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At least 667 records · Page 37Linked to original sources
USGS2019

Improving pressure-limited CO2 storage capacity in saline formations by means of brine extraction

The carbon dioxide (CO 2 ) storage capacity of saline formations may be constrained by reservoir pressure limitations. Brine extraction could be necessary to increase the CO 2 storage capacity of a given formation, manage the extent of the underground CO 2 plume and induced pressure front, and control the migration direction. To estimate the additional CO 2 storage capacity of a saline formation that can be made accessible by extraction of in-situ brines, a three-dimensional (3D) generic cubic cell containing one CO 2 injector in the middle surrounded by four brine extractors at each corner of the cell was assumed. A series of Tough2-ECO2N reservoir simulations were constructed with varying reservoir properties and run. Based on a series of scenarios, a mechanism was developed and demonstrated that resulted in derivation of a function to provide estimates of the ratio of total CO 2 injection over the brine extraction rate for a given scenario. We selected multiple saline formations in U.S. basins and evaluated the potential to increase the combined dynamic CO 2 storage capacity of the selected saline formations to over 1000 million metric tonnes per year (Mt/yr) of CO 2 for 100 years by means of brine extraction. Such storage capacities may be adequate to accommodate the CO 2 injection rates suggested for the United States under a “beyond two-degree Celsius scenario” (B2DS) that has been proposed to maintain global temperature rise to less than 2°C above pre-industrial reported levels. The results suggest that B2DS goals could be achieved with a volume ratio of brine extraction to CO 2 injection as low as 1:4, which is far lower than the ratios that have been commonly assumed in the literature.

International Journal of Greenhouse Gas Control↗
USGS2013

Bactericidal efficacy of elevated pH on fish pathogenic and environmental bacteria

Ship ballast water is a recognized medium for transfer and introductions of nonindigenous species. There is a need for new ballast water treatment methods that effectively and safely eliminate or greatly minimize movements of these species. The present study employed laboratory methods to evaluate the bactericidal efficacy of increased pH (pH 10.0–12.0) for exposure durations of up to 72 h to kill a variety of Gram-negative and Gram-positive bacteria including fish pathogens (Aeromonas spp., Yersinia ruckeri, Edwardsiella ictaluri, Serratia liquefaciens, Carnobacterium sp.), other common aquatic-inhabitant bacteria (Serratia marcescens, Pseudomonas fluorescens, Staphylococcus sp., Bacillus sp.) and indicators listed in International Maritime Organization D2 Standards; namely, Vibrio cholera (an environmental isolate from fish), Escherichia coli and Enterococcus faecalis. Volumes of 5 N NaOH were added to tryptic soy broth to obtain desired pH adjustments. Viable cells were determined after 0, 4, 12, 24, 48, and 72 h. Initial (0 h) cell numbers ranged from 3.40 × 10 4 cfu/mL for Bacillus sp. to 2.44 × 10 7 cfu/mL for E. faecalis. The effective endpoints of pH and treatment duration necessary to realize 100% bactericidal effect varied; however, all bacteria tested were killed within 72 h at pH 12.0 or lower. The lowest parameters examined, 4 h at pH 10.0, were bactericidal to V. cholera, E. ictaluri, three of four isolates of E. coli, and (three of four) Aeromonas salmonicida subsp. salmonicida. Bactericidal effect was attained at pH 10.0 within 12 h for the other A. salmonicida subsp. salmonicida, and within 24 h for P. fluorescens, and the remaining E. coli.

Journal of Advanced Research↗
USGS2014

In vivo and in vitro phenotypic differences between Great Lakes VHSV genotype IVb isolates with sequence types vcG001 and vcG002

Viral hemorrhagic septicemia virus (VHSV) is an aquatic rhabdovirus first recognized in farmed rainbow trout in Denmark. In the past decade, a new genotype of this virus, IVb was discovered in the Laurentian Great Lakes basin and has caused several massive die-offs in some of the 28 species of susceptible North American freshwater fishes. Since its colonization of the Great Lakes, several closely related sequence types within genotype IVb have been reported, the two most common of which are vcG001 and vcG002. These sequence types have different spatial distributions in the Great Lakes. The aim of this study was to determine whether the genotypic differences between representative vcG001 (isolate MI03) and vcG002 (isolate 2010-030 #91) isolates correspond to phenotypic differences in terms of virulence using both in vitro and in vivo approaches. In vitro infection of epithelioma papulosum cyprini (EPC), bluegill fry (BF-2), and Chinook salmon embryo (CHSE) cells demonstrated some differences in onset and rate of growth in EPC and BF-2 cells, without any difference in the quantity of RNA produced. In vivo infection of round gobies ( Neogobius melanostomus ) via immersion exposure to different concentrations of vcG001 or vcG002 caused a significantly greater mortality in round gobies exposed to 10 2 plaque forming units ml − 1 of vcG001. These experiments suggest that there are phenotypic differences between Great Lakes isolates of VHSV genotype IVb.

Journal of Great Lakes Research↗
USGS2019

Defensible standardized ploidy assessments for Grass Carp (Ctenopharyngodon idella, Cyprinidae) intercepted from the commercial supply chain

Although methods are in place through the U.S. Fish and Wildlife (USFWS) program for ploidy testing of feral caught Grass Carp ( Ctenopharyngodon idella ) and black carp ( Mylopharyngodon piceus ), no guidelines exist for carp hauled across state lines. Using 1200 Grass Carp purchased by undercover Ohio law enforcement during 2015–2016, we developed a standardized protocol for discriminating ploidy by using two parameters, nuclear size and DNA content. Bead standards at 2 μm or 4 μm were used to establish nuclear size from Nile Tilapia ( Oreochromis niloticus ), known diploid ( n = 20) and triploid (n = 20) Grass Carp blood, and cells derived from eyeballs of purchased field carp. The control for establishing DNA content was cryopreserved or fresh tilapia blood (2.40 pg). Time postmortem indicated nuclear size was similar over 4 days, but DNA quality from triploids was best at 24 h. Occasionally, only size or DNA content was measurable. Tilapia mean nuclear size ( n = 501 samples) was 4.61 μm (SE 0.05) (R 2 = 0.94). Known diploid and triploid blood nuclear sizes, compared with tilapia size, were 3.62 μm (SE 0.13) (R 2 = 0.96) and 7.58 μm (SE 0.27) (R 2 = 0.96), respectively. Mean field carp eye nuclear size was 5.83 μm (SE 0.13). Mean DNA content of cells from field carp eyes ( n = 698 fish) was 3.51 pg (SE 0.06). No diploid Grass Carp were detected in the USFWS certified triploid Grass Carp transports. This standard protocol reliably discriminates ploidy and can be used for enforcement of regulations that differ among state jurisdictions.

Journal of Great Lakes Research↗
USGS2012

Histological observations in the Hawaiian reef coral, Porites compressa, affected by Porites bleaching with tissue loss

The scleractinian finger coral Porites compressa is affected by the coral disease Porites bleaching with tissue loss (PBTL). This disease initially manifests as bleaching of the coenenchyme (tissue between polyps) while the polyps remain brown with eventual tissue loss and subsequent algal overgrowth of the bare skeleton. Histopathological investigation showed a loss of symbiont and melanin-containing granular cells which was more pronounced in the coenenchyme than the polyps. Cell counts confirmed a 65% reduction in symbiont density. Tissue loss was due to tissue fragmentation and necrosis in affected areas. In addition, a reduction in putative bacterial aggregate densities was found in diseased samples but no potential pathogens were observed.

Journal of Invertebrate Pathology↗
USGS2014

Gross and microscopic pathology of lesions in Pocillopora spp. from the subtropical eastern Pacific

Coral reefs are threatened by a variety of factors including diseases that have caused significant damage in some regions such as in the Caribbean. At present, no data are available on coral diseases in the Mexican Pacific where Pocillopora spp. is a dominant component of coral communities. Here, we describe gross and microscopic morphology of lesions found in pocilloporids at four sites in the Mexican Pacific. Corals were identified and their lesions photographed and quantified in the field. Tissue samples were collected from healthy and affected colonies for histopathology. We recorded seven species of pocilloporids at the study sites with Isla Isabel being the location with the highest coral diversity ( H ′ = 1.27). Lesions were present in 42% of the colonies and included discoloration (32%), predation-induced tissue loss (30%), unexplained tissue loss (3%) and overgrowth by sponges or algae (35%). The most affected species, P . damicornis (50%), was also one of the most common in the region. No species was more prone to a particular lesion, but there was a significant association between location and the presence of lesions. Northern Islas Marietas (61%) and Isla Isabel (41%) had the highest prevalence of lesions, followed by Manzanillo (37%) and Bahías de Huatulco (23%). Histological changes included atrophy of the surface body wall with depletion of zooxanthellae (91%) in corals with discoloration (bleaching). Ablation of tissue from mesoglea (18%) was also observed. Colonies with unexplained tissue loss showed atrophy and thinning of the epidermis (89%), characterized by cuboidal instead of pseudocolumnar cells normally found in healthy pseudocolumnar ciliated epithelium. Bacterial aggregates between the mesoglea and gastrodermis (11%) were very conspicuous in healthy and diseased corals. Lesions produced by fish bites and gastropods were associated with tissue atrophy (40%) and, in some cases, algal overgrowth near the lesion (20%). No infectious agents associated with cell pathology were detected microscopically. Bleaching and overgrowth by algae and sponges, as well as unexplained tissue loss, are common in Pocillopora . These lesions and anatomical changes warrant further study since their incidence is potentially indicative of reef degradation.

Mexican Pacific↗
USGS2010

Dramatic beach and nearshore morphological changes due to extreme flooding at a wave-dominated river mouth

Record flooding on the Santa Clara River of California (USA) during January 2005 injected ∼ 5 million m 3 of littoral-grade sediment into the Santa Barbara Littoral Cell, approximately an order of magnitude more than both the average annual river loads and the average annual alongshore littoral transport in this portion of the cell. This event appears to be the largest sediment transport event on record for a Southern California river. Over 170 m of local shoreline (mean high water (MHW)) progradation was observed as a result of the flood, followed by 3 years of rapid local shoreline recession. During this post-flood stage, linear regression-determined shoreline change rates are up to −45 m a − 1 on the subaerial beach (MHW) and − 114 m a − 1 on the submarine delta (6 m isobath). Starting approximately 1 km downdrift of the river mouth, shoreline progradation persisted throughout the 3-year post-flood monitoring period, with rates up to + 19 m a − 1 . Post-flood bathymetric surveys show nearshore (0 to 12 m depth) erosion on the delta exceeding 400 m 3 /m a − 1 , more than an order of magnitude higher than mean seasonal cross-shore sediment transport rates in the region. Changes were not constant with depth, however; sediment accumulation and subsequent erosion on the delta were greatest at − 5 to − 8 m, and accretion in downdrift areas was greatest above –2 m. Thus, this research shows that the topographic bulge (or “wave”) of sediment exhibited both advective and diffusive changes with time, although there were significant variations in the rates of change with depth. The advection and diffusion of the shoreline position was adequately reproduced with a simple “one line” model, although these modeling techniques miss the important cross-shore variations observed in this area. This study illustrates the importance of understanding low-frequency, high volume coastal discharge events for understanding short- and long-term sediment supply, littoral transport, and beach and nearshore evolution in coastal systems adjacent to river mouths.

Marine Geology↗
USGS2008

Transcriptional profiling of MHC class I genes in rainbow trout infected with infectious hematopoietic necrosis virus

Major histocompatibility complex (MHC) molecules are important mediators of cell-mediated immunity in vertebrates. MHC class IA molecules are important for host anti-viral immunity as they present intracellular antigens and regulate natural killer cell (NK) activity. MHC class Ib molecules on the other hand are less understood and have demonstrated diverse immune and non-immune functions in mammals. Rainbow trout possess a single classical MHC IA locus ( Onmy -UBA) that is believed to function similar to that of mammalian MHC class Ia. Numerous MHC class Ib genes with undetermined functions have also been described in trout. Here we utilize quantitative reverse transcriptase PCR (qRT-PCR) techniques to survey the levels of basal and inducible transcription for selected trout MHC class Ib genes, sIgM and sentinels of IFN induction in response to viral infection. Basal transcription of all the class Ib genes examined in this study was lower than Onmy -UBA in naïve fish. UBA, along with all of the non-classical genes were induced in fish infected with virus but not in control fish. Our results support a non-classical designation for the majority of the class IB genes surveyed in this study based upon expression levels while also indicating that they may play an important role in anti-viral immunity in trout.

Molecular Immunology↗
USGS2012

Ocean-atmosphere dynamics during Hurricane Ida and Nor'Ida: An application of the coupled ocean-;atmosphere–wave–sediment transport (COAWST) modeling system

The coupled ocean–atmosphere–wave–sediment transport (COAWST) modeling system was used to investigate atmosphere–ocean–wave interactions in November 2009 during Hurricane Ida and its subsequent evolution to Nor'Ida, which was one of the most costly storm systems of the past two decades. One interesting aspect of this event is that it included two unique atmospheric extreme conditions, a hurricane and a nor'easter storm, which developed in regions with different oceanographic characteristics. Our modeled results were compared with several data sources, including GOES satellite infrared data, JASON-1 and JASON-2 altimeter data, CODAR measurements, and wave and tidal information from the National Data Buoy Center (NDBC) and the National Tidal Database. By performing a series of numerical runs, we were able to isolate the effect of the interaction terms between the atmosphere (modeled with Weather Research and Forecasting, the WRF model), the ocean (modeled with Regional Ocean Modeling System (ROMS)), and the wave propagation and generation model (modeled with Simulating Waves Nearshore (SWAN)). Special attention was given to the role of the ocean surface roughness. Three different ocean roughness closure models were analyzed: DGHQ (which is based on wave age), TY2001 (which is based on wave steepness), and OOST (which considers both the effects of wave age and steepness). Including the ocean roughness in the atmospheric module improved the wind intensity estimation and therefore also the wind waves, surface currents, and storm surge amplitude. For example, during the passage of Hurricane Ida through the Gulf of Mexico, the wind speeds were reduced due to wave-induced ocean roughness, resulting in better agreement with the measured winds. During Nor'Ida, including the wave-induced surface roughness changed the form and dimension of the main low pressure cell, affecting the intensity and direction of the winds. The combined wave age- and wave steepness-based parameterization (OOST) provided the best results for wind and wave growth prediction. However, the best agreement between the measured (CODAR) and computed surface currents and storm surge values was obtained with the wave steepness-based roughness parameterization (TY2001), although the differences obtained with respect to DGHQ were not significant. The influence of sea surface temperature (SST) fields on the atmospheric boundary layer dynamics was examined; in particular, we evaluated how the SST affects wind wave generation, surface currents and storm surges. The integrated hydrograph and integrated wave height, parameters that are highly correlated with the storm damage potential, were found to be highly sensitive to the ocean surface roughness parameterization.

Ocean Modelling↗
USGS2013

Reproductive health of yellow perch Perca flavescens in selected tributaries of the Chesapeake Bay

Reduced recruitment of yellow perch has been noted for a number of years in certain urbanized watersheds (South and Severn Rivers) of the Chesapeake Bay. Other rapidly developing watersheds such as Mattawoman Creek are more recently showing evidence of reduced recruitment of anadromous fishes. In this study, we used a battery of biomarkers to better document the reproductive health of adult yellow perch collected during spring spawning in 2007–2009. Perch were collected in the South and Severn Rivers, Mattawoman Creek and the less developed Choptank and Allen's Fresh watersheds for comparison. Gonadosomatic indices, plasma reproductive hormone concentrations, plasma vitellogenin concentrations and gonad histology were evaluated in mature perch of both sexes. In addition, sperm quantity (cell counts) and quality (total and progressive motility, spermatogenic stage and DNA integrity), were measured in male perch. Many of these biomarkers varied annually and spatially, with some interesting statistical results and trends. Male perch from the Choptank and Allen's Fresh had generally higher sperm counts. In 2008 counts were significantly lower in the perch from the Severn when compared to other sites. The major microscopic gonadal abnormality in males was the proliferation of putative Leydig cells, observed in testes from Severn and less commonly, Mattawoman Creek perch. Observations that could significantly impact egg viability were an apparent lack of final maturation, abnormal yolk and thin, irregular zona pellucida. These were observed primarily in ovaries from Severn, South and less commonly Mattawoman Creek perch. The potential association of these observations with urbanization, impervious surface and chemical contaminants is discussed.

Maryl;Virginia↗
USGS2023

Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio

A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow ( Tachycineta bicolor ) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling ( HMGCS2 , SLC22A5 ), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids.

Ohio↗
USGS2024

Hormetic and transcriptomic responses of the toxic alga Prymnesium parvum to glyphosate

Growth of the toxic alga Prymnesium parvum is hormetically stimulated with environmentally relevant concentrations of glyphosate. The mechanisms of glyphosate hormesis in this species, however, are unknown. We evaluated the transcriptomic response of P. parvum to glyphosate at concentrations that stimulate maximum growth and where growth is not different from control values, the zero-equivalent point (ZEP). Maximum growth occurred at 0.1 mg l −1 and the ZEP was 2 mg l −1 . At 0.1 mg l −1 , upregulated transcripts outnumbered downregulated transcripts by one order of magnitude. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that the upregulated transcriptome is primarily associated with metabolism and biosynthesis. Transcripts encoding heat shock proteins and co-chaperones were among the most strongly upregulated, and several others were associated with translation, Redox homeostasis, cell replication, and photosynthesis. Although most of the same transcripts were also upregulated at concentrations ≥ZEP, the proportion of downregulated transcripts greatly increased as glyphosate concentrations increased. At the ZEP, downregulated transcripts were associated with photosynthesis, cell replication, and anion transport, indicating that specific interference with these processes is responsible for the nullification of hormetic growth. Transcripts encoding the herbicidal target of glyphosate, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), were upregulated at concentrations ≥ZEP but not at 0.1 mg l −1 , indicating that disruption of EPSPS activity occurred at high concentrations and that nullification of hormetic growth involves the direct interaction of glyphosate with this enzyme. Results of this study may contribute to a better understanding of glyphosate hormesis and of anthropogenic factors that influence P. parvum biogeography and bloom formation.

Science of the Total Environment↗
USGS2012

Viral tropism and pathology associated with viral hemorrhagic septicemia in larval and juvenile Pacific herring

Viral hemorrhagic septicemia virus (VHSV) genotype IVa causes mass mortality in wild Pacific herring, a species of economic value, in the Northeast Pacific Ocean. Young of the year herring are particularly susceptible and can be carriers of the virus. To understand its pathogenesis, tissue and cellular tropisms of VHSV in larval and juvenile Pacific herring were investigated with immunohistochemistry, transmission electron microscopy, and viral tissue titer. In larval herring, early viral tropism for epithelial tissues (6d post-exposure) was indicated by foci of epidermal thickening that contained heavy concentrations of virus. This was followed by a cellular tropism for fibroblasts within the fin bases and the dermis, but expanded to cells of the kidney, liver, pancreas, gastrointestinal tract and meninges in the brain. Among wild juvenile herring that underwent a VHS epizootic in the laboratory, the disease was characterized by acute and chronic phases of death. Fish that died during the acute phase had systemic infections in tissues including the submucosa of the gastrointestinal tract, spleen, kidney, liver, and meninges. The disease then transitioned into a chronic phase that was characterized by the appearance of neurological signs including erratic and corkscrew swimming and darkening of the dorsal skin. During the chronic phase viral persistence occurred in nervous tissues including meninges and brain parenchymal cells and in one case in peripheral nerves, while virus was mostly cleared from the other tissues. The results demonstrate the varying VHSV tropisms dependent on the timing of infection and the importance of neural tissues for the persistence and perpetuation of chronic infections in Pacific herring.

Veterinary Microbiology↗
USGS2013

Experimental infection studies demonstrating Atlantic salmon as a host and reservoir of viral hemorrhagic septicemia virus type IVa with insights into pathology and host immunity

In British Columbia, Canada (BC), aquaculture of finfish in ocean netpens has the potential for pathogen transmission between wild and farmed species due to the sharing of an aquatic environment. Viral hemorrhagic septicemia virus (VHSV) is enzootic in BC and causes serious disease in wild Pacific herring, Clupea pallasii, which often enter and remain in Atlantic salmon, Salmo salar, netpens. Isolation of VHSV from farmed Atlantic salmon has been previously documented, but the effects on the health of farmed salmon and the wild fish sharing the environment are unknown. To determine their susceptibility, Atlantic salmon were exposed to a pool of 9 isolates of VHSV obtained from farmed Atlantic salmon in BC by IP-injection or by waterborne exposure and cohabitation with diseased Pacific herring. Disease intensity was quantified by recording mortality, clinical signs, histopathological changes, cellular sites of viral replication, expression of interferon-related genes, and viral tissue titers. Disease ensued in Atlantic salmon after both VHSV exposure methods. Fish demonstrated gross disease signs including darkening of the dorsal skin, bilateral exophthalmia, light cutaneous hemorrhage, and lethargy. The virus replicated within endothelial cells causing endothelial cell necrosis and extensive hemorrhage in anterior kidney. Infected fish demonstrated a type I interferon response as seen by up-regulation of genes for IFNα, Mx, and ISG15. In a separate trial infected salmon transmitted the virus to sympatric Pacific herring. The results demonstrate that farmed Atlantic salmon can develop clinical VHS and virus can persist in the tissues for at least 10 weeks. Avoiding VHS epizootics in Atlantic salmon farms would limit the potential of VHS in farmed Atlantic salmon, the possibility for further host adaptation in this species, and virus spillback to sympatric wild fishes.

Veterinary Microbiology↗
USGS2018

An update on Toxoplasma gondii infections in northern sea otters (Enhydra lutris kenyoni) from Washington State, USA

Toxoplasmosis in marine mammals is epidemiologically and clinically important. Toxoplasma gondii antibodies (by modified agglutination test, cut-off ≥1:25) were detected in serum of 65 of 70 (92.9%) northern sea otters ( Enhydra lutris kenyoni ) from Washington State, USA. Brains and/or muscles of 44 sea otters were bioassayed in mice (INF-γ knock-out [KO], Swiss Webster outbred [SW]) and viable T. gondii was isolated from 22 of 44 (50%); T. gondii strains were lethal to KO mice but not SW mice. These T. gondii isolates were further propagated in cell culture. Multi-locus PCR-RFLP genotyping of cell culture-derived tachyzoites revealed four different genotypes among 22 isolates including ToxoDB PCR-RFLP genotype #5 (14 isolates), #1 (three isolates), #3 (four isolates), and #167 (one isolate). PCR-DNA sequencing based genotyping using polymorphic gene GRA6 revealed one of four different alleles. Among the 14 RFLP genotype #5 strains, 10 have GRA6 sequences that match with the Type A, one match with the Type X, two strains did not generate sequence data, and one strain had double peaks at known polymorphic sites indicating a mixed infection. The seven strains belong to genotypes #1 and #3, all have identical sequences to T. gondii Type II reference isolate ME49. Genotype #167 strain has identical sequence to Type I reference strain. In summary, we observed high seroprevalence, and high rate of isolation of T. gondii from northern sea otters and predominant genotype #5 that has been previously reported a dominant and widespread strain among terrestrial wildlife in North America. GRA6 sequence analysis of the genotype #5 isolates indicated the dominance of Type A lineage in sea otters in Washington State.

Washington↗
USGS2011

A novel member of the family Hepeviridae from cutthroat trout ( Oncorhynchus clarkii )

Beginning in 1988, the Chinook salmon embryo (CHSE-214) cell line was used to isolate a novel virus from spawning adult trout in the state of California, USA. Termed the cutthroat trout ( Oncorhynchus clarkii ) virus (CTV), the small, round virus was not associated with disease, but was subsequently found to be present in an increasing number of trout populations in the western USA, likely by a combination of improved surveillance activities and the shipment of infected eggs to new locations. Here, we report that the full length genome of the 1988 Heenan Lake isolate of CTV consisted of 7269 nucleotides of positive-sense, single-stranded RNA beginning with a 5' untranslated region (UTR), followed by three open reading frames (ORFs), a 3' UTR and ending in a polyA tail. The genome of CTV was similar in size and organization to that of Hepatitis E virus (HEV) with which it shared the highest nucleotide and amino acid sequence identities. Similar to the genomes of human, rodent or avian hepeviruses, ORF 1 encoded a large, non-structural polyprotein that included conserved methyltransferase, protease, helicase and polymerase domains, while ORF 2 encoded the structural capsid protein and ORF 3 the phosphoprotein. Together, our data indicated that CTV was clearly a member of the family Hepeviridae , although the level of amino acid sequence identity with the ORFs of mammalian or avian hepeviruses (13-27%) may be sufficiently low to warrant the creation of a novel genus. We also performed a phylogenetic analysis using a 262. nt region within ORF 1 for 63 isolates of CTV obtained from seven species of trout reared in various geographic locations in the western USA. While the sequences fell into two genetic clades, the overall nucleotide diversity was low (less than 8.4%) and many isolates differed by only 1-2 nucleotides, suggesting an epidemiological link. Finally, we showed that CTV was able to form persistently infected cultures of the CHSE-214 cell line that may have use in research on the biology or treatment of hepevirus infections of humans or other animals.

Virus Research↗
USGS1997

Fungal life-styles and ecosystem dynamics: Biological aspects of plant pathogens, plant endophytes and saprophytes

This chapter discusses various biochemical, genetic, ecological, and evolutionary aspects of fungi that express either symbiotic or saprophytic life-styles. An enormous pool of potential pathogens exists in both agricultural and natural ecosystems, and virtually all plant species are susceptible to one or more fungal pathogens. Fungal pathogens have the potential to impact on the genetic structure of populations of individual plant species, the composition of plant communities and the process of plant succession. Endophytic fungi exist for at least part of their life cycles within the tissues of a plant host. This group of fungi is distinguished from plant pathogens because they do not elicit significant disease symptoms. However, endophytes do maintain the genetic and biochemical mechanisms required for infection and colonization of plant hosts. Fungi that obtain chemical nutrients from dead organic matter are known as saprophytes and are critical to the dynamics and resilience of ecosystems. There are two modes of saprophytic growth: one in which biomolecules that are amenable to transport across cell walls and membranes are directly absorbed, and another in which fungi must actively convert complex biopolymers into subunit forms amenable to transportation into cells. Regardless of life-style, fungi employ similar biochemical mechanisms for the acquisition and conversion of nutrients into complex biomolecules that are necessary for vegetative growth, production and dissemination of progeny, organismal competition, and survival during periods of nutrient deprivation or environmental inclemency.

Advances in Botanical Research↗
USGS1999

Lanthanide, yttrium, and zirconium anomalies in the Fire Clay coal bed, Eastern Kentucky

The Fire Clay coal bed in the Central Appalachian basin region contains a laterally-persistent tonstein that is found in the coal throughout most of its areal extent. The tonstein contains an array of minerals, including sanidine, ??-quartz, anatase and euhedral zircon, thhat constitutes strong evidence for a volcanic origin of the parting. For this study, five samples of the tonstein and four sets of coal samples underlying the tonstein were collected from five sites in eastern Kentucky. Inductively coupled plasma-mass spectroscopy (ICP-MS) analysis of the tonstein and underlying coal collected from four sites in eastern Kentucky show that although Zr concentrations are high in the tonstein (570-1820 ppm on a coal-ash basis (cab)), they are highest in the coal directly underlying the tonstein (2870-4540 ppm (cab)). A similar enrichment pattern is observed in the concentration of Y plus the sum of the rare earth elements (Y + ??REE): total Y + ??REE concentrations in the five tonstein samples range from 511 to 565 ppm (cab). However, Y + ??REE contents are highest in the coals directly underlying the tonsteins: values range from 1965 to 4198 ppm (cab). Scanning electron microscopy of samples from coal which directly underlies two of the tonstein samples show that REE-rich phosphate, tentatively identified as monazite, commonly infills cracks in clays and cells in clarain and vitrain. Zircon is rare and commonly subhedral. On the basis of coal chemistry and grain morphology, we suggest that volcanic components in the tonstein were leached by ground water. The leachate, rich in Y and REE precipitated as authigenic mineral phases in the underlying coal.The Fire Clay coal bed in the Central Appalachian basin region contains a laterally-persistent tonstein that is found in the coal throughout most of its areal extent. The tonstein contains an array of minerals, including sanidine, ??-quartz, anatase and euhedral zircon, that constitutes strong evidence for a volcanic origin of the parting. For this study, five samples of the tonstein and four sets of coal samples underlying the tonstein were collected from five sites in eastern Kentucky. Inductively coupled plasma-mass spectroscopy (ICP-MS) analysis of the tonstein and underlying coal collected from four sites in eastern Kentucky show that although Zr concentrations are high in the tonstein (570-1820 ppm on a coal-ash basis (cab)), they are highest in the coal directly underlying the tonstein (2870-4540 ppm (cab)). A similar enrichment pattern is observed in the concentration of Y plus the sum of the rare earth elements (Y+???REE): total Y+???REE concentrations in the five tonstein samples range from 511 to 565 ppm (cab). However, Y+???REE contents are highest in the coals directly underlying the tonsteins: values range from 1965 to 4198 ppm (cab). Scanning electron microscopy of samples from coal which directly underlies two of the tonstein samples show that REE-rich phosphate, tentatively identified as monazite, commonly infills cracks in clays and cells in clarain and vitrain. Zircon is rare and commonly subhedral. On the basis of coal chemistry and grain morphology, we suggest that volcanic components in the tonstein were leached by ground water. The leachate, rich in Y and REE precipitated as authigenic mineral phases in the underlying coal.

International Journal of Coal Geology↗