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Recent advances in the utilization of hydrogen as an alternative fuel source to conventional fossil fuels have led to a search for a renewable process of producing hydrogen. Most hydrogen today is produced from hydrocarbons in a process that also releases high levels of carbon dioxide and carbon monoxide, two established greenhouse gasses; because of this harmful means of production, research has been directed toward using anaerobic digestion to produce useful levels of hydrogen gas. Anaerobic systems have been shown to produce a biogas that is easily used in producing energy, but certain processes can be performed to further enhance the concentrations of hydrogen. These processes include the inhibition of microorganisms that lower hydrogen concentrations and the constant removal of hydrogen to promote hydrogen-producing bacteria. Experimental designs and large-scale applications have shown this process to be environmentally viable with limited, but promising, economic potential. With a constant increase for the need of hydrogen gas, the sustainable production of hydrogen is becoming more important. This review explores some of the recent research on this topic and explores the processes behind using anaerobic digestion for hydrogen production.

PURPOSE OF REVIEW: Glycopeptide antibiotics such as vancomycin are frequently utilized to treat resistant Gram-positive infections such as methicillin-resistant Staphylococcus aureus. The current literature on glycopeptide and lipoglycopeptide structure, hypersensitivity and potential cross-reactivity was reviewed, highlighting implications for safe prescribing. RECENT FINDINGS: Structurally similar, glycopeptides could theoretically cross-react. Immediate reactions to vancomycin include non-IgE-mediated reactions (e.g. red man syndrome) and IgE-mediated hypersensitivity (e.g. anaphylaxis), sharing clinical features. Vancomycin can activate mast cells via MAS-related G-protein-coupled receptor X2, an IgE-independent receptor implicated in non-IgE reactions. In-vivo and in-vitro testing for suspected IgE-mediated reactions to glycopeptides remain ill-defined. Vancomycin is increasingly recognized to cause severe cutaneous adverse reactions (SCAR), with drug reaction with eosinophilia and systemic symptoms (DRESS) predominantly reported. Vancomycin DRESS has been associated with HLA-A32:-01, with a number needed to prevent of 1 in 74. Data demonstrating cross-reactivity amongst glycopeptides and lipoglycopeptides is limited to case reports/series. SUMMARY: Further studies and in-vivo/in-vitro diagnostics are required for better differentiation between IgE and non-IgE glycopeptide reactions. Despite its association with vanomycin DRESS, utility of pharmacogenomic screening for HLA-A32: 01 is ill-defined. Although HLA-A32:01 has been associated with vancomycin DRESS, its utility for pharmacogenomic screening is ill defined. Further clinical and immunological cross-reactivity data for glycopeptide/lipoglycopeptide antibiotics is required.

Nicotinamide riboside (NR) is a naturally occurring form of vitamin B3 shown to preferentially elevate the nicotinamide adenine dinucleotide (NAD+) metabolome compared to other vitamin B3 forms (nicotinic acid and nicotinamide). Although daily requirements of vitamin B3 are typically met through the diet, recent studies have shown that additional supplementation with NR may be an effective method to counter the age-related decline in NAD+ levels as NR bypasses the rate-limiting step in NAD+ biosynthesis. Furthermore, pharmaceutical applications of NR for age-related disorders have been proposed. In this study, the safety of a high-purity, nature-identical, synthetic NR (NR-E), manufactured under the guidelines of good manufacturing practices for dietary supplements (21 CFR 111) as well as for drugs (21 CFR 210), was investigated in a 90-day oral toxicity study in Sprague Dawley rats at 300, 500, and 1,200 mg/kg/d. There were no mortality or clinical observations attributable to the test substance at any dose. A small but statistically significant decrease in body weight was observed at day 92 in the 1,200 mg/kg/d NR-treated male rats only. In contrast to a previously published safety assessment using a different synthetic NR (NIAGEN), whose no-observed-adverse-effect-level (NOAEL) was reported to be 300 mg/kg/d, there were no adverse changes in clinical pathology parameters and no notable macroscopic or microscopic findings or treatment-related effects at similar doses. In the current study, the NOAEL for systemic toxicity of NR-E in Sprague-Dawley rats was conservatively determined to be 500 mg/kg/d for males (solely based on body weight) and 1,200 mg/kg/d for females.

Microbial extracellular electron transfer plays an important role in diverse biogeochemical cycles, metal corrosion, bioelectrochemical technologies, and anaerobic digestion. Evaluation of electron uptake from pure Fe(0) and stainless steel indicated that, in contrast to previous speculation in the literature, Desulfovibrio ferrophilus and Desulfopila corrodens are not able to directly extract electrons from solid-phase electron-donating surfaces. D. ferrophilus grew with Fe(III) as the electron acceptor, but Dp. corrodens did not. D. ferrophilus reduced Fe(III) oxide occluded within porous alginate beads, suggesting that it released a soluble electron shuttle to promote Fe(III) oxide reduction. Conductive atomic force microscopy revealed that the D. ferrophilus pili are electrically conductive and the expression of a gene encoding an aromatics-rich putative pilin was upregulated during growth on Fe(III) oxide. The expression of genes for multi-heme c-type cytochromes was not upregulated during growth with Fe(III) as the electron acceptor, and genes for a porin-cytochrome conduit across the outer membrane were not apparent in the genome. The results suggest that D. ferrophilus has adopted a novel combination of strategies to enable extracellular electron transport, which may be of biogeochemical and technological significance.

Tissue culture approaches are widely used in crop plants for the purposes of micropropagation, regeneration of plants through organogenesis, obtaining pathogen-free plantlets from meristem culture, and developing genetically modified plants. In this research, we evaluated variables that can influence the success of shoot growth and plantlet production in tissue cultures of drug-typeCannabis sativaL. (marijuana). Various sterilization methods were tested to ensure shoot development from nodal explants by limiting the frequency of contaminating endophytes, which otherwise caused the death of explants. Seven commercially grown tetrahydrocannabinol (THC)-containing cannabis genotypes (strains) showed significant differences in response to shoot growth from meristems and nodal explants on Murashige and Skoog (MS) medium containing thidiazuron (1 μM) and naphthaleneacetic acid (0.5 μM) plus 1% activated charcoal. The effect of Driver and Kuniyuki Walnut (DKW) or MS basal salts in media on shoot length and leaf numbers from nodal explants was compared and showed genotype dependency with regard to the growth response. To obtain rooted plantlets, shoots from meristems and nodal explants of genotype Moby Dick were evaluated for rooting, following the addition of sodium metasilicate, silver nitrate, indole-3-butyric acid (IBA), kinetin, or 2,4-D. Sodium metasilicate improved the visual appearance of the foliage and improved the rate of rooting. Silver nitrate also promoted rooting. Following acclimatization, plantlet survival in hydroponic culture, peat plugs, and rockwool substrate was 57, 76, and 83%, respectively. The development of plantlets from meristems is described for the first time inC. sativaand has potential for obtaining pathogen-free plants. The callogenesis response of leaf explants of 11 genotypes on MS medium without activated charcoal was 35% to 100%, depending on the genotype; organogenesis was not observed. The success in recovery of plantlets from meristems and nodal explants is influenced by cannabis genotype, degree of endophytic contamination of the explants, and frequency of rooting. The procedures described here have potential applications for research and commercial utility to obtain plantlets in stage 1 tissue cultures ofC. sativa.

Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H2 and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron transfer because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Heterologous expression of the putative S. aciditrophicus type IV pilin gene in Geobacter sulfurreducens yielded conductive pili of the same diameter (4 nm) and conductance of the native S. aciditrophicus pili and enabled long-range electron transport in G. sulfurreducens. S. aciditrophicus lacked abundant c-type cytochromes often associated with DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.Access opt

The gas-phase unimolecular reactions of C2D5CHFCl molecules with 94 kcal mol-1 of vibrational energy have been studied by the chemical-activation experimental technique and by electronic-structure computations. Products from the reaction of C2D5CHFCl molecules, formed by the recombination of C2D5 and CHFCl radicals in a room temperature bath gas, were measured by gas chromatography-mass spectrometry. The 2,1-DCl (81%) and 1,1-HCl (17%) elimination reactions are the principal processes, but 2,1-DF and 1,1-HF elimination reactions also are observed. Comparison of experimental rate constants to calculated statistical rate constants provides threshold energies. The potential surfaces associated with C2D5(F)C: + HCl and C2D5(Cl)C: + HF reactions are of special interest because hydrogen-bonded adducts with HCl and HF with dissociation energies of 6.4 and 9.3 kcal mol-1, respectively, are predicted by calculations. The relationship between the geometries and threshold energies of transition states for 1,1-HCl elimination and carbene:HCl adducts is complex, and previous studies of related molecules, such as CD3CHFCl, CD2ClCHFCl, C2D5CHCl2, and halogenated methanes are included in the computational analysis. Extensive calculations for CH3CHFCl as a model for 1,1-HCl reactions illustrate properties of the exit-channel potential energy surface. Since the 1,1-HCl transition state is submerged relative to dissociation of the adduct, inner and outer transition states should be considered for analysis of rate constants describing 1,1-HCl elimination and addition reactions of carbenes to HCl.

Heterotrophic nitrifying and aerobic denitrifying bacteria (HNADB) are important for partial nitrification treatment of high strength ammonium leachate. However, conditions for their optimal performance in mixed reactor systems have yet to be determined. In this study, optimal parameters were identified and included free ammonia (FA) concentrations below 40 mg/L, a dissolved oxygen concentration of 1.2 mg/L, a carbon to nitrogen ratio of 5 and a reflux ratio of 4. These conditions were applied to a continuous anoxic/oxic membrane moving biofilm reactor treating raw incineration leachate with high total ammonium nitrogen (TAN = 1400 mg/L). Ammonium conversion and nitrogen removal efficiencies of 99% and 86% were achieved. Autotrophic ammonia oxidizing bacteria were inhibited at FA concentrations above 25 mg/L. HNADB, particularly Paracoccus species, contributed to ammonium conversion at high FA (25–40 mg/L). These results show that leachate with high TAN and FA can be treated using parameters that support the growth of HNADB.

High concentrations of nitrous oxide were recovered from partial nitrification treated leachate in a microbial electrolysis cell (MEC) inoculated with a nosZ-deficient strain of Pseudomonas aeruginosa. N2O conversion efficiencies > 90% were achieved when a potential of 0.8 V was applied to the MEC. The ΔnosZ strain was enriched in the 0.8 V MEC, but Achromobacter dominated the non-current control. Nitric oxide reductase genes were highly expressed by ΔnosZ cells growing in the 0.8 V MEC, consistent with enhanced nitrous oxide production rates. Concentrations of phenazine derivatives and transcripts from phenazine biosynthesis genes were also high in the 0.8 V MEC. Phenazine derivatives are known to act as electron shuttles, enhance biofilm formation, and help ward off competitors, thereby increasing the survivability of the ΔnosZ strain in the MEC. These results show that applied current stabilized growth of the ΔnosZ strain in the reactor and allowed it to sustainably generate high concentrations of nitrous oxide.

Cholesterol seems to play a central role in the augmentation of saporin-based immunotoxin (IT) cytotoxicity by triterpenoid saponins. Endolysosomal escape has been proposed as one mechanism for the saponin-mediated enhancement of targeted toxins. We investigated the effects of lipid depletion followed by repletion on Saponinum album (SA)-induced endolysosomal escape of Alexa Fluor labelled saporin and the saporin-based immunotoxin OKT10-SAP, directed against CD38, in Daudi lymphoma cells. Lipid deprived cells showed reduced SA-induced endolysosomal escape at two concentrations of SA, as determined by a flow cytometric method. The repletion of membrane cholesterol by low density lipoprotein (LDL) restored SA-induced endolysosomal escape at a concentration of 5 &micro, g/mL SA but not at 1 &micro, g/mL SA. When LDL was used to restore the cholesterol levels in lipid deprived cells, the SA augmentation of OKT10-SAP cytotoxicity was partially restored at 1 &micro, g/mL SA and fully restored at 5 &micro, g/mL SA. These results suggest that different mechanisms of action might be involved for the two different concentrations of SA and that endosomal escape may not be the main mechanism for the augmentation of saporin IT cytotoxicity by SA at the sub-lytic concentration of 1 &micro, g/mL SA.

Anaerobically treated leachate from municipal solid waste incineration plants contains extremely high free ammonia (FA) concentrations, which can hinder short-cut nitrification. pH adjustments made...

Solid supported colorimetric sensing arrays have the advantage of portability and ease of use when deployed in the field, such as crime scenes, disaster zones, or in war zones, but many sensor arrays require complex fabrication methods. Here, we report a practical method for the fabrication of 4 × 4 colorimetric sensor arrays, which are printed on nylon membranes, using a commercially available inkjet printer. In order to test the efficacy of the printed arrays, they were exposed to 43 analytes at concentrations ranging from 0.001 to 3.0 M for a total of 559 samples of inorganic and organic acids or bases including hydrochloric, acetic, phthalic, malonic, picric, and trifluoroacetic acid, ammonium hydroxide, sodium hydroxide, lysine, and water as the control. Colorimetric data from the imaged arrays was analyzed with linear discriminant analysis and k-nearest neighbors to determine the analyte and concentration with ∼88-90% accuracy. Overall, the arrays have impressive analytical power to identify a variety of analytes at different concentrations while being simple to fabricate.

The recombination of CF3 and CHF2 radicals in a room-temperature bath gas was used to prepare vibrationally excited CF3CHF2* molecules with 101 kcal mol–1 of vibrational energy. The subsequent 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions were observed as a function of bath gas pressure by following the CHF3, CF3(F)C: and C2F4 product concentrations by gas chromatography using a mass spectrometer as the detector. The singlet CF3(F)C: concentration was measured by trapping the carbene with trans-2-butene. The experimental rate constants are 3.6 × 104, 4.7 × 104, and 1.1 × 104 s–1 for the 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions, respectively. These experimental rate constants were matched to statistical RRKM calculated rate constants to assign threshold energies (E0) of 88 ± 2, 88 ± 2, and 87 ± 2 kcal mol–1 to the three reactions. Pentafluoroethane is the only fluoroethane that has a competitive H atom transfer decomposition reaction, and it is the only example with...

Growth of bacterial and archaeal species capable of interspecies electron exchange was stimulated by addition of conductive materials (carbon cloth or granular activated carbon (GAC)) to anaerobic digesters treating dog food (a substitute for the dry-organic fraction of municipal solid waste (OFMSW)). Methane production (772-1428mmol vs

In this study, nitrous oxide was recovered from a lab-scale moving-bed biofilm reactor (MBBR) treating partial nitrification-treated leachate supplemented with a nosZ-deficient strain of Pseudomonas aeruginosa. Batch culture tests with the nosZ-deficient strain determined that the threshold for free nitrous acid (FNA) inhibition was 0.016 mg/L and that FNA concentrations above this threshold severely inhibited denitrification and transcription of genes from the dissimilatory nitrate reduction pathway (narG, nirS, and norB). High nitrite removal and N2O conversion efficiencies (>95%) were achieved with long-term operation of this MBBR. N2O accounted for the majority of biogas (80%) produced when the MBBR was fed partial nitrification-treated leachate with high nitrite concentrations and the drainage ratio was adjusted to 30%. Bacterial community analysis revealed that the nosZ-deficient Pseudomonas strain remained metabolically active and was primarily responsible for denitrification processes in the reactor. This study presents a promising method for N2O recovery from incineration leachate.

In order to illustrate the impact that application of positive or negative potential to conductive materials can have on direct interspecies electron transfer (DIET) and reactor performance under high organic loading rates, three continuous laboratory-scale reactors with carbon-cloth electrodes poised at +0.7 V, −0.7 V (vs. Ag/AgCl) and no-potential were fed high concentrations of ethanol wastewater. While exoelectrogens and methanogens that are capable of DIET were significantly enriched in poised reactors, they performed worse than the non-current control. Volatile fatty acids (VFAs) accumulated more rapidly in the positively then negatively poised reactor, but neither could withstand high-loading rates. These results demonstrate that applying potential to conductive materials had a negative effect on anaerobic digestion under high-loading conditions.

While studies have shown that anaerobic co-digestion of chicken manure (CM) and corn stover (CS) is an efficient method to treat these agricultural wastes, the microbial ecology of these systems and optimal parameters for the digestion process are yet to be determined. In this study, the effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion and microbial community structure were evaluated. Results demonstrated that both the highest cumulative methane yields and methane production rates were obtained from reactors with a CS : CM ratio of 1 : 1 during hemi-solid-state anaerobic digestion (HSS-AD). Cumulative methane yields and methane production rates were 24.8% and 42% lower in solid-state anaerobic digestion (SS-AD) reactors using the same CS : CM ratios. Analysis of microbial community structures revealed that cellulolytic bacteria and a diversity of syntrophic microorganisms capable of direct interspecies electron transfer (DIET) and hydrogen interspecies transfer (HIT) were enriched in the best-performing reactors. Methanosarcina species also dominated during HSS-AD, and their presence was positively correlated with methane production in the reactors.

Bioelectrochemical conversion of CO2 to CH4 is a promising way to increase the calorific value of biogas produced during anaerobic digestion. There are two groups of methanogens enriched in these systems, hydrogenotrophs and acetoclastic methanogens that can also directly accept electrons from an electrode or another microorganism. In this study, a microbial electrolysis cell (MEC) poised at −500 mV (vs. SHE) was operated for biogas upgrading. Methane content in the biogas increased from 71% to >90%, and 8.2% of the CO2 was converted to methane. Methanothrix, an acetoclastic methanogen that can participate in direct electron transfer (DET), and Azonexus, an acetate-oxidizing electrogen, were enriched on the cathode. Transcriptomics revealed that Methanothrix on the cathode were using the CO2 reduction pathway, while Methanothrix in the bulk sludge were using the acetate decarboxylation pathway for production of methane. These results show that stimulation of DET in MEC enhances biogas-upgrading processes.

The glucocorticoid receptor (GR) binds the noncoding RNA Gas5 via its DNA-binding domain (DBD) with functional implications in pro-apoptosis signaling. Here, we report a comprehensive in vitro binding study where we have determined that GR-DBD is a robust structure-specific RNA-binding domain. GR-DBD binds to a diverse range of RNA hairpin motifs, both synthetic and biologically derived, with apparent mid-nanomolar affinity while discriminating against uniform dsRNA. As opposed to dimeric recognition of dsDNA, GR-DBD binds to RNA as a monomer and confers high affinity primarily through electrostatic contacts. GR-DBD adopts a discrete RNA-bound state, as assessed by NMR, distinct from both free and DNA-bound. NMR and alanine mutagenesis suggest a heightened involvement of the C-terminal α-helix of the GR-DBD in RNA-binding. RNA competes for binding with dsDNA and occurs in a similar affinity range as dimer binding to the canonical DNA element. Given the prevalence of RNA hairpins within the transcriptome, our findings strongly suggest that many RNAs have potential to impact GR biology.

The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of the strains studied can also use H2 as an electron donor for growth, which is known to be abiotically produced from Fe(0). Furthermore, no proteins definitely shown to function as extracellular electrical contacts with Fe(0) were identified. The studies described here demonstrate that direct electron transfer from Fe(0) can support anaerobic respiration. They also map out a simple genetic approach to the study of iron corrosion mechanisms in other microorganisms. A better understanding of how microorganisms promote iron corrosion is expected to lead to the development of strategies that can help reduce adverse impacts from this process., The concept that anaerobic microorganisms can directly accept electrons from Fe(0) has been controversial because direct metal-microbe electron transfer has previously only been indirectly inferred. Fe(0) oxidation was studied with Geobacter sulfurreducens strain ACL, an autotrophic strain that was previously shown to grow with electrons derived from a graphite cathode as the sole electron donor. Strain ACL grew with Fe(0) as the sole electron donor and fumarate as the electron acceptor. However, it appeared that at least a portion of the electron transfer was via H2 produced nonenzymatically from the oxidation of Fe(0) to Fe(II). H2, which accumulated in abiotic controls, was consumed during the growth of strain ACL, the cells were predominately planktonic, and genes for the uptake hydrogenase were highly expressed. Strain ACLHF was constructed to prevent growth on H2 or formate by deleting the genes for the uptake of hydrogenase and formate dehydrogenases from strain ACL. Strain ACLHF also grew with Fe(0) as the sole electron donor, but H2 accumulated in the culture, and cells heavily colonized Fe(0) surfaces with no visible planktonic growth. Transcriptomics suggested that the outer surface c-type cytochromes OmcS and OmcZ were important during growth of strain ACLHF on Fe(0). Strain ACLHF did not grow on Fe(0) if the gene for either of these cytochromes was deleted. The specific attachment of strain ACLHF to Fe(0), coupled with requirements for known extracellular electrical contacts, suggest that direct metal-microbe electron transfer is the most likely option for Fe(0) serving as an electron donor.

Biogas produced from anaerobic digestion usually contains 30%-50% CO2, much of which must be removed, before utilization. Bioelectrochemical biogas upgrading approaches show promise, however, they have not yet been optimized for practical applications. In this study, a bioelectrochemical system with low energy input (applied cathode potential of -0.5 V vs. standard hydrogen electrode, SHE) was used for in-situ biogas upgrading. High efficiency CO2 conversion (318.5 mol/d/m2) was achieved when the system was operated with an organic load of 1.7 kgCOD/(m3 d). Methane content in the upgraded biogas was 97.0% and CO2 concentrations stayed below 3%, which is comparable to biogas upgraded with more expensive and less sustainable physiochemical approaches. The high efficiency of this approach could likely be attributed to a significant enrichment of Methanothrix (92.7%) species on the cathode surface that were expressing genes involved in both acetogenic methanogenesis and direct electron transfer (DET). Electromethanogenesis by these organisms also increased proton consumption and created a higher pH that increased the solubility of CO2 in the bioreactor. In addition, CO2 removal from the biogas was likely further enhanced by an enrichment of Actinobacillus species known to be capable of CO2 fixation. Artificial neural network (ANN) models were also used to estimate CH4 production under different loading conditions. The ANN architecture with 10 neurons at hidden layers fit best with a mean square error of 6.06 × 10−3 and R2 of 0.99.

In this study, an Escherichia coli (E. coli) whole-cell biosensor for the specific detection of bioavailable arsenic was developed by placing a green fluorescent protein (GFP) reporter gene under the control of the ArsR1 (GSU2952) regulatory circuit from Geobacter sulfurreducens. E. coli cells only emitted green fluorescence in the presence of arsenite and were more sensitive to arsenite when they were grown in M9 supplemented medium compared to LB medium. Under optimal test conditions, the Geobacter arsR1 promoter had a detection limit of 0.01 μM arsenite and the GFP expression was linear within a range of 0.03–0.1 μM (2.25–7.5 μg/l). These values were well below World Health Organization’s drinking water quality standard, which is 10 μg/l. The feasibility of using this whole-cell biosensor to detect arsenic in water samples, such as arsenic polluted tap water and landfill leachate was verified. The biosensor was determined to be just as sensitive as atomic fluorescence spectrometry. This study examines the potential applications of biosensors constructed with Geobacter ArsR-Pars regulatory circuits and provides a rapid and cost-effective tool that can be used for arsenic detection in water samples.

The recombination of ·CHF2 radicals in a room-temperature bath gas was used to generate CHF2CHF2* (where * indicates vibrational excitation) molecules with 96 kcal mol–1 of vibrational energy. The CHF2CHF2* molecules decompose by four-centered 1,2-HF elimination and by three-centered 1,1-HF elimination reactions to give HF and either CHF═CF2 or :CFCHF2, respectively. The 1,1-HF component was identified by trapping the :CFCHF2 carbene with trans-2-butene that forms 1-fluoro-1-difluoromethyl-2,3-dimethylcyclopropane. The total rate constant for the decomposition of CHF2CHF2* was 6.0 × 105 s–1, and the rate constant for the 1,1-HF pathway forming the carbene, as measured by the 1-fluoro-1-difluoromethyl-2,3-dimethylcyclopropane yield, was 1.4 × 105 s–1. On the basis of matching the experimental rate constants to calculated statistical rate constants, the threshold energies for the four-centered and three-centered reactions are 78 and ≤85 kcal mol–1, respectively.

Chemically activated C2D5CHCl2 molecules were generated with 88 kcal mol–1 of vibrational energy by the recombination of C2D5 and CHCl2 radicals in a room temperature bath gas. The competing 2,1-DCl and 1,1-HCl unimolecular reactions were identified by the observation of the CD3CD═CHCl and CD3CD═CDCl products. The initial CD3CD2C—Cl carbene product from 1,1-HCl elimination rearranges to CD3CD═CDCl under the conditions of the experiments. The experimental rate constants were 2.7 × 107 and 0.47 × 107 s–1 for 2,1-DCl and 1,1-HCl elimination reactions, respectively, which corresponds to branching fractions of 0.84 and 0.16. The experimental rate constants were compared to calculated statistical rate constants to assign threshold energies of 54 and ≈66 kcal mol–1 for the 1,2-DCl and 1,1-HCl reactions, respectively. The statistical rate constants were obtained from models developed from electronic-structure calculations for the molecule and its transition states. The rate constant (5.3 × 107 s–1) for the unimol...

Direct interspecies electron transfer (DIET) is important in diverse methanogenic environments, but how methanogens participate in DIET is poorly understood. Therefore, the transcriptome of Methanosarcina barkeri grown via DIET in co-culture with Geobacter metallireducens was compared with its transcriptome when grown via H2 interspecies transfer (HIT) with Pelobacter carbinolicus. Notably, transcripts for the F420H2 dehydrogenase, Fpo, and the heterodisulfide reductase, HdrABC, were more abundant during growth on DIET. A model for CO2 reduction was developed from these results in which electrons delivered tomethanophenazine in the cell membrane are transferred to Fpo. The external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for Fpo-catalyzed F420 reduction is derived from protons released from G. metallireducens metabolism. Reduced F420 is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB. Expression of genes for putative redox-active proteins predicted to be localized on the outer cell surface was higher during growth on DIET, but further analysis will be required to identify the electron transfer route to methanophenazine. The results indicate that the pathways for electron and proton flux for CO2 reduction during DIET are substantially different than for HIT and suggest that gene expression patterns may also be useful for determining whether Methanosarcina are directly accepting electrons from other extracellular electron donors, such as corroding metals or electrodes.

BACKGROUND: Although use of nonsteroidal antiinflammatory drugs and low-dose irradiation has demonstrated efficacy in preventing heterotopic ossification (HO) after THA and surgical treatment of acetabular fractures, these modalities have not been assessed after traumatic blast amputations where HO is a common complication that can arise in the residual limb. QUESTIONS/PURPOSES: The purpose of this study was to investigate the effectiveness of indomethacin and irradiation in preventing HO induced by high-energy blast trauma in a rat model. METHODS: Thirty-six Sprague-Dawley rats underwent hind limb blast amputation with a submerged explosive under water followed by irrigation and primary wound closure. One group (n = 12) received oral indomethacin for 10 days starting on postoperative Day 1. Another group (n = 12) received a single dose of 8 Gy irradiation to the residual limb on postoperative Day 3. A control group (n = 12) did not receive either. Wound healing and clinical course were monitored in all animals until euthanasia at 24 weeks. Serial radiographs were taken immediately postoperatively, at 10 days, and every 4 weeks thereafter to monitor the time course of ectopic bone formation until euthanasia. Five independent graders evaluated the 24-week radiographs to quantitatively assess severity and qualitatively assess the pattern of HO using a modified Potter scale from 0 to 3. Assessment of grading reproducibility yielded a Fleiss statistic of 0.41 and 0.37 for severity and type, respectively. By extrapolation from human clinical trials, a minimum clinically important difference in HO severity was empirically determined to be two full grades or progression of absolute grade to the most severe. RESULTS: We found no differences in mean HO severity scores among the three study groups (indomethacin 0.90 ± 0.46 [95% confidence interval {CI}, 0.60-1.19]; radiation 1.34 ± 0.59 [95% CI, 0.95-1.74]; control 0.95 ± 0.55 [95% CI, 0.60-1.30]; p = 0.100). For qualitative HO type scores, the radiation group had a higher HO type than both indomethacin and controls, but indomethacin was no different than controls (indomethacin 1.08 ± 0.66 [95% CI, 0.67-1.50]; radiation 1.89 ± 0.76 [95% CI, 1.38-2.40]; control 1.10 ± 0.62 [95% CI, 0.70-1.50]; p = 0.013). The lower bound of the 95% CI on mean severity in the indomethacin group and the upper bound of the radiation group barely spanned a full grade and involved only numeric grades < 2, suggesting that even if a small difference in severity could be detected, it would be less than our a priori-defined minimum clinically important difference and any differences that might be present are unlikely to be clinically meaningful. CONCLUSIONS: This work unexpectedly demonstrated that, compared with controls, indomethacin and irradiation provide no effective prophylaxis against HO in the residual limb after high-energy blast amputation in a rat model. Such an observation is contrary to the civilian experience and may be potentially explained by either a different pathogenesis for blast-induced HO or a stimulus that overwhelms conventional regimens used to prevent HO in the civilian population. CLINICAL RELEVANCE: HO in the residual limb after high-energy traumatic blast amputation will likely require novel approaches for prevention and management.

Chemical warfare agents pose significant threats in the 21st century, especially for armed forces. A colorimetric detection array was developed to identify warfare mimics, including mustard gas and nerve agents. In total, 188 sensors were screened to determine the best sensor performance, in order to identify warfare mimics 2-chloro ethyl ethylsulfide, 2-2&prime, thiodiethanol, trifluoroacetic acid, methylphosphonic acid, dimethylphosphite, diethylcyanophosphonate, and diethyl (methylthiomethyl)phosphonate. The highest loadings in the principle component analysis (PCA) plots were used to identify the sensors that were most effective in analyzing the RGB data to classify the warfare mimics. The dataset was reduced to only twelve sensors, and PCA results gave comparable results as the large data did, demonstrating that only twelve sensors are needed to classify the warfare mimics.

Insoluble extracellular electron donors are important sources of energy for anaerobic respiration in biogeochemical cycling and in diverse practical applications. The previous lack of a genetically tractable model microorganism that could be grown to high densities under anaerobic conditions in pure culture with an insoluble extracellular electron donor has stymied efforts to better understand this form of respiration. We report here on the design of a strain of Geobacter sulfurreducens, designated strain ACL, which grows as thick (ca. 35 μm) confluent biofilms on graphite cathodes poised at -500 mV (versus Ag/AgCl) with fumarate as the electron acceptor. Sustained maximum current consumption rates were >0.8 A/m2, which is >10-fold higher than the current consumption of the wild-type strain. The improved function on the cathode was achieved by introducing genes for an ATP-dependent citrate lyase, completing the complement of enzymes needed for a reverse TCA cycle for the synthesis of biosynthetic precursors from carbon dioxide. Strain ACL provides an important model organism for elucidating the mechanisms for effective anaerobic growth with an insoluble extracellular electron donor and may offer unique possibilities as a chassis for the introduction of synthetic metabolic pathways for the production of commodities with electrons derived from electrodes.

Highlights • Sediment influence on hydrate dissolution was studied in the field and lab • In the field, CH4(aq) concentrations were at or below theoretical saturation • Dissolution of natural hydrate blanketed by 15 cm thick sediment was measured • This covered hydrate dissolved at a slower rate than nearby exposed hydrates • In the lab, exposed hydrate dissolved faster than covered hydrate Abstract Dissolution rates of naturally occurring gas hydrates vary by orders of magnitude across studies suggesting that environmental factors may influence hydrate dissolution. To determine the role that sediment cover plays in hydrate dissolution, we used a mini-pore fluid array sampler (mPFA) to continuously collect sediment porewater adjacent to a hydrate outcrop and maintain it at in situ pressure for later analysis. This allowed us to measure in situ dissolved hydrocarbon concentrations in the porewater over time without sample loss due to degassing. We deployed the mPFA at a hydrate outcrop at Barkley Canyon on the Cascadia Margin for nine months. This novel approach yielded concentration data that were used to determine the steady-state dissolution rate of the hydrate outcrop and test predictions of the diffusion-control model for dissolution in the field. In the lab, we conducted a series of experiments with artificial hydrate to directly compare dissolution rates between exposed and sediment-covered hydrate. The dissolution rate of the natural hydrate outcrop covered with sediment was 0.06 cm y− 1. The laboratory experiments of sediment-covered hydrate yielded dissolution rates of 0.6 ± 0.5 cm y− 1 (n = 5). In both laboratory and field observations, the dissolution rate of hydrates exposed directly to bulk water (3.9 ± 1.7 cm y− 1 and 3.5 cm y− 1 respectively) was at least an order of magnitude faster than the dissolution rate of sediment covered hydrate. These results are consistent with expectations of diffusion-control and support this model of hydrate dissolution. In nature, sediment may account for the persistence of hydrate in otherwise methane-depleted environments by increasing the diffusive boundary layer and slowing the rate of molecular diffusion via porosity/tortuosity effects. We provide a number of “Lessons Learned” for improving the instrument design and for consideration during future studies.

Objective This study aims to examine the potential of radiomimetic compounds as antimicrobial therapeutics, as the recent advances in radiomimetic targeting as well as rapid increase of multidrug resistant bacteria make these compounds attractive for future development. Methods Representative radiomimetics from each of the three major categories was examined; C-1027 and neocarzinostatin from the protein-chromophore enediyne family; Calicheamicin from the non-protein chromophore enediyne family and Bleomycin and Tallysomycin S10b from the glycopeptide family. The activity of these compounds was examined against 12 distinct bacteria species. Inhibition was determined using disc diffusion assays and a subsequent examination of minimum inhibitory concentration of a representative organism. The onset of action of the compounds was also determined by incubating the organisms with drug in liquid media, before plating, and then determining if growth occurred. Results We found that the radiomimetic glycopeptides were more active against Gram-negative species, while the enediynes were more effective against Gram-positive species. The radiomimetics also maintained their rapid onset of action, working as quickly as 5 min. Conclusions Radiomimetic compounds have activity against a wide variety of microorganisms and would support the development of radiomimetic–antibody conjugates as potential antibiotics as an option against severe bacterial infections.

The recombination of CHF2 and C2D5 radicals was used to produce CD3CD2CHF2* molecules with 96 kcal mol(-1) of vibrational energy in a room temperature bath gas. The formation of CD3CD═CHF and CD3CD═CDF was used to identify the 1,2-DF and 1,1-HF unimolecular elimination channels; CD3CD═CDF is formed by isomerization of the singlet-state CD3CD2CF carbene. The total unimolecular rate constant is 1.6 × 10(6) s(-1), and the branching ratio for 1,1-HF elimination is 0.25. Threshold energies of 64 ± 2 and 73 ± 2 kcal mol(-1) were assigned to the 1,2-DF and 1,1-HF reaction channels. The E and Z isomers of 1-fluoropropene were observed for each reaction; approximately 30% of the CD3CD═CDF molecules derived from 1,1-HF elimination retained enough energy to undergo cis-trans isomerization. Electronic structure calculations with density-functional theory were used to characterize the transition-state structures and the H atom migration barrier for CD3CD2CF. Adjustment of the rate constants to account for kinetic-isotope effects suggest that the branching ratio would be 0.20 for 1,1-HF elimination from C2H5CHF2. The results from an earlier study of CD3CHF2 and CH3CHF2 are also reinterpreted to assign a threshold energy of 74 kcal mol(-1) for the 1,1-HF elimination reaction. Because CHF2CHF2* is generated in the photolysis system, the 1,1-and 1,2-HF-elimination reactions of CHF2CHF2* are discussed. The 1,1-HF channel was identified by trapping the CF2HCF carbene with cis-butene-2.

Chemically activated CF3SH, CFCl2SH, and CF2ClSH were formed through combination of SH and CF3, CFCl2, and CF2Cl radicals, respectively. The SH radical was prepared by abstraction of an H-atom from H2S by the halocarbon radical produced during photolysis of (CF3)2C=O, (CFCl2)2C=O, or (CF2Cl)2C=O. 1,2-HX (X = F, Cl) elimination reactions were observed from CF3SH, CFCl2SH, and CF2ClSH with products detected by GC-MS. The combination reaction of CF2Cl radicals with SH radicals prepared CF2ClSH molecules with approximately 318 kJ/mol of internal energy. The experimental rate constants for elimination of HCl and HF from CF2ClSH were 3 ± 3 × 1010 and 2 ± 1 × 109 s−1, respectively. Comparison to Rice–Ramsperger–Kassel–Marcus (RRKM) calculated rate constants assigned the threshold energies as 171 ± 12 and 205 ± 12 kJ/mol for the unimolecular elimination of HCl and HF, respectively. Theoretical calculations using the B3PW91, MP2, and M062X methods with the 6311+G(2d,p) and 6-31G(d',p') basis sets established that for a specific method the threshold energies differ by only 4 kJ/mol between the two different basis sets. There was wide variation among the three methods, but the M062X approach appeared to give threshold energies closest to the experimental values. Chemically activated CF3SH and CFCl2SH were also prepared with about 318 kcal mol−1 of internal energy, and the HX (X = F, Cl) elimination reactions were observed. Only HCl loss was detected from CFCl2SH, but the rate was too fast to measure with our kinetic method; however, based on our detection limit the HF elimination channel is at least 50 times slower.

The hyperthermophilic archaeon Ferroglobus placidus can utilize a wide variety of electron donors, including hydrocarbons and aromatic compounds, with Fe(III) serving as an electron acceptor. In Fe(III)-reducing bacteria that have been studied to date, this process is mediated by c -type cytochromes and type IV pili. However, there currently is little information available about how this process is accomplished in archaea. In silico analysis of the F. placidus genome revealed the presence of 30 genes coding for putative c -type cytochrome proteins (more than any other archaeon that has been sequenced to date), five of which contained 10 or more heme-binding motifs. When cell extracts were analyzed by SDS-PAGE followed by heme staining, multiple bands corresponding to c -type cytochromes were detected. Different protein expression patterns were observed in F. placidus cells grown on soluble and insoluble iron forms. In order to explore this result further, transcriptomic studies were performed. Eight genes corresponding to multiheme c -type cytochromes were upregulated when F. placidus was grown with insoluble Fe(III) oxide compared to soluble Fe(III) citrate as an electron acceptor. Numerous archaella (archaeal flagella) also were observed on Fe(III)-grown cells, and genes coding for two type IV pilin-like domain proteins were differentially expressed in Fe(III) oxide-grown cells. This study provides insight into the mechanisms for dissimilatory Fe(III) respiration by hyperthermophilic archaea.

Background Preclinical and postmortem studies have implicated the metabotropic glutamate receptor 5 (mGluR5) in the pathophysiology of major depressive disorder (MDD). The goal of the current study was to determine the role of mGluR5 in a large group of individuals with MDD compared with healthy control subjects (HCs) in vivo with 3-[ 18 F]FPEB and positron emission tomography. Furthermore, we sought to determine the role glutamate plays in mGluR5 availability in MDD. Methods A total of 65 participants (30 individuals with MDD and 35 HCs) completed 3-[ 18 F]FPEB positron emission tomography to estimate the primary outcome measure, mGluR5 volume of distribution, and the secondary outcome measure, mGluR5 distribution volume ratio. A subgroup of 39 participants (16 individuals with MDD and 23 HCs) completed proton magnetic resonance spectroscopy to estimate anterior cingulate cortex glutamate, glutamine, and glutamate + glutamine levels relative to creatine. Results No significant between-group differences were observed in mGluR5 volume of distribution or distribution volume ratio. Compared with HCs, individuals with MDD had higher anterior cingulate cortex glutamate, glutamine, and glutamate + glutamine levels. Importantly, the anterior cingulate cortex mGluR5 distribution volume ratio negatively correlated with glutamate/creatine and glutamate + glutamine/creatine levels. Conclusions In this novel in vivo examination, we show an inverse relationship between mGluR5 availability and glutamate levels. These data highlight the need to further investigate the role of the glutamatergic system in depression.

Plant root exudates are important mediators in the interactions that occur between plants and microorganisms in the soil, yet much remains to be learned about spatial and temporal variation in their production. This work outlines a method utilizing a novel colorimetric paper to detect spatial and temporal changes in the production of nitrogen-containing compounds on the root surface. While existing methods have made it possible to conduct detailed analysis of root exudate composition, relatively less is known about where in the root system exudates are produced and how this localization changes as the root grows. Furthermore, there is much to learn about how exudate localization and composition varies in response to stress. Root exudates are chemically diverse secretions composed of organic acids, amino acids, proteins, sugars, and other metabolites. The sensor utilized for the method, ninhydrin, is a colorless substance in solution that reacts with free amino groups to form a purple dye. A detection paper was developed by formulating ninhydrin into a print solution that was uniformly deposited onto paper with a commercial ink jet printer. This “ninhydrin paper” was used to analyze the chemical makeup of root surfaces from maize seedlings grown vertically on germination paper. Through contact between the ninhydrin paper and seedling root surfaces, combined with images of both the seedlings and dried ninhydrin papers captured using a standard flatbed scanner, nitrogen-containing substances on the root surface can be localized and concentration of signal estimated for over two weeks of development. The method was found to be non-inhibiting to plant growth over the analysis period although damage to root hairs was observed. The method is sensitive in the detection of free amines at concentrations as little as 140 µM. Furthermore, ninhydrin paper is stable, showing consistent color changes up to two weeks after printing. The method is expandable to the detection of other relevant compounds produced during root development. This relatively simple, low-cost method could contribute to a better understanding of root exudates and mechanisms used by plants to interact with the complex soil environment during growth and development.

The formation of disinfection by-products (DBPs) in drinking water occurs when chemical disinfectants such as chlorine and chloramine react with natural organic matter and anthropogenic pollutants. Some DBPs have been linked to bladder cancer and infertility; however, the underlying mechanism of action is unknown. One possibility is disruption of the endocrine system, with DBPs binding to the androgen receptor and subsequently altering gene expression. Using the androgen receptor-binding assay and in silico molecular docking, the binding affinity of 21 suspected and known DBPs were tested individually at concentrations over the range 0.1 nM–2 mM. 14 DBPs were found to bind at IC 50 values ranging from 1.86 mM for 2,3-dichloropropionamide to 13.5 μM for 3,4,5,6-tetrachloro-benzoquinone as compared to the positive control, 4- n -nonylphenol which bound at 31.6 μM. Since DBPs are present in drinking waters as mixtures, the question of how IC 50 values for individual DBPs might be affected by the presence of other chemicals is addressed. Seven of the chemicals with the strongest binding affinities and one chemical with no binding affinity were tested in binary mixtures with 4- n -nonylphenol, a known androgenic chemical found in some surface waters. In these binary mixtures, concentration additive binding was observed. While typical levels of individual androgenic DBPs in drinking water are below their measured IC 50 values, their combined binding abilities in mixtures could be a source of androgen disruption.

The possibility that bacteria other than Geobacter species might contain genes for electrically conductive pili (e-pili) was investigated by heterologously expressing pilin genes of interest in Geobacter sulfurreducens. Strains of G. sulfurreducens producing high current densities, which are only possible with e-pili, were obtained with pilin genes from Flexistipes sinusarabici, Calditerrivibrio nitroreducens, and Desulfurivibrio alkaliphilus. The conductance of pili from these strains was comparable to native G. sulfurreducens e-pili. The e-pili derived from C. nitroreducens, and D. alkaliphilus pilin genes are the first examples of relatively long (> 100 amino acids) pilin monomers assembling into e-pili. The pilin gene from Desulfofervidus auxilii did not yield e-pili, suggesting that the hypothesis that this sulfate reducer wires itself to ANME-1 microbes with e-pili to promote anaerobic methane oxidation should be reevaluated. A high density of aromatic amino acids and a lack of substantial aromatic-free gaps along the length of long pilins may be important characteristics leading to e-pili. This study demonstrates a simple method to screen pilin genes from difficult-to-culture microorganisms for their potential to yield e-pili; reveals new potential sources for biologically based electronic materials; and suggests that a wide phylogenetic diversity of microorganisms may employ e-pili for extracellular electron exchange.

Triterpenoid saponins from Saponinum Album (SA) exert potent lytic effects on eukaryotic cell plasma membranes and, when used at sub-lytic concentrations, significantly augment the cytotoxicity of saporin-based immunotoxins (IT). To help elucidate the mechanism(s) behind these two phenomena we investigated the role of cholesterol to both. Human Daudi lymphoma cells were lipid deprived using a combination of three different approaches. Following treatment, the total cellular lipid content was analyzed by electrospray ionization mass spectrometry (ESI-MS) and plasma membrane (PM) cholesterol content measured using the lipophilic fluorescent probe NR12S. Maximal lipid deprivation of cells resulted in a complete loss of sensitivity to lysis by SA. Similarly augmentation of the anti-CD19 immunotoxin (IT) BU12-SAPORIN by SA was lost but without a concomitant loss of intrinsic IT cytotoxicity. The lytic activity of SA was restored following incubation of lipid deprived Daudi cells with Synthecol or LDL. The augmentative effect of SA on IT cytotoxicity for Daudi cells was restored following repletion of PM cholesterol levels with LDL. NR12S fluorescence and ESI-MS analysis of cellular lipids demonstrated that restoration of SA lytic activity by Synthecol was entirely due to increased PM cholesterol levels. Restoration of cellular and PM cholesterol levels by LDL also restored the augmentative effect of SA for IT, an effect associated with repletion of PM cholesterol with minor changes in some phospholipid species. These results indicate that the lytic and IT augmentative properties of SA are cholesterol-dependent in contrast to intrinsic IT cytotoxicity that is at least partially cholesterol independent.

Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system ( ars operon), and several have genes required for arsenic respiration ( arr operon) and methylation ( arsM ). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens ; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. IMPORTANCE This study examines arsenic transformation mechanisms utilized by Geobacter , a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system ( ars operon), and some also have genes required for arsenic respiration ( arr operon) and arsenic methylation ( arsM ).

Ferroglobus placiduswas discovered to oxidize completely the aromatic amino acids tyrosine, phenylalanine and tryptophan when Fe(III) oxide was provided as an electron acceptor. This property had not been reported previously for a hyperthermophilic archaeon. It appeared thatF. placidusfollows a pathway for phenylalanine and tryptophan degradation similar to that of mesophilic nitrate-reducing bacteria,Thauera aromaticaandAromatoleum aromaticumEbN1. Phenylacetate, 4-hydroxyphenylacetate and indole-3-acetate were formed during anaerobic degradation of phenylalanine, tyrosine and tryptophan, respectively. Candidate genes for enzymes involved in the anaerobic oxidation of phenylalanine to phenylacetate (phenylalanine transaminase, phenylpyruvate decarboxylase and phenylacetaldehyde : ferredoxin oxidoreductase) were identified in theF. placidusgenome. In addition, transcription of candidate genes for the anaerobic phenylacetate degradation, benzoyl-CoA degradation and glutaryl-CoA degradation pathways was significantly upregulated in microarray and quantitative real-time-PCR studies comparing phenylacetate-grown cells with acetate-grown cells. These results suggested that the general strategies for anaerobic degradation of aromatic amino acids are highly conserved amongst bacteria and archaea living in both mesophilic and hyperthermophilic environments. They also provided insights into the diverse metabolism ofArchaeoglobaceaespecies living in hyperthermophilic environments.

The recombination of CCl3 radicals with CH3, CH3CH2, and CF3CH2 radicals was used to generate CH3CCl3, CH3CH2CCl3, and CF3CH2CCl3 molecules with approximately 87 kcal mol(-1) of vibrational energy in a bath gas at room temperature. The competition between collisional deactivation and unimolecular reaction by HCl elimination was used to obtain the experimental rate constants for each molecule. These experimental rate constants were matched to calculated statistical unimolecular rate constants to assign threshold energies to the three HCl elimination reactions. The models needed for the calculations of the rate constants were obtained from molecular structure calculations using density functional theory (DFT) with the hybrid density-functional MO6-2X recommended by Truhlar for transition states. The assigned threshold energies are 52 ± 2, 50 ± 2, and 52 ± 2 kcal mol(-1) for CH3CCl3, CH3CH2CCl3, and CF3CH2CCl3, respectively, and the CH3 and CF3 groups have only a minor effect on the threshold energies for HCl elimination. The DFT calculated threshold energies are in agreement with the experimentally assigned values. The addition of Cl atoms to the same carbon atom lowers the threshold energy for HCl elimination in the CH3CH2Cl, CH3CHCl2, and CH3CCl3 series. This trend, which is the opposite of that for CH3CH2F, CH3CHF2, and CH3CF3, is discussed in terms of transition-state structure and correlated with the relative stabilities of CH3CH2(+), CH3CHCl(+), and CH3CCl2(+) ions; the relative stabilities are based on the hydride affinities obtained from calculations. Comparison of the reactions of CH3CCl3 and CH2ClCHCl2 shows that the threshold energy is much higher for the isomer with chlorine atoms on both carbon atoms.

The work described herein examines a rapid mix-and-measure method called DETECHIP suitable for screening of steroids and metabolites. The addition of steroids and metabolites to reactive arrays of colorimetric sensors generated characteristic color “fingerprints” that were used to identify the analyte. A color analysis tool was used to identify the analyte pool that now includes biologically relevant analytes. The mix-and-measure arrays allowed the detection of disease metabolites, orotic acid and argininosuccinic acid; and the steroids androsterone, 1,4-androstadiene, testosterone, stanozolol, and estrone. The steroid 1,4-androstadiene was also detected by this method while dissolved in synthetic urine. Some of the steroids, such as androstadiene, stanozolol, and androsterone were co-dissolved with (2-hydroxypropyl)-β-cyclodextrin in order to increase solubility in aqueous buffered solutions. The colorimetric arrays do not intend to eliminate ELISA or mass spectroscopy based screening, but to possibly provide an alternative analytical detection method for steroids and metabolites.

Aspirin has a range of antineoplastic properties linked to inhibition of cyclooxygenase enzymes in tumor cells, platelet inhibition and to inhibition of angiogenesis. We undertook a prospective study to determine the influence of a 45‐day course of aspirin therapy on circulating and intraplatelet levels of selected proangiogenic (vascular endothelial growth factor [VEGF]) and antiangiogenic (thrombospondin‐1 [TSP‐1]) proteins, and platelet protein release in women diagnosed with breast cancer who were receiving tamoxifen therapy. Initiation of aspirin therapy increases serum and intraplatelet levels of TSP‐1 without a corresponding increase in VEGF levels. Following aspirin therapy, VEGF levels decreased (relative to pretreatment levels) while TSP‐1 returned to pretreatment levels. Plasma TSP‐1 and VEGF levels did not change on aspirin therapy. Aspirin use also decreased thrombin receptor mediated release of TSP‐1 and VEGF from platelets. The selective impact on platelet angiogenic protein content and release supports one mechanism by which aspirin can modify the angiogenic balance in women receiving tamoxifen therapy. Aspirin therapy appears to favor an overall antiangiogenic balance in women with breast cancer who are receiving tamoxifen therapy.

Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0 m(-2) tubing day(-1). Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.

Previous studies ofin situbioremediation of uranium-contaminated groundwater with acetate injections have focused on the role ofGeobacterspecies in U(VI) reduction because of a lack of other abundant known U(VI)-reducing microorganisms. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genusMethanosarcinawere enriched after 40 days of acetate amendment. The increased abundance ofMethanosarcinacorresponded with an accumulation of methane in the groundwater. An enrichment culture dominated by aMethanosarcinaspecies with the sameMethanosarcina mcrAsequence that predominated in the field experiment could effectively convert acetate to methane. In order to determine whetherMethanosarcinaspecies could be participating in U(VI) reduction in the subsurface, cell suspensions ofM. barkeriwere incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically activeM. barkericells, however, no U(VI) reduction was observed in inactive controls. These results demonstrate thatMethanosarcinaspecies could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth ofGeobacterspecies. The results also suggest thatMethanosarcinahave the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.

Platelets and their granular contents influence both angiogenesis and breast cancer progression. This study was performed to assess the effect of breast cancer and its treatment on platelet biology and the response to inhibition of the platelet P2Y12 receptor. Receptor-specific platelet activation and inhibition was studied for three platelet-associated proteins important in cancer angiogenesis and progression, vascular endothelial growth factor (VEGF), thrombospondin1 (TSP1), and transforming growth factor beta 1 (TGF-β1). Twenty-four women with active breast cancer and 10 healthy controls not receiving antiplatelet therapy participated in the study. Ex vivo activation of platelets in whole blood was accomplished using PAR1AP, PAR4AP, convulxin, and ADP. Platelet inhibition was accomplished using the P2Y12 receptor antagonist cangrelor (the in vitro equivalent of clopidogrel). VEGF, TSP1, and TGF-β1 were measured using standard ELISA. Platelet activation by ADP, PAR1, PAR4, and collagen receptors increased VEGF, TSP1, and TGF-β1 secretion in patients with breast cancer. Agonist-induced release of VEGF was greater in cancer patients as compared to healthy controls (p = 0.02 for ADP, p < 0.001 for PAR1AP, PAR4AP, and convulxin) despite a decrease in the efficiency of VEGF secretion in patients with breast cancer. These differences were not observed for TSP1 and TGF-β1 secretion. P2Y12 receptor inhibition decreased VEGF, TSP1, and TGF-β1 secretion. In patients with cancer, cangrelor inhibited TSP1 release to a greater extent than VEGF and TGF-β1 release. In patients with breast cancer, the magnitude of platelet inhibition achieved by cangrelor was greater than that achieved with healthy controls for all agonists and platelet proteins studied. While platelets are known to influence progression of breast cancer, our results show that breast cancer and its treatment influence the platelet phenotype by increasing the secretion of pro-angiogenic proteins following platelet activation, modulating the efficiency of platelet protein release as well as increasing the response to antiplatelet therapy.

Using UV-vis absorption and circular dichroism (CD) spectroscopies, we explored the binding interactions of 3,3'-diethylthiatricarbocyanine iodide (Cy7) with polynucleotides of different sequences and helicity. CD showed to be a very diagnostic tool giving different spectroscopic chiroptical signatures for all explored DNA sequences upon Cy7 binding. Cy7 was able to spectroscopically discriminate between the right handed B-DNA of poly(dG-dC)(2) and its left handed Z-DNA counterpart induced by spermine or Co(III)hexamine via nearly opposite induced circular dichroic signal.

Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [ 14 C]benzene to [ 14 C]carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism, and [ 14 C]benzoate was produced from [ 14 C]benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not upregulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- than in benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus . This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much-needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.