Applications of Cathodoluminescence of Quartz and Feldspar to Sedimentary Petrology

Cathodoluminescence (CL), the emission of visible light during electron bombardment, was first used in sandstone petrology in the mid-1960\u27s. CL techniques are especially useful for determining the origin and source of quartz and feldspar, two of the most common constituents in elastic rocks. CL properties of both minerals are dependent on their temperature of crystallization, duration of cooling, and/or history of deformation. Detrital quartz and feldspar are typically derived from igneous and metamorphic sources and luminesce in the visible range whereas authigenic quartz and feldspar form at low temperatures and do not luminesce. Quantification of luminescent and non-luminescent quartz and feldspar with the scanning electron microscope, electron microprobe, or a commercial CL device can allow for the determination of origin, diagenesis, and source of elastic rocks when used in conjunction with field and other petrographic analyses. Future expansion and documentation of the classifications and causes of CL in these minerals may increase the usefulness of CL techniques in sandstone petrology

Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase

Human immunodeficiency virus (HIV-1) is, like most pathogens, under selective pressure to escape the immune system of its host. In particular, HIV-1 can avoid recognition by cytotoxic T lymphocytes (CTLs) by altering the binding affinity of viral peptides to human leukocyte antigen (HLA) molecules, the role of which is to present those peptides to the immune system. It is generally assumed that HLA escape mutations carry a replicative fitness cost, but these costs have not been quantified. In this study, we assess the replicative cost of mutations which are likely to escape presentation by HLA molecules in the region of HIV-1 protease and reverse transcriptase. Specifically, we combine computational approaches for prediction of in vitro replicative fitness and peptide binding affinity to HLA molecules. We find that mutations which impair binding to HLA-A molecules tend to have lower in vitro replicative fitness than mutations which do not impair binding to HLA-A molecules, suggesting that HLA-A escape mutations carry higher fitness costs than non-escape mutations. We argue that the association between fitness and HLA-A binding impairment is probably due to an intrinsic cost of escape from HLA-A molecules, and these costs are particularly strong for HLA-A alleles associated with efficient virus control. Counter-intuitively, we do not observe a significant effect in the case of HLA-B, but, as discussed, this does not argue against the relevance of HLA-B in virus control. Overall, this article points to the intriguing possibility that HLA-A molecules preferentially target more conserved regions of HIV-1, emphasizing the importance of HLA-A genes in the evolution of HIV-1 and RNA viruses in general

The HLA-A*0201-Restricted H-Y Antigen Contains a Posttranslationally Modified Cysteine That Significantly Affects T Cell Recognition.

AbstractA peptide recognized by two cytotoxic T cell clones specific for the human minor histocompatibility antigen H-Y and restricted by HLA-A*0201 was identified. This peptide originates from SMCY, as do two other H-Y epitopes, supporting the importance of this protein as a major source of H-Y determinants in mice and humans. In naturally processed peptides, T cells only recognize posttranslationally altered forms of this peptide that have undergone modification of a cysteine residue in the seventh position. One of these modifications involves attachment of a second cysteine residue via a disulfide bond. This modification has profound effects on T cell recognition and also occurs in other class I MHC-associated peptides, supporting its general importance as an immunological determinant

When using small samples to evaluate hydrocarbon reservoirs, proceed with caution

Small-angle neutron scattering (SANS) and ultra-small angle neutron scattering (USANS) with contrast matching techniques (Melnichenko and others, 2012) were used to investigate size distribution and gas accessibility in pores in an approximately 10.6 cm long Mississippian \ud Barnett Shale butt core from the Fort Worth Basin, \ud Texas, USA. SANS and USANS measurements record scattering from all pores, both open and closed, in the size range 10nm - ~10 μ. The techniques can also be used to determine the material that contains pores and the number of pores as a function of size. By injecting deuterated methane gas (CD4) at contrast matching pressure it is possible to distinguish which pores are accessible, or open, to fluids and which ones are not

Porosity of the Marcellus Shale: A contrast matching small-angle neutron scattering study

Neutron scattering techniques were used to determine the effect of mineral matter on the accessibility of water and toluene to pores in the Devonian Marcellus Shale. Three Marcellus Shale samples, representing quartz-rich, clay-rich, and carbonate-rich facies, were examined using contrast matching small-angle neutron scattering (CM-SANS) at ambient pressure and temperature. Contrast matching compositions of H2O, D2O and toluene, deuterated toluene were used to probe open and closed pores of these three shale samples. Results show that although the mean pore radius was approximately the same for all three samples, the fractal dimension of the quartz-rich sample was higher than for the clay-rich and carbonate-rich samples, indicating different pore size distributions among the samples. The number density of pores was highest in the clay-rich sample and lowest in the quartz-rich sample. Contrast matching with water and toluene mixtures shows that the accessibility of pores to water and toluene also varied among the samples. In general, water accessed approximately 70–80% of the larger pores (>80 nm radius) in all three samples. At smaller pore sizes (~5–80 nm radius), the fraction of accessible pores decreases. The lowest accessibility to both fluids is at pore throat size of ~25 nm radii with the quartz-rich sample exhibiting lower accessibility than the clay- and carbonate-rich samples. The mechanism for this behaviour is unclear, but because the mineralogy of the three samples varies, it is likely that the inaccessible pores in this size range are associated with organics and not a specific mineral within the samples. At even smaller pore sizes (~<2.5 nm radius), in all samples, the fraction of accessible pores to water increases again to approximately 70–80%. Accessibility to toluene generally follows that of water; however, in the smallest pores (~<2.5 nm radius), accessibility to toluene decreases, especially in the clay-rich sample which contains about 30% more closed pores than the quartz- and carbonate-rich samples. Results from this study show that mineralogy of producing intervals within a shale reservoir can affect accessibility of pores to water and toluene and these mineralogic differences may affect hydrocarbon storage and production and hydraulic fracturing characteristics

Partitioning of selected trace elements in coal combustion products from two coal-burning power plants in the United States

Samples of feed coal (FC), bottom ash (BA), economizer fly ash(EFA), and fly ash (FA) were collected from power plants in the Central Appalachian basin and Colorado Plateau to determine the partitioning of As, Cr, Hg, Pb, and Se in coal combustion products (CCPs). The Appalachian plant burns a high-sulfur (about 3.9 wt.%) bituminous coal from the Upper Pennsylvanian Pittsburgh coal bed and operates with electrostatic precipitators(ESPs), with flue gas temperatures of about 163 °C in the ESPs. At this plant, As, Pb, Hg, and Se have the greatest median concentrations in FA samples, compared to BA and EFA. A mass balance (not including the FGD process) suggests that the following percentages of trace elements are captured in FA: As (48%), Cr (58%), Pb (54%), Se (20%), and Hg (2%). The relatively high temperatures of the flue gas in the ESPs and low amounts of unburned C in FA (0.5% loss-on-ignition for FA) may have led to the low amount of Hg captured in FA. The Colorado Plateau plant burns a blend of three low-S (about 0.74 wt.%) bituminous coals from the Upper Cretaceous Fruitland Formation and operates with fabric filters (FFs). Flue gas temperatures in the baghouses are about 104 °C. The elements As, Cr, Pb, Hg, and Se have the greatest median concentrations in the fine-grained fly ash product (FAP) produced by cyclone separators, compared to the other CCPs at this plant. The median concentration of Hg in FA (0.0983 ppm) at the Colorado Plateau plant is significantly higher than that for the Appalachian plant (0.0315 ppm); this higher concentration is related to the efficiency of FFs in Hg capture, the relatively low temperatures of flue gas in the baghouses (particularly in downstream compartments), and the amount of unburned C in FA (0.29% loss-on-ignition for FA)

A USANS/SANS study of the accessibility of pores in the barnett shale to methane and water

Shale is an increasingly important source of natural gas in the United States. The gas is held in fine pores that need to be accessed by horizontal drilling and hydrofracturing techniques. Understanding the nature of the pores may provide clues to making gas extraction more efficient. We have investigated two Mississippian Barnett Shale samples, combining small-angle neutron scattering (SANS) and ultrasmall-angle neutron scattering (USANS) to determine the pore size distribution of the shale over the size range 10 nm to 10 μm. By adding deuterated methane (CD4) and, separately, deuterated water (D2O) to the shale, we have identified the fraction of pores that are accessible to these compounds over this size range. The total pore size distribution is essentially identical for the two samples. At pore sizes >250 nm, >85% of the pores in both samples are accessible to both CD4 and D2O. However, differences in accessibility to CD4 are observed in the smaller pore sizes (∼25 nm). In one sample, CD4 penetrated the smallest pores as effectively as it did the larger ones. In the other sample, less than 70% of the smallest pores (<25 nm) were accessible to CD4, but they were still largely penetrable by water, suggesting that small-scale heterogeneities in methane accessibility occur in the shale samples even though the total porosity does not differ. \ud An additional study investigating the dependence of scattered intensity with pressure of CD4 allows for an accurate estimation of the pressure at which the scattered intensity is at a minimum. This study provides information about the composition of the material immediately surrounding the pores. Most of the accessible (open) pores in the 25 nm size range can be associated with either mineral matter or high reflectance organic material. However, a complementary scanning electron microscopy investigation shows that most of the pores in these shale samples are contained in the organic components. The neutron scattering results indicate that the pores are not equally proportioned in the different constituents within the shale. There is some indication from the SANS results that the composition of the pore-containing material varies with pore size; the pore size distribution associated with mineral matter is different from that associated with organic phases.\u