Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules

AbstractMass spectrometry instrumentation providing unit resolution and 10-ppm mass accuracy for molecules larger than 10 kDa was first reported in 1991. This instrumentation has now been improved with a 6.2-T magnet replacing that of 2.8 T, a more efficient vacuum system, ion injection with controlled ion kinetic energies, accumulated ion trapping with an open-cylindrical ion cell, acquisition of 2M data points, and updated electrospray apparatus. The resulting capabilities include resolving power of 5 × 105 for a 29-kDa protein, less than 1-ppm mass measuring error, and dissociation of protein molecular ions to produce dozens of fragment ions whose exact masses can be identified from their mass-to-charge ratio values and isotopic peak spacing

Rapid Identification of Emerging Pathogens: Coronavirus

New surveillance approach can analyze >900 polymerase chain reactions per day

Combining biomarker and bulk compositional gradient analysis to assess reservoir connectivity

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 41 (2010): 812-821, doi:10.1016/j.orggeochem.2010.05.003.Hydraulic connectivity of petroleum reservoirs represents one of the biggest uncertainties for both oil production and petroleum system studies. Here, a geochemical analysis involving bulk and detailed measures of crude oil composition is shown to constrain connectivity more tightly than is possible with conventional methods. Three crude oils collected from different depths in a single well exhibit large gradients in viscosity, density, and asphaltene content. Crude oil samples are collected with a wireline sampling tool providing samples from well‐defined locations and relatively free of contamination by drilling fluids; the known provenance of these samples minimizes uncertainties in the subsequent analysis. The detailed chemical composition of almost the entire crude oil is determined by use of comprehensive two‐dimensional gas chromatography (GC×GC) to interrogate the nonpolar fraction and negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT‐ICR MS) to interrogate the polar fraction. The simultaneous presence of 25‐ norhopanes and mildly altered normal and isoprenoid alkanes is detected, suggesting that the reservoir has experienced multiple charges and contains a mixture of oils biodegraded to different extents. The gradient in asphaltene concentration is explained by an equilibrium model considering only gravitational segregation of asphaltene nanoaggregates; this grading can be responsible for the observed variation in viscosity. Combining these analyses yields a consistent picture of a connected reservoir in which the observed viscosity variation originates from gravitational segregation of asphaltene nanoaggregates in a crude oil with high asphaltene concentration resulting from multiple charges, including one charge that suffered severe biodegradation. Observation of these gradients having appropriate magnitudes suggests good reservoir connectivity with greater confidence than is possible with traditional techniques alone.The mass spectrometry work was supported by the NSF Division of Materials Research through DMR‐06‐54118, and the State of Florida

Use of an Electrochemical Split Cell Technique to Evaluate the Influence of Shewanella oneidensis Activities on Corrosion of Carbon Steel

Microbially induced corrosion (MIC) is a complex problem that affects various industries. Several techniques have been developed to monitor corrosion and elucidate corrosion mechanisms, including microbiological processes that induce metal deterioration. We used zero resistance ammetry (ZRA) in a split chamber configuration to evaluate the effects of the facultatively anaerobic Fe(III) reducing bacterium Shewanella oneidensis MR-1 on the corrosion of UNS G10180 carbon steel. We show that activities of S. oneidensis inhibit corrosion of steel with which that organism has direct contact. However, when a carbon steel coupon in contact with S. oneidensis was electrically connected to a second coupon that was free of biofilm (in separate chambers of the split chamber assembly), ZRA-based measurements indicated that current moved from the S. oneidensis-containing chamber to the cell-free chamber. This electron transfer enhanced the O2 reduction reaction on the coupon deployed in the cell free chamber, and consequently, enhanced oxidation and corrosion of that electrode. Our results illustrate a novel mechanism for MIC in cases where metal surfaces are heterogeneously covered by biofilms

Microbially-mediated reduction and oxidation of uranium: Implications for the bioremediation of uranium(VI)-contaminated aquifers.

Mechanisms of nitrate-dependent U(IV) were assessed by incubating biogenic U(IV) with nitrite or Fe(III). Fe(III) rapidly but incompletely oxidized U(IV) since Fe(II) accumulated during the reaction and inhibited any further U(IV) oxidation. Nitrite alone was a poor oxidant of U(IV), but the addition of a small amount of Fe(II) to nitrite- and U(IV)-containing incubations lead to complete U(IV) oxidation, suggesting that Fe shuttles electrons from U(IV) to nitrite. A nitrate-dependent acetate- and Fe(II)-oxidizing bacterium was isolated from a nitrate- and U(VI)-contaminated aquifer. U(IV) was oxidized by this organism in site groundwater at a greater rate and to a greater extent in the presence of acetate and Fe(II) (where nitrite accumulated to high levels) than under Fe(II)-oxidizing conditions. This activity was due to mineralogical difference in Fe(III) produced under the two conditions. Goethite was produced by enzymatic, nitrate-dependent Fe(II) oxidation and amorphous Fe(III) was produced by the reaction of Fe(II) with nitrite. The latter Fe(III) mineral was a more effective oxidant of U(IV).We assessed in situ microbial U(VI) reduction. U(VI) immobilization was observed in situ and confirmed as reduction in laboratory sediment incubations. Sulfate neither enhanced nor inhibited U(VI) reduction, but nitrate inhibited U(VI) reduction. U(VI) reduction occurred only after complete consumption of nitrate. The addition of nitrate to U(IV)-containing sediments lead to the oxidation and remobilization of uranium. The addition of intermediates of dissimilatory nitrate reduction (nitrite and nitrous oxide) to heat-inactivated U(IV)-containing sediment slurries lead to the oxidation of U(IV), suggesting that the accumulation of these reactive compounds during dissimilatory nitrate reduction is responsible for nitrate-dependent U(IV) oxidation. Nitrate-dependent U(IV) oxidation may also be catalyzed by Fe(III) that is produced by nitrate-dependent U(IV)-oxidizing bacteria, or by the direct, enzymatic, nitrate-dependent oxidation of U(IV).Geochemical controls on nitrate-dependent U(IV) oxidation were determined in landfill leachate-impacted sediments. Organotrophic (glucose-oxidizing) and Fe(II)-oxidizing nitrate-reducing bacteria were more abundant in these sediments than organisms that coupled U(IV) oxidation to nitrate reduction for growth, suggesting that U(IV) is ultimately oxidized by Fe(III). In sediment incubations, nitrate concentration exerted a strong influence on the extent, but not the rate of nitrate-dependent U(IV) oxidation. The addition of reductants (acetate, sulfide, soluble Fe(II), and FeS) to sediment incubations lead to lower extents and rates of nitrate-dependent U(IV) oxidation. Fe(II) was the strongest inhibitor of nitrate-dependent U(IV) oxidation.The effect of Fe(II) form and Fe(II) oxidation rate on Fe(III) mineralogy were determined. Fe(III) from FeS oxidation was amorphous, while Fe(III) from soluble Fe(II) was identified as predominantly goethite. High initial rates of Fe(II) oxidation lead to amorphous Fe(III), and with decreasing rates of Fe(II) oxidation, more crystalline goethite was formed

Effect of Oxidation Rate and Fe(II) State on Microbial Nitrate-Dependent Fe(III) Mineral Formation

A nitrate-dependent Fe(II)-oxidizing bacterium was isolated and used to evaluate whether Fe(II) chemical form or oxidation rate had an effect on the mineralogy of biogenic Fe(III) (hydr)oxides resulting from nitrate-dependent Fe(II) oxidation. The isolate (designated FW33AN) had 99% 16S rRNA sequence similarity to Klebsiella oxytoca. FW33AN produced Fe(III) (hydr)oxides by oxidation of soluble Fe(II) [Fe(II)(sol)] or FeS under nitrate-reducing conditions. Based on X-ray diffraction (XRD) analysis, Fe(III) (hydr)oxide produced by oxidation of FeS was shown to be amorphous, while oxidation of Fe(II)(sol) yielded goethite. The rate of Fe(II) oxidation was then manipulated by incubating various cell concentrations of FW33AN with Fe(II)(sol) and nitrate. Characterization of products revealed that as Fe(II) oxidation rates slowed, a stronger goethite signal was observed by XRD and a larger proportion of Fe(III) was in the crystalline fraction. Since the mineralogy of Fe(III) (hydr)oxides may control the extent of subsequent Fe(III) reduction, the variables we identify here may have an effect on the biogeochemical cycling of Fe in anoxic ecosystems

Microbial reduction of chlorite and uranium followed by air oxidation

To evaluate the stability of biogenic nanoparticulate U(IV) in the presence of an Fe(II)-rich iron-bearing phyllosilicate, we examined the reduction of structural Fe(III) in chlorite CCa-2 and uranium(VI) by Shewanella oneidensis MR-1, and the reoxidation of these minerals (after pasteurization) via the introduction of oxygen. Bioreduction experiments were conducted with combinations of chlorite, U(VI), and anthraquinone-2,6-disulfonate (AQDS). Abiotic experiments were conducted to quantify the reduction of U(VI) by chemically-reduced chlorite-associated Fe(II), the oxidation of nanoparticulate U(IV) by unaltered structural Fe(III) in chlorite, and the sorption of U(VI) to chlorite, to elucidate interactions between U(VI)/ U(IV) and Fe(II)/Fe(III)-chlorite. Solids were characterized by X-ray diffraction, scanning electron microscopy, and X-ray absorption spectroscopy to confirm Fe and U reduction and reoxidation. U(VI) enhanced the reduction of structural Fe(III) in chlorite and nanoparticulate U(IV) was oxidized by structural Fe(III) in chlorite, demonstrating that U served as an effective electron shuttle from S. oneidensis MR-1 to chlorite-Fe(III). Abiotic reduction of U(VI) by chlorite-associated Fe(II) was very slow compared to biological U(VI) reduction. The rate of nanoparticulate U(IV) oxidation by dissolved oxygen increased in the presence of chlorite-associated Fe(II), but the extent of U(IV) oxidation decreased as compared to no-chlorite controls. In identical experiments conducted with bioreduced suspensions of nanoparticulate U(IV) and nontronite (another iron-bearing phyllosilicate), the rate of U(IV) oxidation by dissolved oxygen increased in the presence of nontronite-associated Fe(II). In summary, we found that structural Fe(III) in chlorite delayed the onset of U(VI) loss from solution, while chlorite-associated Fe(II) enhanced the oxidation rate of U(IV) by dissolved oxygen, indicating that chlorite-associated Fe(II) could not protect nanoparticulate U(IV) from oxygen intrusion but instead increased the oxidation rate of U(IV)

Microbial communities associated with wet flue gas desulfurization systems

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal fired electricity generation facilities were evaluated using culture-dependent and –independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems

Response of Soil-Associated Microbial Communities to Intrusion of Coal Mine-Derived Acid Mine Drainage

A system has been identified in which coal mine-derived acid mine drainage (AMD) flows as a 0.5-cm-deep sheet over the terrestrial surface. This flow regime enhances the activities of Fe­(II) oxidizing bacteria, which catalyze the oxidative precipitation of Fe from AMD. These activities give rise to Fe­(III) (hydr)­oxide-rich deposits (referred to as an iron mound) overlying formerly pristine soil. This iron mound has developed with no human intervention, indicating that microbiological activities associated with iron mounds may be exploited as an inexpensive and sustainable approach to remove Fe­(II) from AMD. To evaluate the changes in microbial activities and communities that occur when AMD infiltrates initially pristine soil, we incubated AMD-unimpacted soil with site AMD. Continuous exposure of soil to AMD induced progressively greater rates of Fe­(II) biooxidation. The development of Fe­(II) oxidizing activities was enhanced by inoculation of soil with microorganisms associated with mature iron mound sediment. Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. Our results indicate that upon mixing of AMD with pristine soil, microbial communities develop that mediate rapid oxidative precipitation of Fe from AMD