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At least 739 records · Page 41Linked to original sources

USGS2016

Bedrock morphology and structure, upper Santa Cruz Basin, south-central Arizona, with transient electromagnetic survey data

The upper Santa Cruz Basin is an important groundwater basin containing the regional aquifer for the city of Nogales, Arizona. This report provides data and interpretations of data aimed at better understanding the bedrock morphology and structure of the upper Santa Cruz Basin study area which encompasses the Rio Rico and Nogales 1:24,000-scale U.S. Geological Survey quadrangles. Data used in this report include the Arizona Aeromagnetic and Gravity Maps and Data referred to here as the 1996 Patagonia Aeromagnetic survey, Bouguer gravity anomaly data, and conductivity-depth transforms (CDTs) from the 1998 Santa Cruz transient electromagnetic survey (whose data are included in appendixes 1 and 2 of this report). Analyses based on magnetic gradients worked well to identify the range-front faults along the Mt. Benedict horst block, the location of possibly fault-controlled canyons to the west of Mt. Benedict, the edges of buried lava flows, and numerous other concealed faults and contacts. Applying the 1996 Patagonia aeromagnetic survey data using the horizontal gradient method produced results that were most closely correlated with the observed geology. The 1996 Patagonia aeromagnetic survey was used to estimate depth to bedrock in the upper Santa Cruz Basin study area. Three different depth estimation methods were applied to the data: Euler deconvolution, horizontal gradient magnitude, and analytic signal. The final depth to bedrock map was produced by choosing the maximum depth from each of the three methods at a given location and combining all maximum depths. In locations of rocks with a known reversed natural remanent magnetic field, gravity based depth estimates from Gettings and Houser (1997) were used. The depth to bedrock map was supported by modeling aeromagnetic anomaly data along six profiles. These cross sectional models demonstrated that by using the depth to bedrock map generated in this study, known and concealed faults, measured and estimated magnetic susceptibilities of rocks found in the study area, and estimated natural remanent magnetic intensities and directions, reasonable geologic models can be built. This indicates that the depth to bedrock map is reason-able and geologically possible. Finally, CDTs derived from the 1998 Santa Cruz Basin transient electromagnetic survey were used to help identify basin structure and some physical properties of the basin fill in the study area. The CDTs also helped to confirm depth to bedrock estimates in the Santa Cruz Basin, in particular a region of elevated bedrock in the area of Potrero Canyon, and a deep basin in the location of the Arizona State Highway 82 microbasin. The CDTs identified many concealed faults in the study area and possibly indicate deep water-saturated clay-rich sediments in the west-central portion of the study area. These sediments grade to more sand-rich saturated sediments to the south with relatively thick, possibly unsaturated, sediments at the surface. Also, the CDTs may indicate deep saturated clay-rich sediments in the Highway 82 microbasin and in the Mount Benedict horst block from Proto Canyon south to the international border.

Arizona↗

USGS2015

Quantification of 15 bile acids in lake charr feces by ultra-high performance liquid chromatography–tandem mass spectrometry

Many fishes are hypothesized to use bile acids (BAs) as chemical cues, yet quantification of BAs in biological samples and the required methods remain limited. Here, we present an UHPLC–MS/MS method for simultaneous, sensitive, and rapid quantification of 15 BAs, including free, taurine, and glycine conjugated BAs, and application of the method to fecal samples from lake charr ( Salvelinus namaycush ). The analytes were separated on a C 18 column with acetonitrile–water (containing 7.5 mM ammonium acetate and 0.1% formic acid) as mobile phase at a flow rate of 0.25 mL/min for 12 min. BAs were monitored with a negative electrospray triple quadrupole mass spectrometer (Xevo TQ-S™). Calibration curves of 15 BAs were linear over the concentration range of 1.00–5,000 ng/mL. Validation revealed that the method was specific, accurate, and precise. The method was applied to quantitative analysis of feces extract of fry lake charr and the food they were eating. The concentrations of analytes CA, TCDCA, TCA, and CDCA were 242.3, 81.2, 60.7, and 36.2 ng/mg, respectively. However, other taurine conjugated BAs, TUDCA, TDCA, and THDCA, were not detected in feces of lake charr. Interestingly, TCA and TCDCA were detected at high concentrations in food pellets, at 71.9 and 38.2 ng/mg, respectively. Application of the method to feces samples from lake charr supported a role of BAs as chemical cues, and will enhance further investigation of BAs as chemical cues in other fish species.

Journal of Chromatography B: Analytical Technologi↗

USGS1981

A transient laboratory method for determining the hydraulic properties of 'tight' rocks-I. Theory

Transient pulse testing has been employed increasingly in the laboratory to measure the hydraulic properties of rock samples with low permeability. Several investigators have proposed a mathematical model in terms of an initial-boundary value problem to describe fluid flow in a transient pulse test. However, the solution of this problem has not been available. In analyzing data from the transient pulse test, previous investigators have either employed analytical solutions that are derived with the use of additional, restrictive assumptions, or have resorted to numerical methods. In Part I of this paper, a general, analytical solution for the transient pulse test is presented. This solution is graphically illustrated by plots of dimensionless variables for several cases of interest. The solution is shown to contain, as limiting cases, the more restrictive analytical solutions that the previous investigators have derived. A method of computing both the permeability and specific storage of the test sample from experimental data will be presented in Part II.

International Journal of Rock Mechanics and Mining↗

USGS2014

Estimating landscape resistance to dispersal

Dispersal is an inherently spatial process that can be affected by habitat conditions in sites encountered by dispersers. Understanding landscape resistance to dispersal is important in connectivity studies and reserve design, but most existing methods use resistance functions with cost parameters that are subjectively chosen by the investigator. We develop an analytic approach allowing for direct estimation of resistance parameters that folds least cost path methods typically used in simulation approaches into a formal statistical model of dispersal distributions. The core of our model is a frequency distribution of dispersal distances expressed as least cost distance rather than Euclidean distance, and which includes terms for feature-specific costs to dispersal and sex (or other traits) of the disperser. The model requires only origin and settlement locations for multiple individuals, such as might be obtained from mark–recapture studies or parentage analyses, and maps of the relevant habitat features. To evaluate whether the model can estimate parameters correctly, we fit our model to data from simulated dispersers in three kinds of landscapes (in which resistance of environmental variables was categorical, continuous with a patchy configuration, or continuous in a trend pattern). We found maximum likelihood estimators of resistance and individual trait parameters to be approximately unbiased with moderate sample sizes. We applied the model to a small grizzly bear dataset to demonstrate how this approach could be used when the primary interest is in the prediction of costs and found that estimates were consistent with expectations based on bear ecology. Our method has important practical applications for testing hypotheses about dispersal ecology and can be used to inform connectivity planning efforts, via the resistance estimates and confidence intervals, which can be used to create a data-driven resistance surface.

Landscape Ecology↗

USGS2001

Detection of pesticides and pesticide metabolites using the cross reactivity of enzyme immunoassays

Enzyme immunoassay is an important environmental analysis method that may be used to identify many pesticide analytes in water samples. Because of similarities in chemical structure between various members of a pesticide class, there often may be an unwanted response that is characterized by a percentage of cross reactivity. Also, there may be cross reactivity caused by degradation products of the target analyte that may be present in the sample. In this paper, the concept of cross reactivity caused by degradation products or by nontarget analytes is explored as a tool for identification of metabolites or structurally similar compounds not previously known to be present in water samples. Two examples are examined in this paper from various water quality studies. They are alachlor and its metabolite, alachlor ethane sulfonic acid, and atrazine and its class members, prometryn and propazine. A method for using cross reactivity for the detection of these compounds is explained in this paper.

Journal of AOAC International↗

USGS2025

Glass laser ablation-inductively coupled plasma-mass spectrometry analysis methods, precision, and accuracy data for tephra studies in Alaska

This publication reports the analytical conditions, standard reference material (SRM) results, and preferred post-processing methodologies for laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) measurements supporting tephra studies in Alaska between 2018 and 2024. We evaluate the long-term accuracy and precision of our methodologies by comparing our calculated SRM concentrations to the Geological and Environmental Reference Materials database (GeoReM) preferred concentration values for the following SRMs: BCR-2G, BHVO-2G, ATHO-G, NIST-612, GSD-1G, and GSE-1G. We show that our LA-ICP-MS methodologies produce accurate and consistent measurements across numerous analytical sessions, even when instrumentation changed. Overall, these results indicate that Alaska tephra matrix glass measurements, like SRM measurements, are accurate, precise, and comparable between analytical sessions. This work allows us to better correlate tephra units from Alaska volcanoes throughout the Alaska-Aleutian arc, ultimately enhancing our understanding of spatiotemporal patterns of volcanism in the region. This enhanced understanding will aid in refining volcanic hazard classification and response strategies. Future versions of this dataset will provide updates to SRM results or analytical routines for sessions that have transpired since the publishing of this version.

Alaska↗

USGS2022

Optimizing trilateration estimates for tracking fine-scale movement of wildlife using automated radio telemetry networks

A major advancement in the use of radio telemetry has been the development of automated radio tracking systems (ARTS), which allow animal movements to be tracked continuously. A new ARTS approach is the use of a network of simple radio receivers (nodes) that collect radio signal strength (RSS) values from animal-borne radio transmitters. However, the use of RSS-based localization methods in wildlife tracking research is new, and analytical approaches critical for determining high-quality location data have lagged behind technological developments. We present an analytical approach to optimize RSS-based localization estimates for a node network designed to track fine-scale animal movements in a localized area. Specifically, we test the application of analytical filters (signal strength, distance among nodes) to data from real and simulated node networks that differ in the density and configuration of nodes. We evaluate how different filters and network configurations (density and regularity of node spacing) may influence the accuracy of RSS-based localization estimates. Overall, the use of signal strength and distance-based filters resulted in a 3- to 9-fold increase in median accuracy of location estimates over unfiltered estimates, with the most stringent filters providing location estimates with a median accuracy ranging from 28 to 73 m depending on the configuration and spacing of the node network. We found that distance filters performed significantly better than RSS filters for networks with evenly spaced nodes, but the advantage diminished when nodes were less uniformly spaced within a network. Our results not only provide analytical approaches to greatly increase the accuracy of RSS-based localization estimates, as well as the computer code to do so, but also provide guidance on how to best configure node networks to maximize the accuracy and capabilities of such systems for wildlife tracking studies.

Ecology and Evolution↗

USGS2011

College and university environmental programs as a policy problem (Part 2): Strategies for improvement

Environmental studies and environmental sciences programs in American and Canadian colleges and universities seek to ameliorate environmental problems through empirical enquiry and analytic judgment. In a companion article (Part 1) we describe the environmental program movement (EPM) and discuss factors that have hindered its performance. Here, we complete our analysis by proposing strategies for improvement. We recommend that environmental programs re-organize around three principles. First, adopt as an overriding goal the concept of human dignity—defined as freedom and social justice in healthy, sustainable environments. This clear higher-order goal captures the human and environmental aspirations of the EPM and would provide a more coherent direction for the efforts of diverse participants. Second, employ an explicit, genuinely interdisciplinary analytical framework that facilitates the use of multiple methods to investigate and address environmental and social problems in context. Third, develop educational programs and applied experiences that provide students with the technical knowledge, powers of observation, critical thinking skills and management acumen required for them to become effective professionals and leaders. Organizing around these three principles would build unity in the EPM while at the same time capitalizing on the strengths of the many disciplines and diverse local conditions involved.

Environmental Management↗

USGS1991

Petrography of Permian “Gondwana” coals from boreholes in northwestern Bangladesh, based on semiautomated reflectance scanning

Drilling through Quaternary alluvium and Tertiary cover at low-gravity anomalies in northwestern Bangladesh showed the presence of Permian sedimentary rocks in depressions that may be as much as a thousand meters deep in the crystalline basement. These Permian strata include low-sulfur, high-volatile bituminous coals in beds as thick as 15 m. The maceral group composition of these coals was determined by semiautomated reflectance scanning with a motorized microscope stage, rather than by point counting. This method was chosen to give objectively recorded raw analytical data and to provide a graphical picture of each sample. The coals are mostly “Gondwana” type (poorly layered “plum pudding” with abundant minerals and inertinite in a vitrinite groundmass) that would be classed as semi-dull (inerto-gelitite) coals. However, six samples have more than 70% vitrinite. None of the samples would be classed as sapropelic (liptinitic). The upper, middle, and lower main seams in borehole GDH-45 were sampled in 10 benches (0.1–3 m thick) each. Inertinite ranges from 7 to 100 vol% (mineral free basis) in individual benches, but composite seam averages are 41, 54 and 67%. Inertinite increases toward the top of two main seams so the bottom would yield the most valuable first mine slices. Some benches with extremely high inertinite content, such as the top 7 m of the lower thick seam, might be mined specially for blending with foreign low-inert coals to increase coke strength. The free swelling index reaches 7.5 in several vitrinite-rich benches, which can indicate good coking coal. Much of the vitrinite is fluorescent, which indicates secondary bituminization characteristic of vitrinite in good coking coals. Ash yields range from 8 to 52%, with composite seam averages of 15, 14 and 24%. Rare visible pyrite is in veinlets or small nodules; framboids and dispersed pyrite are absent. In borehole GDH-40 near Barapukuria (200–500 m depth), the mean random reflectance of vitrinite “A” ranges from 0.60 to 0.80% R o and vitrinite “B” ranges from 0.55 to 0.65%. In borehole GDH-45 near Khalaspir (287–442 m), the reflectance of vitrinite ranges from 0.79 to 0.94%. In individual cases, the vitrinite is difficult to define because of semivitrinite at higher reflectance (forming a separate peak on several reflectograms) and because of surface bitumen films or resinous (?) inclusions at lower reflectance. On the basis of vitrinite reflectance, the coals can be considered to have entered the “main phase of bitumen generation” of organic thermal maturation as understood in petroleum geochemistry.

Organic Geochemistry↗

USGS1994

Analysis of larval trematode communities

We can compare natural communities with null models of communities to indicate how they differ from random assemblages of species (i.e., how much structure is present). However, because null models draw on observed values of species' prevalences, whatever structure already exists in natural communities affects the composition of a null model and weakens its comparative power. To address this, we developed formulae to estimate "pre—interactive" species prevalences permitting a more sensitive quantification of community structure. Nonetheless, if a null model deviates from the community that we base it on, it is difficult to separate the effects of heterogeneity in recruitment from competition. We have developed a method to test for each independently. Applying our analytical techniques to a well—studied guild of larval trematodes in the salt marsh snail Cerithidea californica revealed that competitive interactions among species were the most significant structuring force. Interestingly, spatial heterogeneity acted to significantly intensify species co—occurrences. This differs from previous studies, which argued that the isolating effects of spatial heterogeneity, not competition, structure these communities by reducing co—occurrences.

Ecology↗

USGS2007

Major- and Trace-Element Concentrations in Soils from Two Geochemical Surveys (1972 and 2005) of the Denver, Colorado, Metropolitan Area

Introduction This report contains major- and trace-element concentration data for soil samples collected in 1972 and 2005 from the Denver, Colorado, metropolitan area. A total of 405 sites were sampled in the 1972 study from an area approximately bounded by the suburbs of Golden, Thornton, Aurora, and Littleton to the west, north, east, and south, respectively. This data set included 34 duplicate samples collected in the immediate vicinity of the primary sample. In 2005, a total of 464 sites together with 34 duplicates were sampled from the same approximate localities sampled in 1972 as well as additional sites in east Aurora and the area surrounding the Rocky Mountain Arsenal. Sample density for both surveys was on the order of 1 site per square mile. At each site, sample material was collected from a depth of 0-5 inches. Each sample collected was analyzed for near-total major- and trace-element composition by the following methods: (1) inductively coupled plasma-mass spectrometry (ICP-MS) and inductively coupled plasma-atomic emission spectrometry (ICP-AES) for aluminum, antimony, arsenic, barium, beryllium, bismuth, cadmium, calcium, cerium, cesium, chromium, cobalt, copper, gallium, indium, iron, lanthanum, lead, lithium, magnesium, manganese, molybdenum, nickel, niobium, phosphorus, potassium, rubidium, scandium, silver, sodium, strontium, sulfur, tellurium, thallium, thorium, tin, titanium, tungsten, uranium, vanadium, yttrium, and zinc; and (2) hydride generation-atomic absorption spectrometry for selenium. The samples collected in 2005 were also analyzed by a cold vapor-atomic absorption method for mercury. This report makes available the analytical results of these studies.

Data Series↗

USGS2004

Analytical results from ground-water sampling using a direct-push technique at the Dover National Test Site, Dover Air Force Base, Delaware, June-July 2001

A joint study by the Dover National Test Site and the U.S. Geological Survey was conducted from June 27 through July 18, 2001 to determine the spatial distribution of the gasoline oxygenate additive methyl tert-butyl ether and selected water-quality constituents in the surficial aquifer underlying the Dover National Test Site at Dover Air Force Base, Delaware. The study was conducted to support a planned enhanced bio-remediation demonstration and to assist the Dover National Test Site in identifying possible locations for future methyl tert-butyl ether remediation demonstrations. This report presents the analytical results from ground-water samples collected during the direct-push ground-water sampling study. A direct-push drill rig was used to quickly collect 115 ground-water samples over a large area at varying depths. The ground-water samples and associated quality-control samples were analyzed for volatile organic compounds and methyl tert-butyl ether by the Dover National Test Site analytical laboratory. Volatile organic compounds were above the method reporting limits in 59 of the 115 ground-water samples. The concentrations ranged from below detection limits to maximum values of 12.4 micrograms per liter of cis-1,2-dichloroethene, 1.14 micrograms per liter of trichloroethene, 2.65 micrograms per liter of tetrachloroethene, 1,070 micrograms per liter of methyl tert-butyl ether, 4.36 micrograms per liter of benzene, and 1.8 micrograms per liter of toluene. Vinyl chloride, ethylbenzene, p,m-xylene, and o-xylene were not detected in any of the samples collected during this investigation. Methyl tert-butyl ether was detected in 47 of the 115 ground-water samples. The highest methyl tert-butyl ether concentrations were found in the surficial aquifer from -4.6 to 6.4 feet mean sea level, however, methyl tert-butyl ether was detected as deep as -9.5 feet mean sea level. Increased methane concentrations and decreased dissolved oxygen concentrations were found in samples that contained methyl tert-butyl ether.

Open-File Report↗

USGS1991

Accuracy of selected techniques for estimating ice-affected streamflow

This paper compares the accuracy of selected techniques for estimating streamflow during ice‐affected periods. The techniques are classified into two categories—subjective and analytical—depending on the degree of judgment required. Discharge measurements have been made at three streamflow‐gauging sites in Iowa during the 1987–88 winter and used to establish a baseline streamflow record for each site. Using data based on a simulated six‐week field‐trip schedule, selected techniques are used to estimate discharge during the ice‐affected periods. For the subjective techniques, three hydrographers have independently compiled each record. Three measures of performance are used to compare the estimated streamflow records with the baseline streamflow records: the average discharge for the ice‐affected period, and the mean and standard deviation of the daily errors. Based on average ranks for three performance measures and the three sites, the analytical and subjective techniques are essentially comparable. For two of the three sites, Kruskal‐Wallis one‐way analysis of variance detects significant differences among the three hydrographers for the subjective methods, indicating that the subjective techniques are less consistent than the analytical techniques. The results suggest analytical techniques may be viable tools for estimating discharge during periods of ice effect, and should be developed further and evaluated for sites across the United States.

Journal of Hydraulic Engineering↗

USGS1986

Estimation of recharge rates to the sand and gravel aquifer using environmental tritium, Nantucket Island, Massachusetts

Estimation of the average annual rate of ground-water recharge to sand and gravel aquifers using elevated tritium concentrations in ground water is an alternative to traditional steady-state and water-balance recharge-rate methods. The concept of the tritium tracer method is that the average annual rate of ground-water recharge over a period of time can be calculated from the depth of the peak tritium concentration in the aquifer. Assuming that ground-water flow is vertically downward and that aquifer properties are reasonably homogeneous, and knowing the date of maximum tritium concentration in precipitation and the current depth to the tritium peak from the water table, the average recharge rate can be calculated. The method, which is a direct-measurement technique, was applied at two sites on Nantucket Island, Massachusetts. At site 1, the average annual recharge rate between 1964 and 1983 was 26.1 inches per year, or 68 percent of the average annual precipitation, and the estimated uncertainty is ?15 percent. At site 2, the multilevel water samplers were not constructed deep enough to determine the peak concentration of tritium in ground water. The tritium profile at site 2 resembles the upper part of the tritium profile at site 1 and indicates that the average recharge rate was at least 16 .7 inches per year, or at least 44 percent of the average annual precipitation. The Nantucket tritium recharge rates clearly are higher than rates determined elsewhere in southeastern Massachusetts using the tritium, water-table-fluctuation, and water-balance (Thornthwaite) methods, regardless of the method or the area. Because the recharge potential on Nantucket is so high (runoff is only 2 percent of the total water balance), the tritium recharge rates probably represent the effective upper limit for ground-water recharge in this region. The recharge-rate values used by Guswa and LeBlanc (1985) and LeBlanc (1984) in their ground-water-flow computer models of Cape Cod are 20 to 30 percent lower than this upper limit. The accuracy of the tritium method is dependent on two key factors: the accuracy of the effective-porosity data, and the sampling interval used at the site. For some sites, the need for recharge-rate data may require a determination as statistically accurate as that which can be provided by the tritium method. However, the tritium method is more costly and more time consuming than the other methods because numerous wells must be drilled and installed and because many water samples must be analyzed for tritium, to a very small level of analytical detection. For many sites, a less accurate, less expensive, and faster method of recharge-rate determination might be more satisfactory. The factor that most seriously limits the usefulness of the tritium tracer method is the current depth of the tritium peak. Water with peak concentrations of tritium entered the ground more than 20 years ago, and, according to the Nantucket data, that water now is more than 100 feet below the land surface. This suggests that the tracer method will work only in sand and gravel aquifers that are exceedingly thick by New England standards. Conversely, the results suggest that the method may work in areas where saturated thicknesses are less than 100 feet and the rate of vertical ground-water movement is relatively slow, such as in till and in silt- and clay-rich sand and gravel deposits.

Massachusetts↗

USGS1997

Matrix-enhanced degradation of p,p'-DDT during gas chromatographic analysis: A consideration

Analysis of p,p ‘-DDT in environmental samples requires monitoring the GC-derived breakdown of this insecticide, which produces p,p ‘-DDD and/or p,p ‘-DDE, both also primary environmental degradation products. A performance evaluation standard (PES) containing p,p ‘-DDT but not p,p ‘-DDD or p,p ‘-DDE can be injected at regular intervals throughout an analytical sequence to monitor GC degradation. Some U.S. EPA methods limit GC breakdown of DDT in the PES to ≤20%. GC/MS analysis of large-volume natural water samples fortified with deuterium- and 13 C-labeled p,p ‘-DDT exhibited up to 65% DDT breakdown by the GC inlet. These matrix-enhanced GC degradation amounts substantially exceeded the <20% breakdown levels indicated by bracketing injections of the PES containing unlabeled and labeled DDT. Substantial matrix-enhanced GC degradation was not observed during analysis of a limited number of fractionated bed-sediment extracts containing labeled DDT. Use of isotopically labeled DDT seems to provide an effective tool for monitoring sample-specific DDT breakdown during GC/MS analysis. However, analyte co-elutions render impractical their use in GC/ECD analysis. The oc currence of matrix-enhanced GC degradation might have important implications on data quality and the resultant interpretations of the environmental degradation of DDT and other thermolabile contaminants.

Environmental Science & Technology↗

USGS1998

Rapid-estimation method for assessing scour at highway bridges

A method was developed by the U.S. Geological Survey for rapid estimation of scour at highway bridges using limited site data and analytical procedures to estimate pier, abutment, and contraction scour depths. The basis for the method was a procedure recommended by the Federal Highway Administration for conducting detailed scour investigations, commonly referred to as the Level 2 method. Using pier, abutment, and contraction scour results obtained from Level 2 investigations at 122 sites in 10 States, envelope curves and graphical relations were developed that enable determination of scour-depth estimates at most bridge sites in a matter of a few hours. Rather than using complex hydraulic variables, surrogate variables more easily obtained in the field were related to calculated scour-depth data from Level 2 studies. The method was tested by having several experienced individuals apply the method in the field, and results were compared among the individuals and with previous detailed analyses performed for the sites. Results indicated that the variability in predicted scour depth among individuals applying the method generally was within an acceptable range, and that conservatively greater scour depths generally were obtained by the rapid-estimation method compared to the Level 2 method. The rapid-estimation method is considered most applicable for conducting limited-detail scour assessments and as a screening tool to determine those bridge sites that may require more detailed analysis. The method is designed to be applied only by a qualified professional possessing knowledge and experience in the fields of bridge scour, hydraulics, and flood hydrology, and having specific expertise with the Level 2 method.

Conference Paper↗

USGS2018

Analytical and diagnostic performance of a qPCR assay for Ichthyophonus spp. compared to the tissue culture ‘gold standard’

Parasites of the genus Ichthyophonus infect many fish species and have a non-uniform distribution within host tissues. Due in part to this uneven distribution, the comparative sensitivity and accuracy of using molecular-based detection methods versus culture to estimate parasite prevalence is under debate. We evaluated the analytical and diagnostic performance of an existing qPCR assay in comparison to the ‘gold standard’ culture method using Pacific herring Clupea pallasii with known exposure history. We determined that the assay is suitable for use in this host, and diagnostic specificity was consistently high (>98%) in both heart and liver tissues. Diagnostic sensitivity could not be fully assessed due to low infection rates, but our results suggest that qPCR is not as sensitive as culture under all circumstances. Diagnostic sensitivity of qPCR relative to culture is likely affected by the amount of sample processed. The prevalence values estimated by the 2 methods were not significantly different when sample amounts were equal (heart tissue), but when the assayed sample amounts were unequal (liver tissue), the culture method detected a significantly higher prevalence of the parasite than qPCR. Further, culture of liver also detected significantly more Ichthyophonus infections than culture of heart, suggesting that the density and distribution of parasites in tissues also plays a role in assay sensitivity. This sensitivity issue would be most problematic for fish with light infections. Although qPCR does not detect the presence of a live organism, DNA-based pathogen detection methods provide the opportunity for alternate testing strategies when culture is not possible.

Diseases of Aquatic Organisms↗

USGS2008

Heat as a tracer to determine streambed water exchanges

This work reviews the use of heat as a tracer of shallow groundwater movement and describes current temperature-based approaches for estimating streambed water exchanges. Four common hydrologic conditions in stream channels are graphically depicted with the expected underlying streambed thermal responses, and techniques are discussed for installing and monitoring temperature and stage equipment for a range of hydrological environments. These techniques are divided into direct-measurement techniques in streams and streambeds, groundwater techniques relying on traditional observation wells, and remote sensing and other large-scale advanced temperature-acquisition techniques. A review of relevant literature suggests researchers often graphically visualize temperature data to enhance conceptual models of heat and water flow in the near-stream environment and to determine site-specific approaches of data analysis. Common visualizations of stream and streambed temperature patterns include thermographs, temperature envelopes, and one-, two-, and three-dimensional temperature contour plots. Heat and water transport governing equations are presented for the case of transport in streambeds, followed by methods of streambed data analysis, including simple heat-pulse arrival time and heat-loss procedures, analytical and time series solutions, and heat and water transport simulation models. A series of applications of these methods are presented for a variety of stream settings ranging from arid to continental climates. Progressive successes to quantify both streambed fluxes and the spatial extent of streambeds indicate heat-tracing tools help define the streambed as a spatially distinct field (analogous to soil science), rather than simply the lower boundary in stream research or an amorphous zone beneath the stream channel.

Water Resources Research↗