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At least 127 records · Page 7Linked to original sources
USGS2007

Effect of compost age and composition on the atrazine removal from solution

Compost samples from two composting facilities, the Urbana (Illinois) Landscape Recycling Center (ULRC) and Illinois State University (ISU), were selected to examine the effect of compost age on atrazine removal from solution. The ULRC samples were made from yard waste without an additional nitrogen source. The ISU samples were made from yard waste or sawdust with the addition of manure. The 6-month-old ULRC compost had the greater capacity to remove atrazine from solution, which we attributed to its greater organic carbon content. The addition of nitrate into ULRC compost could influence the extent of atrazine removal, but did not have a significant impact on atrazine removal when applied to ISU compost, probably because manure was added to the yard waste to produce the compost. For both ULRC and ISU samples, the presence of sodium azide inhibited atrazine removal, suggesting that microbial activity contributed to the atrazine removal. Metabolic analysis demonstrated that hydroxyatrazine was the major identified metabolite that accumulated in solution before significant ring mineralization could occur. When compared with the ISU compost, the ULRC compost sample had a greater capacity to remove atrazine from solution during the 120 days of study because of the larger humic acid content. The experimental results suggested that less-mature compost may be better suited for environmental applications such as removing atrazine from tile-drainage waters. ?? 2006 Elsevier B.V. All rights reserved.

Journal of Hazardous Materials↗
USGS2007

The feasibility of applying immature yard-waste compost to remove nitrate from agricultural drainage effluents: A preliminary assessment

Nitrate is a major agricultural pollutant found in drainage waters. Immature yard-waste compost was selected as a filter media to study its feasibility for removing nitrate from drainage water. Different operation parameters were tested to examine the denitrification efficiency, including the amounts of compost packed in columns, the flow rate, and the compost storage periods. The experimental results suggested that hydraulic retention time was the major factor to determine the extent of nitrate removal, although the amount of compost packed could also contribute to the nitrate removal efficiency. The effluent nitrate concentration increased as the flow rate decreased, and the compost column reduced nitrate concentrations from 20 mg/L to less than 5 mg/L within 1.5 h. The solution pH increased at the onset of experiment because of denitrification, but stabilized at a pH of about 7.8, suggesting that the compost had a buffering capacity to maintain a suitable pH for denitrification. Storing compost under air-dried conditions may diminish the extent nitrate removed initially, but the effects were not apparent after longer applications. It appeared that immature yard-waste compost may be a suitable material to remove nitrate from tile drainage water because of its relatively large organic carbon content, high microbial activity, and buffering capacity. ?? 2006 Elsevier B.V. All rights reserved.

Journal of Hazardous Materials↗
USGS2021

Months-long spike in aqueous Arsenic following domestic well installation and disinfection: Short- and long-term drinking water quality implications

Exposure to high concentration geogenic arsenic via groundwater is a worldwide health concern. Well installation introduces oxic drilling fluids and hypochlorite (a strong oxidant) for disinfection, thus inducing geochemical disequilibrium. Well installation causes changes in geochemistry lasting 12 + months, as illustrated in a recent study of 250 new domestic wells in Minnesota, north-central United States. One study well had extremely high initial arsenic (1550 µg/L) that substantially decreased after 15 months (5.2 µg/L). The drilling and development of the study well were typical and ordinary; nothing observable indicated the very high initial arsenic concentration. We hypothesized that oxidation of arsenic-containing sulfides (which lowers pH) combined with low pH dissolution of arsenic-bearing Fe (oxyhydr)oxides caused the very high arsenic concentration. Geochemical equilibrium considerations and modeling supported our hypothesis. Groundwater equilibrium redox conditions are poised at the Fe(III) (s) /Fe(II) (aq) stability boundary, indicating arsenic-bearing Fe (oxyhydr)oxide mineral sensitivity to pH and redox changes. Changing groundwater geochemistry can have negative implications for home water treatment (e.g., reduced arsenic removal efficiency, iron fouling), which can lead to ongoing but unrecognized hazard of arsenic exposure from domestic well water. Our results may inform arsenic mobilization processes and geochemical sensitivity in similarly complex aquifers in Southeast Asia and elsewhere.

Minnesota↗
USGS2004

Overland flow generation in two lithologically distinct rainforest catchments

Streams on uniformly rainforest-covered, but lithologically very diverse Barro Colorado Island in central Panama?? show remarkable differences in their runoff response to rainfall. This lithological diversity is reflected in equally diverse soilscapes, and our objective was to test the hypothesis that contrasting runoff responses derive from soilscape features that control the generation of overland flow. We determined the soil saturated hydraulic conductivity (Ks) of two neighboring, but hydrologically contrasting catchments (Lutz Creek with a flashy and Conrad Trail with a delayed response to rainfall), and quantified the spatial and temporal frequency of overland flow occurrence. The median Ks values at a depth of 12.5 cm are large enough to rule out Hortonian overland flow, but a marked decrease in K s in Lutz Creek catchment at 30 cm suggests the formation of a perched water table and the generation saturation overland flow; the decrease in Ks in the Conrad Trail catchment is more gradual, and a perched water table is expected to form only at depths below 50 cm. In Lutz Creek, overland flow was generated frequently in time and space and regardless of topographic position, including near the interfluve, with very low thresholds of storm magnitude, duration, intensity and antecedent wetness, whereas in Conrad Trail, overland flow was generated much less frequently and then only locally. We conclude that soilscape features and microtopography are important controls of overland flow generation in these catchments. Our results contribute to the growing evidence that overland flow and forests are not a priori a contradiction in terms. ?? 2004 Elsevier B.V. All rights reserved.

Journal of Hydrology↗
USGS2007

Comparison of local- to regional-scale estimates of ground-water recharge in Minnesota, USA

Regional ground-water recharge estimates for Minnesota were compared to estimates made on the basis of four local- and basin-scale methods. Three local-scale methods (unsaturated-zone water balance, water-table fluctuations (WTF) using three approaches, and age dating of ground water) yielded point estimates of recharge that represent spatial scales from about 1 to about 1000 m 2 . A fourth method (RORA, a basin-scale analysis of streamflow records using a recession-curve-displacement technique) yielded recharge estimates at a scale of 10–1000s of km 2 . The RORA basin-scale recharge estimates were regionalized to estimate recharge for the entire State of Minnesota on the basis of a regional regression recharge (RRR) model that also incorporated soil and climate data. Recharge rates estimated by the RRR model compared favorably to the local and basin-scale recharge estimates. RRR estimates at study locations were about 41% less on average than the unsaturated-zone water-balance estimates, ranged from 44% greater to 12% less than estimates that were based on the three WTF approaches, were about 4% less than the age dating of ground-water estimates, and were about 5% greater than the RORA estimates. Of the methods used in this study, the WTF method is the simplest and easiest to apply. Recharge estimates made on the basis of the UZWB method were inconsistent with the results from the other methods. Recharge estimates using the RRR model could be a good source of input for regional ground-water flow models; RRR model results currently are being applied for this purpose in USGS studies elsewhere.

Minnesota↗
USGS2013

Export of dissolved organic carbon from the Penobscot River basin in north-central Maine

Dissolved organic carbon (DOC) flux from the Penobscot River and its major tributaries in Maine was determined using continuous discharge measurements, discrete water sampling, and the LOADEST regression software. The average daily flux during 2004–2007 was 71 kg C ha −1 yr −1 (392 Mt C d −1 ), an amount larger than measured in most northern temperate and boreal rivers. Distinct seasonal variation was observed in the relation between concentration and discharge (C–Q). During June through December (summer/fall), there was a relatively steep positive C–Q relation where concentration increased by a factor of 2–3 over the approximately 20-fold range of observed stream discharge for the Penobscot River near Eddington, Maine. In contrast, during January through May (winter/spring), DOC concentration did not increase with increasing discharge. In addition, we observed a major shift in the C–Q between 2004–2005 and 2006–2007, apparently resulting from unprecedented rainfall, runoff, and soil flushing beginning in late fall 2005. The relative contribution to the total Penobscot River basin DOC flux from each tributary varied dramatically by season, reflecting the role of large regulated reservoirs in certain basins. DOC concentration and flux per unit watershed area were highest in tributaries containing the largest areas in palustrine wetlands. Tributary DOC concentration and flux was positively correlated to percentage wetland area. Climatic or environmental changes that influence the magnitude or timing of river discharge or the abundance of wetlands will likely affect the export of DOC to the near-coastal ocean.

Maine↗
USGS2013

Increases in flood magnitudes in California under warming climates

Downscaled and hydrologically modeled projections from an ensemble of 16 Global Climate Models suggest that flooding may become more intense on the western slopes of the Sierra Nevada mountains, the primary source for California’s managed water system. By the end of the 21st century, all 16 climate projections for the high greenhouse-gas emission SRES A2 scenario yield larger floods with return periods ranging 2–50 years for both the Northern Sierra Nevada and Southern Sierra Nevada, regardless of the direction of change in mean precipitation. By end of century, discharges from the Northern Sierra Nevada with 50-year return periods increase by 30–90% depending on climate model, compared to historical values. Corresponding flood flows from the Southern Sierra increase by 50–100%. The increases in simulated 50 year flood flows are larger (at 95% confidence level) than would be expected due to natural variability by as early as 2035 for the SRES A2 scenario.

California↗
USGS2015

Groundwater recharge assessment at local and episodic scale in a soil mantled perched karst aquifer in southern Italy

Groundwater recharge assessment of karst aquifers, at various spatial and temporal scales, is a major scientific topic of current importance, since these aquifers play an essential role for both socio-economic development and fluvial ecosystems. In this study, groundwater recharge was estimated at local and episodic scales in a representative perched karst aquifer in a region of southern Italy with a Mediterranean climate. The research utilized measurements of precipitation, air temperature, soil water content, and water-table depth, obtained in 2008 at the Acqua della Madonna test area (Terminio Mount karst aquifer, Campania region). At this location the aquifer is overlain by ash-fall pyroclastic soils. The Episodic Master Recession (EMR) method, an improved version of the Water Table Fluctuation (WTF) method, was applied to estimate the amount of recharge generated episodically by individual rainfall events. The method also quantifies the amount of precipitation generating each recharge episode, thus permitting calculation of the Recharge to the Precipitation Ratio (RPR) on a storm-by-storm basis. Depending on the seasonally varying air temperature, evapotranspiration, and precipitation patterns, calculated values of RPR varied between 35% and 97% among the individual episodes. A multiple linear correlation of the RPR with both the average intensity of recharging rainfall events and the antecedent soil water content was calculated. Given the relatively easy measurability of precipitation and soil water content, such an empirical model would have great hydrogeological and practical utility. It would facilitate short-term forecasting of recharge in karst aquifers of the Mediterranean region and other aquifers with similar hydrogeological characteristics. By establishing relationships between the RPR and climate-dependent variables such as average storm intensity, it would facilitate prediction of climate-change effects on groundwater recharge. The EMR methodology could further be applied to other aquifers for evaluating the relationship of recharge to various hydrometeorological and hydrogeological processes.

Journal of Hydrology↗
USGS2019

Evidence for conservative transport of dissolved organic carbon in major river basins in the Gulf of Maine Watershed

Transport and fate of dissolved organic carbon (DOC) in rivers are important aspects of the carbon cycle and the critical linkage between terrestrial, aquatic, and marine systems. Recent studies have quantified fluvial export to the marine environment in many systems, but in-stream losses of DOC are poorly constrained. This study compares DOC yields (kg C/ha) between the area-weighted averages of several tributaries within larger watersheds with the DOC yields of the larger watersheds to gain insight on in-stream losses in larger river systems. Four large watersheds, 22 tributaries to those watersheds, and 5 additional main stem locations in Maine were studied during 1 April to 15 November in 2011 through 2013. There were no significant differences in the area-weighted average DOC yield of the tributaries and the larger watersheds indicating little net in-stream loss in the main stems of the larger rivers. It is unlikely that inputs of DOC from un-gauged areas compensated for losses from gauged tributaries based on similarity in DOC yield longitudinally along the main stems of two of the rivers. In addition, wetland abundance, which is associated with higher DOC yield in this environment, did not consistently increase from tributaries to the larger watershed or longitudinally along the main stems. This geographic distribution of wetlands therefore also indicates that it is unlikely that inputs of DOC from un-gauged areas compensated for losses from gauged tributaries. These findings suggest that in-stream losses of DOC in these larger river systems are minimal and that the vast majority of DOC in major rivers in Maine is transported conservatively to the coastal ocean.

Maine↗
USGS2021

Summer runoff generation in foothill catchments of the Colorado Front Range

Climatic shifts, disturbances, and land-use change can alter hydrologic flowpaths, water quality, and water supply to downstream communities. Prior research investigating streamflow generation processes in mountainous areas has largely focused on high-elevation alpine and subalpine catchments; less is known about these processes in lower-elevation foothills and montane catchments. In these lower-elevation ecoregions, precipitation shifts seasonally from snow to rain, which can result in differing seasonal flowpaths. We analyzed stream water for electrical conductivity, SiO 2 , Ca, Mg, Na, Cl, SO 4 , K, and dissolved organic carbon on both a weekly and storm event basis from April to August 2018 in three small (<10 km 2 ) foothill catchments, and one larger (63.2 km 2 ) catchment extending from the foothills to the subalpine ecoregions, in the Colorado Front Range. Using two end-member hydrograph separations and concentration-runoff relationships, we inferred the dominant catchment-scale flowpaths of precipitation to the streams. We selected catchments with varying land use to investigate the relationship between these characteristics and hydrologic flowpaths. We observed that concentrations of lithogenic constituents generally increased and dissolved organic carbon decreased as seasonal runoff decreased in the three foothill catchments, reflecting a transition from shallow subsurface flowpaths to deeper subsurface flowpaths. Elevated SO 4 and Cl concentrations during low-flow periods in two of our catchments suggest that historical or current anthropogenic activities, such as mining, application of road salt, and/or near-stream septic systems, affect local stream and groundwater chemistry. In a foothill catchment with anthropogenic and geologic impervious surfaces, streamflow during storm responses was sourced from faster, surficial flowpaths compared to a less disturbed neighboring catchment, highlighting the influence of anthropogenic land-use on runoff generation. This study provides insight into the fundamental hydrology of foothill catchments and how they may function in the future with human development, precipitation shifts and disturbances.

Colorado↗
USGS2021

The influence of land cover and storm magnitude on hydrologic flowpath activation and runoff generation in steep tropical catchments of central Panama

Despite abundant research documenting that land use/land cover (LULC) have substantial impacts on the hydrology of humid tropical systems, field-based evidence for the physical mechanisms behind these impacts are still lacking. In particular, our understanding of the hydrologic flowpaths that generate runoff in these systems, and how they vary with respect to LULC is insufficient to inform both physically-based hydrologic modeling and land-use decision-making. In this study, we use end-member mixing analysis (EMMA) of stream chemistry, and hydrometric characterizations of hillslope soil moisture to identify hydrologic flowpaths in humid tropical steep-land catchments of varying LULC: mature tropical forest, young secondary tropical forest, cattle pasture. EMMA was applied to data from 14 storm events (six at the mature forest, five at the young secondary forest, and three at the cattle pasture) that were intensively sampled during the 2017 wet season representing a wide range of rainfall magnitudes and intensities. Additionally, volumetric-soil-moisture responses at multiple depths were characterized during and after 74 storm events occurring from 2015 to 2017. EMMA results indicated that lateral preferential flow within the top 30 cm of the soil profile was a dominant source of runoff generation at the two forested catchments, with the contribution of this flow path increasing with rainfall magnitude and intensity. This was corroborated by volumetric-soil-moisture data, that showed that a perched zone of saturation developed at 30 cm at the time of peak storm runoff during the largest events and lasted for the remaining duration of the event. EMMA indicated that runoff was a combination of infiltration-excess overland flow and lateral subsurface flow in the actively grazed pastoral catchment. There, overland flow contributed 62 % of runoff during the highest runoff rate sampled (35.3 mm/hr) and this contribution increased substantially with storm magnitude. This flowpath identification was also supported by volumetric-soil-moisture data at the pasture, with peak saturation at all depths during the largest storm events occurring up to 30 min after peak runoff. These results provide a mechanistic explanation for previously observed hydrologic differences among tropical LULCs. Additionally, the wide range of hydrologic conditions during these storm events provide a basis for understanding how future changes to this, and similar humid tropical regions will impact hydrological processes and water availability.

Journal of Hydrology↗
USGS2010

Predicting potentially toxigenic Pseudo-nitzschia blooms in the Chesapeake Bay

Harmful algal blooms are now recognized as a significant threat to the Chesapeake Bay as they can severely compromise the economic viability of important recreational and commercial fisheries in the largest estuary of the United States. This study describes the development of empirical models for the potentially domoic acid-producing Pseudo-nitzschia species complex present in the Bay, developed from a 22-year time series of cell abundance and concurrent measurements of hydrographic and chemical properties. Using a logistic Generalized Linear Model (GLM) approach, model parameters and performance were compared over a range of Pseudo-nitzschia bloom thresholds relevant to toxin production by different species. Small-threshold blooms (???10cellsmL-1) are explained by time of year, location, and variability in surface values of phosphate, temperature, nitrate plus nitrite, and freshwater discharge. Medium- (100cellsmL-1) to large- threshold (1000cellsmL-1) blooms are further explained by salinity, silicic acid, dissolved organic carbon, and light attenuation (Secchi) depth. These predictors are similar to other models for Pseudo-nitzschia blooms on the west coast, suggesting commonalities across ecosystems. Hindcasts of bloom probabilities at a 19% bloom prediction point yield a Heidke Skill Score of -53%, a Probability of Detection ~75%, a False Alarm Ratio of ~52%, and a Probability of False Detection ~9%. The implication of possible future changes in Baywide nutrient stoichiometry on Pseudo-nitzschia blooms is discussed. ?? 2010 Elsevier B.V.

Journal of Marine Systems↗
USGS2018

The geochemistry of loess: Asian and North American deposits compared

Loess is widely distributed over Asia and North America and constitutes one of the most important surficial deposits that serve as terrestrial records of the Quaternary. The oldest Pleistocene loess in China is likely ∼2.6 Ma, thus spanning much or all of the Pleistocene. In North America, most loess is no older than the penultimate glacial period, with the exception of Alaska, where the record may go back to ∼3.0 Ma. On both continents, loess deposits date primarily to glacial periods, and interglacial or interstadial periods are represented by paleosols. Both glacial and non-glacial sources of silts that comprise the bulk of loess deposits are found on both continents. Although loess has been considered to be representative of the average upper continental crust, there are regionally distinctive compositions of loess in both Asia and North America. Loess deposits in Asia from Yakutia, Tajikistan, and China have compositionally distinct major element compositions, due to varying abundances of silicate minerals, carbonate minerals, and clay minerals. In North America, loess in the Mississippi River valley, the Great Plains, and Alaska are also distinguishable with regard to major element composition that reflects highly diverse source sediments. Trace element geochemistry (Sc-Th-Zr and the rare earth elements) also shows regional diversity of loess bodies, in both Asia and North America. On both continents, most loess bodies show significant contributions from later-cycle, altered sedimentary rocks, as opposed to direct derivation from igneous rocks. Further, some loess bodies have detectable contributions from mafic igneous rocks as well as major contributions from average, upper-crustal, felsic rocks. Intercalated paleosols in loess sections show geochemical compositions that differ significantly from the underlying loess parent materials. Ratios of soluble-to-insoluble elements show depletions in paleosols due to chemical weathering losses of calcite, dolomite, plagioclase, mica, apatite, and smectite. In Asia and North America, the last interglacial paleosol is more weathered than equivalent modern soils, which could be due either to a climate that was warmer and more humid, a longer period of pedogenesis, or both. In Asia, early Pleistocene loess and paleosols are both more weathered than those from the middle and late Pleistocene, forming prior to a mid-Pleistocene aridification of Asia from uplift of the Tibetan Plateau. Understanding the geochemistry of loess and paleosols can tell us much about past atmospheric circulation, past temperature and moisture regimes, and even tectonic processes.

Journal of Asian Earth Sciences↗
USGS2010

Interpretation and analysis of planetary structures

Structural geology is an integral part of planetary science. Planetary structures provide the framework for determining the character and sequence of crustal deformation while simultaneously establishing the observational basis required to test geodynamic hypotheses for the deformation of planetary and satellite lithospheres. The availability of datasets that record spatial and topographic information with a resolution that matches or, in many cases, exceeds, what is available for Earth-based studies permits the deformation of several planets and satellites to be investigated down to the local or outcrop scales. The geometry and kinematics of common planetary structures such as joints, igneous dikes, deformation bands, faults, and folds can be determined with confidence from their distinctive morphologic and topographic signatures, enabling the structural histories and deformation magnitudes to be determined. Segmentation, displacement profiles, relay ramps, footwall anticlines, displacement-controlled depocenters, and other well-known characteristics of terrestrial normal fault and graben systems reveal the sequence and processes of fault growth in numerous planetary examples. Systems of thrust faults having both blind and surface-breaking components are important elements on several bodies including Mercury, the Moon, and Mars. Strike-slip faults have been identified on bodies including Mars and Europa with oblique extension found on Ganymede. Using field-based studies of Earth-based structures as a guide, planetary structures provide a means to explore and evaluate the causative stresses. Despite the wide range in structural styles across the solar system, plate tectonics is recognized only on the Earth, with the other planets and satellites deforming in the absence of large-scale horizontal motions and attendant plate recycling.

Journal of Structural Geology↗
USGS2012

Observed source parameters for dynamic rupture with non-uniform initial stressand relatively high fracture energy

We have conducted dynamic rupture propagation experiments to establish the relations between in-source stress drop, fracture energy and the resulting particle velocity during slip of an unconfined 2 m long laboratory fault at normal stresses between 4 and 8 MPa. To produce high fracture energy in the source we use a rough fault that has a large slip weakening distance. An artifact of the high fracture energy is that the nucleation zone is large such that precursory slip reduces fault strength over a large fraction of the total fault length prior to dynamic rupture, making the initial stress non-uniform. Shear stress, particle velocity, fault slip and acceleration were recorded coseismically at multiple locations along strike and at small fault-normal distances. Stress drop increases weakly with normal stress. Average slip rate depends linearly on the fault strength loss and on static stress drop, both with a nonzero intercept. A minimum fracture energy of 1.8 J/m 2 and a linear slip weakening distance of 33 μm are inferred from the intercept. The large slip weakening distance also affects the average slip rate which is reduced by in-source energy dissipation from on-fault fracture energy. Because of the low normal stress and small per event slip (∼86 μm), no thermal weakening such as melting or pore fluid pressurization occurs in these experiments. Despite the relatively high fracture energy, and the very low heat production, energy partitioning during these laboratory earthquakes is very similar to typical earthquake source properties. The product of fracture energy and fault area is larger than the radiated energy. Seismic efficiency is low at ∼2%. The ratio of apparent stress to static stress drop is ∼27%, consistent with measured overshoot. The fracture efficiency is ∼33%. The static and dynamic stress drops when extrapolated to crustal stresses are 2–7.3 MPa and in the range of typical earthquake stress drops. As the relatively high fracture energy reduces the slip velocities in these experiments, the extrapolated average particle velocities for crustal stresses are 0.18–0.6 m/s. That these experiments are consistent with typical earthquake source properties suggests, albeit indirectly, that thermal weakening mechanisms such as thermal pressurization and melting which lead to near complete stress drops, dominate earthquake source properties only for exceptional events unless crustal stresses are low.

Journal of Structural Geology↗
USGS2018

Frictional properties and 3-D stress analysis of the southern Alpine Fault, New Zealand

New Zealand's Alpine Fault (AF) ruptures quasi-periodically in large-magnitude earthquakes. Paleoseismological evidence suggests that about half of all recognized AF earthquakes terminated at the boundary between the Central and South Westland sections of the fault. There, fault geometry and the polarity of uplift change. The South Westland AF exhibits oblique-normal fault motion on a structure oriented 052°/82°SE that, for at least 35 km along strike, contains saponite-rich principal slip zone gouges. New hydrothermal friction experiments reveal that the saponite fault gouge is frictionally weak, exhibiting friction coefficients between μ = 0.12 and μ = 0.16 for a range of temperatures ( T = 25–210 °C) and effective normal stresses ( σ n ' = 31.2–93.6 MPa). The saponite gouge is rate-strengthening in all velocity steps performed at velocities between 0.01 and 3.0 μm/s, behavior conducive to aseismic creep. A three-dimensional stress analysis shows that the South Westland AF is favorably oriented with respect to the regional stress field for slip within the frictionally weak saponite fault gouge. Geometrically, the fault is severely misoriented for slip in any fault-forming materials with friction coefficients exceeding μ ∼0.5. The combination of weak gouges prone to aseismic creep, strong asperities , and low resolved shear stress may impede earthquake rupture propagation along the South Westland Alpine Fault.

Journal of Structural Geology↗
USGS2006

Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus

The fish rhabdovirus, Infectious hematopoietic necrosis virus (IHNV), is an important pathogen of salmonids. Cell culture assays have traditionally been used to quantify levels of IHNV in samples; however, real-time or quantitative RT-PCR assays have been proposed as a rapid alternative. For viruses having a single-stranded, negative-sense RNA genome, standard qRT-PCR assays do not distinguish between the negative-sense genome and positive-sense RNA species including mRNA and anti-genome. Thus, these methods do not determine viral genome copy number. This study reports development of strand-specific, qRT-PCR assays that use tagged primers for enhancing strand specificity during cDNA synthesis and quantitative PCR. Protocols were developed for positive-strand specific (pss-qRT-PCR) and negative-strand specific (nss-qRT-PCR) assays for IHNV glycoprotein (G) gene sequences. Validation with synthetic RNA transcripts demonstrated the assays could discriminate the correct strand with greater than 1000-fold fidelity. The number of genome copies in livers of IHNV-infected fish determined by nss-qRT-PCR was, on average, 8000-fold greater than the number of infectious units as determined by plaque assay. We also compared the number of genome copies with the quantity of positive-sense RNA and determined that the ratio of positive-sense molecules to negative-sense genome copies was, on average, 2.7:1. Potential future applications of these IHNV strand-specific qRT-PCR assays are discussed.

Journal of Virological Methods↗
USGS2006

Sustained long-period seismicity at Shishaldin Volcano, Alaska

From September 1999 through April 2004, Shishaldin Volcano, Aleutian Islands, Alaska, exhibited a continuous and extremely high level of background seismicity. This activity consisted of many hundreds to thousands of long-period (LP; 1–2 Hz) earthquakes per day, recorded by a 6-station monitoring network around Shishaldin. The LP events originate beneath the summit at shallow depths (0–3 km). Volcano tectonic events and tremor have rarely been observed in the summit region. Such a high rate of LP events with no eruption suggests that a steady state process has been occurring ever since Shishaldin last erupted in April–May 1999. Following the eruption, the only other signs of volcanic unrest have been occasional weak thermal anomalies and an omnipresent puffing volcanic plume. The LP waveforms are nearly identical for time spans of days to months, but vary over longer time scales. The observations imply that the spatially close source processes are repeating, stable and non-destructive. Event sizes vary, but the rate of occurrence remains roughly constant. The events range from magnitude ∼0.1 to 1.8, with most events having magnitudes <1.0. The observations suggest that the conduit system is open and capable of releasing a large amount of energy, approximately equivalent to at least one magnitude 1.8–2.6 earthquake per day. The rate of observed puffs (1 per minute) in the steam plume is similar to the typical seismic rates, suggesting that the LP events are directly related to degassing processes. However, the source mechanism, capable of producing one LP event about every 0.5–5 min, is still poorly understood. Shishaldin's seismicity is unusual in its sustained high rate of LP events without accompanying eruptive activity. Every indication is that the high rate of seismicity will continue without reflecting a hazardous state. Sealing of the conduit and/or change in gas flux, however, would be expected to change Shishaldin's behavior.

Alaska↗