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At least 325 records · Page 18Linked to original sources
USGS2006

Evolution of the CD4 family: teleost fish possess two divergent forms of CD4 in addition to lymphocyte activation gene-3

The T cell coreceptor CD4 is a transmembrane glycoprotein belonging to the Ig superfamily and is essential for cell-mediated immunity. Two different genes were identified in rainbow trout that resemble mammalian CD4. One (trout CD4) encodes four extracellular Ig domains reminiscent off mammalian CD4, whereas the other (CD4REL) codes for two Ig domains. Structural motifs within the amino acid sequences suggest that the two Ig domains of CD4REL duplicated to generate the four-domain molecule of CD4 and the related gene, lymphocyte activation gene-3. Here we present evidence that both of these molecules in trout are homologous to mammalian CD4 and that teleosts encode an additional CD4 family member, lymphocyte activation gene-3, which is a marker for activated T cells. The syntenic relationships of similar genes in other teleost and non-fish genomes provide evidence for the likely evolution of CD4-related molecules in vertebrates, with CD4REL likely representing the primordial form in fish. Expression of both CD4 genes is highest in the thymus and spleen, and mRNA expression of these genes is limited to surface IgM- lymphocytes, consistent with a role for T cell functionality. Finally, the intracellular regions of both CD4 and CD4REL possess the canonical CXC motif involved in the interaction off CD4 with p56LCK, implying that similar mechanisms for CD4 + T cell activation are present in all vertebrates. Our results therefore raise new questions about T cell development and functionality in lower vertebrates that cannot be answered by current mammalian models and, thus, is of fundamental importance for understanding the evolution of cell-mediated immunity in gnathosomes. Copyright ?? 2006 by The American Association of Immunologists, Inc.

Journal of Immunology↗
USGS2023

Examining dynamic occupancy of gray wolves in Idaho after a decade of managed harvest

Gray wolves ( Canis lupus ) were reintroduced to Idaho, USA, in 1995–1996. The removal of Endangered Species Act protections in 2011 transferred wolf management to the state where wolves were subsequently classified as a harvested (i.e., hunted, trapped) big game species. We implemented a camera-based survey across Idaho from 2016–2021 as part of a population monitoring program. We used the resulting camera images in multi-year, dynamic and single-season occupancy models to examine potential changes in the asymptotic proportion of area occupied by wolves and assess the effect of cumulative wolf harvest from 2016–2021 on occupancy in the last year of the study, 2021. We also wanted to understand how habitat, prey, humans, harvest, livestock, and prey-related wolf removals affected wolf occupancy through their effects on colonization and extinction of occupancy cells through time. Statewide wolf occupancy did not change appreciably over the course of our study, with the proportion of survey cells occupied at an estimated high of 0.44 ± 0.03 (SE) in 2018 and a low of 0.39 ± 0.03 in 2020. Wolf colonization (i.e., probability that a cell switched from unoccupied to occupied between years) was positively associated with forest cover, images of humans, and the percent of neighboring cells that were occupied. Cell extinction (i.e., probability of switching from occupied to unoccupied between years) was negatively associated with neighboring cell occupancy. There were non-linear relationships between wolf harvest, colonization, and extinction. The single-season occupancy model demonstrated a positive relationship between harvest and occupancy at low to moderate levels of harvest (10–30%), but there was also evidence that high levels of harvest (>30%) reduce occupancy. Our results indicate that although harvest might influence wolf occupancy at local scales, wolf occupancy remained relatively constant across the state and wolves remained well distributed across Idaho during the study.

Idaho↗
USGS2001

Effects of maturation-inducing hormone on heterologous gap junctional coupling in ovarian follicles of Atlantic croaker

A previous ultrastructural study of heterologous (granulosa cell-oocyte) gap junction (GJ) contacts in ovarian follicles of Atlantic croaker suggested that these contacts disappear late during the process of resumption of oocyte meiosis. This observation suggested that, unlike scenarios proposed for a number of other species, uncoupling of GJ is not necessary for the onset of meiotic resumption in croaker follicles. However, the functionality of heterologous GJ contacts and the temporal association between maturation-inducing hormone (MIH)-induced changes in heterologous coupling and resumption of oocyte meiosis have not been examined in Atlantic croaker. These questions were addressed with a cell-cell coupling assay that is based on the transfer of a GJ marker, Lucifer Yellow, from oocytes to granulosa cells. Follicle-enclosed oocytes injected with Lucifer Yellow allowed transfer of the dye into the follicle cell layer, thus confirming that there is functional heterologous coupling between the oocyte and the granulosa cells. Dye transfer was observed in vitellogenic, full-grown/maturation-incompetent, and full-grown /maturation-competent follicles. Treatment of maturation-competent follicles with MIH caused a time-dependent decline in the number of follicles transferring dye. However, although GJ uncoupling in some of the follicles was observed before germinal vesicle breakdown (GVBD, index of meiotic resumption), about 50% of the follicles maintained the ability to transfer dye even after GVBD had occurred. Further, a known GJ inhibitor (phorbol 12-myristate 13-acetate) blocked heterologous GJ within a time frame similar to that seen with MIH but without inducing any of the morphological changes (including GVBD) associated with follicular maturation. In conclusion, uncoupling of heterologous GJ seems insufficient and unnecessary for the onset of meiotic resumption in ovarian follicles of Atlantic croaker. ?? 2001 Elsevier Science.

General and Comparative Endocrinology↗
USGS1992

Determining baselines and variability of elements in plants and soils near the Kenai National Wildlife Refuge, Alaska

Recent investigations on the Kenai Peninsula had two major objectives: (1) to establish elemental baseline concentrations ranges for native vegetation and soils; and, (2) to determine the sampling density required for preparing stable regional geochemical maps for various elements in native plants and soils. These objectives were accomplished using an unbalanced, nested analysis-of-variance (ANOVA) barbell sampling design. Hylocomium splendens (Hedw.) BSG (feather moss, whole plant), Picea glauca (Moench) Voss (white spruce, twigs and needles), and soil horizons (02 and C) were collected and analyzed for major and trace total element concentrations. Using geometric means and geometric deviations, expected baseline ranges for elements were calculated. Results of the ANOVA show that intensive soil or plant sampling is needed to reliably map the geochemistry of the area, due to large local variability. For example, producing reliable element maps of feather moss using a 50 km cell (at 95% probability) would require sampling densities of from 4 samples per cell for Al, Co, Fe, La, Li, and V, to more than 15 samples per cell for Cu, Pb, Se, and Zn.Recent investigations on the Kenai Peninsula had two major objectives: (1) to establish elemental baseline concentrations ranges for native vegetation and soils; and, (2) to determine the sampling density required for preparing stable regional geochemical maps for various elements in native plants and soils. These objectives were accomplished using an unbalanced, nested analysis-of-variance (ANOVA) barbell sampling design. Hylocomium splendens (Hedw.) BSG (feather moss, whole plant), Picea glauca (Moench) Voss (white spruce, twigs and needles), and soil horizons (02 and C) were collected and analyzed for major and trace total element concentrations. Using geometric means and geometric deviations, expected baseline ranges for elements were calculated. Results of the ANOVA show that intensive soil or plant sampling is needed to reliably map the geochemistry of the area, due to large local variability. For example, producing reliable element maps of feather moss using a 50 km cell (at 95% probability) would require sampling densities of from 4 samples per cell Al, Co, Fe, La, Li, and V, to more than 15 samples per cell for Cu, Pb, Se, and Zn.

Water, Air, & Soil Pollution↗
USGS2005

Factors affecting the toxicity of methylmercury injected into eggs

We developed a standardized protocol for comparing the sensitivities of the embryos of different bird species to methylmercury when methylmercury was injected into their eggs. During the course of developing this protocol, we investigated the effects of various factors on the toxicity of the injected methylmercury. Most of our experiments were done with chicken ( Gallus domesticus ), mallard ( Anas platyrhynchos ), and ring-necked pheasant ( Phasianus colchicus ) eggs, all of which were purchased in large numbers from game farms. A smaller amount of work was done with double-crested cormorant ( Phalacrocorax auritus ) eggs collected from the wild. Several solvents were tested, and corn oil at a rate of 1 μl/g egg contents was selected for the final standardized protocol because it had minimal toxicity to embryos and because methylmercury dissolved in corn oil yielded a dose–response curve in a range of egg concentrations that was similar to the range that causes reproductive impairment when the mother deposits methylmercury into her own eggs. The embryonic stage at which eggs were injected with corn oil altered mercury toxicity; at early stages, the corn oil itself was toxic. Therefore, in the final protocol we standardized the time of injection to occur when each species reached the morphologic equivalent of a 3-day-old chicken embryo. Although solvents can be injected directly into the albumen of an egg, high embryo mortality can occur in the solvent controls because of the formation of air bubbles in the albumen. Our final protocol used corn oil injections into the air cell, which are easier and safer than albumen injections. Most of the methylmercury, when dissolved in corn oil, injected into the air cell passes through the inner shell membrane and into the egg albumen. Most commercial incubators incubate eggs in trays with the air cell end of the egg pointing upward, but we discovered that mercury-induced mortality was too great when eggs were held in this orientation. In addition, some species of bird eggs require incubation on their sides with the eggs being rolled 180° for them to develop normally. Therefore, we adopted a procedure of incubating the eggs of all species on their sides and rolling them 180° every hour. Little has been published about the conditions of temperature, humidity, and the movements to which eggs of wild birds need to be subjected for them to hatch optimally under artificial incubation. Not unexpectedly, hatching success in an artificial incubator is generally less than what natural incubation by the parents can achieve. However, the survival of control embryos of most wild bird species was good (generally ≥ 80%) up to within 1 or 2 days of hatching when we incubated the eggs at 37.5°C (or 37.6°C for gallinaceous species) at a relative humidity that resulted in an approximate 15% to 16% loss in egg weight by the end of incubation and by incubating the eggs on their sides and rolling them 180°/h. To improve statistical comparisons, we used survival through 90% of incubation as our measurement to compare survival of controls with survival of eggs injected with graded concentrations of mercury.

Archives of Environmental Contamination and Toxico↗
USGS2020

Modeling three-dimensional flow over spur-and-groove morphology

Spur-and-groove (SAG) morphology characterizes the fore reef of many coral reefs worldwide. Although the existence and geometrical properties of SAG have been well documented, an understanding of the hydrodynamics over them is limited. Here, the three-dimensional flow patterns over SAG formations, and a sensitivity of those patterns to waves, currents, and SAG geometry were characterized using the physics-based Delft3D-FLOW and SWAN models. Shore-normal shoaling waves over SAG formations were shown to drive two circulation cells: a cell on the lower fore reef with offshore flow over the spurs and onshore flow over the grooves, except near the seabed where velocities were always onshore, and a cell on the upper fore reef with offshore surface velocities and onshore bottom currents, which result in depth-averaged onshore and offshore flow over the spurs and grooves, respectively. The mechanism driving this flow results from the net of the radiation stress gradients and pressure gradient, which is balanced by the Reynolds stress gradients and bottom friction that differ over the spur and over the groove. Waves were the primary driver of variations in modelled flow over SAG, with the flow strength increasing for increasing wave heights and periods. Spur height, SAG wavelength, and the water depth at peak spur height were the dominant influences on the hydrodynamics, with spur heights directly proportional to the strength of SAG circulation cells. SAG formations with shorter SAG wavelengths only presented one circulation cell on the shallower portion of the reef, as opposed to the two circulation cells for longer SAG wavelengths. SAG formations with peak spur heights occurring in shallower water had stronger circulation than those with peak spur heights occurring in deeper water. These hydrodynamic patterns also likely affect coral and reef development through sediment and nutrient fluxes.

Coral Reefs↗
USGS2008

Downflow limestone beds for treatment of net-acidic, oxic, iron-laden drainage from a flooded Anthracite Mine, Pennsylvania, USA: 1. Field evaluation

Passive-treatment systems that route acidic mine drainage (AMD) through crushed limestone and/or organic-rich substrates have been used to remove the acidity and metals from various AMD sources, with a wide range of effects. This study evaluates treatment of net-acidic, oxic, iron-laden AMD with limestone alone, and with organic-rich compost layered with the limestone. In the fall of 2003, a treatment system consisting of two parallel, 500-m2 downflow cells followed by a 400-m2 aerobic settling pond and wetland was installed to neutralize the AMD from the Bell Mine, a large source of AMD and baseflow to the Schuylkill River in the Southern Anthracite Coalfield, in east-central Pennsylvania. Each downflow cell consisted of a lower substrate layer of 1,090 metric tons (t) of dolomitic limestone (60 wt% CaCO3) and an upper layer of 300 t of calcitic limestone (95 wt% CaCO3); one of the downflow cells also included a 0.3 m thick layer of mushroom compost over the limestone. AMD with pH of 3.5-4.3, dissolved oxygen of 6.6-9.9 mg/L, iron of 1.9-5.4 mg/L, and aluminum of 0.8-1.9 mg/L flooded each cell to a depth 0.65 m above the treatment substrates, percolated through the substrates to underlying, perforated outflow pipes, and then flowed through the aerobic pond and wetland before discharging to the Schuylkill River. Data on the flow rates and chemistry of the effluent for the treatment system indicated substantial neutralization by the calcitic limestone but only marginal effects from the dolomitic limestone or compost. Because of its higher transmissivity, the treatment cell containing only limestone neutralized greater quantities of acidity than the cell containing compost and limestone. On average, the treatment system removed 62% of the influent acidity, 47% of the dissolved iron, 34% of the dissolved aluminum, and 8% of the dissolved manganese. Prior to treatment of the Bell Discharge, the Schuylkill River immediately below its confluence with the discharge had pH as low as 4.1 and supported few, if any, fish. However, within the first year of treatment, the pH was maintained at values of 5.0 or greater and native brook trout were documented immediately below the treatment system, though not above. ?? 2008 Springer-Verlag.

Mine Water and the Environment↗
USGS1985

Sorption of lead onto two gram-negative marine bacteria in seawater

Laboratory adsorption experiments performed at environmentally significant lead (Pb) and cell concentrations indicate that the marine bacteria examined have significant binding capacities for Pb. However, the behavior governing Pb sorption onto gram-negative bacteria in seawater may be quite complex. The sorption kinetics appear to involve two distinct phases, i.e., a rapid removal of Pb from solution within the first few minutes, followed by a slow but nearly constant removal over many hours. Also, the average binding coefficient, calculated for Pb sorption onto bacteria and a measure of binding intensity, increases with decreasing sorption density (amounts of bacteria-associated Pb per unit bacterial surface) at low cell concentrations (10 5 cells ml −1 ), but decreases with decreasing sorption density at higher cell concentrations (10 7 cells ml −1 ). The latter effect is apparently due to the production of significant amounts of extra-cellular organics at high cell concentrations that compete directly with bacterial surfaces for available lead. Lead toxicity and active uptake by marine bacteria did not appear significant at the Pb concentrations used.

Marine Chemistry↗
USGS2000

Microscopic functional anatomy: Integumentary system: Chapter 17

Many of the features of the fish integument can only be observed microscopically. Because there are over 20,000 living fishes, mostly higher bony fishes (teleosts), a great diversity exists in the microscopic anatomy of the integument. This chapter presents several examples from varied taxonomic groups to illustrate the variation in morphological features. As in all vertebrate epidermis, the fundamental structural unit is the epithelial cell. This is the only constant feature, as a great diversity of cell types exists in the various fish taxa. Some of these include apocrine mucous cells and a variety of other secretory cells, ionocytes, sensory cells, and wandering cells such as leukocytes. The dermis consists essentially of two sets of collagen fibers arranged in opposing geodesic spirals around the body. The dermis of most fishes is divided into two major layers. The upper (outer) layer, the stratum spongiosum or stratum laxum, is a loose network of connective tissue, whereas the lower layer, the stratum compactum, is a dense layer consisting primarily of orthogonal collagen bands. There are also specialized dermal elements such as chromatophores scales, and fin rays.

Book chapter↗
USGS2018

Respiratory hazard assessment of combined exposure to complete gasoline exhaust and respirable volcanic ash in a multicellular human lung model at the air-liquid interface

Communities resident in urban areas located near active volcanoes can experience volcanic ash exposures during, and following, an eruption, in addition to sustained exposures to high concentrations of anthropogenic air pollutants ( e.g., vehicle exhaust emissions). Inhalation of anthropogenic pollution is known to cause the onset of, or exacerbate, respiratory and cardiovascular diseases. It is further postulated similar exposure to volcanic ash can also affect such disease states. Understanding of the impact of combined exposure of volcanic ash and anthropogenic pollution to human health, however, remains limited. The aim of this study was to assess the biological impact of combined exposure to respirable volcanic ash (from Soufrière Hills volcano (SHV), Montserrat and Chaitén volcano (ChV), Chile; representing different magmatic compositions and eruption styles) and freshly-generated complete exhaust from a gasoline vehicle. A multicellular human lung model (an epithelial cell-layer composed of A549 alveolar type II-like cells complemented with human blood monocyte-derived macrophages and dendritic cells cultured at the air-liquid interface) was exposed to diluted exhaust (1:10) continuously for 6 h, followed by immediate exposure to the ash as a dry powder (0.54 ± 0.19 μg/cm 2 and 0.39 ± 0.09 μg/cm 2 for SHV and ChV ash, respectively). After an 18 h incubation, cells were exposed again for 6 h to diluted exhaust, and a final 18 h incubation (at 37 °C and 5% CO 2 ). Cell cultures were then assessed for cytotoxic, oxidative stress and (pro-)inflammatory responses. Results indicate that, at all tested (sub-lethal) concentrations, co-exposures with both ash samples induced no significant expression of genes associated with oxidative stress ( HMOX1, NQO1 ) or production of (pro-)inflammatory markers (IL-1β, IL-8, TNF-α) at the gene and protein levels. In summary, considering the employed experimental conditions, combined exposure of volcanic ash and gasoline vehicle exhaust has a limited short-term biological impact to an advanced lung cell in vitro model.

Environmental Pollution↗
USGS2002

An unusual occurrence of arsenic-bearing pyrite in the Upper Freeport coal bed, West-Central Pennsylvania

Scanning electron microscopy and electron microprobe analysis were used to identify a rare type of As-bearing pyrite in selected specific gravity separates from the Pennsylvanian age Upper Freeport coal bed, west-central Pennsylvania. Arsenic was detected mainly in cell-wall replacement pyrite where concentrations ranged from nondetectable to 1.9 wt %. Although the majority of arsenic-bearing pyrite in the Upper Freeport coal bed is concentrated in massive and late diagenetic pyrite morphologies, the rarer As-bearing cell-replacement pyrite was observed in both light and heavy gravity separates from the three coal facies examined. Arsenic was occasionally detected in cell-filling replacement pyrite, but this As appears to be an artifact produced by signals from underlying and/or adjacent As-bearing cell-wall replacement pyrite. It is postulated that some plants of the Upper Freeport paleoswamp may have biomethylated As, which later could have been converted to dimethylarsine or other volatile organoarsenic compounds by either biologically or chemically driven processes. Once liberated, the arsenic may have been incorporated into pyrite during pyritization of the cell walls. The As incorporation occurred early, before significant compaction of the peat, because the pyritized cell walls are not compacted.

Pennsylvania↗
USGS1998

Closing the gap between regional and global travel time tomography

Recent global travel time tomography studies by Zhou [1996] and van der Hilst et al . [1997] have been performed with cell parameterizations of the order of those frequently used in regional tomography studies (i.e., with cell sizes of 1°–2°). These new global models constitute a considerable improvement over previous results that were obtained with rather coarse parameterizations (5° cells). The inferred structures are, however, of larger scale than is usually obtained in regional models, and it is not clear where and if individual cells are actually resolved. This study aims at resolving lateral heterogeneity on scales as small as 0.6° in the upper mantle and 1.2°–3° in the lower mantle. This allows for the adequate mapping of expected small-scale structures induced by, for example, lithosphere subduction, deep mantle upwellings, and mid-ocean ridges. There are three major contributions that allow for this advancement. First, we employ an irregular grid of nonoverlapping cells adapted to the heterogeneous sampling of the Earth's mantle by seismic waves [ Spakman and Bijwaard , 1998]. Second, we exploit the global data set of Engdahl et al . [1998], which is a reprocessed version of the global data set of the International Seismological Centre. Their reprocessing included hypocenter redetermination and phase reidentification. Finally, we combine all data used ( P , pP , and pwP phases) into nearly 5 million ray bundles with a limited spatial extent such that averaging over large mantle volumes is prevented while the signal-to-noise ratio is improved. In the approximate solution of the huge inverse problem we obtain a variance reduction of 57.1%. Synthetic sensitivity tests indicate horizontal resolution on the scale of the smallest cells (0.6° or 1.2°) in the shallow parts of subduction zones decreasing to approximately 2°–3° resolution in well-sampled regions in the lower mantle. Vertical resolution can be worse (up to several hundreds of kilometers) in subduction zones with rays predominantly pointing along dip. Important features of the solution are as follows: 100–200 km thick high-velocity slabs beneath all major subduction zones, sometimes flattening in the transition zone and sometimes directly penetrating into the lower mantle; large high-velocity anomalies in the lower mantle that have been attributed to subduction of the Tethys ocean and the Farallon plate; and low-velocity anomalies continuing across the 660 km discontinuity to hotspots at the surface under Iceland, east Africa, the Canary Islands, Yellowstone, and the Society Islands. Our findings corroborate that the 660 km boundary may resist but not prevent (present day) large-scale mass transfer from upper to lower mantle or vice versa. This observation confirms the results of previous, global mantle studies that employed coarser parameterizations.

Journal of Geophysical Research B: Solid Earth↗
USGS2003

Importance of the predator's ecological neighborhood in modeling predation on migrating prey

Most mathematical descriptions of predator-prey interactions fail to take into account the spatio-temporal structures of the populations, which can lead to errors or misinterpretations. For example, a compact pulse of prey migrating through a field of quasi-stationary predators may not be well described by standard predator-prey models, because the predators and prey are unlikely to be well mixed; that is, the prey may be exposed to only a fraction of the predator population at a time. This underscores the importance of properly accounting for the ecological neighborhood, or effective feeding range, of predators in models. We illustrate this situation with a series of models of salmon smolts migrating through a reservoir arrayed with predators. The reservoir is divided into a number of longitudinal compartments or spatial cells, the length of each cell representing the upstream-downstream range over which predators can forage. In this series of models a 100-km-long reservoir is divided, successively into 2, 5, 10, 25, 50, 100, 200, and 400 cells, with respective cell lengths of 50, 20, 10, 4, 2, 1, 0.5, and 0.25 km. We used a detailed individual-based simulation model at first, but to ensure robustness of results we supplemented this with a simple analytic model. Both models showed sharp differences in the predicted mortality to a compact pulse of smolt prey moving through the reservoir, depending on the number of spatial cells in the model. In particular, models with fewer than about 10 cells vastly overpredicted the amount of mortality due to predators with activity ranges of not more than a few kilometers. These results corroborate recent theoretical and simulation studies on the importance of spatial scale and behavior in modeling predator-prey dynamics.

Oikos↗
USGS2007

Anemia and mechanism of erythrocyte destruction in ducks with acute Leucocytozoon infections

In the anemia which accompanies infection by Leucocytozoon simondi in Pekin ducks there was a far greater loss of erythrocytes than could be accounted for as a result of direct physical rupture by the parasite. Erythrocyte loss began at the same time the 1st parasites appeared in the blood and was severest just prior to maximum parasitemia. Blood replacement and parasite loss occurred simultaneously. Examination of the spleen and bone marrow revealed that erythrophagocytosis was not the cause of anemia as reported for infections of Plasmodium, Babesia and Anaplasma . An anti-erythrocyte (A-E) factor was found in the serum of acutely infected ducks which agglutinated and hemolyzed normal untreated duck erythrocytes as well as infected cells. This A-E factor appeared when the 1st red cell loss was detected and reached its maximum titer just prior to the greatest red cell loss. Titers of the A-E factor were determined using normal uninfected erythrocytes at temperatures between 4 and 42 C. Cells agglutinated below 25 C and hemolyzed at 37 and 42 C. These results indicated that the A-E factor could be responsible for loss of cells other than those which were infected and could thus produce an excess loss of red cells.

Journal of Protozoology↗
USGS2012

On modeling weak sinks in MODPATH

Regional groundwater flow systems often contain both strong sinks and weak sinks. A strong sink extracts water from the entire aquifer depth, while a weak sink lets some water pass underneath or over the actual sink. The numerical groundwater flow model MODFLOW may allow a sink cell to act as a strong or weak sink, hence extracting all water that enters the cell or allowing some of that water to pass. A physical strong sink can be modeled by either a strong sink cell or a weak sink cell, with the latter generally occurring in low resolution models. Likewise, a physical weak sink may also be represented by either type of sink cell. The representation of weak sinks in the particle tracing code MODPATH is more equivocal than in MODFLOW. With the appropriate parameterization of MODPATH, particle traces and their associated travel times to weak sink streams can be modeled with adequate accuracy, even in single layer models. Weak sink well cells, on the other hand, require special measures as proposed in the literature to generate correct particle traces and individual travel times and hence capture zones. We found that the transit time distributions for well water generally do not require special measures provided aquifer properties are locally homogeneous and the well draws water from the entire aquifer depth, an important observation for determining the response of a well to non-point contaminant inputs.

Ground Water↗
USGS2019

Changes in the active, dead, and dormant microbial community structure across a Pleistocene permafrost chronosequence

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19 thousand years (K), 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous ‘relic’ DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provides insights into the survival of microbial communities in ancient permafrost.

Alaska↗
USGS1993

Aerobic and anaerobic degradation of a range of alkyl sulfides by a denitrifying marine bacterium

A pure culture of a bacterium was obtained from a marine microbial mat by using an anoxic medium containing dimethyl sulfide (DMS) and nitrate. The isolate grew aerobically or anaerobically as a denitrifier on alkyl sulfides, including DMS, dimethyl disulfide, diethyl sulfide (DES), ethyl methyl sulfide, dipropyl sulfide, dibutyl sulfide, and dibutyl disulfide. Cells grown on an alkyl sulfide or disulfide also oxidized the corresponding thiols, namely, methanethiol, ethanethiol, propanethiol, or butanethiol. Alkyl sulfides were metabolized by induced or derepressed cells with oxygen, nitrate, or nitrite as electron acceptor. Cells grown on DMS immediately metabolized DMS, but there was a lag before DES was consumed; with DES-grown cells, DES was immediately used but DMS was used only after a lag. Chloramphenicol prevented the eventual use of DES by DMS-grown cells and DMS use by DES-grown cells, respectively, indicating separate enzymes for the metabolism of methyl and ethyl groups. Growth was rapid on formate, acetate, propionate, and butyrate but slow on methanol. The organism also grew chemolithotrophically on thiosulfate with a decrease in pH; growth required carbonate in the medium. Growth on sulfide was also carbonate dependent but slow. The isolate was identified as a Thiobacillus sp. and designated strain ASN-1. It may have utility for removing alkyl sulfides, and also nitrate, nitrite, and sulfide, from wastewaters.

Georgia↗
USGS1967

Low-temperature incubation using a water supply

Cell and tissue culture has been concerned primarily with homiothermic vertebrate cells which require incubation at about 37 C, and there is a great variety of incubators designed to maintain temperatures which are usually above ambient. The culture of poikilothermic vertebrate cells--and invertebrate, plant, and some microbial cells--can often be carried out at ambient temperatures, but for some work cooler conditions must be provided. Variety among the so-called low-temperature incubators is somewhat restricted; there are no small units, and all require a power source to maintain temperatures below ambient. We have used a gravity-fed water supply for 5 years to provide trouble-free, constant, low-temperature incubation of stock cultures of fish and amphibian cells. Though it is but a small part of our low-temperature incubator capacity, it has no power requirements and it provides maximal protection against temperature rises which could be lethal to some of the cell lines. Though the system has limitations, there is a considerable likelihood that the domestic water supply in other laboratories can also be used to provide low-temperature incubation.

Applied Microbiology↗