scholarly journals Enzyme specific isotope effects of the Nap and Nar nitrate reductases

2020 ◽  
Author(s):  
Ciara K. Asamoto ◽  
Kaitlin R. Rempfert ◽  
Victoria H. Luu ◽  
Adam D. Younkin ◽  
Sebastian H. Kopf
Keyword(s):  
Nitrogen Isotopes ◽  
Isotope Effects ◽  
Terrestrial Ecosystems ◽  
Isotopic Signature ◽  
Main Process ◽  
Isotopic Signatures ◽  
Isotopic Pattern ◽  
Almost All ◽  
End Members ◽  
Nitrate Reductases

AbstractDissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR fractionates the stable isotopes of nitrogen (14N, 15N) and oxygen (16O, 18O) and thus imparts an isotopic signature on residual pools of nitrate in many environments. Data on the relationship between the resulting isotopic pattern in oxygen versus nitrogen isotopes (18ε / 15ε) suggests systematic differences exist between marine and terrestrial ecosystems that are not fully understood. DNR can be catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases, and previous work has revealed differences in their 18ε / 15ε isotopic signatures. In this study, we thus examine the 18ε / 15ε of six different nitrate-reducing microorganisms that encode Nar, Nap or both enzymes, as well gene deletion mutants of the enzymes’ catalytic subunits (NarG and NapA) to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of the 18ε / 15ε fractionation ratios of all examined nitrate reductases form two distinct, non-overlapping peaks centered around a 18ε / 15ε proportionality of 0.55 and a 18ε / 15ε proportionality of 0.91, respectively. All Nap reductases studied to date cluster around the lower proportionality (0.55) and none exceed a 18ε / 15ε proportionality of 0.68. Almost all Nar reductases, on the contrary, cluster tightly around the higher proportionality (0.91) with no values below a 18ε / 15ε proportionality of 0.84 with the notable exception of the Nar reductases from the genus Bacillus which fall around 0.62 and thus closely resemble the isotopic fingerprints of the Nap reductases. Our findings confirm the existence of two remarkably distinct isotopic end-members in the dissimilatory nitrate reductases that could indeed explain differences in coupled N and O isotope fractionation between marine and terrestrial systems, and almost but not fully match reductase phylogeny.

scholarly journals Isotopic signatures of production and uptake of H<sub>2</sub> by soil

2015 ◽  
Vol 15 (22) ◽  
pp. 13003-13021 ◽  
Author(s):  
Q. Chen ◽  
M. E. Popa ◽  
A. M. Batenburg ◽  
T. Röckmann
Keyword(s):  
Isotope Effects ◽  
Deposition Velocity ◽  
Isotopic Fractionation ◽  
Isotopic Signature ◽  
Deuterium Content ◽  
Forest Site ◽  
Fractionation Factor ◽  
Isotopic Signatures ◽  
The Difference ◽  
Isotope Equilibrium

Abstract. Molecular hydrogen (H2) is the second most abundant reduced trace gas (after methane) in the atmosphere, but its biogeochemical cycle is not well understood. Our study focuses on the soil production and uptake of H2 and the associated isotope effects. Air samples from a grass field and a forest site in the Netherlands were collected using soil chambers. The results show that uptake and emission of H2 occurred simultaneously at all sampling sites, with strongest emission at the grassland sites where clover (N2 fixing legume) was present. The H2 mole fraction and deuterium content were measured in the laboratory to determine the isotopic fractionation factor during H2 soil uptake (αsoil) and the isotopic signature of H2 that is simultaneously emitted from the soil (δDsoil). By considering all net-uptake experiments, an overall fractionation factor for deposition of αsoil = kHD / kHH = 0.945 ± 0.004 (95 % CI) was obtained. The difference in mean αsoil between the forest soil 0.937 ± 0.008 and the grassland 0.951 ± 0.026 is not statistically significant. For two experiments, the removal of soil cover increased the deposition velocity (vd) and αsoil simultaneously, but a general positive correlation between vd and αsoil was not found in this study. When the data are evaluated with a model of simultaneous production and uptake, the isotopic composition of H2 that is emitted at the grassland site is calculated as δDsoil = (−530 ± 40) ‰. This is less deuterium depleted than what is expected from isotope equilibrium between H2O and H2.

scholarly journals Isotopic signatures of production and uptake of H<sub>2</sub> by soil

2015 ◽  
Vol 15 (17) ◽  
pp. 23457-23506 ◽  
Author(s):  
Q. Chen ◽  
M. E. Popa ◽  
A. M. Batenburg ◽  
T. Röckmann
Keyword(s):  
Isotope Effects ◽  
Deposition Velocity ◽  
Isotopic Fractionation ◽  
Isotopic Signature ◽  
Deuterium Content ◽  
Forest Site ◽  
Fractionation Factor ◽  
Isotopic Signatures ◽  
The Difference ◽  
Isotope Equilibrium

Abstract. Molecular hydrogen (H2) is the second most abundant reduced trace gas (after methane) in the atmosphere, but its biogeochemical cycle is not well understood. Our study focuses on the soil production and uptake of H2 and the associated isotope effects. Air samples from a grass field and a forest site in the Netherlands were collected using soil chambers. The results show that uptake and emission of H2 occurred simultaneously at all sampling sites, with strongest emission at the grassland sites where clover (N2 fixing legume) was present. The H2 mole fraction and deuterium content were measured in the laboratory to determine the isotopic fractionation factor during H2 soil uptake (αsoil) and the isotopic signature of H2 that is simultaneously emitted from the soil (δDsoil). By considering all net-uptake experiments, an overall fractionation factor for deposition of αsoil = kHD/kHH = 0.945 ± 0.004 (95 % CI) was obtained. The difference in mean αsoil between the forest soil 0.937 ± 0.008 and the grassland 0.951 ± 0.025 is not statistically significant. For two experiments, the removal of soil cover increased the deposition velocity (vd) and αsoil simultaneously, but a general positive correlation between vd and αsoil was not found in this study. When the data are evaluated with a model of simultaneous production and uptake, the isotopic composition of H2 that is emitted at the grassland site is calculated as δDsoil = (−530 ± 40) ‰. This is less deuterium-depleted than what is expected from isotope equilibrium between H2O and H2.

scholarly journals The δ13C, δ18O and Δ47 records in biogenic, pedogenic and geogenic carbonate types from paleosol-loess sequence and their paleoenvironmental meaning

2021 ◽  
pp. 1-17
Author(s):  
Kazem Zamanian ◽  
Alex R. Lechler ◽  
Andrew J. Schauer ◽  
Yakov Kuzyakov ◽  
Katharine W. Huntington
Keyword(s):  
Land Snail ◽  
Isotopic Signature ◽  
Sediment Layer ◽  
Isotopic Signatures ◽  
Pedogenic Carbonates ◽  
Rhine Valley ◽  
Clumped Isotope ◽  
Time Specific ◽  
Sediment Layers ◽  
Paleoenvironmental Reconstructions

Abstract Paleoenvironmental reconstructions are commonly based on isotopic signatures of a variety of carbonate types, including rhizoliths and land-snail shells, present in paleosol-loess sequences. However, various carbonate types are formed through distinct biotic and abiotic processes over various periods, and therefore may record diverging environmental information in the same sedimentological layer. Here, we investigate the effects of carbonate type on δ13C, δ18O, and clumped isotope-derived paleotemperature [T(Δ47)] from the Quaternary Nussloch paleosol-loess sequence (Rhine Valley, SW Germany). δ13C, δ18O, and T(Δ47) values of co-occurring rhizoliths (-8.2‰ to -5.8‰, -6.1‰ to -5.9‰, 12–32°C, respectively), loess dolls (-7.0‰, -5.6‰, 23°C), land-snail shells (-8.1‰ to -3.2‰, -4.0‰ to -2.2‰, 12–38°C), earthworm biospheroliths (-11‰, -4.7‰, 8°C), and “bulk” carbonates (-1.9‰ to -0.5‰, -5.6‰ to -5.3‰, 78–120°C) from three sediment layers depend systematically on the carbonate type, admixture from geogenic carbonate, and the duration of formation periods. Based on these findings, we provide a comprehensive summary for the application of the three isotopic proxies of δ13C, δ18O, and Δ47 in biogenic and pedogenic carbonates present in the same sediment layer to reconstruct paleoenvironments (e.g., local vegetation, evaporative conditions, and temperature). We conclude that bulk carbonates in Nussloch loess should be excluded from paleoenvironmental reconstructions. Instead, pedogenic and biogenic carbonates should be used to provide context for interpreting the isotopic signature for detailed site- and time-specific paleoenvironmental information.

scholarly journals Isotopic hydrograph separation in two small mountain catchments during multiple events

2018 ◽  
Vol 44 (2) ◽  
pp. 453 ◽  
Author(s):  
L. Holko ◽  
S. Bičárová ◽  
J. Hlavčo ◽  
M. Danko ◽  
Z. Kostka
Keyword(s):  
Isotopic Composition ◽  
Elevation Gradient ◽  
Rain Gauge ◽  
Windward Side ◽  
Storm Event ◽  
Hydrograph Separation ◽  
Tatra Mountains ◽  
Isotopic Signatures ◽  
Water Fractions ◽  
End Members

Two-component isotopic hydrograph separation (IHS) was developed to determine the event- and pre-event components of a single storm event. Its application for several sucessive events requires repeated determination of isotopic signatures of end-members (precipitation, pre-event component) for each event. The existence of several possible alternative signatures results in differences in calculated contributions of event-/pre- event components. This article addresses the question of how big the differences could be in small mountain catchments with different methods for detemining the end member signatures. We analyzed data on isotopic composition of daily/event precipitation at different elevations in two catchments located in the highest part of the Carpathians in July 2014.The isotopic composition of streamflow sampled every 4-6 hours was analyzed as well. Elevational gradients of δ18O and δ2H in precipitation in the study period were -0.18 ‰ 100 m-1 and -1.1 ‰ 100 m-1, respectively. An elevation gradient in deuterium excess (0.29 ‰ 100 m-1) was also found. Precipitation on the windward side of the mountains was isotopically lighter than expected for a given rain gauge elevation. Five large rainfall-runoff events occurred in the study period in the meso-scale catchment of the Jalovecký creek (Western Tatra Mountains, area 22.2 km2) and in the headwater catchment of the Škaredý creek (High Tatra Mountains, area 1.4 km2). Isotopic hydrograph separation was conducted using eight options for the isotopic signatures of event and pre-event water. The isotopic signature of the event water (rainfall) was alternatively represented by data from high or low elevations. Pre-event water was represented either by the streamflow before the event or by the value taken from the statistics of the long-term data on isotopic composition of the stream. Both isotopes (18O and 2H) were used to calculate event water fractions during peak flows of individual events. Calculated peak flow event water fractions were below 0.2-0.3 for most events. However, the differences in calculated event water fractions for alternative isotopic composition of end-members were significant even if we did not take into account changes in isotopic composition during individual rainfalls. Coefficients of variation for event water fractions calculated for various options varied during individual events from 0.14 to 0.36. It is therefore perhaps better to use a range of possible values instead of a single accurate number to interpret the IHS results. Hydrograph separations based on 18O and 2H provided similar results.

scholarly journals The Moroccan Massive Sulphide Deposits: Evidence for a Polyphase Mineralization

Minerals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 156 ◽  
Author(s):  
Abderrahim Essaifi ◽  
Kathryn Goodenough ◽  
Fernando Tornos ◽  
Abdelhak Outigua ◽  
Abdelmalek Ouadjou ◽  
...  
Keyword(s):  
Lead Isotopes ◽  
Shear Zones ◽  
Structural Features ◽  
Isotopic Signature ◽  
Ore Deposits ◽  
Massive Sulphide ◽  
Isotopic Signatures ◽  
Crustal Block ◽  
Massive Sulphide Deposits ◽  
Sulphide Deposits

This work provides an overview of the geological, geochemical, and metallogenic data available up to date on the Moroccan massive sulphide deposits, including some new results, and then discusses the evidences for the epigenetic and syngenetic hypotheses. All of the ore deposits are located within a crustal block located at the intersection between two major shear zones and are characterized by a sustained and long-lived magmatic activity. The ore deposits are located within second-order shear zones, which played an important role in controlling the geometry of the mineralization. The mineralization lacks the unequivocal textural and structural features that are indicative of a sedimentary or diagenetic origin, and a syntectonic to late-tectonic pyrite-rich assemblage is superimposed on an earlier, pretectonic to syntectonic pyrrhotite-rich mineralization. Each deposit has a distinctive pyrrhotite sulfur isotopic signature, while the sulfur isotopic signature of pyrite is similar in all deposits. Lead isotopes suggest a shift from a magmatic source during the pyrrhotite-rich mineralization to a source that is inherited from the host shales during the pyrite-rich mineralization. The O/H isotopic signatures record a predominance of fluids of metamorphic derivation. These results are consistent with a model in which an earlier pyrrhotite-rich mineralization, which formed during transtension, was deformed and then remobilized to pyrite-rich mineralization during transpression.

scholarly journals Exploring the Diversity of the Marine Environment for New Anti-cancer Compounds

2021 ◽  
Vol 7 ◽  
Author(s):  
Divya L. Dayanidhi ◽  
Beatrice C. Thomas ◽  
Joshua S. Osterberg ◽  
Mallissa Vuong ◽  
Giselle Vargas ◽  
...  
Keyword(s):  
Terrestrial Ecosystems ◽  
Cancer Therapies ◽  
Clinical Use ◽  
Marine Environments ◽  
Cancer Drugs ◽  
Hallmarks Of Cancer ◽  
Natural Sources ◽  
Anti Cancer ◽  
Almost All ◽  
Untapped Resource

Marine ecosystems contain over 80% of the world’s biodiversity, and many of these organisms have evolved unique adaptations enabling survival in diverse and challenging environments. The biodiversity within the world’s oceans is a virtually untapped resource for the isolation and development of novel compounds, treatments, and solutions to combat human disease. In particular, while over half of our anti-cancer drugs are derived from natural sources, almost all of these are from terrestrial ecosystems. Yet, even from the limited analyses to date, a number of marine-derived anti-cancer compounds have been approved for clinical use, and several others are currently in clinical trials. Here, we review the current suite of marine-derived anti-cancer drugs, with a focus on how these compounds act upon the hallmarks of cancer. We highlight potential marine environments and species that could yield compounds with unique mechanisms. Continued exploration of marine environments, along with the characterization and screening of their inhabitants for unique bioactive chemicals, could prove fruitful in the hunt for novel anti-cancer therapies.

The aqueous chemistry of uranium minerals. Part I. Divalent cation zippeïte

1979 ◽  
Vol 43 (328) ◽  
pp. 539-541 ◽  
Author(s):  
David F. Haacke ◽  
Peter A. Williams
Keyword(s):  
Metal Ion ◽  
Metal Speciation ◽  
Divalent Metal ◽  
Free Energies ◽  
Naturally Occurring ◽  
Solution Studies ◽  
Chemical Studies ◽  
Divalent Metal Ion ◽  
Almost All ◽  
End Members

SynopsisFree energies of formation of divalent metal ion zippeïtes, M2(UO2)6(SO4)3(OH)10 ·nH2O, M = Mg,Co,Ni,Zn have been determined from solution studies and metal speciation calculations, in water. It is found that in the compounds, the number of molecules of water of crystallization is equal to 8. This is at variance with a previous report (Frondel et al., 1976), but it has been found that some at least of the water content of zippeite is either nonessential or very loosely bound in the structure. Based on the octahydrate formulation, values are −3506, −12695, −12683 and −12870±4 kJ mol−1 for the Mg,Co,Ni and Zn end-members, respectively. Almost all of the differences in the values are accounted for by those values for the metal ions alone with the exception of Znzippeïte where a discrepancy of some 22 kJ mol−1 is found. Even this value is small however, and the chemical studies indicate that extensive mutual solid solution between all end members is to be expected. These findings agree perfectly with observations on the composition of naturally occurring zippeite minerals of this group.

scholarly journals Kinetic isotope effects of <sup>12</sup>CH<sub>3</sub>D  + OH and <sup>13</sup>CH<sub>3</sub>D  + OH from 278 to 313 K

2016 ◽  
Vol 16 (7) ◽  
pp. 4439-4449 ◽  
Author(s):  
L. M. T. Joelsson ◽  
J. A. Schmidt ◽  
E. J. K. Nilsson ◽  
T. Blunier ◽  
D. W. T. Griffith ◽  
...  
Keyword(s):  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
State Theory ◽  
Atmospheric Methane ◽  
Isotopic Signatures ◽  
Budget Analysis ◽  
Kinetic Isotope ◽  
Methane Budget ◽  
Source Signal ◽  
Clumped Isotope

Abstract. Methane is the second most important long-lived greenhouse gas and plays a central role in the chemistry of the Earth's atmosphere. Nonetheless there are significant uncertainties in its source budget. Analysis of the isotopic composition of atmospheric methane, including the doubly substituted species 13CH3D, offers new insight into the methane budget as the sources and sinks have distinct isotopic signatures. The most important sink of atmospheric methane is oxidation by OH in the troposphere, which accounts for around 84 % of all methane removal. Here we present experimentally derived methane + OH kinetic isotope effects and their temperature dependence over the range of 278 to 313 K for CH3D and 13CH3D; the latter is reported here for the first time. We find kCH4/kCH3D = 1.31 ± 0.01 and kCH4/k13CH3D = 1.34 ± 0.03 at room temperature, implying that the methane + OH kinetic isotope effect is multiplicative such that (kCH4/k13CH4)(kCH4/kCH3D) = kCH4/k13CH3D, within the experimental uncertainty, given the literature value of kCH4/k13CH4 = 1.0039 ± 0.0002. In addition, the kinetic isotope effects were characterized using transition state theory with tunneling corrections. Good agreement between the experimental, quantum chemical, and available literature values was obtained. Based on the results we conclude that the OH reaction (the main sink of methane) at steady state can produce an atmospheric clumped isotope signal (Δ(13CH3D) = ln([CH4][13CH3D]/[13CH4][CH3D])) of 0.02 ± 0.02. This implies that the bulk tropospheric Δ(13CH3D) reflects the source signal with relatively small adjustment due to the sink signal (i.e., mainly OH oxidation).

Investigating the diet of the omnivorous mirid Dicyphus hesperus using stable isotopes

2009 ◽  
Vol 99 (4) ◽  
pp. 347-358 ◽  
Author(s):  
J.A. Bennett ◽  
D.R. Gillespie ◽  
S.L. VanLaerhoven
Keyword(s):  
Nitrogen Isotopes ◽  
Trophic Position ◽  
Isotope Analysis ◽  
Isotopic Signature ◽  
Encarsia Formosa ◽  
Verbascum Thapsus ◽  
Diet Variability ◽  
Feeding Trials ◽  
Plant Sources ◽  
Over Time

AbstractOmnivory involves numerous feeding relationships and a complex web of interactions. When using omnivores in biocontrol, these interactions need to be understood to maximize feeding on the target species and minimize non-target interactions. Dicyphus hesperus is used along with Encarsia formosa for biocontrol of whiteflies in greenhouse tomato crops. Dicyphus hesperus is a generalist omnivore which feeds on all components of the system. To quantify these interactions, stable isotope analysis was used to identify trophic position with nitrogen isotopes (δ15N) and plant sources with carbon isotopes (δ13C). Feeding trials were used to establish baseline isotopic data for D. hesperus and their diet, including Verbascum thapsus, an alternative plant food. Cage trials were used to monitor population abundances and the isotopic signature of D. hesperus. In feeding trials, D. hesperus were enriched relative to their food, suggesting an elevated trophic position. However, large amounts of isotopic variation were found within all diet components, with only V. thapsus exhibiting a distinct signature. In cage trials, the average δ15N and δ13C of the omnivore declined over time, coinciding with declines in total available prey, though it may be confounded by changes in temperature. The range of δ13C, but not the range of δ15N, also declined over time. This suggests a change in the plant source within the diet, but also some unquantified variability within the population. We suggest that diet variability exists within D. hesperus populations, declining as prey become less abundant.

scholarly journals Matrix Expression of Convolution and Its Generalized Continuous Form

Symmetry ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1791
Author(s):  
Young Hee Geum ◽  
Arjun Kumar Rathie ◽  
Hwajoon Kim
Keyword(s):  
Neural Networks ◽  
Integral Transforms ◽  
Main Process ◽  
Continuous Form ◽  
Core Technology ◽  
New Variant ◽  
The Matrix ◽  
Matrix Expression ◽  
Almost All ◽  
Laplace Type

In this paper, we consider the matrix expression of convolution, and its generalized continuous form. The matrix expression of convolution is effectively applied in convolutional neural networks, and in this study, we correlate the concept of convolution in mathematics to that in convolutional neural network. Of course, convolution is a main process of deep learning, the learning method of deep neural networks, as a core technology. In addition to this, the generalized continuous form of convolution has been expressed as a new variant of Laplace-type transform that, encompasses almost all existing integral transforms. Finally, we would, in this paper, like to describe the theoretical contents as detailed as possible so that the paper may be self-contained.

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