Intact Core Research Articles

Colloid Mobilization in a Fractured Soil: Effect of Pore-Water Exchange between Preferential Flow Paths and Soil Matrix.

Exchange of water and solutes between contaminated soil matrix and bulk solution in preferential flow paths has been shown to contribute to the long-term release of dissolved contaminants in the subsurface, but whether and how this exchange can affect the release of colloids in a soil are unclear. To examine this, we applied rainfall solutions of different ionic strength on an intact soil core and compared the resulting changes in effluent colloid concentration through multiple sampling ports. The exchange of water between soil matrix and the preferential flow paths leading to each port was characterized on the basis of the bromide (conservative tracer) breakthrough time at the port. At individual ports, two rainfalls of a certain ionic strength mobilized different amounts of colloids when the soil was pre-exposed to a solution of lower or higher ionic strength. This result indicates that colloid mobilization depended on rainfall solution history, which is referred as colloid mobilization hysteresis. The extent of hysteresis was increased with increases in exchange of pore water and solutes between preferential flow paths and matrix. The results indicate that the soil matrix exchanged the old water from the previous infiltration with new infiltrating water during successive infiltration and changed the pore water chemistry in the preferential flow paths, which in turn affected the release of soil colloids. Therefore, rainfall solution history and soil heterogeneity must be considered to assess colloid mobilization in the subsurface. These findings have implications for the release of colloids, colloid-associated contaminants, and pathogens from soils.

One-pot preparation of hydrophobic cellulose nanocrystals in an ionic liquid

The facile one-pot preparation of hydrophobic cellulose nanocrystals (CNCs) from wood pulpboard in an ionic liquid is reported in the present paper. This process employed a so-called amorphous cellulose solvent system capable of dissolving the majority of the amorphous regions in cellulose while maintaining the crystalline domains essentially intact, and consisting of tetrabutylammonium acetate with dimethylacetamide. These solvents were mixed at a mass ratio of 1:9 in conjunction with acetic anhydride to prepare CNCs via surface acetylation. The rod-like morphology and nanometer-scale dimensions of the resulting CNCs were ascertained by atomic force microscopy and transmission electron microscopy. Successful surface acetylation while maintaining an intact crystalline core was confirmed by Fourier transform infrared, 13C CP/MAS NMR and X-ray photoelectron spectroscopy in addition to X-ray diffraction. Finally, the thermal stability and hydrophobic behavior of the hydrophobic CNCs were characterized using thermal gravimetric analysis and water contact-angle measurements, respectively.

Enhanced Chiroptical Activity in Glutathione-Protected Bimetallic (AuAg)18 Nanoclusters with Almost Intact Core–Shell Configuration

We here focus on the chiroptical response of a glutathione (GS)-protected bimetallic (AuAg)18 nanocluster containing comparable amounts of Au and Ag atoms. X-ray photoelectron spectroscopy (XPS) as well as the electrophoretic pattern allow us to determine the chemical composition of the nanocluster as Au8.5Ag9.5(SG)14. Chiroptical activity of the Au8.5Ag9.5 nanocluster is enhanced as compared to that of the corresponding monometallic Au counterpart, whereas that of bimetallic (AuAg)18 nanocluster with the atomic ratio of Au/Ag = 4.0 (Au14.4Ag3.6) decreases. Since thiolate-protected Au18 nanocluster has recently been revealed to consist of a face-fused Au9 bioctahedral kernel protected by one Au4(SR)5 tetramer, one Au2(SR)3 dimer, and three Au(SR)2 monomers, we use density functional theory (DFT) calculations to predict the lowest-energy structure of a model cluster compound Au9Ag9(SH)14 on the basis of this geometry, yielding a Agcore–Austaple intact core–shell configuration. This structure is in good agr...

Frequency and Characteristics of Dust Sediments in Core Samples from Hashylan Wetland, Kermanshah, Iran

Dust phenomenon is one of the biggest environmental problems in arid and semiarid regions. In these areas, lakes and wetlands are natural dust traps and core sampling method can be an appropriate way to assess the phenomenon of the dust. Therefore, the purpose of this study is the study of frequency and characteristics of dust sediments in core samples from Hashilan wetlands, Kermanshah. Four intact core samples were taken from different parts of the Hashilan wetland in Kermanshah. Physical, chemical and micromorphological analysis were done. Also clay mineralogy was performed using X-ray analysis (XRD) and shape of particles was photographed by scanning electron microscope (SEM). Considering that four samples had been taken from different parts of the wetland, the quantitative differences in dust amount are likely due to the location of the samples. The results of XRD and thin sections show that the dominant mineralogical composition of dust particles was clay minerals, quartz and calcite. SEM results for core sample 1 revealed that most particles had the size between 2 to 50 mm which ranged from fine silt to coarse silt. Considering the similarities between SEM images for core sample 1 and those from Kermanshah dust measurement station, it could be said that fine rounded particles detected at top 30 cm of core samples had Aeolian origin. These findings were in accordance with the results from dust measurement and weather station of Kermanshah about increased dust activities in the study area over past 10 years.

Mercury transformation and release differs with depth and time in a contaminated riparian soil during simulated flooding

Riparian soils are an important environment in the transport of mercury in rivers and wetlands, but the biogeochemical factors controlling mercury dynamics under transient redox conditions in these soils are not well understood. Mercury release and transformations in the Oa and underlying A horizons of a contaminated riparian soil were characterized in microcosms and an intact soil core under saturation conditions. Pore water dynamics of total mercury (HgT), methylmercury (MeHg), and dissolved gaseous mercury (Hg0(aq)) along with selected anions, major elements, and trace metals were characterized across redox transitions during 36d of flooding in microcosms. Next, HgT dynamics were characterized over successive flooding (17d), drying (28d), and flooding (36d) periods in the intact core. The observed mercury dynamics exhibit depth and temporal variability. At the onset of flooding in microcosms (1–3d), mercury in the Oa horizon soil, present as a combination of ionic mercury (Hg(II)) bound to thiol groups in the soil organic matter (SOM) and nanoparticulate metacinnabar (β-HgS), was mobilized with organic matter of high molecular weight. Subsequently, under anoxic conditions, pore water HgT declined coincident with sulfate (3–11d) and the proportion of nanoparticulate β-HgS in the Oa horizon soil increased slightly. Redox oscillations in the intact Oa horizon soil exhausted the mobile mercury pool associated with organic matter. In contrast, mercury in the A horizon soil, present predominantly as nanoparticulate β-HgS, was mobilized primarily as Hg0(aq) under strongly reducing conditions (5–18d). The concentration of Hg0(aq) under dark reducing conditions correlated positively with byproducts of dissimilatory metal reduction (∑(Fe,Mn)). Mercury dynamics in intact A horizon soil were consistent over two periods of flooding, indicating that nanoparticulate β-HgS was an accessible pool of mobile mercury over recurrent reducing conditions. The concentration of MeHg increased with flooding time in both the Oa and A horizon pore waters. Temporal changes in pore water constituents (iron, manganese, sulfate, inorganic carbon, headspace methane) all implicate microbial control of redox transitions. The mobilization of mercury in multiple forms, including HgT associated with organic matter, MeHg, and Hg0(aq), to pore waters during periodic soil flooding may contribute to mercury releases to adjacent surface waters and the recycling of the legacy mercury to the atmosphere.

KLF15 Establishes the Landscape of Diurnal Expression in the Heart.

Circadian rhythms offer temporal control of anticipatory physiologic adaptations in animals. In the mammalian cardiovascular system, the importance of these rhythms is underscored by increased cardiovascular disease in shift workers, findings recapitulated in experimental animal models. However, a nodal regulator that allows integration of central and peripheral information and coordinates cardiac rhythmic output has been elusive. Here, we show that kruppel-like factor 15 (KLF15) governs a biphasic transcriptomic oscillation in the heart with a maximum ATP production phase and a remodeling and repair phase corresponding to the active and resting phase of a rodent. Depletion of KLF15 in cardiomyocytes leads to a disorganized oscillatory behavior without phasic partition despite an intact core clock. Thus, KLF15 is a nodal connection between the clock and meaningful rhythmicity in the heart.

Phosphite flux at the sediment–water interface in northern Lake Taihu

Phosphite (H2PO3−, HPO32−, +3 valence), a reduced form of phosphorus (P), has been widely detected in water environments. The role of phosphite in the P biogeochemical cycle has not been investigated systematically and quantitative results on phosphite fluxes are lacking. In this study, intact sediment core simulation was employed to measure the flux of phosphite at the sediment–water interface in northern Lake Taihu. Phosphite fluxes (μmolm−2d−1) ranged from −38.21±1.14 to 7.10±2.18, with an annual average of −4.72±10.40. On the whole, phosphite migrated from water into sediment and the sediment was primarily a sink. The highest seasonal negative phosphite fluxes (μmolm−2d−1) occurred in winter (−10.44±18.63), followed by summer (−8.04±5.61) and spring (−2.61±4.17). In autumn, phosphite flux was 2.20±4.07. Higher annual average negative fluxes of phosphite (μmolm−2d−1) appeared in site ZSB (−12.70±17.96), which contained the highest content of total soluble P. The average yearly migration of phosphite in Lake Taihu from water to sediment was estimated to be (4.04±8.88)×106moly−1. The transfer of phosphite from water into sediment usually occurs in winter may due to the season's natural tendency to create more favorable conditions for phosphite biogeochemical reactions. Phosphite fluxes showed significant negative correlations with the original phosphite concentration in water (r=−0.840, p<0.01), as well as organic matter (r=−0.720, p<0.01) and phosphate bound to Ca (Ca-Ps) (r=−0.632, p<0.05) in sediment. These results indicate that microbiological processes and P species bound to Ca may play an important role in the P redox cycle. No significant correlations between phosphite fluxes and dissolved oxygen or oxidation-reduction potential were observed.

Correlating physico-mechanical properties of intact rocks with P-wave velocity

The physico-mechanical properties of five different intact rock types including sandstone, arkoses and limestone were determined through standardized laboratory tests. Ninety six specimens were tested to obtain the relationships between P-wave velocity (Vp), dry unit weight (DUW), uniaxial compressive strength (UCS), point load index Is(50), Brazilian tensile strength (TS), porosity (Φ), and Schmidt hardness (RN). This study also reviews some recent correlations between P-wave velocity and physico-mechanical properties as well as investigates the reliability of these correlations. Findings show the results of the experimental tests are in good agreement with previous studies. Statistical equations have been determined for estimating the physico-mechanical properties of rocks using nondestructive and indirect test methods. Results of regression analysis showed satisfactory correlations. Based on the results, new strong correlation with correlation coeffecients above (R2 > 0.80) are introduced for predicting the UCS, Is(50), Φ and RN and reasonable good correlations (R2 ≥ 0.78) are introduced to predict TS and DUW from P-wave velocity of different intact rock core samples. There is a discrepancy between P-wave velocity (Vp) in situ values with laboratory results. The large reductions in Vp in situ values are clearly the functions of fractures and natural joints.

FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2.

The Fanconi anemia (FA)-BRCA pathway mediates repair of DNA interstrand crosslinks. The FA core complex, a multi-subunit ubiquitin ligase, participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins, FANCD2 and FANCI (or the ID complex). However, the regulation of the FA core complex itself is poorly understood. Here we show that the FA core complex proteins are recruited to sites of DNA damage and form nuclear foci in S and G2 phases of the cell cycle. ATR kinase activity, an intact FA core complex and FANCM-FAAP24 were crucial for this recruitment. Surprisingly, FANCI, but not its partner FANCD2, was needed for efficient FA core complex foci formation. Monoubiquitination or ATR-dependent phosphorylation of FANCI were not required for the FA core complex recruitment, but FANCI deubiquitination by USP1 was. Additionally, BRCA1 was required for efficient FA core complex foci formation. These findings indicate that FANCI functions upstream of FA core complex recruitment independently of FANCD2, and alter the current view of the FA-BRCA pathway.

EUS-Guided Liver Fine Needle Biopsy With a 19-Gauge SharkCore Needle in Patients Undergoing EUS to Evaluate for Biliary Disease

Introduction: Non Malignant Liver biopsies are currently performed via a percutaneous approach and transjugular approach. EUS guided liver fine needle Aspiration FNA of non malignant liver disease has been reported in the literature. EUS guided liver biopsy using a novel 19 Gauge Fine Needle Biopsy (FNB) (SharkCore, Medtronic) offers an alternative to produce a biopsy with preserved tissue architecture. Our aim is to describe the initial experience using a novel FNB needle in the evaluation of liver disease in patients undergoing EUS for biliary disease evaluation in the setting of abnormal liver function tests. Methods: This is a retrospective case series from April 2015 to May 2015, in a tertiary medical center of patients referred for EUS evaluation of biliary disease in the setting of abnormal liver function tests. We reviewed six patients with abnormal liver function tests, who had normal biliary EUS evalutions. Two passes with 19 Gauge FNB SharkCore needle using the saline wet technique and high suction (20cc) were used. The specimens were put in formalin and sent for pathology evaluation, number of intact portal triads, intact core specimen length, stage and grade of liver disease. Post EUS FNB complications were monitor at one week follow up.Figure 1Figure 2Figure 3Results: We evaluated 6 EUS guided FNB liver biopsies in 6 patients (50% women), ages (33-76) with abnormal liver function tests and a normal biliary EUS evaluation. The pathology was consistent with alcohol liver disease (33.3%), drug induced liver toxicity (16.7%), autoimmune liver disease (16.7%), and NASH (33.3%). The mean number of intact portal tracts 9.83 (range 7-18), all specimens where adequate for pathological evaluation. Median intact core specimen length was 34.4 mm (range 21mm to 65.9mm). The average grade of liver disease 1.7 (range 1-2) and stage 2.2 (range 0-3). Post EUS FNB 33.3% of patient complained of right upper quadrant pain and all resolved after one dose of pain medication. There were no reported complications and persistent pain at one week follow up. Conclusion: A novel EUS guided FNB 19 G needle (SharkCore) provided adequate pathological yield and safety profile. EUS guided FNB is an alternative to liver biopsy in patients undergoing EUS for biliary disease exclusion, it provides adequate tissue architecture it is relatively safe. Larger prospective studies are needed to fully understand the role of EUS guided liver FNB.

An Equation to Evaluate the Unconfined Compressive Strength of Rock from Splitting Tensile Strength Test Results

The unconfined compressive strength (UCS) of rock is a basic parameter for the design of foundations resting on rock. However, it is often very difficult to retrieve intact rock core specimens for the UCS test due to mechanical breaking or natural fracturing of the rock core during the drilling process. In such cases, it becomes obligatory to correlate UCS values based on the point load strength index test results. Correlation between the UCS and the point load strength index test results has been observed to be inconsistent in many instances and hence a need for another such correlation with a relatively higher degree of accuracy to predict UCS values of rock sample has been generated. An endeavor has been made to correlate the UCS value based on the test results of a splitting tensile strength test (STS) by conducting both the tests on various rock samples. Though the UCS test provides compressive strength and the STS test provides tensile strength of a rock, a dimensional analysis technique has been used to correlate these properties. The predicted UCS results are compared with the actual lab UCS test results to validate the mathematical equation thus developed. It has been observed from comparison that this equation can be used to predict UCS values from STS results with a fair degree of accuracy. Thus the Dimensional analysis has established a provisional rule-of-thumb to correlate the UCS with STS test results and further proved that, it is an easy and sufficiently accurate analytical tool.

Influence of temperature, pH, and salinity on membrane lipid composition and TEX86 of marine planktonic thaumarchaeal isolates

Marine ammonia-oxidizing archaea of the phylum Thaumarchaeota are a cosmopolitan group of microorganisms representing a major fraction of the picoplankton in the ocean. The cytoplasmic membranes of Thaumarchaeota consist predominantly of intact polar isoprenoid glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, which may be used as biomarkers for living Thaumarchaeota. Fossil thaumarchaeal GDGT core lipids accumulate in marine sediments and serve as the basis for geochemical proxies such as the TEX86 paleothermometer. Here, we demonstrate that the responses of membrane lipid compositions and resulting TEX86 values to growth temperature strongly diverge in three closely related thaumarchaeal pure cultures, i.e., Nitrosopumilus maritimus and two novel strains isolated from South Atlantic surface water, although the inventories of intact polar lipids and core lipids were overall similar in the three strains. N. maritimus and its closely related strain NAOA6 showed linear relationships of TEX86 and growth temperature but no correlation of TEX86 and temperature was observed in the more distantly related strain NAOA2. In contrast, the weighted average number of cycloalkyl moieties (ring index) was linearly correlated with growth temperature in all strains. This disparate relationship of TEX86 to growth temperature among closely related Thaumarchaeota suggests that the ring index but not the TEX86 ratio represents a universal response to growth temperature in marine planktonic Thaumarchaeota. Furthermore, the distinct TEX86-temperature relationships in the cultivated strains indicate that environmental GDGT signals may include an ecological component, which has important implications for ocean temperature reconstructions using the TEX86 proxy. In contrast, different growth medium salinities in the range 27–51‰ tested for N. maritimus showed no systematic effect on intact polar GDGT composition and TEX86. Similarly, N. maritimus showed only small changes in intact polar GDGT composition and TEX86 when grown at different medium pH in the range 7.3–7.9. Overall, our pure culture studies suggest that the TEX86 paleotemperature proxy is not solely dependent on growth temperature, but may amalgamate physiological, environmental, and ecological factors.

Reversible 26S proteasome disassembly upon mitochondrial stress

In eukaryotic cells, proteasomes exist primarily as 26S holoenzymes, the most efficient configuration for ubiquitinated protein degradation. Here, we show that acute oxidative stress caused by environmental insults or mitochondrial defects results in rapid disassembly of 26S proteasomes into intact 20S core and 19S regulatory particles. Consequently, polyubiquitinated substrates accumulate, mitochondrial networks fragment, and cellular reactive oxygen species (ROS) levels increase. Oxidation of cysteine residues is sufficient to induce proteasome disassembly, and spontaneous reassembly from existing components is observed both in vivo and in vitro upon reduction. Ubiquitin-dependent substrate turnover also resumes after treatment with antioxidants. Reversible attenuation of 26S proteasome activity induced by acute mitochondrial or oxidative stress may be a short-term response distinct from adaptation to long-term ROS exposure or changes during aging.

Temporal effects of food waste compost on soil physical quality and productivity

Reynolds, W. D., Drury, C. F., Tan, C. S. and Yang, X. M. 2015. Temporal effects of food waste compost on soil physical quality and productivity. Can. J. Soil Sci. 95: 251–268. The benefits of compost additions on soil organic carbon content and crop productivity are extant in the literature, but detailed studies of compost effects on soil physical quality (SPQ) are limited. The objective of this study was therefore to describe how one-time additions of compost impact the immediate, mid-term and long-term SPQ and crop yields of an agricultural soil. Food waste compost (FWC) was incorporated once into the top 10 cm of a humid-temperate Brookston clay loam soil at rates of 0 (Control), 75 dry t ha−1 (FWC-75), 150 dry t ha−1 (FWC–150) and 300 dry t ha−1 (FWC-300); measurements of SPQ parameters and corn yield were then made annually over the next 11 yr. The SPQ parameters included bulk density (BD), organic carbon content (OC), air capacity (AC), plant-available water capacity (PAWC), relative field capacity (RFC), and saturated hydraulic conductivity (KS), which were obtained from intact (undisturbed) soil core samples. Prior to compost addition, BD, OC, AC, PAWC, RFC and KS were substantially non-optimal, and BD had increased relative to virgin soil by 46%, while OC, AC and PAWC had decreased relative to virgin soil by 60, 56 and 43%, respectively. Improvements in SPQ 1 yr after compost addition were negligible or small for FWC-75 and FWC-150, but FWC-300 generated optimal values for BD, OC, AC, PAWC and RFC. The SPQ parameters degraded with time, but 11 yr after compost addition, OC and AC under FWC-300 were still within their optimal ranges, as well as significantly (P&lt;0.05) greater than the Control values by 65 and 26%, respectively. Soil cracks and biopores apparently induced substantial annual variation in KS, but average KS nevertheless increased with increasing compost addition rate. Corn grain yield varied substantially among years, which was likely due to weather and compost effects; however, 11-yr cumulative yields from the compost treatments were greater than the Control by 2200–6500 kg ha−1.

Vegetated canals mitigate nitrogen surplus in agricultural watersheds

Within irrigated agricultural watersheds, canal networks may play a crucial role as nitrogen (N) sink. This is due to the intertwined action of macrophytes and microbial communities occurring in the dense net of small watercourses. We hypothesize that vegetated canals may buffer relevant fractions of excess N from agriculture via microbial denitrification, and that vegetation provides multiple interfaces that greatly support the activity of bacteria. To test these hypotheses, we measured net dinitrogen (N2) fluxes in bare sediments and at the reach-scale in vegetated ditches. As study areas we selected canals subjected to diffuse N pollution, laying in a lowland sub-basin of the Po River (northern Italy). Denitrification was evaluated on the basis of changes in dissolved N2:Ar, measured by Membrane Inlet Mass Spectrometry. Complementary data were obtained via upstream–downstream inorganic N balances and intact core incubations targeting sedimentary N fluxes. Denitrification was the major pathway for N removal, with rates at the reach-scale (5–25mmolNm−2d−1) up to one order of magnitude higher than in sediment alone (3–7mmolNm−2 d−1). Results highlighted that N uptake by macrophyte stands was quantitatively small; however, aquatic vegetation provided multiple interfaces for microbial growth and N-related processes. Our data suggest that 1ha of vegetated canal may remove between 150 and 560kgNyr−1. In the study area, an average canal density of ∼0.05 linear kmha−1 of agricultural land has the potential to buffer 5–17% of the excess N from agriculture (∼60kgNha−1yr−1).The results of this study suggest the central role of emergent vegetation in promoting microbial N-transformation and canal self-depuration. Innovative management of the canal networks should couple hydraulic needs with the maintenance of emergent vegetation.

Phosphorus mobility under short-term anoxic conditions in two shallow eutrophic coastal systems (Curonian and Sacca di Goro lagoons)

The effects of short-term anoxia on phosphorus mobility were investigated in estuarine sediments collected from two eutrophic European lagoons. Study areas differ with regard to climate and salinity: the boreal Curonian Lagoon (Lithuania) is oligohaline while the Mediterranean Sacca di Goro (Italy) is mesohaline. In each lagoon two sites were chosen representing areas impacted by river plume discharge and areas impacted by high organic matter deposition. Benthic fluxes of dissolved oxygen, inorganic phosphorus (DIP), iron (Fe2+) and manganese (Mn2+) were measured by dark intact core incubations in oxic and anoxic conditions. The latter were induced by incubation prolonged by up to 40 h depending on oxygen consumption rates. Solid phase P pools and pore water profiles of DIP, Fe2+, Mn2+ and sulfides were also measured before and after the induction of anoxia. Although incubation temperature and organic matter content were similar in plume and organic impacted areas of the two estuaries, higher benthic oxygen consumption rates were observed in Sacca di Goro, suggesting higher reactivity of the organic pool. Short-term anoxia had a significant effect on benthic fluxes of DIP (sulfide and Fe2+) only at the organic-rich and saline site of Sacca di Goro while internal buffers prevented inorganic P regeneration at the remaining sites. However, the analysis of pore water and solid phase pools revealed large variations during the transition and provided insights on the mechanisms controlling P dynamics. Both stations influenced by river plume deposition had high total inorganic P content (but most of it was refractory) and high reactive Mn pools, continuously regenerated by ventilation and irrigation of sediments by macrofauna. In these sites, oxygen depletion resulted in large accumulation of reduced Mn in the pore water but high fluxes of Mn2+ were also measured in the oxic part of the incubation suggesting the relevance of this respiration process. Thus Mn reduction preserved oxidized Fe pool and ultimately prevent P mobilization. Our results suggest that fluxes of DIP across the sediment–water interface are controlled by an array of different and site-specific mechanisms. These biogeochemical buffers are effective and contrast massive P release to the water column in highly productive systems as coastal lagoons, where episodes of transient oxygen shortage are frequent.

Using Ground and Intact Coal Samples To Evaluate Hydrocarbon Fate during Supercritical CO2 Injection into Coal Beds: Effects of Particle Size and Coal Moisture

To investigate the potential for mobilizing organic compounds from coal beds during geologic carbon dioxide (CO2) storage (sequestration), a series of solvent extractions using dichloromethane (DCM) and using supercritical CO2 (40 °C and 10 MPa) were conducted on a set of coal samples collected from Louisiana and Ohio. The coal samples studied range in rank from lignite A to high volatile A bituminous, and were characterized using proximate, ultimate, organic petrography, and sorption isotherm analyses. Sorption isotherm analyses of gaseous CO2 and methane show a general increase in gas storage capacity with coal rank, consistent with findings from previous studies. In the solvent extractions, both dry, ground coal samples and moist, intact core plug samples were used to evaluate effects of variations in particle size and moisture content. Samples were spiked with perdeuterated surrogate compounds prior to extraction, and extracts were analyzed via gas chromatography–mass spectrometry. The DCM extracts generally contained the highest concentrations of organic compounds, indicating the existence of additional hydrocarbons within the coal matrix that were not mobilized during supercritical CO2 extractions. Concentrations of aliphatic and aromatic compounds measured in supercritical CO2 extracts of core plug samples generally are lower than concentrations in corresponding extracts of dry, ground coal samples, due to differences in particle size and moisture content. Changes in the amount of extracted compounds and in surrogate recovery measured during consecutive supercritical CO2 extractions of core plug samples appear to reflect the transition from a water-wet to a CO2-wet system. Changes in coal core plug mass during supercritical CO2 extraction range from 3.4% to 14%, indicating that a substantial portion of coal moisture is retained in the low-rank coal samples. Moisture retention within core plug samples, especially in low-rank coals, appears to inhibit accessibility of supercritical CO2 to coal matrix porosity, limiting the extent to which hydrocarbons are mobilized. Conversely, the enhanced recovery of some surrogates from core plugs relative to dry, ground coal samples might indicate that, once mobilized, supercritical CO2 is capable of transporting these constituents through coal beds. These results underscore the need for using intact coal samples, and for better characterization of forms of water in coal, to understand fate and transport of organic compounds during supercritical CO2 injection into coal beds.

Practical Investigations on Use of Weighted Joint Density to Decrease the Limitations of RQD Measurements

Various techniques have been established in geotechnical engineering to determine the quality of rock drilled out from a borehole. These simple and inexpensive methods include total core recovery (TCR), solid core recovery (SCR), and rock quality designation (RQD). Among these, RQD provides a general indication of rock mass quality and is widely used as an index to evaluate rock quality by expressing the degree of fracturing in drill cores. The RQD was modified from the TCR method by Deere (1963) to indirectly measure the number of fractures and amount of softening or/and alteration in rock mass for engineering applications. Its simplicity, low cost, and reproducibility generally resulted in quick development of the RQD for a wide variety of rock engineering applications, such as tunnels, mining engineering, and large caverns. Nowadays, this method is considered as a standard method in drill core logging and forms a basic element of the most widely used rock mass classification systems, such as the rock mass rating (RMR) and Q-system (Bieniawski 1989; Barton 1995). However, a number of limitations such as dependence on borehole orientation and the selected threshold value for the minimum intact core length restrict the consistency of the measured values. Accordingly, several methods have been established to overcome these limitations, such as the corrected rock quality designation (RQDc) (Li et al. 2009), volumetric joint density (Jv) (Palmstrom 1982, 1985, 1986; Sen and Eissa 1992), cumulative core index (Sen 1990), and weighted joint density (WJD) (Palmstrom 1995, 2005). Although such new methods have been developed, the RQD is still used with the initial definition, without correction, in many geotechnical engineering applications, e.g., rock mass classification, rock mass strength, and modulus of elasticity. This paper reviews the conventional RQD measurement techniques by Deere (1963) and RQD measurements from the WJD (hereafter called RQDWJD) by Palmstrom (2005) using rock cores drilled out from directional boreholes at the Bakhtiary Dam site. In this way, the RQD values from different methods were compared, and a new modification is proposed, called RQDM-WJD.

Single-Nucleotide Polymorphisms Found in the migA and wbpX Glycosyltransferase Genes Account for the Intrinsic Lipopolysaccharide Defects Exhibited by Pseudomonas aeruginosa PA14.

Pseudomonas aeruginosa PA14 is widely used by researchers in many laboratories because of its enhanced virulence over strain PAO1 in a wide range of hosts. Although lipopolysaccharide (LPS) is an important virulence factor of all P. aeruginosa strains, the LPS of PA14 has not been characterized fully. A recent study showed that the structure of its O-specific antigen (OSA) belongs to serotype O19. We found that the OSA gene cluster of PA14 shares ∼99% identity with those of the O10/O19 group. These two serotypes share the same O-unit structure, except for an O-acetyl substitution in one of the sugars in O10. Here we showed that both PA14 and O19 LPS cross-reacted with the O10-specific monoclonal antibody MF76-2 in Western blots. Analysis by SDS-PAGE and silver staining showed that PA14 LPS exhibited modal chain lengths that were different from those of O19 LPS, in that only "very long" and "short" chain lengths were observed, while "medium" and "long" chain lengths were not detected. Two other novel observations included the lack of the uncapped core oligosaccharide epitope and of common polysaccharide antigen (CPA) LPS. The lack of the uncapped core oligosaccharide was caused by point mutations in the glycosyltransferase gene migA, while the CPA-negative phenotype was correlated with a single amino acid substitution, G20R, in the glycosyltransferase WbpX. Additionally, we showed that restoring CPA biosynthesis in PA14 significantly stimulated mature biofilm formation after 72 h, while outer membrane vesicle production was not affected. P. aeruginosa PA14 is a clinical isolate that has become an important reference strain used by many researchers worldwide. LPS of PA14 has not been characterized fully, and hence, confusion about its phenotype exists in the literature. In the present study, we set out to characterize the O-specific antigen (OSA), the common polysaccharide antigen (CPA), and the core oligosaccharide produced by PA14. We present evidence that PA14 produces an LPS consisting of "very-long-chain" and some "short-chain" OSA belonging to the O19 serotype but is devoid of CPA and the uncapped core oligosaccharide epitope. These intrinsic defects in PA14 LPS were due to single-nucleotide polymorphisms (SNPs) in the genes that encode glycosyltransferases in the corresponding biosynthesis pathways. Since sugars in CPA and the uncapped core are receptors for different bacteriocins and pyocins, the lack of CPA and an intact core may contribute to the increased virulence of PA14. Restoring CPA production in PA14 was found to stimulate mature biofilm formation.

Whole vitreous humor dissection for vitreodynamic analysis.

The authors propose an effective technique to isolate whole, intact vitreous core and cortex from post mortem enucleated porcine eyes. While previous studies have shown the results of such dissections, the detailed steps have not been described, precluding researchers outside the field from replicating their methods. Other studies harvest vitreous either through aspiration, which does not maintain the vitreous structure anatomy, or through partial dissection, which only isolates the vitreous core. The proposed method isolates the whole vitreous body, with the vitreous core and cortex intact, while maintaining vitreous anatomy and structural integrity. In this method, a full thickness scleral flap in an enucleated porcine eye is first created and through this, the choroid tissue can be separated from the sclera. The scleral flap is then expanded and the choroid is completely separated from the sclera. Finally the choroid-retina tissue is peeled off the vitreous to leave an isolated intact vitreous body. The proposed vitreous dissection technique can be used to study physical properties of the vitreous humor. In particular, this method has significance for experimental studies involving drug delivery, vitreo-retinal oxygen transport, and intraocular convection.