Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments – which are of great interest due to the potential to stimulate microbial methane generation – contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to low biomass oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 h apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment

1,2-Dichlorohexafluoro-Cyclobutane (1,2-c-C4F6Cl2, R-316c) a Potent Ozone Depleting Substance and Greenhouse Gas: Atmospheric Loss Processes, Lifetimes, and Ozone Depletion and Global Warming Potentials for the (E) and (Z) stereoisomers

The atmospheric processing of (E)- and (Z)-1,2-dichlorohexafluorocyclobutane (1,2-c-C4F6Cl2, R-316c) was examined in this work as the ozone depleting (ODP) and global warming (GWP) potentials of this proposed replacement compound are presently unknown. The predominant atmospheric loss processes and infrared absorption spectra of the R-316c isomers were measured to provide a basis to evaluate their atmospheric lifetimes and, thus, ODPs and GWPs. UV absorption spectra were measured between 184.95 to 230 nm at temperatures between 214 and 296 K and a parametrization for use in atmospheric modeling is presented. The Cl atom quantum yield in the 193 nm photolysis of R- 316c was measured to be 1.90 +/- 0.27. Hexafluorocyclobutene (c-C4F6) was determined to be a photolysis co-product with molar yields of 0.7 and 1.0 (+/-10%) for (E)- and (Z)-R-316c, respectively. The 296 K total rate coefficient for the O(1D) + R-316c reaction, i.e., O(1D) loss, was measured to be (1.56 +/- 0.11) 10(exp 10)cu cm/ molecule/s and the reactive rate coefficient, i.e., R-316c loss, was measured to be (1.36 +/- 0.20) 10(exp 10)cu cm/molecule/s corresponding to a approx. 88% reactive yield. Rate coefficient upper-limits for the OH and O3 reaction with R-316c were determined to be <2.3 10(exp 17) and <2.0 10(exp 22)cu cm/molecule/s, respectively, at 296 K. The quoted uncertainty limits are 2(sigma) and include estimated systematic errors. Local and global annually averaged lifetimes for the (E)- and (Z)-R-316c isomers were calculated using a 2-D atmospheric model to be 74.6 +/- 3 and 114.1 +/-10 years, respectively, where the estimated uncertainties are due solely to the uncertainty in the UV absorption spectra. Stratospheric photolysis is the predominant atmospheric loss process for both isomers with the O(1D) reaction making a minor, approx. 2% for the (E) isomer and 7% for the (Z) isomer, contribution to the total atmospheric loss. Ozone depletion potentials for (E)- and (Z)-R-316c were calculated using the 2-D model to be 0.46 and 0.54, respectively. Infrared absorption spectra for (E)- and (Z)-R-316c were measured at 296 K and used to estimate their radiative efficiencies (REs) and GWPs; 100-year time-horizon GWPs of 4160 and 5400 were obtained for (E)- and (Z)-R-316c, respectively. Both isomers of R-316c are shown in this work to be long-lived ozone depleting substances and potent greenhouse gases

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

BISULFATE (HSO4−_{4}^{-}) DEHYDRATION AT THE VAPOR/SOLUTION INTERFACE PROBED BY VIBRATIONAL SUM FREQUENCY GENERATION SPECTROSCOPY

Author Institution: Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210With perspective towards atmospheric chemistry, ion behavior at vapor/solution interfaces has important implications for understanding aqueous aerosols as reactions at this interface control the growth and uptake of the aerosol. Sulfate species are a major ionic component of aqueous acidic tropospheric aerosols with bisulfate (HSO$_{4}^{-}$) being the major sulfate species at pH values lower than 2. The application of inherently interface specific spectroscopic methods such as vibrational sum frequency generation (VSFG) allows for resolution of interfacial chemical species versus the bulk species facilitating a clearer understanding of chemical phenomena taking place at vapor/solution interfaces. Here we present VSFG results on the effects that cation identity have toward the molecular environment experienced by bisulfate anions residing within the vapor/solution interface for aqueous H$_{2}$SO$_{4}$, Na$_{2}$SO$_{4}$, and MgSO$_{4}$ solutions. By probing the $\nu_{\mathrm{SS}}$-SO$_{3}$ vibrational mode of interfacial bisulfate anions directly we are able to elucidate the influence that Na$^{+}$ and Mg$^{2+}$ ions have toward bisulfate hydration within the interface. Our results indicate that Na$^{+}$ and Mg$^{2+}$ perturb the hydration of interfacial bisulfate anions but do not form ion-pair complexes. Mg$^{2+}$ is found to exhibit a larger net influence on bisulfate hydration relative to Na$^{+}$

Sulfate Adsorption at the Buried Fluorite–Solution Interface Revealed by Vibrational Sum Frequency Generation Spectroscopy

Understanding the structure and energetics of adsorbed ions at buried mineral/solution interfaces has great importance to the geochemical and atmospheric chemistry communities. Vibrational spectroscopy is a powerful tool for the study of mineral/solution interfaces as these techniques can be applied in situ, are sensitive to surface structures, and are generally nondestructive. The use of vibrational sum frequency generation spectroscopy (VSFG), which is inherently interface-specific, is applied here to study the adsorption of sulfate at the buried fluorite (CaF₂)/Na₂SO₄ solution surface at pH 7 and 298 K in the presence of an aqueous background electrolyte, NaCl. The use of VSFG allowed for the resolution of adsorbed sulfate complexes from sulfate molecules which reside in the interfacial electric double layer yet remain fully solvated. The sulfate anion is found to adsorb with a bidentate inner-sphere structure at the fluorite surface with an average surface free energy of adsorption of −31 ± 3 kJ/mol for pH 7 solutions at 298 K

ION ORGANIZATION AND REVERSED ELECTRIC FIELD AT AIR/AQUEOUS INTERFACES REVEALED BY HETERODYNE-DETECTED SUM FREQUENCY GENERATION SPECTROSCOPY

Author Institution: Department of Chemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210Sum frequency generation (SFG) is a second order optical spectroscopy that probes regions of non centrosymmetry, interfaces, and allows for the understanding of molecular organization at air/aqueous interfaces. An overview of our work in this area is presented with emphasis on phase-sensitive SFG (PS-SFG) spectroscopy. PS-SFG is a variant of SFG and is used in our laboratory to investigate the average direction of the transition dipole of interfacial water molecules. The orientation of water at air/aqueous inorganic salts interfaces of CaCl$_{2}$, NaCl, Na$_{2}$SO$_{4}$, (NH$_{4}$)$_{2}$SO$_{4}$, and Na$_{2}$CO$_{3}$ is inferred from the direct measurement of the transition dipole moment. We find that charge separation at the air/water interface is most obvious for the aqueous ammonium sulfate solution where the local electric field has a greater magnitude at this interface relative to the other salt solutions. The magnitude of the electric field in the surface extending to the subsurface regions decreases in the order: (NH$_{4}$)$_{2}$SO$_{4}$ $>$ Na$_{2}$SO$_{4}$ $>$ Na$_{2}$CO$_{3}$ $\geq$ CaCl$_{2}$ $>$ NaCl; the electric field is opposite in direction for the sulfates and carbonate relative to the chloride salts

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments – which are of great interest due to the potential to stimulate microbial methane generation – contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to low biomass oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 h apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment

Cathodoluminescence differentiates sedimentary organic matter types

Abstract High-resolution scanning electron microscopy (SEM) visualization of sedimentary organic matter is widely utilized in the geosciences for evaluating microscale rock properties relevant to depositional environment, diagenesis, and the processes of fluid generation, transport, and storage. However, despite thousands of studies which have incorporated SEM methods, the inability of SEM to differentiate sedimentary organic matter types has hampered the pace of scientific advancement. In this study, we show that SEM-cathodoluminescence (CL) properties can be used to identify and characterize sedimentary organic matter at low thermal maturity conditions. Eleven varied mudstone samples with a broad array of sedimentary organic matter types, ranging from the Paleoproterozoic to Eocene in age, were investigated. Sedimentary organic matter fluorescence intensity and CL intensity showed an almost one-to-one correspondence, with certain exceptions in three samples potentially related to radiolytic alteration. Therefore, because CL emission can be used as a proxy for fluorescence emission from sedimentary organic matter, CL emission during SEM visualization can be used to differentiate fluorescent from non-fluorescent sedimentary organic matter. This result will allow CL to be used as a visual means to quickly differentiate sedimentary organic matter types without employing correlative optical microscopy and could be widely and rapidly adapted for SEM-based studies in the geosciences