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At least 109 records · Page 6Linked to original sources

USGS2011

Experimental determination of the phase boundary between kornelite and pentahydrated ferric sulfate at 0.1MPa

Recent findings of various ferric sulfates on Mars emphasize the importance of understanding the fundamental properties of ferric sulfates at temperatures relevant to that of Martian surface. In this study, the phase boundary between kornelite (Fe2(SO4)3.7H2O) and pentahydrated ferric sulfate (Fe2(SO4)3.5H2O) was experimentally determined using the humidity-buffer technique together with gravimetric measurements and Raman spectroscopy at 0.1MPa in the 36-56??C temperature range. Through the thermodynamic analysis of our experimental data, the enthalpy change (-290.8??0.3kJ/mol) and the Gibbs free energy change (-238.82??0.02kJ/mol) for each water molecule of crystallization in the rehydration of pentahydrated ferric sulfate to kornelite were obtained. ?? 2011 Elsevier B.V.

Chemical Geology↗

USGS2010

Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss)

Induction of innate immune pathways is critical for early anti-microbial defense but there is limited understanding of how teleosts recognize microbial molecules and activate these pathways. In mammals, Toll-like receptors (TLR) 1 and 2 form a heterodimer involved in recognizing peptidoglycans and lipoproteins of microbial origin. Herein, we identify and describe the rainbow trout (Oncorhynchus mykiss) TLR1 gene ortholog and its mRNA expression. Two TLR1 loci were identified from a rainbow trout bacterial artificial chromosome (BAC) library using DNA sequencing and genetic linkage analyses. Full length cDNA clone and direct sequencing of four BACs revealed an intact omTLR1 open reading frame (ORF) located on chromosome 14 and a second locus on chromosome 25 that contains a TLR1 pseudogene. The duplicated trout loci exhibit conserved synteny with other fish genomes that extends beyond the TLR1 gene sequences. The omTLR1 gene includes a single large coding exon similar to all other described TLR1 genes, but unlike other teleosts it also has a 5' UTR exon and intron preceding the large coding exon. The omTLR1 ORF is predicted to encode an 808 amino-acid protein with 69% similarity to the Fugu TLR1 and a conserved pattern of predicted leucine-rich repeats (LRR). Phylogenetic analysis grouped omTLR1 with other fish TLR1 genes on a separate branch from the avian TLR1 and mammalian TLR1, 6 and 10. omTLR1 expression levels in rainbow trout anterior kidney leukocytes were not affected by the human TLR2/6 and TLR2/1 agonists diacylated lipoprotein (Pam2CSK4) and triacylated lipoprotein (Pam3CSK4). However, due to the lack of TLR6 and 10 genes in teleost genomes and up-regulation of TLR1 mRNA in response to LPS and bacterial infection in other fish species we hypothesize an important role for omTLR1 in anti-microbial immunity. Therefore, the identification of a TLR2 ortholog in rainbow trout and the development of assays to measure ligand binding and downstream signaling are critical for future elucidation of omTLR1 functions.

Fish and Shellfish Immunology↗

USGS2016

Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha

Adult Chinook salmon ( Oncorhynchus tshawytscha ) migrate from salt water to freshwater streams to spawn. Immune responses in migrating adult salmon are thought to diminish in the run up to spawning, though the exact mechanisms for diminished immune responses remain unknown. Here we examine both adaptive and innate immune responses as well as pathogen burdens in migrating adult Chinook salmon in the Upper Willamette River basin. Messenger RNA transcripts encoding antibody heavy chain molecules slightly diminish as a function of time, but are still present even after fish have successfully spawned. In contrast, the innate anti-bacterial effector proteins present in fish plasma rapidly decrease as spawning approaches. Fish also were examined for the presence and severity of eight different pathogens in different organs. While pathogen burden tended to increase during the migration, no specific pathogen signature was associated with diminished immune responses. Transcript levels of the immunosuppressive cytokines IL-10 and TGF beta were measured and did not change during the migration. These results suggest that loss of immune functions in adult migrating salmon are not due to pathogen infection or cytokine-mediated immune suppression, but is rather part of the life history of Chinook salmon likely induced by diminished energy reserves or hormonal changes which accompany spawning.

Oregon↗

USGS2020

Investigating the effects of broad ion beam milling to sedimentary organic matter: Surface flattening or heat-induced aromatization and condensation?

Previous work has proposed transfer of kinetic heat energy from low-energy broad ion beam (BIB) milling causes thermal alteration of sedimentary organic matter, resulting in increases of organic matter reflectance. Whereas, other studies have suggested the organic matter reflectance increase from BIB milling is due to decreased surface roughness. To test if reflectance increases to sedimentary organic matter (vitrinite) caused by BIB milling were related to molecular aromatization and condensation, Raman and Fourier transform infrared (FTIR) spectroscopies were used to evaluate potential compositional changes in the same vitrinite locations pre- and post-BIB milling. The same locations also were examined by atomic force microscopy (AFM) to determine topographic changes caused by BIB milling (as quantified by the areal root-mean-square roughness parameter S q ). Samples consisted of four medium volatile bituminous coals. A non-aggressive BIB milling approach was used with conditions of 5 min, 4 keV, 15°incline, 360° rotation at 25 rpm and 100% focus (1.5 kV discharge; ∼100 μA). This gentle BIB milling caused vitrinite reflectance (VR o ) increases of 12 to 36% of the original values determined optically before milling (average 26% increase). When molecular proxies from FTIR (A- and C-factor, branching ratio) were plotted against each other for the same vitrinite locations pre- and post-milling, mean data points for each sample generally lie within error of a 1:1 line. Likewise, mean Raman thermal proxy [full-width half maximum of G-band (G-FWHM), Raman band separation (RBS) and D1/G band intensity ratio] values were similar for pre- and post-milled locations, also plotting within error of a 1:1 line. AFM confirms the majority (24 of 36) of pre- and post-ion milled surface pairs were smoother (lower S q values) after BIB milling. These results are interpreted to indicate VR o increase induced by the gentle BIB milling conditions used in this study is an effect of decreased diffuse reflectance due to flatter surfaces, causing more photons to reflect directly back to the detector. Little evidence was observed for molecular aromatization and condensation of vitrinite molecules following BIB milling (with the conditions used). The presence of milling-induced artifacts, including differential milling effects dependent on location and the development of self-organized patterned structures, indicate much work remains in standardization of BIB milling before its promulgation as a routine sample preparation technique for organic petrography. These results provide better understanding of anthropogenic-induced changes to geological samples caused by the now widespread adoption of BIB milling as a disruptive innovation in sample preparation.

Fuel↗

USGS2006

Experiments on δ 34 S mixing between organic and inorganic sulfur species during thermal maturation

Reduced sulfur species were studied to constrain isotopic exchange-mixing with synthetic polysulfide cross-linked macromolecules (PCLM), model sulfur containing molecules and natural sulfur-rich kerogen, asphalt and oil of the Dead Sea area. PCLM represents protokerogens that are rich in sulfur and thermally unstable. Mixing rates of PCLM with HS-(aq) (added as (NH 4 ) 2 S (aq) ) at low to moderate temperatures (50–200 °C) are rapid. Elemental sulfur and H 2 S (gas) fully mix isotopes with PCLM during pyrolysis conditions at 200 °C. During these reactions significant structural changes of the PCLM occur to form polysulfide dimers, thiolanes and thiophenes. As pyrolysis temperatures or reaction times increase, the PCLM thermal products are transformed to more aromatic sulfur compounds. Isotopic mixing rates increase with increasing pyrolysis temperature and time. Polysulfide bonds (S–S) in the PCLM are responsible for most of these structural and isotopic changes because of their low stability. Conversely, sulfur isotope mixing does not occur between dibenzothiophene (aromatic S) or hexadecanthiol (C–SH) and HS-(aq) at 200 °C after 48 h. This shows that rates of sulfur isotope mixing are strongly dependent on the functionality of the sulfur in the organic matter. The order of isotopic mixing rates for organic matter is kerogen > asphalt > oil, which is inverse to their sulfur thermal stability. Asphalt and oil with more refractory sulfur show significantly lower isotopes mixing rates than the kerogen with more labile sulfur. Based on the findings of the present study we suggest that sulfur isotopes mixing can occur from early diagenesis into catagenesis and result in isotopic homogenization of the inorganic and organic reduced sulfur pools.

Geochimica et Cosmochimica Acta↗

USGS2016

Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

Seasonal (spring freshet, summer–autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV–visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64–74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63–77%) and TPIA (54–78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OC np , OC np O and C q , 13–17% of HPOA and 15–20% of TPIA) and isolated O–CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (&sim;5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C–O and O–C–O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

Alaska, Yukon↗

USGS2018

Equilibrium and non-equilibrium controls on the abundances of clumped isotopologues of methane during thermogenic formation in laboratory experiments: Implications for the chemistry of pyrolysis and the origins of natural gases

Multiply isotopically substituted molecules (‘clumped’ isotopologues) can be used as geothermometers because their proportions at isotopic equilibrium relative to a random distribution of isotopes amongst all isotopologues are functions of temperature. This has allowed measurements of clumped-isotope abundances to be used to constrain formation temperatures of several natural materials. However, kinetic processes during generation, modification, or transport of natural materials can also affect their clumped-isotope compositions. Herein, we show that methane generated experimentally by closed-system hydrous pyrolysis of shale or nonhydrous pyrolysis of coal yields clumped-isotope compositions consistent with an equilibrium distribution of isotopologues under some experimental conditions (temperature–time conditions corresponding to ‘low,’ ‘mature,’ and ‘over-mature’ stages of catagenesis), but can have non-equilibrium (i.e., kinetically controlled) distributions under other experimental conditions (‘high’ to ‘over-mature’ stages), particularly for pyrolysis of coal. Non-equilibrium compositions, when present, lead the measured proportions of clumped species to be lower than expected for equilibrium at the experimental temperature, and in some cases to be lower than a random distribution of isotopes (i.e., negative Δ 18 values). We propose that the consistency with equilibrium for methane formed by relatively low temperature pyrolysis reflects local reversibility of isotope exchange reactions involving a reactant or transition state species during demethylation of one or more components of kerogen. Non-equilibrium clumped-isotope compositions occur under conditions where ‘secondary’ cracking of retained oil in shale or wet gas hydrocarbons (C 2-5 , especially ethane) in coal is prominent. We suggest these non-equilibrium isotopic compositions are the result of the expression of kinetic isotope effects during the irreversible generation of methane from an alkyl precursor. Other interpretations are also explored. These findings provide new insights into the chemistry of thermogenic methane generation, and may provide an explanation of the elevated apparent temperatures recorded by the methane clumped-isotope thermometer in some natural gases. However, it remains unknown if the laboratory experiments capture the processes that occur at the longer time and lower temperatures of natural gas formation.

Geochimica et Cosmochimica Acta↗

USGS2020

Position-specific distribution of hydrogen isotopes in natural propane: Effects of thermal cracking, equilibration and biodegradation

Intramolecular isotope distributions, including isotope clumping and position specific fractionation, can provide proxies for the formation temperature and formation and destruction pathways of molecules. In this study, we explore the position-specific hydrogen isotope distribution in propane. We analyzed propane samples from 10 different petroleum systems with high-resolution molecular mass spectrometry. Our results show that the hydrogen isotope fractionation between central and terminal positions of natural propanes ranges from −102‰ to +205‰, a much larger range than that expected for thermodynamic equilibrium at their source and reservoir temperatures (36–63‰). Based on these findings, we propose that the hydrogen isotope structure of catagenic propane is largely controlled by irreversible processes, expressing kinetic isotope effects (KIEs). Kinetic control on hydrogen isotope composition of the products of thermal cracking is supported by a hydrous pyrolysis experiment using the Woodford Shale as substrate, in which we observed isotopic disequilibrium in the early stage of pyrolysis. We make a more general prediction of KIE signatures associated with kerogen cracking by simulating this chemistry in a kinetic Monte Carlo model for different types of kerogens. In contrast, unconventional shale fluids or hot conventional reservoirs contain propane with an isotopic structure close to equilibrium, presumably reflecting internal and/or heterogeneous exchange during high temperature storage (ca. 100–150 °C). In relatively cold (<100 °C) conventional gas accumulations, propane can discharge from its source to a colder reservoir, rapidly enough to preserve disequilibrium signatures even if the source rock thermal maturity is high. These findings imply that long times at elevated temperatures are required to equilibrate the hydrogen isotopic structure of propane in natural gas host rocks and reservoirs. We further defined the kinetics of propane equilibration through hydrogen isotope exchange experiments under hydrous conditions; these experiments show that hydrogen in propane is exchangeable over laboratory timescales when exposed to clay minerals such as kaolinite. This implies rather rapid transfer of propane from sources to cold reservoirs in some of the conventional petroleum systems. Propane is also susceptible to microbial degradation in both oxic and anoxic environments. Biodegradation of propane in the Hadrian and Diana Hoover oil fields (Gulf of Mexico) results in strong increases in central-terminal hydrogen isotope fractionation. This reflects preferential attack on the central position, consistent with previous studies.

Geochimica et Cosmochimica Acta↗

USGS2010

Phosphorus dynamics in soils irrigated with reclaimed waste water or fresh water - A study using oxygen isotopic composition of phosphate

Transformations of phosphate (Pi) in different soil fractions were tracked using the stable isotopic composition of oxygen in phosphate ( δ 18 O p ) and Pi concentrations. Clay soil from Israel was treated with either reclaimed waste water (secondary, low grade) or with fresh water amended with a chemical fertilizer of a known isotopic signature. Changes of δ 18 O p and Pi within different soil fractions, during a month of incubation, elucidate biogeochemical processes in the soil, revealing the biological and the chemical transformation impacting the various P pools. P in the soil solution is affected primarily by enzymatic activity that yields isotopic equilibrium with the water molecules in the soil solution. The dissolved P interacts rapidly with the loosely bound P (extracted by bicarbonate). The oxides and mineral P fractions (extracted by NaOH and HCl, respectively), which are considered as relatively stable pools of P, also exhibited isotopic alterations in the first two weeks after P application, likely related to the activity of microbial populations associated with soil surfaces. Specifically, isotopic depletion which could result from organic P mineralization was followed by isotopic enrichment which could result from preferential biological uptake of depleted P from the mineralized pool. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with reclaimed waste water compared to the fertilizer treated soil.

Geoderma↗

USGS2004

Cassini observations of Io's visible aurorae

More than 500 images of Io in eclipse were acquired by the Cassini spacecraft in late 2000 and early 2001 as it passed through the jovian system en route to Saturn (Porco et al., 2003, Science 299, 1541-1547). Io's bright equatorial glows were detected in Cassini's near-ultraviolet filters, supporting the interpretation that the visible emissions are predominantly due to molecular SO2. Detailed comparisons of laboratory SO2 spectra with the Cassini observations indicate that a mixture of gases contribute to the equatorial emissions. Potassium is suggested by new detections of the equatorial glows at near-infrared wavelengths from 730 to 800 nm. Neutral atomic oxygen and sodium are required to explain the brightness of the glows at visible wavelengths. The molecule S2 is postulated to emit most of the glow intensity in the wavelength interval from 390 to 500 nm. The locations of the visible emissions vary in response to the changing orientation of the external magnetic field, tracking the tangent points of the jovian magnetic field lines. Limb glows distinct from the equatorial emissions were observed at visible to near-infrared wavelengths from 500 to 850 nm, indicating that atomic O, Na, and K are distributed across Io's surface. Stratification of the atmosphere is demonstrated by differences in the altitudes of emissions at various wavelengths: SO2 emissions are confined to a region close to Io's surface, whereas neutral oxygen emissions are seen at altitudes that reach up to 900 km, or half the radius of the satellite. Pre-egress brightening demonstrates that light scattered into Jupiter's shadow by gases or aerosols in the giant planet's upper atmosphere contaminates images of Io taken within 13 minutes of entry into or emergence from Jupiter's umbra. Although partial atmospheric collapse is suggested by the longer timescale for post-ingress dimming than pre-egress brightening, Io's atmosphere must be substantially supported by volcanism to retain auroral emissions throughout the duration of eclipse. ?? 2004 Elsevier Inc. All rights reserved.

Icarus↗

USGS2008

Hydrocarbons on Saturn's satellites Iapetus and Phoebe

Material of low geometric albedo (pV ??? 0.1) is found on many objects in the outer Solar System, but its distribution in the saturnian satellite system is of special interest because of its juxtaposition with high-albedo ice. In the absence of clear, diagnostic spectral features, the composition of this low-albedo (or "dark") material is generally inferred to be carbon-rich, but the form(s) of the carbon is unknown. Near-infrared spectra of the low-albedo hemisphere of Saturn's satellite Iapetus were obtained with the Visible-Infrared Mapping Spectrometer (VIMS) on the Cassini spacecraft at the fly-by of that satellite of 31 December 2004, yielding a maximum spatial resolution on the satellite's surface of ???65 km. The spectral region 3-3.6 ??m reveals a broad absorption band, centered at 3.29 ??m, and concentrated in a region comprising about 15% of the low-albedo surface area. This is identified as the C{single bond}H stretching mode vibration in polycyclic aromatic hydrocarbon (PAH) molecules. Two weaker bands attributed to {single bond}CH2{single bond} stretching modes in aliphatic hydrocarbons are found in association with the aromatic band. The bands most likely arise from aromatic and aliphatic units in complex macromolecular carbonaceous material with a kerogen- or coal-like structure, similar to that in carbonaceous meteorites. VIMS spectra of Phoebe, encountered by Cassini on 11 June 2004, also show the aromatic hydrocarbon band, although somewhat weaker than on Iapetus. The origin of the PAH molecular material on these two satellites is unknown, but PAHs are found in carbonaceous meteorites, cometary dust particles, circumstellar dust, and interstellar dust. ?? 2007 Elsevier Inc. All rights reserved.

Icarus↗

USGS2019

Isotopic ratios of Saturn's rings and satellites: Implications for the origin of water and Phoebe

Isotopic ratios have long been used to learn about physical processes acting over a wide range of geological environments, and in constraining the origin and/or evolution of planetary bodies. We report the spectroscopic detection of deuterium in Saturn's rings and satellites, and use these measurements to determine the (D/H) ratios in their near-surface regions. Saturn's moons, Phoebe and Iapetus, show a strong signature of CO2 and the 13C component of this molecule is detected and quantified. Large averages of spectra obtained by the Cassini Visual and Infrared Mapping Spectrometer, VIMS, were computed for the rings and icy satellites. The observed intensities of the infrared absorptions in H2O and CO2 and their isotopes were calibrated using laboratory data and radiative transfer models to derive the D/H and 13C/12C ratios. We find that the D/H in Saturn's rings and satellites is close to the Vienna Standard Mean Ocean Water (VSMOW) and bulk Earth (4% lower than VSMOW) value except for Phoebe, which is 8.3 times the VSMOW value. This is the highest value for any Solar-System surface yet measured, and suggests that Phoebe formed from material with a different D/H ratio than the other satellites in the Saturn system. Phoebe’s 13C/12C ratio is also unusual: 4.7 times greater than terrestrial, and greater than values measured for the interstellar medium and the galactic center. The high 13C abundance in the CO2 suggests that Phoebe was never warm enough for the large D/H ratio in its surface to have originated by evaporative fractionation of its waterice (e.g., from heating in the inner Solar System before its eventual capture by Saturn). We also report the detection of a probable O-D stretch absorption due to OD in minerals on Phoebe at 3.62 μm. This absorption is not detected on other Saturnian satellites. Stronger signatures of bound water absorptions are found in the dark material of Iapetus and we report a new detection of bound water at 1.9 μm. The position of this absorption matches that seen in spectra of hydrated iron oxides but does not match absorptions seen in spectra of tholins. Despite the strong bound water signature in the Iapetus dark material, no 3.62-μm OD absorption is seen in the spectra, further indicating the high deuterium level on Phoebe is unusual. As such, it is likely that Phoebe originated in a colder part of the outer Solar System, relative to the prevailing temperatures at Saturn’s distance from the Sun.

Icarus↗

USGS2006

Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus

The fish rhabdovirus, Infectious hematopoietic necrosis virus (IHNV), is an important pathogen of salmonids. Cell culture assays have traditionally been used to quantify levels of IHNV in samples; however, real-time or quantitative RT-PCR assays have been proposed as a rapid alternative. For viruses having a single-stranded, negative-sense RNA genome, standard qRT-PCR assays do not distinguish between the negative-sense genome and positive-sense RNA species including mRNA and anti-genome. Thus, these methods do not determine viral genome copy number. This study reports development of strand-specific, qRT-PCR assays that use tagged primers for enhancing strand specificity during cDNA synthesis and quantitative PCR. Protocols were developed for positive-strand specific (pss-qRT-PCR) and negative-strand specific (nss-qRT-PCR) assays for IHNV glycoprotein (G) gene sequences. Validation with synthetic RNA transcripts demonstrated the assays could discriminate the correct strand with greater than 1000-fold fidelity. The number of genome copies in livers of IHNV-infected fish determined by nss-qRT-PCR was, on average, 8000-fold greater than the number of infectious units as determined by plaque assay. We also compared the number of genome copies with the quantity of positive-sense RNA and determined that the ratio of positive-sense molecules to negative-sense genome copies was, on average, 2.7:1. Potential future applications of these IHNV strand-specific qRT-PCR assays are discussed.

Journal of Virological Methods↗

USGS2009

Assessment of the UV camera sulfur dioxide retrieval for point source plumes

Digital cameras, sensitive to specific regions of the ultra-violet (UV) spectrum, have been employed for quantifying sulfur dioxide (SO 2 ) emissions in recent years. The instruments make use of the selective absorption of UV light by SO 2 molecules to determine pathlength concentration. Many monitoring advantages are gained by using this technique, but the accuracy and limitations have not been thoroughly investigated. The effect of some user-controlled parameters, including image exposure duration, the diameter of the lens aperture, the frequency of calibration cell imaging, and the use of the single or paired bandpass filters, have not yet been addressed. In order to clarify methodological consequences and quantify accuracy, laboratory and field experiments were conducted. Images were collected of calibration cells under varying observational conditions, and our conclusions provide guidance for enhanced image collection. Results indicate that the calibration cell response is reliably linear below 1500 ppm m, but that the response is significantly affected by changing light conditions. Exposure durations that produced maximum image digital numbers above 32 500 counts can reduce noise in plume images. Sulfur dioxide retrieval results from a coal-fired power plant plume were compared to direct sampling measurements and the results indicate that the accuracy of the UV camera retrieval method is within the range of current spectrometric methods. ?? 2009 Elsevier B.V.

Journal of Volcanology and Geothermal Research↗

USGS2021

The structure and volume of large geysers in Yellowstone National Park, USA and the mineralogy and chemistry of their silica sinter deposits

Siliceous sinter is formed by biogenic and abiogenic opal deposition around hot springs and geysers. Using Structure-from-Motion photogrammetry we generated three-dimensional models of Giant and Castle Geysers from the Upper Geyser Basin of Yellowstone National Park. We use these models to calculate an approximate mass of sinter for each (~2 and ~ 5 kton, respectively) and estimate a range of plausible long-term deposition rates for Castle Geyser (470 to 940 kg·yr −1 ). We estimate ~2% of the silica discharged from Castle Geyser is deposited as sinter in the cone and proximal terraces. We collected 15 sinter samples following the stratigraphy of each geyser from an older terrace to a younger cone and examined them using a variety of analytical methods. We find that young opaline sinter with a water content of <12 wt% (from loss on ignition) contains higher concentrations of major and trace elements, notably As, Sb, Rb, Ga and Cs, relative to older dehydrated sinter. Rare earth element (REE) concentrations in sinter are 2–3 orders of magnitude higher than in the thermal water from which they are deposited. Sinter deposits are enriched in light REE, Gd and Yb when normalized to concentrations in thermal water and enriched in Eu, Tm, and Yb when normalized to the underlying rhyolite. Sinter samples with the highest REE concentrations are also enriched in organic material, implying either microbial uptake of REE, or that organic molecules are efficient ligands that form metal complexes.

Wyoming↗

USGS2023

Book review: Quasispecies as a unifying concept in population dynamics

The quasispecies concept had two independent origins. One source was the theoretical ideas of Manfred Eigen and Peter Schuster in the 1970s. Studying the self-organization and evolution of primitive RNA molecules, they defined quasispecies as a distribution of mutant viral genomes generated by the mutation-selection process. In particular, the quasispecies nucleotide distribution consists of a singular fittest genotype, called the master sequence, surrounded by similar mutant spectra. The other source of the quasispecies concept can be traced to the growing empirical knowledge on RNA viruses formulated around the same time. Genomic sequencing of viral RNA indicated a variety of nucleotide sequences, or a distribution of sequences. Mutations in both Eigen’s theoretical system in the RNA viruses are not rare, as RNA is structurally less stable than RNA, but common, preventing the fittest genotype from becoming dominant. Virologists have adopted the quasispecies concept, with some papers on Covid-19 using the construct to explain that virus’s behavior.

Mathematical Biosciences↗

USGS2006

Carbon isotopic fractionation of CH4 and CO2 during canister desorption of coal

Canister desorption of coal gas from freshly sampled coal is commonly used for exploratory assessment of the coalbed methane (CBM) potential of a basin or prospect, as well as for the sampling of gas for isotopic determination of the gas origin. Compositional and ??13C isotopic time-series of desorbing CBM and carbon dioxide (CO2) over 3-4 months demonstrate considerable compositional and isotopic shifts over time. Non-stationary chemical and isotopic characteristics are due to differences in diffusivity and adsorbance behavior of gas molecules and must be taken into account when attempting to reproducibly sample coal gases. Off-line gas processing on a vacuum line and on-line GC/MS analyses were performed on coal gas samples from the Springfield and Seelyville Coal Members of the Pennsylvanian age that were cored in the SE Illinois Basin in SW Indiana, USA. The coals cover a narrow range of maturity from 0.54% to 0.64% vitrinite reflectance. Methane initially desorbed faster than CO2, resulting in a 50% increase of the CO 2 content in bulk desorbing gas on the 50th day relative to the first day of desorption. After 50 days of desorption, about 90% of all coal gas was desorbed. Over the same time period, ??13C values of incrementally sampled coal gas increased by 2??? and 9???, for CH 4 and CO2, respectively, testifying to the greater retention of 13CH4 and 13CO2 relative to 12CH4 and 12CO2. An isotopic mass balance of the individual, sequentially desorbed and sampled gas amounts yielded weighted mean ??13CCH4 and ??13CCO2 values for characterizing the cumulatively desorbed gas. The overall mean ??13C values were equivalent to ??13C values of gases that desorbed at a time when half of the potentially available gas had been desorbed from coal, corresponding in this study to a time between day 5 and day 12 of canister desorption at 15-18??C. The total expected gas volume and the ???50% midpoint can thus be approximated for a desorbing coal gas sample, based on a dynamic prediction after the first five days of canister desorption. ?? 2005 Elsevier Ltd. All rights reserved.

Organic Geochemistry↗

USGS2008

Distinguishing solid bitumens formed by thermochemical sulfate reduction and thermal chemical alteration

Insoluble solid bitumens are organic residues that can form by the thermal chemical alteration (TCA) or thermochemical sulfate reduction (TSR) of migrated petroleum. TCA may actually encompass several low temperature processes, such as biodegradation and asphaltene precipitation, followed by thermal alteration. TSR is an abiotic redox reaction where petroleum is oxidized by sulfate. It is difficult to distinguish solid bitumens associated with TCA of petroleum from those associated with TSR when both processes occur at relatively high temperature. The focus of the present work was to characterize solid bitumen samples associated with TCA or TSR using X-ray photoelectron spectroscopy (XPS). XPS is a surface analysis conducted on either isolated or in situ (>25 ??m diameter) solid bitumen that can provide the relative abundance and chemical speciation of carbon, organic and inorganic heteroatoms (NSO). In this study, naturally occurring solid bitumens from three locations, Nisku Fm. Brazeau River area (TSR-related), LaBarge Field Madison Fm. (TSR-related), and the Alaskan Brooks range (TCA-related), are compared to organic solids generated during laboratory simulation of the TSR and TCA processes. The abundance and chemical nature of organic nitrogen and sulfur in solid bitumens can be understood in terms of the nature of (1) petroleum precursor molecules, (2) the concentration of nitrogen by way of thermal stress and (3) the mode of sulfur incorporation. TCA solid bitumens originate from polar materials that are initially rich in sulfur and nitrogen. Aromaticity and nitrogen increase as thermal stress cleaves aliphatic moieties and condensation reactions take place. Organic sulfur in TCA organic solids remains fairly constant with increasing maturation (<3.4 sulfurs per 100 carbons) due to offsetting preservation and H2S elimination reactions. In contrast, TSR solid bitumens are sulfur rich and nitrogen poor solids. These heteroatom distributions are attributed to the ability of TSR to incorporate copious amounts of inorganic sulfur (>3.5 to ???17 sulfur per 100 carbons) into aromatic structures and to the low levels of nitrogen in their hydrocarbon precursors. Hence, XPS results provide organic chemical composition information that helps to distinguish whether solid bitumen, either in situ or removed and concentrated from the rock matrix, was formed via the TCA or TRS process. ?? 2008 Elsevier Ltd.

Organic Geochemistry↗