USGS Science⌕ Search

SEARCH · USGS Science

Results for “Cells”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 595 records · Page 33Linked to original sources

Examining the occupancy–density relationship for a low-density carnivore

The challenges associated with monitoring low-density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Non-invasive sampling techniques and advanced statistical approaches have alleviated some of these challenges and can even allow for spatially explicit estimates of density, one of the most valuable wildlife monitoring tools. For some species, individual identification comes at no cost when unique attributes (e.g. pelage patterns) can be discerned with remote cameras, while other species require viable genetic material and expensive laboratory processing for individual assignment. Prohibitive costs may still force monitoring efforts to use species distribution or occupancy as a surrogate for density, which may not be appropriate under many conditions. Here, we used a large-scale monitoring study of fisher Pekania pennanti to evaluate the effectiveness of occupancy as an approximation to density, particularly for informing harvest management decisions. We combined remote cameras with baited hair snares during 2013–2015 to sample across a 70 096-km 2 region of western New York, USA. We fit occupancy and Royle–Nichols models to species detection–non-detection data collected by cameras, and spatial capture–recapture (SCR) models to individual encounter data obtained by genotyped hair samples. Variation in the state variables within 15-km 2 grid cells was modelled as a function of landscape attributes known to influence fisher distribution. We found a close relationship between grid cell estimates of fisher state variables from the models using detection–non-detection data and those from the SCR model, likely due to informative spatial covariates across a large landscape extent and a grid cell resolution that worked well with the movement ecology of the species. Fisher occupancy and density were both positively associated with the proportion of coniferous-mixed forest and negatively associated with road density. As a result, spatially explicit management recommendations for fisher were similar across models, though relative variation was dampened for the detection–non-detection data. Synthesis and applications . Our work provides empirical evidence that models using detection–non-detection data can make similar inferences regarding relative spatial variation of the focal population to models using more expensive individual encounters when the selected spatial grain approximates or is marginally smaller than home range size. When occupancy alone is chosen as a cost-effective state variable for monitoring, simulation and sensitivity analyses should be used to understand how inferences from detection–non-detection data will be affected by aspects of study design and species ecology.

Journal of Applied Ecology↗

Extending the MODPATH algorithm to rectangular unstructured grids

The recent release of MODFLOW-USG, which allows model grids to have irregular, unstructured connections, requires a modification of the particle-tracking algorithm used by MODPATH. This paper describes a modification of the semi-analytical particle-tracking algorithm used by MODPATH that allows it to be extended to rectangular-based unstructured grids by dividing grid cells with multi-cell face connections into sub-cells. The new method will be incorporated in the next version of MODPATH which is currently under development.

Ground Water↗

Time-lapse three-dimensional inversion of complex conductivity data using an active time constrained (ATC) approach

Induced polarization (more precisely the magnitude and phase of impedance of the subsurface) is measured using a network of electrodes located at the ground surface or in boreholes. This method yields important information related to the distribution of permeability and contaminants in the shallow subsurface. We propose a new time-lapse 3-D modelling and inversion algorithm to image the evolution of complex conductivity over time. We discretize the subsurface using hexahedron cells. Each cell is assigned a complex resistivity or conductivity value. Using the finite-element approach, we model the in-phase and out-of-phase (quadrature) electrical potentials on the 3-D grid, which are then transformed into apparent complex resistivity. Inhomogeneous Dirichlet boundary conditions are used at the boundary of the domain. The calculation of the Jacobian matrix is based on the principles of reciprocity. The goal of time-lapse inversion is to determine the change in the complex resistivity of each cell of the spatial grid as a function of time. Each model along the time axis is called a ‘reference space model’. This approach can be simplified into an inverse problem looking for the optimum of several reference space models using the approximation that the material properties vary linearly in time between two subsequent reference models. Regularizations in both space domain and time domain reduce inversion artefacts and improve the stability of the inversion problem. In addition, the use of the time-lapse equations allows the simultaneous inversion of data obtained at different times in just one inversion step (4-D inversion). The advantages of this new inversion algorithm are demonstrated on synthetic time-lapse data resulting from the simulation of a salt tracer test in a heterogeneous random material described by an anisotropic semi-variogram.

Geophysical Journal International↗

Isolation of viral haemorrhagic septicaemia virus from muskellunge, Esox masquinongy (Mitchill), in Lake St Clair, Michigan, USA reveals a new sublineage of the North American genotype

Viral haemorrhagic septicaemia virus (VHSV) was isolated from muskellunge, Esox masquinongy (Mitchill), caught from the NW portion of Lake St Clair, Michigan, USA in 2003. Affected fish exhibited congestion of internal organs; the inner wall of the swim bladder was thickened and contained numerous budding, fluid-filled vesicles. A virus was isolated using fish cell lines inoculated with a homogenate of kidney and spleen tissues from affected fish. Focal areas of cell rounding and granulation appeared as early as 24 h post-inoculation and expanded rapidly to destroy the entire cell sheet by 96 h. Electron microscopy revealed virions that were 170-180 nm in length by 60-70 nm in width having a bullet-shaped morphology typical of rhabdoviruses. The virus was confirmed as VHSV by reverse transcriptase-polymerase chain reaction. Sequence analysis of the entire nucleoprotein and glycoprotein genes revealed the virus was a member of the North American genotype of VHSV; however, the isolate was sufficiently distinct to be considered a separate sublineage, suggesting its origin may have been from marine species inhabiting the eastern coastal areas of the USA or Canada.

Michigan↗

Bacterial dominance in subseafloor sediments characterized by methane hydrates

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10 3 –10 5 cells cm −3 ). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.

FEMS Microbiology Ecology↗

Stochastic Ground Water Flow Simulation with a Fracture Zone Continuum Model

A method is presented for incorporating the hydraulic effects of vertical fracture zones into two-dimensional cell-based continuum models of ground water flow and particle tracking. High hydraulic conductivity features are used in the model to represent fracture zones. For fracture zones that are not coincident with model rows or columns, an adjustment is required for the hydraulic conductivity value entered into the model cells to compensate for the longer flowpath through the model grid. A similar adjustment is also required for simulated travel times through model cells. A travel time error of less than 8% can occur for particles moving through fractures with certain orientations. The fracture zone continuum model uses stochastically generated fracture zone networks and Monte Carlo analysis to quantify uncertainties with simulated advective travel times. An approach is also presented for converting an equivalent continuum model into a fracture zone continuum model by establishing the contribution of matrix block transmissivity to the bulk transmissivity of the aquifer. The methods are used for a case study in west-central Florida to quantify advective travel times from a potential wetland rehydration site to a municipal supply wellfield. Uncertainties in advective travel times are assumed to result from the presence of vertical fracture zones, commonly observed on aerial photographs as photolineaments.

Ground Water↗

Simulation and analysis of conjunctive use with MODFLOW's farm process

The extension of MODFLOW onto the landscape with the Farm Process (MF-FMP) facilitates fully coupled simulation of the use and movement of water from precipitation, streamflow and runoff, groundwater flow, and consumption by natural and agricultural vegetation throughout the hydrologic system at all times. This allows for more complete analysis of conjunctive use water-resource systems than previously possible with MODFLOW by combining relevant aspects of the landscape with the groundwater and surface water components. This analysis is accomplished using distributed cell-by-cell supply-constrained and demand-driven components across the landscape within " water-balance subregions" comprised of one or more model cells that can represent a single farm, a group of farms, or other hydrologic or geopolitical entities. Simulation of micro-agriculture in the Pajaro Valley and macro-agriculture in the Central Valley are used to demonstrate the utility of MF-FMP. For Pajaro Valley, the simulation of an aquifer storage and recovery system and related coastal water distribution system to supplant coastal pumpage was analyzed subject to climate variations and additional supplemental sources such as local runoff. For the Central Valley, analysis of conjunctive use from different hydrologic settings of northern and southern subregions shows how and when precipitation, surface water, and groundwater are important to conjunctive use. The examples show that through MF-FMP's ability to simulate natural and anthropogenic components of the hydrologic cycle, the distribution and dynamics of supply and demand can be analyzed, understood, and managed. This analysis of conjunctive use would be difficult without embedding them in the simulation and are difficult to estimate a priori. Journal compilation ?? 2010 National Ground Water Association. No claim to original US government works.

Ground Water↗

Approaches to the simulation of unconfined flow and perched groundwater flow in MODFLOW

Various approaches have been proposed to manage the nonlinearities associated with the unconfined flow equation and to simulate perched groundwater conditions using the MODFLOW family of codes. The approaches comprise a variety of numerical techniques to prevent dry cells from becoming inactive and to achieve a stable solution focused on formulations of the unconfined, partially-saturated, groundwater flow equation. Keeping dry cells active avoids a discontinuous head solution which in turn improves the effectiveness of parameter estimation software that relies on continuous derivatives. Most approaches implement an upstream weighting of intercell conductance and Newton-Raphson linearization to obtain robust convergence. In this study, several published approaches were implemented in a stepwise manner into MODFLOW for comparative analysis. First, a comparative analysis of the methods is presented using synthetic examples that create convergence issues or difficulty in handling perched conditions with the more common dry-cell simulation capabilities of MODFLOW. Next, a field-scale three-dimensional simulation is presented to examine the stability and performance of the discussed approaches in larger, practical, simulation settings.

Ground Water↗

Use of dietary yeast Saccharomyces cerevisiae nitrogen by lake trout

In a 12 week experiment, lake trout ( Salvelinus namaycush ) were fed diets in which 50% of the nitrogen was provided by one of six preparations of Saccharomyces yeast. Fish fed baker's yeast with disrupted cell walls grew at a rate equal to that of fish fed the control diet and faster than fish fed intact yeast cells. Fish fed a diet containing disrupted yeast cells previously washed in a saline solution did not perform as well. The results of this study indicated that it may be possible to use more than 50% yeast in the diets of salmonid fishes.

Journal of the World Aquaculture Society↗

Gene transcription in sea otters (Enhydra lutris); development of a diagnostic tool for sea otter and ecosystem health

Gene transcription analysis for diagnosing or monitoring wildlife health requires the ability to distinguish pathophysiological change from natural variation. Herein, we describe methodology for the development of quantitative real-time polymerase chain reaction (qPCR) assays to measure differential transcript levels of multiple immune function genes in the sea otter ( Enhydra lutris ); sea otter-specific qPCR primer sequences for the genes of interest are defined. We establish a ‘reference’ range of transcripts for each gene in a group of clinically healthy captive and free-ranging sea otters. The 10 genes of interest represent multiple physiological systems that play a role in immuno-modulation, inflammation, cell protection, tumour suppression, cellular stress response, xenobiotic metabolizing enzymes, antioxidant enzymes and cell–cell adhesion. The cycle threshold (C T ) measures for most genes were normally distributed; the complement cytolysis inhibitor was the exception. The relative enumeration of multiple gene transcripts in simple peripheral blood samples expands the diagnostic capability currently available to assess the health of sea otters in situ and provides a better understanding of the state of their environment.

Molecular Ecology Resources↗

Accuracy of histology, endoscopy, ultrasonography, and plasma sex steroids in describing the population reproductive structure of hatchery-origin and wild white sturgeon

Hatchery-origin white sturgeon Acipenser transmontanus in the lower Columbia River, Canada are approaching puberty, and describing the reproductive structure of the population is critical to determine if they are capable of contributing to spawning events in the wild, a key management uncertainty. Few studies have compared the accuracy of available tools (histology, ultrasound, endoscopy, and plasma sex steroids) used to assign sex and stage of maturity within the same population of prepubertal and post-pubertal sturgeon. Population reproductive structure was described using these tools in 332 hatchery-origin and 75 wild individuals over 2 years (2017 and 2018). True sex was determined using histological analysis of gonadal tissue, which is 100% accurate at assigning sex and stage of maturity in fish when germ cells are present in the biopsy. All hatchery-origin fish assessed had not reached puberty and were pre-meiotic males ( n = 158) or pre-vitellogenic females ( n = 174). Assignment of true sex using histology was 97% in hatchery-origin and 94% in wild fish as several biopsies did not contain germ cells. Fish with gonadal biopsies that did not contain germ cells and intersex fish ( n = 3) were not included in further analyses of other tools. Accuracy in assigning sex to both the hatchery-origin (98%) and wild (100%) fish was highest using endoscopy (an otoscope). The other tools evaluated were less accurate, with 69% accuracy in hatchery-origin and 74% accuracy in wild fish for plasma sex steroids and 57% accuracy in hatchery-origin and 70% accuracy in wild fish for ultrasonography. Based on these results, endoscopy was the most reliable tool for assigning sex in both prepubertal and post-pubertal fish and can be easily complimented with histology when determining stage of maturity or describing population reproductive structure.

British Columbia, Washington↗

Description of an estuarine methylotrophic methanogen, which grows on dimethyl sulfite

Characteristics of an obligately methylotrophic coccoid methanogen (strain GS-16) previously isolated from estuarine sediment are described. Growth was demonstrated on dimethyl sulfide (DMS) or trimethylamine (TMA), but not on methane thiol, methane thiol plus hydrogen, dimethyl disulfide, or methionine. DMS-grown cells were able to metabolize DMS and TMA simultaneously when inoculated into media containing substrate levels of these compounds. However, TMA-grown cells could not metabolize [ 14 C]DMS to 14 CH 4 , although they could convert [ 14 C]methanol to 14 CH 4 . These results suggest that metabolism of DMS proceeds along a somewhat different route than that of TMA and perhaps also that of methanol. The organism exhibited doubling times of 23 and 32 h for growth (25°C) in mineral media on TMA and DMS, respectively. Doubling times were more rapid (∼6 h) when the organisms were grown on TMA in complex broth. In mineral media, the fastest growth on DMS occurred between pH levels of 7.0 and 8.7, at 29°C, and with 0.2 to 0.4 M Na + and 0.04 M Mg 2+ . Somewhat different results occurred for growth on TMA in complex broth. Cells had a moles percent G+C value of 44.5% for their DNA. Growth on DMS, TMA, and methanol yielded stable carbon isotope fractionation factors of 1.044, 1.037, and 1.063, respectively. Fractionation factors for hydrogen were 1.203 (DMS) and 1.183 (TMA).

Applied and Environmental Microbiology↗

Fish viruses: Buffers and methods for plaquing eight agents under normal atmosphere

A universal procedure was sought for plaque assay of eight fish viruses (bluegill myxovirus, channel catfish virus, eel virus, Egtved virus, infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, lymphocystis virus, and the agent of spring viremia of carp ( Rhabdovirus carpio ), in dish cultures of various fish cells. Eagle minimal essential medium with sodium bicarbonate-CO 2 buffer (Earle’s salt solution) was compared with minimal essential medium buffered principally with tris (hydroxymethyl)aminomethane or N -2-hydroxyethylpiperazine-N′-2′-ethanesulfonic acid at a pH or in the range of 7.6 to 8.0 depending upon temperature. Five fish cell lines collectively capable of replicating all fish viruses thus far isolated were tested and quantitatively found to grow comparably well in the three media. Two-phase (gel-liquid) media incorporating the various buffer systems allowed plaquing at 15 to 33 C either in partial pressures of CO 2 or in normal atmosphere, but greater efficiency and sensitivity were obtained with the organic buffers, and, overall, the best results were obtained with tris(hydroxymethyl)aminomethane. Epizootiological data, specific fish cell line response, and plaque morphology permit presumptive identification of most of the agents. At proper pH, use of organic buffers obviates the need for CO 2 incubators.

Applied Microbiology↗

Detection and identification of aquatic birnaviruses by PCR assay

A reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for the detection and identification of aquatic birnaviruses. The four sets of primers (PrA, PrB, PrC, and PrD) that we used are specific for regions of cDNA coded by genome segment A of aquatic birnaviruses. PrA identifies a large fragment (1,180 bp) within the pVP2-coding region, and PrB identifies a 524-bp fragment within the sequence amplified by PrA. Primer set PrC frames a genome fragment (339 bp) within the NS-VP3-coding region, and PrD identifies a 174-bp sequence within the fragment identified by PrC. PrB and PrD amplified cDNAs from all nine recognized serotypes of aquatic birnavirus serogroup A as well as the N1 isolate that may represent a 10th serotype. These results indicate that these three primer sequences are highly conserved and can be used in PCR assays for group identification of these viruses. PrA routinely produced amplification products from eight serotypes but exhibited variable results with one serotype, and primer PrC identified 6 of the 11 virus isolates tested. The qualitative sensitivity of the RT-PCR assay was evaluated by comparison of the results with those of cell culture isolation assays. With the exception of one sample, the RT-PCR assay with primer PrD was as accurate as cell culture isolation for detecting virus in kidney and spleen tissues from naturally infected, asymptomatic carrier fish. These results indicate that the RT-PCR assay can be a rapid and reliable substitute for cell culture methods for the detection of aquatic birnaviruses.

Journal of Clinical Microbiology↗

Herpesvirus salmonis: Characterization of a new pathogen of rainbow trout

A new agent, provisionally designated Herpesvirus salmonis , was isolated from post-spawning rainbow trout ( Salmo gairdneri ) and studied primarily in the RTG-2 rainbow trout cell line. Infection of RTG-2 cells resulted in the formation of syncytia and Cowdry type A intranuclear inclusions. Replication occurred regularly at 5 and 10°C, but was inconsistent at 15°C, largely inhibited at 0°C, and completely inhibited at 20°C or higher. The virus was acid, heat, ether, and chloroform labile, but stable to freezing and thawing. It did not hemagglutinate. Viral DNA had a buoyant density of 1.709 g/cm 3 and a guanine-cytosine value of 50%. Hexagonal nucleocapsids had a diameter of 90 nm and were first seen in nuclei at 36 h. Enveloped forms measured about 150 nm and occurred both cytoplasmically and extracellularly. At 10°C, a one-step growth culture required about 96 h; cell-associated virus peaked at about 10 5 PFU/ml and exceeded released virus by a factor of about 10.

Journal of Virology↗

Modeling rainfall conditions for shallow landsliding in Seattle, Washington

We describe the results from an application of a distributed, transient infiltration–slope-stability model for an 18 km 2 area of southwestern Seattle, Washington, USA. The model (TRIGRS) combines an infinite slope-stability calculation and an analytic, one-dimensional solution for pore-pressure diffusion in a soil layer of finite depth in response to time-varying rainfall. The transient solution for pore-pressure response can be superposed on any steady-state groundwater-flow field that is consistent with model assumptions. Applied over digital topography, the model computes a factor of safety for each grid cell at any time during a rainstorm. Input variables may vary from cell to cell, and the rainfall rate can vary in both space and time. For Seattle, topographic slope derived from an airborne laser swath mapping (ALSM)–based 3 m digital elevation model (DEM), maps of soil and water-table depths derived from geotechnical borings, and hourly rainfall intensities were used as model inputs. Material strength and hydraulic properties used in the model were determined from field and laboratory measurements, and a tension-saturated initial condition was assumed. Results are given in terms of a destabilizing intensity and duration of rainfall, and they were evaluated by comparing the locations of 212 historical landslides with the area mapped as potentially unstable. Because the equations of groundwater flow are explicitly solved with respect to time, the results from TRIGRS simulations can be portrayed quantitatively to assess the potential landslide hazard based on rainfall conditions.

Washington↗

The offshore export of sand during exceptional discharge from California rivers

Littoral cells along active tectonic margins receive large inputs of sand and gravel from coastal watersheds and commonly lose this sediment to submarine canyons. One hypothesis is that the majority of coarse (sand and gravel) river sediment discharge will be emplaced within and immediately “resupply” local littoral cells. A competing hypothesis is that the infrequent, large floods that supply the majority of littoral sediment may discharge water-sediment mixtures within negatively buoyant hyperpycnal plumes that transport sediment offshore of the littoral cell. Here we summarize pre- and post-flood surveys of two wave-dominated California (United States) river deltas during record to near-record floods to help evaluate these hypotheses: the 1982–1983 delta at the San Lorenzo River mouth and the 2005 delta at the Santa Clara River mouth. Flood sedimentation at both deltas resulted in several meters of aggradation and hundreds of meters of offshore displacement of isobaths. One substantial difference between these deltas was the thick (>2 m) aggradation of sand on the inner shelf of the Santa Clara River delta that contained substantial amounts (∼50%) of littoral-grade sediment. Once deposited on the inner shelf, only a fraction (∼20%) of this river sand was observed to migrate toward the beach over the following 5 yr. Furthermore, simple hypopycnal plume behavior could not explain deposition of this sand on the inner shelf. Thus, during an exceptional flood a substantial amount of littoral-grade sand was exported offshore of the littoral system at the Santa Clara River mouth—likely from hyperpycnal plume processes—and was deposited on the inner shelf.

California↗

Pathophysiology of infectious hematopoietic necrosis virus disease in rainbow trout (Salmo gairdneri): early changes in blood and aspects of the immune Response after Injection of IHN Virus

Juvenile rainbow trout ( Salmo gairdneri ) were injected with infectious hematopoietic necrosis (IHN) virus and various hematological and blood chemical changes were monitored over 9 days. The packed cell volume, hemoglobin, red blood cell count, and plasma bicarbonate were significantly depressed by day 4. Plasma chloride, calcium, phosphorus, total protein, and blood cell types did not change during the 9 days. Furthermore, plasma LDH isozyme was significantly increased by the fourth day, and fish infected with infectious pancreatic necrosis virus, Vibrio anguillarum , Aeromonas salmonicida , and redmouth bacterium did not show specific LDH isozyme alterations. Acid-base alterations occurred at 10 C but not at 18 C. The acid-base imbalance and elevation of the LDH isozyme were consistently associated with the early development of the disease.The immune response after injection of IHN virus was determined and protection from disease was tested by passive immunization. Actively immunized fish developed IHN-neutralizing antibodies within 54 days after injection of virus, and the antibodies were protective when juvenile fish were passively immunized and experimentally challenged with IHN virus.

Journal of the Fisheries Research Board of Canada↗