SEARCH · Geology Reports

Results for “Cells”

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

SourceResearch connectionFrom yearThrough year

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

At least 739 records · Page 41Linked to original sources

USGS2004

Structural and spectral features of selenium nanospheres produced by Se-respiring bacteria

Certain anaerobic bacteria respire toxic selenium oxyanions and in doing so produce extracellular accumulations of elemental selenium [Se(0)]. We examined three physiologically and phylogenetically diverse species of selenate- and selenite-respiring bacteria, Sulfurospirillum barnesii, Bacillus selenitireducens, and Selenihalanaerobacter shriftii, for the occurrence of this phenomenon. When grown with selenium oxyanions as the electron acceptor, all of these organisms formed extracellular granules consisting of stable, uniform nanospheres (diameter, ???300 nm) of Se(0) having monoclinic crystalline structures. Intracellular packets of Se(0) were also noted. The number of intracellular Se(0) packets could be reduced by first growing cells with nitrate as the electron acceptor and then adding selenite ions to washed suspensions of the nitrate-grown cells. This resulted in the formation of primarily extracellular Se nanospheres. After harvesting and cleansing of cellular debris, we observed large differences in the optical properties (UV-visible absorption and Raman spectra) of purified extracellular nanospheres produced in this manner by the three different bacterial species. The spectral properties in turn differed substantially from those of amorphous Se(0) formed by chemical oxidation of H2Se and of black, vitreous Se(0) formed chemically by reduction of selenite with ascorbate. The microbial synthesis of Se(0) nanospheres results in unique, complex, compacted nanostructural arrangements of Se atoms. These arrangements probably reflect a diversity of enzymes involved in the dissimilatory reduction that are subtly different in different microbes. Remarkably, these conditions cannot be achieved by current methods of chemical synthesis.

Applied and Environmental Microbiology↗

USGS1967

Dechlorination of 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane by Aerobacter aerogenes: I. Metabolic products

Whole cells or cell-free extracts of Aerobacter aerogenes catalyze the degradation of 1,1,1-trichloro-2,2-bis( p -chlorophenyl)ethane (DDT) in vitro to at least seven metabolites: 1,1-dichloro-2,2-bis( p -chlorophenyl)ethylene (DDE); 1,1-dichloro-2,2-bis( p -chlorophenyl)ethane (DDD); 1-chloro-2,2-bis( p -chlorophenyl)ethylene (DDMU); 1-chloro-2,2-bis( p -chlorophenyl)ethane (DDMS); unsym-bis( p -chlorophenyl)ethylene (DDNU); 2,2-bis( p -chlorophenyl)acetate (DDA); and 4,4′-dichlorobenzophenone (DBP). The use of metabolic inhibitors together with p H and temperature studies indicated that discrete enzymes are involved. By use of the technique of sequential analysis, the metabolic pathway was shown to be: DDT → DDD →DDMU →DDMS → DDNU → DDA → DBP, or DDT → DDE. Dechlorination was marginally enhanced by light-activated flavin mononucleotide.

Applied Microbiology↗

USGS1987

Rainfall, ground-water flow, and seasonal movement at Minor Creek landslide, northwestern California: Physical interpretation of empirical relations

Simple ground-water flow analyses can clarify complex empirical relations between rainfall and landslide motion. Here we present detailed data on rainfall, ground-water flow, and repetitive seasonal motion that occurred from 1982 to 1985 at Minor Creek landslide in northwestern California, and we interpret these data in the context of physically based theories. We find that landslide motion is closely regulated by the direction and magnitude of near-surface hydraulic gradients and by waves of pore pressure caused by intermittent rainfall. Diffusive propagation of pore-pressure waves accompanies downward ground-water flow along nearly vertical hydraulic gradients that exist in most of the landslide. Field data combined with a pore-pressure diffusion analysis show that single rainstorms typically produce short-period waves that attenuate before reaching the landslide base. In contrast, seasonal rainfall cycles produce long-period waves that modify basal pore pressures, but only after time lags that range from weeks to months. Such tune lags can depend on antecedent moisture storage and can explain variable delays between the onset of the wet season and seasonal landslide motion. Limit-equilibrium analysis shows that when seasonal pressure waves reach the landslide base, they establish a critical distribution of effective stress that delicately triggers landslide motion. The critical effective-stress balance is extremely sensitive to the direction and magnitude of hydraulic gradients. Although pervasively downward gradients instigate seasonal motion, we infer from theory and limited data that ground water also may circulate locally in near-surface cells. The circulation can further reduce the landslide's frictional strength, particularly in areas of nearly horizontal ground-water flow that occur beneath steep faces of hummocks. Hummocky topography that results from slope instability may therefore cause ground-water flow that perpetuates instability. Diffusive propagation of pore-pressure waves accompanies downward ground-water flow along nearly vertical hydraulic gradients that exist in most of the landslide. Field data combined with a pore-pressure diffusion analysis show that single rainstorms typically produce short-period waves that attenuate before reaching the landslide base. In contrast, seasonal rainfall cycles produce long-period waves that modify basal pore pressures, but only after time lags that range from weeks to months. Such tune lags can depend on antecedent moisture storage and can explain variable delays between the onset of the wet season and seasonal landslide motion. Limit-equilibrium analysis shows that when seasonal pressure waves reach the landslide base, they establish a critical distribution of effective stress that delicately triggers landslide motion. The critical effective-stress balance is extremely sensitive to the direction and magnitude of hydraulic gradients. Although pervasively downward gradients instigate seasonal motion, we infer from theory and limited data that ground water also may circulate locally in near-surface cells. The circulation can further reduce the landslide's frictional strength, particularly in areas of nearly horizontal ground-water flow that occur beneath steep faces of hummocks. Hummocky topography that results from slope instability may therefore cause ground-water flow that perpetuates instability.

California↗

USGS2015

Association of anatase (TiO2) and microbes: unusual fossilization effect or a potential biosignature?

We combined microbial paleontology and molecular biology methods to study the Eyreville B drill core from the 35.3-Ma-old Chesapeake Bay impact structure,Virginia, USA. The investigated sample is a pyrite vein collected from the 1353.81-1353.89 m depth interval, located within a section of biotite granite. The granite is a pre-impact rock that was disrupted by the impact event. A search for inorganic (mineral) biosignatures revealed the presence of micron-size rod morphologies of anatase (TiO2) embedded in chlorite coatings on pyrite grains. Neither the Acridine Orange microbial probe nor deoxyribonucleic acid (DNA) extraction followed by polymerase chain reaction (PCR) amplifi cation showed the presence of DNA or ribonucleic acid (RNA) at the location of anatase rods, implying the absence of viable cells in the investigated area. A Nile Red microbial probe revealed the presence of lipids in the rods. Because most of the lipids are resistant over geologic time spans, they are good biomarkers, and they are an indicator of biogenicity for these possibly 35-Ma-old microbial fossils. The mineral assemblage suggests that rod morphologies are associated with low-temperature (<100 °C) hydrothermal alteration that involved aqueous fl uids. The temporal constraints on the anatase fossils are still uncertain because pre-impact alteration of the granite and postimpact heating may have provided identical conditions for anatase precipitation and microbial preservation.

Geological Society of America Bulletin↗

USGS2004

Microbial precipitation of dolomite in methanogenic groundwater

We report low-temperature microbial precipitation of dolomite in dilute natural waters from both field and laboratory experiments. In a freshwater aquifer, microorganisms colonize basalt and nucleate nonstoichiometric dolomite on cell walls. In the laboratory, ordered dolomite formed at near-equilibrium conditions from groundwater with molar Mg:Ca ratios of <1; dolomite was absent in sterile experiments. Geochemical and microbiological data suggest that methanogens are the dominant metabolic guild in this system and are integral to dolomite precipitation. We hypothesize that the attached microbial consortium reacts with the basalt surface, releasing Mg and Ca into solution, which drives dolomite precipitation via nucleation on the cell wall. These findings provide insight into the long-standing dolomite problem and suggest a fundamental role for microbial processes in the formation of dolomite across a wide range of environmental conditions.

Geology↗

USGS2010

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Geology↗

USGS2015

Localization and seasonal variation of blue pigment (sandercyanin) in walleye (Sander vitreus)

Several fish species, including the walleye ( Sander vitreus ), have “yellow” and “blue” color morphs. In S. vitreus , one source of the blue color has been identified as a bili-binding protein pigment (sandercyanin), found in surface mucus of the fish. Little is known about the production of the pigment or about its functions. We examined the anatomical localization and seasonal variation of sandercyanin in S. vitreus from a population in McKim Lake, northwestern Ontario, Canada. Skin sections were collected from 20 fish and examined histologically. Mucus was collected from 306 fish over 6 years, and the amount of sandercyanin was quantified spectrophotometrically. Sandercyanin was found solely on dorsal surfaces of the fish and was localized to novel cells in the epidermis, similar in appearance to secretory sacciform cells. Sandercyanin concentrations were significantly higher in fish collected in summer versus other seasons. Yellow and blue morphs did not differ in amounts of sandercyanin, suggesting that the observed blue color, in fact, arises from lack of yellow pigmentation in blue morphs. The function of the sandercyanin remains unclear, but roles in photoprotection and countershading are consistent with available data.

Ontario↗

USGS2006

Geochemical evidence for the origin of late Quaternary loess in central Alaska

Loess is extensive in central Alaska, but there are uncertainties about its source and the direction of paleo-winds that deposited it. Both northerly and southerly winds have been inferred. The most likely sources of loess are the Tanana River (south), the Nenana River (southeast), and the Yukon River (north). Late Quaternary loess in central Alaska has immobile trace-element compositions (Cr/Sc, Th/Ta, Th/ Sc, Th/U, Eu/Eu*, GdN/YbN) that indicate derivation mostly from the Tanana River. However, other ratios (As/Sb, Zr/Hf, LaN/YbN) and quantitative modeling indicate that the Yukon River was also a source. During the last glacial period, there may have been a longer residence time of the Siberian and Canadian high-pressure cells, along with a strengthened Aleutian low-pressure cell. This would have generated regional-scale northeasterly winds and explains derivation of loess from the Yukon River. However, superim-posed upon this synoptic-scale circulation, there may have been strong, southerly katabatic winds from expanded glaciers on the northern flank of the Alaska Range. These winds could have provided eolian silt from the Tanana River. Yukon River and Tanana River sediments are highly calcareous, whereas Fairbanks-area loess is not. This suggests that carbonate leaching in loess kept ahead of sedimentation and that late Quaternary loess in central Alaska was deposited relatively slowly. ?? 2006 NRC Canada.

Canadian Journal of Earth Sciences↗

USGS1970

Morphology of certain viruses of Salmonid fishes. II. In vivo studies of infectious Hematopoietic Necrosis Virus

Juvenile sockeye salmon ( Oncorhynchus nerka ) were injected with the infectious hematopoietic necrosis (IHN) virus, and tissue samples from the anterior kidney, spleen, liver, intestine, and pyloric caeca of moribund fish were prepared for electron microscopy. Bullet-shaped virus particles measuring 158&ensp;×&ensp;90&ensp;mμ were observed in the hematopoietic tissues of the anterior kidney and spleen. Virus particles were also observed in the outer connective tissues of the pancreas or pyloric caeca, or both. No virus was found in the intestine or liver. The healthy appearance of erythrocytes, reticular cells, and endothelial cells in necrotic areas of the spleen and anterior kidney, and the absence of lymphocytes in these areas, suggested that lymphocytes might be one source of the virus.

Journal of the Fisheries Research Board of Canada↗

USGS1979

Fish viruses: A double-stranded RNA icosahedral virus from a North American cyprinid

A previously unreported virus disease of cultured golden shiners ( Notemigonus crysoleucas ) is described. The condition is called golden shiner virus (GSV) disease. The virus is icosahedral, measures approximately 70 nm, is ether and heat resistant, stable at pH 3, 7, and 10, and appears to have a double stranded RNA core. It was not neutralized by infectious pancreatic necrosis virus specific antiserum. GSV causes syncytial like cytopathic effect in fathead minnow cells but not brown bullhead, rainbow trout gonad (RTG-2) or channel catfish ovary cells. Severe mortalities in golden shiner culture ponds do not appear to be associated with GSV infections.

Journal of the Fisheries Research Board of Canada↗

USGS1980

Viral erythrocytic necrosis: Some physiological consequences of infection in chum salmon ( Oncorhynchus keta )

Erythroid cells in chum salmon ( Oncorhynchus keta ) susceptible to infection with erythrocytic necrosis virus (ENV) were examined by light and electron microscopy. Cells of stages II, III, IV, V, and VI contained complete eyrthrocytic necrosis virions in the cytoplasm. Viruses closely resembling ENV were also detected in the nuclei of some erythroblasts. Some secondary consequences of ENV infection were a threefold greater mortality rate from vibriosis, a significantly decreased tolerance to oxygen depletion, and a decreased ability to regulate serum sodium and potassium in saltwater.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1995

Metals-contaminated benthic invertebrates in the Clark Fork River, Montana: Effects on age-0 brown trout and rainbow trout

Benthic organisms in the upper Clark Fork River have recently been implicated as a dietary source of metals that may be a chronic problem for young-of-the-year rainbow trout ( Oncorhynchus mykiss ). In this present study, early life stage brown trout ( Salmo trutta ) and rainbow trout were exposed for 88&ensp;d to simulated Clark Fork River water and a diet of benthic invertebrates collected from the river. These exposures resulted in reduced growth and elevated levels of metals in the whole body of both species. Concentrations of As, Cd, Cu, and Pb increased in whole brown trout; in rainbow trout, As and Cd increased in whole fish, and As also increased in liver. Brown trout on the metals-contaminated diets exhibited constipation, gut impaction, increased cell membrane damage (lipid peroxidation), decreased digestive enzyme production (zymogen), and a sloughing of intestinal mucosal epithelial cells. Rainbow trout fed the contaminated diets exhibited constipation and reduced feeding activity. We believe that the reduced standing crop of trout in the Clark Fork River results partly from chronic effects of metals contamination in benthic invertebrates that are important as food for young-of-the-year fish.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1992

Seasonal patterns of weight, hematology, and serum characteristics of free-ranging female white-tailed deer in Minnesota

Weights, hematology, and serum profIles of white-tailed does in the central Superior National Forest of northeastern Minnesota were examined year-around to determine seasonal patterns of nutritional condition and metabolism. Deer were initially captured by Clover trap or rocket net. Between 15 February 1989 and 23 January 1990, we recaptured 12 adult (> 1.5 years) female deer 1-9 times each (a total of 59 recaptures) using a radio-controlled capture collar. Monthly weights of deer exhibited a cyclic seasonal pattern. Mean weight declined 22 % from February to an annual minimum during May, then steadily increased 45 % to a maximum in October. Seasonal patterns were most evident for hemoglobin concentration, red blood cells, packed cell volume, serum total protein, urea nitrogen, creatinine, the urea N to creatinine ratio, triiodothyronine, cortisol, and potassium. Wide seasonal variations of these characteristics were indicative of shifts in the deer's metabolic physiology. Although seasonal metabolic shifts are partially attributable to an endogenous rhythm, the intensity of, their expression was most likely affected by nutritional changes and concomitant alterations of body condition. Annual changes in seasonal trends of blood characteristics may be useful in investigating nutritional effects of specific environmental and demographic factors. We compare our findings with those reported for deer on ranges farther south.

Minnesota↗

USGS2000

Coupled atmosphere-biophysics-hydrology models for environmental modeling

The formulation and implementation of LEAF-2, the Land Ecosystem–Atmosphere Feedback model, which comprises the representation of land–surface processes in the Regional Atmospheric Modeling System (RAMS), is described. LEAF-2 is a prognostic model for the temperature and water content of soil, snow cover, vegetation, and canopy air, and includes turbulent and radiative exchanges between these components and with the atmosphere. Subdivision of a RAMS surface grid cell into multiple areas of distinct land-use types is allowed, with each subgrid area, or patch, containing its own LEAF-2 model, and each patch interacts with the overlying atmospheric column with a weight proportional to its fractional area in the grid cell. A description is also given of TOPMODEL, a land hydrology model that represents surface and subsurface downslope lateral transport of groundwater. Details of the incorporation of a modified form of TOPMODEL into LEAF-2 are presented. Sensitivity tests of the coupled system are presented that demonstrate the potential importance of the patch representation and of lateral water transport in idealized model simulations. Independent studies that have applied LEAF-2 and verified its performance against observational data are cited. Linkage of RAMS and TOPMODEL through LEAF-2 creates a modeling system that can be used to explore the coupled atmosphere–biophysical–hydrologic response to altered climate forcing at local watershed and regional basin scales.

Journal of Applied Meteorology↗

USGS2012

Safety of florfenicol administered in feed to tilapia (Oreochromis sp.)

The safety of Aquaflor® (50% w/w florfenicol [FFC]) incorporated in feed then administered to tilapia for 20 days (2x the recommended duration) at 0, 15, 45, or 75 mg/kg body weight/day (0, 1, 3, or 5x the recommended dose of 15 mg FFC/kg BW/d) was investigated. Mortality, behavioral change, feed consumption, body size, and gross and microscopic lesions were determined. Estimated delivered doses were >96.9% of target. Three unscheduled mortalities occurred but were considered incidental since FFC-related findings were not identified. Feed consumption was only affected during the last 10 dosing days when the 45 and 75 mg/kg groups consumed only 62.5% and 55.3% of the feed offered, respectively. There were significant, dose-dependent reductions in body size in the FFC-dose groups relative to the controls. Treatment-related histopathological findings included increased severity of lamellar epithelial hyperplasia, increased incidence of lamellar adhesions, decreased incidence of lamellar telangiectasis in the gills, increased glycogen-type and lipid-type hepatocellular vacuolation in the liver, decreased lymphocytes, increased blast cells, and increased individual cell necrosis in the anterior kidney, and tubular epithelial degeneration and mineralization in the posterior kidney. These changes are likely to be of minimal clinical relevance, given the lack of mortality or morbidity observed. This study has shown that FFC, when administered in feed to tilapia at the recommended dose (15 mg FFC/kg BW/day) for 10 days would be well tolerated.

Toxicologic Pathology↗

USGS2014

Dynamics of virus shedding and in situ confirmation of chelonid herpesvirus 5 in Hawaiian green turtles with Fibropapillomatosis

Cancers in humans and animals can be caused by viruses, but virus-induced tumors are considered to be poor sites for replication of intact virions (lytic replication). Fibropapillomatosis (FP) is a neoplastic disease associated with a herpesvirus, chelonid herpesvirus 5 (ChHV5), that affects green turtles globally. ChHV5 probably replicates in epidermal cells of tumors, because epidermal intranuclear inclusions (EIIs) contain herpesvirus-like particles. However, although EIIs are a sign of herpesvirus replication, they have not yet been firmly linked to ChHV5. Moreover, the dynamics of viral shedding in turtles are unknown, and there are no serological reagents to confirm actual presence of the specific ChHV5 virus in tissues. The investigators analyzed 381 FP tumors for the presence of EIIs and found that overall, about 35% of green turtles had lytic replication in skin tumors with 7% of tumors showing lytic replication. A few (11%) turtles accounted for more than 30% cases having lytic viral replication, and lytic replication was more likely in smaller tumors. To confirm that turtles were actively replicating ChHV5, a prerequisite for shedding, the investigators used antiserum raised against F-VP26, a predicted capsid protein of ChHV5 that localizes to the host cell nucleus during viral replication. This antiserum revealed F-VP26 in EIIs of tumors, thus confirming the presence of replicating ChHV5. In this light, it is proposed that unlike other virus-induced neoplastic diseases, FP is a disease that may depend on superspreaders, a few highly infectious individuals growing numerous small tumors permissive to viral production, for transmission of ChHV5.

Veterinary Pathology↗

USGS2017

Natural infections with pigeon paramyxovirus serotype 1: Pathologic changes in Eurasian collared-doves (Streptopelia decaocto) and rock pigeons (Columba livia) in the United States

Pigeon paramyxovirus serotype 1 (PPMV-1) is a globally distributed, virulent member of the avian paramyxovirus serotype 1 serogroup that causes mortality in columbiformes and poultry. Following introduction into the United States in the mid-1980s, PPMV-1 rapidly spread causing numerous mortality events in Eurasian collared-doves ( Streptopelia decaocto ) (ECDOs) and rock pigeons ( Columba livia ) (ROPIs). The investigators reviewed pathological findings of 70 naturally infected, free-ranging columbiforms from 25 different mortality events in the United States. Immunohistochemistry targeting PPMV-1 nucleoprotein was used to determine the tissue distribution of the virus in a subset of 17 birds from 10 of the studied outbreaks. ECDOs (61 birds) and ROPIs (9 birds) were the only species in which PPMV-1-associated disease was confirmed by viral isolation and presence of histologic lesions. Acute to subacute tubulointerstitial nephritis and necrotizing pancreatitis were the most frequent histologic lesions, with immunolabeling of viral antigen in renal tubular epithelial cells and pancreatic acinar epithelium. Lymphoid depletion of bursa of Fabricius and spleen was common, but the presence of viral antigen in these organs was inconsistent among infected birds. Hepatocellular necrosis was occasionally present with immunolabeling of hypertrophic Kupffer cells, and immunopositive eosinophilic intracytoplasmic inclusion bodies were present in hepatocytes of 1 ECDO. Immunopositive lymphocytic choroiditis was present in 1 ECDO, while lymphocytic meningoencephalitis was frequent in ROPIs in absence of immunolabeling. This study demonstrates widespread presence of PPMV-1 antigen in association with histologic lesions, confirming the lethal potential of this virus in these particular bird species.

Veterinary Pathology↗

USGS1998

Comparison of the membrane-filtration fluorescent antibody test, the enzyme-linked immunosorbent assay, and the polymerase chain reaction to detect Renibacterium salmoninarum in salmon ovarian fluid

Ovarian fluid samples from naturally infected chinook salmon ( Oncorhynchus tshawytscha ) were examined for the presence of Renibacterium salmoninarum by the membrane-filtration fluorescent antibody test (MF-FAT), an antigen capture enzyme-linked immunosorbent assay (ELISA), and a nested polymerase chain reaction (PCR). On the basis of the MF-FAT, 64% (66/103) samples contained detectable levels of R. salmoninarum cells. Among the positive fish, the R. salmoninarum concentrations ranged from 25 cells/ml to 4.3 × 10 9 cells/ml. A soluble antigenic fraction of R. salmoninarum was detected in 39% of the fish (40/103) by the ELISA. The ELISA is considered one of the most sensitive detection methods for bacterial kidney disease in tissues, yet it did not detect R. salmoninarum antigen consistently at bacterial cell concentrations below about 1.3 × 10 4 cells/ml according to the MF-FAT counts. When total DNA was extracted and tested in a nested PCR designed to amplify a 320-base-pair region of the gene encoding a soluble 57-kD protein of R. salmoninarum , 100% of the 100 samples tested were positive. The results provided strong evidence that R. salmoninarum may be present in ovarian fluids thought to be free of the bacterium on the basis of standard diagnostic methods.

Journal of Veterinary Diagnostic Investigation↗