The time of sands: Quartz-rich sand deposits as renewable resource
[No abstract available]
Electronic Green Journal↗
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Utilization of integrated correlative light and electron microscopy (iCLEM) for imaging sedimentary organic matter
We report here a new microscopic technique for imaging and identifying sedimentary organic matter in geologic materials that combines inverted fluorescence microscopy with scanning electron microscopy and allows for sequential imaging of the same region of interest without transferring the sample between instruments. This integrated correlative light and electron microscopy technique is demonstrated with observations from an immature lacustrine oil shale from the Eocene Green River Mahogany Zone and mid‐oil window paralic shale from the Upper Cretaceous Tuscaloosa Group. This technique has the potential to allow for identification and characterization of organic matter in shale hydrocarbon reservoirs that is not possible using either light or electron microscopy alone, and may be applied to understanding the organic matter type and thermal regime in which organic nanoporosity forms, thereby reducing uncertainty in the estimation of undiscovered hydrocarbon resources.
Journal of Microscopy↗
Identification of a small, naked virus in tumor-like aggregates in cell lines derived from a green turtle, Chelonia mydas, with fibropapillomas
Serial cultivation of cell lines derived from lung, testis, periorbital and tumor tissues of a green turtle (Chelonia mydas) with fibropapillomas resulted in the in vitro formation of tumor-like cell aggregates, ranging in size from 0.5 to 2.0 mm in diameter. Successful induction of tumor-like aggregates was achieved in a cell line derived from lung tissue of healthy green turtles, following inoculation with cell-free media from these tumor-bearing cell lines, suggesting the presence of a transmissible agent. Thin-section electron microscopy of the cell aggregates revealed massive collagen deposits and intranuclear naked viral particles, measuring 5095 nm in diameter. These findings, together with the morphological similarity between these tumor-like cell aggregates and the naturally occurring tumor, suggest a possible association between this novel virus and the disease. Further characterization of this small naked virus will clarify its role in etiology of green turtle fibropapilloma, a life-threatening disease of this endangered marine species.
Journal of Virological Methods↗
Regional oxygen reduction and denitrification rates in groundwater from multi-model residence time distributions, San Joaquin Valley, USA
Rates of oxygen and nitrate reduction are key factors in determining the chemical evolution of groundwater. Little is known about how these rates vary and covary in regional groundwater settings, as few studies have focused on regional datasets with multiple tracers and methods of analysis that account for effects of mixed residence times on apparent reaction rates. This study provides insight into the characteristics of residence times and rates of O 2 reduction and denitrification (NO 3 − reduction) by comparing reaction rates using multi-model analytical residence time distributions (RTDs) applied to a data set of atmospheric tracers of groundwater age and geochemical data from 141 well samples in the Central Eastern San Joaquin Valley, CA. The RTD approach accounts for mixtures of residence times in a single sample to provide estimates of in-situ rates. Tracers included SF 6 , CFCs, 3 H, He from 3 H (tritiogenic He), 14 C, and terrigenic He. Parameter estimation and multi-model averaging were used to establish RTDs with lower error variances than those produced by individual RTD models. The set of multi-model RTDs was used in combination with NO 3 − and dissolved gas data to estimate zero order and first order rates of O 2 reduction and denitrification. Results indicated that O 2 reduction and denitrification rates followed approximately log-normal distributions. Rates of O 2 and NO 3 − reduction were correlated and, on an electron milliequivalent basis, denitrification rates tended to exceed O 2 reduction rates. Estimated historical NO 3 − trends were similar to historical measurements. Results show that the multi-model approach can improve estimation of age distributions, and that relatively easily measured O 2 rates can provide information about trends in denitrification rates, which are more difficult to estimate.
California↗
Morphologic and cytochemical characteristics of blood cells from Hawaiian green turtles
Objective - To identify and characterize blood cells from free-ranging Hawaiian green turtles, Chelonia mydas. Sample Population - 26 green turtles from Puako on the island of Hawaii and Kaneohe Bay on the island of Oahu. Procedure - Blood was examined, using light and electron microscopy and cytochemical stains that included benzidine peroxidase, chloroacetate esterase, alpha naphthyl butyrate esterase, acid phosphatase, Sudan black B, periodic acid-Schiff, and toluidine blue. Results - 6 types of WBC were identified: lymphocytes, monocytes, thrombocytes, heterophils, basophils, and eosinophils (small and large). Morphologic characteristics of mononuclear cells and most granulocytes were similar to those of cells from other reptiles except that green turtles have both large and small eosinophils. Conclusions - Our classification of green turtle blood cells clarifies imporoper nomenclature reported previously and provides a reference for future hematologic studies in this species.
Hawai'i↗
Limited occurrence of denitrification in four shallow aquifers in agricultural areas of the United States
The ability of natural attenuation to mitigate agricultural nitrate contamination in recharging aquifers was investigated in four important agricultural settings in the United States. The study used laboratory analyses, field measurements, and flow and transport modeling for monitoring well transects (0.5 to 2.5 km in length) in the San Joaquin watershed, California, the Elkhorn watershed, Nebraska, the Yakima watershed, Washington, and the Chester watershed, Maryland. Ground water analyses included major ion chemistry, dissolved gases, nitrogen and oxygen stable isotopes, and estimates of recharge date. Sediment analyses included potential electron donors and stable nitrogen and carbon isotopes. Within each site and among aquifer-based medians, dissolved oxygen decreases with ground water age, and excess N 2 from denitrification increases with age. Stable isotopes and excess N 2 imply minimal denitrifying activity at the Maryland and Washington sites, partial denitrification at the California site, and total denitrification across portions of the Nebraska site. At all sites, recharging electron donor concentrations are not sufficient to account for the losses of dissolved oxygen and nitrate, implying that relict, solid phase electron donors drive redox reactions. Zero-order rates of denitrification range from 0 to 0.14 μmol N L −1 d −1 , comparable to observations of other studies using the same methods. Many values reported in the literature are, however, orders of magnitude higher, which is attributed to a combination of method limitations and bias for selection of sites with rapid denitrification. In the shallow aquifers below these agricultural fields, denitrification is limited in extent and will require residence times of decades or longer to mitigate modern nitrate contamination.
Journal of Environmental Quality↗
Green turtles ( Chelonia mydas ) have novel asymmetrical antibodies
Igs in vertebrates comprise equally sized H and L chains, with exceptions such as H chain–only Abs in camels or natural Ag receptors in sharks. In Reptilia, Igs are known as IgYs. Using immunoassays with isotype-specific mAbs, in this study we show that green turtles ( Chelonia mydas ) have a 5.7S 120-kDa IgY comprising two equally sized H/L chains with truncated Fc and a 7S 200-kDa IgY comprised of two differently sized H chains bound to L chains and apparently often noncovalently associated with an antigenically related 90-kDa moiety. Both the 200- and 90-kDa 7S molecules are made in response to specific Ag, although the 90-kDa molecule appears more prominent after chronic Ag stimulation. Despite no molecular evidence of a hinge, electron microscopy reveals marked flexibility of Fab arms of 7S and 5.7S IgY. Both IgY can be captured with protein G or melon gel, but less so with protein A. Thus, turtle IgY share some characteristics with mammalian IgG. However, the asymmetrical structure of some turtle Ig and the discovery of an Ig class indicative of chronic antigenic stimulation represent striking advances in our understanding of immunology.
Journal of Immunology↗
Microprobe analysis of biotites - A method of correlating tuff beds in the Green River Formation, Colorado and Utah
Quantitative electron microprobe analyses of biotite grains for iron, magnesium, and titanium from tuff beds in the lacustrine Green River Formation (Eocene) of Colorado and Utah provide a tentative method of identification and a permissive stratigraphic correlation of tuffs. Tuff beds that have been identified and correlated by stratigraphic means were sampled at five localities in Colorado and Utah to determine if microprobe analyses of biotite could be used as a method of correlation. Although most of the original phenocrysts and glass shards of these pyroclastic beds have undergone extensive postdepositional alteration, biotite seems to have been unaffected. The iron, magnesium, and titanium contents of the biotite do not uniquely characterize individual tuff beds, but when the proportions of these elements are compared in a continuous stratigraphic sequence of beds, correlation of individual tuffs or groups of tuffs is possible over areas exceeding several hundred square miles. The method may be used for detailed correlation of pyroclastic beds where stratigraphic, faunal, and radiometric methods have been unsatisfactory.
Colorado, Utah↗
Evaluating aromatization of solid bitumen generated in the presence and absence of water: Implications for solid bitumen reflectance as a thermal proxy
Geological models for petroleum generation suggest thermal conversion of oil-prone sedimentary organic matter in the presence of water promotes increased liquid saturate yield, whereas absence of water causes formation of an aromatic, cross-linked solid bitumen residue. To test the influence of hydrogen from water, organic-rich (22 wt% total organic carbon , TOC) mudrock samples from the Eocene lacustrine Green River Formation Mahogany zone oil shale were pyrolyzed under hydrous and anhydrous conditions in closed system batch reactors at temperatures between 300 and 370 °C for 72 h. Pre- and post-pyrolysis samples were characterized using petrographic approaches including optical microscopy , reflectance, Raman spectroscopy , and scanning electron and transmission electron microscopy to quantify differences in relative appearance, abundance, and composition of solid bitumen newly generated during the pyrolysis experiments. Petrographic analyses were supplemented by geochemical screening measurements (TOC content and programmed temperature pyrolysis). Results show post-hydrous pyrolysis residues contain lower TOC, are comprised of solid bitumen with greater aromaticity , and have textures indicative of lower viscosities, relative to anhydrous residues from the same temperature pyrolysis conditions. These observations suggest solid bitumen forming from thermal conversion of oil-prone sedimentary organic matter under anhydrous conditions may be less aromatic, although more cross-linked, than solid bitumen forming under hydrous conditions at the same time-temperature combination. To explain these results, we suggest that a radical disproportionation mechanism is favored in the presence of hydrogen donated from water, and that this disproportionation promotes aromatization in the solid residue with concomitant expulsion of saturated hydrocarbons.
International Journal of Coal Geology↗
In-vitro replication of Chelonid herpesvirus 5 in organotypic skin cultures from Hawaiian green turtles (Chelonia mydas)
Fibropapillomatosis (FP) is a tumor disease of marine turtles associated with Chelonid herpesvirus 5 (ChHV5) that has historically been refractory to growth in tissue culture. Here, we show for the first time de novo formation of ChHV5-positive intranuclear inclusions in cultured green turtle cells, which is indicative for active lytic replication of the virus. The minimal requirements to achieve lytic replication in cultured cells included 1) either in-vitro culturing of ChHV5-positive tumor biopsies (plugs) or organotypic cultures (rafts) consisting of ChHV5-positive turtle fibroblasts in collagen rafts seeded with turtle keratinocytes and 2) keratinocyte maturation induced by raising raft or biopsy cultures to the air-liquid interface. Virus growth was confirmed by detailed electron microscopic studies revealing intranuclear sun-shaped capsid factories, tubules, various stages of capsid formation, nuclear export by budding into the perinuclear space, tegumentation, and envelopment to complete de novo virus production. Membrane synthesis was also observed as a sign for active viral replication. Interestingly, cytoplasmic particles became associated with keratin filaments, a feature not seen in conventional monolayer cell cultures where most studies of herpesvirus replication have been performed. Our findings draw a rich and realistic picture of ChHV5 replication in cells derived from its natural host and may be crucial not only to better understand ChHV5 circulation but also to eventually complete Koch's postulates for FP. Moreover, the principles described here may serve as model to culture other viruses that are resistant to replication in conventional cell culture.
Hawai'i↗
Scanning electron microscopic evaluation of broad ion beam milling effects to sedimentary organic matter: Sputter-induced artifacts or naturally occurring porosity?
Research examining organic-matter hosted porosity has significantly increased during the last decade due to greater focus on understanding hydrocarbon migration and storage in source-rock reservoirs, and technological advances in scanning electron microscopy (SEM) capabilities. The examination of nanometer-scale organic-matter hosted porosity by SEM requires the preparation of exceptionally flat geologic samples beyond the abilities of traditional mechanical polishing, which can deform or otherwise obscure organic surfaces. To meet this demand, broad ion beam (BIB) milling was introduced as a sample preparation technique for SEM petrographic analysis of geologic samples. As with any sample preparation technique, there can be unintended consequences. In this study, we examined the development of nanometer-scale sputter-induced voids caused by BIB milling of thermoset plastic binder material [poly(methyl methacrylate), PMMA] used for the mounting of geologic samples, and artifact sputter-induced voids in the organic matter of Green River Formation and Kimmeridge Clay Formation source rocks. Development of artifact sputter-induced voids was evaluated in relation to variations in the slope of the sample examination surface (0.0–4.9% slope), effectively varying the angle of ion incidence. The results indicate that only minor variations in the angle of ion incidence can generate sputter-induced voids in both PMMA (10.0–386.2 nm diameter sputter-induced voids) and sample sedimentary organic matter (solid bitumen; 12.2–103.6 nm diameter sputter-induced voids). Overall, average artifact pore diameters increased with increasing ion incidence angle within PMMA. Although sputter-induced voids within solid bitumen in the Green River Formation sample were only found in limited extent, the size of these void artifacts falls within the same size range as naturally occurring meso-macroporosity. That is, the pore-like artifacts could easily be misconstrued as naturally developed organic porosity, which is a major concern for SEM-based porosity evaluation methods. This study describes the factors that contribute to the creation of artifact sputter-induced voids, their distinguishing characteristics, and best practices for avoiding the creation of ion-induced artifacts.
International Journal of Coal Geology↗
Reaction kinetics and accelerant effects of sulfides in early mature hydrocarbon generation using hydrous pyrolysis
Hydrocarbon generation in organic-rich sediments is influenced by the molecular organic composition and relative abundance of associated minerals. Certain mineral-derived elements act as catalysts and reaction intermediaries, facilitating early-stage hydrocarbon formation in potential source rocks. This study investigated the role of sulfur contributed from pyrite as an accelerant in thermal reaction, focusing on its effects on early maturation and consequent hydrocarbon generation from gilsonite (low-sulfur solid petroleum). Hydrous pyrolysis (HP) experiments were conducted on mixtures of gilsonite and pyrite in varying ratios (1:0.1, 1:0.5, 1:1, 1:2, and 1:10 w/w gilsonite:pyrite) at 320, 350, and 370 °C for 72 h. Untreated and thermally altered residues were analyzed using solid bitumen reflectance (BR o , %), total organic carbon (TOC) content, programmed temperature pyrolysis, scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS), and X-ray diffraction (XRD) to evaluate the potential accelerant role of pyritic sulfur in hydrocarbon formation. The results show HP residues at 320 and 350 °C with greater pyrite concentrations had higher BR o , while reflectance values were similar in the 370 °C residues, regardless of pyrite concentration, suggesting enhanced reaction at lower thermal conditions. Increasing pyrite content systematically decreased hydrogen index (HI) values while increasing the transformation ratio (TR) and production index (PI), indicating enhanced conversion of organic matter to hydrocarbons with increasing pyrite concentrations. Gas yields increased with pyrite addition, particularly at 350 °C, confirming secondary cracking effects. However, gas production stabilized or declined at higher pyrite loadings (1:10), suggesting alternative reaction pathways such as coke formation. Our data indicate the presence of pyrite lowers the activation energy for thermal cracking, shifting peak experimental hydrocarbon generation temperatures downward by 20–30 °C, with the most pronounced accelerant effects observed at moderate pyrite concentrations (1:0.5 and 1:1). The thermodynamic framework reveals that pyrite stability is influenced by experimental conditions, with pyrrhotite formation favored in the presence of gilsonite due to reduced oxygen fugacity. Pyrite transformation to pyrrhotite, as observed through XRD, SEM-EDS, and predicted by thermodynamic data, further supports the accelerant role of S, as pyrrhotite exhibits a higher hydrogen transfer potential, promoting early oil generation. These findings highlight the importance of pyrite in modulating hydrocarbon generation pathways in organic-rich systems.
Journal of Analytical and Applied Pyrolysis↗
Multiple hydrothermal and metamorphic events in the Kidd Creek volcanogenic massive sulphide deposit, Timmins, Ontario: evidence from tourmalines and chlorites
Tourmaline and chlorite are the principal ferromagnesian silicate minerals in the Kidd Creek massive sulphide deposit. Tourmaline is most common in sphalerite-rich peripheral margins of the chalcopyrite stringer zone. Within the north orebody, samples typically contain <1% tourmaline, but small areas (hand-specimen scale) may have 10–20%. Chlorite is more widely distributed and in places constitutes 30–50% of rock volumes. Associated assemblages may include quartz, sulphides (principally chalcopyrite, sphalerite, and (or) pyrite), carbonate, albite, sericite, and rare fluorite, allanite, or zoisite(?).The tourmalines and chlorites record a series of multiple hydrothermal and metamorphic events. Paragenetic studies suggest that tourmaline was deposited during several discrete stages of mineralization, as evidenced by brecciation and cross-cutting relationships. Most of the tourmalines have two concentric growth zones defined by different colours (green, brown, blue, yellow). Some tourmalines also display pale discordant rims that cross-cut and embay the inner growth zones and polycrystalline, multiple-extinction domains. Late sulphide veinlets (chalcopyrite, pyrrhotite) transect the inner growth zones and pale discordant rims of many crystals. The concentric growth zones are interpreted as primary features developed by the main ore-forming hydrothermal system, whereas the discordant rims, polycrystalline domains, and cross-cutting sulphide veinlets reflect post-ore metamorphic processes.Detailed electron microprobe analyses of tourmalines show a wide compositional range, from Fe-rich dravite nearly to end-member schorl, with Fe/(Fe + Mg) ratios varying from 0.33 to 0.92; only minor amounts of Ca are present, yielding uniformly high Na/(Na + Ca) ratios of 0.84–0.99. Two sets of chemical zoning trends are identified in the tourmalines, involving systematic changes in Fe/(Fe + Mg), Na/(Na + Ca), Al, and Ti that are believed to reflect internal coupled substitutions (e.g., + Ti = Na + Al) and local mineral equilibria (e.g., tourmaline–chlorite). Analyses of the pale discordant reaction rims show consistent depletion of Fe, Ca, and Ti, presumably by fluid–solid reactions during post-ore metamorphism.Chlorites also show an extensive range in composition, from ripidolite nearly to end-member daphnite, with Fe/(Fe + Mg) ratios of 0.43–0.98 and Si cation values of 5.00–5.39. Chlorites from the fringes of the footwall stringer zone have narrow compositional ranges, whereas chlorites near footwall rhyolite sills in the core of the stringer zone display major variations in Fe/(Fe + Mg) ratios, including one sample with a range of 0.68–0.95. The former group of chlorites has Fe/(Fe + Mg) ratios that correlate well with those of coexisting tourmalines (exclusive of late reaction rims). Data for the latter group, in contrast, fall off equilibrium K D curves, indicating that the tourmalines and chlorites within these samples are not in chemical equilibrium. The chlorites are believed to have been altered (overprinted) by Fe-rich hydrothermal fluids apparently generated during intrusion of the rhyolite sills. The tourmalines, however, are unaffected and retain primary chemical signatures.Variations in mineral proportions and mineral chemistry within the deposit mainly depend on fluctuations in temperature, pH, water/rock ratios, and amounts of entrained seawater. The major proposed control is mixing between high-temperature, Fe-rich end-member hydrothermal fluids and cold, Mg-rich entrained seawater. Fe/(Fe + Mg) variations in footwall tourmalines (and equilibrium chlorites) are believed to largely reflect the progressive infiltration of Mg-rich seawater into the margins and top of the hydrothermal system. The more Fe-rich compositions of Kidd Creek tourmalines relative to those from sediment-hosted massive sulphide deposits (e.g., Sullivan, British Columbia) may be related to the preferential generation of end-member hydrothermal fluids in proximal volcanic environments like that at Kidd Creek.
Ontario↗