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At least 55 records · Page 3Linked to original sources
USGS2000

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↗
USGS2023

Evidence for infection influencing survival of the freshwater copepod Salmincola californiensis, a parasite of Pacific salmon and trout

Objective We explore apparent infection of Salmincola californiensis arising during investigations involving this lernaeopodid copepod parasitic on Pacific salmon and trout Oncorhynchus spp. Methods We noted occasional unusual coloration of adult female copepods collected from the wild. These females were bright blue and pink in contrast to the cream white coloration characteristic of the copepod. We also observed that similar color patterns developed under laboratory settings when copepod eggs were held for hatching. In paired egg cases, we found consistent hatching failure of blue and pink eggs and patterns in apparent disease development that would be consistent with both vertical and horizontal transmission. Result Attempts to identify the cause of the apparent infection using genetic methods and transmission electron microscopy were inconclusive. Conclusion Iridovirus infection was initially suspected, but bacterial infection is also plausible. This apparent reduced hatching success of S. californiensis warrants further exploration as it could reduce local abundances. Given the potential importance of a disease impacting this copepod, a parasite that itself affects endangered and commercially important Pacific salmon and trout, future research would benefit from clarification of the apparent infection through additional sequencing, primer development, visualization, and exploration into specificity and transmission.

Journal of Aquatic Animal Health↗
USGS2017

Otolith marking of juvenile shortnose gar by immersion in oxytetracycline

Oxytetracycline (OTC) has been used to mark a variety of fish species at multiple developmental stages; however, there is little information on batch-marking Lepisosteidae. Juvenile Shortnose Gar Lepisosteus platostomus (53 ± 3 mm TL) were seined from an Oklahoma State University research pond and transported to the Oklahoma Fishery Research Lab. Juvenile Shortnose Gar were exposed to a range of OTC concentrations—0, 500, 600, and 700 mg/L—for 4, 5, or 6 h. Lapillus and sagitta otoliths were examined 14 d postexposure for mark presence and evaluation using fluorescent microscopy. Overall, 93.3% of otoliths exposed to OTC exhibited a mark. Concentration of OTC affected the mean mark quality, whereas duration and otolith type examined did not. However, as concentration increased, so did mortality, suggesting a balance is needed to achieve marking goals. Based on our findings, batch marking of Shortnose Gar can be successful at OTC concentrations from 500 to 700 mg/L for 4–6 h, although mark quality may vary and mortality rates increase at the higher concentrations and longer durations.

North American Journal of Fisheries Management↗
USGS2016

Structured heterogeneity in a marine terrace chronosequence: Upland mottling

Soil mottles generally are interpreted as a product of reducing conditions during periods of water saturation. The upland soils of the Santa Cruz, CA, marine terrace chronosequence display an evolving sequence of reticulate mottling from the youngest soil (65 ka) without mottles to the oldest soil (225 ka) with well-developed mottles. The mottles consist of an interconnected network of clay and C-enriched regions (gray, 2.5Y 6/1) bordered by leached parent material (white, 2.5Y 8/1) within a diminishing matrix of oxidized parent material (orange, 7.5YR 5/8). The mottles develop in soils that formed from relatively uniform nearshore sediments and occur below the depth of soil bioturbation. To explore how a presumably wetland feature occurs in an unsaturated upland soil, physical and chemical characteristics of mottle separates (orange, gray, and white) were compared through the deep time represented by the soil chronosequence. Mineralogical, isotopic, and surface-area differences among mottle separates indicate that rhizogenic centimeter-scale mass transfer acting across millennia is an integral part of weathering, pedogenesis, and C and nutrient transfer. Elemental analysis, electron microscopy, and Fe-isotope systematics indicate that mottle development is driven by deep roots together with their fungal and microbial symbionts. Taken together, these data suggest that deep soil horizons on old stable landforms can develop reticulate mottling as the long-term imprint of rhizospheric processes. The processes of rhizogenic mottle formation appear to regulate pedogenesis, nutrients, and C sequestration at depth in unsaturated zones.

California↗
USGS1975

Thin-section electron microscopy of mature Myxosoma cerebralis (Myxosporidea) spores

The morphology of purified, mature Myxosoma cerebralis spores was examined by thin-section electron microscopy. Surface architecture corresponded closely to that described in an earlier scanning electron microscopy study of this organism (Lom and Hoffman, 1971). A uniformly thick spore wall is composed of finely granular, electron-lucent material. Intrawall "valvoplasm" at the sutural border region contains small, light spheroidal profiles with dense centers situated in a background matrix; such structures are absent in the intermediate wall areas. Ovoid polar capsules contain complex filamentous profiles within the peripheral matrix region. Individual filaments appear twisted into S-shaped configurations and contain moderately electron-opaque material within their lumina.

Journal of Parasitology↗
USGS1970

Morphology of certain viruses of Salmonid fishes. II. In vivo studies of infectious Hematopoietic Necrosis Virus

Juvenile sockeye salmon ( Oncorhynchus nerka ) were injected with the infectious hematopoietic necrosis (IHN) virus, and tissue samples from the anterior kidney, spleen, liver, intestine, and pyloric caeca of moribund fish were prepared for electron microscopy. Bullet-shaped virus particles measuring 158 × 90 mμ were observed in the hematopoietic tissues of the anterior kidney and spleen. Virus particles were also observed in the outer connective tissues of the pancreas or pyloric caeca, or both. No virus was found in the intestine or liver. The healthy appearance of erythrocytes, reticular cells, and endothelial cells in necrotic areas of the spleen and anterior kidney, and the absence of lymphocytes in these areas, suggested that lymphocytes might be one source of the virus.

Journal of the Fisheries Research Board of Canada↗
USGS2022

Microbially induced anaerobic oxidation of magnetite to maghemite in a hydrocarbon-contaminated aquifer

Iron mineral transformations occurring in hydrocarbon-contaminated sites are linked to the biodegradation of the hydrocarbons. At a hydrocarbon-contaminated site near Bemidji, Minnesota, USA, measurements of magnetic susceptibility (MS) are useful for monitoring the natural attenuation of hydrocarbons related to iron cycling. However, a transient MS, previously observed at the site, remains poorly understood and the iron mineral phases acting as reactants and products associated with this MS perturbation remain largely unknown. To address these unknowns, we acquired mineral magnetism measurements, including hysteresis loops, backfield curves, and isothermal remanent magnetizations on sediment core samples retrieved from the site and magnetite-filled mineral packets installed within the aquifer. Our data show that the core samples and magnetite packs display decreasing magnetization with time and that this loss in magnetization is accompanied by increasing bulk coercivity consistent with decreased average grain size and/or partial oxidation. Low-temperature magnetometry on all samples displayed behavior consistent with magnetite, but samples within the plume also show evidence of maghemitization. This interpretation is supported by the occurrence of shrinkage cracks on the surface of the grains imaged via scanning electron microscopy. Magnetite transformation to maghemite typically occurs under oxic conditions, here, we propose that maghemitization occurs within the anoxic portions of the plume via microbially mediated anaerobic oxidation. Mineral dissolution also occurs within the plume. Microorganisms capable of such anaerobic oxidation have been identified within other areas at the Bemidji site, but additional microbiological studies are needed to link specific anaerobic iron oxidizers with this loss of magnetization.

Minnesota↗
USGS2011

Microanatomy of passerine hard-cornified tissues: Beak and claw structure of the black-capped chickadee (Poecile atricapillus)

The microanatomy of healthy beaks and claws in passerine birds has not been well described in the literature, despite the importance of these structures in avian life. Histological processing of hard‐cornified tissues is notoriously challenging and only a few reports on effective techniques have been published. An emerging epizootic of beak deformities among wild birds in Alaska and the Pacific Northwest region of North America recently highlighted the need for additional baseline information about avian hard‐cornified structures. In this study, we examine the beak and claw of the Black‐capped Chickadee ( Poecile atricapillus ), a common North American passerine that is affected by what has been described as “avian keratin disorder.” We use light and scanning electron microscopy and high‐magnification radiography to document the healthy microanatomy of these tissues and identify features of functional importance. We also describe detailed methods for histological processing of avian hard‐cornified structures and discuss the utility of special stains. Results from this study will assist in future research on the functional anatomy and pathology of hard‐cornified structures and will provide a necessary reference for ongoing investigations of avian keratin disorder in Black‐capped Chickadees and other wild passerine species.

Journal of Morphology↗
USGS2019

Marking otoliths of Alligator Gar by immersion in oxytetracycline

Alligator Gar Atractosteus spatula are increasingly being stocked to restore populations, making the need to identify stocked individuals important for monitoring. Oxytetracycline (OTC) immersion allows for large numbers of fish to be marked simultaneously, thus eliminating the need to handle fish individually, but protocols for doing so have not been investigated fully for this species. In this study, we sought to identify dosages of OTC (concentration and duration of exposure) that would successfully mark juvenile Alligator Gar while minimizing mortality as a result of the marking procedures. Juvenile Alligator Gar (38 ± 4.4 mm [mean ± SE]) were collected from raceways at Tishomingo National Fish Hatchery 18–22 d after hatch and were marked during transport to the Oklahoma Fishery Research Laboratory. Ten individuals per treatment (360 total individuals) were randomly placed into one of three replicates containing one of four concentration × duration combinations of Pennox 343 OTC solution. Juvenile Alligator Gar were exposed to an OTC concentration of 0 (control), 500, 600, or 700 mg/L for a duration of 4, 5, or 6 h. Asteriscus, lapillus, and sagittal otoliths were examined for mark presence at 14 d postexposure by using fluorescent microscopy. The OTC concentration and duration both affected mean mark quality similarly among otolith types. Mortality increased with increasing OTC concentration, suggesting that a balance between concentration and duration is needed to achieve marking goals. Based on our findings, batch marking of Alligator Gar was successful at OTC concentrations from 500 to 700 mg/L for 4–6 h, although immersion at 500 mg/L for 6 h and 600 mg/L for 4–6 h produced the best balance between high mark quality and low associated mortality.

North American Journal of Fisheries Management↗
USGS2014

Anatomy of the lamprey ear: morphological evidence for occurrence of horizontal semicircular ducts in the labyrinth of Petromyzon marinus

In jawed (gnathostome) vertebrates, the inner ears have three semicircular canals arranged orthogonally in the three Cartesian planes: one horizontal (lateral) and two vertical canals. They function as detectors for angular acceleration in their respective planes. Living jawless craniates, cyclostomes (hagfish and lamprey) and their fossil records seemingly lack a lateral horizontal canal. The jawless vertebrate hagfish inner ear is described as a torus or doughnut, having one vertical canal, and the jawless vertebrate lamprey having two. These observations on the anatomy of the cyclostome (jawless vertebrate) inner ear have been unchallenged for over a century, and the question of how these jawless vertebrates perceive angular acceleration in the yaw (horizontal) planes has remained open. To provide an answer to this open question we reevaluated the anatomy of the inner ear in the lamprey, using stereoscopic dissection and scanning electron microscopy. The present study reveals a novel observation: the lamprey has two horizontal semicircular ducts in each labyrinth. Furthermore, the horizontal ducts in the lamprey, in contrast to those of jawed vertebrates, are located on the medial surface in the labyrinth rather than on the lateral surface. Our data on the lamprey horizontal duct suggest that the appearance of the horizontal canal characteristic of gnathostomes (lateral) and lampreys (medial) are mutually exclusive and indicate a parallel evolution of both systems, one in cyclostomes and one in gnathostome ancestors.

Journal of Anatomy↗
USGS1989

Pulmonary lesions in disseminated visceral coccidiosis of sandhill and whooping cranes

Fifty cranes, consisting of 46 sandhill (Grus canadensis) and four whooping cranes (Grus americana), were studied. Eighteen sandhill cranes and the four whooping cranes were naturally infected with disseminated visceral coccidiosis (DVC). The remaining sandhill cranes were chicks experimentally infected with oocysts of Eimeria reichenowi and/or E. gruis; five chicks served as controls. There were no clinical signs attributed to respiratory infection. Necropsy of naturally infected adult birds revealed nodules in many organs, including the lung, air sacs, trachea and nares. Artificially infected sandhill cranes and the whooping crane chicks that died from DVC had congestion and consolidated areas in the lung with frothy fluid in the airways. Grossly visible nodules were observed from 10 days postinoculation. Granulomatous pneumonia and tracheitis were observed with light microscopy. Lesions were associated with merogonic and gametogonic stages of eimerian coccidia. Granulomas and granulomatous foci contained parasitized large mononuclear cells. Merogonic stages were seen in lymphoid cells by ultrastructural examination. Oocysts were observed in the trachea and bronchial mucosa and admixed with exudate in the airways, indicating that crane eimerians can complete their life cycle at these sites. Of the few eimeriid coccidia that have extraintestinal stages of development in birds and mammals, only the species in cranes complete their life cycle in both the digestive and respiratory tracts.

Journal of Wildlife Diseases↗
USGS2019

Optical characterization of two cyanobacteria genera, Aphanizomenon and Microcystis, with hyperspectral microscopy.

Cyanobacterial blooms are a nuisance and a potential hazard in freshwater systems worldwide. Remote sensing has been used to detect cyanobacterial blooms, but few studies have distinguished between genera of cyanobacteria. Because some genera are more likely to be toxic than others, this is a useful distinction.In this study, hyperspectral imaging reflectance microscopy was used to examine cyanobacteria from Upper Klamath Lake, Oregon, USA, at high spatial and spectral resolution to determine if two species found commonly in the lake, Aphanizomenon flos-aquae and Microcystis aeruginosa, can be separated spectrally. Of the analytical methods applied, a spectral shape algorithm applied to the derivative was found to be most successful in classifying these species in microscope scenes. Further work is required to determine if the spectral characterization of cyanobacterial genera can be scaled up to other remote sensing applications.

Oregon↗
USGS1998

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↗
USGS2011

Halloysite nanotubes and bacteria at the saprolite-bedrock interface, Rio Icacos watershed, Puerto Rico

Quartz diorite bedrock underlying the Luquillo Mountains of eastern Puerto Rico undergoes weathering at one of the fastest documented rates for granitic rocks in the world. Although tropical temperatures and precipitation promote rapid weathering in this location, increased bacterial densities in the regolith immediately above the bedrock suggest that microorganisms contribute to mineral weathering as well. Deep saprolite and saprock samples were obtained at the bedrock interface in an upland location (Guaba Ridge) in the Rio Icacos watershed for examination by environmental scanning electron microscopy (ESEM). In ESEM images, mineral nanotubes were observed to occur frequently in association with coccus- and rod-shaped structures resembling bacteria. These nanotubes (50–140-nm width and 150–2700-nm length) were identified as halloysite using transmission electron microscopy. Observations of multiple nanotubes on the surfaces of an individual cell are consistent with the cell's exterior functional groups interacting with Si in pore water to facilitate halloysite nucleation. We propose that one mechanism by which bacteria contribute to the rapid weathering of quartz diorite minerals in this regolith is by lowering the free energy for secondary mineral formation. The presence of bacterial surfaces may result in more rapid removal of Si from solution, thereby increasing the dissolution rates of primary minerals.

Puerto Rico↗
USGS1986

Phase relations in the CuVS system

Phase relations in the system Cu-V-S were studied by using a sealedcapsule technique, reflected-light microscopy, X-ray powder diffraction and electron microprobe analysis. In the temperature range between 300 and 900 ??C, six vanadium sulfides exist in the V-S system. These are VS, V7S8, V3S4, V5S8, V3S5 and VS4. In the Cu-V-S system, three Cu-V sulfides are stable. Both Cu3VS4 (sulvanite) and CuV2S4 are cubic with a = 5.391 ?? 0.005 A ?? and a = 9.789 ?? 0.005 A ?? respectively, and the third has a composition Cu0.8V1.1S2. CuV2S4 forms equilibrium assemblages with all vanadium sulfides, which restricts their effects on the phase relations in the system to a small region. ?? 1986.

Journal of the Less-Common Metals↗
USGS1999

Geochemical heterogeneity of a gasoline-contaminated aquifer

The scale of biogeochemical reactions was studied in a physically and chemically heterogeneous surficial Coastal Plain aquifer contaminated by a gasoline spill. The physical heterogeneity of the aquifer is manifested in two hydrologic units, a shallow local aquifer of perched water and a regional sandy aquifer. Over the studied vertical interval of 21.3 ft (6.5 m), concentrations of reactive species varied by orders of magnitude, and the impact of biodegradation was expressed to widely varying degrees. A thin (3 ft thick) section of the perched-water zone was the most contaminated; total aromatic hydrocarbons were as high as 19.4 mg/l. Hydrocarbons were degraded by microbially mediated reactions that varied over short vertical distances and time. Anaerobic processes dominated within the low-permeability clay unit, whereas in the more permeable sandy layers nitrate reduction and aerobic degradation occurred. Hydrocarbons were more persistent over time in the low-permeability layer due to the limited availability of electron acceptors for degradation. The microbial degradation of hydrocarbons was linked to sulfate and iron reduction in the clay unit and led to alterations in the aquifer solids; electron microscopy revealed the presence of FeS minerals encrusting primary aquifer grains. High concentrations of Fe 2+ in groundwater, up to 34.5 mg/l, persist in kinetic disequilibrium in the presence of elevated H 2 S levels of 1.0 mg/l. Assessment of aquifer heterogeneities and groundwater contamination was possible due to sample discrimination at a scale of approximately 2 ft (∼0.6 m), a much finer resolution than is attempted in many remedial investigations of polluted aquifers. The information obtained in this type of study is essential to the development of models capable of estimating the fate of hydrocarbons at a site scale.

Journal of Contaminant Hydrology↗
USGS2019

Reflectance increase from broad beam ion milling of coals and organic-rich shales due to increased surface flatness

Broad ion beam (BIB) milling is useful in organic petrology because it can yield flat sample surfaces and avert the ‘smearing’ of organic matter (OM) that results from traditional mechanical polishing. This potentially makes BIB especially useful in the study of nano-porosity, where even minor mechanical disruption of the sample surface distorts the sample characteristic of interest—the pore structure. However, several studies have observed an OM reflectance increase after BIB milling, concluding that ion milling may cause thermal alteration to OM surfaces. To better understand ion milling effects on organic matter, coal (subbituminous, high volatile bituminous, medium volatile bituminous, anthracite) and shale [Bakken Formation, Ohio Shale-Huron Member (5), Kimmeridge Clay Formation, Alum Shale, New Albany Shale] samples were prepared using traditional mechanical polishing methods. Reflectance measurements (% Ro) were gathered on all maceral types present before BIB milling, followed by re-measurement of OM reflectance at the same locations after milling. Most OM increased in reflectance after BIB milling, with some exceptions in high maturity samples. Liptinite macerals in both coal and shale samples showed the greatest percent reflectance increase on average (+133%; n=338), followed by solid bitumen (+49%; n=313), vitrinite (+26%; n=413), and inertinite (+9%; n=220). Despite the increases to OM reflectance caused by BIB milling, no evidence was found for kerogen conversion (e.g., change in maceral abundances), or for migration of newly generated petroleum (e.g., pseudomorphic replacement of kerogen by solid bitumen). Such changes occur when samples are thermally altered from immature conditions into the oil window (e.g., by hydrous pyrolysis), and, if the increases in OM reflectance were thermally driven (by BIB milling), they should have been observed in the above experiments. Herein, we also used atomic force microscopy to document a decrease in surface roughness of correlative locations of OM on pre- and post-ion milled samples. This improved surface polish caused by BIB milling appears to be the root cause of increased OM reflectance, as no other supporting evidence of thermal alteration could be found. That is, the fraction of light formerly lost to oblique scatter in diffuse reflectance from a mechanically polished surface is converted to specular reflectance after BIB ion milling. Thus the light leaves the surface at a near normal angle and returns to the detector, resulting in increased OM reflectance.

International Journal of Coal Geology↗
USGS2016

Application of organic petrography in North American shale petroleum systems: A review

Organic petrography via incident light microscopy has broad application to shale petroleum systems, including delineation of thermal maturity windows and determination of organo-facies. Incident light microscopy allows practitioners the ability to identify various types of organic components and demonstrates that solid bitumen is the dominant organic matter occurring in shale plays of peak oil and gas window thermal maturity, whereas oil-prone Type I/II kerogens have converted to hydrocarbons and are not present. High magnification SEM observation of an interconnected organic porosity occurring in the solid bitumen of thermally mature shale reservoirs has enabled major advances in our understanding of hydrocarbon migration and storage in shale, but suffers from inability to confirm the type of organic matter present. Herein we review organic petrography applications in the North American shale plays through discussion of incident light photographic examples. In the first part of the manuscript we provide basic practical information on the measurement of organic reflectance and outline fluorescence microscopy and other petrographic approaches to the determination of thermal maturity. In the second half of the paper we discuss applications of organic petrography and SEM in all of the major shale petroleum systems in North America including tight oil plays such as the Bakken, Eagle Ford and Niobrara, and shale gas and condensate plays including the Barnett, Duvernay, Haynesville-Bossier, Marcellus, Utica, and Woodford, among others. Our review suggests systematic research employing correlative high resolution imaging techniques and in situ geochemical probing is needed to better document hydrocarbon storage, migration and wettability properties of solid bitumen at the pressure and temperature conditions of shale reservoirs.

International Journal of Coal Geology↗