Synthesis of 18O-labeled RNA for application to kinetic studies and imaging

Radioisotopes and fluorescent compounds are frequently used for RNA labeling but are unsuitable for clinical studies of RNA drugs because of the risk from radiation exposure or the nonequivalence arising from covalently attached fluorophores. Here, we report a practical phosphoramidite solid-phase synthesis of ¹⁸O-labeled RNA that avoids these disadvantages, and we demonstrate its application to quantification and imaging. The synthesis involves the introduction of a nonbridging ¹⁸O atom into the phosphate group during the oxidation step of the synthetic cycle by using ¹⁸O water as the oxygen donor. The ¹⁸O label in the RNA was stable at pH 3–8.5, while the physicochemical and biological properties of labeled and unlabeled short interfering RNA were indistinguishable by circular dichroism, melting temperature and RNA-interference activity. The ¹⁸O/¹⁶O ratio as measured by isotope ratio mass spectrometry increased linearly with the concentration of ¹⁸O-labeled RNA, and this technique was used to determine the blood concentration of ¹⁸O-labeled RNA after administration to mice. ¹⁸O-labeled RNA transfected into human A549 cells was visualized by isotope microscopy. The RNA was observed in foci in the cytoplasm around the nucleus, presumably corresponding to endosomes. These methodologies may be useful for kinetic and cellular-localization studies of RNA in basic and pharmaceutical studies.     

Enhancing the stability of O-labeled peptides through removal of immobilized trypsin by ZipTips

Trypsin-catalyzed ¹⁸O labeling is increasingly used in shotgun proteomics for relative peptide/protein quantitation. However, precise quantitative measurements are often complicated by the instability of ¹⁸O-labeled peptides caused mainly by oxygen back-exchange. Although a number of attempts have been made to reduce or prevent oxygen back-exchange, there is still room for improvement. Here we demonstrate that the removal of immobilized trypsin by filtration using ZipTips can efficiently minimize oxygen back-exchange and enhance the stability of ¹⁸O-labeled peptides under various pH conditions. The ¹⁸O-labeled peptides processed by the approach were successfully separated by immobilized pH gradient–isoelectric focusing (IPG–IEF), and no marked decrease in the extent of labeling was observed. The results also demonstrated that there was no correlation between the extent of ¹⁸O labeling and molecular weight or isoelectric point (pI). The approach presented here is especially applicable to microscale samples. Its ability to generate stably ¹⁸O-labeled samples without back-exchange should expand the application scope of the ¹⁸O-labeling technique.     

Novel Pathway of Toluene Catabolism in the Trichloroethylene-Degrading Bacterium G4

o-Cresol and 3-methylcatechol were identified as successive transitory intermediates of toluene catabolism by the trichloroethylene-degrading bacterium G4. The absence of a toluene dihydrodiol intermediate or toluene dioxygenase and toluene dihydrodiol dehydrogenase activities suggested that G4 catabolizes toluene by a unique pathway. Formation of a hybrid species of ¹⁸O- and ¹⁶O-labeled 3-methylcatechol from toluene in an atmosphere of ¹⁸O₂ and ¹⁶O₂ established that G4 catabolizes toluene by successive monooxygenations at the ortho and meta positions. Detection of trace amounts of 4-methylcatechol from toluene catabolism suggested that the initial hydroxylation of toluene was not exclusively at the ortho position. Further catabolism of 3-methylcatechol was found to proceed via catechol-2,3-dioxygenase and hydroxymuconic semialdehyde hydrolase activities.     

Synthesis of <Superscript>18</Superscript>O-labeled photosynthetically active chlorophylls at the 3- or 7-carbonyl group with high regioselectivity

The 3- and 7-formyl groups of chlorophyll-d (Chl-d) and bacteriochlorophyll-e (BChl-e), respectively, were regioselectively labeled with an isotopically stable oxygen-18 (¹⁸O) atom to give 3¹-¹⁸O-labeled Chl-d and 7¹-¹⁸O-labeled BChl-e (ca. 90% ¹⁸O) by exchanging the carbonyl oxygen atoms in the presence of acidic H₂ ¹⁸O (ca. 95% ¹⁸O). Another photosynthetically active chlorophyll, BChl-a possessing the 3-acetyl group was treated under similar acidic conditions to afford a trace amount of 3¹-¹⁸O-labeled BChl-a and further demetallated compound, the corresponding 3¹-¹⁸O-labeled bacteriopheophytin-a as the major product with 55% ¹⁸O-degree. The FT-IR spectra of ¹⁸O-(un)labeled chlorophylls in the solution and the solid states showed that the 3- and 7-carbonyl stretching vibration modes moved to about a 30-cm⁻¹ lower wavenumber by ¹⁸O-labeling at the 3¹- and 7¹-oxo moieties. In artificial chlorosome-like self-aggregates of BChl-e, the ¹⁸O-labeled 7-carbonyl stretching mode was completely resolved from the specially hydrogen-bonded 13-C=O stretching mode, evidently indicating no interaction of the 7-CHO with other functional groups in the supramolecules.     

Kinetics of BTEX biodegradation by a coculture of <Emphasis Type="Italic">Pseudomonas putida</Emphasis> and<Emphasis Type="Italic"> Pseudomonas fluorescens</Emphasis> under hypoxic conditions

Pseudomonas putida and Pseudomonas fluorescens present as a coculture were studied for their abilities to degrade benzene, toluene, ethylbenzene, and xylenes (collectively known as BTEX) under various growth conditions. The coculture effectively degraded various concentrations of BTEX as sole carbon sources. However, all BTEX compounds showed substrate inhibition to the bacteria, in terms of specific growth, degradation rate, and cell net yield. Cell growth was completely inhibited at 500mgl^–1 of benzene, 600mgl^–1 of o-xylene, and 1000mgl^–1 of toluene. Without aeration, aerobic biodegradation of BTEX required additional oxygen provided as hydrogen peroxide in the medium. Under hypoxic conditions, however, nitrate could be used as an alternative electron acceptor for BTEX biodegradation when oxygen was limited and denitrification took place in the culture. The carbon mass balance study confirmed that benzene and toluene were completely mineralized to CO₂ and H₂O without producing any identifiable intermediate metabolites.     

Kinetics of biodegradation of gasoline and its hydrocarbon constituents

Aerobic biodegradation of gasoline and its constituents, benzene, toluene and ethylbenzene were studied by an enrichment from soil indigenous microbial population. The enrichment culture completely degraded 16.1–660 mg/l gasoline in 2.5–16 days respectively, without accumulation of any by-products. The kinetics of gasoline as well as benzene, toluene and ethylbenzene biodegradation was investigated with initial gasoline concentrations of 16.1–62.6 mg/l. The maximum specific rates of biodegradation of benzene, toluene and ethylbenzene were 0.12, 0.38 and 0.19 mg mg biomass⁻¹ day⁻¹ respectively. When benzene and toluene were used as sole substrate, the maximum specific rates of their biodegradation were 62.9 and 16.4 times greater than the corresponding values for a mixture (gasoline). The microbial culture was able to mineralize up to 200 mg/l pure toluene and benzene. Maximum mineralization efficiencies of benzene and toluene were 76.7 ± 5.1% and 76.8 ± 1.3% respectively. Self-inhibition and competitive inhibition patterns were observed during the biodegradation of benzene and toluene alone and in the mixture respectively. The observed kinetics was modeled according to Andrews' inhibition model. Received: 6 August 1997 / Received revision: 18 November 1997 / Accepted: 29 November 1997     

Thermophilic biodegradation of BTEX by two consortia of anaerobic bacteria

Two thermophilic anaerobic bacterial consortia (ALK-1 and LLNL-1), capable of degrading the aromatic fuel hydrocarbons, benzene, toluene, ethylbenzene, and the xylenes (BTEX compounds), were developed at 60 °C from the produced water of ARCO'S Kuparuk oil field at Alaska and the subsurface water at the Lawrence Livermore National Laboratory gasoline-spill site, respectively. Both consortia were found to grow at 45–75 °C on BTEX compounds as their sole carbon and energy sources with 50 °C being the optimal temperature. With 3.5 mg total BTEX added to sealed 50-ml serum bottles, which contained 30 ml mineral salts medium and the consortium, benzene, toluene, ethylbenze, m-xylene, and an unresolved mixture of o- and p-xylenes were biodegraded by 22%, 38%, 42%, 40%, and 38%, respectively, by ALK-1 after 14 days of incubation at 50 °C. Somewhat lower, but significant, percentages of the BTEX compounds also were biodegraded at 60 °C and 70 °C. The extent of biodegradation of these BTEX compounds by LLNL-1 at each of these three temperatures was slightly less than that achieved by ALK-1. Use of [ring-¹⁴C]toluene in the BTEX mixture incubated at 50 °C verified that 41% and 31% of the biodegraded toluene was metabolized within 14 days to water-soluble products by ALK-1 and LLNL-1, respectively. A small fraction of it was mineralized to ¹⁴CO₂. The use of [U-¹⁴C]benzene revealed that 2.6%–4.3% of the biodegraded benzene was metabolized at 50 °C to water-soluble products by the two consortia; however, no mineralization of the degraded [U-¹⁴C]benzene to ¹⁴CO₂ was observed. The biodegradation of BTEX at all three temperatures by both consortia was tightly coupled to sulfate reduction as well as H₂S generation. None was observed when sulfate was omitted from the serum bottles. This suggests that sulfate-reducing bacteria are most likely responsible for the observed thermophilic biodegradation of BTEX in both consortial cultures. Received: 12 July 1996 / Received revision: 31 December 1996 / Accepted: 31 January 1997     

Spontaneous Hydrolysis and Dehydration of Dehydroascorbic Acid in Aqueous Solution

The interaction of water with dehydroascorbic acid was examined by incubating dehydroascorbic acid and ascorbic acid in¹⁸O-labeled water for various amounts of time and then oxidizing the products with hydrogen peroxide or reducing the products with mercaptoethanol, with analysis by gas chromatography mass spectrometry. Based on mass changes, dehydroascorbic acid readily exchanged three oxygen atoms with H₂¹⁸O. When mercaptoethanol was used to reduce dehydroascorbic acid (which had been incubated in H₂¹⁸O) to ascorbic acid, the newly formed ascorbic acid also contained three labeled oxygen atoms. However, ascorbic acid incubated in H₂¹⁸O for the same amount of time under identical conditions exchanged only two labeled oxygen atoms. Electron impact mass spectrometry of derivatized ascorbic acid created a decarboxylation product which had only two labeled oxygen atoms, regardless if 3-oxygen-labeled or 2-oxygen-labeled ascorbic acid was the parent compound, isolating the extra oxygen addition to carbon 1. These data suggest that dehydroascorbic acid spontaneously hydrolyzes and dehydrates in aqueous solution and that the hydrolytic-hydroxyl oxygen is accepted by carbon 1. Ascorbic acid, on the other hand, does not show this same tendency to hydrolyze.     

18O Labeling of Chlorophyll d in Acaryochloris marina Reveals That Chlorophyll a and Molecular Oxygen Are Precursors

The cyanobacterium Acaryochloris marina was cultured in the presence of either H₂¹⁸O or ¹⁸O₂, and the newly synthesized chlorophylls (Chl a and Chl d) were isolated using high performance liquid chromatography and analyzed by mass spectroscopy. In the presence of H₂¹⁸O, newly synthesized Chl a and d, both incorporated up to four isotopic ¹⁸O atoms. Time course H₂¹⁸O labeling experiments showed incorporation of isotopic ¹⁸O atoms originating from H₂¹⁸O into Chl a, with over 90% of Chl a ¹⁸O-labeled at 48 h. The incorporation of isotopic ¹⁸O atoms into Chl d upon incubation in H₂¹⁸O was slower compared with Chl a with ∼50% ¹⁸O-labeled Chl d at 115 h. The rapid turnover of newly synthesized Chl a suggested that Chl a is the direct biosynthetic precursor of Chl d. In the presence of ¹⁸O₂ gas, one isotopic ¹⁸O atom was incorporated into Chl a with approximately the same kinetic incorporation rate observed in the H₂¹⁸O labeling experiment, reaching over 90% labeling intensity at 48 h. The incorporation of two isotopic ¹⁸O atoms derived from molecular oxygen (¹⁸O₂) was observed in the extracted Chl d, and the percentage of double isotopic ¹⁸O-labeled Chl d increased in parallel with the decrease of non-isotopic-labeled Chl d. This clearly indicated that the oxygen atom in the C3¹-formyl group of Chl d is derived from dioxygen via an oxygenase-type reaction mechanism.     

Metabolic diversity of aromatic hydrocarbon-degrading bacteria from a petroleum-contaminated aquifer

We characterized bacteria from contaminated aquifers for their ability to utilize aromatic hydrocarbons under hypoxic (oxygen-limiting) conditions (initial dissolved oxygen concentration about 2 mg/l) with nitrate as an alternate electron acceptor. This is relevant to current intense efforts to establish favorable conditions forin situ bioremediation. Using samples of granular activated carbon slurries from an operating groundwater treatment system, we isolated bacteria that are able to use benzene, toluene, ethylbenzene, orp-xylene as their sole source of carbon under aerobic or hypoxic-denitrifying conditions. Direct isolation on solid medium incubated aerobically or hypoxically with the substrate supplied as vapor yielded 10³ to 10⁵ bacteria ml^–1 of slurry supernatant, with numbers varying little with respect to isolation substrate or conditions. More than sixty bacterial isolates that varied in colony morphology were purified and characterized according to substrate utilization profiles and growth condition (i.e., aerobic vs. hypoxic) specificity. Strains with distinct characteristics were obtained using benzene compared with those isolated on toluene or ethylbenzene. In general, isolates obtained from direct selection on benzene minimal medium grew well under aerobic conditions but poorly under hypoxic conditions, whereas many ethylbenzene isolates grew well under both incubation conditions. We conclude that the conditions of isolation, rather than the substrate used, will influence the apparent characteristic substrate utilization range of the isolates obtained. Also, using an enrichment culture technique, we isolated a strain ofPseudomonas fluorescens, designated CFS215, which exhibited nitrate dependent degradation of aromatic hydrocarbons under hypoxic conditions.Abbreviations BTEX benzene, toluene, ethylbenzene, andp-xylene - HPLC high performance liquid chromatography - GAC granular activated carbon     

A Newly Isolated Organic Solvent Tolerant Staphylococcus saprophyticus M36 Produced Organic Solvent-Stable Lipase

Thirty-eight high lipase activity strains were isolated from soil, seawater, and Brassica napus. Among them, a novel organic solvent tolerant bacterium (strain M36) was isolated from the seawater in Jiangsu, China. Isolate M36 was able to grow at high concentration of benzene or toluene up to 40% (vol/vol), and later identified as Staphylococcus saprophyticus by biochemical test and 16s ribosomal DNA sequence. No work on Staphylococcus producing lipase with organic solvent tolerance has been reported so far. The lipase of strain M36 whose activity in liquid medium was 42 U mL⁻¹ at 24-h incubation time was stable in the presence of 25% (vol/vol) p-xylene, benzene, toluene, and hexane.     

Design of a biofilter packed with crab shell and operation of the biofilter fed with leaf mold solution as a nutrient

After measuring toluene adsorption (15.7 mg-toluene/g-material), water holding capacity (18.5%), organic content (53.8%), specific surface area (18.1 m²/g-material), and microbial attachment, crab shells were chosen as the main packing material for a biofilter design. The crab shells, cheap and abundant in the Gangneung area, also have relatively rigid structure, low density, and ability to neutralize acids generated during mineralization of toluene. Since towel scraps have water holding capacity as high as 301.2%, 10% of the total packing was supplemented with them to compensate for low water holding capacity of the crab shells. The biofilter fed with defined chemical medium under 0.8∼1.3 mg/L of inlet toluene concentration and 18 seconds of residence time showed satisfactory removal efficiency of over 97% and 72.8 g/h·m³ of removal capacity. For the purpose of deceasing operation costs, leaf mold solution was tried as an alternative nutrient instead of a defined chemical medium. The removal efficiency and removal capacity were 85% and 56.3 g/h·m³, respectively, using the same inlet toluene concentration and residence time. This research shows the possibility of recycling crab shell waste as packing material for biofilter. In addition, leaf mold was able to serve as an alternative nutrient, which remarkably decreased the operating cost of the biofilter.     

Inhibition of benzene,toluene, phenol and benzoate in single and combination on Anammox activity: implication to the denitrification–Anammox synergy

A previous study demonstrated that denitrification synergized with Anammox could accelerate the anaerobic degradation of benzene. The inhibitory effects of benzene, toluene, phenol and benzoate in single and combination on Anammox activity were investigated by short-term batch tests. The results indicated that the inhibition of single compounds on Anammox could be well fitted with the extended non-competitive and Luong inhibition kinetic models. The inhibitions of the individual compound were in order as follows: benzene?>?toluene?>?phenol?>?benzoate. The joint inhibitions of bi-component mixtures of benzene with toluene, benzene with phenol and benzene with benzoate on Anammox activity were additive; the joint inhibition of a tri-component mixture (benzene, toluene and phenol) was partly additive; and the joint inhibition of a multicomponent mixture (benzene, toluene, phenol and benzoate) was synergistic. The effect of benzoate on the denitrification–Anammox synergy for benzene degradation was evaluated using a long-term test. Although the average rate of benzene degradation decreased by 13% with the addition of 10 mg L^?1 benzoate, the average rate of NO₃^? and NH₄⁺ increased by approximately 1- and 0.56-fold, respectively, suggesting that benzoate favors the stability of the denitrification–Anammox synergy. The carboxylation of benzene would be a more favorable pathway for the anaerobic degradation of benzene under denitrification synergized with Anammox.     

Microbial communities and biodegradation in lab-scale BTEX-contaminated groundwater remediation using an oxygen-releasing reactive barrier

To remediate benzene, toluene, ethylbenzene and xylene (BTEX) -contaminated groundwater, a biotreatment process including biostimulation and bioaugmentation was simulated using oxygen-releasing reactive barriers (ORRB) and water with added BTEX in a lab-scale system. The results showed that the capability for BTEX removal decreases in the order of benzene, toluene, p-xylene, ethylbenzene for both added-nitrogen and no-added-nitrogen under BTEX concentrations at 30 mg l⁻¹. The removal efficiencies in ORRB systems were higher in the nitrogen-added condition for biostimulation compared with the no-nitrogen-added condition; moreover, an increased pattern for removal was observed during the bioaugmentation process. The oxygen content was found to be inversely proportional to the distance from the ORRB, as evidenced by observing that the average bacteria densities were two orders higher when located at 15 cm compared with 30 cm from the ORRB. The microbial community structure was similar in both cases of added-nitrogen and the no-added-nitrogen conditions.     

How dry are anhydrous enzymes? Measurement of residual and buried 18O-labeled water molecules using mass spectrometry

There is continual debate over the central role of water in protein folding, structure, stability, and dynamics. Catalytic activity has been demonstrated in organic media with, apparently “anhydrous” enzymes. Hence there is considerable discussion over whether there are a few residual water molecules or if the enzymes are demonstrating activity in the complete absence of water. Here we present measurements designed to test this hypothesis based on the detection of ¹⁸O-labeled water by mass spectrometry. This extremely sensitive technique avoids many of the potential errors associated with published methods for measuring water content such as gravimetry or Karl Fischer titrations. We have also explored the mass spectrometric detection of ²H-enriched water and found that lyophilization of deuteron-labeled protein can lead to extensive loss of the isotopic label during the drying process. “Anhydrous” protein was produced by extended drying, over P₂O₅, of lyophilized powders hydrated through the vapor phase with ¹⁸O-labeled water. Redissolution in standard water released the remaining protein-bound ¹⁸O-labeled water molecules, and the isotopic enrichment of the water was used to calculate the number of bound molecules per mole of protein. In the cases of lysozyme and subtilisin Carlsberg, 4 ± 2 and 15 ± 2 waters per mole were found, respectively. Comparisons with crystal structures showed these values correspond closely to the expected number of buried water molecules in these proteins. This is consistent with the idea that water physically entrapped within the rigid protein structure is retained but all the other more accessible surface-bound hydration molecules can be removed by the drying process. Such anhydrous subtilisin Carlsberg preparations have been found to be weakly catalytic and therefore it appears that additional water molecules on the surface of the enzyme are not essential for this level of enzyme activity. © 1997 John Wiley & Sons, Inc.     

4株苯系物降解菌菌株的筛选鉴定、降解特性及其降解基因研究

分别以苯、甲苯为碳源,从厦门污水处理厂活性污泥中富集筛选获得了2株苯降解菌B1、B2和2株甲苯降解菌J2、J6。16S rRNA基因鉴定结果表明B1、J2属于假单胞菌属(Pseudomonassp.),B2、J6属于不动杆菌属(Acinetobactersp.)。研究表明,这些菌在pH7~10的碱性范围内能很好生长。在以0.1%(V/V)苯或甲苯为唯一碳源的无机盐培养基中,B1、B2菌在72小时内对苯的降解率分别为67.7%、94.2%,J2、J6菌对甲苯的降解率分别为92.4%、84.8%。简并PCR扩增、序列分析表明,这些菌含有相同的苯双加氧酶基因,表明苯降解基因在这些降解菌中可能存在水平转移。此外,J2,J6两株菌还含有甲苯双加氧酶基因,而且J2能在甲苯浓度为70%(V/V)的LB培养基中生长。这些降解菌在苯、甲苯污染的生物治理中有应用前景。     

Hydroperoxide-dependent oxygenation of trans-7,8-dihydroxy-7,8-dihydrobenzo[a]pyrene by ram seminal vesicle microsomes. Source of the oxygen

Incubation of 15-hydroperoxy-5,8,11,13-eicosatetraenoic acid with ram seminal vesicle microsomes (RSVM) triggers the oxygenation of $\text{trans}$-7,8-dihydroxy-7,8-dihydrobenzo[a]pyrene (BP-7,8-diol). The principal oxidation products are 7,8,9,10-tetrahydroxy-7,8,9,10-tetrahydrobenzo[a]pyrenes which are non-enzymatic hydrolysis products of r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene. At short incubation times, an additional product is isolated which is identified as r-7,t-8,t-9-trihydroxy-c-10-methoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. This product appears to arise by solvolysis of the extracted diolepoxide during high performance liquid chromatography using methanol-water solvent systems. The incubation of ¹⁸O-labeled 15-hydroperoxy-5,8,11,13-eicosatetraenoic acid with BP-7,8-diol and RSVM leads to very little incorporation of ¹⁸O into the stable solvolysis products (analyzed by gc-ms of their peracetates). Parallel incubations conducted with ¹⁶O-labeled hydroperoxide under an ¹⁸O₂ atmosphere indicate that the principle source of the epoxide oxygen is molecular oxygen.     

Effect of Hydrologic and Geochemical Conditions on Oxygen-Enhanced Bioremediation in a Gasoline-Contaminated Aquifer

Oxygen addition to enhance bioremediation of gasoline-contaminated ground water was performed in two locations of a shallow aquifer in South Carolina characterized by benzene, toluene, and methyl tert-butyl ether (MTBE) at concentrations greater than 1 mg/L, respectively. Oxygen addition with an oxygen-release compound (a proprietary form of magnesium peroxide [MgO₂]) produced markedly different results with respect to dissolved oxygen (DO) generation and contaminant decrease in the two locations. Oxygen-release compound injected at the former underground storage tank (UST) source area did not significantly change measured concentrations of DO, benzene, toluene, or MTBE. Conversely, oxygen-release compound injected 200 m downgradient of the former UST source area rapidly increased DO levels, and benzene, toluene, and MTBE concentrations decreased substantially. The different results can be related to differences in hydrologic and geochemical conditions that characterized the two locations prior to oxygen addition. For example, the contaminated aquifer downgradient of the former UST source area was anoxic, but frequently received oxygen-saturated recharge during rainfall events. As such, the aquifer was characterized by low concentrations of reduced species (such as ferrous iron (Fe²⁺), as well as relatively high numbers of aerobic heterotrophic bacteria (as most probable number [MPN] per milliliter). In contrast, recharge does not occur in the paved, former UST source area. The anoxic aquifer was characterized by higher concentrations of Fe²⁺ that exerted a significant chemical oxygen demand on the oxygen injected, and much lower numbers of aerobic heterotrophic bacteria. The results of this investigation indicate the important role that pre-existing hydrologic, geochemical, and microbiologic conditions have on the outcome of oxygen-based remediation strategies, and suggest that these properties should be evaluated prior to the implementation of oxygen-based remedial strategies.     

Stimulating the anaerobic degradation of aromatic hydrocarbons in contaminated sediments by providing an electrode as the electron acceptor

The possibility that electrodes might serve as an electron acceptor to simulate the degradation of aromatic hydrocarbons in anaerobic contaminated sediments was investigated. Initial studies with Geobacter metallireducens demonstrated that although toluene was rapidly adsorbed onto the graphite electrodes it was rapidly oxidized to carbon dioxide with the electrode serving as the sole electron acceptor. Providing graphite electrodes as an electron acceptor in hydrocarbon‐contaminated sediments significantly stimulated the removal of added toluene and benzene. Rates of toluene and benzene removal accelerated with continued additions of toluene and benzene. [¹⁴C]‐Toluene and [¹⁴C]‐benzene were quantitatively recovered as [¹⁴C]‐CO₂, demonstrating that even though the graphite adsorbed toluene and benzene they were degraded. Introducing an electrode as an electron acceptor also accelerated the loss of added naphthalene and [¹⁴C]‐naphthalene was converted to [¹⁴C]‐CO₂. The results suggest that graphite electrodes can serve as an electron acceptor for the degradation of aromatic hydrocarbon contaminants in sediments, co‐localizing the contaminants, the degradative organisms and the electron acceptor. Once in position, they provide a permanent, low‐maintenance source of electron acceptor. Thus, graphite electrodes may offer an attractive alternative for enhancing contaminant degradation in anoxic environments.     

Conformational changes of recombinant monoclonal antibodies by limited proteolytic digestion,stable isotope labeling,and liquid chromatography–mass spectrometry

Limited proteolytic digestion is a method with a long history that has been used to study protein domain structures and conformational changes. A method of combining limited proteolytic digestion, stable isotope labeling, and mass spectrometry was established in the current study to investigate protein conformational changes. Recombinant monoclonal antibodies with or without the conserved oligosaccharides, and with or without oxidation of the conserved methionine residues, were used to test the newly proposed method. All of the samples were digested in ammonium bicarbonate buffer prepared in normal water. The oxidized deglycosylated sample was also digested in ammonium bicarbonate buffer prepared in ¹⁸O-labeled water. The sample from the digestion in ¹⁸O–water was spiked into each sample digested in normal water. Each mixed sample was subsequently analyzed by liquid chromatography–mass spectrometry (LC–MS). The molecular weight differences between the peptides digested in normal water versus ¹⁸O–water were used to differentiate peaks from the samples. The relative peak intensities of peptides with or without the C-terminal incorporation of ¹⁸O atoms were used to determine susceptibility of different samples to trypsin and chymotrypsin. The results demonstrated that the method was capable of detecting local conformational changes of the recombinant monoclonal antibodies caused by deglycosylation and oxidation.