bong-Hyun; Kim, Yong-Kweon; Hong Jeong, Dae; Lee, Yoon-Sik

2015-05-28

Recently, preparation and screening of compound libraries remain one of the most challenging tasks in drug discovery, biomarker detection, and biomolecular profiling processes. So far, several distinct encoding/decoding methods such as chemical encoding, graphical encoding, and optical encoding have been reported to identify those libraries. In this paper, a simple and efficient surface-enhanced Raman spectroscopic (SERS) barcoding method using highly sensitive SERS nanoparticles (SERS ID) is presented. The 44 kinds of SERS IDs were able to generate simple codes and could possibly generate more than one million kinds of codes by incorporating combinations of different SERS IDs. The barcoding method exhibited high stability and reliability under bioassay conditions. The SERS ID encoding based screening platform can identify the peptide ligand on the bead and also quantify its binding affinity for specific protein. We believe that our SERS barcoding technology is a promising method in the screening of one-bead-one-compound (OBOC) libraries for drug discovery.

Reversible RNA adenosine methylation in biological regulation

PubMed Central

Jia, Guifang; Fu, Ye; He, Chuan

2012-01-01

N6-methyladenosine (m6A) is a ubiquitous modification in messenger RNA (mRNA) and other RNAs across most eukaryotes. For many years, however, the exact functions of m6A were not clearly understood. The discovery that the fat mass and obesity associated protein (FTO) is an m6A demethylase indicates that this modification is reversible and dynamically regulated, suggesting it has regulatory roles. In addition, it has been shown that m6A affects cell fate decisions in yeast and plant development. Recent affinity-based m6A profiling in mouse and human cells further showed that this modification is a widespread mark in coding and non-coding RNA transcripts and is likely dynamically regulated throughout developmental processes. Therefore, reversible RNA methylation, analogous to reversible DNA and histone modifications, may affect gene expression and cell fate decisions by modulating multiple RNA-related cellular pathways, which potentially provides rapid responses to various cellular and environmental signals, including energy and nutrient availability in mammals. PMID:23218460

GW100: Benchmarking G0W0 for Molecular Systems.

PubMed

van Setten, Michiel J; Caruso, Fabio; Sharifzadeh, Sahar; Ren, Xinguo; Scheffler, Matthias; Liu, Fang; Lischner, Johannes; Lin, Lin; Deslippe, Jack R; Louie, Steven G; Yang, Chao; Weigend, Florian; Neaton, Jeffrey B; Evers, Ferdinand; Rinke, Patrick

2015-12-08

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW. The use of these three codes allows for a quantitative comparison of the type of basis set (plane wave or local orbital) and handling of unoccupied states, the treatment of core and valence electrons (all electron or pseudopotentials), the treatment of the frequency dependence of the self-energy (full frequency or more approximate plasmon-pole models), and the algorithm for solving the quasi-particle equation. Primary results include reference values for future benchmarks, best practices for convergence within a particular approach, and average error bars for the most common approximations.

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

PubMed

Liberek, K; Osipiuk, J; Zylicz, M; Ang, D; Skorko, J; Georgopoulos, C

1990-02-25

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.

PubMed

Zhou, X Edward; He, Yuanzheng; de Waal, Parker W; Gao, Xiang; Kang, Yanyong; Van Eps, Ned; Yin, Yanting; Pal, Kuntal; Goswami, Devrishi; White, Thomas A; Barty, Anton; Latorraca, Naomi R; Chapman, Henry N; Hubbell, Wayne L; Dror, Ron O; Stevens, Raymond C; Cherezov, Vadim; Gurevich, Vsevolod V; Griffin, Patrick R; Ernst, Oliver P; Melcher, Karsten; Xu, H Eric

2017-07-27

G protein-coupled receptors (GPCRs) mediate diverse signaling in part through interaction with arrestins, whose binding promotes receptor internalization and signaling through G protein-independent pathways. High-affinity arrestin binding requires receptor phosphorylation, often at the receptor's C-terminal tail. Here, we report an X-ray free electron laser (XFEL) crystal structure of the rhodopsin-arrestin complex, in which the phosphorylated C terminus of rhodopsin forms an extended intermolecular β sheet with the N-terminal β strands of arrestin. Phosphorylation was detected at rhodopsin C-terminal tail residues T336 and S338. These two phospho-residues, together with E341, form an extensive network of electrostatic interactions with three positively charged pockets in arrestin in a mode that resembles binding of the phosphorylated vasopressin-2 receptor tail to β-arrestin-1. Based on these observations, we derived and validated a set of phosphorylation codes that serve as a common mechanism for phosphorylation-dependent recruitment of arrestins by GPCRs. Copyright © 2017 Elsevier Inc. All rights reserved.

Scale-4 Analysis of Pressurized Water Reactor Critical Configurations: Volume 2-Sequoyah Unit 2 Cycle 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowman, S.M.

1995-01-01

The requirements of ANSI/ANS 8.1 specify that calculational methods for away-from-reactor criticality safety analyses be validated against experimental measurements. If credit for the negative reactivity of the depleted (or spent) fuel isotopics is desired, it is necessary to benchmark computational methods against spent fuel critical configurations. This report summarizes a portion of the ongoing effort to benchmark away-from-reactor criticality analysis methods using critical configurations from commercial pressurized-water reactors. The analysis methodology selected for all the calculations reported herein is based on the codes and data provided in the SCALE-4 code system. The isotopic densities for the spent fuel assemblies inmore » the critical configurations were calculated using the SAS2H analytical sequence of the SCALE-4 system. The sources of data and the procedures for deriving SAS2H input parameters are described in detail. The SNIKR code module was used to extract the necessary isotopic densities from the SAS2H results and provide the data in the format required by the SCALE criticality analysis modules. The CSASN analytical sequence in SCALE-4 was used to perform resonance processing of the cross sections. The KENO V.a module of SCALE-4 was used to calculate the effective multiplication factor (k{sub eff}) of each case. The SCALE-4 27-group burnup library containing ENDF/B-IV (actinides) and ENDF/B-V (fission products) data was used for all the calculations. This volume of the report documents the SCALE system analysis of three reactor critical configurations for the Sequoyah Unit 2 Cycle 3. This unit and cycle were chosen because of the relevance in spent fuel benchmark applications: (1) the unit had a significantly long downtime of 2.7 years during the middle of cycle (MOC) 3, and (2) the core consisted entirely of burned fuel at the MOC restart. The first benchmark critical calculation was the MOC restart at hot, full-power (HFP) critical conditions. The other two benchmark critical calculations were the beginning-of-cycle (BOC) startup at both hot, zero-power (HZP) and HFP critical conditions. These latter calculations were used to check for consistency in the calculated results for different burnups and downtimes. The k{sub eff} results were in the range of 1.00014 to 1.00259 with a standard deviation of less than 0.001.« less

Chromium and titanium isotopes produced in photonuclear reactions of vanadium, revisited

NASA Astrophysics Data System (ADS)

Sakamoto, K.; Yoshida, M.; Kubota, Y.; Fukasawa, T.; Kunugise, A.; Hamajima, Y.; Shibata, S.; Fujiwara, I.

1989-10-01

Photonuclear production yields of 51Ti und 51,49,48Cr from 51V were redetermined for bremsstrahlung end-point energies ( E0) of 30 to 1000 or 1050 MeV with the aid of radiochemical separation of Cr. The yield curves for 51Ti, 51Cr, 49Cr and 48Cr show a clear evidence for two components in the production process; one tor secondary-proton reactions at E0 < Qπ and the other for photopion reactions, at E0 > Q, Qπ being Q-values for (γ, π +) and ( γ, π+xn) reactions. The contributions of the secondary reactions for production of the Ti and Cr isotopes at E0 > Qπ were then estimated by fitting calculated secondary yields to the observed ones at E0 < Qπ, and found to be about 40%, 20%, 4% and 4% for 51Ti, 51Cr, 49Cr and 48Cr, respectively, at E0 = 400 to 1000 MeV. The calculation of the secondary yields was based on the excitation functions for 51V(n, p) and (p, x'n) calculated with the ALICE code and the reported photoneutron and photoproton spectra from 12C and some other complex nuclei. The present results for 49Cr are close to the reported ones, while the present 48Cr yields differ by a factor of about 50. For the 51Ti and 51Cr yields, there are some discrepancies between the present and reported ones. The yield corrected for the secondaries, in units of μb/equivalent quantum, were unfolded into cross sections per photon, in units of μb, as a function ol monochromatic photon energy with the LOUHI-82 code. The results for the 51Ti and 49Cr are in disagreement in both the magnitude and shape with the theoretical predictions based on DWIA and PWIA. A Monte Carlo calculation based on the PICA code by Gabriel and Alsmiller does reproduce the gross feature of the present results.

Single-tube, non-isotopic, multiplex PCR/OLA assay and sequence-coded separation for simultaneous screening of 31 cystic fibrosis mutations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brinson, E.C.; Adriano, T.; Bloch, W.

1994-09-01

We have developed a rapid, single-tube, non-isotopic assay that screens a patient sample for the presence of 31 cystic fibrosis (CF) mutations. This assay can identify these mutations in a single reaction tube and a single electrophoresis run. Sample preparation is a simple, boil-and-go procedure, completed in less than an hour. The assay is composed of a 15-plex PCR, followed by a 61-plex oligonucleotide ligation assay (OLA), and incorporates a novel detection scheme, Sequence Coded Separation. Initially, the multiplex PCR amplifies 15 relevant segments of the CFTR gene, simultaneously. These PCR amplicons serve as templates for the multiplex OLA, whichmore » detects the normal or mutant allele at all loci, simultaneously. Each polymorphic site is interrogated by three oligonucleotide probes, a common probe and two allele-specific probes. Each common probe is tagged with a fluorescent dye, and the competing normal and mutant allelic probes incorporate different, non-nucleotide, mobility modifiers. These modifiers are composed of hexaethylene oxide (HEO) units, incorporated as HEO phosphoramidite monomers during automated DNA synthesis. The OLA is based on both probe hybridization and the ability of DNA ligase to discriminate single base mismatches at the junction between paired probes. Each single tube assay is electrophoresed in a single gel lane of a 4-color fluorescent DNA sequencer (Applied Biosystems, Model 373A). Each of the ligation products is identified by its unique combination of electrophoretic mobility and one of three colors. The fourth color is reserved for the in-lane size standard, used by GENESCAN{sup TM} software (Applied Biosystems) to size the OLA electrophoresis products. The Genotyper{sub TM} software (Applied Biosystems) decodes these Sequence-Coded-Separation data to create a patient summary report for all loci tested.« less

Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle

PubMed Central

Zhang, Youjun; Beard, Katherine F. M.; Swart, Corné; Bergmann, Susan; Krahnert, Ina; Nikoloski, Zoran; Graf, Alexander; Ratcliffe, R. George; Sweetlove, Lee J.; Fernie, Alisdair R.; Obata, Toshihiro

2017-01-01

Protein complexes of sequential metabolic enzymes, often termed metabolons, may permit direct channelling of metabolites between the enzymes, providing increased control over metabolic pathway fluxes. Experimental evidence supporting their existence in vivo remains fragmentary. In the present study, we test binary interactions of the proteins constituting the plant tricarboxylic acid (TCA) cycle. We integrate (semi-)quantitative results from affinity purification-mass spectrometry, split-luciferase and yeast-two-hybrid assays to generate a single reliability score for assessing protein–protein interactions. By this approach, we identify 158 interactions including those between catalytic subunits of sequential enzymes and between subunits of enzymes mediating non-adjacent reactions. We reveal channelling of citrate and fumarate in isolated potato mitochondria by isotope dilution experiments. These results provide evidence for a functional TCA cycle metabolon in plants, which we discuss in the context of contemporary understanding of this pathway in other kingdoms. PMID:28508886

Comparison of three quantitative phosphoproteomic strategies to study receptor tyrosine kinase signaling.

PubMed

Zhang, Guoan; Neubert, Thomas A

2011-12-02

There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or immobilized metal affinity chromatography; (2) phosphotyrosine sites following anti- phosphotyrosine antibody enrichment of phosphotyrosine peptides; or (3) phosphotyrosine proteins and their binding partners following anti-phosphotyrosine protein immunoprecipitation. However, it is not clear from literature which strategy is more effective. In this study, we assessed the utility of these three phosphoproteomic strategies in RTK signaling studies by using EphB receptor signaling as an example. We used all three strategies with stable isotope labeling with amino acids in cell culture (SILAC) to compare changes in phosphoproteomes upon EphB receptor activation. We used bioinformatic analysis to compare results from the three analyses. Our results show that the three strategies provide complementary information about RTK pathways.

Basal Adare volcanics, Robertson Bay, North Victoria Land, Antarctica: Late Miocene intraplate basalts of subaqueous origin

USGS Publications Warehouse

Mortimer, N.; Dunlap, W.J.; Isaac, M.J.; Sutherland, R.P.; Faure, K.

2007-01-01

Late Cenozoic lavas and associated hyaloclastite breccias of the Adare volcanics (Hallett volcanic province) in Robertson Bay, North Victoria Land rest unconformably on Paleozoic greywackes. Abundant hyaloclastite breccias are confined to a paleovalley; their primary geological features, and the stable isotope ratios of secondary minerals, are consistent with eruption in a subaqueous environment with calcite formation probably involving seawater. In contrast, the lavas which stratigraphically overlie the hyaloclastites on Mayr Spur probably were erupted subaerially. K-Ar dating of eight samples from this basal sequence confirms the known older age limit (Late Miocene) of the Hallett volcanic province. Geochemical data reveal an ocean island basalt-like affinity, similar to other Cenozoic igneous rocks of the Hallett volcanic province. If a submarine eruptive paleoenvironment is accepted then there has been net tectonic or isostatic post-Late Miocene uplift of a few hundred metres in the Robertson Bay-Adare Peninsula area

The late Cretaceous Arman flora of Magadan oblast, Northeastern Russia

NASA Astrophysics Data System (ADS)

Herman, A. B.; Golovneva, L. B.; Shczepetov, S. V.; Grabovsky, A. A.

2016-12-01

The Arman flora from the volcanogenic-sedimentary beds of the Arman Formation is systematically studied using materials from the Arman River basin and the Nelkandya-Khasyn interfluve (Magadan oblast, Northeastern Russia). Seventy-three species of fossil plants belonging to 49 genera are described. They consist of liverworts, horsetails, ferns, seed ferns, cycadaleans, bennettitaleans, ginkgoaleans, czekanowskialeans, conifers, gymnosperms of uncertain systematic affinity, and angiosperms. The Arman flora shows a unique combination, with relatively ancient Early Cretaceous ferns and gymnosperms occurring alongside younger Late Cretaceous plants, primarily angiosperms. The similarity of the Arman flora to the Penzhina and Kaivayam floras of northwestern Kamchatka and the Tylpegyrgynai flora of the Pekul'nei Ridge allows the Arman flora to be dated as Turonian and Coniacian (Late Cretaceous), which is corroborated by isotopic (U-Pb and 40Ar/39Ar) age determination for the plant-bearing layers.

Mercury dilution by autochthonous organic matter in a fertilized mangrove wetland.

PubMed

Machado, Wilson; Sanders, Christian J; Santos, Isaac R; Sanders, Luciana M; Silva-Filho, Emmanoel V; Luiz-Silva, Wanilson

2016-06-01

A dated sediment core from a highly-fertilized mangrove wetland located in Cubatão (SE Brazil) presented a negative correlation between mercury (Hg) and organic carbon contents. This is an unusual result for a metal with well-known affinity to organic matter. A dilution of Hg concentrations by autochthonous organic matter explained this observation, as revealed by carbon stable isotopes signatures (δ(13)C). Mercury dilution by the predominant mangrove-derived organic matter counterbalanced the positive influences of algal-derived organic matter and clay contents on Hg levels, suggesting that deleterious effects of Hg may be attenuated. Considering the current paradigm on the positive effect of organic matter on Hg concentrations in coastal sediments and the expected increase in mangrove organic matter burial due to natural and anthropogenic stimulations of primary production, predictions on the influences of organic matter on Hg accumulation in mangrove wetlands deserve caution. Copyright © 2016 Elsevier Ltd. All rights reserved.

Production mechanism of new neutron-rich heavy nuclei in the 136Xe +198Pt reaction

NASA Astrophysics Data System (ADS)

Li, Cheng; Wen, Peiwei; Li, Jingjing; Zhang, Gen; Li, Bing; Xu, Xinxin; Liu, Zhong; Zhu, Shaofei; Zhang, Feng-Shou

2018-01-01

The multinucleon transfer reaction of 136Xe +198Pt at Elab = 7.98 MeV/nucleon is investigated by using the improved quantum molecular dynamics model. The quasielastic, deep-inelastic, and quasifission collision mechanisms are studied via analyzing the angular distributions of fragments and the energy dissipation processes during the collisions. The measured isotope production cross sections of projectile-like fragments are reasonably well reproduced by the calculation of the ImQMD model together with the GEMINI code. The isotope production cross sections for the target-like fragments and double differential cross sections of 199Pt, 203Pt, and 208Pt are calculated. It is shown that about 50 new neutron-rich heavy nuclei can be produced via deep-inelastic collision mechanism, where the production cross sections are from 10-3 to 10-6 mb. The corresponding emission angle and the kinetic energy for these new neutron-rich nuclei locate at 40∘-60∘ and 100-200 MeV, respectively.

Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium.

PubMed

Plaga, W; Lottspeich, F; Oesterhelt, D

1992-04-01

An improved purification procedure, including nickel chelate affinity chromatography, is reported which resulted in a crystallizable pyruvate:ferredoxin oxidoreductase preparation from Halobacterium halobium. Crystals of the enzyme were obtained using potassium citrate as the precipitant. The genes coding for pyruvate:ferredoxin oxidoreductase were cloned and their nucleotide sequences determined. The genes of both subunits were adjacent to one another on the halobacterial genome. The derived amino acid sequences were confirmed by partial primary structure analysis of the purified protein. The structural motif of thiamin-diphosphate-binding enzymes was unequivocally located in the deduced amino acid sequence of the small subunit.

Cyborg lectins: novel leguminous lectins with unique specificities.

PubMed

Yamamoto, K; Maruyama, I N; Osawa, T

2000-01-01

Bauhinia purpurea lectin (BPA) is one of the beta-galactose-binding leguminous lectins. Leguminous lectins contain a long metal-binding loop, part of which determines their carbohydrate-binding specificities. Random mutations were introduced into a portion of the cDNA coding BPA that corresponds to the carbohydrate-binding loop of the lectin. An library of the mutant lectin expressed on the surface of lambda foo phages was screened by the panning method. Several phage clones with an affinity for mannose or N-acetylglucosamine were isolated. These results indicate the possibility of making artificial lectins (so-called "cyborg lectins") with distinct and desired carbohydrate-binding specificities.

Carbohydrate-dependent binding of langerin to SodC, a cell wall glycoprotein of Mycobacterium leprae.

PubMed

Kim, Hee Jin; Brennan, Patrick J; Heaslip, Darragh; Udey, Mark C; Modlin, Robert L; Belisle, John T

2015-02-01

Langerhans cells participate in the immune response in leprosy by their ability to activate T cells that recognize the pathogen, Mycobacterium leprae, in a langerin-dependent manner. We hypothesized that langerin, the distinguishing C-type lectin of Langerhans cells, would recognize the highly mannosylated structures in pathogenic Mycobacterium spp. The coding region for the extracellular and neck domain of human langerin was cloned and expressed to produce a recombinant active trimeric form of human langerin (r-langerin). Binding assays performed in microtiter plates, by two-dimensional (2D) Western blotting, and by surface plasmon resonance demonstrated that r-langerin possessed carbohydrate-dependent affinity to glycoproteins in the cell wall of M. leprae. This lectin, however, yielded less binding to mannose-capped lipoarabinomannan (ManLAM) and even lower levels of binding to phosphatidylinositol mannosides. However, the superoxide dismutase C (SodC) protein of the M. leprae cell wall was identified as a langerin-reactive ligand. Tandem mass spectrometry verified the glycosylation of a recombinant form of M. leprae SodC (rSodC) produced in Mycobacterium smegmatis. Analysis of r-langerin affinity by surface plasmon resonance revealed a carbohydrate-dependent affinity of rSodC (equilibrium dissociation constant [KD] = 0.862 μM) that was 20-fold greater than for M. leprae ManLAM (KD = 18.69 μM). These data strongly suggest that a subset of the presumptively mannosylated M. leprae glycoproteins act as ligands for langerin and may facilitate the interaction of M. leprae with Langerhans cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Carbohydrate-Dependent Binding of Langerin to SodC, a Cell Wall Glycoprotein of Mycobacterium leprae

PubMed Central

Kim, Hee Jin; Brennan, Patrick J.; Heaslip, Darragh; Udey, Mark C.; Modlin, Robert L.

2014-01-01

Langerhans cells participate in the immune response in leprosy by their ability to activate T cells that recognize the pathogen, Mycobacterium leprae, in a langerin-dependent manner. We hypothesized that langerin, the distinguishing C-type lectin of Langerhans cells, would recognize the highly mannosylated structures in pathogenic Mycobacterium spp. The coding region for the extracellular and neck domain of human langerin was cloned and expressed to produce a recombinant active trimeric form of human langerin (r-langerin). Binding assays performed in microtiter plates, by two-dimensional (2D) Western blotting, and by surface plasmon resonance demonstrated that r-langerin possessed carbohydrate-dependent affinity to glycoproteins in the cell wall of M. leprae. This lectin, however, yielded less binding to mannose-capped lipoarabinomannan (ManLAM) and even lower levels of binding to phosphatidylinositol mannosides. However, the superoxide dismutase C (SodC) protein of the M. leprae cell wall was identified as a langerin-reactive ligand. Tandem mass spectrometry verified the glycosylation of a recombinant form of M. leprae SodC (rSodC) produced in Mycobacterium smegmatis. Analysis of r-langerin affinity by surface plasmon resonance revealed a carbohydrate-dependent affinity of rSodC (equilibrium dissociation constant [KD] = 0.862 μM) that was 20-fold greater than for M. leprae ManLAM (KD = 18.69 μM). These data strongly suggest that a subset of the presumptively mannosylated M. leprae glycoproteins act as ligands for langerin and may facilitate the interaction of M. leprae with Langerhans cells. PMID:25422308

Cross Sections of the 36Ar(d,α)34mCl, 40Ar(d,α)38Cl and 40Ar(d,p)41Ar Nuclear Reactions below 8.4 MeV

PubMed Central

Engle, J W; Severin, G W; Barnhart, T E; Knutson, L D; Nickles, R J

2011-01-01

We have measured the cross section for production of the medically interesting isotope 34mCl, along with 38Cl and 41Ar, using deuteron bombardments of 36Ar and 40Ar below 8.4 MeV. ALICE/ASH analytical codes were employed to determine the shape of nuclear excitation functions, and experiments were performed using the University of Wisconsin tandem electrostatic accelerator to irradiate thin targets of argon gas. PMID:22041299

Calculation evaluation of multiplying properties of LWR with thorium fuel

NASA Astrophysics Data System (ADS)

Shamanin, I. V.; Grachev, V. M.; Knyshev, V. V.; Bedenko, S. V.; Novikova, N. G.

2017-01-01

The results of multiplying properties design research of the unit cell and LWR fuel assembly with the high temperature gas-cooled thorium reactor fuel pellet are presented in the work. The calculation evaluation showed the possibility of using thorium in LWR effectively. In this case the amount of fissile isotope is 2.45 times smaller in comparison with the standard loading of LWR. The research and numerical experiments were carried out using the verified accounting code of the program MCU5, modern libraries of evaluated nuclear data and multigroup approximations.

How high do ion fluxes go? A re-evaluation of the two-mechanism model of K(+) transport in plant roots.

PubMed

Coskun, Devrim; Britto, Dev T; Kochian, Leon V; Kronzucker, Herbert J

2016-02-01

Potassium (K(+)) acquisition in roots is generally described by a two-mechanism model, consisting of a saturable, high-affinity transport system (HATS) operating via H(+)/K(+) symport at low (<1mM) external [K(+)] ([K(+)]ext), and a linear, low-affinity system (LATS) operating via ion channels at high (>1mM) [K(+)]ext. Radiotracer measurements in the LATS range indicate that the linear rise in influx continues well beyond nutritionally relevant concentrations (>10mM), suggesting K(+) transport may be pushed to extraordinary, and seemingly limitless, capacity. Here, we assess this rise, asking whether LATS measurements faithfully report transmembrane fluxes. Using (42)K(+)-isotope and electrophysiological methods in barley, we show that this flux is part of a K(+)-transport cycle through the apoplast, and masks a genuine plasma-membrane influx that displays Michaelis-Menten kinetics. Rapid apoplastic cycling of K(+) is corroborated by an absence of transmembrane (42)K(+) efflux above 1mM, and by the efflux kinetics of PTS, an apoplastic tracer. A linear apoplastic influx, masking a saturating transmembrane influx, was also found in Arabidopsis mutants lacking the K(+) transporters AtHAK5 and AtAKT1. Our work significantly revises the model of K(+) transport by demonstrating a surprisingly modest upper limit for plasma-membrane influx, and offers insight into sodium transport under salt stress. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Differential 14-3-3 affinity capture reveals new downstream targets of phosphatidylinositol 3-kinase signaling.

PubMed

Dubois, Fanny; Vandermoere, Franck; Gernez, Aurélie; Murphy, Jane; Toth, Rachel; Chen, Shuai; Geraghty, Kathryn M; Morrice, Nick A; MacKintosh, Carol

2009-11-01

We devised a strategy of 14-3-3 affinity capture and release, isotope differential (d(0)/d(4)) dimethyl labeling of tryptic digests, and phosphopeptide characterization to identify novel targets of insulin/IGF1/phosphatidylinositol 3-kinase signaling. Notably four known insulin-regulated proteins (PFK-2, PRAS40, AS160, and MYO1C) had high d(0)/d(4) values meaning that they were more highly represented among 14-3-3-binding proteins from insulin-stimulated than unstimulated cells. Among novel candidates, insulin receptor substrate 2, the proapoptotic CCDC6, E3 ubiquitin ligase ZNRF2, and signaling adapter SASH1 were confirmed to bind to 14-3-3s in response to IGF1/phosphatidylinositol 3-kinase signaling. Insulin receptor substrate 2, ZNRF2, and SASH1 were also regulated by phorbol ester via p90RSK, whereas CCDC6 and PRAS40 were not. In contrast, the actin-associated protein vasodilator-stimulated phosphoprotein and lipolysis-stimulated lipoprotein receptor, which had low d(0)/d(4) scores, bound 14-3-3s irrespective of IGF1 and phorbol ester. Phosphorylated Ser(19) of ZNRF2 (RTRAYpS(19)GS), phospho-Ser(90) of SASH1 (RKRRVpS(90)QD), and phospho- Ser(493) of lipolysis-stimulated lipoprotein receptor (RPRARpS(493)LD) provide one of the 14-3-3-binding sites on each of these proteins. Differential 14-3-3 capture provides a powerful approach to defining downstream regulatory mechanisms for specific signaling pathways.

Differential 14-3-3 Affinity Capture Reveals New Downstream Targets of Phosphatidylinositol 3-Kinase Signaling*

PubMed Central

Dubois, Fanny; Vandermoere, Franck; Gernez, Aurélie; Murphy, Jane; Toth, Rachel; Chen, Shuai; Geraghty, Kathryn M.; Morrice, Nick A.; MacKintosh, Carol

2009-01-01

We devised a strategy of 14-3-3 affinity capture and release, isotope differential (d0/d4) dimethyl labeling of tryptic digests, and phosphopeptide characterization to identify novel targets of insulin/IGF1/phosphatidylinositol 3-kinase signaling. Notably four known insulin-regulated proteins (PFK-2, PRAS40, AS160, and MYO1C) had high d0/d4 values meaning that they were more highly represented among 14-3-3-binding proteins from insulin-stimulated than unstimulated cells. Among novel candidates, insulin receptor substrate 2, the proapoptotic CCDC6, E3 ubiquitin ligase ZNRF2, and signaling adapter SASH1 were confirmed to bind to 14-3-3s in response to IGF1/phosphatidylinositol 3-kinase signaling. Insulin receptor substrate 2, ZNRF2, and SASH1 were also regulated by phorbol ester via p90RSK, whereas CCDC6 and PRAS40 were not. In contrast, the actin-associated protein vasodilator-stimulated phosphoprotein and lipolysis-stimulated lipoprotein receptor, which had low d0/d4 scores, bound 14-3-3s irrespective of IGF1 and phorbol ester. Phosphorylated Ser19 of ZNRF2 (RTRAYpS19GS), phospho-Ser90 of SASH1 (RKRRVpS90QD), and phospho- Ser493 of lipolysis-stimulated lipoprotein receptor (RPRARpS493LD) provide one of the 14-3-3-binding sites on each of these proteins. Differential 14-3-3 capture provides a powerful approach to defining downstream regulatory mechanisms for specific signaling pathways. PMID:19648646

Fingerprints of the Paleotethyan back-arc basin in Central Hainan, South China: geochronological and geochemical constraints on the Carboniferous metabasites

NASA Astrophysics Data System (ADS)

He, Huiying; Wang, Yuejun; Zhang, Yanhua; Qian, Xin; Zhang, Yuzhi

2018-03-01

Hainan of Southeast Asia has been regarded as a key area for understanding the Late Paleozoic tectonic regime and amalgamation process of the Indochina with South China Blocks that are not well constrained. This paper presents a set of new geochronological, elemental, and Sr-Nd isotopic data for the Paleozoic Bangxi and Chenxing metabasites in Central Hainan. The geochronological data show that the representative samples yield the 40Ar/39Ar plateau age of 328.1 ± 2.6 Ma and zircon U-Pb age of 330.7 ± 4.4 Ma, respectively. They are SiO2- and TiO2-poor, Al2O3-rich mafic rocks. The Chenxing samples are characterized by left-sloping chondrite-normalized REE and N-MORB-like multi-elemental patterns. The Bangxi samples have the E-MORB-like geochemical affinity. All samples show high ɛ Nd(t) values ranging from +5.61 to +9.85. Such signatures suggest their origination of a MORB-like source with the input of subduction-derived components. Our investigation has verified the presence of the Carboniferous metabasites with both MORB- and arc- like geochemical affinities at the Bangxi-Chenxing area in Central Hainan. In combination with the available data from the Jinshajiang, Ailaoshan, and Song Ma suture zones, it is proposed for the development of a Carboniferous back-arc basin along the Ailaoshan-Song Ma and Central Hainan suture zones in response to the subduction of the Paleotethyan main Ocean.

Optimization of post-run corrections for water stable isotope measurements by laser spectroscopy

NASA Astrophysics Data System (ADS)

van Geldern, Robert; Barth, Johannes A. C.

2013-04-01

Light stable isotope analyses of hydrogen and oxygen of water are used in numerous aquatic studies from various scientific fields. The advantage of using stable isotope ratios is that water molecules serve as ubiquitous and already present natural tracers. Traditionally, the samples were analyzed in the laboratory by isotope ratio mass spectrometry (IRMS). Within recent years these analyses have been revolutionized by the development of new isotope ratio laser spectroscopy (IRIS) systems that are said to be cheaper, more robust and mobile compared to IRMS. Although easier to operate, laser systems also need thorough calibration with international reference materials and raw data need correction for analytical effects. A major issue in systems that use liquid injection via a vaporizer module is the memory effect, i.e. the carry-over from the previous analyzed sample in a sequence. This study presents an optimized and simple post-run correction procedure for liquid water injection developed for a Picarro water analyzer. The Excel(TM) template will rely exclusively on standard features implemented in MS Office without the need to run macros, additional code written in Visual Basic for Applications (VBA) or to use a database-related software such as MS Access or SQL Server. These protocols will maximize precision, accuracy and sample throughput via an efficient memory correction. The number of injections per unknown sample can be reduced to 4 or less. This procedure meets the demands of faster throughput with reduced costs per analysis. Procedures were verified by an international proficiency test and traditional IRMS techniques. The template is available free for scientific use from the corresponding author or the journals web site (van Geldern and Barth, 2012). References van Geldern, R. and Barth, J.A.C. (2012) Limnol. Oceanogr. Methods 10:1024-1036 [doi: 10.4319/lom.2012.10.1024

Impact investigation of reactor fuel operating parameters on reactivity for use in burnup credit applications

NASA Astrophysics Data System (ADS)

Sloma, Tanya Noel

When representing the behavior of commercial spent nuclear fuel (SNF), credit is sought for the reduced reactivity associated with the net depletion of fissile isotopes and the creation of neutron-absorbing isotopes, a process that begins when a commercial nuclear reactor is first operated at power. Burnup credit accounts for the reduced reactivity potential of a fuel assembly and varies with the fuel burnup, cooling time, and the initial enrichment of fissile material in the fuel. With regard to long-term SNF disposal and transportation, tremendous benefits, such as increased capacity, flexibility of design and system operations, and reduced overall costs, provide an incentive to seek burnup credit for criticality safety evaluations. The Nuclear Regulatory Commission issued Interim Staff Guidance 8, Revision 2 in 2002, endorsing burnup credit of actinide composition changes only; credit due to actinides encompasses approximately 30% of exiting pressurized water reactor SNF inventory and could potentially be increased to 90% if fission product credit were accepted. However, one significant issue for utilizing full burnup credit, compensating for actinide and fission product composition changes, is establishing a set of depletion parameters that produce an adequately conservative representation of the fuel's isotopic inventory. Depletion parameters can have a significant effect on the isotopic inventory of the fuel, and thus the residual reactivity. This research seeks to quantify the reactivity impact on a system from dominant depletion parameters (i.e., fuel temperature, moderator density, burnable poison rod, burnable poison rod history, and soluble boron concentration). Bounding depletion parameters were developed by statistical evaluation of a database containing reactor operating histories. The database was generated from summary reports of commercial reactor criticality data. Through depletion calculations, utilizing the SCALE 6 code package, several light water reactor assembly designs and in-core locations are analyzed in establishing a combination of depletion parameters that conservatively represent the fuel's isotopic inventory as an initiative to take credit for fuel burnup in criticality safety evaluations for transportation and storage of SNF.

2nd-order optical model of the isotopic dependence of heavy ion absorption cross sections for radiation transport studies

NASA Astrophysics Data System (ADS)

Cucinotta, Francis A.; Yan, Congchong; Saganti, Premkumar B.

2018-01-01

Heavy ion absorption cross sections play an important role in radiation transport codes used in risk assessment and for shielding studies of galactic cosmic ray (GCR) exposures. Due to the GCR primary nuclei composition and nuclear fragmentation leading to secondary nuclei heavy ions of charge number, Z with 3 ≤ Z ≥ 28 and mass numbers, A with 6 ≤ A ≥ 60 representing about 190 isotopes occur in GCR transport calculations. In this report we describe methods for developing a data-base of isotopic dependent heavy ion absorption cross sections for interactions. Calculations of a 2nd-order optical model solution to coupled-channel solutions to the Eikonal form of the nucleus-nucleus scattering amplitude are compared to 1st-order optical model solutions. The 2nd-order model takes into account two-body correlations in the projectile and target ground-states, which are ignored in the 1st-order optical model. Parameter free predictions are described using one-body and two-body ground state form factors for the isotopes considered and the free nucleon-nucleon scattering amplitude. Root mean square (RMS) matter radii for protons and neutrons are taken from electron and muon scattering data and nuclear structure models. We report on extensive comparisons to experimental data for energy-dependent absorption cross sections for over 100 isotopes of elements from Li to Fe interacting with carbon and aluminum targets. Agreement between model and experiments are generally within 10% for the 1st-order optical model and improved to less than 5% in the 2nd-order optical model in the majority of comparisons. Overall the 2nd-order optical model leads to a reduction in absorption compared to the 1st-order optical model for heavy ion interactions, which influences estimates of nuclear matter radii.

Remanent Activation in the Mini-SHINE Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Micklich, Bradley J.

2015-04-16

Argonne National Laboratory is assisting SHINE Medical Technologies in developing a domestic source of the medical isotope 99Mo through the fission of low-enrichment uranium in a uranyl sulfate solution. In Phase 2 of these experiments, electrons from a linear accelerator create neutrons by interacting in a depleted uranium target, and these neutrons are used to irradiate the solution. The resulting neutron and photon radiation activates the target, the solution vessels, and a shielded cell that surrounds the experimental apparatus. When the experimental campaign is complete, the target must be removed into a shielding cask, and the experimental components must bemore » disassembled. The radiation transport code MCNPX and the transmutation code CINDER were used to calculate the radionuclide inventories of the solution, the target assembly, and the shielded cell, and to determine the dose rates and shielding requirements for selected removal scenarios for the target assembly and the solution vessels.« less

Design of self-coded combinatorial libraries to facilitate direct analysis of ligands by mass spectrometry.

PubMed

Hughes, I

1998-09-24

The direct analysis of selected components from combinatorial libraries by sensitive methods such as mass spectrometry is potentially more efficient than deconvolution and tagging strategies since additional steps of resynthesis or introduction of molecular tags are avoided. A substituent selection procedure is described that eliminates the mass degeneracy commonly observed in libraries prepared by "split-and-mix" methods, without recourse to high-resolution mass measurements. A set of simple rules guides the choice of substituents such that all components of the library have unique nominal masses. Additional rules extend the scope by ensuring that characteristic isotopic mass patterns distinguish isobaric components. The method is applicable to libraries having from two to four varying substituent groups and can encode from a few hundred to several thousand components. No restrictions are imposed on the manner in which the "self-coded" library is synthesized or screened.

Generation of 238U Covariance Matrices by Using the Integral Data Assimilation Technique of the CONRAD Code

NASA Astrophysics Data System (ADS)

Privas, E.; Archier, P.; Bernard, D.; De Saint Jean, C.; Destouche, C.; Leconte, P.; Noguère, G.; Peneliau, Y.; Capote, R.

2016-02-01

A new IAEA Coordinated Research Project (CRP) aims to test, validate and improve the IRDF library. Among the isotopes of interest, the modelisation of the 238U capture and fission cross sections represents a challenging task. A new description of the 238U neutrons induced reactions in the fast energy range is within progress in the frame of an IAEA evaluation consortium. The Nuclear Data group of Cadarache participates in this effort utilizing the 238U spectral indices measurements and Post Irradiated Experiments (PIE) carried out in the fast reactors MASURCA (CEA Cadarache) and PHENIX (CEA Marcoule). Such a collection of experimental results provides reliable integral information on the (n,γ) and (n,f) cross sections. This paper presents the Integral Data Assimilation (IDA) technique of the CONRAD code used to propagate the uncertainties of the integral data on the 238U cross sections of interest for dosimetry applications.

Symmetry-Based Variance Reduction Applied to 60Co Teletherapy Unit Monte Carlo Simulations

NASA Astrophysics Data System (ADS)

Sheikh-Bagheri, D.

A new variance reduction technique (VRT) is implemented in the BEAM code [1] to specifically improve the efficiency of calculating penumbral distributions of in-air fluence profiles calculated for isotopic sources. The simulations focus on 60Co teletherapy units. The VRT includes splitting of photons exiting the source capsule of a 60Co teletherapy source according to a splitting recipe and distributing the split photons randomly on the periphery of a circle, preserving the direction cosine along the beam axis, in addition to the energy of the photon. It is shown that the use of the VRT developed in this work can lead to a 6-9 fold improvement in the efficiency of the penumbral photon fluence of a 60Co beam compared to that calculated using the standard optimized BEAM code [1] (i.e., one with the proper selection of electron transport parameters).

Development of a multispectral autoradiography using a coded aperture

NASA Astrophysics Data System (ADS)

Noto, Daisuke; Takeda, Tohoru; Wu, Jin; Lwin, Thet T.; Yu, Quanwen; Zeniya, Tsutomu; Yuasa, Tetsuya; Hiranaka, Yukio; Itai, Yuji; Akatsuka, Takao

2000-11-01

Autoradiography is a useful imaging technique to understand biological functions using tracers including radio isotopes (RI's). However, it is not easy to describe the distribution of different kinds of tracers simultaneously by conventional autoradiography using X-ray film or Imaging plate. Each tracer describes each corresponding biological function. Therefore, if we can simultaneously estimate distribution of different kinds of tracer materials, the multispectral autoradiography must be a quite powerful tool to better understand physiological mechanisms of organs. So we are developing a system using a solid state detector (SSD) with high energy- resolution. Here, we introduce an imaging technique with a coded aperture to get spatial and spectral information more efficiently. In this paper, the imaging principle is described, and its validity and fundamental property are discussed by both simulation and phantom experiments with RI's such as 201Tl, 99mTc, 67Ga, and 123I.

Archean recycled oceanic crust sampled in Azores lavas

NASA Astrophysics Data System (ADS)

Beguelin, P.; Bizimis, M.; Beier, C.; Turner, S.

2016-12-01

Azores lava compositions extend below the mantle array in ɛNd-ɛHf space and define the steepest slope of all plume provinces [1], but this pattern is largely controlled by low ɛHf lavas from Eastern São Miguel island (SM). Here we present new Hf isotope data on well-characterized on-land and submarine Azores lavas from several islands, the Terceira Rift and João do Castro seamount (JdC), in order to further constrain this trend. While Azores lavas fall along the mantle array with relatively steep slopes (e.g. São Jorge slope = 2.1), both SM and JdC fall below the mantle array as two distinct steep arrays with slopes of 2.0 and 2.6 respectively, extending to ɛHf = 0 at ɛNd = 2 (SM) and 4 (JdC). This is a unique feature in OIBs. The new Hf-Nd data overlaps the HIMU-type Mangaia and St Helena compositions. However, SM and JdC have distinctly less radiogenic and more variable Pb isotopes (e.g. 206Pb/204Pb = 18.8 to 20.2) than HIMU. Hf-Nd isotope decoupling below the mantle array is therefore not an exclusive HIMU signature. The coupled Hf-Nd-Pb-Sr isotope compositions of the enriched SM and JdC end-members can be modeled by recycled 2.5-3.0 Ga N-MORB, with some E-MORB affinity for SM. Unlike HIMU however, no Pb-loss during subduction is required for recycled MORB to explain their Pb isotopes. The relatively high κ (232Th/238U 4.3) required by the Azores data is also consistent with a high Th/U Archean mantle [2]. Aged, metasomatised mantle lithosphere based on a global peridotite and pyroxenite compilation is too variable and only fortuitously could explain the Azores compositions. Both enriched JdC and SM endmembers can therefore be explained by a recycled Archean oceanic crust that is locally heterogeneous, as presently observed in some MOR segments where N-and E-MORB exist closely [3, 4]. The lack of mixing between SM and JdC end-members some 100 km apart further implies that this recycled crust has retained its distinct signature through mantle convection and stirring for 2.5-3.0 Ga. [1] Salters et al. (2011) G3 12(8): Q08001. [2] Elliott et al. (1999) EPSL 169(1), 129-145. [3] Donnelly et al. (2004) EPSL 226(3), 347-366. [4] Gale et al. (2013) EPSL 365, 209-220.

Evolution of the lithospheric mantle beneath Mt. Baekdu (Changbaishan): Constraints from geochemical and Sr-Nd-Hf isotopic studies on peridotite xenoliths in trachybasalt

NASA Astrophysics Data System (ADS)

Park, Keunsu; Choi, Sung Hi; Cho, Moonsup; Lee, Der-Chuen

2017-08-01

Major and trace element compositions of minerals as well as Sr-Nd-Hf isotopic compositions of clinopyroxenes from spinel peridotite xenoliths entrained in Late Cenozoic trachybasalt from Mt. Baekdu (Changbaishan) were used to elucidate lithospheric mantle formation and evolution in the eastern North China Craton (NCC). The analyzed peridotites were mainly spinel lherzolites with rare harzburgites. They consisted of olivine (Fo89.3-91.0), enstatite (Wo1-2En88-90Fs8-11), diopside (Wo45-50En45-51Fs4-6), and spinel (Cr# = 8.8-54.7). The peridotite residues underwent up to 25% partial melting in fertile mid-ocean-ridge basalt (MORB) mantle. Plots of the Cr# in spinel against the Mg# in coexisting olivine or spinel suggested an affinity with abyssal peridotites. Comparisons of Cr# and TiO2 in spinel were also compatible with an abyssal peridotite-like composition; however, harzburgites were slightly enriched in TiO2 because of the reaction with MORB-like melt. Temperatures estimated using two-pyroxene thermometry ranged from 750 to 1010 °C, reflecting their lithospheric mantle origin. The rare earth element (REE) patterns in clinopyroxenes of the peridotites varied from light REE (LREE) depleted to spoon shaped to LREE enriched, reflecting secondary overprinting effects of metasomatic melts or fluids on the residues from primordial melting. The calculated trace element pattern of metasomatic melt equilibrated with clinopyroxene in Mt. Baekdu peridotite showed strong enrichment in large-ion lithophile elements, Th and U together with slight fractionation in heavy REEs (HREEs) and considerable depletion in Nb and Ti. The Sr-Nd-Hf isotopic compositions of clinopyroxenes separated from the peridotites varied from more depleted than present-day MORB to bulk Earth values. However, some clinopyroxene showed a decoupling between Nd and Sr isotopes, deviating from the mantle array with a high 87Sr/86Sr ratio. This sample also showed a significant Nd-Hf isotope decoupling lying well above the mantle array. The Lu-Hf and Sm-Nd model ages of residual clinopyroxenes yielded Early Proterozoic to Phanerozoic ages. No signature of Archean cratonic mantle was present. Therefore, Mt. Baekdu peridotite is residual lithospheric mantle that has undergone variable degrees of diachronous melt extraction and infiltration metasomatism involving subduction-related, fluid-bearing silicate melts. The predominance of Phanerozoic Hf model ages indicates that the lherzolites represent lithospheric mantle fragments newly accreted underneath the eastern NCC.

Ages and origins of rocks of the Killingworth dome, south-central Connecticut: Implications for the tectonic evolution of southern New England

USGS Publications Warehouse

Aleinikoff, J.N.; Wintsch, R.P.; Tollo, R.P.; Unruh, D.M.; Fanning, C.M.; Schmitz, M.D.

2007-01-01

The Killingworth dome of south-central Connecticut occurs at the southern end of the Bronson Hill belt. It is composed of tonalitic and trondhjemitic orthogneisses (Killingworth complex) and bimodal metavolcanic rocks (Middletown complex) that display calc-alkaline affinities. Orthogneisses of the Killingworth complex (Boulder Lake gneiss, 456 ?? 6 Ma; Pond Meadow gneiss, ???460 Ma) were emplaced at about the same time as eruption and deposition of volcanic-sedimentary rocks of the Middletown complex (Middletown Formation, 449 ?? 4 Ma; Higganum gneiss, 459 ?? 4 Ma). Hidden Lake gneiss (339 ?? 3 Ma) occurs as a pluton in the core of the Killingworth dome, and, on the basis of geochemical and isotopic data, is included in the Killingworth complex. Pb and Nd isotopic data suggest that the Pond Meadow, Boulder Lake, and Hidden Lake gneisses (Killingworth complex) resulted from mixing of Neoproterozoic Gander terrane sources (high 207Pb/204Pb and intermediate ??Nd) and less radiogenic (low 207Pb/204Pb and low ??Nd) components, whereas Middletown Formation and Higganum gneiss (Middletown complex) were derived from mixtures of Gander basement and primitive (low 207Pb/204Pb and high ??Nd) sources. The less radiogenic component for the Killingworth complex is similar in isotopic composition to material from Laurentian (Grenville) crust. However, because published paleomagnetic and paleontologic data indicate that the Gander terrane is peri-Gondwanan in origin, the isotopic signature of Killingworth complex rocks probably was derived from Gander basement that contained detritus from non-Laurentian sources such as Amazonia, Baltica, or Oaxaquia. We suggest that the Killingworth complex formed above an east-dipping subduction zone on the west margin of the Gander terrane, whereas the Middletown complex formed to the east in a back-arc rift environment. Subsequent shortening, associated with the assembly of Pangea in the Carboniferous, resulted in Gander cover terranes over the Avalon terrane in the west; and in the Middletown complex over the Killingworth complex in the east. Despite similarities of emplacement age, structural setting, and geographic continuity of the Killingworth dome with Oliverian domes in central and northern New England, new and published isotopic data suggest that the Killingworth and Middletown complexes were derived from Gander crust, and are not part of the Bronson Hill arc that was derived from Laurentian crust. The trace of the Ordovician Iapetan suture (the Red Indian line) between rocks of Laurentian and Ganderian origin probably extends from Southwestern New Hampshire west of the Pelham dome of northcentral Massachusetts and is coverd by Mesozoic rocks of the Hartford basin.

Volatiles in High-K Lunar Basalts

NASA Technical Reports Server (NTRS)

Barnes, Jessica J.; McCubbin, Francis M.; Messenger, Scott R.; Nguyen, Ann; Boyce, Jeremy

2017-01-01

Chlorine is an unusual isotopic system, being essentially unfractionated ((delta)Cl-37 approximately 0 per mille ) between bulk terrestrial samples and chondritic meteorites and yet showing large variations in lunar (approximately -4 to +81 per mille), martian, and vestan (HED) samples. Among lunar samples, the volatile-bearing mineral apatite (Ca5(PO4)3[F,Cl,OH]) has been studied for volatiles in K-, REE-, and P (KREEP), very high potassium (VHK), low-Ti and high-Ti basalts, as well as samples from the lunar highlands. These studies revealed a positive correlation between in-situ (delta)Cl-37 measurements and bulk incompatible trace elements (ITEs) and ratios. Such trends were interpreted to originate from Cl isotopic fractionation during the degassing of metal chlorides during or shortly after the differentiation of the Moon via a magma ocean. In this study, we investigate the volatile inventories of a group of samples for which new-era volatile data have yet to be reported - the high-K (greater than 2000 ppm bulk K2O), high-Ti, trace element-rich mare basalts. We used isotope imaging on the Cameca NanoSIMS 50L at JSC to obtain the Cl isotopic composition [((Cl-37/(35)Clsample/C-37l/(35)Clstandard)-1)×1000, to get a value in per thousand (per mille)] which ranges from approximately -2.7 +/- 2 per mille to +16.1 +/- 2 per mille (2sigma), as well as volatile abundances (F & Cl) of apatite in samples 10017, 10024 & 10049. Simply following prior models, as lunar rocks with high bulk-rock abundances of ITEs we might expect the high-K, high-Ti basalts to contain apatite characterized by heavily fractionated (delta)Cl-37 values, i.e., Cl obtained from mixing between unfractionated mantle Cl (approximately 0 per mille) and the urKREEP reservoir (possibly fractionated to greater than +25 per mille.). However, the data obtained for the studied samples do not conform to either the early degassing or mixing models. Existing petrogentic models for the origin of the high-K, high-Ti basalts do not include urKREEP assimilation into their LMO cumulate sources. Therefore, Cl in these basalts either originated from source region heterogeneity or through assimilation or metasomatism by volatile and incompatible trace element rich materials. The new data presented here could provide evidence for the existence of region(s) in the lunar interior that are ITE-enriched and contain Cl that does not share isotopic affinities with lunar urKREEP, possibly representing the composition of the purported 'neuKREEP'.

Deletion of SLC19A2, the high affinity thiamine transporter, causes selective inner hair cell loss and an auditory neuropathy phenotype.

PubMed

Liberman, M C; Tartaglini, E; Fleming, J C; Neufeld, E J

2006-09-01

Mutations in the gene coding for the high-affinity thiamine transporter Slc19a2 underlie the clinical syndrome known as thiamine-responsive megaloblastic anemia (TRMA) characterized by anemia, diabetes, and sensorineural hearing loss. To create a mouse model of this disease, a mutant line was created with targeted disruption of the gene. Cochlear function is normal in these mutants when maintained on a high-thiamine diet. When challenged with a low-thiamine diet, Slc19a2-null mice showed 40-60 dB threshold elevations by auditory brainstem response (ABR), but only 10-20 dB elevation by otoacoustic emission (OAE) measures. Wild-type mice retain normal hearing on either diet. Cochlear histological analysis showed a pattern uncommon for sensorineural hearing loss: selective loss of inner hair cells after 1-2 weeks on low thiamine and significantly greater inner than outer hair cell loss after longer low-thiamine challenges. Such a pattern is consistent with the observed discrepancy between ABR and OAE threshold shifts. The possible role of thiamine transport in other reported cases of selective inner hair cell loss is considered.

In vivo expression and purification of aptamer-tagged small RNA regulators

PubMed Central

Said, Nelly; Rieder, Renate; Hurwitz, Robert; Deckert, Jochen; Urlaub, Henning; Vogel, Jörg

2009-01-01

Small non-coding RNAs (sRNAs) are an emerging class of post-transcriptional regulators of bacterial gene expression. To study sRNAs and their potential protein interaction partners, it is desirable to purify sRNAs from cells in their native form. Here, we used RNA-based affinity chromatography to purify sRNAs following their expression as aptamer-tagged variants in vivo. To this end, we developed a family of plasmids to express sRNAs with any of three widely used aptamer sequences (MS2, boxB, eIF4A), and systematically tested how the aptamer tagging impacted on intracellular accumulation and target regulation of the Salmonella GcvB, InvR or RybB sRNAs. In addition, we successfully tagged the chromosomal rybB gene with MS2 to observe that RybB-MS2 is fully functional as an envelope stress-induced repressor of ompN mRNA following induction of sigmaE. We further demonstrate that the common sRNA-binding protein, Hfq, co-purifies with MS2-tagged sRNAs of Salmonella. The presented affinity purification strategy may facilitate the isolation of in vivo assembled sRNA–protein complexes in a wide range of bacteria. PMID:19726584

Argonaute pull-down and RISC analysis using 2'-O-methylated oligonucleotides affinity matrices.

PubMed

Jannot, Guillaume; Vasquez-Rifo, Alejandro; Simard, Martin J

2011-01-01

During the last decade, several novel small non-coding RNA pathways have been unveiled, which reach out to many biological processes. Common to all these pathways is the binding of a small RNA molecule to a protein member of the Argonaute family, which forms a minimal core complex called the RNA-induced silencing complex or RISC. The RISC targets mRNAs in a sequence-specific manner, either to induce mRNA cleavage through the intrinsic activity of the Argonaute protein or to abrogate protein synthesis by a mechanism that is still under investigation. We describe here, in details, a method for the affinity chromatography of the let-7 RISC starting from extracts of the nematode Caenorhabditis elegans. Our method exploits the sequence specificity of the RISC and makes use of biotinylated and 2'-O-methylated oligonucleotides to trap and pull-down small RNAs and their associated proteins. Importantly, this technique may easily be adapted to target other small RNAs expressed in different cell types or model organisms. This method provides a useful strategy to identify the proteins associated with the RISC, and hence gain insight in the functions of small RNAs.

Rapid production of functionalized recombinant proteins: marrying ligation independent cloning and in vitro protein ligation.

PubMed

Kushnir, Susanna; Marsac, Yoann; Breitling, Reinhard; Granovsky, Igor; Brok-Volchanskaya, Vera; Goody, Roger S; Becker, Christian F W; Alexandrov, Kirill

2006-01-01

Functional genomics and proteomics have been very active fields since the sequencing of several genomes was completed. To assign a physiological role to the newly discovered coding genes with unknown function, new generic methods for protein production, purification, and targeted functionalization are needed. This work presents a new vector, pCYSLIC, that allows rapid generation of Escherichia coli expression constructs via ligation-independent cloning (LIC). The vector is designed to facilitate protein purification by either Ni-NTA or GSH affinity chromatography. Subsequent proteolytic removal of affinity tags liberates an N-terminal cysteine residue that is then used for covalent modification of the target protein with different biophysical probes via protein ligation. The described system has been tested on 36 mammalian Rab GTPases, and it was demonstrated that recombinant GTPases produced with pCYSLIC could be efficiently modified with fluorescein or biotin in vitro. Finally, LIC was compared with the recently developed In-Fusion cloning method, and it was demonstrated that In-Fusion provides superior flexibility in choice of expression vector. By the application of In-Fusion cloning Cys-Rab6A GTPase with an N-terminal cysteine residue was generated employing unmodified pET30a vector and TVMV protease.

Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination

PubMed Central

Nicolas, Laura; Cols, Montserrat; Choi, Jee Eun; Chaudhuri, Jayanta; Vuong, Bao

2018-01-01

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity. PMID:29744038

Codes in the codons: construction of a codon/amino acid periodic table and a study of the nature of specific nucleic acid-protein interactions.

PubMed

Benyo, B; Biro, J C; Benyo, Z

2004-01-01

The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a common periodic table of codons and amino acids, where the nucleic acid table showed perfect axial symmetry for codons and the corresponding amino acid table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The table indicates that the middle (2/sup nd/) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

Multimodal molecular imaging reveals high target uptake and specificity of 111In and 68Ga labeled fibrin-binding probes for thrombus detection in rats

PubMed Central

Oliveira, Bruno L.; Blasi, Francesco; Rietz, Tyson A.; Rotile, Nicholas J.; Day, Helen; Caravan, Peter

2016-01-01

We recently showed the high target specificity and favorable imaging properties of 64Cu and Al18F positron emission tomography (PET) probes for non-invasive imaging of thrombosis. Here, our aim was to evaluate new derivatives labeled with either with 68Ga, 111In, or 99mTc as thrombus imaging agents for PET and single-photon emission computed tomography (SPECT). In this study, the feasibility and potential of these probes for thrombus imaging was assessed in detail in two animal models of arterial thrombosis. The specificity of the probes was further evaluated using a triple-isotope approach with multimodal SPECT/PET/CT imaging. Methods Radiotracers were synthesized using a known fibrin-binding peptide conjugated to NODAGA, DOTA-MA, or a diethylenetriamine ligand (DETA-PA), followed by labeling with 68Ga (FBP14, 68Ga-NODAGA), 111In (FBP15, 111In-DOTA-MA) or 99mTc (FBP16, 99mTc(CO)3-DETA-PA), respectively. PET or SPECT imaging, biodistribution, pharmacokinetics and metabolic stability were evaluated in rat models of mural and occlusive carotid artery thrombosis. In vivo target specificity was evaluated by comparing the distribution of the SPECT and PET probes with preformed 125I-labeled thrombi and with a non-binding control probe using SPECT/PET/CT imaging. Results All three radiotracers showed similar affinity to soluble fibrin fragment DD(E) (Ki = 0.53–0.83 μM). After the kidneys, the highest uptake of 68Ga-FBP14 and 111In-FBP15 was in the thrombus (1.0 ± 0.2% ID/g) with low off-target accumulation. Both radiotracers underwent fast systemic elimination (t1/2 = 8-15 min) through the kidneys, which led to highly conspicuous thrombi on PET and SPECT images. 99mTc-FBP16 displayed low target uptake and distribution consistent with aggregation and/or degradation. Triple isotope imaging experiments showed that both 68Ga-FBP14 and 111In-FBP15, but not the nonbinding derivative 64Cu-D-Cys-FBP8, detected the location of the 125I-labeled thrombus, confirming high target specificity. Conclusion 68Ga-FBP14 and 111In-FBP15 have high fibrin affinity and thrombus specificity, and represent useful PET and SPECT probes for thrombus detection. PMID:26251420

2H Kinetic Isotope Effects and pH Dependence of Catalysis as Mechanistic Probes of Rat Monoamine Oxidase A: Comparisons with the Human Enzyme‡

PubMed Central

Wang, Jin; Edmondson, Dale E.

2011-01-01

Monoamine oxidase A (MAO A) is a mitochondrial outer membrane-bound flavoenzyme important in the regulation of serotonin and dopamine levels. Since the rat is extensively used as an animal model in drug studies, it is important to understand how rat MAO A behaves in comparison with the more extensively studied human enzyme. For many reversible inhibitors, rat MAO A exhibits Ki values similar to those of human MAO A. The pH profile of kcat for rat MAO A shows a pKa of 8.2±0.1 for the benzylamine ES complex and pKa values of 7.5±0.1 and 7.6±0.1 for the respective ES complexes with p-CF3-1H and p-CF3-2H-benzylamine. In contrast to the human enzyme, the rat enzyme exhibits a single pKa value (8.3±0.1) with kcat/Km benzylamine vs. pH and pKa values of 7.8±0.1 and 8.1±0.2 are found for the ascending limbs, respectively, of kcat/Km vs. pH profiles for p-CF3-1H and p-CF3-2H-benzylamine and 9.3±0.1 and 9.1±0.2 for their respective descending limbs. The oxidation of para-substituted benzylamine substrate analogues by rat MAO A exhibit large deuterium kinetic isotope effects on kcat and on kcat/Km. These effects are pH-independent, and range from 7 to 14, demonstrating a rate-limiting α-C-H bond cleavage step in catalysis. Quantitative structure-activity correlations of log kcat with the electronic substituent parameter (σ) at pH 7.5 and at 9.0 show a dominant contribution with positive ρ values (+1.2 – 1.3) and a pH-independent negative contribution from the steric term. Quantitative structure-activity relationship analysis of the binding affinities of the para-substituted benzylamine analogues to rat MAO A show an increased van der Waals volumes (Vw) increases the affinity of the deprotonated amine for the enzyme. These results demonstrate that rat MAO A exhibits similar but not identical functional properties with the human enzyme and provide additional support for C-H bond cleavage via a polar nucleophilic mechanism. PMID:21819071

Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation.

PubMed

Sun, Ying-Chieh; Hsu, Wen-Chi; Hsu, Chia-Jen; Chang, Chia-Ming; Cheng, Kai-Hsiang

2015-11-01

Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand-which is seldom addressed in the literature-is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length. The pair of ligand-p38 kinase complexes examined in this work (pdb codes: 3d7z and 3lhj, respectively) were ideal for investigating this effect. The experimentally determined binding energy for the ref ligand with the untagged p38 kinase was -10.9 kcal mol(-1), while that for the analog ligand with the tagged p38 kinase was -11.9 kcal mol(-1). The present TI-MD simulation of the mutation of the ref ligand into the analog ligand while the ligand is bound to the untagged p38 kinase predicted that the binding affinity of the analog ligand is 2.0 kcal mol(-1) greater than that of the ref ligand. A similar simulation also indicated that the same was true for ligand binding to the tagged protein, but in this case the binding affinity for the analog ligand is 2.5 kcal mol(-1) larger than that for the ref ligand. These results therefore suggest that the presence of the peptide tag on p38 kinase increased the difference in the binding energies of the ligands by a small amount of 0.5 kcal mol(-1). This result supports the assumption that the presence of a peptide tag has only a minor effect on ΔG values. The error bars in the computed ΔG values were then estimated via confidence interval analysis and a time autocorrelation function for the quantity dV/dλ. The estimated correlation time was ~0.5 ps and the error bar in the ΔG values estimated using nanosecond-scale simulations was ±0.3 kcal mol(-1) at a confidence level of 95%. These predicted results can be verified in future experiments and should prove useful in subsequent similar studies. Graphical Abstract Thermodynamic cycles for binding of two analogous ligands with untagged and tagged p38 kinases and associated Gibbs free energy.

Integrated elemental and Sr-Nd-Pb-Hf isotopic studies of Mesozoic mafic dykes from the eastern North China Craton: implications for the dramatic transformation of lithospheric mantle

NASA Astrophysics Data System (ADS)

Liu, Shen; Feng, Caixia; Santosh, M.; Feng, Guangying; Coulson, Ian M.; Xu, Mengjing; Guo, Zhuang; Guo, Xiaolei; Peng, Hao; Feng, Qiang

2018-02-01

Evolution of the lithospheric mantle beneath the North China Craton (NCC) from its Precambrian cratonic architecture until Paleozoic, and the transformation to an oceanic realm during Mesozoic, with implications on the destruction of cratonic root have attracted global attention. Here we present geochemical and isotopic data on a suite of newly identified Mesozoic mafic dyke swarms from the Longwangmiao, Weijiazhuang, Mengjiazhuang, Jiayou, Huangmi, and Xiahonghe areas (Qianhuai Block) along the eastern NCC with an attempt to gain further insights on the lithospheric evolution of the region. The Longwangmiao dykes are alkaline with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N > 4.3) and EM1-like Sr-Nd-Pb-Hf isotopic signature ((87Sr/86Sr) i > 0.706; ε Nd (t) < -6.3, (206Pb/204Pb) i > 16.6, (207Pb/204Pb) i > 15.4, (208Pb/204Pb) i > 36.8, ε Hf (t) < -22.4). The Weijiazhuang dykes are sub-alkaline with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N > 3.7), and display similar EM1-like isotopic features ((87Sr/86Sr) i > 0.706; ε Nd (t) < -7.0, (206Pb/204Pb) i > 16.7, (207Pb/204Pb) i > 15.4, (208Pb/204Pb) i > 36.9, ε Hf (t) < -23.3). The Mengjiazhuang dykes are also sub-alkaline with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N > 2.4) and EM1-like isotopic features((87Sr/86Sr) i > 0.706; ε Nd (t) < -18.4, (206Pb/204Pb) i > 16.7, (207Pb/204Pb) i > 15.4, (208Pb/204Pb) i > 36.9, ε Hf (t) < -8.6). The Jiayou dykes also display sub-alkaline affinity with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N > 3.7) and EM1-like Sr-Nd-Pb-Hf isotopic features ((87Sr/86Sr) i > 0.706; ε Nd(t) < -15.3, (206Pb/204Pb) i > 16.7, (207Pb/204Pb) i > 15.4, (208Pb/204Pb) i > 36.9, ε Hf (t) < -18.4). The Huangmi dykes are alkaline (with Na2O + K2O ranging to more than 5.9 wt.%)) with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N > 9.3) and EM1-like isotopic composition ((87Sr/86Sr) i > 0.705; ε Nd (t) < -15.1, (206Pb/204Pb) i > 16.9, (207Pb/204Pb) i > 15.5, (208Pb/204Pb) i > 36.9, ε Hf (t) < -12.2). The Xiahonghe dykes are alkaline with LILE (Ba and K)- and LREE-enrichment ((La/Yb) N = 2.12-2.84) and similar EM1-like Sr-Nd-Pb-Hf isotopic signature ((87Sr/86Sr) i > 0.705; ε Nd (t)<-18.0, (206Pb/204Pb) i > 16.9, (207Pb/204Pb) i > 15.5, (208Pb/204Pb) i > 36.9, ε Hf (t) < -8.6). Our data from the various mafic dyke suites suggest that the magmas were derived from EM1-like lithospheric mantle, corresponding to lithospheric mantle modified by the previously foundered lower crust beneath the eastern NCC. Our results suggest contrasting lithospheric evolution from Triassic (212 Ma) to Cretaceous (123 Ma) beneath the NCC. These mafic dykes mark an important phase of lithospheric thinning in the eastern North China Craton.

Mantle source beneath Turrialba volcano (Costa Rica): a geochemical investigation

NASA Astrophysics Data System (ADS)

Di Piazza, A.; Rizzo, A. L.; Barberi, F.; Carapezza, M. L.; Sortino, F.; De Astis, G.; Romano, C.

2014-12-01

In this study we analysed rocks and noble gas composition of fluid inclusions (FIs) hosted in olivine crystals contained in a suite of eruptive products of the last 10ka of activity of Turrialba volcano, Cordillera Central, Costa Rica. The suite of analyzed rocks display a calc-alkaline affinity, ranging in composition from basaltic-andesite to dacite. Trace element patterns indicate a typical behavior of subduction-related magmas and also the clear contribution of an OIB-like signature at source. A group of andesites displays also adakite-like geochemical features, as evidenced by their constant depletion in HFSE elements. Sr isotope (0.703593 - 0.703678) and Nd isotope ratios (0.512960 - 0.512968) suggest that Turrialba magmas belong to one of the less contaminated mantle source of Central America. The 3He/4He ratio of fluid inclusions from the most mafic eruptive products (basaltic-andesites) varies from 7.86 to 8.07 Ra, while that from andesite lavas varies from 7.03 to 7.18 Ra. In order to understand the mantle source feeding Turrialba volcano, we performed a geochemical investigation on fumarolic gases of summit craters. The He isotope composition of dry gases of Turrialba volcano is characterized by extremely high R/Ra values (7.08-7.96 Ra). The highest 3He/4He ratios were measured at both West and Central Craters (7.93-7.96 Ra and 7.78-7.88 Ra, respectively), and are the highest values of the entire Central America. Despite the observed variability, the 3He/4He ratio of fumarolic gases and FIs from Turrialba volcano is well in the range of arc related volcanism (~7-8 Ra; Hilton et al., 2002), and represents the signature of a mantle wedge in which the contamination by crustal fluids is small to negligible. In addition the occurrence of recent adakite-like magmatism suggests the presence of an abnormal heating of the subducting lithosphere under Turrialba volcano, allowing even old or cold oceanic crust to melt.

Petrogenesis of granodiorite in the Balong region, eastern Kunlun Orogen, China: Constraints from zircon U-Pb geochronology, geochemistry and Sr-Nd-Hf isotopes

NASA Astrophysics Data System (ADS)

Huang, X.; Li, H.; Wang, Y.; Liu, Y.

2017-12-01

Numerous granitoid intrusions that close to the Balong region have great scientific significance to reveal tectonic evolution and geodynamic background of eastern Kunlun Orogen (EKO). Balong granodiorite (BLG) is located at the northern of the EKO. It generally emplaced into the Proterozoic to Lower Palaeozoic rocks and contains abundant mafic microgranular enclaves. LA-ICP-MS zircon U-Pb dating of the BLG gives a 206Pb/238U age of 230.7±1.9 Ma, indicating that it was emplaced in the Late Triassic. The BLG is high-K calc-alkaline series and metaluminous, with SiO2 of 59.86 61.83%, K2O+Na2O of 5.98 6.40%, CaO of 4.95 5.77% and P2O5 of 0.14% 0.18%. The granodioritic rocks are enriched in LILE (Ba, Rb, Sr), but depleted in HFSE (Nb, Ta, P, Ti), with weak negative Eu anomalies (δEu=0.70 0.82). Mineralogy and geochemistry of the rocks show an affinity to I-type granite. The BLG, having (87Sr/86Sr)i ratios of 0.70819 to 0.70832, ɛNd(t) values of -5.27 to -5.75, and zircon ɛHf(t) values ranging from -3.86 to -1.34. The whole-rock Nd isotopic model ages (1432 1471 Ma) and zircon Hf isotopic model ages (1205 1357 Ma) indicate that the BLG is generated by partial melting of lower crust (Precambrian metabasaltic basement rocks) with different degree of involvement of mantle material. Combined with regional geological data, the granodiorite was derived from dehydration melting of mafic lower crustal rocks during the subduction of the Anyemaqen ocean lithosphere at Late Permian-Triassic in a subduction setting. Basaltic magma underplating and crust-mantle mixing are main mechanisms for the origin of large-scale I-type granitoid in Balong.

Early Jurassic mafic dykes from the Aigao uranium ore deposit in South China: Geochronology, petrogenesis and relationship with uranium mineralization

NASA Astrophysics Data System (ADS)

Zhang, Di; Zhao, Kui-Dong; Chen, Wei; Jiang, Shao-Yong

2018-05-01

Mafic dykes are abundant and widely distributed in many granite-hosted uranium ore deposits in South China. However, their geochronology, petrogenesis and relationship with uranium mineralization were poorly constrained. In this study, apatite U-Pb dating, whole-rock major and trace element and Sr-Nd-Pb isotope analysis were conducted for the dolerite dykes from the Aigao uranium ore deposit. Apatite U-Pb isotopic data indicate that the mafic dykes were emplaced at Early Jurassic (189 ± 4 Ma), which provides new evidence for the rarely identified Early Jurassic magmatism in South China. Pyroxene from the dykes is mainly augite, and plagioclase belongs to albite. The dolerite samples have relatively low SiO2 contents (45.33-46.79 wt%), relatively high total alkali contents (K2O + Na2O = 4.11-4.58 wt%) and Al2O3 contents (13.39-13.80 wt%), and medium MgO contents (4.29-5.16 wt%). They are enriched in Nb, Ta, Ti, rare earth elements and depleted in Rb, K, Sr, Th, showing the typical OIB-like geochemical affinity. All the dolerite samples show homogeneous Sr-Nd-Pb isotopic compositions, with (87Sr/86Sr)i varying from 0.706049 to 0.707137, εNd(t) from +4.6 to +5.2, 206Pb/204Pb from 19.032 to 19.126 and 207Pb/204Pb from 15.641 to 15.653. The mafic dykes in the Aigao deposit should be derived from the partial melting of the asthenospheric mantle and formed in a within-plate extensional environment. The emplacement age of the mafic dykes is older than the uranium mineralization age. Therefore, CO2 in ore-forming fluids couldn't originate from the basaltic magma as suggested by previous studies. The dolerite dykes might only provide a favorable reducing environment to promote the precipitation of uraninite from oxidize hydrothermal fluids.

An Early Permian epithermal gold system in the Tulasu Basin in North Xinjiang, NW China: Constraints from in situ oxygen-sulfur isotopes and geochronology

NASA Astrophysics Data System (ADS)

Dong, Leilei; Wan, Bo; Deng, Chen; Cai, Keda; Xiao, Wenjiao

2018-03-01

The Axi and Jingxi-Yelmand gold deposits, being the largest gold deposits in the Chinese North Tianshan, NW China, are located ca. l0 km apart in the Tulasu Basin, and are hosted by the Late Devonian - Early Carboniferous Dahalajunshan Formation. In situ LA-ICP-MS titanium analyses on quartz from the Axi and Jingxi-Yelmand deposits are broadly identical. Accordingly, the calculated ore-forming temperatures by Ti-in-quartz thermometer give average temperatures of 279 °C and 294 °C, respectively. Results of in situ SIMS analyses of oxygen and sulfur isotopes on quartz and pyrite from these two deposits are similar. Temperature-corrected fluids of the Axi deposit have δ18O values of 2.6-8.1‰ and δ34S values of 0.8-2.4‰, whereas the fluids of the Jingxi-Yelmand deposit have δ18O of 6.4-8.9‰ and δ34S of -0.4 to 4.0‰. The oxygen and sulfur isotopes from the two deposits indicate a magmatic origin. LA-ICP-MS zircon U-Pb ages of Aqialehe Formation sandstone provided a lower limit for the mineralization timing of the Axi deposit (288 Ma). In situ SIMS U-Pb analyses on entrapped zircon (297 Ma) and newly recognized 284.5 Ma columnar rhyolite implies that the Jingxi-Yelmand deposit formed in the Early Permian. Based on the magmatic affinity of the ore fluids, similar age and ore-formation temperatures, we propose that the Axi and Jingxi-Yelmand deposits comprise an epithermal gold system, which was driven by the same Permian magma in the Tulasu Basin. The ore geological features together with our new results indicate that the Axi and Jingxi-Yelmand deposits are intermediate and high sulfidation type epithermal deposits, respectively.

Middle Neoproterozoic (ca. 705-716 Ma) arc to rift transitional magmatism in the northern margin of the Yangtze Block: Constraints from geochemistry, zircon U-Pb geochronology and Hf isotopes

NASA Astrophysics Data System (ADS)

Wang, Ruirui; Xu, Zhiqin; Santosh, M.; Xu, Xianbing; Deng, Qi; Fu, Xuehai

2017-09-01

The South Qinling Belt in Central China is an important window to investigate the Neoproterozoic tectono-magmatic processes along the northern margin of the Yangtze Block. Here we present whole-rock geochemistry, zircon U-Pb geochronology and Lu-Hf isotopes of a suite of Middle Neoproterozoic intrusion from the Wudang Uplift in South Qinling. Zircon LA-ICP-MS U-Pb ages reveal that these rocks were formed at ca. 705-716 Ma. Geochemical features indicate that the felsic magmatic rocks are I-type granitoids, belong to calcic- to calc-alkaline series, and display marked negative Nb, Ta and Ti anomalies. Moreover, the enrichment of light rare earth elements (LREEs) and large ion lithophile elements (LILEs), combined with depletion of heavy rare earth elements (HREEs) support that these rocks have affinity to typical arc magmatic rocks formed in Andean-type active continental margins. The REE patterns are highly to moderately fractionated, with (La/Yb)N = 5.13-8.10 in meta-granites, and 2.32-2.35 in granodiorite. The granitoids have a wide range of zircon εHf(t) values (-29.91 to 14.76) and zircon Hf two-stage model ages (696-3482 Ma). We suggest that the ca. 705-716 Ma granitoids were sourced from different degrees of magma mixing between partial melting of the overlying mantle wedge triggered by hydrous fluids released from subducted materials and crustal melting. The hybrid magmas were emplaced in the shallow crust accompanied by assimilation and fractional crystallization (AFC). Both isotopic and geochemical data suggest that the ca. 705-716 Ma felsic magmatic rocks were formed along a continental arc. These rocks as well as the contemporary A-type granite may mark a transitional tectonic regime from continental arc to rifting, probably related to slab rollback during the oceanic subduction beneath the northern margin of Yangtze Block.

The Means: Cytometry and Mass Spectrometry Converge in a Single Cell Deep Profiling Platform

PubMed Central

Weis-Garcia, Frances; Bandura, Dmitry; Baranov, Vladimir; Ornatsky, Olga; Tanner, Scott

2013-01-01

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is a distinct flavor of mass spectrometry that has had little association with cell biology: it remains the state of the art for the determination of the atomic composition of materials. Unrelatedly, flow cytometry is the superior method for distinguishing the heterogeneity of cells through the determination of antigen signatures using tagged antibodies. Simply replacing fluorophore tags with stable isotopes of the heavy metals, and measuring these cell-by-cell with ICP-MS, dramatically increases the number of probes that can be simultaneously measured in cytometry and enables a transformative increase in the resolution of rare cell populations in complex biological samples. While this can be thought of as a novel incarnation of single-cell targeted proteomics, the metal-labeling reagents, ICP-MS of single cells, and accompanying informatics comprise a new field of technology termed Mass Cytometry. While the conception of mass cytometry is simple the embodiment to address the issues of multi-parameter flow cytometry has been far more challenging. There are many elements, and many more stable isotopes of those elements, that might be used as distinct reporter tags. Still, there are many approaches to conjugating metals to antibodies (or other affinity reagents) and work in this area along with developing new applications is ongoing. The mass resolution and linear (quantitative) dynamic range of ICP-MS allows those many stable isotopes to be measured simultaneously and without the spectral overlap issues that limit fluorescence assay. However, the adaptation of ICP-MS to allow high-speed simultaneous measurement with single cell distinction at high throughput required innovation of the cell introduction system, ion optics (sampling, transmission and beam-shaping), mass analysis, and signal handling and processing. An overview of “the nuts and bolts” of Mass Cytometry is presented.

Mantle xenoliths hosted in alkali basalts in subduction environment: the example of the SE Alps (Italy)

NASA Astrophysics Data System (ADS)

Gasperini, D.; Maffei, K.; Bosch, D.; Braga, R.; Macera, P.; Morten, L.

2003-04-01

We present petrographic, geochemical, and isotopic (Sr, Nd, and Pb) data of a representative suite of spl-peridotite xenoliths (mg# >88) hosted in alkali basalts from numerous outcrops in the Tertiary Veneto Volcanic Province (VVP; SE Alps, Italy), compared to various world-wide mafic inclusions (French Massif, Australia, China, Philippines, Russia, Kerguelen). The VVP spl-harzburgites and -lherzolites carry textures ranging from protogranular, porphyroclastic, granuloblastic to pyrometamorfic. These samples are characterized by a continuous depletion trend from the cpx-rich lherzolites to harzburgites, with CaO, Al_2O_3, TiO_2, and Na_2O contents decreasing with mg# increasing (Morten, 1987; Beccaluva et al., 2001). Then, the VVP xenoliths spinels show a strong Cr/(Cr+Al) ratio increase at a slight Mg/(Mg+Fe2+) ratio decrease, thus reflecting a variably depleted mantle source. The VVP xenoliths display a large range of enrichment in LREE, K, Rb, Sr and P, suggesting post depletion metasomatic episodes (Morten et al., 2002). Whereas most of the VVP xenoliths' multi-element spectra, incompatible element and isotope ratios are similar to the VVP host basalts, thus with a strong HIMU signature (Macera et al. submitted), some depleted samples show geochemical features typical of crust derived material. These characteristics cannot be related to significant interaction with the local lower continental crust, as represented by several analyzed gabbroic xenoliths. Nevertheless negative Nb and Ta anomalies in analogous peridotitic samples have been previously ascribed to metasomatism inferred by plume rising material in the upper mantle (Bedini et al., 1997). Comparing the VVP peridotites with several mafic xenoliths from various geodynamical environments, we suggest that this crust affinity could be alternatively explained by the presence of a not perfectly homogenized upper crustal component in the source region, probably induced by subduction related episode(s). In this contest, the isotopic composition of the VVP mafic xenoliths is a crucial tool to understand the geochemical history of the Alpine subcontinental mantle.

New Innovations in Highly Ion Specific Media for Recalcitrant Waste stream Radioisotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denton, M. S.; Wilson, J.; Ahrendt, M.

Specialty ion specific media were examined and developed for, not only pre- and post-outage waste streams, but also for very difficult outage waste streams. This work was carried out on first surrogate waste streams, then laboratory samples of actual waste streams, and, finally, actual on-site waste streams. This study was particularly focused on PWR wastewaters such as Floor Drain Tank (FDT), Boron Waste Storage Tank (BWST), and Waste Treatment Tank (WTT, or discharge tank). Over the last half decade, or so, treatment technologies have so greatly improved and discharge levels have become so low, that certain particularly problematic isotopes, recalcitrantmore » to current treatment skids, are all that remain prior to discharge. In reality, they have always been present, but overshadowed by the more prevalent and higher activity isotopes. Such recalcitrants include cobalt, especially Co 58 [both ionic/soluble (total dissolved solids, TDS) and colloidal (total suspended solids, TSS)] and antimony (Sb). The former is present in most FDT and BWST wastewaters, while the Sb is primarily present in BWST waste streams. The reasons Co 58 can be elusive to granulated activated carbon (GAC), ultrafiltration (UF) and ion exchange (IX) demineralizers is that it forms submicron colloids as well as has a tendency to form metal complexes with chelating agents (e.g., ethylene diamine tetraacetic acid, or EDTA). Such colloids and non-charged complexes will pass through the entire treatment skid. Antimony (Sb) on the other hand, has little or no ionic charge, and will, likewise, pass through both the filtration and de-min skids into the discharge tanks. While the latter will sometimes (the anionic vs. the cationic or neutral species) be removed on the anion bed(s), it will slough off (snow-plow effect) when a higher affinity anion (iodine slugs, etc.) comes along; thus causing effluents not meeting discharge criteria. The answer to these problems found in this study, during an actual Nuclear Power Plant (NPP) outage cycle and recovery (four months), was the down-select and development of a number of highly ion specific media for the specific removal of such elusive isotopes. Over three dozen media including standard cation and anion ion exchangers, specialty IX, standard carbons, and, finally, chemically doped media (e.g., carbon and alumina substrates). The latter involved doping with iron, manganese, and even metals. The media down-select was carried out on actual plant waste streams so that all possible outage affects were accounted for, and distribution coefficients (Kd's) were determined (vs. decontamination factors, DF's, or percent removals). Such Kd's, in milliliters of solution per gram of media (mug), produce data indicative of the longevity of the media in that particular waste stream. Herein, the down-select is reported in Pareto (decreasing order) tables. Further affects such as the presence of high cobalt concentrations, high boron concentrations, the presence of hydrazine and chelating agents, and extreme pH conditions. Of particular importance here is to avoid the affinity of competing ions (e.g., a Sb specific media having more than a slight affinity for Co). The latter results in the snow-plow effect of sloughing off 3 to 4 times the cobalt into the effluent as was in the feed upon picking up the Sb. The study was quite successful and resulted in the development of and selection of a resin-type and two granular media for antimony removal, and two resin-types and a granular media for cobalt removal. The decontamination factors for both media were hundreds to thousands of times that of the full filtration and de-min. (authors)« less

Poster - 40: Treatment Verification of a 3D-printed Eye Phantom for Proton Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunning, Chelsea; Lindsay, Clay; Unick, Nick

Purpose: Ocular melanoma is a form of eye cancer which is often treated using proton therapy. The benefit of the steep proton dose gradient can only be leveraged for accurate patient eye alignment. A treatment-planning program was written to plan on a 3D-printed anatomical eye-phantom, which was then irradiated to demonstrate the feasibility of verifying in vivo dosimetry for proton therapy using PET imaging. Methods: A 3D CAD eye model with critical organs was designed and voxelized into the Monte-Carlo transport code FLUKA. Proton dose and PET isotope production were simulated for a treatment plan of a test tumour, generatedmore » by a 2D treatment-planning program developed using NumPy and proton range tables. Next, a plastic eye-phantom was 3D-printed from the CAD model, irradiated at the TRIUMF Proton Therapy facility, and imaged using a PET scanner. Results: The treatment-planning program prediction of the range setting and modulator wheel was verified in FLUKA to treat the tumour with at least 90% dose coverage for both tissue and plastic. An axial isotope distribution of the PET isotopes was simulated in FLUKA and converted to PET scan counts. Meanwhile, the 3D-printed eye-phantom successfully yielded a PET signal. Conclusions: The 2D treatment-planning program can predict required parameters to sufficiently treat an eye tumour, which was experimentally verified using commercial 3D-printing hardware to manufacture eye-phantoms. Comparison between the simulated and measured PET isotope distribution could provide a more realistic test of eye alignment, and a variation of the method using radiographic film is being developed.« less

Zirconium Evaluations for ENDF/B-VII.2 for the Fast Region

NASA Astrophysics Data System (ADS)

Brown, D. A.; Arcilla, R.; Capote, R.; Mughabghab, S. F.; Herman, M. W.; Trkov, A.; Kim, H. I.

2014-04-01

We have performed a new combined set of evaluations for 90-96Zr, including new resolved resonance parameterizations from Said Mughabghab for 90,91,92,94,96Zr and fast region calculations made with EMPIRE-3.1. Because 90Zr is a magic nucleus, stable Zr isotopes are nearly spherical. A new soft-rotor optical model potential is used allowing calculations of the inelastic scattering on low-lying coupled levels of vibrational nature. A soft rotor model describes dynamical deformations of the nucleus around the spherical shape and is implemented in EMPIRE/OPTMAN code. The same potential is used with rigid rotor couplings for odd-A nuclei. This then led to improved elastic angular distributions, helping to resolve improper leakage in the older ENDF/B-VII.1β evaluation in KAPL proprietary, ZPR and TRIGA benchmarks. Another consequence of 90Zr being a magic nucleus is that the level densities in both 90Zr and 91Zr are unusually low causing the (n,el) and (n,tot) cross sections to exhibit large fluctuations above the resolved resonance region. To accommodate these fluctuations, we performed a simultaneous constrained generalized least-square fit to (n,tot) for all isotopic and elemental Zr data in EXFOR, using EMPIRE's TOTRED scaling factor. TOTRED rescales total cross sections so that the optical model calculations are unaltered by the rescaling and the correct competition between channels is maintained. In this fit, all (n,tot) data in EXFOR was used for Ein>100 keV, provided the target isotopic makeup could be correctly understood, including spectrum averaged data and data with broad energy resolution. As a result of our fitting procedure, we will have full cross material and cross reaction covariance for all Zr isotopes and reactions.

Expression and isotopic labelling of the potassium channel blocker ShK toxin as a thioredoxin fusion protein in bacteria.

PubMed

Chang, Shih Chieh; Galea, Charles A; Leung, Eleanor W W; Tajhya, Rajeev B; Beeton, Christine; Pennington, Michael W; Norton, Raymond S

2012-10-01

The polypeptide toxin ShK is a potent blocker of Kv1.3 potassium channels, which play a crucial role in the activation of human effector memory T-cells (T(EM)). Selective blockers constitute valuable therapeutic leads for the treatment of autoimmune diseases mediated by T(EM) cells, such as multiple sclerosis, rheumatoid arthritis, and type-1 diabetes. We have established a recombinant peptide expression system in order to generate isotopically-labelled ShK and various ShK analogues for in-depth biophysical and pharmacological studies. ShK was expressed as a thioredoxin fusion protein in Escherichia coli BL21 (DE3) cells and purified initially by Ni²⁺ iminodiacetic acid affinity chromatography. The fusion protein was cleaved with enterokinase and purified to homogeneity by reverse-phase HPLC. NMR spectra of ¹⁵N-labelled ShK were similar to those reported previously for the unlabelled synthetic peptide, confirming that recombinant ShK was correctly folded. Recombinant ShK blocked Kv1.3 channels with a K(d) of 25 pM and inhibited the proliferation of human and rat T lymphocytes with a preference for T(EM) cells, with similar potency to synthetic ShK in all assays. This expression system also enables the efficient production of ¹⁵N-labelled ShK for NMR studies of peptide dynamics and of the interaction of ShK with Kv1.3 channels. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hydrogeochemical and isotopic investigation and water quality assessment of groundwater in the Sisseb El Alem Nadhour Saouaf aquifer (SANS), northeastern Tunisia

NASA Astrophysics Data System (ADS)

Hamdi, Mohamed; Zagrarni, Mohamed Faouzi; Jerbi, Hamza; Tarhouni, Jamila

2018-05-01

In the Sisseb El Alem Nadhour Saouaf basin (SANS), as in all other arid regions, surface water is scarce and groundwater is the greatest most important source of water for all uses. This study aims to identify the processes governing groundwater mineralization in order to assess the suitability of the groundwater for drinking and agriculture purposes. This research used a geodatabase which includes information on hydrogeology, geochemistry, land cover, and geology. We identified the most important factors involved in the deterioration of water quality, including anhydrite and gypsum dissolution, silicate weathering, downward leakage between aquifers, evaporation, groundwater over-exploitation, and the overuse of fertilizers. Furthermore, the two following important factors were identified: the intrusion of Sebkhat El Kelbia and the vertical flow from the deep aquifer. Results were used to develop a conceptual geochemical model, wherein three geochemical regions were differentiated. Statistical techniques, such as Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) were used to confirm the water affinities and the presence of three different geochemical regions. The water quality index (WQI), Wilcox and Richards's diagrams were performed to assess the suitability of groundwater to drinking and irrigation purposes. These indexes confirm the fact that the groundwater of this aquifer is not suitable for irrigation, neither for drinking. Furthermore, 18O and deuterium isotope data indicate the importance of evaporation in the basin, and the recharge with modern rainfall.

Geology of 1. 7 GA ( ) Baldwin gneiss in the Baldwin Lake type area, San Bernardino Mountains, southern California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barth, A.P.; Ehlig, P.L.; Wooden, J.L.

1993-04-01

Precambrian gneisses in the San Bernardino Mountains were first identified and described in the vicinity of Baldwin Lake by Guillou (1953). Five lithologic units mappable at 1:24,000 scale are recognized: biotite [+-] muscovite quartzofeldspathic gneiss, amphibolite, pyroxene metagabbro, augen gneiss, and biotite [+-] muscovite granitic gneiss. Baldwin gneiss with this L < S tectonite fabric is unconformably overlain by latest Proterozoic, upright, greenschist/hornfels facies quartzite (Big Bear Group). North and northeast of Baldwin Lake, the gneissic fabric is rotated toward the northwest, subparallel to the Doble fault. Along this fault, Baldwin gneiss is structurally underlain by overturned Paleozoic quartzite andmore » marble (Zabriskie Quartzite and Carrara Formation). Regional relations suggest that the Doble fault is a northeast-directed basement thrust fault of pre-Late Cretaceous age, and may be contemporaneous with late Paleozoic deformation and metamorphism of Paleozoic rocks further west in the range. Field relations suggest that Baldwin gneiss in its type area largely retains Proterozoic fabrics and mineral assemblages, despite marginal Phanerozoic reworking. Silver (1971) reported a U-Pb zircon age of ca. 1,730 Ma for Baldwin augen ( ) gneiss, from an unknown locality, and Miller and Morton (1980) reported Late Cretaceous mica K-Ar ages from a sample of augen gneiss. Preliminary Pb isotopic ratios in galena, feldspar and whole rock samples of Baldwin gneiss, and feldspars in Mesozoic plutons suggest isotopic affinity to the Mojave crustal province of Wooden and Miller (1990).« less

An Earth with affinities to Enstatite Chondrites

NASA Astrophysics Data System (ADS)

McDonough, W. F.

2015-12-01

The Enstatite chondrite model for the Earth, as envisaged by Marc Javoy and colleagues, has strengths and weaknesses. The overwhelming evidence against layered mantle scenarios makes the existing enstatite Earth models unacceptable. Increasingly, stable and radiogenic isotope data for the Earth and the range of chondrites find that many (but not all) isotopic ratios are shared between the Earth and enstatite chondrites. This significant amount of overlap in isotope space compels one to reconsider the enstatite chondrite model for the Earth. During early solar system formation (circa +1 Ma) radial inward migration of the Jupiter and Saturn in the disk (e.g., Grand Tack model) would fully disrupted an asteroid belt, resulting in mixing and redistribution of preexisting components, while much later after the disk is gone (e.g., +100 Ma) gravitational scattering by these planets may have transported small bodies from the outer reaches of the solar system inward towards the rocky planets (Nice model). Astromineralogy reveals variations in the proportion of olivine to pyroxene in accretion disks, some with inner disk regions being richer in olivine relative to the disk wide composition, while other disks show the abundance of olivine is greater in the outer (vs the inner) part of the circumstellar disk, with differences in disk mineralogy being relating to type of star (e.g., T Tauri vs Herbig Ae/Be stars). The inner disk regions (a few AU) show higher abundances of large grains and generally higher crystallinity as compared to outer disk regions, suggesting grain growth occurs more rapidly in the inner disk regions. Recent results from geoneutrino measurements are most consistent with geochemical models that predict 20 TW of radiogenic power, less so with existing enstatite Earth models predicting less power in the planet. At 1 AU the Earth accreted a greater proportion of olivine to pyroxene (i.e., Mg/Si of pyrolite) than that available to the known enstatite chondrite parent body. The Earth accreted early in a reduced state, perhaps to the point of differentiating silicides into the core. Later accreted material was increasingly more oxidized. Stirring and mixing in the early solar system created opportunities for the Earth and enstatite chondrites to share some, but not all chemical and isotopic characteristics.

Two Late Cretaceous A-type granites related to the Yingwuling W-Sn polymetallic mineralization in Guangdong province, South China: Implications for petrogenesis, geodynamic setting, and mineralization

NASA Astrophysics Data System (ADS)

Zheng, Wei; Mao, Jingwen; Zhao, Haijie; Zhao, Caisheng; Yu, Xiaofei

2017-03-01

Major and trace elements, whole rock Sr-Nd-Pb isotopes, LA-ICP-MS U-Pb zircon dating, zircon trace elements and Hf isotope data are reported for a suite of A-type granites from Yingwuling pluton in western Guangdong province, South China. Zircon U-Pb ages obtained by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) show that biotite granite and alkali feldspar granite were emplaced in 81.3 ± 0.6 Ma and 80.6 ± 0.5 Ma, respectively. Both of the two suites have the petrographic and geochemical characteristics of A-type granite. These granitic rocks are metaluminous to weakly peraluminous and have pronounced contents of total alkalis (Na2O + K2O = 7.80-8.84%), Fe2O3T/MgO and Ga/Al ratios. They exhibit low MgO, CaO and TiO2 contents, enrichment in some LILEs and HFSEs (except for Zr, Eu and Y), depletion in Ba, Sr, P and Ti. They show A2 subtype affinity and were probably formed a temperature of 800 °C. The Yingwuling biotite granite has relatively high (87Sr/86Sr)i ratios of 0.70655 to 0.70928, low εNd(t) values of - 5.8 to - 4.2 and zircon εHf(t) values (- 5.70-1.37). Whole-rock Nd isotopic and zircon Hf isotopic two-stages model ages mostly vary from 1057 to 1506 Ma. The alkali feldspar granite display bulk rock εNd(t) values and (87Sr/86Sr)i ratios in the range of - 6.6 to - 6.1 and 0.70640 to 0.71077, respectively, and zircon εHf(t) values from - 5.44 to 0.54, with Mesoproterozoic T2DM for both Nd and Hf isotopes. Geochemical and isotopic data indicate the Yingwuling A-type granitic magmas were drived from mantle-crust interaction. Zircon grains of Yingwuling granites have relatively low Eu/Eu* and Ce4 +/Ce3 + ratios, indicating low oxygen fugacity. The visible tetrad effect in the Yingwuling granites indicates that it experienced strong fractionation and is close relationship to the W-Sn mineralization. Our new data together with previous published data indicate that Late Mesozoic A-type granitiods or alkaline intrusive rocks in South China can be grouped into four pulses: 195-180 Ma, 180-149 Ma, 136-116 Ma and 110-79 Ma. After 135 Ma, with a change in the polarity of the subduction of paleo-Pacific plate, the crust and lithospheric mantle in eastern China became progressively thinned causing the upwelling of asthenosphere, which would have triggered crustal rocks to partially melt and generate Yingwuling A-type granitic magmas.

The complete mitochondrial genome sequence of Eimeria innocua (Eimeriidae, Coccidia, Apicomplexa).

PubMed

Hafeez, Mian Abdul; Vrba, Vladimir; Barta, John Robert

2016-07-01

The complete mitochondrial genome of Eimeria innocua KR strain (Eimeriidae, Coccidia, Apicomplexa) was sequenced. This coccidium infects turkeys (Meleagris gallopavo), Bobwhite quails (Colinus virginianus), and Grey partridges (Perdix perdix). Genome organization and gene contents were comparable with other Eimeria spp. infecting galliform birds. The circular-mapping mt genome of E. innocua is 6247 bp in length with three protein-coding genes (cox1, cox3, and cytb), 19 gene fragments encoding large subunit (LSU) rRNA and 14 gene fragments encoding small subunit (SSU) rRNA. Like other Apicomplexa, no tRNA was encoded. The mitochondrial genome of E. innocua confirms its close phylogenetic affinities to Eimeria dispersa.

Functional analysis of human aromatic amino acid transporter MCT10/TAT1 using the yeast Saccharomyces cerevisiae.

PubMed

Uemura, Satoshi; Mochizuki, Takahiro; Kurosaka, Goyu; Hashimoto, Takanori; Masukawa, Yuki; Abe, Fumiyoshi

2017-10-01

Tryptophan is an essential amino acid in humans and an important serotonin and melatonin precursor. Monocarboxylate transporter MCT10 is a member of the SLC16A family proteins that mediates low-affinity tryptophan transport across basolateral membranes of kidney, small intestine, and liver epithelial cells, although the precise transport mechanism remains unclear. Here we developed a simple functional assay to analyze tryptophan transport by human MCT10 using a deletion mutant for the high-affinity tryptophan permease Tat2 in Saccharomyces cerevisiae. tat2Δtrp1 cells are defective in growth in YPD medium because tyrosine present in the medium competes for the low-affinity tryptophan permease Tat1 with tryptophan. MCT10 appeared to allow growth of tat2Δtrp1 cells in YPD medium, and accumulate in cells deficient for Rsp5 ubiquitin ligase. These results suggest that MCT10 is functional in yeast, and is subject to ubiquitin-dependent quality control. Whereas growth of Tat2-expressing cells was significantly impaired by neutral pH, that of MCT10-expressing cells was nearly unaffected. This property is consistent with the transport mechanism of MCT10 via facilitated diffusion without a need for pH gradient across the plasma membrane. Single-nucleotide polymorphisms (SNPs) are known to occur in the human MCT10 coding region. Among eight SNP amino acid changes in MCT10, the N81K mutation completely abrogated tryptophan import without any abnormalities in the expression or localization. In the MCT10 modeled structure, N81 appeared to protrude into the putative trajectory of tryptophan. Plasma membrane localization of MCT10 and the variant proteins was also verified in human embryonic kidney 293T cells. Copyright © 2017 Elsevier B.V. All rights reserved.

BADGER v1.0: A Fortran equation of state library

NASA Astrophysics Data System (ADS)

Heltemes, T. A.; Moses, G. A.

2012-12-01

The BADGER equation of state library was developed to enable inertial confinement fusion plasma codes to more accurately model plasmas in the high-density, low-temperature regime. The code had the capability to calculate 1- and 2-T plasmas using the Thomas-Fermi model and an individual electron accounting model. Ion equation of state data can be calculated using an ideal gas model or via a quotidian equation of state with scaled binding energies. Electron equation of state data can be calculated via the ideal gas model or with an adaptation of the screened hydrogenic model with ℓ-splitting. The ionization and equation of state calculations can be done in local thermodynamic equilibrium or in a non-LTE mode using a variant of the Busquet equivalent temperature method. The code was written as a stand-alone Fortran library for ease of implementation by external codes. EOS results for aluminum are presented that show good agreement with the SESAME library and ionization calculations show good agreement with the FLYCHK code. Program summaryProgram title: BADGERLIB v1.0 Catalogue identifier: AEND_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEND_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 41 480 No. of bytes in distributed program, including test data, etc.: 2 904 451 Distribution format: tar.gz Programming language: Fortran 90. Computer: 32- or 64-bit PC, or Mac. Operating system: Windows, Linux, MacOS X. RAM: 249.496 kB plus 195.630 kB per isotope record in memory Classification: 19.1, 19.7. Nature of problem: Equation of State (EOS) calculations are necessary for the accurate simulation of high energy density plasmas. Historically, most EOS codes used in these simulations have relied on an ideal gas model. This model is inadequate for low-temperature, high-density plasma conditions; the gaseous and liquid phases; and the solid phase. The BADGER code was developed to give more realistic EOS data in these regimes. Solution method: BADGER has multiple, user-selectable models to treat the ions, average-atom ionization state and electrons. Ion models are ideal gas and quotidian equation of state (QEOS), ionization models are Thomas-Fermi and individual accounting method (IEM) formulation of the screened hydrogenic model (SHM) with l-splitting, electron ionization models are ideal gas and a Helmholtz free energy minimization method derived from the SHM. The default equation of state and ionization models are appropriate for plasmas in local thermodynamic equilibrium (LTE). The code can calculate non-LTE equation of state (EOS) and ionization data using a simplified form of the Busquet equivalent-temperature method. Restrictions: Physical data are only provided for elements Z=1 to Z=86. Multiple solid phases are not currently supported. Liquid, gas and plasma phases are combined into a generalized "fluid" phase. Unusual features: BADGER divorces the calculation of average-atom ionization from the electron equation of state model, allowing the user to select ionization and electron EOS models that are most appropriate to the simulation. The included ion ideal gas model uses ground-state nuclear spin data to differentiate between isotopes of a given element. Running time: Example provided only takes a few seconds to run.

Cross sections of the 36Ar(d,α)34mCl, 40Ar(d,α)38Cl, and 40Ar(d,p)41Ar nuclear reactions below 8.4 MeV.

PubMed

Engle, J W; Severin, G W; Barnhart, T E; Knutson, L D; Nickles, R J

2012-02-01

We have measured the cross section for production of the medically interesting isotope (34m)Cl, along with (38)Cl and (41)Ar, using deuteron bombardments of (36)Ar and (40)Ar below 8.4 MeV. ALICE/ASH analytical codes were employed to determine the shape of nuclear excitation functions, and experiments were performed using the University of Wisconsin tandem electrostatic accelerator to irradiate thin targets of argon gas. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comparison between experimental data and Monte-Carlo simulations of neutron production in spallation reactions of 0.7-1.5 GeV protons on a thick, lead target

NASA Astrophysics Data System (ADS)

Krása, A.; Majerle, M.; Krízek, F.; Wagner, V.; Kugler, A.; Svoboda, O.; Henzl, V.; Henzlová, D.; Adam, J.; Caloun, P.; Kalinnikov, V. G.; Krivopustov, M. I.; Stegailov, V. I.; Tsoupko-Sitnikov, V. M.

2006-05-01

Relativistic protons with energies 0.7-1.5 GeV interacting with a thick, cylindrical, lead target, surrounded by a uranium blanket and a polyethylene moderator, produced spallation neutrons. The spatial and energetic distributions of the produced neutron field were measured by the Activation Analysis Method using Al, Au, Bi, and Co radio-chemical sensors. The experimental yields of isotopes induced in the sensors were compared with Monte-Carlo calculations performed with the MCNPX 2.4.0 code.

Confirmation of shutdown cooling effects

NASA Astrophysics Data System (ADS)

Sato, Kotaro; Tabuchi, Masato; Sugimura, Naoki; Tatsumi, Masahiro

2015-12-01

After the Fukushima accidents, all nuclear power plants in Japan have gradually stopped their operations and have long periods of shutdown. During those periods, reactivity of fuels continues to change significantly especially for high-burnup UO2 fuels and MOX fuels due to radioactive decays. It is necessary to consider these isotopic changes precisely, to predict neutronics characteristics accurately. In this paper, shutdown cooling (SDC) effects of UO2 and MOX fuels that have unusual operation histories are confirmed by the advanced lattice code, AEGIS. The calculation results show that the effects need to be considered even after nuclear power plants come back to normal operation.

Annual Report on the Activities and Publications of the DHS-DNDO-NTNFC Sponsored Post-doctoral Fellow at Los Alamos National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rim, Jung Ho; Tandon, Lav

This report is a summary of the projects Jung Rim is working on as a DHS postdoctoral fellow at Los Alamos National Laboratory. These research projects are designed to explore different radioanalytical methods to support nuclear forensics applications. The current projects discussed here include development of alpha spectroscopy method for 240/239Pu Isotopic ratio measurement, non-destructive uranium assay method using gamma spectroscopy, and 236U non-destructive uranium analysis using FRAM code. This report documents the work that has been performed since the start of the postdoctoral appointment.

Design of a setup for 252Cf neutron source for storage and analysis purpose

NASA Astrophysics Data System (ADS)

Hei, Daqian; Zhuang, Haocheng; Jia, Wenbao; Cheng, Can; Jiang, Zhou; Wang, Hongtao; Chen, Da

2016-11-01

252Cf is a reliable isotopic neutron source and widely used in the prompt gamma ray neutron activation analysis (PGNAA) technique. A cylindrical barrel made by polymethyl methacrylate contained with the boric acid solution was designed for storage and application of a 5 μg 252Cf neutron source. The size of the setup was optimized with Monte Carlo code. The experiments were performed and the results showed the doses were reduced with the setup and less than the allowable limit. The intensity and collimating radius of the neutron beam could also be adjusted through different collimator.

Robust 3D face landmark localization based on local coordinate coding.

PubMed

Song, Mingli; Tao, Dacheng; Sun, Shengpeng; Chen, Chun; Maybank, Stephen J

2014-12-01

In the 3D facial animation and synthesis community, input faces are usually required to be labeled by a set of landmarks for parameterization. Because of the variations in pose, expression and resolution, automatic 3D face landmark localization remains a challenge. In this paper, a novel landmark localization approach is presented. The approach is based on local coordinate coding (LCC) and consists of two stages. In the first stage, we perform nose detection, relying on the fact that the nose shape is usually invariant under the variations in the pose, expression, and resolution. Then, we use the iterative closest points algorithm to find a 3D affine transformation that aligns the input face to a reference face. In the second stage, we perform resampling to build correspondences between the input 3D face and the training faces. Then, an LCC-based localization algorithm is proposed to obtain the positions of the landmarks in the input face. Experimental results show that the proposed method is comparable to state of the art methods in terms of its robustness, flexibility, and accuracy.

The effect of prolonged treatment with imipramine on the biosynthesis and functional characteristics of D2 dopamine receptors in the rat caudate putamen

PubMed Central

Dziedzicka-Wasylewska, Marta; Rogoż, Renata

1998-01-01

The present study shows the effects of imipramine in a single dose (10 mg kg−1, p.o.) or following repeated (14 days, twice a day) treatment on the level of mRNA coding for D2 dopamine receptors in the rat caudate putamen (CP). Repeated administration of imipramine resulted in the increase of the level of mRNA coding for D2 dopamine receptors. Radioligand binding studies with the D2 receptor agonist, [3H]-N-0437, indicated, that following imipramine administration, the affinity of the agonist for the D2 dopamine receptor significantly increased, though without any alterations in the Bmax. Pharmacological manipulations (by use of forskolin, GppNHp and quinpirole) of the cyclic AMP generating system, ex vivo following administration of imipramine indicated that an up-regulation of factors inhibiting cyclic GMP formation takes place. Most probably it is the D2 dopamine receptor which undergoes functional up-regulation, resulting from the enhancement of its biosynthesis. PMID:9535010

Petrologic evolution of Miocene-Pliocene mafic volcanism in the Kangal and Gürün basins (Sivas-Malatya), central east Anatolia: Evidence for Miocene anorogenic magmas contaminated by continental crust

NASA Astrophysics Data System (ADS)

Kocaarslan, Ayça; Ersoy, E. Yalçın

2018-06-01

This study discusses the geochemical features of the Early-Middle Miocene and Pliocene basaltic (SiO2 = 46-52; MgO = 6-10 wt%) to andesitic (SiO2 = 59; MgO = 4 wt%) rocks exposed in the Gürün and Kangal basins (Sivas, eastern part of central Anatolia), respectively. The basaltic rocks are characterized by alkaline to tholeiitic affinities, while the more evolved andesitic samples show calc-alkaline affinity. Trace element variations reveal that they can be evaluated in three sub-groups, each represented by different contents of trace elements for given Nb contents. Primary magmas of each groups were likely produced by different degrees of partial melting ( 1-2, 2-3, 7-10% respectively) from a common mantle source, subsequently underwent different degrees of fractionation and crustal contamination. Derivation from a common mantle source of the primitive magmas of each group is supported by similar Sr, Nd and Pb isotopic ratios. Increasing degrees of partial melting seem to be responsible for the alkaline to tholeiitic variation among the basaltic samples, while higher degrees of crustal contamination (AFC) resulted in calc-alkaline affinity of the more evolved samples. Most primitive Pliocene samples show intra-plate (anorogenic) geochemical features, while the more evolved Miocene calc-alkaline samples resemble geochemically subduction-related (orogenic) magmatic rocks. However, on the basis of detailed geochemical models, we propose that the calc-alkaline affinity among the Miocene samples can also be gained by crustal contamination of their primary magmas which were also anorogenic in character. If this is true, overall, the Miocene and Pliocene basaltic to andesitic rocks in the Gürün and Kangal basins appear to may have formed by variable degrees of partial melting of a common anorogenic mantle that had not been subject to subduction-related metasomatism. This is an alternative approach to the general view assuming the Early-Middle Miocene magmatic activity in the region was derived from subduction-modified mantle sources in response to subduction of the Arabian Plate under the Anatolian Plate. This hypothesis further implies that either delamination of the sub-continental lithosphere or slab break-off processes beneath the central to eastern Anatolia might took place well before the Miocene, thus allowing upwelling unaltered mantle to provide the source of the Miocene to Pliocene volcanic rocks.

[Identification of the interacting proteins with S100A8 or S100A9 by affinity purification and mass spectrometry].

PubMed

Wang, Jing; Zhang, Xuemei; Li, Zheng; Li, Xiayu; Ma, Jian; Shen, Shourong

2017-04-28

To identify the interacting proteins with S100A8 or S100A9 in HEK293 cell line by flag-tag affinity purification and liquid chromatography mass spectrometry/mass spectrometry (LC-MS/MS).
 Methods: The p3×Flag-CMV-S100A8 and p3×Flag-CMV-S100A9 expression vectors were constructed by inserting S100A8 or S100A9 coding sequence. The recombinant plasmids were then transfected into HEK293 cells. Affinity purification and LC-MS/MS were applied to identify the proteins interacting with S100A8 or S100A9. Bioinformatics analysis was used to seek the gene ontology of the interacting proteins. Co-immunoprecipitation (Co-IP) was applied to confirm the proteins interacted with S100A8 or S100A9.
 Results: Fourteen proteins including pyruvate kinase, muscle (PKM), nucleophosmin (NPM1) and eukaryotic translation initiation factor 5A (EIF5A), which potentially interacted with S100A8, were successfully identified by Flag-tag affinity purification followed by LC-MS/MS analysis. Six proteins, such as tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon (14-3-3ε) and PKM, which potentially interacted with S100A9, were successfully identified. Gene ontology analysis of the identified proteins suggested that proteins interacted with S100A8 or S100A9 were involved in several biological pathways, including canonical glycolysis, positive regulation of NF-κB transcription factor activity, negative regulation of apoptotic process, cell-cell adhesion, etc. Co-IP experiment confirmed that PKM2 can interact with both S100A8 and S100A9, and 14-3-3ε can interact with S100A8.
 Conclusion: PKM2 is identified to interact with both S100A8 and S100A9, while 14-3-3ε can interact with S100A9. These results may provide a new clue for the role of S100A8 or S100A9 in the progression of colitis-associated colorectal cancer.

Covalent attachment of Arc repressor subunits by a peptide linker enhances affinity for operator DNA.

PubMed

Robinson, C R; Sauer, R T

1996-01-09

By designing a recombinant gene containing tandem copies of the arc coding sequence with intervening DNA encoding the linker sequence GGGSGGGTGGGSGGG, the two subunits of the P22 Are repressor dimer have been covalently linked to form a single-chain protein called Arc-L1-Arc. The 15-residue linker joins the C-terminus of one monomer to the N-terminus of the second, a distance of approximately 45 A in the Arc-operator cocrystal structure. Arc-L1-Arc is expressed at high levels in Escherichia coli, with no evidence of degradation or proteolytic clipping of the linker, and is more active than wild-type Arc in repression assays. The purified Arc-L1-Arc protein has the molecular weight expected for the designed protein and unfolds cooperatively, reversibly, and with no concentration dependence in thermal-denaturation studies. Arc-L1-Arc protects operator DNA in a manner indistinguishable from that of wild-type Arc in DNase I and copper-phenanthroline footprinting studies, but the covalent attachment of the two monomers results in enhanced affinity for operator DNA. Arc-L1-Arc binds operator DNA half-maximally at a concentration of 1.7 pM, compared with the wild-type value of 185 pM, and also binds DNA fragments containing the left or right operator half-sites more tightly than wild type. Because wild-type Arc is monomeric at sub-nanomolar concentrations and must dimerize before binding to the operator, it was anticipated that Arc-L1-Arc would exhibit a lower half-maximal binding concentration. However, even when the change from a monomeric to a dimeric species is taken into account, the affinity of Arc-L1-Arc for operator and half-operator DNA is greater than the wild-type affinity. This tighter binding appears to result from slower dissociation, as Arc-L1-Arc DNA complexes with full or half-site operators dissociate at rates 5-10 times slower than the corresponding Arc--DNA complexes. Hence, the activity of the designed Arc-L1-Arc protein is substantially increased relative to wild-type Arc in a variety of assays.