Search USGS⌕ Search

SEARCH · Search USGS

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 73 records · Page 4Linked to original sources
USGS2015

Classification of rocky headlands in California with relevance to littoral cell boundary delineation

Despite extensive studies of hydrodynamics and sediment flux along beaches, there is little information on the processes, pathways and timing of water and sediment transport around rocky headlands. In this study, headlands along the California coast are classified to advance understanding of headland dynamics and littoral cell boundaries in support of improved coastal management decisions. Geomorphological parameters for 78 headlands were quantified from geological maps, remote-sensing imagery, navigational charts, and shoreline geospatial databases. K -means cluster analysis grouped the headlands into eight distinct classes based on headland perimeter, bathymetric slope ratio, and the headland apex angle. Wave data were used to investigate the potential for sediment transport around the headland types and determine the efficacy of the headland as a littoral cell boundary. Four classes of headland appear to function well as littoral cell boundaries, with headland size (e.g., perimeter or area) and a marked change in nearshore bathymetry across the headland being relevant attributes. About half of the traditional California littoral cell boundaries align with headland classes that are expected to perform poorly in blocking alongshore sediment transport, calling into question these boundaries. Better definition of these littoral cell boundaries is important for regional sediment management decisions.

California↗
USGS2010

Granular cell tumor in an endangered Puerto Rican Amazon parrot (Amazon vittata)

A 3 cm diameter mass from the metacarpus of a Puerto Rican Amazon parrot was diagnosed as a granular cell tumour based on light microscopy. The cytoplasmic granules were periodic-acid Schiff positive and diastase resistant. Ultrastructural characteristics of the cells included convoluted nuclei and the presence of numerous cytoplasmic tertiary lysosomes. This is only the second granular cell tumour reported in a bird. We speculate that most granular cell tumours are derived from cells that are engaged in some type of cellular degradative process, creating a similar morphologic appearance, but lacking a uniform histogenesis.

Avian Pathology↗
USGS2010

The H4IIE cell bioassay as an indicator of dioxin-like chemicals in wildlife and the environment

The H4IIE cell bioassay has proven utility as a screening tool for planar halogenated hydrocarbons (PHHs) and structurally similar chemicals accumulated in organisms from the wild. This bioassay has additional applications in hazard assessment of PHH exposed populations. In this review, the toxicological principles, current protocols, performance criteria, and field applications for the assay are described. The H4IIE cell bioassay has several advantages over the analytical measurement of PHHs in environmental samples, but conclusions from studies can be strengthened when both bioassay and analytical chemistry data are presented together. Often, the bioassay results concur with biological effects in organisms and support direct measures of PHHs. For biomonitoring purposes and prioritization of PHH-contaminated environments, the H4IIE bioassay may be faster and less expensive than analytical measurements. The H4IIE cell bioassay can be used in combination with other biomarkers such as in vivo measurements of CYP1A1 induction to help pinpoint the sources and identities of dioxin-like chemicals. The number of studies that measure H4IIE-derived TCDD-EQs continues to increase, resulting in subtle improvements over time. Further experiments are required to determine if TCDD-EQs derived from mammalian cells are adequate predictors of toxicity to non-mammalian species. The H4IIE cell bioassay has been used in over 300 published studies, and its combination of speed, simplicity, and ability to integrate the effects of complex containment mixtures makes it a valuable addition to hazard assessment and biomonitoring studies.

Critical Reviews in Toxicology↗
USGS2025

Accurate simulation of flow through dipping aquifers with MODFLOW 6 using enhanced cell connectivity

In simulations of groundwater flow through dipping aquifers, layers of model cells are often “deformed” to follow the top and bottom elevations of the aquifers. When this approach is used in MODFLOW, adjacent cells within the same model layer are vertically offset from one another, and the standard conductance-based (two-point) formulation for flow between cells does not rigorously account for these offsets. The XT3D multi-point flow formulation in MODFLOW 6 is designed to account for geometric irregularities in the grid, including vertical offsets, and to provide accurate results for both isotropic and anisotropic groundwater flow. A recent study evaluated the performance of the standard formulation and XT3D using a simple, synthetic benchmark model of a steeply dipping aquifer. Although XT3D generally improved the accuracy of flow simulations relative to the standard formulation as expected, neither formulation produced accurate flows in cases that involved large vertical offsets. In this paper, we explain that the inability of XT3D to produce accurate flows in the steeply dipping aquifer benchmark was not due to an inherent limitation of the flow formulation, but rather to the limited cell connectivity inherent in the most commonly used discretization packages in MODFLOW 6. Furthermore, we demonstrate that XT3D is able to produce the expected accuracy when adequate cell connectivity is introduced using MODFLOW's unstructured grid type and the aquifer is discretized vertically using at least two model layers.

Groundwater↗
USGS2014

Biological effects of desert dust in respiratory epithelial cells and a murine model

As a result of the challenge of recent dust storms to public health, we tested the postulate that desert dust collected in the southwestern United States imparts a biological effect in respiratory epithelial cells and an animal model. Two samples of surface sediment were collected from separate dust sources in northeastern Arizona. Analysis of the PM 20 fraction demonstrated that the majority of both dust samples were quartz and clay minerals (total SiO 2 of 52 and 57%). Using respiratory epithelial and monocytic cell lines, the two desert dusts increased oxidant generation, measured by Amplex Red fluorescence, along with carbon black (a control particle), silica, and NIST 1649 (an ambient air pollution particle). Cell oxidant generation was greatest following exposures to silica and the desert dusts. Similarly, changes in RNA for superoxide dismutase-1, heme oxygenase-1, and cyclooxygenase-2 were also greatest after silica and the desert dusts supporting an oxidative stress after cell exposure. Silica, desert dusts, and the ambient air pollution particle NIST 1649 demonstrated a capacity to activate the p38 and ERK1/2 pathways and release pro-inflammatory mediators. Mice, instilled with the same particles, showed the greatest lavage concentrations of pro-inflammatory mediators, neutrophils, and lung injury following silica and desert dusts. We conclude that, comparable to other particles, desert dusts have a capacity to (1) influence oxidative stress and release of pro-inflammatory mediators in respiratory epithelial cells and (2) provoke an inflammatory injury in the lower respiratory tract of an animal model. The biological effects of desert dusts approximated those of silica.

Inhalation Toxicology↗
USGS1993

Effects of salinity on chloride cells and Na+ K+-ATPase activity in the teleost Gillchthys mirabilis

1. Longjawed mudsuckers, Gillichthys mirabilis , in 30ppt seawater (SW) were transferred to 1.5, 30 and 60ppt SW. 2. In the first 1–3 days after transfer, plasma chloride level and plasma osmolarity rose in the 60ppt SW fish, and decreased in the 1.5ppt SW fish. 3. By day 21, however, plasma chloride and osmolarity were at or near the levels seen in the controls (30ppt). 4. Branchial and jawskin Na + , K + -ATPase activities were high in all salinities, and did not differ significantly among treatments. 5. The vital fluorescent stains DASPEI and anthroylouabain were used to detect mitochondria and Na + , K + -ATPase, respectively, in chloride cells. 6. Both stains indicated that jawskin chloride cell density did not differ among treatment groups. 7. In contrast, chloride cell size increased significantly with increasing salinity. 8. The chloride cells of fish in 60 ppt SW were noticeably angular in outline, whereas those of both the 1.5 and 30ppt SW fish were circular. 9. The results are discussed in relation to the ion transport requirements encountered in the intertidal habitat of the mudsucker.

Comparative Biochemistry and Physiology, Part A: P↗
USGS2025

Establishment of a cell culture from Daphnia magna as an in vitro model for (eco)toxicology assays: Case study using Bisphenol A as a representative cytotoxic and endocrine disrupting chemical

Bisphenol A (BPA) is a widely used industrial compound found in polycarbonate plastics, epoxy resin, and various polymer materials, leading to its ubiquitous presence in the environment. The toxicity of BPA to aquatic organisms has been well documented following in vivo exposure scenarios, with known cytotoxic and endocrine-disrupting effects. As such, BPA was used in this study as a well-characterized chemical to implement more ethical and resource-efficient scientific practices in toxicity testing through new approach methods (NAMs). Due to the frequent use of Daphnia spp. as a model organism in toxicology, we developed an in vitro cell culture system from Daphnia magna embryos, with optimized medium to support cell longevity. The cultures were maintained for up to two months, demonstrating their stability and suitability for cytotoxicity studies. Using this novel system, lethal concentration 50 (LC 50 ) values were determined at the 24 and 48 h time points following BPA exposure. Subsequently, oxidative stress, endocrine disruption, and DNA damage were assessed through gene expression, activity assays, and a comet assay in BPA-exposed cells. LC 50 values of 52 µM and 20 µM BPA were calculated after 24 and 48 h exposures, respectively. BPA cells exposed to 20 and 52 µM had significantly increased GSH, GPx, and GST activity levels. mRNA expression analysis revealed significant upregulations in the expression of hsp70, hsp90, gst, gpx, vtg1 , and cyp4 , with downregulations of sod, cat , and ecr following BPA exposure. Furthermore, comet assays showed a significantly higher level of DNA damage induced by BPA compared to controls, with greater comet and tail lengths. This study established a novel in vitro Daphnia model, using BPA as a case study for determining toxic effects, further highlighting the importance and applicability of utilizing alternative methods in ecotoxicological research through reducing animal use.

Aquatic Toxicology↗
USGS2012

Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development

Thiamin pyrophosphokinase (TPK) converts thiamin to its active form, thiamin diphosphate. In humans, TPK expression is down-regulated in some thiamin deficiency related syndrome, and enhanced during pregnancy. Rainbow trout are also vulnerable to thiamin deficiency in wild life and are useful models for thiamin metabolism research. We identified the tpk gene transcript including seven splice variants in the rainbow trout. Almost all cell lines and tissues examined showed co-expression of several tpk splice variants including a potentially major one at both mRNA and protein levels. However, relative to other tissues, the longest variant mRNA expression was predominant in the ovary and abundant in embryos. During embryogenesis, total tpk transcripts increased abruptly in early development, and decreased to about half of the peak shortly after hatching. In rainbow trout, the tpk transcript complex is ubiquitously expressed for all tissues and cells examined, and its increase in expression could be important in the early-middle embryonic stages. Moreover, decimated tpk expression in a hepatoma cell line relative to hepatic and gonadal cell lines appears to be consistent with previously reported down-regulation of thiamin metabolism in cancer.

Comparative Biochemistry and Physiology, Part B: B↗
USGS2014

Lectins stain cells differentially in the coral, Montipora capitata

A limitation in our understanding of coral disease pathology and cellular pathogenesis is a lack of reagents to characterize coral cells. We evaluated the utility of plant lectins to stain tissues of a dominant coral, Montipora capitata , from Hawaii. Of 22 lectins evaluated, nine of these stained structures in the upper or basal body wall of corals. Specific structures revealed by lectins that were not considered distinct or evident on routine hematoxylin and eosin sections of coral tissues included apical and basal granules in gastrodermis and epidermis, cnidoglandular tract and actinopharynx cell surface membranes, capsules of mature holotrichous isorhizas, and perivitelline and periseminal cells. Plant lectins could prove useful to further our understanding of coral physiology, anatomy, cell biology, and disease pathogenesis.

Hawai'i↗
USGS2002

Shape functions for velocity interpolation in general hexahedral cells

Numerical methods for grids with irregular cells require discrete shape functions to approximate the distribution of quantities across cells. For control-volume mixed finite-element (CVMFE) methods, vector shape functions approximate velocities and vector test functions enforce a discrete form of Darcy's law. In this paper, a new vector shape function is developed for use with irregular, hexahedral cells (trilinear images of cubes). It interpolates velocities and fluxes quadratically, because as shown here, the usual Piola-transformed shape functions, which interpolate linearly, cannot match uniform flow on general hexahedral cells. Truncation-error estimates for the shape function are demonstrated. CVMFE simulations of uniform and non-uniform flow with irregular meshes show first- and second-order convergence of fluxes in the L2 norm in the presence and absence of singularities, respectively.

Computational Geosciences↗
USGS2012

A rapid compatibility analysis of potential offshore sand sources for beaches of the Santa Barbara Littoral Cell

The beaches of the Santa Barbara Littoral Cell, which are narrow as a result of either natural and/or anthropogenic factors, may benefit from nourishment. Sand compatibility is fundamental to beach nourishment success and grain size is the parameter often used to evaluate equivalence. Only after understanding which sand sizes naturally compose beaches in a specific cell, especially the smallest size that remains on the beach, can the potential compatibility of source areas, such as offshore borrow sites, be accurately assessed. This study examines sediments on the beach and in the nearshore (5-20m depth) for the entire Santa Barbara Littoral Cell east of Point Conception. A digital bed sediment camera, the Eyeball??, and spatial autocorrelation technique were used to determine sediment grain size. Here we report on whether nearshore sediments are comparable and compatible with beach sands of the Santa Barbara Littoral Cell. ?? 2007 ASCE.

Conference Paper↗
USGS2006

Mycoplasma contamination in fish cell lines: An evaluation of detection by differential incorporation of 3H-uridine and 14C-uracil

Differential incorporation of uridine and uracil was used to assay for mycoplasma contamination in five fish cell lines: bluegill fry (BF-2), chinook salmon embryo (CHSE-214), epithelioma papillosum cyprini (EPC), fathead minnow (FHM) and rainbow trout gonad (RTG-2). The method was not suitable for monitoring BF-2, CHSE-214, FHM, and RTG-2 cell lines because they incorporated uracil. Differential incorporation of uridine and uracil may be applicable for screening EPC cells because only this cell line could distinguish cultures experimentally infected with Mycoplasma orale from cultures known to be free from microbial contaminants.

Journal of Fish Diseases↗
USGS2003

Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water

Quantitative PCR (QPCR) technology, incorporating fluorigenic 5′ nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida ( C. albicans , C. tropicalis , C. krusei , C. parapsilosis , C. glabrata and C. lusitaniae ) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.

Applied and Environmental Microbiology↗
USGS2010

Release of infectious cells from epidermal ulcers in Ichthyophonus sp.–infected Pacific Herring (Clupea pallasii): Evidence for multiple mechanisms of transmission

A common clinical sign of ichthyophoniasis in herring and trout is “sandpaper” skin, a roughening of the epidermis characterized by the appearance of small papules, followed by ulceration and sloughing of the epithelium; early investigators hypothesized that these ulcers might be a means of transmitting the parasite, Ichthyophonus sp ., without the necessity of ingesting an infected host. We examined the cells associated with the epidermal lesions and confirmed that they were viable Ichthyophonus sp. cells that were readily released from the skin into the mucous layer and ultimately into the aquatic environment. The released cells were infectious when injected into the body cavity of specific-pathogen-free herring. Our hypothesis is that different mechanisms of transmission occur in carnivorous and planktivorous hosts: Planktonic feeders become infected by ingestion of ulcer-derived cells, while carnivores become infected by ingestion of whole infected fish.

Journal of Parasitology↗
USGS2022

Compilation of existing data for sand resource studies in Federal and California State Waters of the San Francisco, Oceanside, and Silver Strand littoral cell study areas along the continental shelf of California—Strategy for field studies and sand resource assessment

Executive Summary The Sand Resources Project was established through collaborative agreements between the U.S. Geological Survey (USGS), the Bureau of Ocean Energy Management (BOEM), and the California Ocean Protection Council (OPC) with the purpose of evaluating sand and gravel resources in Federal and California State Waters for potential use in future beach-nourishment projects. Project partners worked in collaboration with California Coastal Sediment Management Workgroup (CSMW) members to define priority study areas for this work based on the potential for finding sand within the broader region and the needs for this sand as shown by beach erosion areas of concern in the adjacent littoral cells. The final study areas were defined to be (1) the San Francisco Littoral Cell, (2) the Oceanside Littoral Cell, and (3) the Silver Strand Littoral Cell. A two-stage approach was used to assess the study areas. This report addresses the initial stage, which is a synthesis of the existing geophysical and sediment-sampling data in each area. This allowed for evaluations of the data availability, data gaps, and general patterns of sediment thickness and grain size. This report provides a description of the methods and results of this synthesis. The findings from this work were used to refine study area boundaries and develop sampling plans for stage two of the project. Stage two of the project, the results of which will be published separately, will be the collection, processing, and synthesis of new data, including high-resolution geophysical surveys and sediment cores within the three study areas. The data collected will provide new information about the three study areas including sediment thickness, grain-size distributions, and total organic carbon. The description and results of stage two of the work is included in another USGS report (Warrick and others, 2022).

California↗
USGS2004

Detection of Clostridium botulinum type C cells in the gastrointestinal tracts of Mozambique tilapia (Oreochromis mossambicus) by polymerase chain reaction

We established a method of directly detecting Clostridium botulinum type C cells, while minimizing spore detection, in the intestinal contents of Mozambique tilapia ( Oreochromis mossambicus ). This technique involved extraction of predominantly cellular DNA from tilapia intestinal tracts and used a polymerase chain reaction assay to detect presence of type C 1 toxin gene. We consistently detected C. botulinum type C cells in tilapia gastrointestinal contents at a level of 7.5×10 4 cells per 0.25 g material or 1.9×10 3 cells. This technique is useful for determining prevalence of the potentially active organisms within a given population of fish and may be adapted to other types of C. botulinum and vertebrate populations as well.

California↗
USGS1998

Morphologic and cytochemical characteristics of blood cells from Hawaiian green turtles

Objective - To identify and characterize blood cells from free-ranging Hawaiian green turtles, Chelonia mydas. Sample Population - 26 green turtles from Puako on the island of Hawaii and Kaneohe Bay on the island of Oahu. Procedure - Blood was examined, using light and electron microscopy and cytochemical stains that included benzidine peroxidase, chloroacetate esterase, alpha naphthyl butyrate esterase, acid phosphatase, Sudan black B, periodic acid-Schiff, and toluidine blue. Results - 6 types of WBC were identified: lymphocytes, monocytes, thrombocytes, heterophils, basophils, and eosinophils (small and large). Morphologic characteristics of mononuclear cells and most granulocytes were similar to those of cells from other reptiles except that green turtles have both large and small eosinophils. Conclusions - Our classification of green turtle blood cells clarifies imporoper nomenclature reported previously and provides a reference for future hematologic studies in this species.

Hawai'i↗
USGS2003

Trace-metal sources and their release from mine wastes: examples from humidity cell tests of hardrock mine waste and from Warrior Basin coal

To assess the potential impact of metal and acid contamination from mine-waste piles, it is important to identify the mineralogic source of trace metals and their mode of occurrence. Microscopic analysis of mine-waste samples from both hard-rock and coalmine waste samples demonstrate a microstructural control, as well as mineralogic control, on the source and release of trace metals into local water systems. The samples discussed herein show multiple periods of sulfide mineralization with varying concentrations of trace metals. In the first case study, two proprietary hard-rock mine-waste samples exposed to a series of humidity cell tests (which simulate intense chemical weathering conditions) generated acid and released trace metals. Some trace elements of interest were: arsenic (45-120 ppm), copper (60-320 ppm), and zinc (30-2,500 ppm). Untested and humidity cell-exposed samples were studied by X-ray diffraction, scanning electron microscope with energy dispersive X-ray (SEM/EDX), and electron microprobe analysis. Studies of one sample set revealed arsenic-bearing pyrite in early iron- and magnesium-rich carbonate-filled microveins, and iron-, copper-, arsenic-, antimony-bearing sulfides in later crosscutting silica-filled microveins. Post humidity cell tests indicated that the carbonate minerals were removed by leaching in the humidity cells, exposing pyrite to oxidative conditions. However, sulfides in the silica-filled veins were more protected. Therefore, the trace metals contained in the sulfides within the silica-filled microveins may be released to the surface and (or) ground water system more slowly over a greater time period. In the second case study, trace metal-rich pyrite-bearing coals from the Warrior Basin, Alabama were analyzed. Arsenic-bearing pyrite was observed in a late-stage pyrite phase in microfaults and microveins that crosscut earlier arsenic.

Conference Paper↗