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 1,009 records · Page 56Linked to original sources

USGS2002

Persistence of tidally-oriented vertical migration by zooplankton in a temperate estuary

Tidal vertical migration by zooplankton is a common phenomenon in estuaries, usually associated with landward movement of meroplankton or position maintenance of holoplankton. Little is known about the persistence of this behavior, its spatial variability, or its response to changing environmental conditions. We extended a previous study of tidal movements of zooplankton in the low-salinity zone (LSZ) of the San Francisco estuary in 1994 to include data from two additional years with very different hydrology. Freshwater flow during sampling in 1995 was about 7-fold greater than in 1994; the LSZ was about 28 km further seaward, and gravitational circulation in the LSZ was strong. In 1996 freshwater flow and LSZ position were intermediate but, because the LSZ was in shallower water in 1996 than in 1995, gravitational circulation was uncommon. Behavior of copepods in both years was similar to that reported in 1994 with some tidal migration observed during most cruises. An exception was the introduced carnivorous copepod Tortanus dextrilobatus , which did not migrate and maintained a position deep in the water column (1995 only). In 1996, mysids mainly stayed near the bottom with evidence for vertical migration from only 1 of 6 data sets, whereas amphipods migrated slightly on a diel schedule; these behaviors contrasted with the tidal migration observed in 1994. The bay shrimp Crangon franciscorum did not appear to migrate, but was more abundant in the water column during both ebb and flood, suggesting passive vertical dispersal. Zooplankton did not appear to maintain position by interactions with lateral circulation cells. The results for copepods suggest rigidity in behavior with little or no relaxation of the vertical movement in 1995 when strong gravitational circulation would have made upstream movement relatively easy. Mysids and amphipods altered their behavior depending on local conditions related to freshwater flow.

California↗

USGS1998

Photoprotective substance occurs primarily in outer layers of fish skin

Methanol extracts of dorsal skin layers, eyes, gills, and livers from ultraviolet-B (UVB) radiation-sensitive and UVB-tolerant species of freshwater fish were examined for a substance that appears to be photoprotective. Significantly larger amounts of this substance were found in extracts of outer dorsal skin layers from both UVB-sensitive and UVB-tolerant fish when compared with extracts of inner dorsal skin layers. This substance occurred in minor amounts or was not detected in eye, gill, and liver extracts. The apparent primary function of this substance in fish is to protect the cells in outer dorsal skin layers from harmful levels of UVB radiation.

Environmental Science and Pollution Research↗

USGS2005

The inverse problem of refraction travel times, part II: Quantifying refraction nonuniqueness using a three-layer model

This paper is the second of a set of two papers in which we study the inverse refraction problem. The first paper, "Types of Geophysical Nonuniqueness through Minimization," studies and classifies the types of nonuniqueness that exist when solving inverse problems depending on the participation of a priori information required to obtain reliable solutions of inverse geophysical problems. In view of the classification developed, in this paper we study the type of nonuniqueness associated with the inverse refraction problem. An approach for obtaining a realistic solution to the inverse refraction problem is offered in a third paper that is in preparation. The nonuniqueness of the inverse refraction problem is examined by using a simple three-layer model. Like many other inverse geophysical problems, the inverse refraction problem does not have a unique solution. Conventionally, nonuniqueness is considered to be a result of insufficient data and/or error in the data, for any fixed number of model parameters. This study illustrates that even for overdetermined and error free data, nonlinear inverse refraction problems exhibit exact-data nonuniqueness, which further complicates the problem of nonuniqueness. By evaluating the nonuniqueness of the inverse refraction problem, this paper targets the improvement of refraction inversion algorithms, and as a result, the achievement of more realistic solutions. The nonuniqueness of the inverse refraction problem is examined initially by using a simple three-layer model. The observations and conclusions of the three-layer model nonuniqueness study are used to evaluate the nonuniqueness of more complicated n-layer models and multi-parameter cell models such as in refraction tomography. For any fixed number of model parameters, the inverse refraction problem exhibits continuous ranges of exact-data nonuniqueness. Such an unfavorable type of nonuniqueness can be uniquely solved only by providing abundant a priori information. Insufficient a priori information during the inversion is the reason why refraction methods often may not produce desired results or even fail. This work also demonstrates that the application of the smoothing constraints, typical when solving ill-posed inverse problems, has a dual and contradictory role when applied to the ill-posed inverse problem of refraction travel times. This observation indicates that smoothing constraints may play such a two-fold role when applied to other inverse problems. Other factors that contribute to inverse-refraction-problem nonuniqueness are also considered, including indeterminacy, statistical data-error distribution, numerical error and instability, finite data, and model parameters. ?? Birkha??user Verlag, Basel, 2005.

Pure and Applied Geophysics↗

USGS2010

Aftershock distribution as a constraint on the geodetic model of coseismic slip for the 2004 Parkfield earthquake

Several studies of the 2004 Parkfield earthquake have linked the spatial distribution of the event’s aftershocks to the mainshock slip distribution on the fault. Using geodetic data, we find a model of coseismic slip for the 2004 Parkfield earthquake with the constraint that the edges of coseismic slip patches align with aftershocks. The constraint is applied by encouraging the curvature of coseismic slip in each model cell to be equal to the negative of the curvature of seismicity density. The large patch of peak slip about 15 km northwest of the 2004 hypocenter found in the curvature-constrained model is in good agreement in location and amplitude with previous geodetic studies and the majority of strong motion studies. The curvature-constrained solution shows slip primarily between aftershock “streaks” with the continuation of moderate levels of slip to the southeast. These observations are in good agreement with strong motion studies, but inconsistent with the majority of published geodetic slip models. Southeast of the 2004 hypocenter, a patch of peak slip observed in strong motion studies is absent from our curvature-constrained model, but the available GPS data do not resolve slip in this region. We conclude that the geodetic slip model constrained by the aftershock distribution fits the geodetic data quite well and that inconsistencies between models derived from seismic and geodetic data can be attributed largely to resolution issues.

California↗

USGS1996

Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAl-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c -type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAl-1 differs from all other described bacteria, and represents the type strain of a new genus and species, Geovibrio ferrireducens .

Archives of Microbiology↗

USGS2005

Dissolved saxitoxin causes transient inhibition of sensorimotor function in larval Pacific herring (Clupea harengus pallasi) Kathi A. Lefebvre , N

Herring ( Clupea harengus pallasi ) spawning sites in Puget Sound, Washington overlap spatially and temporally with blooms of Alexandrium catenella , a toxic dinoflagellate species responsible for paralytic shellfish poisoning. Consequently, newly hatched herring larvae may be regularly exposed to the suite of dissolved paralytic shellfish toxins that are released into the water column from toxic cells during blooms. To date, virtually nothing is known about the impacts of these neurotoxins on early developmental stages of marine fish. In the present study, herring larvae at three ages, 0 days post hatch (dph), 4 dph, and 11 dph, were exposed to dissolved saxitoxin (STX) in 24-h and multi-day exposures. All larvae were examined for sensorimotor function (i.e. spontaneous swimming behavior and touch response). Significant reductions in spontaneous and touch-activated swimming behavior occurred within 1 h of exposure. EC 50 s at 1 h of exposure were 1,500, 840, and 700 μg STX equiv. l −1 for larvae introduced to STX at 0, 4, and 11 dph, respectively. This progressive age-specific increase in STX-induced paralysis suggests that older larvae were more sensitive to the toxin than younger larvae. Interestingly, herring larvae at all ages exhibited a significant degree of neurobehavioral recovery within 4–24 h of continuous exposure relative to the 1-h time point. This recovery of normal motor behaviors was not observed in previous studies with freshwater zebrafish ( Danio rerio ) larvae under the same continuous exposure conditions, suggesting that an adaptive detoxification or toxin sequestration mechanism may have evolved in some species of marine fish larvae. Our data reveal that (1) dissolved STX is bioavailable to marine finfish larvae, (2) the toxin is a paralytic agent with potencies that differ between developmental stages, and (3) STX-induced sensorimotor inhibition occurs rapidly but is transient in marine larvae. Collectively, these results suggest that dissolved algal toxins may have important sublethal effects on marine fish populations.

Marine Biology↗

USGS1997

Assimilation efficiencies and turnover rates of trace elements in marine bivalves: A comparison of oysters, clams and mussels

Assimilation efficiencies (AEs) and physiological turnover-rate constants ( k ) of six trace elements (Ag, Am, Cd, Co, Se, Zn) in four marine bivalves ( Crassostrea virginica Gmelin, Macoma balthica Linnaeus, Mercenaria mercenaria Linnaeus, and Mytilus edulis Linnaeus) were measured in radiotracer-depuration experiments. Egestion rates of unassimilated elements were highest during the first 24 h of depuration and declined thereafter. Significant egestion of unassimilated Co, however, continued for up to 5 d in Macoma balthica , Mercenaria mercenaria and Mytilus edulis . With the exception of the extremely low values for 110 m Ag, 109 Cd, and 65 Zn in C. virginica , physiological turnover-rate constants ( k ) showed no general pattern of variation among elements, bivalve species or food types, and were relatively invariant. Values from  ≤0.001 to 0.1 d −1 were observed, but excluding those for Co, most values were  ≤0.04 d −1 . In all four species, the AEs of Ag, Am, and Co were generally lower than those of Cd, Se, and Zn. The AEs of Ag, Cd, Se, and Zn in these bivalves are directly related to the proportion of each element in the cytoplasmic fraction of ingested phytoplankton, indicating that >80% of elements in a prey alga's cytoplasm was assimilated. C. virginica , Macoma balthica , and Mercenaria mercenaria assimilated &sim;36% of the Ag and Cd associated with the non-cytoplasmic (membrane/organelle) fraction of ingested cells in addition to the cytoplasmic fraction. The ratio of AE: k , which is proportional to the consumer–prey trace-element bioaccumulation factor (concentration in consumer:concentration in prey) was generally greater for Cd, Se, and Zn than for Ag, Am, and Co. This ratio was lowest in Mytilus edulis , suggesting that this bivalve, the most widely employed organism in global biomonitoring, is relatively inefficient at accumulating important elements such as Ag, Cd, and Zn from ingested phytoplankton.

Marine Biology↗

USGS2013

Toxic exposure of songbirds to lead in the Southeast Missouri Lead Mining District

Mining and smelting in the Southeast Missouri Lead Mining District has caused widespread contamination of soils with lead (Pb) and other metals. Soils from three study sites sampled in the district contained from approximately 1,000–3,200 mg Pb/kg. Analyses of earthworms [33–4,600 mg Pb/kg dry weight (dw)] collected in the district showed likely high Pb exposure of songbirds preying on soil organisms. Mean tissue Pb concentrations in songbirds collected from the contaminated sites were greater (p < 0.05) than those in songbirds from reference sites by factors of 8 in blood, 13 in liver, and 23 in kidney. Ranges of Pb concentrations in livers (mg Pb/kg dw) were as follows: northern cardinal (Cardinalis cardinalis) = 0.11–3.0 (reference) and 1.3–30 (contaminated) and American robin (Turdus migratorius) = 0.43–8.5 (reference) and 7.6–72 (contaminated). Of 34 adult and juvenile songbirds collected from contaminated sites, 11 (32 %) had hepatic Pb concentrations that were consistent with adverse physiological effects, 3 (9 %) with systemic toxic effects, and 4 (12 %) with life-threatening toxic effects. Acid-fast renal intranuclear inclusion bodies, which are indicative of Pb poisoning, were detected in kidneys of two robins that had the greatest renal Pb concentrations (952 and 1,030 mg/kg dw). Mean activity of the enzyme delta-aminolevulinic acid dehydratase (ALAD) in red blood cells, a well-established bioindicator of Pb poisoning in birds, was decreased by 58–82 % in songbirds from the mining sites. We conclude that habitats within the mining district with soil Pb concentrations of ≥1,000 mg Pb/kg are contaminated to the extent that they are exposing ground-feeding songbirds to toxic concentrations of Pb.

Missouri↗

USGS2000

Field evaluation of lead effects on Canada geese and mallards in the Coeur d'Alene River Basin, Idaho

Hatch year (HY) mallards ( Anas platyrhynchos ) in the Coeur d'Alene (CDA) River Basin had higher concentrations of lead in their blood than HY Western Canada geese ( Branta canadensis moffitti ) (geometric means 0.98 versus 0.28 μg/g, wet weight). The pattern for adults of both species was similar, although geometric means (1.77 versus 0.41 μg/g) were higher than in HY birds. HY mallards captured in the CDA River Basin in 1987 contained significantly lower lead concentrations in their blood than in 1994–95 (0.36 versus 0.98 μg/g); however, some very young mallards were sampled in 1987, and concentrations in adults were not significantly different in 1987, 1994, or 1995 (1.52, 2.07, 1.55 μg/g, respectively). Both species in the CDA River Basin in 1994–95 showed significantly reduced red blood cell delta-aminolevulinic acid dehydratase (ALAD) activity compared to the reference areas: Canada geese (HY −65.4 to −86.0%, adults −82.3%), and mallards (HY −90.7 to −95.5%, adults −94.1%). Canada goose goslings were divided into size classes, and the two smaller classes from the CDA River Basin had significantly elevated free erythrocyte protoporphyrin (protoporphyrin) levels compared to the reference area (15.2× and 6.9×). HY and adult mallards both had significantly elevated protoporphyrin (5.9× and 7.5×). Recognizing that interspecific differences exist in response and sensitivity to lead, it appears (at least for hemoglobin and hematocrit) that Canada geese were more sensitive to lead than mallards, i.e ., adverse hematologic effects occur at lower blood lead concentrations. Only Canada geese from the CDA River Basin, in spite of lower blood lead concentrations, had significantly reduced mean hemoglobin and hematocrit values. No euthanized Canada geese (all HYs) from CDA River Basin were classified as clinically lead poisoned, but 38 Canada geese found dead in the CDA River Basin during a concurrent study succumbed to lead poisoning between 1992 and 1997. Only 6 (15.8%) of these 38 contained ingested lead shot, which contrasts greatly with the 75–94% incidence of ingested lead shot when mortality was due to lead shot ingestion. Lead from other contaminated sources ( i.e ., sediments and vegetation) in the CDA River Basin was strongly implicated in most Canada goose deaths. Based on the 31 live mallards and Canada geese collected in the CDA River Basin, which were representative of the live populations blood sampled only, the prevalence of subclinical and clinical lead poisoning (as determined by liver lead concentrations, excluding birds with ingested lead shot) was higher in mallards: subclinical (4 of 8, 50% HYs and 6 of 11, 55% adults); clinical (0% HYs and 4 of 11, 36% adults), with less data available for Canada geese (only 1 of 9, 11% HYs marginally subclinical). The clinically lead-poisoned mallards had extremely high concentrations of lead in blood (2.69–8.82 μg/g) and liver (6.39–17.89 μg/g). Eight mallards found dead in the CDA River Basin during a concurrent study were diagnosed as lead poisoned, and only one (12.5%) contained ingested lead shot, which again strongly implicates other lead sources. The finding of dead lead poisoned Canada geese together with the high percentage of live mallards classified as subclinically or clinically lead poisoned, in combination with the low incidence of ingested lead shot causes us concern for both of these species, which live in association with lead-contaminated sediment in the CDA River Basin.

Idaho↗

USGS2000

Developmental toxicity of lead-contaminated sediment to mallard ducklings

Sediment ingestion has been identified as an important exposure route for toxicants in waterfowl. The toxicity of lead-contaminated sediment from the Coeur d'Alene River Basin (CDARB) in Idaho was examined on posthatching development of mallard ( Anas platyrhynchos ) ducklings for 6 weeks. Day-old ducklings received either untreated control diet, clean sediment (24%) supplemented control diet, CDARB sediment (3,449 μg/g lead) supplemented diets at 12% or 24%, or a positive control diet containing lead acetate equivalent to that found in 24% CDARB. The 12% CDARB diet resulted in a geometric mean blood lead concentration of 1.41 ppm (WW) with over 90% depression of red blood cell ALAD activity and over threefold elevation of free erythrocyte protoporphyrin concentration. The 24% CDARB diet resulted in blood lead of 2.56 ppm with over sixfold elevation of protoporphyrin and lower brain weight. In this group the liver lead concentration was 7.92 ppm (WW), and there was a 40% increase in hepatic reduced glutathione concentration. The kidney lead concentration in this group was 7.97 ppm, and acid-fast inclusion bodies were present in the kidneys of four of nine ducklings. The lead acetate positive control group was more adversely affected in most respects than the 24% CDARB group. With a less optimal diet (mixture of two thirds corn and one third standard diet), CDARB sediment was more toxic; blood lead levels were higher, body growth and liver biochemistry (TBARS) were more affected, and prevalence of acid-fast inclusion bodies increased. Lead from CDARB sediment accumulated more readily in duckling blood and liver than reported in goslings, but at given concentrations was generally less toxic to ducklings. Many of these effects are similar to ones reported in wild mallards and geese within the CDARB.

Idaho↗

USGS2001

Development of marine toxicity data for ordnance compounds

A toxicity database for ordnance compounds was generated using eight compounds of concern and marine toxicity tests with five species from different phyla. Toxicity tests and endpoints included fertilization success and embryological development with the sea urchin Arbacia punctulata ; zoospore germination, germling length, and cell number with the green macroalga Ulva fasciata ; survival and reproductive success of the polychaete Dinophilus gyrociliatus ; larvae hatching and survival with the redfish Sciaenops ocellatus ; and survival of juveniles of the opossum shrimp Americamysis bahia (formerly Mysidopsis bahia ). The studied ordnance compounds were 2,4- and 2,6-dinitrotoluene, 2,4,6-trinitrotoluene, 1,3-dinitrobenzene, 1,3,5-trinitrobenzene, 2,4,6-trinitrophenylmethylnitramine (tetryl), 2,4,6-trinitrophenol (picric acid), and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). The most sensitive toxicity test endpoints overall were the macroalga zoospore germination and the polychaete reproduction tests. The most toxic ordnance compounds overall were tetryl and 1,3,5-trinitrobenzene. These were also the most degradable compounds, often being reduced to very low or below-detection levels at the end of the test exposure. Among the dinitro- and trinitrotoluenes and benzenes, toxicity tended to increase with the level of nitrogenation. Picric acid and RDX were the least toxic chemicals tested overall.

Archives of Environmental Contamination and Toxico↗

USGS1998

The influence of extraction procedure on ion concentrations in sediment pore water

Sediment pore water has the potential to yield important information on sediment quality, but the influence of isolation procedures on the chemistry and toxicity are not completely known and consensus on methods used for the isolation from sediment has not been reached. To provide additional insight into the influence of collection procedures on pore water chemistry, anion (filtered only) and cation concentrations were measured in filtered and unfiltered pore water isolated from four sediments using three different procedures: dialysis, centrifugation, and vacuum. Peepers were constructed using 24-cell culture plates and cellulose membranes and vacuum extractors consisted of fused-glass air stones attached with airline tubing to 60-cc syringes. Centrifugation was accomplished at two speeds (2,500 and 10,000 g ) for 30 min in a refrigerated centrifuge maintained at 4°C. Only minor differences in chemical characteristics and cation and anion concentrations were found among the different collecting methods with differences being sediment-specific. Filtering of the pore water did not appreciably reduce major cation concentrations, but trace metals (Cu and Pb) were markedly reduced. Although the extraction methods evaluated produced pore waters of similar chemistries, the vacuum extractor provided the following advantages over the other methods: ease of extraction, volumes of pore water isolated, minimal preparation time, and least time required for extraction of pore water from multiple samples at one time.

Archives of Environmental Contamination and Toxico↗

USGS2000

Mixed-function oxygenases, oxidative stress, and chromosomal damage measured in lesser scaup wintering on the Indiana Harbor Canal

During the winter of 1993-1994, male lesser scaup ( Aythya alfinis ) were collected on the heavily polluted Indiana Harbor Canal, East Chicago, Indiana, and examined for several bioindicators of chemical exposure. Livers were analyzed for activities of three cytochrome P450-associated monooxygenases and four measures of oxidative stress. Blood and spleen were analyzed by flow cytometry for chromosomal damage. In a concurrent study, scaup tissues were analyzed for organic and inorganic contaminants. Ethoxyresomfm-O-dealkylase (EROD) activity in livers of scaup collected in January 1994 was significantly higher than in livers of scaup collected in March 1994 or in livers of reference birds. Three hepatic monooxygenase activities were each significantly correlated with polycyclic aromatic hydrocarbon (PAH) concentrations in scaup carcasses. Thiobarbituric acid (TBA) activity in scaup livers was positively correlated with iron, boron, and lead concentrations in livers and polychlorinated biphenyl concentrations in carcasses. TBA activity was negatively correlated with protein-bound thiol activity and mercury concentrations in livers. The coefficient of variation of DNA content in scaup blood cells was correlated with PAH concentrations in scaup carcasses. This is the first field study with birds to demonstrate a correlation between liver monooxygenase activity and carcass PAH concentrations and to show a direct correlation between PAH concentrations in tissues and somatic chromosomal damage in blood.

Indiana↗

USGS2004

The occurrence of lysogenic bacteria and microbial aggregates in the lakes of the McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys of Antarctica form the coldest and driest ecosystem on Earth. Within this region there are a number of perennially ice-covered (3–6 m thick) lakes that support active microbial assemblages and have a paucity of metazoans. These lakes receive limited allochthonous input of carbon and nutrients, and primary productivity is limited to only 6 months per year owing to an absence of sunlight during the austral winters. In an effort to establish the role that bacteria and their associated viruses play in carbon and nutrient cycling in these lakes, indigenous bacteria, free bacteriophage, and lysogen abundances were determined. Total bacterial abundances (TDC) ranged from 3.80 × 10 4 to 2.58 × 10 7 cells mL −1 and virus-like particle (VLP) abundances ranged from 2.26 × 10 5 to 5.56 × 10 7 VLP mL −1 . VLP abundances were significantly correlated ( P < 0.05) with TDC, bacterial productivity (TdR), chlorophyll a (Chl a ), and soluble reactive phosphorus (SRP). Lysogenic bacteria, determined by induction with mitomycin C, made up between 2.0% and 62.5% of the total population of bacteria when using significant decreases and increases in TDC and VLP abundances, respectively, and 89.5% when using increases in VLP abundances as the sole criterion for a successful induction event. The contribution of viruses released from induced lysogens contributed <0.015% to the total viral production rate. Carbohydrate and protein based organic aggregates were abundant within the water column of the lakes and were heavily colonized by bacteria and VLPs. Alkaline phosphatase activity was detected within the matrix of the aggregates, implying phosphorus deficiency and consortial nutrient exchanges among microorganisms.

Microbial Ecology↗

USGS2012

Free tropospheric transport of microorganisms from Asia to North America

Microorganisms are abundant in the troposphere and can be transported vast distances on prevailing winds. This study measures the abundance and diversity of airborne bacteria and fungi sampled at the Mt. Bachelor Observatory (located 2.7 km above sea level in North America) where incoming free tropospheric air routinely arrives from distant sources across the Pacific Ocean, including Asia. Overall deoxyribonucleic acid (DNA) concentrations for microorganisms in the free troposphere, derived from quantitative polymerase chain reaction assays, averaged 4.94 × 10(-5) ng DNA m(-3) for bacteria and 4.77 × 10(-3) ng DNA m(-3) for fungi. Aerosols occasionally corresponded with microbial abundance, most often in the springtime. Viable cells were recovered from 27.4 % of bacterial and 47.6 % of fungal samples (N = 124), with 49 different species identified by ribosomal DNA gene sequencing. The number of microbial isolates rose significantly above baseline values on 22-23 April 2011 and 13-15 May 2011. Both events were analyzed in detail, revealing distinct free tropospheric chemistries (e.g., low water vapor, high aerosols, carbon monoxide, and ozone) useful for ruling out boundary layer contamination. Kinematic back trajectory modeling suggested air from these events probably originated near China or Japan. Even after traveling for 10 days across the Pacific Ocean in the free troposphere, diverse and viable microbial populations, including presumptive plant pathogens Alternaria infectoria and Chaetomium globosum, were detected in Asian air samples. Establishing a connection between the intercontinental transport of microorganisms and specific diseases in North America will require follow-up investigations on both sides of the Pacific Ocean.

Microbial Ecology↗

USGS2006

Identification and regulatory analysis of rainbow trout tapasin and tapasin-related genes

Tapasin (TAPBP) is a key member of MHC class Ia antigen-loading complexes, bridging the class Ia molecule to the transporter associated with antigen presentation (TAP). As part of an ongoing study of MHC genomics in rainbow trout, we have identified two rainbow trout TAPBP genes (Onmy-TAPBP.a and .b) and a similar but distinct TAPBP-related gene (Onmy-TAPBP-R) that had previously only been described in mammals. Physical and genetic mapping indicate that Onmy-TAPBP.a is on chromosome 18 in the MHC class Ia region and that Onmy-TAPBP.b resides on chromosome 14 in the MHC class Ib region. There are also at least two copies of TAPBP-R, Onmy-TAPBP-R.a and Onmy-TAPBP-R.b, located on chromosomes 2 and 3, respectively. Due to the central role of TAPBP expression during acute viral infection, we have characterized the transcriptional profile and regulatory regions for both Onmy-TAPBP and Onmy-TAPBP-R. Transcription of both genes increased during acute infection with infectious hematapoeitic necrosis virus (IHNV) in a fashion indicative of interferon-mediated regulation. Promoter-reporter assays in STE-137 cells demonstrate that the trout TAPBP and TAPBP-R promoters respond to interferon regulatory factors, Onmy-IRF1 and Onmy-IRF2. Overall, TAPBP is expressed at higher levels than TAPBP-R in nai??ve tissues and TAPBP transcription is more responsive to viral infection and IRF1 and 2 binding. ?? Springer-Verlag 2006.

Immunogenetics↗

USGS2017

Extensive shared polymorphism at non-MHC immune genes in recently diverged North American prairie grouse

Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time, but under strong balancing selection it may persist for millions of years beyond species divergence (balanced trans-species polymorphism), as in the case of the major histocompatibility complex (MHC) genes. However, balancing selection is much less likely to act on non-MHC immune genes. The aim of this study was to investigate the patterns of shared polymorphism and selection at non-MHC immune genes in five grouse species from Centrocercus and Tympanuchus genera. For this purpose, we genotyped five non-MHC immune genes that do not interact directly with pathogens, but are involved in signaling and regulate immune cell growth. In contrast to previous studies with MHC, we found no evidence for balancing selection or balanced trans-species polymorphism among the non-MHC immune genes. No haplotypes were shared between genera and in most cases more similar allelic variants sorted by genus. Between species within genera, however, we found extensive shared polymorphism, which was most likely attributable to introgression or incomplete lineage sorting following recent divergence and large ancestral effective population size (i.e., weak genetic drift). Our study suggests that North American prairie grouse may have attained relatively low degree of reciprocal monophyly at nuclear loci and reinforces the rarity of balancing selection in non-MHC immune genes.

Immunogenetics↗

USGS2019

Functional variation at an expressed MHC class IIß locus associates with Ranavirus infection intensity in larval anuran populations

Infectious diseases are causing catastrophic losses to biodiversity globally. Iridoviruses in the genus Ranavirus are among the leading causes of amphibian disease-related mortality. Polymorphisms in major histocompatibility complex (MHC) genes are significantly associated with variation in amphibian susceptibility to pathogens. MHC genes encode diverse cell-surface molecules that can recognize and bind to a wide array of pathogen peptides, and are divided into two classes. While MHC class I genes are the classic mediators of viral acquired immunity, larval amphibians do not express them. However, MHC class II gene diversity may be an important predictor of Ranavirus susceptibility in larval amphibians, the life stage most susceptible to Ranavirus. We surveyed natural populations of larval wood frogs (Lithobates sylvaticus), which are highly susceptible to Ranavirus, across 17 ponds and two years in Maryland, USA. We sequenced the peptide-binding region of an expressed MHC class IIß locus and assessed allelic and genetic diversity. We converted alleles to functional supertypes and determined if physiochemical properties of peptide-binding regions influenced host responses to Ranavirus. Among 334 sampled individuals, 26% were infected with Ranavirus, and among infected individuals the average intensity was 7.12 x 107 virus copies. We recovered 20 unique MHC class IIß alleles that fell into two deeply diverged clades and seven functional supertypes. Variation in MHC supertypes were associated with Ranavirus infection intensity, but not prevalence. MHC supertype heterozygotes and individuals with the MHC supertype genotype ST1/ST7 had significantly lower Ranavirus infection intensity compared to homozygotes and all other genotypes. We conclude that MHC class IIß functional genetic variation is an important component of Ranavirus susceptibility. Identifying immune system gene signatures linked to variation in disease susceptibility can inform mitigation strategies for combatting global amphibian declines.

Immunogenetics↗