A Set of In Situ Informed Simulated Medium Formats for Culturing Environmentally Acquired Anaerobic Microorganisms.

Culture-dependent research of anaerobic microorganisms rests upon methodological competence. These methods must create and maintain suitable growth conditions (e.g., pH and carbon sources) for anaerobic microorganisms while also allowing samples to be extracted without compromising the artificial environment. To this end, methods that are informed by and simulate an in situ environment can be of great aid in culturing microorganisms from that environment. Here, we outline an in situ informed and simulated anaerobic method for culturing terrestrial surface and subsurface microorganisms, emphasizing anaerobic sample collection with minimal perturbation. This protocol details the production of a customizable anaerobic liquid medium, and the environmental acquisition and in vitro growth of anaerobic microorganisms. The protocol also covers critical components of an anaerobic bioreactor used for environmental simulations of sediment and anaerobic liquid media for environmentally acquired cultures. We have included preliminary Next Generation Sequencing data from a maintained microbiome over the lifespan of a bioreactor where the active culture dynamically adjusted in response to an experimental carbon source.

Equilibrated Gas and Carbonate Standard-Derived Dual (Δ47 and Δ48) Clumped Isotope Values.

Carbonate clumped isotope geochemistry has primarily focused on mass spectrometric determination of m/z 47 CO2 for geothermometry, but theoretical calculations and recent experiments indicate paired analysis of the m/z 47 (13C18O16O) and m/z 48 (12C18O18O) isotopologues (referred to as Δ47 and Δ48) can be used to study non-equilibrium isotope fractionations and refine temperature estimates. We utilize 5,448 Δ47 and 3,400 Δ48 replicate measurements of carbonate samples and standards, and 183 Δ47 and 195 Δ48 replicate measurements of gas standards from 2015 to 2021 from a multi-year and multi-instrument data set to constrain Δ47 and Δ48 values for 27 samples and standards, including Devils Hole cave calcite, and study equilibrium Δ47-Δ48, Δ47-temperature, and Δ48-temperature relationships. We compare results to previously published findings and calculate equilibrium regressions based on data from multiple laboratories. We report acid digestion fractionation factors, Δ*63-47 and Δ*64-48, and account for their dependence on the initial clumped isotope values of the mineral.

Alpine permafrost could account for a quarter of thawed carbon based on Plio-Pleistocene paleoclimate analogue.

Estimates of the permafrost-climate feedback vary in magnitude and sign, partly because permafrost carbon stability in warmer-than-present conditions is not well constrained. Here we use a Plio-Pleistocene lacustrine reconstruction of mean annual air temperature (MAAT) from the Tibetan Plateau, the largest alpine permafrost region on the Earth, to constrain past and future changes in permafrost carbon storage. Clumped isotope-temperatures (Δ47-T) indicate warmer MAAT (~1.2 °C) prior to 2.7 Ma, and support a permafrost-free environment on the northern Tibetan Plateau in a warmer-than-present climate. Δ47-T indicate ~8.1 °C cooling from 2.7 Ma, coincident with Northern Hemisphere glacial intensification. Combined with climate models and global permafrost distribution, these results indicate, under conditions similar to mid-Pliocene Warm period (3.3-3.0 Ma), ~60% of alpine permafrost containing ~85 petagrams of carbon may be vulnerable to thawing compared to ~20% of circumarctic permafrost. This estimate highlights ~25% of permafrost carbon and the permafrost-climate feedback could originate in alpine areas.

What are the competency requirements for clinical pharmacist verification of systemic anti-cancer therapy (SACT) prescribed within a clinical trial? A consensus study.

BACKGROUND: Since 2005 it has been a legal requirement in Scotland to have a suitably trained pharmacist verify SACT prescriptions. Published information for verification of SACT does not currently cover SACT prescribed within a clinical trial and the additional knowledge this requires. This poses the question of how pharmacists are deemed suitably trained to competently verify SACT prescribed within a clinical trial to ensure patient safety and service efficiency. AIM: To determine and gain consensus on the competency requirements for clinical pharmacist verification of SACT prescribed within a clinical trial. METHOD: A two stage process was adopted. Firstly, a Nominal Group Technique (NGT) was conducted with a multi-disciplinary expert panel (n = 7) from National Health Service (NHS) Lothian, part of the South East Scotland Cancer Network (SCAN). Secondly, a national survey was distributed to expert cancer care pharmacists with experience in clinical trial verification across NHS Scotland (n = 86). RESULTS: Of the 28 competencies proposed, 100% achieved consensus and were deemed important by the expert panel during the NGT. From the national survey, 26 (92.9%) of the competencies achieved national agreement and were considered transferable across Scotland. The final national competencies were split into four categories: general trial background (n = 13); calculations, laboratory results and toxicity assessments (n = 7); administration details (n = 3); prescription and patient details (n = 3). Based on the themes identified during the NGT the final national competencies were further split into two suggested complexity levels; Level 1 (core) and Level 2 (advanced). CONCLUSION: The competency requirements for clinical pharmacist verification of SACT prescribed within a clinical trial were defined for national use across Scotland. The competencies were split into four categories and two complexity levels. Further work will be required to identify training requirements, develop a training programme to support these and to determine how these competencies should be assessed. In addition, further work could be undertaken to develop a United Kingdom wide competency framework based on the results of this study.

Carbonate clumped isotope analysis (Δ47 ) of 21 carbonate standards determined via gas-source isotope-ratio mass spectrometry on four instrumental configurations using carbonate-based standardization and multiyear data sets.

RATIONALE: Clumped isotope geochemistry examines the pairing or clumping of heavy isotopes in molecules and provides information about the thermodynamic and kinetic controls on their formation. The first clumped isotope measurements of carbonate minerals were first published 15 years ago, and since then, interlaboratory offsets have been observed, and laboratory and community practices for measurement, data analysis, and instrumentation have evolved. Here we briefly review historical and recent developments for measurements, share Tripati Lab practices for four different instrument configurations, test a recently published proposal for carbonate-based standardization on multiple instruments using multi-year data sets, and report values for 21 different carbonate standards that allow for recalculations of previously published data sets. METHODS: We examine data from 4628 standard measurements on Thermo MAT 253 and Nu Perspective IS mass spectrometers, using a common acid bath (90°C) and small-sample (70°C) individual reaction vessels. Each configuration was investigated by treating some standards as anchors (working standards) and the remainder as unknowns (consistency standards). RESULTS: We show that different acid digestion systems and mass spectrometer models yield indistinguishable results when instrument drift is well characterized. For linearity correction, mixed gas-and-carbonate standardization or carbonate-only standardization yields similar results. No difference is observed in the use of three or eight working standards for the construction of transfer functions. CONCLUSIONS: We show that all configurations yield similar results if instrument drift is robustly characterized and validate a recent proposal for carbonate-based standardization using large multiyear data sets. Δ47 values are reported for 21 carbonate standards on both the absolute reference frame (ARF; also refered to as the Carbon Dioxide Equilibrated Scale or CDES) and the new InterCarb-Carbon Dioxide Equilibrium Scale (I-CDES) reference frame, facilitating intercomparison of data from a diversity of labs and instrument configurations and restandardization of a broad range of sample sets between 2006, when the first carbonate measurements were published, and the present.

Factors controlling the oxygen isotopic composition of lacustrine authigenic carbonates in Western China: implications for paleoclimate reconstructions.

In the carbonate-water system, at equilibrium, the oxygen isotopic composition of carbonate is dependent not only on the temperature but also on the isotopic composition of host water in which the carbonate is formed. In this study, lake surface sediment and water samples were collected from 33 terminal lakes in Western China to evaluate controls on the oxygen isotopic composition of lacustrine authigenic carbonates (δ18Ocarb) and its spatial distribution. Our results show that water oxygen isotopic composition (δ18Owater) rather than lake summer water temperature (Twater), is the main determinant of δ18Ocarb, irrespective of whether oxygen isotope equilibrium is achieved. There are significant linear correlations between δ18Ocarb and elevation, as well as that between δ18Ocarb and latitude for lakes located on the Tibetan Plateau. In Western China, the spatial distribution of δ18Ocarb is consistent with that of δ18Owater, and is ultimately controlled by the isotopic composition of local precipitation (δ18Oprecipitation) that depends on the source of water vapor. Therefore, changes in δ18Ocarb can be predominantly interpreted as variations of δ18Owater, which in turn represent changes in δ18Oprecipitation for paleoclimate reconstructions in this region, and may be relevant to studies of other areas.

High resolution spectral analysis of oxygen. III. Laboratory investigation of the airglow bands.

We report the first high spectral resolution laboratory measurements of simulated oxygen A-band night glow. Our static discharge system approximates the conditions of the mesospheric oxygen night glow--suggesting O((1)D) + O2 (X(3)Σg(-)) → O((3)P) + O2 (b(1)Σg(+)) → O2 (X(3)Σg(-)) + hν as the primary source of the emission. Additionally, use of the static cell has enabled us to collect spectra for all six molecular oxygen isotopologues using isotopically enriched samples. The (0,0), (0,1), and (1,1) b - X vibrational bands were observed for all six isotopologues. The (1,2) and (2,2) bands were also observed for (16)O2. The frequencies of the observed (0,1) transitions resolved discrepancies in Raman data for (16)O(17)O, (17)O2, and (17)O(18)O, enabling us to improve the vibrational parameterization of the ground electronic state global fit. Rotationally resolved intensities were determined for the (0,0), (0,1), and (1,1) bands. The experimental band intensity ratios I(0,0)/I(0,1) = 13.53(24); I(1,1)/I(1,0) = 11.9(65); I(0,0)/I(0,2) = 503(197); and I(1,1)/I(1,2) = 5.6(19) are in excellent agreement with the recent mesospheric remote sensing data and calculated Franck-Condon factors.

How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Anharmonicities and isotopic effects in the vibrational spectra of X-.H2O, .HDO, and .D2O [X = Cl, Br, and I] binary complexes.

Vibrational predissociation spectra of the argon-tagged halide monohydrates, X(-) .H(2)O.Ar (X = Cl, Br, or I), are recorded from approximately 800 to 3800 cm(-1) by monitoring the loss of the argon atom. We use this set of spectra to investigate how the spectral signatures of the hydrogen-bonding and large-amplitude hindered rotations of the water molecule are affected by incremental substitution of the hydrogen atoms by deuterium. All six vibrational modes of the X(-).H(2)O complexes are assigned through fundamental transitions, overtones, or combination bands. To complement the experimental study, harmonic and reduced-dimensional calculations of the vibrational spectra are performed based on the MP2/aug-cc-pVTZ level of theory and basis set. Comparison of these results with those from the converged six-dimensional calculations of Rheinecker and Bowman [J. Chem. Phys. 2006, 125, 133206.] show good agreement, with differences smaller than 30 cm(-1). The simpler method has the advantage that it can be readily extended to the heavier halides and was found to accurately recover the wide range of behaviors displayed by this series, including the onset of tunneling between equivalent minima arising from the asymmetrical (single ionic hydrogen-bonded) equilibrium structures of the complexes.

Vibrationally induced interconversion of H-bonded NO2(-) x H2O isomers within NO2(-) x H2O x Ar(m) clusters using IR-IR pump-probe through the OH and NO stretching vibrations.

We introduce a method based on sequential application of vibrational predissociation spectroscopy to explore the high-amplitude rearrangements available in a small H-bonded complex that is vibrationally excited within a larger Ar cluster. The weakly bound Ar atoms play the role of a solvent in mediating the energy content of the embedded system, ultimately quenching it into local minima through evaporation. We demonstrate the approach on the NO(2)(-) x H(2)O binary hydrate, which is known to occur in two nearly isoenergetic isomeric forms. The scheme involves three stages of mass separation to select a particular NO(2)(-) x H(2)O x Ar(m) parent ion cluster prior to vibrational excitation and then isolate the NO(2)(-) x H(2)O x Ar fragment ions for interrogation using resonant vibrational predissociation with a second infrared laser. The initial vibrational excitation selectively energizes one of the isomers through one of its characteristic resonances while the predissociation spectrum of the NO(2)(-) x H(2)O x Ar fragment encodes the distribution of isomers present after Ar evaporation. Isomerization from the front- to backside form is found to occur upon excitation of the NO stretch near 1200 cm(-1); although the reverse reaction is not observed upon excitation of the NO stretch, it is observed upon excitation of the higher-energy OH stretching fundamental near 3000 cm(-1). We discuss these observations in the context of the calculated isomerization energetics, which focus on the minimum energy structures for the isomers as well as the transition states for their interconversion.

Isolating the spectra of cluster ion isomers using Ar-"tag" -mediated IR-IR double resonance within the vibrational manifolds: Application to NO2- *H2O.

We demonstrate a method for isolating the vibrational predissociation spectra of different structural isomers of mass-selected cluster ions based on a population-labeling double resonance scheme. This involves a variation on the "ion dip" approach and is carried out with three stages of mass selection in order to separate the fragment ion signals arising from a fixed-frequency population-monitoring laser and those generated by a scanned laser that removes population of species resonant in the course of the scan. We demonstrate the method on the Ar-tagged NO(2) (-)H(2)O cluster, where we identify the spectral patterns arising from two isomers. One of these structures features accommodation of the water molecule in a double H-bond arrangement, while in the other, H(2)O attaches in a single ionic H-bond motif where the nominally free OH group is oriented toward the N atom of NO(2) (-). Transitions derived from both the NO(2) (-) and H(2)O constituents are observed for both isomers, allowing us to gauge the distortions suffered by both the ion and solvent molecules in the different hydration arrangements.

Why does argon bind to deuterium? Isotope effects and structures of Ar x H5O2(+) complexes.

Recently, we reported the spectrum of Ar x D4HO2(+) [McCunn; et, al. J. Phys. Chem. B 2008, 112, 321], and here, we extend that work to include the Ar x H4DO2(+) isotopologue in order to explore why the Ar atom has a much greater propensity for attachment to a dangling OD group than it does for OH, even when many more of the latter binding sites are available. Calculated (MP2/6-311+G(d,p) level of theory/basis) harmonic frequencies reproduce the observed multiplet patterns of OH and OD stretches and confirm the presence of various isomers arising from the different Ar binding sites. The preferential bonding of Ar to OD is traced to changes in the frequencies of the wag and rock modes of the H5O2(+) moiety rather than to shifts in the oscillator that directly binds the Ar atom.

Probing isomer interconversion in anionic water clusters using an Ar-mediated pump-probe approach: Combining vibrational predissociation and velocity-map photoelectron imaging spectroscopies.

We present the first results from an experiment designed to explore barriers for interconversion between isomers of cluster anions using an Ar-cluster mediated pump-probe technique. In this approach, anions are generated with many Ar atoms attached, and one of the isomers present is selectively excited by tuning an infrared laser to one of the isomer's characteristic vibrational resonances. The excited cluster is then cooled by evaporation of Ar atoms, and the isomer distribution in the lighter daughter ions is measured after secondary mass selection by recording their photoelectron spectra using velocity-map imaging. We apply the method to the water hexamer anion, (H(2)O)(6) (-), which is known to occur in two isomeric forms with different electron-binding energies. We find that conversion of the high-binding (type I) form to the low-binding (type II) isomer is not efficiently driven in (H(2)O)(6) (-) with excitation energies in the 0.4 eV range even though it is possible to create both isomers in abundance in the ion source. This observation is discussed in the context of the competition between isomerization and electron autodetachment, which depends on the relative positions of the neutral and ionic potential surfaces along the isomerization pathway. Application of the method to the more complex heptamer ion, however, does reveal that interconversion is available among the highest binding isomer classes (I and I(')).

MX3(-) superhalogens (M = Be, Mg, Ca; X = Cl, Br): a photoelectron spectroscopic and ab initio theoretical study.

Gas-phase alkaline earth halide anions, MgX3(-) and CaX3(-) (X = Cl, Br), were produced using electrospray and investigated using photoelectron spectroscopy at 157 nm. Extremely high electron binding energies were observed for all species and their first vertical detachment energies were measured as 6.60 +/- 0.04 eV for MgCl3(-), 6.00 +/- 0.04 eV for MgBr3(-), 6.62 +/- 0.04 eV for CaCl3(-), and 6.10 +/- 0.04 eV for CaBr3(-). The high electron binding energies indicate these are very stable anions and they belong to a class of anions, called superhalogens. Theoretical calculations at several levels of theory were carried out on these species, as well as the analogous BeX3(-). Vertical detachment energy spectra were predicted to compare with the experimental observations, and good agreement was obtained for all species. The first adiabatic detachment energies were found to be substantially lower (by about 1 eV) than the corresponding vertical detachment energies for all the MX3(-) species, indicating extremely large geometry changes between MX3(-) and MX3. We found that all the MX3(-) anions possess D3h ((1)A1') structures and are extremely stable against dissociation into MX2 and X-. The corresponding neutral species MX3, however, were found to be only weakly bound with respect to dissociation toward MX2 + X. The global minimum structures of all the MX3 neutrals were found to be C2v ((2)B2), which can be described as (X2(-))(MX+) charge-transfer complexes, whereas the MX2...X (C2v, (2)B1) van der Waals complexes were shown to be low-lying isomers.

The oxygen-rich carboxide series: COn (n = 3, 4, 5, 6, 7, or 8).

The lowest-energy isomers of the high-order carboxide series, COn (n = 3-8), have been elucidated via ab initio quantum chemical calculations. The structures of the lowest order of these (3 and 4) are in close agreement with previous calculations and with experimental data. The structures of the higher-order species are elucidated and correlated to the previous structures, showing similarities in structure and reactivity pathways. The reaction energies of the formation of all products are shown to be related. Exothermic pathways of formation often involve a C2v form of CO2, which was shown to be metastable. The newly identified species could be intermediates in atmospheric reactions. The calculated vibrational frequencies and IR intensities may be used to identify these metastable species.

Ab initio probing of the aromatic oxygen cluster O4(2+).

The structure of the O(4)(2+) dication has been studied theoretically using a few conventional theoretical methods. We found the O(4)(2+) dication to be a metastable species with a perfect square structure. The molecular orbital analysis reveals that this dication is the first all-oxygen aromatic system with 6pi electrons. Although the O(4)(2+) dication is highly thermodynamically unstable, we believe that appropriate counteranions with very high electron detachment energy (superhalogens) can be found to form a solid-state compound containing O(4)(2+). Another way to probe the planar aromatic tetra oxygen dication could be a double-photoionization process of the (O(2))(2) dimer.

Ozonic acid and its ionic salts: ab initio probing of the O(4)(2)(-) dianion.

The pyramidal O(4)(2)(-) dianion is valence isoelectronic to the well-known ClO(3)(-) and SO(3)(2)(-) anions, and yet it has not been observed. The synthesis of any molecule containing such a dianion would represent a major breakthrough in making molecules containing more than three covalently bound oxygen atoms. We found that the parent H(2)O(4) ozonic acid is unstable in the form of the valence isoelectronic sulfurous acid H(2)SO(3). Our quantum chemical probing of the Li(2)O(4) ionic salt molecule is inconclusive. However, we found that the specially designed FLi(3)O(4) gas phase molecule is a true metastable species and could be considered as the first molecule containing the O(4)(2)(-) dianion. Our theoretical prediction of the first compound containing the tetraatomic covalently bound O(4)(2)(-) dianion opens the possibility to even more oxygen rich compounds, which will have a great potential as high density oxygen storage.

In search of covalently bound tetra- and penta-oxygen species: a photoelectron spectroscopic and Ab initio investigation of MO4- and MO5- (M = Li, Na, K, Cs).

Although neutral and ionic O4(0/-/+) species have been observed experimentally and considered for energetic materials, O4(2-) and O5(2-) dianions have not yet been explored. O4(2-) is valent isoelectronic to the well-known ClO3- and SO3(2-) anions, and O5(2-) is valent isoelectronic to ClO4- and SO4(2-). All are stable, common anions in solutions and inorganic salts. In this article, we explore the possibility of making covalently bound O4(2-) and O5(2-) species stabilized in the forms of M+O4(2-) and M+O5(2-) (M = Li, Na, K, Cs) in the gas phase. Laser vaporization experiments using M-containing targets and an O2-seeded carrier gas yielded very intense mass peaks corresponding to MO4- and MO5-. To elucidate the structure and bonding of the newly observed MO4- and MO5- species, we measured their photoelectron spectra and then compared them with ab initio calculations and the spectra of ClO3-, Na+SO3(2-), ClO4-, and Na+SO4(2-). Careful analyses of the experimental and ab initio results showed, however, that the observed species are of the forms, O2-M+O2- and O2-M+O3-. The more interesting M+O4(2-) and M+O5(2-) species were found to be higher-energy isomers, but they are true minima on the potential energy surfaces, which suggests that it might be possible to synthesize bulk materials containing covalently bound tetra- and pentatomic oxygen building blocks.