Search tips
Search criteria

Results 1-21 (21)

Clipboard (0)

Select a Filter Below

Year of Publication
more »
1.  Peptide Biomarkers as Evidence of Perchlorate Biodegradation▿ †  
Perchlorate is a known health hazard for humans, fish, and other species. Therefore, it is important to assess the response of an ecosystem exposed to perchlorate contamination. The data reported here show that a liquid chromatography-mass spectrometry-based proteomics approach for the detection of perchlorate-reducing enzymes can be used to measure the ability of microorganisms to degrade perchlorate, including determining the current perchlorate degradation status. Signature peptides derived from chlorite dismutase (CD) and perchlorate reductase can be used as biomarkers of perchlorate presence and biodegradation. Four peptides each derived from CD and perchlorate reductase subunit A (PcrA) and seven peptides derived from perchlorate reductase subunit B (PcrB) were identified as signature biomarkers for perchlorate degradation, as these sequences are conserved in the majority of the pure and mixed perchlorate-degrading microbial cultures examined. However, chlorite dismutase signature biomarker peptides from Dechloromonas agitata CKB were found to be different from those in other cultures used and should also be included with selected CD biomarkers. The combination of these peptides derived from the two enzymes represents a promising perchlorate presence/biodegradation biomarker system. The biomarker peptides were detected at perchlorate concentrations as low as 0.1 mM and at different time points both in pure cultures and within perchlorate-reducing environmental enrichment consortia. The peptide biomarkers were also detected in the simultaneous presence of perchlorate and an alternate electron acceptor, nitrate. We believe that this technique can be useful for monitoring bioremediation processes for other anthropogenic environmental contaminants with known metabolic pathways.
PMCID: PMC3028743  PMID: 21115710
2.  Design, Synthesis and Biological Evaluation of A Novel Class of Anticancer Agents: Anthracenylisoxazole Lexitropsin Conjugates 
Bioorganic & medicinal chemistry  2008;17(4):1671-1680.
The synthesis and in vitro anti-tumor 60 cell lines screen of a novel series of anthracenyl isoxazole amides (AIMs)¥ (22–33) is described. The molecules consist of an isoxazole that pre-organizes a planar aromatic moiety and a simple amide and/or lexitropsin-oligopeptide. The new conjugate molecules were prepared via doubly activated amidation modification of Weinreb’s amide formation technique, using SmCl3 as an activating agent which produces improved yields for sterically hindered 3-aryl-4-isoxazolecarboxylic esters. The results of the National Cancer Institute’s (NCI) 60 cell line screening assay show a distinct structure activity relationship (SAR), wherein a trend of the highest activity for molecules with one N-methylpyrrole peptide. Evidence consistent with a mechanism of action via the interaction of these compounds with G-quadruplex (G4) DNA, and a structural based rational for the observed selectivity of the AIMs for G4 over B-DNA is presented.
PMCID: PMC2978248  PMID: 19167892
Anthracene; Antitumor; G-quadruplex; Isoxazole; Pyrrole
3.  Pyridine-2,6-Bis(Thiocarboxylic Acid) Produced by Pseudomonas stutzeri KC Reduces and Precipitates Selenium and Tellurium Oxyanions 
The siderophore of Pseudomonas stutzeri KC, pyridine-2,6-bis(thiocarboxylic acid) (pdtc), is shown to detoxify selenium and tellurium oxyanions in bacterial cultures. A mechanism for pdtc's detoxification of tellurite and selenite is proposed. The mechanism is based upon determination using mass spectrometry and energy-dispersive X-ray spectrometry of the chemical structures of compounds formed during initial reactions of tellurite and selenite with pdtc. Selenite and tellurite are reduced by pdtc or its hydrolysis product H2S, forming zero-valent pdtc selenides and pdtc tellurides that precipitate from solution. These insoluble compounds then hydrolyze, releasing nanometer-sized particles of elemental selenium or tellurium. Electron microscopy studies showed both extracellular precipitation and internal deposition of these metalloids by bacterial cells. The precipitates formed with synthetic pdtc were similar to those formed in pdtc-producing cultures of P. stutzeri KC. Culture filtrates of P. stutzeri KC containing pdtc were also active in removing selenite and precipitating elemental selenium and tellurium. The pdtc-producing wild-type strain KC conferred higher tolerance against selenite and tellurite toxicity than a pdtc-negative mutant strain, CTN1. These observations support the hypothesis that pdtc not only functions as a siderophore but also is involved in an initial line of defense against toxicity from various metals and metalloids.
PMCID: PMC1472348  PMID: 16672449
4.  Microbial Diversity and Its Relationship to Planetary Protection 
PMCID: PMC1183353  PMID: 16085798
5.  Use of Stochastic Models To Assess the Effect of Environmental Factors on Microbial Growth 
We present a novel application of a stochastic ecological model to the study and analysis of microbial growth dynamics as influenced by environmental conditions in an extensive experimental data set. The model proved to be useful in bridging the gap between theoretical ideas in ecology and an applied problem in microbiology. The data consisted of recorded growth curves of Escherichia coli grown in triplicate in a base medium with all 32 possible combinations of five supplements: glucose, NH4Cl, HCl, EDTA, and NaCl. The potential complexity of 25 experimental treatments and their effects was reduced to 22 as just the metal chelator EDTA, the presumed osmotic pressure imposed by NaCl, and the interaction between these two factors were enough to explain the variability seen in the data. The statistical analysis showed that the positive and negative effects of the five chemical supplements and their combinations were directly translated into an increase or decrease in time required to attain stationary phase and the population size at which the stationary phase started. The stochastic ecological model proved to be useful, as it effectively explained and summarized the uncertainty seen in the recorded growth curves. Our findings have broad implications for both basic and applied research and illustrate how stochastic mathematical modeling coupled with rigorous statistical methods can be of great assistance in understanding basic processes in microbial ecology.
PMCID: PMC1087571  PMID: 15870322
6.  Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer 
PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus Methylocystis. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.
PMCID: PMC1082543  PMID: 15812034
7.  Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library 
Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing uncultured microorganisms. However, conventional library-screening techniques permit characterization of relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities. A cosmid library derived from a microcosm of groundwater microorganisms was used to construct a microarray (COSMO) containing ∼1-kb PCR products amplified from the inserts of 672 cosmids plus a set of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance, including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified species of microorganisms.
PMCID: PMC169101  PMID: 12902288
8.  Potassium ferrate [Fe(VI)] does not mediate self-sterilization of a surrogate mars soil 
BMC Microbiology  2003;3:4.
Martian soil is thought to be enriched with strong oxidants such as peroxides and/or iron in high oxidation states that might destroy biological materials. There is also a high flux of ultraviolet radiation at the surface of Mars. Thus, Mars may be inhospitable to life as we know it on Earth. We examined the hypothesis that if the soil of Mars contains ferrates [Fe(VI)], the strongest of the proposed oxidizing species, and also is exposed to high fluxes of UV radiation, it will be self-sterilizing.
Under ambient conditions (25°C, oxygen and water present) K2FeO4 mixed into sand mineralized some reactive organic molecules to CO2, while less reactive compounds were not degraded. Dried endospores of Bacillus subtilis incubated in a Mars surrogate soil comprised of dry silica sand containing 20% by weight K2FeO4 and under conditions similar to those now on Mars (extreme desiccation, cold, and a CO2-dominated atmosphere) were resistant to killing by the ferrate-enriched sand. Similar results were observed with permanganate. Spores in oxidant-enriched sand exposed to high fluxes of UV light were protected from the sporocidal activity of the radiation below about 5 mm depths.
Based on our data and previously published descriptions of ancient but dormant life forms on Earth, we suggest that if entities resembling bacterial endospores were produced at some point by life forms on Mars, they might still be present and viable, given appropriate germination conditions. Endospores delivered to Mars on spacecraft would possibly survive and potentially compromise life detection experiments.
PMCID: PMC153549  PMID: 12694634
9.  Measurement of microbial activity in soil by colorimetric observation of in situ dye reduction: an approach to detection of extraterrestrial life 
BMC Microbiology  2002;2:22.
Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa. Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain). We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life. The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry.
Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature. We measured the ability of soil microbial communities to reduce artificial electron acceptors. Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP) and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT). Uninoculated or sterilized controls did not reduce the dyes. A soil from Antarctica that was determined by chemical signature and DNA analysis to be sterile also did not reduce the dyes.
Observation of dye reduction, supplemented with extraction and identification of only a few specific signature redox-active biochemicals such as porphyrins or quinones, provides a simplified means to detect a signature of life in the soils of other planets or their moons.
PMCID: PMC119848  PMID: 12150716
10.  Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid) 
Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc.
Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species.
The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.
PMCID: PMC115864  PMID: 11972321
11.  Optimization of Simultaneous Chemical and Biological Mineralization of Perchloroethylene† 
Optimization of the simultaneous chemical and biological mineralization of perchloroethylene (PCE) by modified Fenton’s reagent and Xanthobacter flavus was investigated by using a central composite rotatable experimental design. Concentrations of PCE, hydrogen peroxide, and ferrous iron and the microbial cell number were set as variables. Percent mineralization of PCE to CO2 was investigated as a response. A second-order, quadratic response surface model was generated and fit the data adequately, with a correlation coefficient of 0.72. Analysis of the results showed that the PCE concentration had no significant effect within the tested boundaries of the model, while the other variables, hydrogen peroxide and iron concentrations and cell number, were significant at α = 0.05 for the mineralization of PCE. The 14C radiotracer studies showed that the simultaneous chemical and biological reactions increased the extent of mineralization of PCE by more than 10% over stand-alone Fenton reactions.
PMCID: PMC91416  PMID: 10347081
12.  Toxic Effects of Modified Fenton Reactions on Xanthobacter flavus FB71† 
Applied and Environmental Microbiology  1998;64(10):3759-3764.
The toxic effects of modified Fenton reactions on Xanthobacter flavus FB71, measured as microbial survival rates, were determined as part of an investigation of simultaneous abiotic and biotic oxidations of xenobiotic chemicals. A central composite, rotatable experimental design was developed to study the survival rates of X. flavus under various concentrations of hydrogen peroxide and iron(II) and at different initial cell populations. A model based on the experimental results, relating microorganism survival to the variables of peroxide, iron, and cellular concentrations was formulated and fit the data reasonably well, with a coefficient of determination of 0.76. The results of this study indicate that the use of simultaneous abiotic and biotic processes for the treatment of xenobiotic compounds may be possible.
PMCID: PMC106541  PMID: 9758796
13.  Preparation of Encapsulated Microbial Cells for Environmental Applications † 
An improved method for the encapsulation of bacteria into microspheres of alginate, agarose, or polyurethane is described. Cell suspensions were passed through a low-pressure nozzle into an aqueous phase where matrix polymerization or gelation yielded beads 2 to 50 μm in diameter. Trials with a chlorophenol-degrading Flavobacterium species showed that cells entrapped by these procedures were as catabolically active as free cells. These types of beads should have numerous applications in the fields of environmental science and engineering.
PMCID: PMC195313  PMID: 16348656
14.  Biodegradation of Dinoseb (2-sec-Butyl-4,6-Dinitrophenol) in Several Idaho Soils with Various Dinoseb Exposure Histories † 
We examined the ability of native microorganisms in various Idaho soils to degrade dinoseb and studied some physical and chemical soil characteristics which might affect the biodegradation process. Dinoseb biodegradation rates were higher in silt-loam soils than in loamy-sand soils. Biodegradation rates were not influenced by previous exposure of the soils to dinoseb. Bacterial numbers, measured by standard plate counts on soil extract agar, were the best predictors of biodegradation rates, accounting for 53% of the variability between soils. Soil nitrate-N inhibited dinoseb biodegradation and accounted for 39% of the variability. Sorption of dinoseb to soil surfaces also appeared to influence biodegradation rates. No other soil parameter contributed significantly to the variability in biodegradation rates. Persistence of dinoseb in one soil was due to inhibition of biodegradation by nitrate, while in another soil persistence appeared to be due to lack of native degradative microorganisms.
PMCID: PMC183261  PMID: 16348086
15.  Delignification of Wood Chips and Pulps by Using Natural and Synthetic Porphyrins: Models of Fungal Decay † 
Kraft pulps, prepared from softwoods, and small chips of birch wood were treated with heme and tert-butyl hydroperoxide in aqueous solutions at reflux temperature. Analyses of treated pulps showed decreases in kappa number (a measure of lignin content) from about 36 to less than 2, with concomitant increases in brightness (80% increase in the better samples). Analyses of treated wood chips revealed selective delignification and removal of hemicelluloses. After 48 h of treatment, lignin losses from the wood chips approached 40%, and xylose/mannose (hemicellulose) losses approached 70%, while glucose (cellulose) losses were less than 10%. Examination of delignified chips by transmission electron microscopy showed that the removal of lignin occurred in a manner virtually indistinguishable from that seen after decay by white rot fungi. Various metalloporphyrins, which act as biomimetic catalysts, were compared to horseradish peroxidase and fungal manganese peroxidase in their abilities to oxidize syringaldazine in an organic solvent, dioxane. The metalloporphyrins and peroxidases behaved similarly, and it appeared that the activities of the peroxidases resulted from the extraction of heme into the organic phase, rather than from the activities of the enzymes themselves. We concluded that heme-tert-butyl hydroperoxide systems in the absence of a protein carrier mimic the decay of lignified tissues by white rot fungi.
PMCID: PMC202397  PMID: 16347540
16.  Methanogenic Bacteria, Including an Acid-Tolerant Strain, from Peatlands 
Five pure cultures of methanogenic bacteria were isolated from Minnesota peatlands by enrichment culture techniques. One strain, identified as a member of the family Methanobacteriaceae by antigenic fingerprinting, was acid tolerant and able to produce methane at pH 3.1. Growth could not be demonstrated at pH less than 5.3.
PMCID: PMC238796  PMID: 16346955
17.  Methane Production in Minnesota Peatlands 
Rates of methane production in Minnesota peats were studied. Surface (10- to 25-cm) peats produced an average of 228 nmol of CH4 per g (dry weight) per h at 25°C and ambient pH. Methanogenesis rates generally decreased with depth in ombrotrophic peats, but on occasion were observed to rise within deeper layers of certain fen peats. Methane production was temperature dependent, increasing with increasing temperature (4 to 30°C), except in peats from deeper layers. Maximal methanogenesis from these deeper regions occurred at 12°C. Methane production rates were also pH dependent. Two peats with pHs of 3.8 and 4.3 had an optimum rate of methane production at pH 6.0. The addition to peat of glucose and H2-CO2 stimulated methanogenesis, whereas the addition of acetate inhibited methanogenesis. Cysteine-sulfide, nitrogen-phosphorus-trace metals, and vitamins-yeast extract affected methane production very little. Various gases were found to be trapped or dissolved (or both) within peatland waters. Dissolved methane increased linearly to a depth of 210 cm. The accumulation of metabolic end products produced within peat bogs appears to be an important mechanism limiting carbon turnover in peatland environments.
PMCID: PMC240215  PMID: 16346565
18.  Lignin Degradation by Streptomyces viridosporus: Isolation and Characterization of a New Polymeric Lignin Degradation Intermediate † 
A new, quantitatively significant intermediate formed during lignin degradation by Streptomyces viridosporus T7A was isolated and characterized. In Streptomyces-inoculated cultures, the intermediate, an acid-precipitable, polyphenolic, polymeric lignin (APPL), accumulated in the growth medium. The APPL was a water-soluble polymer probably consisting of a heterogeneous mixture of molecular weight components of ≥20,000. APPLs were precipitable from culture filtrates after they had been acidified to pH <3 to 5. Noninoculated controls yielded little APPL, but supernatant solutions from inoculated cultures produced quantities of APPL that correlated with the biodegradability of the lignocellulose type. Maximal recovery of APPL was obtained from corn lignocellulose, reaching 30% of the initial lignin present in the substrate. APPLs contained small amounts of carbohydrate, organic nitrogen, and inorganic materials. The lignin origin of APPLs was confirmed by chemical analyses, which included acidolysis, permanganate oxidation, elemental analyses, functional group analyses, nuclear magnetic resonance spectroscopy, and 14C isotopic techniques. Analyses of APPLs from corn lignocelluloses showed that S. viridosporus-degraded APPLs were lignin derived but significantly different in structure from APPLs derived from uninoculated controls or from a standard corn milled-wood lignin. Degraded APPLs were enriched in phenolic hydroxyl groups and, to a small extent, in carboxyl groups. Degradative changes appeared to be largely oxidative and were thought to involve substantial cleavage of p-hydroxy ether linkages and methoxyl groups in the lignin.
PMCID: PMC242390  PMID: 16346253
19.  Preparation of Specifically Labeled 14C-(Lignin)- and 14C-(Cellulose)-Lignocelluloses and Their Decomposition by the Microflora of Soil 1 
Microbial decomposition of lignocellulose in soil was studied using radioisotope techniques. Natural lignocelluloses containing 14C in either their lignin or cellulose (glucan) components were prepared by feeding plants l-[U-14C]phenylalanine or d-[U-14C]glucose, respectively, through their cut stems. Detailed chemical and chromatographic characterization of labeled lignocelluloses from three hardwood and three softwood species showed that those labeled by the [14C]glucose incorporation method contained specifically labeled cellulosic components, whereas those labeled by the [14C]phenylalanine incorporation method contained specifically labeled lignin components. Microbial degradation of these differentially labeled lignocelluloses was followed by monitoring 14CO2 evolution from selected soil samples incubated with known amounts of radiolabeled lignocelluloses. The lignin components of the six woods were shown to be decomposed in soil 4 to 10 times more slowly than their cellulosic components. These rates of mineralization were comparable to the generalized patterns previously reported in the literature. The present technique, however, was thought to be simpler, more sensitive, and less prone to interference than methods previously available.
PMCID: PMC170865  PMID: 16345246
20.  Microbial Degradation of Lignocellulose: the Lignin Component 
A new procedure was developed for the study of lignin biodegradation by pure or mixed cultures of microorganisms. Natural lignocelluloses were prepared containing 14C in primarily their lignin components by feeding plants l-[U-14C]phenylalanine through their cut stems. Lignin degradation was observed in numerous soils by monitoring evolution of 14CO2 from [14C]lignin-labeled oak (Quercus albus), maple (Acer rubrum), and cattail (Typha latifola). An organism (Thermonospora fusca ATCC 27730) that is known to degrade cellulose but not lignin was shown to grow on lignocellulose in the presence of [14C]lignocelluloses without evolution of 14CO2. A known lignin degrader (a white-rot fungus, Polyporus versicolor) was shown to readily evolve 14CO2 from damp 14C-labeled cattail and 14C-labeled maple.
PMCID: PMC291182  PMID: 16345159
21.  Degradation of 3-Hydroxybenzoate by Bacteria of the Genus Bacillus 
Applied Microbiology  1975;30(3):439-444.
The pathway whereby certain bacterial strains of the genus Bacillus degrade m-hydroxybenzoate is delineated. Of 12 strains examined, nine were tentatively classified as representatives of the species Bacillus brevis, two of Bacillus sphaericus and one of Bacillus megaterium. All strains degraded m-hydroxybenzoate via the same pathway. m-Hydroxybenzoate was hydroxylated to 2,5-dihydroxybenzoate (gentisate), which was oxidized by a gentisate 1,2-dioxygenase yielding maleylpyruvate. Maleylpyruvate was hydrolyzed without prior cis, cis to cis, trans isomerization yielding pyruvate and maleic acid. Numerous soils were examined by plate-count procedures and found to contain 104 to 106 aerobic sporeformers able to grow on m-hydroxybenzoate per g of dry soil.
PMCID: PMC187200  PMID: 810087

Results 1-21 (21)