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USGS2022

Acetylenotrophic and diazotrophic Bradyrhizobium sp. strain I71 from TCE-contaminated soils

Abstract Acetylene (C 2 H 2 ) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus’ economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. Importance The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium . These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.

California↗

USGS1966

Tropical lakes, copropel, and oil shale

During a long-continued study of the lacustrine beds of the Eocene Green River Formation, I have tried to interpret past events from observation of present-day processes. After a search of some 40 years, four lakes have been found that are producing a kind of organic ooze judged to be a modern analogue of the precursors of rich oil shale. Two of the lakes are in central Africa and two are in Florida. All four are shallow. The ooze in all four is predominantly algal, entirely in the form of minute fecal pellets, and does not decay in warm, wet, oxidizing environments. Several of the most unusual, mummified microorganisms found in the oil shale of the Green River are illustrated as testament to the inference that the Eocene organic oozes also were resistant to decay. Studies to determine why these algal oozes do not decay are in progress, but as yet no satisfactory explanation is available. The ooze from Mud Lake, Florida, contains very few living bacteria but a great many bacterial spores, suggesting some active inhibitor. Gentle and slow anaerobic decay takes place in the ooze 1 foot or more below the mud-water interface. The algal ooze accumulates slowly. That at a depth of 3 feet below the mud-water interface has a C 14 age of 2280 ± 200 years. If compacted, this 3-foot layer would amount to a layer only about 0.5 inch thick. The air-dried algal mud (from Mud Lake) looks much like oil shale and has a C-H ratio essentially like that of the organic matter in oil shale. The oxygen of the mud, however, is roughly 5 times as high as in oil shale. The calorific value of dried Mud Lake algal ooze is about 6600 cal/g, whereas the organic matter from Green River oil shale averages about 9500 cal/g. Analyses show that the dried algal ooze from Mud Lake contains small quantities of higher fatty acids (C 12 –C 34 ), with C 16 being dominant. It also contains some unsaturated fatty acids and about 0.3 per cent of n-alkanes, predominantly odd carbons, with C 29 being dominant. A few qualitative analyses show that carotenoid pigments and terpenes are also present. A possible source of hydrocarbons is the long branched side chain of the chlorophyll molecule. Small crustaceans liberate this in the form of phytol, which, by dehydration, can go over into a series of saturated and unsaturated hydrocarbons, including phytanc and pristane, both of which are common in Green River oil shale. Search for other precursors of hydrocarbons continues.

GSA Bulletin↗

USGS1974

Garnet-clinopyroxenite from the Red Mountain pluton, Alaska

Several lens-shaped and irregular masses of garnet-clinopyroxenite occur along the north margin of the Red Mountain pluton, near Seldovia, Alaska. The pluton is composed of intercalated dunite, clinopyroxenite, and banded chromite layers. The chromite layers appear to dip toward the center of the mass, but they have been deformed, and in some places display isoclinal overturned folds. The garnet-clinopyroxenite bodies are compositionally layered and appear to have been deformed along with the host peridotite. The garnet-clinopyroxenite bodies have whole-rock compositions analogous to alkali-poor anorthite gabbro or mafic anorthosite. Garnet compositions are dominated by the pyrope, grossularite, and almandine components, and the clinopyroxene bodies are rich in Ca-Tschermaks molecule (CaAl 2 SiO 6 ). Although crystallization from the liquidus is a possibility, textures, structures, and the chemical composition of the constituent mineral phases indicate that the garnet-clinopyroxenite has equilibrated in the solid state at pressures of 15 to 25 kb and temperatures of 1100°C to 1300°C. Such P-T parameters suggest an upper-mantle origin for the garnet-clinopyroxenite and the enclosing pluton.

Alaska↗

USGS2001

Fractionation of Fe isotopes by soil microbes and organic acids

Small natural variations in Fe isotopes have been attributed to biological cycling. However, without understanding the mechanism of fractionation, it is impossible to interpret such variations. Here we show that the δ 56 Fe of Fe dissolved from a silicate soil mineral by siderophore-producing bacteria is as much as 0.8% lighter than bulk Fe in the mineral. A smaller isotopic shift is observed for Fe released abiotically by two chelates, and the magnitude of the shift increases with affinity of the ligand for Fe, consistent with a kinetic isotope effect during hydrolysis of Fe at the mineral surface. Fe dissolved abiotically without chelates shows no isotopic shift. The δ 56 Fe of the exchange fraction on soil grains is also lighter by ~0.6%-1% than Fe from both hornblende and iron oxyhydroxides. The kinetic isotope effect is therefore preserved in open systems such as soils. when recorded in the rock record, Fe isotopic fractionation could document Fe transport by organic molecules or by microbes where such entities were present in the geologic past.

Geology↗

USGS1969

Geology and regional metamorphism of some high-grade cordierite gneisses, Front Range, Colorado

Cordierite is common in regional metamorphic gneisses of Precambrian age in the central part of the Front Range. It occurs in discontinuous stratigraphic units that are structurally a minor component, except locally, of the thick succession of biotite gneisses that comprise the widespread Idaho Springs Formation. The rocks have mineral assemblages, that are characteristic of the sillimanite grade of metamorphism. The cordierite occurs in three principal rock types: (1) potassic feldspar-bearing cordierite-garnet-sillimanite-biotite gneiss, (2) cordierite-biotite gneiss, and (3) cordierite-gedrite-biotite gneiss; each type contains several characteristic mineral assemblages. The rock types are gradational and overlap in areal distribution, and mainly owe their diversity in mineralogy to differences in bulk chemical composition. The field relations are consistent with an interpretation that the diverse cordierite rocks were derived from original sedimentary rocks, largely pelitic sediments. The potassic feldspar-bearing cordierite-garnet gneisses were formed from shales that contained more MgO and FeO than the more abundant sedimentary facies that yielded sillimanitic biotite gneisses. Cordierite-gedrite-biotite gneisses contain much aluminum, iron, and magnesium and little sodium and potassium as compared to the other biotite gneisses; they have an extremely low content of minor elements. Although their chemical compositions are unlike those of known modern sediments, the cordierite-gedrite gneisses are considered also to have been derived from sedimentary rocks. The physical properties and chemical compositions of the mineral phases vary somewhat from one rock type to another. Biotite varies systematically in composition, and the changes are closely related to rock type and thus to bulk composition; the MgO/FeO ratios range from 1.7 in the more mafic cordierite-gedrite rocks to 0.49 in potassic feldspar-bearing cordierite-garnet gneisses. Cordierite is magnesium-rich and intermediate in the range of composition of all analyzed cordierites (Leake, 1960); its MgO/FeO ratio is higher in the gedrite-bearing gneisses than in the potassic feldspar-bearing gneisses. The garnets consist dominantly of the almandine and pyrope molecules, and range from 64 to 75 percent almandine and from 14 to 27 pyrope. These crystals are zoned; their rims are slightly more ferrous and less magnesian than their cores. Both monoclinic and triclinic alkali feldspars coexist in the potassic feldspar-bearing cordierite-garnet gneisses. The potassic feldspars contain from 18 to 27 weight percent NaAlSi 3 O 8 . Plagioclase (oligoclase-andesine) is uncommon in the rocks. Gedrite has an MgO/FeO ratio ranging from 1 to 1.2. Associated minor minerals include iron oxides, andalusite, spinel and its alteration product högbomite, and corundum. The mineral assemblages can be correlated imperfectly with episodes of deformation and metamorphism. Relict staurolite and associated garnet occur locally as remnants of an assemblage formed early in regional metamorphism, presumably early in the first period of deformation. The dominant assemblage biotite-cordierite-garnet-magnetite-plagioclase-potassic feldspar-quartz-sillimanite and associated assemblages having fewer phases, were formed during period one and period two deformations, the principal episodes of regional dynamothermal metamorphism in the central part of the Front Range. A minor assemblage andalusite-biotite-magnetite-plagioclase-quartz was formed later, possibly coincident with a third period of deformation, largely cataclastic in effects, which was more local than the earlier deformations and metamorphism. Phase equilibria studies of the assemblage biotite-cordierite-garnet-magnetite-plagioclase-potassic feldspar-quartz-sillimanite and associated assemblages are interpreted to indicate that the cordierite assemblages approach a state of chemical equilibrium. The scatter of points in a distribution diagram can be interpreted in terms of at least two sets of equilibrium conditions that prevailed during the major plastic deformations. Other discrepancies indicating departure from a homogeneous equilibrium can be explained as a result of mosaic equilibrium involving limited diffusion of iron and magnesium for short distances. The mineral assemblages and the compositions of the ferromagnesian minerals in the cordierite rocks of this region are dependent primarily on the bulk composition of the rocks and variations in the mineral species that comprise the rocks and, to a lesser degree, on the grade of metamorphism. Biotite and cordierite are markedly more magnesian in the more mafic cordierite-gedrite-biotite gneiss than in the potassic feldspar-bearing cordierite-garnet-sillimanite-biotite gneiss. Associated microcline gneiss and biotite-sillimanite gneiss that contains muscovite as a primary stable mineral provides a means to define the metamorphic grade in the area of study. It is concluded from analyses of the assemblages with respect to theoretical phase relations in the system SiO 2 -Al 2 O 3 -Na 2 O-K 2 O-H 2 O that at least some of the rocks in the Central City-Nederland area are above the sillimanite-potassic feldspar isograd as defined by Evans and Guidotti (1966). In rocks of appropriate composition, muscovite is a stable phase in assemblages containing potassic feldspar and sillimanite. The cordierite assemblages and associated rocks are inferred to have formed in an environment having a load pressure of 3–5 kilobars (fluid pressure equaled load pressure) and a temperature somewhat in excess of 620° C.

Colorado↗

USGS2003

Chemosterilization of male sea lampreys ( Petromyzon marinus ) does not affect sex pheromone release

Release of males sterilized by injection with bisazir is an important experimental technique in management of sea lamprey ( Petromyzon marinus ), an invasive, nuisance species in the Laurentian Great Lakes. Sea lampreys are semelparous and sterilization can theoretically eliminate a male's reproductive capacity and, if the ability to obtain mates is not affected, waste the sex products of females spawning with him. It has been demonstrated that spermiating males release a sex pheromone that attracts ovulating females. We demonstrated that sterilized, spermiating males also released the pheromone and attracted ovulating females. In a two-choice maze, ovulating females increased searching behavior and spent more time in the side of the maze containing chemical stimuli from sterilized, spermiating males. This attraction response was also observed in spawning stream experiments. Also, electro-olfactograms showed that female olfactory organs were equally sensitive to chemical stimuli from sterilized and nonsterilized, spermiating males. Finally, fast atom bombardment mass spectrometry showed that extracts from water conditioned with sterilized and nonsterilized, spermiating males contained the same pheromonal molecule at similar levels. We concluded that injection of bisazir did not affect the efficacy of sex pheromone in sterilized males.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1975

Effects of pH on toxicity of antimycin to fish

Detoxification of antimycin at pH 9.5 was caused by two factors. The piscicide was biologically unavailable at the high pH, and this unavailability was reversed by decreasing the pH of water solutions. Simultaneously antimycin detoxified with time, and the resulting loss in toxicity was irreversible. The toxicity of antimycin was related to the amount of un-ionized molecules; however, the dissociation curve resulting from the published pKa of 5.1 does not agree with the implied dissociation when based on toxicity. Toxicity of antimycin decreased gradually from pH 6.5 to 8.5 and abruptly from 8.5 to 9.5 with carp ( Cyprinus carpio ), green sunfish ( Lepomis cyanellus ), and bluegill ( Lepomis macrochirus ). As previously suggested, water hardness had little or no effect on toxicity.

Journal of the Fisheries Research Board of Canada↗

USGS1993

Mitochondrial DNA variation in chinook salmon and chum salmon detected by restriction enzyme analysis of polymerase chain reaction products

We analyze intraspecific mitochondrial DNA variation in chinook salmon from drainages in the Yukon River, the Kenai River, and Oregon and California rivers; and chum salmon from the Yukon River and vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified seperately using the polymerase chain reaction and then digested with at least 19 restrictions enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base subsitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (8) occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rviers and four occurred in the Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock seperation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2012

Thermally dried ink-jet process for 6,13-bis(triisopropylsilylethynyl)-pentacene for high mobility and high uniformity on a large area substrate

In this study we developed a simple ink-jet process for 6,13-bis(triisopropylsilylethynyl)-pentacene (TIPS-pentacene), which is known as a high-mobility soluble organic semiconductor, to achieve relatively high-mobility and high-uniformity performance for large-area applications. We analyzed the behavior of fluorescent particles in droplets and applied the results to determining a method of controlling the behavior of TIPS-pentacene molecules. The grain morphology of TIPS-pentacene varied depending on the temperature applied to the droplets during drying. We were able to obtain large and uniform grains at 46 degrees C without any "coffee stain". The process was applied to a large-size organic thin-film transistor (OTFT) backplane for an electrophoretic display panel containing 192 x 150 pixels on a 6-in.-sized substrate. The average of mobilities of 36 OTFTs, which were taken from different locations of the backplane, was 0.44 +/- 0.08 cm 2 .V -1 .s -1 , with a small deviation of 20%, over a 6-in.-size area comprising 28,800 OTFTs. This process providing high mobility and high uniformity can be achieved by simply maintaining the whole area of the substrate at a specific temperature (46 degrees C in this case) during drying of the droplets.

Japanese Journal of Applied Physics↗

USGS2022

Characterization of arsenic species in microbial mats from an inactive gold mine

Filamentous cyanobacterial mats and Fe oxyhydroxide-rich bacterial mats collected near an inactive gold mine in California are enriched in arsenic (As) approximately 1000-fold relative to the waters in contact with them. The predominant organism in the cyanobacterial mat could not be identified using morphological characteristics, but the unique morphology of the sheath-forming β protobacterium Leptothrix ochracea was used to identify this species in Fe oxyhydroxide mat samples from several sites near the gold mine. Leptothrix sheaths commonly exceed 10 μm in length and have an average diameter of 1 μm . The Fe-oxyhydroxide mats are dominated by L. ochracea sheaths, but use of fluorescently tagged genetic stains reveals the presence of sheathless bacteria that presumably also promote the formation of Fe oxyhydroxide. X-ray absorption fine structure (XAFS) spectroscopy was used to identify As species in these microbial mats. Mat-associated As is predominantly As(V), even when As(III) is the primary dissolved species in contact with the mats. The species of As(V) associated with the cyanobacterial mat could not be conclusively identified; however, it is not associated with Fe oxyhydroxide or other minerals, based on comparison to XAFS spectra of As adsorbed to various substrates. In addition, the cyanobacterial mat XAFS spectrum is different from that of aqueous As(V), suggesting that As(V) in the mat lacks some or all of the coordinating water molecules present in aqueous solution. We hypothesize that As is associated with the exopolysaccharide (EPS) matrix secreted by the cyanobacteria. In Leptothrix -dominated Fe-oxyhydroxide bacterial mats, XAFS analysis clearly indicates that As(V) is associated with the Fe oxyhydroxide as an adsorbed and/or coprecipitated complex.

California↗

USGS2018

A reexamination of the turquoise group: The mineral aheylite, planerite (redefined), turquoise and coeruleolactite

The turquoise group has the general formula: A (sub 0-1) B 6 (PO 4 ) (sub 4-x) (PO 3 OH) x (OH) 8 .4H 2 O, where x = 0-2, and consists of six members: planerite, turquoise, faustite, aheylite, chalcosiderite and an unnamed Fe (super 2+) -Fe (super 3+) analogue. The existence of "coeruleolactite" is doubtful. Planerite is revalidated as a species and is characterized by a dominant A-site vacancy. Aheylite is established as a new member of the group, and is characterized by having Fe (super 2+) dominant in the A-site. Chemical analyses of 15 pure samples of microcrystalline planerite, turquoise, and aheylite show that a maximum of two of the (PO 4 ) groups are protonated (PO 3 OH) in planerite. Complete solid solution exists between planerite and turquoise. Other members of the group show variable A-site vacancy as well. Most samples of "turquoise" are cation-deficient or are planerite. Direct determination of water indicates that there are 4 molecules of water. Planerite, ideally []Al 6 (PO 4 ) 2 (PO 3 OH) 2 (OH) 8 .4H 2 O, is white, pale blue or pale green, and occurs as mamillary, botryoidal crusts as much as several mm thick; may also be massive; microcrystalline, crystals typically 2-4 micrometres, luster chalky to earthy, H. 5, somewhat brittle, no cleavage observed, splintery fracture, D m 2.68(2), D c 2.71, not magnetic, not fluorescent, mean RI about 1.60. a 7.505(2), b 9.723(3), c 7.814(2) Aa, alpha 111.43 degrees , beta 115.56 degrees , Gamma 68.69 degrees , V 464.2(1) Aa 3 , Z = 1. Aheylite, ideally Fe (super 2+) Al 6 (PO 4 ) 4 (OH) 8 .4H 2 O, is pale blue or green, and occurs as isolated and aggregate clumps of hemispherical or spherical, radiating to interlocked masses of crystals that average 3 micrometres in maximum dimension; porcelaneous-subvitreous luster, moderate to brittle tenacity, no cleavage observed, hackly to splintery fracture, not magnetic, not fluorescent, biax. (+), mean RI is about 1.63, D m 2.84(2), D c 2.90. a 7.400(1), b 9.896(1), c 7.627(1) Aa, alpha 110.87 degrees , beta 115.00 degrees , gamma 69.96 degrees , V 460.62(9) Aa 3 , Z = 1.

Mineralogical Magazine↗

USGS2013

Pheromonal bile acid 3-ketopetromyzonol sulfate primes the neuroendocrine system in sea lamprey

Background Vertebrate pheromones are known to prime the endocrine system, especially the hypothalamic-pituitary-gonadal (HPG) axis. However, no known pheromone molecule has been shown to modulate directly the synthesis or release of gonadotropin releasing hormone (GnRH), the main regulator of the HPG axis. We selected sea lamprey (Petromyzon marinus) as a model system to determine whether a single pheromone component alters the output of GnRH. Sea lamprey male sex pheromones contain a main component, 7α, 12α, 24-trihydroxy-5α-cholan-3-one 24-sulfate (3 keto-petromyzonol sulfate or 3kPZS), which has been shown to modulate behaviors of mature females. Through a series of experiments, we tested the hypothesis that 3kPZS modulates both synthesis and release of GnRH, and subsequently, HPG output in immature sea lamprey. Results The results showed that natural male pheromone mixtures induced differential steroid responses but facilitated sexual maturation in both sexes of immature animals (χ2 = 5.042, dF = 1, p < 0.05). Exposure to 3kPZS increased plasma 15α-hydroxyprogesterone (15α-P) concentrations (one-way ANOVA, p < 0.05) and brain gene expressions (genes examined: three lamprey (l) GnRH-I transcripts, lGnRH-III, Jun and Jun N-terminal kinase (JNK); one-way ANOVA, p < 0.05), but did not alter the number of GnRH neurons in the hypothalamus in immature animals. In addition, 3kPZS treatments increased lGnRH peptide concentrations in the forebrain and modulated their levels in plasma. Overall, 3kPZS modulation of HPG axis is more pronounced in immature males than in females. Conclusions We conclude that a single male pheromone component primes the HPG axis in immature sea lamprey in a sexually dimorphic manner.

BMC Neuroscience↗

USGS2010

The impact of hydrate saturation on the mechanical, electrical, and thermal properties of hydrate-bearing sand, silts, and clay

Proper understanding of the physical properties of hydrate-bearing sediments is required for interpretation of borehole logs and exploration geophysical data, the analysis of borehole and submarine slope stability, and the formulation of reservoir simulation and production models. Yet current knowledge of geophysical and geotechnical properties of hydrate-bearing sediments is still largely derived from laboratory experiments conducted on disparate soils at different confining pressures, degrees of water saturation, and hydrate concentrations and with hydrates formed by methods unlike those that predominate in nature. We conducted a comprehensive laboratory program using sand, silts, and clay subjected to various confining effective stress levels in standardized geotechnical laboratory devices and containing carefully controlled saturations of tetrahydrofuran (THF) hydrate formed from the dissolved phase. Here, we undertake complete analysis of the trends in the measured geophysical and geotechnical properties (e.g., seismic velocities, strength, electrical conductivity and permittivity, and thermal conductivity) as a function of hydrate saturation, soil characteristics, and effective stress. Results reveal that the electrical properties of hydrate-bearing sediments are not very sensitive to the laboratory method used to form hydrate, which controls the pore-scale arrangement of hydrate and sediment grains, but are sensitive to hydrate saturation. Mechanical properties are strongly influenced by both soil properties and the hydrate formation method. Thermal conductivity depends on the complex interplay of a variety of factors, including formation history, and cannot be easily predicted by volume average formulations but will remain within physical upper and lower bounds. When hydrate forms from dissolved phase guest molecules, the resulting mathematical trends for all physical properties require that the hydrate saturation Sh in pore space, which is a quantity between 0≤ Sh ≤1.0 , be raised to a power greater than 1. This significantly reduces the impact of low-hydrate saturations on the measured physical parameters, an effect that is particularly pronounced at the hydrate saturations characteristic of many natural systems (<0.2 of pore space).

Book chapter↗

USGS2024

Adsorption of benzene, toluene, and xylene by two tetramethylammonium-smectites having different charge densities

A high-charge smectite from Arizona [cation-exchange capacity (CEC) = 120 meq/100 g] and a low-charge smectite from Wyoming (CEC = 90 meq/100 g) were used to prepare homoionic tetramethylammonium (TMA)-clay complexes. The adsorption of benzene, toluene, and o-xylene as vapors by the dry TMA-clays and as solutes from water by the wet TMA-clays was studied. The adsorption of the organic vapors by the dry TMA-smectite samples was strong and apparently consisted of interactions with both the aluminosilicate mineral surfaces and the TMA exchange ions in the interlayers. In the adsorption of organic vapors, the closer packing of TMA ions in the dry high-charge TMA-smectite, compared with the dry low-charge TMA-smectite, resulted in a somewhat higher degree of shape-selective adsorption of benzene, toluene, and xylene. In the presence of water, the adsorption capacities of both samples for the aromatic compounds were significantly reduced, although the uptake of benzene from water by the low-charge TMA-smectite was still substantial. This lower sorption capacity was accompanied by increased shape-selectivity for the aromatic compounds. The reduction in uptake and increased selectivity was much more pronounced for the water-saturated, high-charge TMA-smectite than for the low-charge TMA-smectite. Hydration of the TMA exchange ions and/or the mineral surfaces apparently reduced the accessibility of the aromatic molecules to interlamellar regions. The resulting water-induced sieving effect was greater for the high-charge TMA-smectite due to the higher density of exchanged TMA-ions. The low-charge Wyoming TMA-smectite was a highly effective adsorbent for removing benzene from water and may be useful for purifying benzene-contaminated water.

Clays and Clay Minerals↗

USGS2012

The genome of Chelonid herpesvirus 5 harbors atypical genes

The Chelonid fibropapilloma-associated herpesvirus (CFPHV; ChHV5) is believed to be the causative agent of fibropapillomatosis (FP), a neoplastic disease of marine turtles. While clinical signs and pathology of FP are well known, research on ChHV5 has been impeded because no cell culture system for its propagation exists. We have cloned a BAC containing ChHV5 in pTARBAC2.1 and determined its nucleotide sequence. Accordingly, ChHV5 has a type D genome and its predominant gene order is typical for the varicellovirus genus within the alphaherpesvirinae . However, at least four genes that are atypical for an alphaherpesvirus genome were also detected, i.e. two members of the C-type lectin-like domain superfamily (F-lec1, F-lec2), an orthologue to the mouse cytomegalovirus M04 (F-M04) and a viral sialyltransferase (F-sial). Four lines of evidence suggest that these atypical genes are truly part of the ChHV5 genome: (1) the pTARBAC insertion interrupted the UL52 ORF, leaving parts of the gene to either side of the insertion and suggesting that an intact molecule had been cloned. (2) Using FP-associated UL52 (F-UL52) as an anchor and the BAC-derived sequences as a means to generate primers, overlapping PCR was performed with tumor-derived DNA as template, which confirmed the presence of the same stretch of “atypical” DNA in independent FP cases. (3) Pyrosequencing of DNA from independent tumors did not reveal previously undetected viral sequences, suggesting that no apparent loss of viral sequence had happened due to the cloning strategy. (4) The simultaneous presence of previously known ChHV5 sequences and F-sial as well as F-M04 sequences was also confirmed in geographically distinct Australian cases of FP. Finally, transcripts of F-sial and F-M04 but not transcripts of lytic viral genes were detected in tumors from Hawaiian FP-cases. Therefore, we suggest that F-sial and F-M04 may play a role in FP pathogenesis

Hawaii↗

USGS2007

Molecular ecology of the big brown bat (Eptesicus fuscus): Genetic and natural history variation in a hybrid zone

Several geographically distinct mitochondrial DNA (mtDNA) lineages of the big brown bat (Eptesicus fuscus) have been documented in North America. Individuals from 2 of these lineages, an eastern and a western form, co-occur within maternity colonies in Colorado. The discovery of 2 divergent mtDNA lineages in sympatry prompted a set of questions regarding possible biological differences between haplotypes. We captured big brown bats at maternity roosts in Colorado and recorded data on body size, pelage color, litter size, roosting and overwintering behaviors, and local distributions. Wing biopsies were collected for genetic analysis. The ND2 region of the mtDNA molecule was used to determine lineage of the bats. In addition, nuclear DNA (nDNA) intron 1 of the ??-globin gene was used to determine if mtDNA lineages are hybridizing. Eastern and western mtDNA lineages differed by 10.3% sequence divergence and examination of genetic data suggests recent population expansion for both lineages. Differences in distribution occur along the Colorado Front Range, with an increasing proportion of western haplotypes farther south. Results from nDNA analyses demonstrated hybridization between the 2 lineages. Additionally, no outstanding distinctiveness was found between the mtDNA lineages in natural history characters examined. We speculate that historical climate changes separated this species into isolated eastern and western populations, and that secondary contact with subsequent interbreeding was facilitated by European settlement. ?? 2007 American Society of Mammalogists.

Journal of Mammalogy↗

USGS1990

Organic matter and thermochemical sulfate reduction in the Viburnum Trend, southeast Missouri

The role of organic matter in Mississippi Valley-type Pb-Zn deposits has been studied by systematically sampling and characterizing various types of organic matter in the Upper Cambrian Bonneterre formation in lead-zinc mines from the Viburnum Trend and from rocks as far as 20 km away from the Trend. Organic matter that is several kilometers from ore consists of insoluble disseminated kerogen in carbonates. Kerogen from brown dolostones yields mainly n-alkane pyrolysis products up to approximately n-C 20 H 42 , whereas gray and white carbonates that are poorer in organic carbon give much smaller quantities of pyrolysis products. Within meters to centimeters of ore in the Milliken mine, at the south end of the Viburnum Trend, organic matter occurs as solid, partly soluble tacky bitumen and insoluble hard blebs of millimeter to centimeter size. These hydrocarbon materials also yield n-alkane pyrolysis products up to C 20 . In contrast, the solid insoluble organic matter in intimate contact (intergrown) with ore (galena and chalcopyrite) is friable and brittle. Products from pyrolysis-gas chromatography-mass spectrometry of this material are quite different from the kerogen in rocks or the hydrocarbon blebs; they are substituted aromatic molecules such as toluene and methyl naphthalene, rather than n-alkanes.The sulfur content of solid organic matter from the Milliken mine varies and is lowest for tacky material away from ore, intermediate for blebs near ore, and highest for friable material in intimate contact with ore.Pyrolysis-gas chromatography of this sample suite documents the progression of kerogen (far from ore) through solid petroleumlike material (near ore) to degraded organic matter (in contact with ore). The change in the organic matter from n-alkane to a hydrogen poorer aromatic character with a higher sulfur content when associated with sulfide ores, suggests that chemical reactions such as nonbiological (thermochemical) sulfate reduction, which consume hydrogen and produce reactive sulfur, were responsible for organic degradation.

Economic Geology↗

USGS1992

Organic matter diagenesis as the key to a unifying theory for the genesis of tabular uranium-vanadium deposits in the Morrison Formation, Colorado Plateau

Interstitial, epigenetic amorphous organic matter is intimately associated with uranium in the Grants uranium region on the southern part of the Colorado Plateau in northwestern New Mexico and is considered essential to genetic models for these deposits. In contrast, uranium minerals are intimately associated with authigenic vanadium chlorite and vanadium oxides in amorphous organic matter-poor ores of the Slick Rock and Henry Mountains mining districts on the northern part of the plateau, and therefore, in some genetic models amorphous organic matter is not considered crucial to the formation of these deposits. Differences in organic matter content can be explained by recognizing that amorphous organic matter-poor deposits have been subjected to more advanced stages of diagenesis than amorphous organic matter-rich deposits, during which organic compounds were broken down, solubilized, and removed during various diagenetic stages (e.g., sulfate reduction, methanogenesis, and organic acid production). Most diagenetic alterations (e.g., dissolution of framework grains and cements and precipitation of coarse-grained coffinite, vanadium clays, and vanadium oxides) characteristic of amorphous organic matter-poor deposits occurred when temperatures exceeded 80 degrees C--a temperature typical of the organic acid stage of diagenesis.Two factors combined to assure that a high percentage of the amorphous organic matter was removed from the Morrison Formation during diagenesis: the fact that the organic matter was humic (and therefore highly oxygenated), and that the juxtaposition of authigenic smectite and amorphous organic matter on grain rims facilitated clay mineral-organic catalysis reactions leading to the breakdown of large organic molecules into smaller, soluble molecules.Evidence that amorphous organic matter was involved in the genesis of organic matter-poor, as well as organic matter-rich, deposits includes the presence of leached iron-titanium oxides and strongly etched garnets (both attributed to leaching by organic acids), the gradation from organic matter-rich to organic matter-poor deposits in the Grants uranium region, the inverse correlation between the amount of amorphous organic matter and the intensity of diagenetic alteration, the ubiquitous occurrence of amorphous organic matter inclusions in coffinite, and the similarity in geometry of tabular uranium-vanadium ores and Holocene humate deposits. By recognizing that amorphous organic matter was crucial to the initial concentration of uranium (even in those deposits that presently contain little amorphous organic matter) and by recognizing the effects of the various stages of diagenesis on the ore, one genetic model may be applied to all of the sandstone-hosted, tabular-type uranium-vanadium deposits in the Morrison Formation on the Colorado Plateau.

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