An Experimental Multi-scale Assessment of Mechanical Properties of Organic-rich Mudrocks, and Impact of the Variability of Their Mineralogical and Organic Components in Their Mechanical Analysis

Reliable evaluation of rock mechanical properties in organic-rich mudrocks is challenging due to their heterogeneity, anisotropy, and complex lithology. It is important to assimilate variable elastic properties and distribution of individual mudrock components, as well as rock fabric in the evaluation of elastic properties of organic-rich mudrocks. Failure to take into consideration their physical and mechanical properties, can result in unreliable geomechanical characterization for wellbore studies and stress prediction for completions design. The objectives of this dissertation are to (a) investigate the impact of anisotropic poroelastic parameters for stress prediction in organic-rich mudrocks; (b) quantify the uncertainties involved in well-log-based evaluation of effective elastic properties of mudrocks using micro-scale mechanical testing; and (c) evaluate the impacts of thermal maturity on elastic properties of kerogen and on effective elastic properties of mudrocks. First, I demonstrated that a thorough depth-by-depth estimation of anisotropic poroelastic parameters is required to estimate stress profile for organic-rich mudrocks. I observed variabilities of up to 30% in estimates of minimum horizontal stress due to vertical heterogeneity, mechanical anisotropy and anisotropic poroelasticity assumptions in organic-rich formations. Next, I evaluated the uncertainties involved in the assessment of effective elastic properties of organic-rich mudrocks. I used nanoindentation tests to quantify the variability in elastic properties of individual rock components, caused by differences in their spatial distribution, size, and rock fabric within the formation. I reported a variability of 25% in Young’s moduli of clay minerals due to their location within the mudrock. I also quantified differences up to 33% between estimates of elastic stiffness coefficients from core measurements and well-log-based estimates of effective elastic stiffness coefficients obtained from nanoindentation tests. Finally, I demonstrated that elastic properties of kerogen vary as the thermal maturity of the formation changes. I evaluated the impacts of thermal maturity on elastic properties of kerogen at the micronscale by using synthetic thermal maturation. I reported differences of up to 44% in magnitudes of Young’s moduli of kerogen at different levels of thermal maturity. Furthermore, I observed that effective elastic properties of the formation varied up to 25% as thermal maturity of kerogen changes from room temperature to 425ºC

Assessment of Fluid Transport Mechanisms in Shale Gas Reservoirs

The complex interplay between the physical and flow properties of shales was investigated. A methodology was developed to estimate free and bound porosity fractions from NMR-T2 experiments on shales, while a second order flow model was proposed to interpret gas permeability data. Slippage effects appeared to be influenced by characteristic pore lengths, while poroelastic behaviour was linked to compositional data. Potential associations emerged between FFI/BVI, pore sizes, fluid dynamic phenomena, and shale composition

ZOOM or Non-ZOOM? Assessing spinal cord diffusion tensor imaging protocols for multi-centre studies

The purpose of this study was to develop and evaluate two spinal cord (SC) diffusion tensor imaging (DTI) protocols, implemented at multiple sites (using scanners from two different manufacturers), one available on any clinical scanner, and one using more advanced options currently available in the research setting, and to use an automated processing method for unbiased quantification. DTI parameters are sensitive to changes in the diseased SC. However, imaging the cord can be technically challenging due to various factors including its small size, patient-related and physiological motion, and field inhomogeneities. Rapid acquisition sequences such as Echo Planar Imaging (EPI) are desirable but may suffer from image distortions. We present a multi-centre comparison of two acquisition protocols implemented on scanners from two different vendors (Siemens and Philips), one using a reduced field-of-view (rFOV) EPI sequence, and one only using options available on standard clinical scanners such as outer volume suppression (OVS). Automatic analysis was performed with the Spinal Cord Toolbox for unbiased and reproducible quantification of DTI metrics in the white matter. Images acquired using the rFOV sequence appear less distorted than those acquired using OVS alone. SC DTI parameter values obtained using both sequences at all sites were consistent with previous measurements made at 3T. For the same scanner manufacturer, DTI parameter inter-site SDs were smaller for the rFOV sequence compared to the OVS sequence. The higher inter-site reproducibility (for the same manufacturer and acquisition details, i.e. ZOOM data acquired at the two Philips sites) of rFOV compared to the OVS sequence supports the idea that making research options such as rFOV more widely available would improve accuracy of measurements obtained in multi-centre clinical trials. Future multi-centre studies should also aim to match the rFOV technique and signal-to-noise ratios in all sequences from different manufacturers/sites in order to avoid any bias in measured DTI parameters and ensure similar sensitivity to pathological changes

The Andrew W. Mellon Foundation Report 2016

Annual Report 201

Nutrient limitation of algae and macrophytes in streams: Integrating laboratory bioassays, field experiments, and field data

Successful eutrophication control strategies need to address the limiting nutrient. We conducted a battery of laboratory and in situ nutrient-limitation tests with waters collected from 9 streams in an agricultural region of the upper Snake River basin, Idaho, USA. Laboratory tests used the green alga Raphidocelis subcapitata, the macrophyte Lemna minor (duckweed) with native epiphytes, and in situ nutrient-limitation tests of periphyton were conducted with nutrient-diffusing substrates (NDS). In the duckweed/epiphyte test, P saturation occurred when concentrations reached about 100 μg/L. Chlorophyll a in epiphytic periphyton was stimulated at low P additions and by about 100 μg/L P, epiphytic periphyton chlorophyll a appeared to be P saturated. Both duckweed and epiphyte response patterns with total N were weaker but suggested a growth stimulation threshold for duckweed when total N concentrations exceeded about 300 μg/L and approached saturation at the highest N concentration tested, 1300 μg/L. Nutrient uptake by epiphytes and macrophytes removed up to 70 and 90% of the N and P, respectively. The green algae and the NDS nutrient-limitation test results were mostly congruent; N and P co-limitation was the most frequent result for both test series. Across all tests, when N:P molar ratios \u3e30 (mass ratios \u3e14), algae or macrophyte growth was P limited; N limitation was observed at N:P molar ratios up to 23 (mass ratios up to 10). A comparison of ambient periphyton chlorophyll a concentrations with chlorophyll a accrued on control artificial substrates in N-limited streams, suggests that total N concentrations associated with a periphyton chlorophyll a benchmark for desirable or undesirable conditions for recreation would be about 600 to 1000 μg/L total N, respectively. For P-limited streams, the corresponding benchmark concentrations were about 50 to 90 μg/L total P, respectively. Our approach of integrating controlled experiments and matched biomonitoring field surveys was cost effective and more informative than either approach alone

Activation of Epidermal Toll-Like Receptor 2 Enhances Tight Junction Function: Implications for Atopic Dermatitis and Skin Barrier Repair

Atopic dermatitis (AD) is characterized by epidermal tight junction (TJ) defects and a propensity for Staphylococcus aureus skin infections. S. aureus is sensed by many pattern recognition receptors, including Toll-like receptor 2 (TLR2). We hypothesized that an effective innate immune response will include skin barrier repair, and that this response is impaired in AD subjects. S. aureus–derived peptidoglycan (PGN) and synthetic TLR2 agonists enhanced TJ barrier and increased expression of TJ proteins, claudin-1 (CLDN1), claudin-23 (CLDN23), occludin, and Zonulae occludens 1 (ZO-1) in primary human keratinocytes. A TLR2 agonist enhanced skin barrier recovery in human epidermis wounded by tape stripping. Tlr2−/− mice had a delayed and incomplete barrier recovery following tape stripping. AD subjects had reduced epidermal TLR2 expression as compared with nonatopic subjects, which inversely correlated (r=-0.654, P=0.0004) with transepidermal water loss (TEWL). These observations indicate that TLR2 activation enhances skin barrier in murine and human skin and is an important part of a wound repair response. Reduced epidermal TLR2 expression observed in AD patients may have a role in their incompetent skin barrier

Regional Stratigraphy, Elemental Chemostratigraphy, and Organic Richness of the Niobrara Member of the Mancos Shale, Piceance Basin, Colorado

The elemental chemostratigraphy of the Upper Cretaceous Niobrara Member of the Mancos Shale shows that six chemostratigraphic zones can be identified in the Piceance Basin, Colorado, based on geochemical data collected from cuttings at 10- , 20-, and 30-ft (3.05, 6.10, and 9.14 m) intervals. Chemostratigraphic correlations of nine wells spaced 20 mi (~32 km) apart closely match lithostratigraphic correlations made using gamma-ray and deep-resistivity logs. Lithologic interpretations made from wireline logs indicate that the Niobrara Member and equivalent strata consist primarily of interbedded calcareous shale and shaley limestone facies that increase in thickness to the northwest of the basin. The geochemical data suggest that during deposition of the Niobrara Member, anoxia and calcium enrichment increased to the east of the basin, whereas terrestrial input and clay enrichment increased to the northwest. Element cross-plots suggest that a large portion of the silicon is detrital and that the Niobrara Member becomes an increasingly more clastic than carbonate system to the west. The Δ Log R-derived total organic carbon (TOC) calculated using a sonic-resistivity overlay analysis technique shows that the Niobrara Member comprises organic-rich and organic-poor deposits. Average TOC values range between 1 (in organic-poor deposits) and 2.37 wt.% (in organic-rich deposits) with higher TOC values recorded in the southern and eastern portions of the basin. Relative-rock brittleness estimates from element and TOC data show the stratigraphic variability of alternating ductile (TOC rich, Ca and Si/Al poor) and brittle intervals (TOC poor, Ca and Si/Al rich) for the Niobrara Member

61st Annual Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 61st annual meeting of the Rocky Mountain Conference on Magnetic Resonance, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Copper Mountain, Colorado, July 25-29, 2022

THE MECHANISM OF RNA INTERFERENCE IN ARTHROPODS

RNA interference (RNAi) is a useful reverse genetics tool for investigation of gene function as well as for practical applications in many fields including medicine and agriculture. Due to the variability in RNAi efficiency, RNAi-based methods are currently being developed for controlling only coleopteran insects which are known to be amenable to RNAi. The first chapter of my thesis includes findings from research to investigate what are the factors that make coleopteran insects relatively more efficient in RNAi. I used Colorado potato beetle (CPB), Leptinotarsa decemlineata and its cell line (Lepd-SL1) as study models to identify genes that play key roles in RNAi pathway. Five genes including Argonaute-1 (microRNA Argonaute) and Aubergine (PiwiRNA Argonaute) were identified as those required for siRNA (short interfering RNA) RNAi pathway. I also found that RNAi is completely blocked in StaufenC knockdown cells. StaufenC belongs to dsRNA binding protein family and binds to dsRNA as shown by gel mobility shift and the pull-down assays. Interestingly, I also found that StaufenC is downregulated in RNAi resistant cells and StaufenC homologous sequences are present in only coleopteran insects where RNAi works efficiently. These data suggest that StaufenC is a major contributor to efficient RNAi in coleopteran insects and is a potential target for RNAi resistance. The second part of my research is to understand the mechanisms of RNAi in those insects refractory to RNAi. The barriers for successful RNAi include the presence of double-stranded ribonucleases (dsRNase) in the lumen and hemolymph that could potentially digest double-stranded RNA (dsRNA) and the variability in the transport of dsRNA into and within the cells. Recent work in our laboratory showed that the dsRNAs are transported into lepidopteran cells, but they are not processed into siRNAs because they are trapped in acidic bodies. I focused on identification of these acidic bodies in which dsRNAs accumulate in Spodoptera frugiperda Sf9 cells. These studies showed that entrapment of internalized dsRNA in endosomes is one of the major factors contributing to inefficient RNAi. Overall, my research revealed important players involved in successful and unsuccessful RNAi in insects