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USGS1990

Ultrastructure of the spleen and head kidney of striped bass

The spleen and head kidney of striped bass Morone saxatilis were examined by electron microscopy, including examination of ultrastructural localization of peroxidase. The spleen is composed of a loosely organized reticulum that supports the red and white pulp. The principal hematopoietic and mature blood cells observed were erythrocytes, erythroblasts, lymphocytes, macrophages, thrombocytes, and aggregates of pigmented macrophages. In addition, limited numbers of neutrophils, neutrophilic myelocytes (immature neutrophils), plasma cells, eosinophils and monocytes were identified. Reticular cells and fibers appeared to provide a structural framework for both cells and blood sinuses in the spleen. Like the spleen, the head kidney contained erythrocytes, macrophages, monocytes, lymphocytes, and other less frequently observed cell types. A distinct difference in the cytologic composition of the two organs, however, was in the greater number of neutrophilic myelocytes found in the head kidney, where these cells were often arranged in groups. Positive peroxidase reactions were observed for neutrophils, neutrophilic myelocytes, macrophage phagolysosomes, and pigmented macrophages in both the spleen and head kidney.

Journal of Aquatic Animal Health↗

USGS2022

Growth of complex volcanic ash aggregates in the Tierra Blanca Joven eruption of Ilopango Caldera, El Salvador

Aggregation processes control both the residence time and dispersal of volcanic ash during eruptions yet remain incompletely understood. The products of aggregation vary from simple ash clusters to large, complexly layered accretionary lapilli. Here we detail the micro-stratigraphy of a single population of accretionary lapilli that grew during the ∼431 CE Tierra Blanca Joven eruption from Ilopango Caldera, El Salvador. The accretionary lapilli were sampled 10 km from the caldera source within a sequence of ash-rich pyroclastic density current deposits and intercalated fall material, known as unit D, which is traceable >40 km from Ilopango. Scanning electron microscopy and image analysis reveal common facies that form distinct layers within the accretionary lapilli. Each facies is distinguished by quantitative and qualitative variations in particle size distribution , porosity, and particle fabric. We infer that these textures resulted from aggregation conditions that differed in terms of liquid water availability, particle concentration and grain size distributions. In our proposed model, a characteristic sequence of facies accreted from core to rim in the accretionary lapilli during passage through ash clouds generated by vent-derived plumes and pyroclastic density currents. The accretionary lapilli are mostly composed of smaller aggregates (ash clusters, ash pellets) and grew predominantly by accretion of already-formed aggregates, rather than by grain-by-grain accretion of individual particles. This finding is consistent with observations of rapid aggregate growth in volcanic plumes, suggesting a common evolutionary pathway for accretionary lapilli formation across diverse eruptions.

Ilopango caldera↗

USGS2022

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↗

USGS2005

Characterization of a C3a receptor in rainbow trout and Xenopus: The first identification of C3a receptors in nonmammalian species

Virtually nothing is known about the structure, function, and evolutionary origins of the C3aR in nonmammalian species. Because C3aR and C5aR are thought to have arisen from the same common ancestor, the recent characterization of a C5aR in teleost fish implied the presence of a C3aR in this animal group. In this study we report the cloning of a trout cDNA encoding a 364-aa molecule (TC3aR) that shows a high degree of sequence homology and a strong phylogenetic relationship with mammalian C3aRs. Northern blotting demonstrated that TC3aR was expressed primarily in blood leukocytes. Flow cytometric analysis and immunofluorescence microscopy showed that Abs raised against TC3aR stained to a high degree all blood B lymphocytes and, to a lesser extent, all granulocytes. More importantly, these Abs inhibited trout C3a-mediated intracellular calcium mobilization in trout leukocytes. A fascinating structural feature of TC3aR is the lack of a significant portion of the second extracellular loop (ECL2). In all C3aR molecules characterized to date, the ECL2 is exceptionally large when compared with the same region of C5aR. However, the exact function of the extra portion of ECL2 is unknown. The lack of this segment in TC3aR suggests that the extra piece of ECL2 was not necessary for the interaction of the ancestral C3aR with its ligand. Our findings represent the first C3aR characterized in nonmammalian species and support the hypothesis that if C3aR and C5aR diverged from a common ancestor, this event occurred before the emergence of teleost fish.

Journal of Immunology↗

USGS2022

Importance of nonindigenous harpacticoids (Crustacea: Copepoda) decrease with depth in Lake Ontario

Harpacticoid copepods can be a substantial component of the meiobenthic community in lakes and serve an ecological role as detritivores. Here we present the first species-level lake-wide quantitative assessment of the harpacticoid assemblage of Lake Ontario with emphasis on the status of nonindigenous species. Additionally, we provide COI-5P sequences of harpacticoid taxa through Barcode of Life Data System (BOLD). Harpacticoids were collected at depths from 0.1 to 184 m and from a range of substrates from August to September 2018 as part of the Cooperative Science and Monitoring Initiative (CSMI) offshore benthic survey. Twenty-six meiobenthic samples were analyzed using microscopy for community composition analysis of harpacticoids. We found thirteen indigenous and three nonindigenous species of harpacticoid, with the introduced species dominating at shallow depths. The community transitioned from nonindigenous to indigenous species dominance as depth increased. Nonindigenous species accounted for 79% of the community (by abundance) at depths <20 m, 55% from 20 to 40 m, and only 24% at depths >40 m. The nonindigenous species encountered included the first detections of Schizopera borutzkyi (Monchenko, 1967) and Heteropsyllus nunni (Coull, 1975) from Lake Ontario. S. borutzkyi was the most abundant harpacticoid species in the lake, approaching a maximum density of 50,000/m 2 and a lake-wide average density of 7,900/m 2 . Numerically important indigenous species included Bryocamptus nivalis (Willey, 1925), Canthocamptus robertcokeri (Wilson, 1958), Canthocamptus staphylinoides (Pearse, 1905), and Moraria cristata (Chappuis, 1929). The prevalence of nonindigenous harpacticoids in the meiobenthos of Lake Ontario suggests further investigations of Great Lakes meiofauna communities are warranted.

Lake Ontario↗

USGS2020

Fluorescence spectroscopy of ancient sedimentary organic matter via confocal laser scanning microscopy (CLSM)

Fluorescence spectroscopy via confocal laser scanning microscopy (CLSM) was used to analyze ancient sedimentary organic matter, including Tasmanites microfossils in Devonian shale and Gloecapsomorpha prisca ( G. prisca ) in Ordovician kukersite from North American basins. We examined fluorescence emission as a function of excitation laser wavelength, sample orientation, and with respect to location within individual organic entities and in transects across bedded organic matter. Results from spectral scans of the same field of view in Tasmanites with different laser lines showed progressive red-shift in emission maxima with longer excitation wavelengths. This result indicates steady-state Tasmanites fluorescence emission is an overlapping combination of emission from multiple fluorophore functions. Stokes shift decreased with increasing excitation wavelength, further suggesting the presence of multiple fluorophore functions with different S 1 → S 0 transition energies. This observation also indicates that at longer excitation wavelengths, less absorbed light energy is dissipated via collisional transfer than at shorter excitation wavelengths and may suggest fewer polar functions are preferentially absorbing. Confirming earlier results, emission spectra observed from high fluorescence intensity regions (fold apices) in individual Tasmanites are blue-shifted relative to emission from other locations in the same microfossil. We suggest high intensity emission is from photoselective alignment of polarized excitation with the fluorophore absorption and emission transition moment. The blue shift observed in regions of high intensity emission may be due to relative absence or realignment of polar species, e.g., bridging ether or ester functions, although variations in O abundance could not be confirmed with preliminary time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis. Tasmanites occurring in consolidated sediments are flattened from original spherical morphology and, in optical microscopy, this burial deformation results in generally parallel extinction (strain-influenced) and positive elongation. The deformation also induces fluorescence anisotropy observed as variations in emission wavelength when individual Tasmanites are measured from their long axis parallel to bedding, whereas this effect is absent in bedding-normal view. Transects from G. prisca -rich source layers into adjacent reservoir layers show decrease in fluorescence intensity and spectral red-shift (increase in full-width half-maximum with increasing red portion of the half-width). These results may suggest an increase in fluorescence quenching across the source-to-reservoir transition zone, consistent with an increase in aromaticity following petroleum expulsion and migration. These observations are supported by increasing reflectance values measured across similar micro-scale transects. Our results highlight the applicability of CLSM as a broad and under-utilized approach for the characterization of sedimentary organic matter and are discussed with perspective toward petroleum processes and thermal indices research.

International Journal of Coal Geology↗

USGS2018

Full-range, solar-reflected hyperspectral microscopy to support earth remote sensing research

Over the past 20 years, hyperspectral microscopy has grown into a robust field of analysis for a number of applications. The visible to near-infrared (VNIR; 400 to 1000 nm) region of the spectrum has demonstrated utility for the characterization of healthy and diseased tissue and of biomolecular indicators at the cellular level. Here, we describe the development of a hyperspectral imaging (HSI) microscope that is aimed at material characterization to complement traditional stand-off, earth remote sensing with hyperspectral sensors. We combine commercial off the shelf technology to build an HSI microscope to collect spectral data with illumination provided by a tunable laser. Hyperspectral imaging microscopy (HIM) facilitates detailed examination of target materials at the subcentimeter spatial scale. The custom-built, laser illumination HSI microscope covers the NIR to shortwave infrared (NIR/SWIR; 900 to 2500 nm) solar-reflected spectral range. It is combined with a separate VNIR sensor (400 to 900 nm) that utilizes quartz–tungsten–halogen lamps for illumination. The combined sensors provide a means to collect <10,000 s of spectra in the full VNIR/SWIR spectral range from both pure substances and precisely engineered linear and nonlinear mixtures. The large abundance of spectra allows for a more detailed understanding of the variability and multivariate probability distributions of spectral signatures. This additional information aids in understanding the variability observed in ground truth spectra collected from portable spectrometers, and it greatly enhances sample description and metadata content. In addition, HIM data cubes can serve as proxies, as “microscenes,” for systems engineering applications such as trade studies for HSI acquired by air- and space-borne sensors.

Journal of Applied Remote Sensing↗

USGS2012

Assessing consumption of bioactive micro-particles by filter-feeding Asian carp

Silver carp Hypophthalmichthys molitrix (SVC) and bighead carp H. nobilis (BHC) have impacted waters in the US since their escape. Current chemical controls for aquatic nuisance species are non-selective. Development of a bioactive micro-particle that exploits filter-feeding habits of SVC or BHC could result in a new control tool. It is not fully understood if SVC or BHC will consume bioactive micro-particles. Two discrete trials were performed to: 1) evaluate if SVC and BHC consume the candidate micro-particle formulation; 2) determine what size they consume; 3) establish methods to evaluate consumption of filter-feeders for future experiments. Both SVC and BHC were exposed to small (50-100 μm) and large (150-200 μm) micro-particles in two 24-h trials. Particles in water were counted electronically and manually (microscopy). Particles on gill rakers were counted manually and intestinal tracts inspected for the presence of micro-particles. In Trial 1, both manual and electronic count data confirmed reductions of both size particles; SVC appeared to remove more small particles than large; more BHC consumed particles; SVC had fewer overall particles in their gill rakers than BHC. In Trial 2, electronic counts confirmed reductions of both size particles; both SVC and BHC consumed particles, yet more SVC consumed micro-particles compared to BHC. Of the fish that ate micro-particles, SVC consumed more than BHC. It is recommended to use multiple metrics to assess consumption of candidate micro-particles by filter-feeders when attempting to distinguish differential particle consumption. This study has implications for developing micro-particles for species-specific delivery of bioactive controls to help fisheries, provides some methods for further experiments with bioactive micro-particles, and may also have applications in aquaculture.

Journal of Aquaculture Research & Development↗

USGS1999

Importance of microscopy in durability studies of solidified and stabilized contaminated soils

Solidification/stabilization (S/S) is recognized by the U.S. EPA as a best demonstrated available technology for the containment of contaminated soils and other hazardous wastes that cannot be destroyed by chemical, thermal, or biological means. Despite the increased use of S/S technologies, little research has been conducted on the weathering and degradation of solidified and stabilized wastes once the treated materials have been buried. Published data to verify the performance and durability of landfilled treated wastes over time are rare. In this preliminary study, optical and electron microscopy (scanning electron microscopy [SEM], transmission electron microscopy [TEM] and electron probe microanalyses [EPMA]) were used to evaluate weathering features associated with metal-bearing contaminated soil that had been solidified and stabilized with Portland cement and subsequently buried on site, stored outdoors aboveground, or achieved in a laboratory warehouse for up to 6 yr. Physical and chemical alteration processes identified include: freeze-thaw cracking, cracking caused by the formation of expansive minerals such as ettringite, carbonation, and the movement of metals from waste aggregates into the cement micromass. Although the extent of degradation after 6 yr is considered slight to moderate, results of this study show that the same environmental concerns that affect the durability of concrete must be considered when evaluating the durability and permanence of the solidification and stabilization of contaminated soils with cement. In addition, such evaluations cannot be based on leaching and chemical analyses alone. The use of all levels of microscopic analyses must be incorporated into studies of the long-term performance of S/S technologies.Solidification/stabilization (S/S) is recognized by the U.S. EPA as a best demonstrated available technology for the containment of contaminated soils and other hazardous wastes that cannot be destroyed by chemical, thermal, or biological means. Despite the increased use of S/S technologies, little research has been conducted on the weathering and degradation of solidified and stabilized wastes once the treated materials have been buried. Published data to verify the performance and durability of landfilled treated wastes over time are rare. In this preliminary study, optical and electron microscopy (scanning electron microscopy [SEM], transmission electron microscopy [TEM] and electron probe microanalyses [EPMA]) were used to evaluate weathering features associated with metal-bearing contaminated soil that had been solidified and stabilized with Portland cement and subsequently buried on site, stored outdoors aboveground, or archived in a laboratory, warehouse for up to 6 yr. Physical and chemical alteration processes identified include: freeze-thaw cracking, cracking caused by the formation of expansive minerals such as ettringite, carbonation, and the movement of metals from waste aggregates into the cement micromass. Although the extent of degradation after 6 yr is considered slight to moderate, results of this study show that the same environmental concerns that affect the durability of concrete must be considered when evaluating the durability and permanence of the solidification and stabilization of contaminated soils with cement. In addition, such evaluations cannot be based on leaching and chemical analyses alone. The use of all levels of microscopic analyses must be incorporated into studies of the long-term performance of S/S technologies.

Soil Science Society of America Journal↗

USGS2014

The fungus Trichophyton redellii sp. nov. causes skin infections that resemble white-nose syndrome of hibernating bats

Before the discovery of white-nose syndrome (WNS), a fungal disease caused by Pseudogymnoascus destructans , there were no reports of fungal skin infections in bats during hibernation. In 2011, bats with grossly visible fungal skin infections similar in appearance to WNS were reported from multiple sites in Wisconsin, USA, a state outside the known range of P. destructans and WNS at that time. Tape impressions or swab samples were collected from affected areas of skin from bats with these fungal infections in 2012 and analyzed by microscopy, culture, or direct DNA amplification and sequencing of the fungal internal transcribed spacer region (ITS). A psychrophilic species of Trichophyton was isolated in culture, detected by direct DNA amplification and sequencing, and observed on tape impressions. Deoxyribonucleic acid indicative of the same fungus was also detected on three of five bat carcasses collected in 2011 and 2012 from Wisconsin, Indiana, and Texas, USA. Superficial fungal skin infections caused by Trichophyton sp. were observed in histopathology for all three bats. Sequencing of the ITS of Trichophyton sp., along with its inability to grow at 25 C, indicated that it represented a previously unknown species, described herein as Trichophyton redellii sp. nov. Genetic diversity present within T. redellii suggests it is native to North America but that it had been overlooked before enhanced efforts to study fungi associated with bats in response to the emergence of WNS.

Journal of Wildlife Diseases↗

USGS2009

Effect of grain-coating mineralogy on nitrate and sulfate storage in the unsaturated zone

Unsaturated-zone sediments and the chemistry of shallow groundwater underlying a small (∼8-km 2 ) watershed were studied to identify the mechanisms responsible for anion storage within the Miocene Bridgeton Formation and weathered Coastal Plain deposits in southern New Jersey. Lower unsaturated-zone sediments and shallow groundwater samples were collected and concentrations of selected ions (including NO 3 − and SO 4 2− ) from 11 locations were determined. Grain size, sorting, and color of the lower unsaturated-zone sediments were determined and the mineralogy of these grains and the composition of coatings were analyzed by petrographic examination, scanning electron microscopy and energy dispersive analysis of x-rays, and quantitative whole-rock x-ray diffraction. The sediment grains, largely quartz and chert (80–94% w/w), are coated with a very fine-grained (<20 μm), complex mixture of kaolinite, halloysite, goethite, and possibly gibbsite and lepidocrocite. The mineral coatings are present as an open fabric, resulting in a large surface area in contact with pore water. Significant correlations between the amount of goethite in the grain coatings and the concentration of sediment-bound SO 4 2− were observed, indicative of anion sorption. Other mineral–chemical relations indicate that negatively charged surfaces and competition with SO 4 2− results in exclusion of NO 3 − from inner sphere exchange sites. The observed NO 3 − storage may be a result of matrix forces within the grain coatings and outer sphere complexation. The results of this study indicate that the mineralogy of grain coatings can have demonstrable effects on the storage of NO 3 − and SO 4 2− in the unsaturated zone.

Vadose Zone Journal↗

USGS2008

Ionoregulatory changes during metamorphosis and salinity exposure of juvenile sea lamprey (Petromyzon marinus L.)

Ammocoetes of the anadromous sea lamprey Petromyzon marinus L. spend many years in freshwater before metamorphosing and migrating to sea. Metamorphosis involves the radical transformation from a substrate-dwelling, filter feeder into a free-swimming, parasitic feeder. In the present work we examined osmoregulatory differences between ammocoetes and transformers (metamorphic juveniles), and the effects of salinity acclimation. We measured the expression of key ion-transporting proteins [Na+/K+-ATPase, vacuolar (V)-type H+-ATPase and carbonic anhydrase (CA)] as well as a number of relevant blood parameters (hematocrit, [Na+] and [Cl -]). In addition, immunofluorescence microscopy was used to identify and characterize the distributions of Na+/K+-ATPase, V-type H+-ATPase and CA immunoreactive cells in the gill. Ammocoetes did not survive in the experiments with salinities greater than 10???, whereas survival in high salinity (???25-35???) increased with increased degree of metamorphosis in transformers. Plasma [Na+] and [Cl -] of ammocoetes in freshwater was lower than transformers and increased markedly at 10???. In transformers, plasma ions increased only at high salinity (>25???). Branchial Na+/K+-ATPase levels were ??? tenfold higher in transformers compared to ammocoetes and salinity did not affect expression in either group. However, branchial H +-ATPase expression showed a negative correlation with salinity in both groups. Na+/K+-ATPase immunoreactivity was strongest in transformers and associated with clusters of cells in the interlamellar spaces. H+-ATPase (B subunit) immunoreactivity was localized to epithelial cells not expressing high Na+/K+-ATPase immunoreactivity and having a similar tissue distribution as carbonic anhydrase. The results indicate that branchial Na+/K+-ATPase and salinity tolerance increase in metamorphosing lampreys, and that branchial H+-ATPase is downregulated by salinity.

Journal of Experimental Biology↗

USGS2015

Characterization of a novel hepadnavirus in the white sucker ( Catostomus commersonii ) from the Great Lakes Region of the USA

The white sucker Catostomus commersonii is a freshwater teleost often utilized as a resident sentinel. Here, we sequenced the full genome of a hepatitis B-like virus that infects white suckers from the Great Lakes Region of the USA. Dideoxysequencing confirmed the white sucker hepatitis B virus (WSHBV) has a circular genome (3542 bp) with the prototypical codon organization of hepadnaviruses. Electron microscopy demonstrated that complete virions of approximately 40 nm were present in the plasma of infected fish. Compared to avi- and orthohepadnaviruses, sequence conservation of the core, polymerase and surface proteins was low and ranged from 16-27% at the amino acid level. An X protein homologue common to the orthohepadnaviruses was not present. The WSHBV genome included an atypical, presumptively non-coding region absent in previously described hepadnaviruses. Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses. The level of divergence in protein sequences between WSHBV other hepadnaviruses, and the identification of an HBV-like sequence in an African cichlid provide evidence that a novel genus of the family Hepadnaviridae may need to be established that includes these hepatitis B-like viruses in fishes. Viral transcription was observed in 9.5% (16 of 169) of white suckers evaluated. The prevalence of hepatic tumors in these fish was 4.9%, of which only 2.4% were positive for both virus and hepatic tumors. These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.

Great Lakes Region↗

USGS2024

Atlas of microscopic images of biochar using reflected light microscopy in biochar characterization

Derived through the thermochemical conversion of biomass, biochar is a carbon-rich substance recognized for its significance in environmental applications and sustainable agriculture. As interest in its utilization continues to rise, it becomes crucial to comprehend how the source material and pyrolysis parameters influence the properties of biochar and, consequently, to research the suitability of various analytical methods for characterizing it. Despite the current utilization of numerous physical and chemical methods, the untapped potential of reflected light microscopy warrants further exploration. While a few recent studies suggest a correlation between certain microscopic characteristics and selected physical and chemical properties of biochar, the data are limited and difficult to compare. This is primarily due to variations in the types of original biomass used and lack of information about pyrolysis conditions. Moreover, because only a limited number of photographs taken under a reflected light microscope are publicly available to-date, it is difficult to evaluate morphological differences between various biochars and other organic materials such as inertinites from coal, charcoal, etc. To address limited availability of publicly available data, this “Atlas of Microscopic Images of Biochar” presents a collection of more than 300 images contributed by researchers from Poland, the United States, Canada, Australia, Brazil, and Denmark. These photomicrographs capture optical characteristics of a diverse array of biochar, demonstrating its unique morphological and structural features. This visual documentation can serve as a valuable resource for researchers, industry professionals, educators, and enthusiasts interested in investigating the complexities of biochar forms.

Indiana Journal of Earth Sciences↗

USGS2022

Pore systems and organic petrology of cretaceous Mowry and Niobrara source-rock reservoirs, Powder River Basin, Wyoming, USA

The Powder River Basin (PRB) is a world-class oil province, in large part thanks to contributions from premier source rocks, Cretaceous Mowry and Niobrara shales. Both formations are also unconventional reservoirs. A critical aspect of evaluating production potential and finding sweet spots is the nature of the pore systems in these fine-grained source-rock reservoirs. Variation by stratigraphic interval is important for selecting optimum target zones for horizontal wells. Understanding variation in pore type, size, and connectivity and relationships with mineralogy and fabric help in determining prospectivity in different parts of the basin. Deciphering controls on pore-system development helps predict intervals and locations of optimum reservoir quality. Imaging of Niobrara and Mowry samples from a range of thermal maturities provided observations and data on pore systems, organic matter (OM) types and associations with mineralogy and fabric, wettability, and microporosity associated with both diagenetic and detrital clays. Imaging techniques included scanning electron microscopy, organic petrography and correlative scanning electron microscopy, and mapping of mineralogy through energy dispersive spectroscopy. Mean solid bitumen (BR o ) and vitrinite reflectance (VR o ) values indicate all samples are in the oil window with values ranging from 0.52 to 1.15%. Organic fluorescence is prominent in amorphous OM, solid bitumen and some vitrinite in the early oil window. The fluorescence is extinguished at higher thermal maturity. Carbonate pellets (in Niobrara) mainly contain migrated solid bitumen and residual live oil and little or no terrigenous OM (vitrinite and inertinite). However, terrigenous OM is common in siliceous/argillaceous laminae in both formations, where it occurs with amorphous OM, some of which has converted in situ to a solid bitumen petroleum residue. One key finding is the widespread presence of migrated OM at very early oil window maturity. Distribution of such OM and associated wettability alteration is fabric-controlled, at all levels of thermal maturity studied. Clay morphology and abundance and supporting rigid mineral grain framework strongly influence pore development, preservation, and connectivity in both formations. Carbonate content is a good proxy for reservoir quality in Niobrara intervals due to association of porous solid bitumen with calcareous fecal pellets. High recrystallized microquartz content is associated with the best reservoir intervals in the Mowry.

Wyoming↗

USGS2018

Pore-types and pore-network evolution in Upper Devonian-Lower Mississippian Woodford and Mississippian Barnett mudstones: Insights from laboratory thermal maturation and organic petrology

Pore-evolution models from immature organic-matter (OM) -rich Barnett (0.42%R o ) and Woodford (0.49%R o ) mudstones were compared with models previously developed from low-maturity OM-lean Boquillas (Eagle Ford-equivalent) mudstones to investigate whether (1) different mineralogy (siliceous vs. calcareous) exerts different catalytic and sorption effects and influences OM-pore origin and evolution; and (2) different types of macerals show different OM pore evolution history. Laboratory gold-tube pyrolysis, scanning electron microscopy (SEM) and thin-section petrography, organic petrography, and geochemical characterization were used to investigate the role of bulk mineralogy, maceral type, and thermal maturation on OM-pore evolution. Results suggest that mineralogy has little impact on OM-pore development and evolution. Macerals, identified using both SEM (platy OM, particulate OM, organic–mineral admixtures, Tasmanites ) and organic petrology (vitrinite, inertinite, amorphous organic matter [AOM]/bituminite, telalginite [ Leiosphaeridia , Tasmanites ]), do affect the origin and evolution of OM pores owing to differences in chemical compositions, generation kinetics, and activation-energy distributions between Tasmanites , matrix bituminite, and other types of macerals. Leiosphaeridia and Tasmanites in Woodford mudstone samples exhibit a delay in onset and a shorter period of petroleum generation and pore development compared to the matrix bituminite in the Barnett and Woodford mudstone samples. Pre-oil solid bitumen was observed to have migrated into initial primary mineral pore networks at the bitumen generation stage in both Barnett and Woodford samples. At higher levels of thermal maturation, the volume of primary mineral pores decreases and the pore volume composed of modified mineral pores and OM pores becomes greater. Pore evolution and pore-type heterogeneity in these mudstones is a function of the initial mineral pore network, types of kerogen and macerals, and generation kinetics of individual macerals upon thermal maturation.

Oklahoma↗

USGS2009

Oxalosis in wild desert tortoises, Gopherus agassizii

We necropsied a moribund, wild adult male desert tortoise ( Gopherus agassizii ) with clinical signs of respiratory disease and elevated plasma biochemical analytes indicative of renal disease (blood urea nitrogen [415 mg/dl], uric acid [11.8 mg/dl], sodium >180 mmol/l] and chloride [139 mmol/l]). Moderate numbers of birefringent oxalate crystals, based on infrared and electron microscopy, were present within renal tubules; small numbers were seen in colloid within thyroid follicles. A retrospective analysis of 66 additional cases of wild desert tortoises was conducted to determine whether similar crystals were present in thyroid and kidney. The tortoises, from the Mojave and Sonoran deserts, were necropsied between 1992 and 2003 and included juveniles and adults. Tortoises were classified as healthy (those that died due to trauma and where no disease was identified after necropsy and evaluation by standard laboratory tests used for other tortoises) or not healthy (having one or more diseases or lesions). For all 67 necropsied tortoises, small numbers of crystals of similar appearance were present in thyroid glands from 44 of 54 cases (81%) and in kidneys from three of 65 cases (5%). Presence of oxalates did not differ significantly between healthy and unhealthy tortoises, between age classes, or between desert region, and their presence was considered an incidental finding. Small numbers of oxalate crystals seen within the kidney of two additional tortoises also were considered an incidental finding. Although the source of the calcium oxalate could not be determined, desert tortoises are herbivores, and a plant origin seems most likely. Studies are needed to evaluate the oxalate content of plants consumed by desert tortoises, and particularly those in the area where the tortoise in renal failure was found.

Journal of Wildlife Diseases↗

USGS2022

Relating systematic compositional variability to the textural occurrence of solid bitumen in shales

This study presents Raman spectroscopic data paired with scanning electron microscopy (SEM) images to assess solid bitumen composition as a function of solid bitumen texture and association with minerals. A series of hydrous pyrolysis experiments (1–103 days, 300–370 °C) using a low maturity (0.25% solid bitumen reflectance, BR o ), high total organic carbon [(TOC), 14.0 wt%] New Albany Shale sample as the starting material yielded pyrolysis residues designed to evaluate the evolution of solid bitumen aromaticity with increasing temperature and heating duration. Solid bitumen was analyzed by Raman spectroscopy wherein point data were collected from accumulations that ranged in size and degree of association with the mineral matrix. Raman spectroscopy results show that with increasing temperature and experimental duration, solid bitumen aromaticity increases and compositional variability decreases. With regards to texture and composition, coarser-grained solid bitumen (>1.3 μm from nearest mineral grain) has consistently higher, but less variable aromaticity than thinner, wispy solid bitumen which is more intimately associated with the mineral matrix. Collocated scanning electron microscope images were used to provide qualitative assessments of porosity hosted by the organic matter. These paired data sets suggest that solid bitumen porosity development and molecular composition are linked, and these parameters are related to the textural relationships of the organic matter within the whole rock. These results are discussed with perspective towards understanding how rock fabric and texture can influence organic matter evolution during thermal maturation of organic-rich marine shales and inform our broader understanding of these important energy resources.

International Journal of Coal Geology↗