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Fault-related clay authigenesis along the Moab Fault: Implications for calculations of fault rock composition and mechanical and hydrologic fault zone properties

The presence of clays in fault rocks influences both the mechanical and hydrologic properties of clay-bearing faults, and therefore it is critical to understand the origin of clays in fault rocks and their distributions is of great importance for defining fundamental properties of faults in the shallow crust. Field mapping shows that layers of clay gouge and shale smear are common along the Moab Fault, from exposures with throws ranging from 10 to ???1000 m. Elemental analyses of four locations along the Moab Fault show that fault rocks are enriched in clays at R191 and Bartlett Wash, but that this clay enrichment occurred at different times and was associated with different fluids. Fault rocks at Corral and Courthouse Canyons show little difference in elemental composition from adjacent protolith, suggesting that formation of fault rocks at those locations is governed by mechanical processes. Friction tests show that these authigenic clays result in fault zone weakening, and potentially influence the style of failure along the fault (seismogenic vs. aseismic) and potentially influence the amount of fluid loss associated with coseismic dilation. Scanning electron microscopy shows that authigenesis promotes that continuity of slip surfaces, thereby enhancing seal capacity. The occurrence of the authigenesis, and its influence on the sealing properties of faults, highlights the importance of determining the processes that control this phenomenon. ?? 2010 Elsevier Ltd.

Journal of Structural Geology↗

A review of spatially resolved techniques and applications of organic petrography in shale petroleum systems

This review examines new techniques and applications of organic petrography in source-rock reservoir petroleum systems that have occurred along with development of the global ‘shale revolution’ in energy resources. The review is limited to techniques and instrumentation that provide spatially resolved information, typically at or below microscales, for dispersed organic matter occurring in situ in samples of shale and mudrock. A brief summary of ion beam sample preparation is followed by discussion of the most common analytical techniques and applications. Advantages and limitations of each technique, including requisite sample preparation, types of information generated [e.g., molecular or elemental (isotopic) abundance], sensitivity, and resolution are discussed. In a few cases, techniques not yet applied to organic petrology of shale or mudrock are described (e.g., X-ray photoelectron spectroscopy imaging), in anticipation of near-term future application. The most common in situ techniques applied for characterization of organic matter in shale and mudrock include optical (including fluorescence) and electron microscopies, Raman, fluorescence, and infrared spectroscopies, and surficial measurements via force microscopy. Techniques that show growing application to organic petrography of shale include tip-enhanced photothermal infrared spectroscopy, mass spectrometry imaging, and synchrotron-based spectroscopies, among others. It is anticipated that the future of dispersed organic matter petrography will hold continued development of integrated instrument techniques (e.g., simultaneous or sequential correlative microscopies and/or spectroscopies of the same location), increased instrumental resolution, increased use of multiscale and multimodal organic petrography investigations, and three-dimensional imaging and chemical speciation mapping applications via multiple analytical approaches.

International Journal of Coal Geology↗

PCR diagnostics underestimate the prevalence of avian malaria ( Plasmodium relictum ) in experimentally-infected passerines

Several polymerase chain reaction (PCR)-based methods have recently been developed for diagnosing malarial infections in both birds and reptiles, but a critical evaluation of their sensitivity in experimentally-infected hosts has not been done. This study compares the sensitivity of several PCR-based methods for diagnosing avian malaria ( Plasmodium relictum ) in captive Hawaiian honeycreepers using microscopy and a recently developed immunoblotting technique. Sequential blood samples were collected over periods of up to 4.4 yr after experimental infection and rechallenge to determine both the duration and detectability of chronic infections. Two new nested PCR approaches for detecting circulating parasites based on P. relictum 18S rRNA genes and the thrombospondin-related anonymous protein (TRAP) gene are described. The blood smear and the PCR tests were less sensitive than serological methods for detecting chronic malarial infections. Individually, none of the diagnostic methods was 100% accurate in detecting subpatent infections, although serological methods were significantly more sensitive (97%) than either nested PCR (61–84%) or microscopy (27%). Circulating parasites in chronically infected birds either disappear completely from circulation or to drop to intensities below detectability by nested PCR. Thus, the use of PCR as a sole means of detection of circulating parasites may significantly underestimate true prevalence.

Journal of Parasitology↗

Characterization of the host response to the myxosporean parasite, Ceratomyxa shasta (Noble), by histology, scanning electron microscopy, and immunological techniques

The tissue response of Salmo gairdneri Richardson, against the myxosporean parasite. Ceratomyxa shasta (Noble), was investigated using histological techniques, scanning electron microscopy and immunological methods. The progress of infection in C. shasta ‐susceptible and resistant steelhead and rainbow trout was examined by standard histological techniques and by indirect fluorescent antibody methods using monoclonal antibodies directed against C. shasta antigens. Trophozoite stages were first observed in the posterior intestine and there was indication that resistance was due to the inability of the parasite to penetrate this tissue rather than to an inflammatory response. Examination of a severely infected intestine by scanning electron microscopy showed extensive destruction of the mucosal folds of the posterior intestine. Western blotting and indirect fluorescent antibody techniques were used to investigate the immunological component of the host response. No antibodies specific for C. shasta were detected by either method.

Journal of Fish Diseases↗

Skin pathology in Hawaiian goldring surgeonfish, Ctenochaetus strigosus (Bennett)

Twenty-eight goldring surgeonfish, Ctenochaetus strigosus (Bennett), manifesting skin lesions and originating from the north-western and main Hawaiian Islands were examined. Skin lesions were amorphous and ranged from simple dark or light discolouration to multicoloured tan to white sessile masses with an undulant surface. Skin lesions covered 2–66% of the fish surface, and there was no predilection for lesions affecting a particular part of the fish. Males appeared over-represented. Microscopy revealed the skin lesions to be hyperplasia, melanophoromas or iridophoromas. The presence of skin tumours in a relatively unspoiled area of Hawaii is intriguing. Explaining their distribution, cause and impact on survivorship of fish all merit further study because C. strigosus is an economically important fish in the region.

Hawai'i↗

Rotifers ingest oocysts of Cryptosporidium parvum

Six genera of rotifers including Philodina, Monostyla, Epiphanes, Euchlanis, Brachionus, and Asplanchna were exposed to oocysts of Cryptosporidium parvum cleaned of fecal debris. Unstained oocysts and those stained with fluorescein-conjugated monoclonal antibody were added to suspensions of viable rotifers and were examined by phase-contrast, differential interference contrast, and fluorescence microscopy. Rotifers of all six genera were observed ingesting oocysts. A maximum of 25 oocysts was observed in the stomachs of Euchlanis and Brachionus. Euchlanis and Epiphanes were observed excreting boluses containing up to eight oocysts. It was not determined whether rotifers digested or otherwise rendered oocysts nonviable.

Journal of Eukaryotic Microbiology↗

Development of a real-time PCR assay for detection of planktonic red king crab ( Paralithodes camtschaticus (Tilesius 1815)) larvae

The Alaskan red king crab ( Paralithodes camtschaticus ) fishery was once one of the most economically important single-species fisheries in the world, but is currently depressed. This fishery would benefit from improved stock assessment capabilities. Larval crab distribution is patchy temporally and spatially, requiring extensive sampling efforts to locate and track larval dispersal. Large-scale plankton surveys are generally cost prohibitive because of the effort required for collection and the time and taxonomic expertise required to sort samples to identify plankton individually via light microscopy. Here, we report the development of primers and a dual-labeled probe for use in a DNA-based real-time polymerase chain reaction assay targeting the red king crab, mitochondrial gene cytochrome oxidase I for the detection of red king crab larvae DNA in plankton samples. The assay allows identification of plankton samples containing crab larvae DNA and provides an estimate of DNA copy number present in a sample without sorting the plankton sample visually. The assay was tested on DNA extracted from whole red king crab larvae and plankton samples seeded with whole larvae, and it detected DNA copies equivalent to 1/10,000th of a larva and 1 crab larva/5mL sieved plankton, respectively. The real-time polymerase chain reaction assay can be used to screen plankton samples for larvae in a fraction of the time required for traditional microscopial methods, which offers advantages for stock assessment methodologies for red king crab as well as a rapid and reliable method to assess abundance of red king crab larvae as needed to improve the understanding of life history and population processes, including larval population dynamics.

Journal of Shellfish Research↗

Relating systematic molecular and textural properties of graptolite pyrolyzed via gold tube hydrous pyrolysis: Implications for thermal proxies in lower Paleozoic marine shales

A series of gold tube pyrolysis experiments (72 h, 300–550 °C, 50 MPa) conducted on a graptolite-rich lower Paleozoic marine shale generated pyrolysis residues for a comprehensive evaluation of the molecular and structural variability of three types of graptolite periderm. Organic petrology, Raman spectroscopy, and field emission scanning electron microscopy (FE-SEM) with energy dispersive spectroscopy (EDS) were combined to evaluate the thermal evolution process. The three types of graptolite periderm, namely granular, non-granular, and nodular graptolite, were analyzed by Raman spectroscopy wherein point measurements were obtained after the maceral was identified and the location verified by organic petrology. Distinct thermal evolution pathways among non-granular, granular, and nodular graptolite periderms were recorded. The evolution patterns of the Raman parameters, particularly D1 and G bands, highlight the differences in geochemical composition of the graptolite periderm types and the alteration of molecular structure with increasing thermal maturity. Raman parameters D1 (position of the D1 peak), G-FWHM (full width at half maximum of the G peak), and ratios D1-FWHM/G-FWHM (full width at half maximum of the D1 peak ratioed to G-FWHM) and A D1 /A G (ratio of D1 and G peak intensities) showed effectiveness in assessing thermal maturity. Bireflectance with increasing gold tube pyrolysis temperature followed a hierarchy: non-granular > granular > nodular, reflecting different molecular alignment intensities. Qualitative FE-SEM evaluation showed that fine-grained mineral inclusions (primarily Fe-sulfide as determined via EDS) were associated with the graptolite populations, with granular graptolite containing greater amounts of coarser-grained (e.g., ∼300–1400 nm) mineral inclusions relative to non-granular and nodular graptolite, which contain finer-grained (e.g., ∼100–200 nm) inclusions difficult to resolve with optical microscopy. These findings are investigated to highlight the mechanisms that drive organic matter evolution within graptolite during thermal maturation, as well as to explore some of the limitations of using spectroscopic parameters as thermal maturity proxies.

International Journal of Coal Geology↗

Complex resistivity signatures of ethanol biodegradation in porous media

Numerous adverse effects are associated with the accidental release of ethanol (EtOH) and its persistence in the subsurface. Geophysical techniques may permit non-invasive, real time monitoring of microbial degradation of hydrocarbon. We performed complex resistivity (CR) measurements in conjunction with geochemical data analysis on three microbial-stimulated and two control columns to investigate changes in electrical properties during EtOH biodegradation processes in porous media. A Debye Decomposition approach was applied to determine the chargeability ( m ), normalized chargeability ( m n ) and time constant ( τ ) of the polarization magnitude and relaxation length scale as a function of time. The CR responses showed a clear distinction between the bioaugmented and control columns in terms of real ( σ′ ) and imaginary ( σ″ ) conductivity, phase ( ϕ ) and apparent formation factor ( F app ). Unlike the control columns, a substantial decrease in σ′ and increase in F app occurred at an early time (within 4 days) of the experiment for all three bioaugmented columns. The observed decrease in σ′ is opposite to previous studies on hydrocarbon biodegradation. These columns also exhibited increases in ϕ (up to ~ 9 mrad) and σ″ (up to two order of magnitude higher) 5 weeks after microbial inoculation. Variations in m and m n were consistent with temporal changes in ϕ and σ″ responses, respectively. Temporal geochemical changes and high resolution scanning electron microscopy imaging corroborated the CR findings, thus indicating the sensitivity of CR measurements to EtOH biodegradation processes. Our results offer insight into the potential application of CR measurements for long-term monitoring of biogeochemical and mineralogical changes during intrinsic and induced EtOH biodegradation in the subsurface.

Journal of Contaminant Hydrology↗

Phase relations in the system CuMoS

Phase relations in the system CuMoS were studied in the temperature range 500-1000 ??C by using the conventional sealed, evacuated glass capsule technique. Reflected-light microscopy, X-ray powder diffraction and electron microprobe analysis were used for phase characterization. The chevrel-type phase, CuxMo3S4, is stable above 600??C, and forms equilibrium assemblages with the cubic Cu2S solid solution, copper, molybdenum, Mo2S3 and MoS2. Its solid solution ranges from Cu1.50-2.00Mo3S4 at 700??C to Cu1.22-2.00Mo3S4 at 1000 ??C. ?? 1990.

Journal of the Less-Common Metals↗

Linking avian malaria parasitemia estimates from quantitative PCR and microscopy reveals new infection patterns in Hawai'i

Plasmodium parasites infect thousands of species and provide an exceptional system for studying host-pathogen dynamics, especially for multi-host pathogens. However, understanding these interactions requires an accurate assay of infection. Assessing Plasmodium infections using microscopy on blood smears often misses infections with low parasitemias (the fractions of cells infected), and biases in malaria prevalence estimates will differ among hosts that differ in mean parasitemias. We examined Plasmodium relictum infection and parasitemia using both microscopy of blood smears and quantitative polymerase chain reaction (qPCR) on 299 samples from multiple bird species in Hawai'i and fit models to predict parasitemias from qPCR cycle threshold (Ct) values. We used these models to quantify the extent to which microscopy underestimated infection prevalence and to more accurately estimate infection patterns for each species for a large historical study done by microscopy. We found that most qPCR-positive wild-caught birds in Hawaii had low parasitemias (Ct scores ≥35), which were rarely detected by microscopy. The fraction of infections missed by microscopy differed substantially among eight species due to differences in species’ parasitemia levels. Infection prevalence was likely 4–5-fold higher than previous microscopy estimates for three introduced species, including Zosterops japonicus , Hawaii’s most abundant forest bird, which had low average parasitemias. In contrast, prevalence was likely only 1.5–2.3-fold higher than previous estimates for Himatione sanguinea and Chlorodrepanis virens , two native species with high average parasitemias. Our results indicate that relative patterns of infection among species differ substantially from those observed in previous microscopy studies, and that differences depend on variation in parasitemias among species. Although microscopy of blood smears is useful for estimating the frequency of different Plasmodium stages and host attributes, more sensitive quantitative methods, including qPCR, are needed to accurately estimate and compare infection prevalence among host species.

Hawai'i↗

A lymphosarcoma of thymic origin in the rainbow trout, Salmo gairdneri Richardson

A rainbow trout with a malignant lymphoma of probable thymic origin showed direct spread of the tumour to the gills, metastases to the liver and head kidney, and the presence of abnormal circulating lymphocytes. The cells of the tumour possessed plasma membrane immunoglobulin detectable by immuno–fluorescence. Examination of the tumour cells by transmission electron microscopy revealed no evidence of virus associated with the cells. Infectious viruses could not be detected in the tumour tissue, and the tumour was not transmissible by injection of live tumour cells into young rainbow trout. Attempts to establish the tumour in long–term culture were unsuccessful.

Journal of Fish Diseases↗

Serological comparison of selected isolates of Aeromonas salmonicida ssp. Salmonicida

Eight isolates of Acronionus salmonicida ssp. salmonicida were collected during furunculosis epizootics in North American Pacific coast states and provinces. Both virulent and avirulent forms of each isolate, confirmed by challenge and electron microscopy, were examined. Serological comparisons by cross-absorption agglutination tests revealed no serological differences between isolates. Using the double diffusion precipitin test, a single band was observed when antigen from a sonicated virulent strain was reacted with antiserum against a sonicated, virulent strain absorbed with homologous, avirulent strain. The presence of the single band was eliminated by excess sonication.

Journal of Fish Diseases↗

Laboratory transmission of adult salmon enteritis and associated pathogens in juvenile Chinook salmon ( Oncorhynchus tshawytscha )

Adult salmon enteritis (ASE), characterised by severe ulcerative enteritis, has been linked to prespawn mortality (PSM) in spring Chinook salmon ( Oncorhynchus tshawytscha ) in certain rivers in Oregon, USA. Catastrophic losses of spring Chinook salmon have resulted from PSM, a significant threat to their population stability. Understanding the causes of ASE is therefore critical for mitigating PSM and supporting conservation. This study investigates the potential infectious aetiology of ASE using a juvenile Chinook salmon model. Fish were immunocompromised with dexamethasone implants, fasted, and exposed to intestinal tissues from ASE-affected adult Chinook. Histopathology of recipient fish revealed mid-intestinal lesions consistent with ASE. The microsporidium Enterocytozoon schreckii , which is observed in ASE-affected adults from rivers, was transmitted for the first time to juvenile Chinook Salmon, making E. schreckii a potential new pathogen of juvenile salmon. Additionally, intranuclear inclusions were identified in enterocytes by histopathology and viral particles were detected by electron microscopy in recipient fish. The study demonstrates that intestinal lesions consistent with ASE can be experimentally induced in juvenile Chinook salmon through oral exposure to infected tissues, supporting an infectious aetiology. Further research is needed to isolate specific pathogens, including viruses and E. schreckii , and to elucidate their roles in ASE development.

Oregon↗

Viral erythrocytic necrosis: Some physiological consequences of infection in chum salmon ( Oncorhynchus keta )

Erythroid cells in chum salmon ( Oncorhynchus keta ) susceptible to infection with erythrocytic necrosis virus (ENV) were examined by light and electron microscopy. Cells of stages II, III, IV, V, and VI contained complete eyrthrocytic necrosis virions in the cytoplasm. Viruses closely resembling ENV were also detected in the nuclei of some erythroblasts. Some secondary consequences of ENV infection were a threefold greater mortality rate from vibriosis, a significantly decreased tolerance to oxygen depletion, and a decreased ability to regulate serum sodium and potassium in saltwater.

Canadian Journal of Fisheries and Aquatic Sciences↗

Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA

Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii . The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.

Journal of Veterinary Diagnostic Investigation↗

Attempts to identify the source of avian vacuolar myelinopathy for waterbirds

Attempts were made to reproduce avian vacuolar myelinopathy (AVM) in a number of test animals in order to determine the source of the causative agent for birds and to find a suitable animal model for future studies. Submerged vegetation, plankton, invertebrates, forage fish, and sediments were collected from three lakes with ongoing outbreaks of AVM and fed to American coots ( Fulica americana ), mallard ducks and ducklings ( Anas platyrhynchos ), quail ( Coturnix japonica ), and laboratory mice either via gavage or ad libitum. Tissues from AVM-affected coots with brain lesions were fed to ducklings, kestrels ( Falco sparverius ), and American crows ( Corvus brachyrhynchos ). Two mallards that ingested one sample of Hydrilla verticillata along with any biotic or abiotic material associated with its external surface developed brain lesions consistent with AVM, although neither of the ducks had clinical signs of disease. Ingestion of numerous other samples of Hydrilla from the AVM affected lakes and a lake with no prior history of AVM, other materials (sediments, algae, fish, invertebrates, and water from affected lakes), or tissues from AVM-affected birds did not produce either clinical signs or brain lesions in any of the other test animals in our studies. These results suggest that waterbirds are most likely exposed to the causative agent of AVM while feeding on aquatic vegetation, but we do not believe the vegetation itself is the agent. We hypothesize that the causative agent of AVM might either be accumulated by aquatic vegetation, such as Hydrilla , or associated with biotic or abiotic material on its external surfaces. In support of that hypothesis, two coots that ingested Hydrilla sampled from a lake with an ongoing AVM outbreak in wild birds developed neurologic signs within 9 days (ataxia, limb weakness, and incoordination), and one of two coots that ingested Hydrilla collected from the same site 13 days later became sick and died within 38 days. None of these three sick coots had definitive brain lesions consistent with AVM by light microscopy, but they had no gross or histologic lesions in other tissues. It is unclear if these birds died of AVM. Perhaps they did not ingest a dose sufficient to produce brain lesions or the lesions were ultrastructural. Alternatively, it is possible that a separate neurotoxic agent is responsible for the morbidity and mortality observed in these coots.

Journal of Wildlife Diseases↗

Comparative morphology of zebra ( Dreissena polymorpha ) and quagga ( Dreissena bugensis ) mussel sperm: Light and electron microscopy

Adult zebra ( Dreissena polymorpha ) and quagga ( Dreissena bugensis ) mussels were induced to release large quantities of live spermatozoa by the administration of 5-hydroxytryptamine (serotonin). Sperm were photographed alive using phase-contrast microscopy and were fixed subsequently with glutaraldehyde followed by osmium tetroxide for eventual examination by transmission or scanning electron microscopy. The sperm of both genera are of the ect-aquasperm type. Their overall dimensions and shape allow for easy discrimination at the light and scanning electron microscopy level. Transmission electron microscopy of the cells reveals a barrel-shaped nucleus in zebra mussel sperm and an elongated nucleus in quagga mussel sperm. In both species, an acrosome is cradled in a nuclear fossa. The ultrastructure of the acrosome and axial body, however, is distinctive for each species. The structures of the midpiece are shown, including a unique mitochondrial "skirt" that includes densely packed parallel cristae and extends in a narrow sheet from the mitochondria.

Canadian Journal of Zoology↗