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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↗

USGS1997

Effects of ultraviolet-B radiation on fish: Histologic comparison of a UVB-sensitive and a UVB-tolerant species

Lahontan cutthroat trout Oncorhynchus clarki henshatvi were sensitive to simulated solar ultraviolet-B radiation (UVB) and exhibited grossly visible signs of sunburn upon exposure. Razorback suckers Xyrauchen texanus , however, were tolerant to simulated solar UVB and showed no grossly visible signs of exposure. Cutthroat trout also had considerably less of an unidentified, possibly photoprotective, substance in the skin than did razorback suckers. In an attempt to characterize the cellular response to simulated solar UVB exposure in the skin of these two species, we examined sections from UVB-exposed fish by light and electron microscopy. Cutthroat trout showed grossly visible signs of sunburn by 48 h. Histologic observations included a sloughing of the mucous cells, necrosis and edema in the epidermis and dermis, and, in some cases, secondary fungal infections. Razorback suckers did not show any visible signs of sunburn during 72 h of experimental exposure. Histologic analyses revealed that cell necrosis had occurred, but the severe necrosis and sloughing noted in cutthroat trout was not observed. An increase in epidermal thickness, apparently due to hypertrophy and hyperplasia of large PAS-negative cells, occurred in the razorback suckers. These cells contained a large central region of low electron density and appeared to be club cells. In some, extensive interdigitation of the electron-lucent cytoplasm with adjacent epithelial cell margins occurred. Near the surface of the epidermis these cells were larger and the interface with epithelial cells lacked complex interdigitation. These cells may contain the substance that appears to protect razorback suckers against UV-B radiation.

Journal of Aquatic Animal Health↗

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↗

USGS1999

Analysis of atmospheric paniculate matter; application of optical and selected geochemical techniques

An increase in particulate matter in the atmosphere has been shown to be linked to increased mortality but this relationship is poorly understood. Light microscopy, electron microscopy , electron microprobe , and micro-FTIR techniques have been applied to study atmospheric particulates in Brisbane, Australia as a part of a study on asthma. The particulate matter samples were collected daily from April to August 1992, and the sampling covered the autumn period which is typically a time of high asthma incidence in Brisbane. Volumetrically, most atmospheric particulate matter is less than 2 μ m in size. The microscopic analysis reveals that this material is composed mainly of combusted and incompletely burned hydrocarbons from motor vehicle exhaust emissions, quiescent spores of Mucorales, soil bacteria, and inorganic matter in the form of quartz and other silicates. Elemental and functional group analyses confirm microscope identification, documenting carbon-rich, aromatic exhaust material, more aliphatic pollen and spore material and inorganic matter. Fungal spores dominate bioaerosol and are very abundant from the end of April through May to mid-June. The cytoplasmic content of pollens or fungal spores is commonly regarded as allergenic. Particulates from the exhaust emissions and crustal material in a sub-micrometer size range may act as carriers or dispersive mechanisms for cytoplasmic material from fungal spores and pollens, perhaps causing periods of the highest exhaust emission to be the most allergenic.

International Journal of Coal Geology↗

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↗

USGS1999

Sperm-cell ultrastructure of North American sturgeons II: The shortnose sturgeon (Acipenser brevirostrum, Lesueur, 1818)

The fine structure of the sperm cell of the shortnose sturgeon ( Acipenser brevirostrum ) was examined using transmission electron microscopy and selected metrics. The cell possesses a distinct acrosome, a defined head region, a midpiece, and a single flagellum. The mean length of the sperm cell body (acrosome + nucleus + midpiece) is approximately 9.71 µm, and the length of the flagellum is about 37 µm, resulting in a total cell length of about 46 µm. The sperm cell of the shortnose sturgeon is much longer and slightly wider than that of the Atlantic sturgeon. The nuclei of shortnose, white, and stellate sturgeon sperm cells are elongate trapezoids with the anterior (acrosome) end narrowest, the opposite of that of the Atlantic sturgeon. Although slightly smaller in total length and width than the sperm cells of the stellate and white sturgeons, that of the shortnose sturgeon is most similar to them in overall ultrastructure, as all three cells have three endonuclear canals. A structural connection of unknown function between the nuclear fossa and the proximal centriole, which is similar to the fibrous body in other species, is present in the shortnose sturgeon sperm cell. Our results suggest a more recent evolutionary link between the shortnose, white, and stellate sturgeons than between any of these and the Atlantic sturgeon. This is the first description of sperm cell ultrastructure in the shortnose sturgeon, an endangered species.

Canadian Journal of Zoology↗

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↗

USGS1998

Sperm-cell ultrastructure of North American sturgeons I: The Atlantic sturgeon (Acipenser oxyrhynchus)

Atlantic sturgeon ( Acipenser oxyrhynchus ) and lake sturgeon ( Acipenser fulvescens ) sperm-cell morphologies were examined using scanning electron microscopy. Major differences were found in four of nine metrics, all in the head region of the cell. Atlantic sturgeon sperm cells were much shorter than those of lake sturgeon. Anterior head width exceeded posterior head width, in contrast to the arrangement in lake sturgeon sperm cells. Lake sturgeon sperm cells are nearer in size to those of other sturgeons than are Atlantic sturgeon sperm cells. Comparisons were made with sperm-cell structures known from other sturgeon species, including the Russian sturgeon ( Acipenser gueldenstaedti colchicus ), stellate sturgeon ( Acipenser stellatus ), Chinese sturgeon ( Acipenser sinensis ), and white sturgeon ( Acipenser transmontanus ). Variation in cell morphology may indicate evolutionary relationships. In addition, the fine structure of Atlantic sturgeon sperm cells was examined using transmission electron microscopy and selected metrics are described. The cell possesses a distinct acrosome, a midpiece, and a single flagellum. A comparison is made with ultrastructural details of the sperm cells of stellate and white sturgeons. Similarities among these species include radial symmetry about the longitudinal axis, an elongate shape, a distinct acrosome, and the presence of endonuclear canals. Noteworthy differences include a smaller total length and width than stellate and white sturgeon sperm cells. The main sperm-cell body is approximately 4 µm long and the flagellum about 37 µm long, resulting in a total cell length of about 41 µm. Also, the Atlantic sturgeon sperm cell possesses only two membraned endonuclear canals, in contrast to the arrangement in white and stellate sturgeons, where three such organelles are found. A structural connection of unknown function between the nuclear fossa and proximal centriole is also present in the Atlantic sturgeon sperm cell. Sperm-cell nuclei of white and stellate sturgeons are elongate trapezoids, with the anterior end narrower, whereas in Atlantic sturgeon the anterior portion of the trapezoid is wider than the posterior. Structural similarities between species may indicate a commonality of ancestral and evolutionary relationships that may have taxonomic implications. Ultrastructure suggests a closer evolutionary relationship between the white and stellate sturgeon than between either of these species and the Atlantic sturgeon. The present findings may be used by biologists studying the reproductive physiology, forensics, taxonomy, and genetics of sturgeons.

Canadian Journal of Zoology↗

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↗

USGS2021

Compositional evolution of organic matter in Boquillas Shale across a thermal gradient at the single particle level

The molecular composition of petroliferous organic matter and its compositional evolution throughout thermal maturation provides insight for understanding petroleum generation. This information is critical for understanding hydrocarbon resources in unconventional reservoirs, as source rock organic matter is highly dispersed, in contact with the surrounding mineral matrix, and may occur as multiple organic matter maceral types. Here, Raman spectroscopy and optical microscopy approaches were applied to a marginally mature (vitrinite reflectance ~0.5%) sample of the Late Cretaceous Boquillas Shale before and after hydrous pyrolysis (HP) at 300 °C and 330 °C for 72 h. This analytical approach allowed for correlative examination of micro-scale changes in organic matter compositional properties (e.g., aromaticity) for a variety of organic matter macerals across a thermal gradient (from marginally mature into the late oil/wet gas window) at the single particle level. Results indicate that while the examined amorphous organic matter, solid bitumen, and vitrinite particles exhibit different aromatic signatures in the unheated shale, they effectively progress along a similar trend through composition space with thermal maturation. Examined inertinite fragments were generally insensitive to the applied thermal stress, reinforcing the idea that reservoir temperature may be secondary for dictating the molecular composition of inertinite. Additional analysis of Raman spectra for individual organic matter macerals was performed using multivariate curve resolution (MCR) and correlation of standard Raman and reflectance-derived thermal maturity proxies against MCR parameters shows consistent trends. This trend suggests that MCR may be a fast and statistically robust method for extracting compositional information from Raman spectra of sedimentary organic matter, and can be used to construct thermal maturity relationships. These findings inform our understanding of how different petroliferous organic matter maceral types evolve throughout thermal reactions and further demonstrate that Raman spectroscopy combined with petrographic analysis can provide complementary estimates of organic matter composition and thermal maturity.

International Journal of Coal Geology↗

USGS2011

Microstructure and crystallographic preferred orientation of polycrystalline microgarnet aggregates developed during progressive creep, recovery, and grain boundary sliding

Optical microscopy, electron probe microanalysis, and electron backscatter diffraction methods have been used to examine a broad range of garnet microstructures within a high strain zone that marks the western margin of a major transpression zone in the southern New England Appalachians. Garnet accommodated variable states of finite strain, expressed as low strain porphyroclasts (Type 1), high strain polycrystalline aggregates (Type 2), and transitional morphologies (Type 3) that range between these end members. Type 1 behaved as rigid porphyroclasts and is characterized by four concentric Ca growth zones. Type 2 help define foliation and lineation, are characterized by three Ca zones, and possess a consistent bulk crystallographic preferred orientation of (100) symmetrical to the tectonic fabric. Type 3 show variable degrees of porphyroclast associated with aggregate, where porphyroclasts display complex compositional zoning that corresponds to lattice distortion, low-angle boundaries, and subgrains, and aggregate CPO mimics porphyroclast orientation. All aggregates accommodated a significant proportion of greenschist facies deformation through grain boundary sliding, grain rotation and impingement, and pressure solution, which lead to a cohesive behavior and overall strain hardening of the aggregates. The characteristic CPO could not have been developed in this manner, and was the result of an older phase of partitioned amphibolite facies dislocation creep, recovery including chemical segregation, and recrystallization of porphyroclasts. This study demonstrates the significance of strain accommodation within garnet and its affect on composition under a range of PT conditions, and emphasizes the importance of utilizing EBSD methods with studies that rely upon a sound understanding of garnet. ?? 2010 Elsevier Ltd.

Journal of Structural Geology↗