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USGS2024

Mixed-layer kaolinite-montmorillonite from the Yucatan Peninsula, Mexico

Clay beds 1–2 m thick and interbedded with marine limestones probably of early Eocene age are composed of nearly pure mixed-layer kaolinite-montmorillonite. Particle size studies, electron micrographs, X-ray diffraction studies, chemical analyses, cation exchange experiments, DTA, and TGA indicate that clays from three different localities contain roughly equal proportions of randomly interlayered kaolinite and montmorillonite layers. The montmorillonite structural formulas average K 0·2 Na 0·2 Ca 0·2 Mg 0·2 (Al 2·5 Fe 1·0 3+ Mg 0·5 )(Al 0·75 Si 7.25 )O 20+ (OH) 4− , with a deficiency of structural (OH) in either the montmorillonite or kaolinite layers. Nonexchangeable K + indicates that a few layers are mica-like. Crystals are mostly round plates 1/10 to 1/20 µ across. The feature most diagnostic of the mixed-layer character is an X-ray reflection near 8 Å after heating at 300°C. The clays are inferred to have developed by weathering of volcanic ash and subsequent erosion and deposition in protected nearshore basins.

Clays and Clay Minerals↗

USGS2024

Interlamellar adsorption of carbon dioxide by smectites

The adsorption of CO 2 at low temperature (∼ −70°C) on thin films of homoionic smectites was studied by X-ray diffraction and by i.r. absorption. An increase in the d 001 spacings of these clay films upon adsorption of CO 2 was observed. In addition, a dichroic effect was readily discernible by comparing the i.r. spectra at two different orientations of the smectite films; i.e. with the film normal and tilted 35° with respect to the i.r. beam. The CO 2 stretching vibration at 2350 cm −1 was used for the i.r. study. These observations conclusively show that CO 2 intercalates the smectite structure rather than being adsorbed only in pores between clay tactoids—the limiting process proposed by other investigators. Adsorption isotherm data from earlier surface area studies are re-examined here through application of the Dubinin equation. Again, intercalation is demonstrated by convergence of the plotted experimental data for smectites containing large monovalent interlayer cations toward a pore volume that is near the calculated theoretical value for a monolayer of intercalated CO 2 . Scanning electron photomicrographs of Li- and Cs- smectites provide additional evidence that aggregation differences are not responsible for the large observed difference in BET surface areas obtained for these smectites with CO 2 as the adsorbate. At low magnification, visual differences in macro-aggregates are apparent, but at high magnification no significant differences are observed in the micro-structure of individual aggregates where the major amount of gas adsorption really occurs.

Clays and Clay Minerals↗

USGS2024

Phosphates in some Missouri refractory clays

This paper describes in detail phosphate minerals occurring in refractory clays of Missouri and their effect on the refractory degree of the clays. The minerals identified include carbonate-fluorapatite (francolite), crandallite, goyazite, wavellite, variscite and strengite. It is emphasized that these phosphates occur only in local isolated concentrations, and not generally in Missouri refractory clays. The Missouri fireclay region comprises 2 districts, northern and southern, separated by the Missouri River. In this region, clay constitutes a major part of the Lower Pennsylvanian Cheltenham Formation. The original Cheltenham mud was an argillic residue derived from leaching and dissolution of pre-Pennsylvanian carbonates. The mud accumulated on a karstic erosion surface truncating the pre-Cheltenham rocks. Fireclays of the northern district consist mainly of poorly ordered kaolinite, with variable but minor amounts of illite, chlorite and fine-grained detrital quartz. Clays of the southern district were subjected to extreme leaching that produced well-ordered kaolinite flint clays. Local desilication formed pockets of diaspore, or more commonly, kaolinite, with oolite-like nubs or burls of diaspore (“burley”" clay). The phosphate-bearing materials have been studied by X-ray diffraction (XRD), scanning electron microscopy-energy dispersive spectral analysis (SEM-EDS) and chemical analysis. Calcian goyazite was identified in a sample of diaspore, and francolite in a sample of flint clay. A veinlet of wavellite occurs in flint clay at one locality, and a veinlet of variscite-strengite at another locality. The Missouri flint-clay-hosted francolite could not have formed in the same manner as marine francolite. The evidence suggests that the Cheltenham francolite precipitated from ion complexes in pore water, nearly simultaneously with crystallization of kaolinite flint clay from an alumina-silica gel. Calcian goyazite is an early diagenetic addition to its diaspore host. The wavellite and variscite-strengite veinlets are secondary, precipitated from ion complexes in ground water percolating along cracks in the flint clay. The flint clay host of the variscite-strengite veinlet contains strontian crandallite. All of the phosphates contain significant amounts of strontium. The source of P, Ca and Sr was the marine carbonates. Dissolution of these carbonates produced the argillic residue that became the primordial Cheltenham paludal mud, which ultimately altered to fireclay. Preliminary firing tests show that the presence of phosphates lowers fusion temperature. However, it is not clear whether poor refractoriness is due to the presence of phosphates, per se, or to Ca, Sr and other alkaline elements present in the phosphates.

Clays and Clay Minerals↗

USGS2024

Crystal structure refinement and Mössbauer spectroscopy of an ordered, triclinic clinochlore

The crystal structure of a natural, ordered IIb-4 triclinic clinochlore has been refined in space group C 1¯ from 4282 unique X-ray intensity measurements of which 3833 are greater than 3 times the statistical counting error (3σ). Unit cell parameters are a = 5.3262(6) Å; b = 9.226(1) Å; c = 14.334(3) Å; α = 90.56(2)°; β = 97.47(2)°; and γ = 89.979(9)°, which represents the greatest deviation from monoclinic symmetry yet recorded for a triclinic chlorite. The final weighted R is 0.059 for reflections with I > 3σ and 0.064 for all reflections. The chemical formula is (Mg 0.966 Fe 0.034 ) M1 (Mg 0.962 Fe 0.038 ) M2 2 (Si 2.96 Al 1.04 )O 10 (OH) 2 (Mg 0.996 Fe 0.004 ) M3 2 (Al 0.841 Fe III 0.102 Cr 0.004 Ti 0.004 ) M4 (OH) 6 , which is consistent with electron microprobe (EMP), wet chemical analyses, Mössbauer spectroscopy and X-ray structure refinement. The high degree of ordering of the divalent versus trivalent octahedral cations in the interlayer is noteworthy, with Fe III and Al in M4 and virtually no Fe in M3. In the 2:1 layer, M1 and M2 each contain similar amounts of Fe. The 2 tetrahedral sites have nearly identical mean oxygen distances and volumes, and thus show no evidence of long-range cation ordering.

Clays and Clay Minerals↗

USGS2024

Measurement of fundamental illite particle thicknesses by X-ray diffraction using PVP-10 intercalation

The thicknesses of fundamental illite particles that compose mixed-layer illite-smectite (I-S) crystals can be measured by X-ray diffraction (XRD) peak broadening techniques (Bertaut-Warren-Averbach [BWA] method and integral peak-width method) if the effects of swelling and XRD background noise are eliminated from XRD patterns of the clays. Swelling is eliminated by intercalating Na-saturated I-S with polyvinylpyrrolidone having a molecular weight of 10,000 (PVP-10). Background is minimized by using polished metallic silicon wafers cut perpendicular to (100) as a substrate for XRD specimens, and by using a single-crystal monochromator. XRD measurements of PVP-intercalated diagenetic, hydrothermal and low-grade metamorphic I-S indicate that there are at least 2 types of crystallite thickness distribution shapes for illite fundamental particles, lognormal and asymptotic; that measurements of mean fundamental illite particle thicknesses made by various techniques (Bertant-Warren-Averbach, integral peak width, fixed cation content, and transmission electron microscopy [TEM]) give comparable results; and that strain (small differences in layer thicknesses) generally has a Gaussian distribution in the log-normal-type illites, but is often absent in the asymptotic-type illites.

Clays and Clay Minerals↗

USGS2024

The role of clay minerals in the preservation of organic matter in sediments of Qinghai Lake, NW China

The role of saline lake sediments in preserving organic matter has long been recognized. In order to further understand the preservation mechanisms, the role of clay minerals was studied. Three sediment cores, 25, 57, and 500 cm long, were collected from Qinghai Lake, NW China, and dissected into multiple subsamples. Multiple techniques were employed, including density fractionation, X-ray diffraction, scanning and transmission electron microscopy (SEM and TEM), total organic carbon (TOC) and carbon compound analyses, and surface area determination. The sediments were oxic near the water-sediment interface, but became anoxic at depth. The clay mineral content was as much as 36.8%, consisting mostly of illite, chlorite, and halloysite. The TEM observations revealed that organic matter occurred primarily as organic matter-clay mineral aggregates. The TOC and clay mineral abundances are greatest in the mid-density fraction, with a positive correlation between the TOC and mineral surface area. The TOC of the bulk sediments ranges from 1 to 3% with the non-hydrocarbon fraction being predominant, followed by bitumen, saturated hydrocarbon, aromatic hydrocarbons, and chloroform-soluble bitumen. The bimodal distribution of carbon compounds of the saturated hydrocarbon fraction suggests that organic matter in the sediments was derived from two sources: terrestrial plants and microorganisms/algae. Depthrelated systematic changes in the distribution patterns of the carbon compounds suggest that the oxidizing conditions and microbial abundance near the water-sediment interface promote degradation of labile organic matter, probably in adsorbed form. The reducing conditions and small microbial biomass deeper in the sediments favor preservation of organic matter, because of the less labile nature of organic matter, probably occurring within clay mineral-organic matter aggregates that are inaccessible to microorganisms. These results have important implications for our understanding of mechanisms of organic matter preservation in saline lake sediments.

Qinghai Lake↗

USGS2024

The formation of illite from nontronite by mesophilic and thermophilic bacterial reaction

The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic ( Shewanella putrefaciens CN32) and thermophilic ( Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65°C) were the most favorable conditions for the formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

Clays and Clay Minerals↗

USGS2024

The influence of oxalate-promoted growth of saponite and talc crystals

The intercalating growth of new silicate layers or metal hydroxide layers in the interlayer space of other clay minerals is known from various mixed-layer clay minerals such as illite-smectite (I-S), chlorite-vermiculite, and mica-vermiculite. In a recent study, the present authors proposed that smectite-group minerals can be synthesized from solution as new 2:1 silicate layers within the low-charge interlayers of rectorite. That study showed how oxalate catalyzes the crystallization of saponite from a silicate gel at low temperatures (60ºC) and ambient pressure. As an extension of this work the aim of the present study was to test the claim that new 2:1 silicate layers can be synthesized as new intercalating layers in the low-charge interlayers of rectorite and whether oxalate could promote such an intercalation synthesis. Two experiments were conducted at 60ºC and atmospheric pressure. First, disodium oxalate solution was added to a suspension of rectorite in order to investigate the effects that oxalate anions have on the structure of rectorite. In a second experiment, silicate gel of saponitic composition (calculated interlayer charge −0.33 eq/O 10 (OH) 2 ) was mixed with a suspension of rectorite and incubated in disodium oxalate solution. The synthesis products were extracted after 3 months and analyzed by X-ray diffraction and high-resolution transmission electron microscopy (HRTEM). The treatment of ultrathin sections with octadecylammonium (n C = 18) cations revealed the presence of 2:1 layer silicates with different interlayer charges that grew from the silicate gel. The oxalate-promoted nucleation of saponite and talc crystallites on the rectorite led to the alteration and ultimately to the destruction of the rectorite structure. The change was documented in HRTEM lattice-fringe images. The crystallization of new 2:1 layer silicates also occurred within the expandable interlayers of rectorite but not as new 2:1 silicate layers parallel to the previous 2:1 silicate layers. Instead, they grew independently of any orientation predetermined by the rectorite crystal substrate and their crystallization was responsible for the destruction of the rectorite structure.

Clays and Clay Minerals↗

USGS2011

Data sharing by scientists: Practices and perceptions

Background Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers – data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region. Conclusions/Significance Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound data management principles.

PLoS ONE↗

USGS2014

Isolation and molecular characterization of a novel picornavirus from baitfish in the USA

During both regulatory and routine surveillance sampling of baitfish from the states of Illinois, Minnesota, Montana, and Wisconsin, USA, isolates (n = 20) of a previously unknown picornavirus were obtained from kidney/spleen or entire viscera of fathead minnows ( Pimephales promelas ) and brassy minnows ( Hybognathus hankinsoni ). Following the appearance of a diffuse cytopathic effect, examination of cell culture supernatant by negative contrast electron microscopy revealed the presence of small, round virus particles (&sim;30–32 nm), with picornavirus-like morphology. Amplification and sequence analysis of viral RNA identified the agent as a novel member of the Picornaviridae family, tentatively named fathead minnow picornavirus (FHMPV). The full FHMPV genome consisted of 7834 nucleotides. Phylogenetic analysis based on 491 amino acid residues of the 3D gene showed 98.6% to 100% identity among the 20 isolates of FHMPV compared in this study while only 49.5% identity with its nearest neighbor, the bluegill picornavirus (BGPV) isolated from bluegill ( Lepomis macrochirus ). Based on complete polyprotein analysis, the FHMPV shared 58% (P1), 33% (P2) and 43% (P3) amino acid identities with BGPV and shared less than 40% amino acid identity with all other picornaviruses. Hence, we propose the creation of a new genus ( Piscevirus ) within the Picornaviridae family. The impact of FHMPV on the health of fish populations is unknown at present.

Illinois, Minnesota, Montana, Wisconsin↗

USGS2014

An integrated approach to the Taxonomic identification of prehistoric shell ornaments

Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.

PLoS ONE↗

USGS2016

The importance of species name synonyms in literature searches

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

PLoS ONE↗

USGS2018

Development and characterization of two cell lines from gills of Atlantic salmon

Gill disease in Atlantic salmon, Salmo salar L., causes big losses in the salmon farming industry. Until now, tools to cultivate microorganisms causing gill disease and models to study the gill responses have been lacking. Here we describe the establishment and characterization of two cell lines from the gills of Atlantic salmon. Atlantic salmon gill cell ASG-10 consisted of cells staining for cytokeratin and e-cadherin and with desmosomes as seen by transmission electron microscopy suggesting the cells to be of epithelial origin. These structures were not seen in ASG-13. The cell lines have been maintained for almost 30 passages and both cell lines are fully susceptible to infection by infectious hematopoietic necrosis virus (IHNV), viral hemorrhagic septicemia virus (VHSV), infectious pancreatic necrosis virus (IPNV), Atlantic salmon reovirus TS (TSRV) and Pacific salmon paramyxovirus (PSPV). While infectious salmon anemia virus (ISAV) did not cause visible CPE, immunofluorescent staining revealed a sub-fraction of cells in both the ASG-10 and ASG-13 lines may be permissive to infection. ASG-10 is able to proliferate and migrate to close scratches in the monolayer within seven days in vitro contrary to ASG-13, which does not appear to do have the same proliferative and migratory ability. These cell lines will be useful in studies of gill diseases in Atlantic salmon and may represent an important contribution for alternatives to experimental animals and studies of epithelial–mesenchymal cell biology.

PLoS ONE↗

USGS1992

Tensiometers: Theory, construction, and use

Standard tensiometers are used to measure matric potential as low as −870 cm of water in the unsaturated zone by creating a saturated hydraulic link between the soil water and a pressure sensor. The direction and, in some cases, quantity of water flux can be determined using multiple installations. A variety of commercial and fabricated tensiometers are commonly used. Saturated porous ceramic materials, which form an interface between the soil water and the bulk water inside the instrument, are available in many shapes, sizes, and pore diameters. A gage, manometer, or electronic pressure transducer is connected to the porous material with small- or large-diameter tubing. Selection of these components allows the user to optimize one or more characteristics, such as accuracy, versatility, response time, durability, maintenance, extent of data collection, and cost. Special designs have extended the normal capabilities of tensiometers, allowing measurement in cold or remote areas, measurement of matric potential as low as −153 m of water (−15 bars), measurement at depths as deep as 6 m (recorded at land surface), and automatic measurement using as many as 22 tensiometers connected to a single pressure transducer. Continuous hydraulic connection between the porous material and soil, and minimal disturbance of the natural infiltration pattern are necessary for successful installation. Avoidance of errors caused by air invasion, nonequilibrium of the instrument, or pressure-sensor inaccuracy will produce reliable values of matric potential, a first step in characterizing unsaturated flow.

Geotechnical Testing Journal↗

USGS2015

Sturgeon in the Sacramento-San Joaquin watershed: new insights to support conservation and management

The goal of a day-long symposium on March 3, 2015, Sturgeon in the Sacramento–San Joaquin Watershed: New Insights to Support Conservation and Management, was to present new information about the physiology, behavior, and ecology of the green (Acipenser medirostris) and white sturgeon (Acipenser transmontanus) to help guide enhanced management and conservation efforts within the Sacramento–San Joaquin watershed. This symposium identified current unknowns and highlighted new electronic tracking technologies and physiological techniques to address these knowledge gaps. A number of presentations, each reviewing ongoing research on the two species, was followed by a round-table discussion, in which each of the participants was asked to share recom-mendations for future research on sturgeon in the watershed. This article presents an in-depth review of the scientific information presented at the sympo-sium with a summary of recommendations for future research.

California↗

USGS1984

Technological innovations in aquaculture

Technology in aquaculture has expanded at a phenomenal rate during the last 50 to 100 years. Based on both this past progress and the present technological advances being made in our society, it is reasonable to expect aquaculturists to profit from the rapid technological advances being made in both hardware and biological systems. These advances will result as spinoffs from medicine, from analytical chemistry, and most importantly, from the evolution of new consumer products such as auto-focus cameras, electronic watches, and microprocessor-monitored automobiles. We can expect to use economical, reliable instrumentation capable of environmental monitoring for predictive purposes and instrumentation that will contain alarm and control circuits. Genetic engineering will result in biological organisms that produce hormones, drugs, and other biological materials as well as detoxify pollutants on demand. When we as aquaculturists identify the need for a product, that product will be developed.

Fisheries↗

USGS1974

A respirometer with controllable oxygen levels

Construction details and operation of a respirometer with capabilities for controlling the oxygen level at preselected levels is described. The interaction of an oxygen sensor and electronic switch energizes an electrolysis cell which replenishes oxygen used by a test organism. Respiration rate of any aquatic or semiaquatic organism may be determined by this apparatus.

Transactions of the American Fisheries Society↗

USGS1990

Ultrastructure of the spleen and head kidney of striped bass

The spleen and head kidney of striped bass Morone saxatilis were examined by electron microscopy, including examination of ultrastructural localization of peroxidase. The spleen is composed of a loosely organized reticulum that supports the red and white pulp. The principal hematopoietic and mature blood cells observed were erythrocytes, erythroblasts, lymphocytes, macrophages, thrombocytes, and aggregates of pigmented macrophages. In addition, limited numbers of neutrophils, neutrophilic myelocytes (immature neutrophils), plasma cells, eosinophils and monocytes were identified. Reticular cells and fibers appeared to provide a structural framework for both cells and blood sinuses in the spleen. Like the spleen, the head kidney contained erythrocytes, macrophages, monocytes, lymphocytes, and other less frequently observed cell types. A distinct difference in the cytologic composition of the two organs, however, was in the greater number of neutrophilic myelocytes found in the head kidney, where these cells were often arranged in groups. Positive peroxidase reactions were observed for neutrophils, neutrophilic myelocytes, macrophage phagolysosomes, and pigmented macrophages in both the spleen and head kidney.

Journal of Aquatic Animal Health↗