@article {3043, title = {Response to Wang et al.: evidence contradicting the cytochrome-only model.}, journal = {Trends Microbiol}, volume = {31}, year = {2023}, month = {2023 Jun}, pages = {548-549}, keywords = {Cytochromes, Electron Transport}, issn = {1878-4380}, doi = {10.1016/j.tim.2023.03.006}, author = {Lovley, Derek R} } @article {3096, title = {Reply to {\textquoteright}Measuring conductivity of living Geobacter sulfurreducens biofilms{\textquoteright}.}, journal = {Nat Nanotechnol}, volume = {11}, year = {2016}, month = {2016 Nov 08}, pages = {913-914}, keywords = {Biofilms, Electric Conductivity, Geobacter}, issn = {1748-3395}, doi = {10.1038/nnano.2016.191}, author = {Malvankar, Nikhil S and Rotello, Vincent M and Tuominen, Mark T and Lovley, Derek R} } @article {1622, title = {Regulation of Clostridium difficile Spore Formation by the SpoIIQ and SpoIIIA Proteins.}, journal = {PLoS Genet}, volume = {11}, year = {2015}, month = {2015 Oct}, pages = {e1005562}, abstract = {

Sporulation is an ancient developmental process that involves the formation of a highly resistant endospore within a larger mother cell. In the model organism Bacillus subtilis, sporulation-specific sigma factors activate compartment-specific transcriptional programs that drive spore morphogenesis. \σG activity in the forespore depends on the formation of a secretion complex, known as the \"feeding tube,\" that bridges the mother cell and forespore and maintains forespore integrity. Even though these channel components are conserved in all spore formers, recent studies in the major nosocomial pathogen Clostridium difficile suggested that these components are dispensable for \σG activity. In this study, we investigated the requirements of the SpoIIQ and SpoIIIA proteins during C. difficile sporulation. C. difficile spoIIQ, spoIIIA, and spoIIIAH mutants exhibited defects in engulfment, tethering of coat to the forespore, and heat-resistant spore formation, even though they activate \σG at wildtype levels. Although the spoIIQ, spoIIIA, and spoIIIAH mutants were defective in engulfment, metabolic labeling studies revealed that they nevertheless actively transformed the peptidoglycan at the leading edge of engulfment. In vitro pull-down assays further demonstrated that C. difficile SpoIIQ directly interacts with SpoIIIAH. Interestingly, mutation of the conserved Walker A ATP binding motif, but not the Walker B ATP hydrolysis motif, disrupted SpoIIIAA function during C. difficile spore formation. This finding contrasts with B. subtilis, which requires both Walker A and B motifs for SpoIIIAA function. Taken together, our findings suggest that inhibiting SpoIIQ, SpoIIIAA, or SpoIIIAH function could prevent the formation of infectious C. difficile spores and thus disease transmission.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005562}, author = {Fimlaid, Kelly A and Jensen, Owen and Donnelly, M Lauren and Siegrist, M Sloan and Shen, Aimee} } @article {1558, title = {Response to Comment on "Environmental Fate of the Next Generation Refrigerant 2,3,3,3-Tetrafluoropropene (HFO-1234yf)".}, journal = {Environ Sci Technol}, volume = {49}, year = {2015}, month = {2015 Jul 7}, pages = {8265-6}, issn = {1520-5851}, doi = {10.1021/acs.est.5b01970}, author = {Im, Jeongdae and Walshe-Langford, Gillian E and Moon, Ji-Won and L{\"o}ffler, Frank E} } @article {1964, title = {A Ribonucleoprotein Complex Protects the Interleukin-6 mRNA from Degradation by Distinct Herpesviral Endonucleases}, journal = {PLOS Pathogens}, volume = {11}, year = {2015}, month = {may}, pages = {e1004899}, doi = {10.1371/journal.ppat.1004899}, url = {https://doi.org/10.1371/journal.ppat.1004899}, author = {Mandy Muller and Stephanie Hutin and Oliver Marigold and Kathy H. Li and Al Burlingame and Britt A. Glaunsinger}, editor = {Nicholas K Conrad} } @article {3112, title = {Real-time monitoring of subsurface microbial metabolism with graphite electrodes.}, journal = {Front Microbiol}, volume = {5}, year = {2014}, month = {2014}, pages = {621}, abstract = {

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μM range. In order to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2-(14)C]-acetate metabolism. There was a direct correlation between current production and the rate that [2-(14)C]-acetate was metabolized to (14)CO2 and (14)CH4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. The results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2014.00621}, author = {Wardman, Colin and Nevin, Kelly P and Lovley, Derek R} } @article {1562, title = {Regulation of ethanol-related behavior and ethanol metabolism by the Corazonin neurons and Corazonin receptor in Drosophila melanogaster.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e87062}, abstract = {

Impaired ethanol metabolism can lead to various alcohol-related health problems. Key enzymes in ethanol metabolism are alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH); however, neuroendocrine pathways that regulate the activities of these enzymes are largely unexplored. Here we identified a neuroendocrine system involving Corazonin (Crz) neuropeptide and its receptor (CrzR) as important physiological regulators of ethanol metabolism in Drosophila. Crz-cell deficient (Crz-CD) flies displayed significantly delayed recovery from ethanol-induced sedation that we refer to as hangover-like phenotype. Newly generated mutant lacking Crz Receptor (CrzR(01) ) and CrzR-knockdown flies showed even more severe hangover-like phenotype, which is causally associated with fast accumulation of acetaldehyde in the CrzR(01) mutant following ethanol exposure. Higher levels of acetaldehyde are likely due to 30\% reduced ALDH activity in the mutants. Moreover, increased ADH activity was found in the CrzR(01) mutant, but not in the Crz-CD flies. Quantitative RT-PCR revealed transcriptional upregulation of Adh gene in the CrzR(01) . Transgenic inhibition of cyclic AMP-dependent protein kinase (PKA) also results in significantly increased ADH activity and Adh mRNA levels, indicating PKA-dependent transcriptional regulation of Adh by CrzR. Furthermore, inhibition of PKA or cAMP response element binding protein (CREB) in CrzR cells leads to comparable hangover-like phenotype to the CrzR(01) mutant. These findings suggest that CrzR-associated signaling pathway is critical for ethanol detoxification via Crz-dependent regulation of ALDH activity and Crz-independent transcriptional regulation of ADH. Our study provides new insights into the neuroendocrine-associated ethanol-related behavior and metabolism.

}, keywords = {Acetaldehyde, Alcohol Dehydrogenase, Aldehyde Dehydrogenase, Alleles, Animals, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Ethanol, Genes, Reporter, Male, Mutation, Neurons, Neuropeptides, Phenotype, Receptors, Neuropeptide, RNA, Messenger, Transcription, Genetic}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087062}, author = {Sha, Kai and Choi, Seung-Hoon and Im, Jeongdae and Lee, Gyunghee G and Loeffler, Frank and Park, Jae H} } @article {1420, title = {Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.}, journal = {Appl Environ Microbiol}, volume = {80}, year = {2014}, month = {2014 Jan}, pages = {281-8}, abstract = {

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

}, keywords = {Agriculture, Bacteria, Biota, Carbon, Cluster Analysis, Conservation of Natural Resources, Human Activities, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen, Nitrogen Fixation, Oxidoreductases, Phylogeny, Sequence Analysis, DNA, Soil, Soil Microbiology, South America, Trees}, issn = {1098-5336}, doi = {10.1128/AEM.02362-13}, author = {Mirza, Babur S and Potisap, Chotima and N{\"u}sslein, Klaus and Bohannan, Brendan J M and Rodrigues, Jorge L M} } @article {408, title = {Real-time spatial gene expression analysis within current-producing biofilms.}, journal = {ChemSusChem}, volume = {5}, year = {2012}, month = {2012 Jun}, pages = {1092-8}, abstract = {

The expression of genes involved in central metabolism and extracellular electron transfer was examined in real-time in current-producing anode biofilms of Geobacter sulfurreducens. Strains of G. sulfurreducens were generated, in which the expression of the gene for a short half-life fluorescent protein was placed under control of the promoter of the genes of interest. Anode biofilms were grown in a chamber that permitted direct examination of the cell fluorescence with confocal scanning laser microscopy. Studies on nifD and citrate synthase expression in response to environmental changes demonstrated that the reporter system revealed initiation and termination of gene transcription. Uniform expression throughout the biofilms was noted for the genes for citrate synthase; PilA, the structural protein of the conductive pili; and OmcZ, a c-type cytochrome essential for optimal current production, which was localized at the anode-biofilm interface. These results demonstrate that even cells at great distance from the anode, or within expected low-pH zones, are metabolically active and likely to contribute to current production and that there are factors other than gene expression differences influencing the distribution of OmcZ. This real-time reporter approach is likely to be a useful tool in optimizing the design of technologies relying on microbe-electrode interactions.

}, keywords = {Bacterial Proteins, Bioelectric Energy Sources, Biofilms, Citrate (si)-Synthase, Cytochrome c Group, Fimbriae Proteins, Fimbriae, Bacterial, Gene Expression Regulation, Bacterial, Geobacter, Quaternary Ammonium Compounds}, issn = {1864-564X}, doi = {10.1002/cssc.201100714}, author = {Franks, Ashley E and Glaven, Richard H and Lovley, Derek R} } @article {355, title = {RNAi: Future in insect management.}, journal = {J Invertebr Pathol}, year = {2012}, month = {2012 Jul 24}, abstract = {RNA interference is a post- transcriptional, gene regulation mechanism found in virtually all plants and animals including insects. The demonstration of RNAi in insects and its successful use as a tool in the study of functional genomics opened the door to the development of a variety of novel, environmentally sound approaches for insect pest management. Here the current understanding of the biogenesis of the two RNAi classes in insects is reviewed. These are microRNAs (miRNAs) and short interfering RNAs (siRNAs). Several other key approaches in RNAi -based for insect control, as well as for the prevention of diseases in insects are also reviewed. The problems and prospects for the future use of RNAi in insects are presented.}, issn = {1096-0805}, doi = {10.1016/j.jip.2012.07.012}, author = {Burand, John P and Hunter, Wayne B} } @article {3148, title = {The Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase essential for autotrophic growth.}, journal = {mBio}, volume = {4}, year = {2012}, month = {2012 Dec 26}, pages = {e00406-12}, abstract = {

UNLABELLED: It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD(+) oxidoreductase which contributes to ATP synthesis by an H(+)-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H(2) as the electron source and CO(2) as the electron acceptor. Heterotrophic growth was hindered in the absence of a functional Rnf complex, as ATP synthesis, proton gradient, and proton motive force were significantly reduced with fructose as the electron donor. Growth of the Rnf-deficient mutant was also inhibited when no source of fixed nitrogen was provided. These results demonstrate that the Rnf complex of C. ljungdahlii is responsible for translocation of protons across the membrane to elicit energy conservation during acetogenesis and is a multifunctional device also implicated in nitrogen fixation.

IMPORTANCE: Mechanisms for energy conservation in the acetogen Clostridium ljungdahlii are of interest because of its potential value as a chassis for the production of biocommodities with novel electron donors such as carbon monoxide, syngas, and electrons derived from electrodes. Characterizing the components implicated in the chemiosmotic ATP synthesis during acetogenesis by C. ljungdahlii is a prerequisite for the development of highly productive strains. The Rnf complex has been considered the prime candidate to be the pump responsible for the formation of an ion gradient coupled with ATP synthesis in multiple acetogens. However, experimental evidence for a proton-pumping Rnf complex has been lacking. This study establishes the C. ljungdahlii Rnf complex as a proton-translocating ferredoxin:NAD(+) oxidoreductase and demonstrates that C. ljungdahlii has the potential of becoming a model organism to study proton translocation, electron transport, and other functions of the Rnf complex in energy conservation or other processes.

}, keywords = {Adenosine Triphosphate, Autotrophic Processes, Clostridium, Energy Metabolism, Fructose, Gene Knockout Techniques, Genes, Essential, Nitrogen, Operon, Oxidoreductases, Proton-Motive Force}, issn = {2150-7511}, doi = {10.1128/mBio.00406-12}, author = {Tremblay, Pier-Luc and Zhang, Tian and Dar, Shabir A and Leang, Ching and Lovley, Derek R} } @article {411, title = {Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 May}, pages = {2248-53}, abstract = {Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O(2). Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O(2)-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens.}, keywords = {Bacterial Proteins, Gene Expression Regulation, Bacterial, Geobacter, Hydrogen Peroxide, Hydrogenase, Mutation, Oxidative Stress, Oxygen, Reactive Oxygen Species, Reverse Transcriptase Polymerase Chain Reaction, Xanthine Oxidase}, issn = {1098-5530}, doi = {10.1128/JB.00044-12}, author = {Tremblay, Pier-Luc and Lovley, Derek R} } @article {760, title = {Resolving the phylogeny of malaria parasites.}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 Aug 9}, pages = {12973-4}, keywords = {Animals, Evolution, Molecular, Malaria, Parasites}, issn = {1091-6490}, doi = {10.1073/pnas.1110141108}, author = {Rich, Stephen M and Xu, Guang} } @article {850, title = {Respiratory Chlamydophyla pneumoniae resides primarily in the lower airway.}, journal = {Eur Respir J}, volume = {38}, year = {2011}, month = {2011 Oct}, pages = {994-5; author reply 995}, keywords = {Asthma, Humans, Pulmonary Medicine}, issn = {1399-3003}, doi = {10.1183/09031936.00071711}, author = {Webley, W C and Hahn, D L} } @article {806, title = {RecA4142 causes SOS constitutive expression by loading onto reversed replication forks in Escherichia coli K-12.}, journal = {J Bacteriol}, volume = {192}, year = {2010}, month = {2010 May}, pages = {2575-82}, abstract = {Escherichia coli initiates the SOS response when single-stranded DNA (ssDNA) produced by DNA damage is bound by RecA and forms a RecA-DNA filament. recA SOS constitutive [recA(Con)] mutants induce the SOS response in the absence of DNA damage. It has been proposed that recA(Con) mutants bind to ssDNA at replication forks, although the specific mechanism is unknown. Previously, it had been shown that recA4142(F217Y), a novel recA(Con) mutant, was dependent on RecBCD for its high SOS constitutive [SOS(Con)] expression. This was presumably because RecA4142 was loaded at a double-strand end (DSE) of DNA. Herein, it is shown that recA4142 SOS(Con) expression is additionally dependent on ruvAB (replication fork reversal [RFR] activity only) and recJ (5{\textquoteright}-->3{\textquoteright} exonuclease), xonA (3{\textquoteright}-->5{\textquoteright} exonuclease) and partially dependent on recQ (helicase). Lastly, sbcCD mutations (Mre11/Rad50 homolog) in recA4142 strains caused full SOS(Con) expression in an ruvAB-, recBCD-, recJ-, and xonA-independent manner. It is hypothesized that RuvAB catalyzes RFR, RecJ and XonA blunt the DSE (created by the RFR), and then RecBCD loads RecA4142 onto this end to produce SOS(Con) expression. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease.}, keywords = {Bacterial Proteins, Deoxyribonucleases, DNA Helicases, DNA Replication, Endodeoxyribonucleases, Escherichia coli K12, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Exonucleases, Microscopy, Fluorescence, Mutation, Rec A Recombinases, SOS Response (Genetics)}, issn = {1098-5530}, doi = {10.1128/JB.01623-09}, author = {Long, Jarukit Edward and Massoni, Shawn C and Sandler, Steven J} } @article {447, title = {Role of Geobacter sulfurreducens outer surface c-type cytochromes in reduction of soil humic acid and anthraquinone-2,6-disulfonate.}, journal = {Appl Environ Microbiol}, volume = {76}, year = {2010}, month = {2010 Apr}, pages = {2371-5}, abstract = {Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.}, keywords = {Anthraquinones, Bacterial Proteins, Cytochromes, Gene Deletion, Genes, Bacterial, Geobacter, Humic Substances, Oxidation-Reduction, Soil, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02250-09}, author = {Voordeckers, James W and Kim, Byoung-Chan and Izallalen, Mounir and Lovley, Derek R} } @article {732, title = {The role of nano-scale heterogeneous electrostatic interactions in initial bacterial adhesion from flow: a case study with Staphylococcus aureus.}, journal = {Colloids Surf B Biointerfaces}, volume = {76}, year = {2010}, month = {2010 Apr 1}, pages = {489-95}, abstract = {This study investigated the initial adhesion of Staphylococcus aureus from flowing buffer onto modified albumin films with the objective of probing the influence of electrostatic heterogeneity on bacterial adhesion. Electrostatic heterogeneity, on the lengthscale of 10-100 nm, was incorporated into the protein film through the irreversible random deposition of small amounts of polycation coils to produce isolated positive "patches" on the otherwise negative albumin surface before exposure to bacteria, which also possess a net negative surface charge. The system was benchmarked against an appropriate analog using 1 microm silica spheres and the same cationic patches on a silica substrate. Bacterial adhesion from flow was measured with the surface oriented vertically to eliminate gravitational forces between the bacteria and collector. In both systems, a threshold in the surface density of polycation patches needed for bacterial (or silica particle) capture indicated multivalent binding: multiple polycation patches were needed to adhere the bacteria (particles). The shifting of the threshold to greater patch concentrations at lower ionic strengths confirmed that the electrostatic interaction area (zone of influence) was a key factor in modulating the interactions. The role of the contact area in this manner is important because it enables a quantitative explanation of counterintuitive bacterial adhesion onto net negative surfaces. The study further revealed a hydrodynamic crossover from a regime where flow aids bacterial adhesion to one where flow impedes adhesion. An explanation is put forth in terms of the relative hydrodynamic and surface forces.}, keywords = {Adsorption, Bacterial Adhesion, Methacrylates, Nylons, Particle Size, Serum Albumin, Bovine, Silicon Dioxide, Staphylococcus aureus, Static Electricity, Surface Properties}, issn = {1873-4367}, doi = {10.1016/j.colsurfb.2009.12.009}, author = {Kalasin, Surachate and Dabkowski, Jeffrey and N{\"u}sslein, Klaus and Santore, Maria M} } @article {812, title = {RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis.}, journal = {Mol Microbiol}, volume = {69}, year = {2008}, month = {2008 Sep}, pages = {1165-79}, abstract = {The Escherichia coli SOS response to DNA damage is modulated by the RecA protein, a recombinase that forms an extended filament on single-stranded DNA and hydrolyzes ATP. The RecA K72R (recA2201) mutation eliminates the ATPase activity of RecA protein. The mutation also limits the capacity of RecA to form long filaments in the presence of ATP. Strains with this mutation do not undergo SOS induction in vivo. We have combined the K72R variant of RecA with another mutation, RecA E38K (recA730). In vitro, the double mutant RecA E38K/K72R (recA730,2201) mimics the K72R mutant protein in that it has no ATPase activity. The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild-type, and do so in the presence of ATP. Unlike recA K72R, the recA E38K/K72R double mutant promotes SOS induction in vivo after UV treatment. Thus, SOS induction does not require ATP hydrolysis by the RecA protein, but does require formation of extended RecA filaments. The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro.}, keywords = {Adenosine Triphosphate, Amino Acid Substitution, Bacterial Proteins, DNA, Bacterial, DNA, Single-Stranded, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Rec A Recombinases, Serine Endopeptidases, SOS Response (Genetics), Ultraviolet Rays}, issn = {1365-2958}, doi = {10.1111/j.1365-2958.2008.06341.x}, author = {Gruenig, Marielle C and Renzette, Nicholas and Long, Edward and Chitteni-Pattu, Sindhu and Inman, Ross B and Cox, Michael M and Sandler, Steven J} } @article {813, title = {Requirements for ATP binding and hydrolysis in RecA function in Escherichia coli.}, journal = {Mol Microbiol}, volume = {67}, year = {2008}, month = {2008 Mar}, pages = {1347-59}, abstract = {RecA is essential for recombination, DNA repair and SOS induction in Escherichia coli. ATP hydrolysis is known to be important for RecA{\textquoteright}s roles in recombination and DNA repair. In vitro reactions modelling SOS induction minimally require ssDNA and non-hydrolyzable ATP analogues. This predicts that ATP hydrolysis will not be required for SOS induction in vivo. The requirement of ATP binding and hydrolysis for SOS induction in vivo is tested here through the study of recA4159 (K72A) and recA2201 (K72R). RecA4159 is thought to have reduced affinity for ATP. RecA2201 binds, but does not hydrolyse ATP. Neither mutant was able to induce SOS expression after UV irradiation. RecA2201, unlike RecA4159, could form filaments on DNA and storage structures as measured with RecA-GFP. RecA2201 was able to form hybrid filaments and storage structures and was either recessive or dominant to RecA(+), depending on the ratio of the two proteins. RecA4159 was unable to enter RecA(+) filaments on DNA or storage structures and was recessive to RecA(+). It is concluded that ATP hydrolysis is essential for SOS induction. It is proposed that ATP binding is essential for storage structure formation and ability to interact with other RecA proteins in a filament.}, keywords = {Adenosine Triphosphate, Chromosomes, Bacterial, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Mutation, Protein Binding, Rec A Recombinases, Ultraviolet Rays}, issn = {1365-2958}, doi = {10.1111/j.1365-2958.2008.06130.x}, author = {Renzette, Nicholas and Sandler, Steven J} } @article {506, title = {Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.}, journal = {Int J Syst Evol Microbiol}, volume = {57}, year = {2007}, month = {2007 Mar}, pages = {463-6}, abstract = {Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1(T)=ATCC BAA-34(T)=JCM 14045(T)) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 degrees C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.}, keywords = {DNA, Bacterial, DNA, Ribosomal, Genes, Bacterial, Geobacter, Phylogeny, RNA, Ribosomal, 16S, Temperature}, issn = {1466-5026}, doi = {10.1099/ijs.0.63408-0}, author = {Nevin, Kelly P and Holmes, Dawn E and Woodard, Trevor L and Covalla, Sean F and Lovley, Derek R} } @article {745, title = {Responses of rhizobia to desiccation in relation to osmotic stress, oxygen, and temperature.}, journal = {Appl Environ Microbiol}, volume = {73}, year = {2007}, month = {2007 Jun}, pages = {3451-9}, keywords = {Adaptation, Physiological, Dehydration, Hot Temperature, Osmotic Pressure, Oxidative Stress, Rhizobiaceae}, issn = {0099-2240}, doi = {10.1128/AEM.02991-06}, author = {Vriezen, Jan Ac and de Bruijn, Frans J and N{\"u}sslein, K} } @article {693, title = {Removal or maintenance of inositol-linked acyl chain in glycosylphosphatidylinositol is critical in trypanosome life cycle.}, journal = {J Biol Chem}, volume = {281}, year = {2006}, month = {2006 Apr 28}, pages = {11595-602}, abstract = {The protozoan parasite Trypanosoma brucei is coated by glycosylphosphatidylinositol (GPI)-anchored proteins. During GPI biosynthesis, inositol in phosphatidylinositol becomes acylated. Inositol is deacylated prior to attachment to variant surface glycoproteins in the bloodstream form, whereas it remains acylated in procyclins in the procyclic form. We have cloned a T. brucei GPI inositol deacylase (GPIdeAc2). In accordance with the acylation/deacylation profile, the level of GPIdeAc2 mRNA was 6-fold higher in the bloodstream form than in the procyclic form. Knockdown of GPIdeAc2 in the bloodstream form caused accumulation of an inositol-acylated GPI, a decreased VSG expression on the cell surface and slower growth, indicating that inositol-deacylation is essential for the growth of the bloodstream form. Overexpression of GPIdeAc2 in the procyclic form caused an accumulation of GPI biosynthetic intermediates lacking inositol-linked acyl chain and decreased cell surface procyclins because of release into the culture medium, indicating that overexpression of GPIdeAc2 is deleterious to the surface coat of the procyclic form. Therefore, the GPI inositol deacylase activity must be tightly regulated in trypanosome life cycle.}, keywords = {Acylation, Animals, Cloning, Molecular, Glycosylphosphatidylinositols, Inositol, Life Cycle Stages, Membrane Glycoproteins, Phosphoric Monoester Hydrolases, Protozoan Proteins, RNA, Messenger, Trypanosoma brucei brucei}, issn = {0021-9258}, doi = {10.1074/jbc.M513061200}, author = {Hong, Yeonchul and Nagamune, Kisaburo and Morita, Yasu S and Nakatani, Fumiki and Ashida, Hisashi and Maeda, Yusuke and Kinoshita, Taroh} } @article {511, title = {Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {188}, year = {2006}, month = {2006 Dec}, pages = {8469-78}, abstract = {Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated rel(Gsu), which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3{\textquoteright},5{\textquoteright}-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of Rel(Gsu) in G. sulfurreducens, a rel(Gsu) mutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type and rel(Gsu) mutant strains. In the wild-type strain, ppGpp and ppGp were produced in response to acetate and nitrogen deprivation, whereas exposure to oxygen resulted in an accumulation of ppGpp alone. Neither ppGpp nor ppGp could be detected in the rel(Gsu) mutant. The rel(Gsu) mutant consistently grew to a higher cell density than the wild type in acetate-fumarate medium and was less tolerant of oxidative stress than the wild type. The capacity for Fe(III) reduction was substantially diminished in the mutant. Microarray and quantitative reverse transcription-PCR analyses indicated that during stationary-phase growth, protein synthesis genes were up-regulated in the rel(Gsu) mutant and genes involved in stress responses and electron transport, including several implicated in Fe(III) reduction, were down-regulated in the mutant. The results are consistent with a role for Rel(Gsu) in regulating growth, stress responses, and Fe(III) reduction in G. sulfurreducens under conditions likely to be prevalent in subsurface environments.}, keywords = {Bacterial Proteins, Culture Media, Ferric Compounds, Gene Expression Regulation, Bacterial, Geobacter, Guanosine Tetraphosphate, Heat-Shock Response, Ligases, Mutation, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction, Sulfur}, issn = {0021-9193}, doi = {10.1128/JB.01278-06}, author = {DiDonato, Laurie N and Sullivan, Sara A and Meth{\'e}, Barbara A and Nevin, Kelly P and England, Reg and Lovley, Derek R} } @article {537, title = {Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens.}, journal = {Microbiology}, volume = {151}, year = {2005}, month = {2005 Jun}, pages = {1761-7}, abstract = {The Fe(III)-reducing micro-organism Geobacter sulfurreducens requires an outer-membrane c-type cytochrome, OmcB, for Fe(III) reduction, but a related cytochrome, OmcC, which is 73 \% identical to OmcB, is not required. The omcB and omcC genes are part of a tandem chromosomal duplication consisting of two repeated clusters of four genes. The 2.7 kb sequences preceding omcB and omcC are identical with the exception of a single base pair change. Studies that combined genetic, Northern blotting and primer extension analyses demonstrated that both omcB and omcC are transcribed as monocistronic and polycistronic (orf1-orf2-omcB/omcC) transcripts. All of the promoters for the various transcripts were found to be located within the 2.7 kb identical region upstream of omcB and omcC. The sequences of the promoter regions for the two monocistronic transcripts are identical and equidistant from the omcB or omcC start codons. The promoters for the two polycistronic transcripts, in contrast, are distinct. One is specific for transcription of orf1-orf2-omcB and the other is associated with transcription of orf1-orf2-omcC. Studies with an RpoS-deficient mutant suggested that transcription from all four promoters is RpoS dependent under one or more growth conditions. Deletion of orfR, a gene immediately upstream of orf1-orf2-omcB that encodes a putative transcriptional regulator, significantly lowered the omcB transcription when Fe(III) was the electron acceptor and partially inhibited Fe(III) reduction. In contrast, levels of omcC transcripts were unaffected in the orfR mutant. These results indicate that omcB and omcC operons represent a rare instance in which duplicated operons, located in tandem on the chromosome, have different transcriptional regulation.}, keywords = {Bacterial Outer Membrane Proteins, Bacterial Proteins, Blotting, Northern, DNA, Bacterial, Gene Deletion, Gene Expression Regulation, Bacterial, Geobacter, Molecular Sequence Data, Operon, Promoter Regions, Genetic, RNA, Bacterial, RNA, Messenger, Sequence Analysis, DNA, Sigma Factor, Transcription, Genetic}, issn = {1350-0872}, doi = {10.1099/mic.0.27870-0}, author = {Leang, Ching and Lovley, Derek R} } @article {528, title = {Remediation and recovery of uranium from contaminated subsurface environments with electrodes.}, journal = {Environ Sci Technol}, volume = {39}, year = {2005}, month = {2005 Nov 15}, pages = {8943-7}, abstract = {Previous studies have demonstrated that Geobacter species can effectively remove uranium from contaminated groundwater by reducing soluble U(VI) to the relatively insoluble U(IV) with organic compounds serving as the electron donor. Studies were conducted to determine whether electrodes might serve as an alternative electron donor for U(VI) reduction by a pure culture of Geobacter sulfurreducens and microorganisms in uranium-contaminated sediments. Electrodes poised at -500 mV (vs a Ag/AgCl reference) rapidly removed U(VI) from solution in the absence of cells. However, when the poise at the electrode was removed, all of the U(VI) returned to solution, demonstrating that the electrode did not reduce U(VI). If G. sulfurreducens was present on the electrode, U(VI) did not return to solution until the electrode was exposed to dissolved oxygen. This suggeststhat G. sulfurreducens on the electrode reduced U(VI) to U(IV) which was stably precipitated until reoxidized in the presence of oxygen. When an electrode was placed in uranium-contaminated subsurface sediments, U(VI) was removed and recovered from groundwater using poised electrodes. Electrodes emplaced in flow-through columns of uranium-contaminated sediments readily removed U(VI) from the groundwater, and 87\% of the uranium that had been removed was recovered from the electrode surface after the electrode was pulled from the sediments. These results suggest that microorganisms can use electrons derived from electrodes to reduce U(VI) and that it may be possible to remove and recover uranium from contaminated groundwater with poised electrodes.}, keywords = {Biodegradation, Environmental, Electrodes, Geobacter, Graphite, Soil Pollutants, Uranium, Water Pollutants, Chemical}, issn = {0013-936X}, author = {Gregory, Kelvin B and Lovley, Derek R} } @article {821, title = {Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12.}, journal = {Genetics}, volume = {169}, year = {2005}, month = {2005 Apr}, pages = {1799-806}, abstract = {Constitutive stable DNA replication (cSDR) is a mechanism for replisome loading in Escherichia coli K-12. This occurs in a dnaA-independent fashion in an rnhA mutant. cSDR is dependent on recA, priA, and transcription. In this report, it is shown that dnaA rnhA mutants using cSDR for initiation of their DNA replication additionally require priB, but not priC, for viability. Two subtle priA missense mutations either eliminated the ability to grow using cSDR (priA301 C479Y) or resulted in very small colonies (priA300 K230R). DnaC809, a priA suppressor, failed to allow priA or priB mutants to grow using cSDR to initiate DNA replication. Furthermore, unlike dnaC(+) strains, dnaC809 strains require priC for cSDR. DnaC809,820, a priC-independent suppressor of priA2::kan phenotypes, allowed priA and priC (but not priB) mutants to grow using cSDR to initiate DNA replication. It is also shown that rep and rnhA mutations are synthetically lethal. DnaC809 and dnaC809,820 mutations suppress this lethality. Rep is further shown to be required for cSDR in a dnaC809 strain. A model whereby these different sets of replication restart proteins interact preferentially with substrates associated with either RecA or SSB during replication restart and cSDR, respectively, is proposed.}, keywords = {Bacterial Proteins, DNA, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Macromolecular Substances, Models, Genetic, Mutation, Mutation, Missense, Phenotype, Rec A Recombinases, RNA, SOS Response (Genetics)}, issn = {0016-6731}, doi = {10.1534/genetics.104.036962}, author = {Sandler, Steven J} } @article {542, title = {Resistance of solid-phase U(VI) to microbial reduction during in situ bioremediation of uranium-contaminated groundwater.}, journal = {Appl Environ Microbiol}, volume = {70}, year = {2004}, month = {2004 Dec}, pages = {7558-60}, abstract = {Speciation of solid-phase uranium in uranium-contaminated subsurface sediments undergoing uranium bioremediation demonstrated that although microbial reduction of soluble U(VI) readily immobilized uranium as U(IV), a substantial portion of the U(VI) in the aquifer was strongly associated with the sediments and was not microbially reducible. These results have important implications for in situ uranium bioremediation strategies.}, keywords = {Acetates, Biodegradation, Environmental, Deltaproteobacteria, Fresh Water, Geologic Sediments, Oxidation-Reduction, Solubility, Uranium, Water Pollutants, Radioactive}, issn = {0099-2240}, doi = {10.1128/AEM.70.12.7558-7560.2004}, author = {Ortiz-Bernad, Irene and Anderson, Robert T and Vrionis, Helen A and Lovley, Derek R} } @article {549, title = {The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {186}, year = {2004}, month = {2004 Aug}, pages = {5543-6}, abstract = {Geobacter sulfurreducens RpoS sigma factor was shown to contribute to survival in stationary phase and upon oxygen exposure. Furthermore, a mutation in rpoS decreased the rate of reduction of insoluble Fe(III) but not of soluble forms of iron. This study suggests that RpoS plays a role in regulating metabolism of Geobacter under suboptimal conditions in subsurface environments.}, keywords = {Adaptation, Physiological, Bacterial Proteins, Base Sequence, Ferric Compounds, Gene Expression Regulation, Bacterial, Genes, Bacterial, Geobacter, Molecular Sequence Data, Mutation, Oxidation-Reduction, Oxidative Stress, Sigma Factor, Transcription Initiation Site}, issn = {0021-9193}, doi = {10.1128/JB.186.16.5543-5546.2004}, author = {N{\'u}{\~n}ez, Cinthia and Adams, Lorrie and Childers, Susan and Lovley, Derek R} } @article {567, title = {Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III).}, journal = {Int J Syst Evol Microbiol}, volume = {53}, year = {2003}, month = {2003 May}, pages = {669-73}, abstract = {To further investigate the diversity of micro-organisms capable of conserving energy to support growth from dissimilatory Fe(III) reduction, Fe(III)-reducing micro-organisms were enriched and isolated from subsurface sediments collected in Oyster Bay, VA, USA. A novel isolate, designated T118(T), was recovered in a medium with lactate as the sole electron donor and Fe(III) as the sole electron acceptor. Cells of T1 18(T) were Gram-negative, motile, short rods with a single polar flagellum. Strain T1 18(T) grew between pH 6.7 and 7.1, with a temperature range of 4-30 degrees C. The optimal growth temperature was 25 degrees C. Electron donors utilized by strain T1 18(T) with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Electron acceptors utilized with either acetate or lactate as the electron donor included Fe(III)-NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic analysis demonstrated that strain T1 18(T) is most closely related to the genus Rhodoferax. Unlike other species in this genus, strain T1 18(T) is not a phototroph and does not ferment fructose. However, phototrophic genes may be present but not expressed under the experimental conditions tested. No Rhodoferax species have been reported to grow via dissimilatory Fe(III) reduction. Based on these physiological and phylogenetic differences, strain T1 18(T) (=ATCC BAA-621(T) = DSM 15236(T)) is proposed as a novel species, Rhodoferax ferrireducens sp. nov.}, keywords = {Acetates, Anaerobiosis, Bacterial Typing Techniques, Betaproteobacteria, Cold Temperature, Culture Media, DNA, Ribosomal, Electron Transport, Ferric Compounds, Fresh Water, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA}, issn = {1466-5026}, author = {Finneran, Kevin T and Johnsen, Claudia V and Lovley, Derek R} } @article {579, title = {Rapid evolution of redox processes in a petroleum hydrocarbon-contaminated aquifer.}, journal = {Ground Water}, volume = {40}, year = {2002}, month = {2002 Jul-Aug}, pages = {353-60}, abstract = {Ground water chemistry data collected over a six-year period show that the distribution of contaminants and redox processes in a shallow petroleum hydrocarbon-contaminated aquifer has changed rapidly over time. Shortly after a gasoline release occurred in 1990, high concentrations of benzene were present near the contaminant source area. In this contaminated zone, dissolved oxygen in ground water was depleted, and by 1994 Fe(III) reduction and sulfate reduction were the predominant terminal electron accepting processes. Significantly, dissolved methane was below measurable levels in 1994, indicating the absence of significant methanogenesis. By 1996, however, depletion of solid-phase Fe(III)-oxyhydrox ides in aquifer sediments and depletion of dissolved sulfate in ground water resulted in the onset of methanogenesis. Between 1996 and 2000, water-chemistry data indicated that methanogenic metabolism became increasingly prevalent. Molecular analysis of 16S-rDNA extracted from sediments shows the presence of a more diverse methanogenic community inside as opposed to outside the plume core, and is consistent with water-chemistry data indicating a shift toward methanogenesis over time. This rapid evolution of redox processes reflects several factors including the large amounts of contaminants, relatively rapid ground water flow (approximately 0.3 m/day [approximately foot/day]), and low concentrations of microbially reducible Fe(III) oxyhydroxides ( approximately 1 micromol/g) initially present in aquifer sediments. These results illustrate that, under certain hydrologic conditions, redox conditions in petroleum hydrocarbon-contaminated aquifers can change rapidly in time and space, and that the availability of solid-phase Fe(III)-oxyhydroxides affects this rate of change.}, keywords = {Hydrocarbons, Iron, Methane, Oxidation-Reduction, Petroleum, Soil Pollutants, Solubility, Sulfates, Water Pollutants, Water Supply}, issn = {0017-467X}, author = {Chapelle, Francis H and Bradley, Paul M and Lovley, Derek R and O{\textquoteright}Neill, Kathleen and Landmeyer, James E} } @article {585, title = {Reduction of Fe(III) oxide by methanogens in the presence and absence of extracellular quinones.}, journal = {Environ Microbiol}, volume = {4}, year = {2002}, month = {2002 Feb}, pages = {115-24}, abstract = {Five methanogens (Methanosarcina barkeri MS, Methanosphaera cuniculi 1R7, Methanobacterium palustre F, Methanococcus voltaei A3 and Methanolobus vulcani PL-12/M) were investigated for their ability to reduce Fe(III) oxide and the soluble quinone anthraquinone-2,6-disulphonate (AQDS). Two species (M. barkeri and M. voltaei) reduced significant amounts of Fe(III) oxide using hydrogen as the electron donor, and 0.1 mM AQDS greatly accelerated Fe(III) reduction by these organisms. Although Fe(III) appeared to inhibit growth and methanogenesis of some strains, hydrogen partial pressures under donor-limited conditions were much lower (<0.5 Pa) in the presence of Fe(III) than in normal media (1-10 Pa) for all species except for M. vulcani. These results demonstrate that electrons were transferred to Fe(III) by hydrogen-utilizing methanogens even when growth and methanogenesis were inhibited. All species except the obligate methylotroph M. vulcani were able to reduce AQDS when their growth substrates were present as electron donors, and rates were highest when organisms used hydrogen as the electron donor. Purified soil humic acids could also be reduced by the AQDS-reducing methanogens. The ability of methanogens to interact with extracellular quinones, humic acids and Fe(III) oxides raises the possibility that this functional group of organ-isms contributes to Fe(III) and humic acid reduction under certain conditions in the environment and provides an alternative explanation for the inhibition of methanogenesis in some Fe(III)-containing ecosystems.}, keywords = {Anthraquinones, Euryarchaeota, Ferric Compounds, Humic Substances, Oxidation-Reduction, Species Specificity}, issn = {1462-2912}, author = {Bond, Daniel R and Lovley, Derek R} } @article {594, title = {Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea.}, journal = {Appl Environ Microbiol}, volume = {67}, year = {2001}, month = {2001 Jul}, pages = {3275-9}, abstract = {Studies with a diversity of hyperthermophilic and mesophilic dissimilatory Fe(III)-reducing Bacteria and Archaea demonstrated that some of these organisms are capable of precipitating gold by reducing Au(III) to Au(0) with hydrogen as the electron donor. These studies suggest that models for the formation of gold deposits in both hydrothermal and cooler environments should consider the possibility that dissimilatory metal-reducing microorganisms can reductively precipitate gold from solution.}, keywords = {Archaea, Bacteria, Chemical Precipitation, Ferric Compounds, Gold, Oxidation-Reduction}, issn = {0099-2240}, doi = {10.1128/AEM.67.7.3275-3279.2001}, author = {Kashefi, K and Tor, J M and Nevin, K P and Lovley, D R} } @article {389, title = {Replication of kinetoplast DNA: an update for the new millennium.}, journal = {Int J Parasitol}, volume = {31}, year = {2001}, month = {2001 May 1}, pages = {453-8}, abstract = {In this review we will describe the replication of kinetoplast DNA, a subject that our lab has studied for many years. Our knowledge of kinetoplast DNA replication has depended mostly upon the investigation of the biochemical properties and intramitochondrial localisation of replication proteins and enzymes as well as a study of the structure and dynamics of kinetoplast DNA replication intermediates. We will first review the properties of the characterised kinetoplast DNA replication proteins and then describe our current model for kinetoplast DNA replication.}, keywords = {Animals, Crithidia fasciculata, DNA Replication, DNA, Kinetoplast, Forecasting}, issn = {0020-7519}, author = {Morris, J C and Drew, M E and Klingbeil, M M and Motyka, S A and Saxowsky, T T and Wang, Z and Englund, P T} } @article {366, title = {Replication of the gonad-specific virus Hz-2V in Ld652Y cells mimics replication in vivo.}, journal = {J Invertebr Pathol}, volume = {77}, year = {2001}, month = {2001 Jan}, pages = {44-50}, abstract = {A newly discovered, nonoccluded insect virus, known as gonad-specific virus or Hz-2V, was found to replicate differently in two insect cell lines derived from ovarian tissues (Tn-368 cells from Trichoplusia ni and Ld652Y from Lymantria dispar). Differences between these two cell lines were observed in virus plaque forming ability, rate of viral DNA replication, time course of infectious virus production, and the mechanism of virus release from infected cells. Replication of Hz-2V in Ld652Y cells was more productive and more closely resembled in vivo virus replication.}, keywords = {Animals, Baculoviridae, Cell Line, DNA Replication, Lepidoptera, Molecular Mimicry, Time Factors, Virus Cultivation, Virus Replication}, issn = {0022-2011}, doi = {10.1006/jipa.2000.4990}, author = {Lu, H and Burand, J P} } @article {614, title = {Reduction of Fe(III), Mn(IV), and toxic metals at 100 degrees C by Pyrobaculum islandicum.}, journal = {Appl Environ Microbiol}, volume = {66}, year = {2000}, month = {2000 Mar}, pages = {1050-6}, abstract = {It has recently been noted that a diversity of hyperthermophilic microorganisms have the ability to reduce Fe(III) with hydrogen as the electron donor, but the reduction of Fe(III) or other metals by these organisms has not been previously examined in detail. When Pyrobaculum islandicum was grown at 100 degrees C in a medium with hydrogen as the electron donor and Fe(III)-citrate as the electron acceptor, the increase in cell numbers of P. islandicum per mole of Fe(III) reduced was found to be ca. 10-fold higher than previously reported. Poorly crystalline Fe(III) oxide could also serve as the electron acceptor for growth on hydrogen. The stoichiometry of hydrogen uptake and Fe(III) oxide reduction was consistent with the oxidation of 1 mol of hydrogen resulting in the reduction of 2 mol of Fe(III). The poorly crystalline Fe(III) oxide was reduced to extracellular magnetite. P. islandicum could not effectively reduce the crystalline Fe(III) oxide minerals goethite and hematite. In addition to using hydrogen as an electron donor for Fe(III) reduction, P. islandicum grew via Fe(III) reduction in media in which peptone and yeast extract served as potential electron donors. The closely related species P. aerophilum grew via Fe(III) reduction in a similar complex medium. Cell suspensions of P. islandicum reduced the following metals with hydrogen as the electron donor: U(VI), Tc(VII), Cr(VI), Co(III), and Mn(IV). The reduction of these metals was dependent upon the presence of cells and hydrogen. The metalloids arsenate and selenate were not reduced. U(VI) was reduced to the insoluble U(IV) mineral uraninite, which was extracellular. Tc(VII) was reduced to insoluble Tc(IV) or Tc(V). Cr(VI) was reduced to the less toxic, less soluble Cr(III). Co(III) was reduced to Co(II). Mn(IV) was reduced to Mn(II) with the formation of manganese carbonate. These results demonstrate that biological reduction may contribute to the speciation of metals in hydrothermal environments and could account for such phenomena as magnetite accumulation and the formation of uranium deposits at ca. 100 degrees C. Reduction of toxic metals with hyperthermophilic microorganisms or their enzymes might be applied to the remediation of metal-contaminated waters or waste streams.}, keywords = {Chromium, Cobalt, Energy Metabolism, Ferric Compounds, Geological Phenomena, Geology, Iron, Manganese, Metals, Heavy, Oxidation-Reduction, Technetium, Thermoproteaceae, Uranium, Water Pollutants, Chemical}, issn = {0099-2240}, author = {Kashefi, K and Lovley, D R} } @article {829, title = {Role of PriA in replication fork reactivation in Escherichia coli.}, journal = {J Bacteriol}, volume = {182}, year = {2000}, month = {2000 Jan}, pages = {9-13}, keywords = {Bacterial Proteins, DNA Primase, DNA Repair, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Models, Genetic, Replication Protein A}, issn = {0021-9193}, author = {Sandler, S J and Marians, K J} } @article {831, title = {Replication fork assembly at recombination intermediates is required for bacterial growth.}, journal = {Proc Natl Acad Sci U S A}, volume = {96}, year = {1999}, month = {1999 Mar 30}, pages = {3552-5}, abstract = {PriA, a 3{\textquoteright} --> 5{\textquoteright} DNA helicase, directs assembly of a primosome on some bacteriophage and plasmid DNAs. Primosomes are multienzyme replication machines that contribute both the DNA-unwinding and Okazaki fragment-priming functions at the replication fork. The role of PriA in chromosomal replication is unclear. The phenotypes of priA null mutations suggest that the protein participates in replication restart at recombination intermediates. We show here that PriA promotes replication fork assembly at a D loop, an intermediate formed during initiation of homologous recombination. We also show that DnaC810, encoded by a naturally arising intergenic suppressor allele of the priA2::kan mutation, bypasses the need for PriA during replication fork assembly at D loops in vitro. These findings underscore the essentiality of replication fork restart at recombination intermediates under normal growth conditions in bacteria.}, keywords = {Bacteria, Bacteriophage phi X 174, Base Sequence, DNA Polymerase III, DNA Replication, DNA-Binding Proteins, Escherichia coli, Molecular Sequence Data, Oligodeoxyribonucleotides, Open Reading Frames, Recombination, Genetic, Replication Protein A, Templates, Genetic}, issn = {0027-8424}, author = {Liu, J and Xu, L and Sandler, S J and Marians, K J} } @article {791, title = {Reply}, journal = {Parasitol Today}, volume = {15}, year = {1999}, month = {1999 Jan}, pages = {39-40}, issn = {0169-4758}, author = {Rich, S M and Ayala, F J} } @article {617, title = {Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction.}, journal = {Appl Environ Microbiol}, volume = {65}, year = {1999}, month = {1999 Sep}, pages = {4252-4}, abstract = {The dissimilatory Fe(III) reducer Geobacter metallireducens reduced Fe(III) bound in humic substances, but the concentrations of Fe(III) in a wide range of highly purified humic substances were too low to account for a significant portion of the electron-accepting capacities of the humic substances. Furthermore, once reduced, the iron in humic substances could not transfer electrons to Fe(III) oxide. These results suggest that other electron-accepting moieties in humic substances, such as quinones, are the important electron-accepting and shuttling agents under Fe(III)-reducing conditions.}, keywords = {Deltaproteobacteria, Electron Transport, Ferric Compounds, Humic Substances, Iron, Oxidation-Reduction}, issn = {0099-2240}, author = {Lovley, D R and Blunt-Harris, E L} } @article {833, title = {RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange.}, journal = {Genes Dev}, volume = {12}, year = {1998}, month = {1998 May 1}, pages = {1248-53}, abstract = {With the discovery that the Saccharomyces cerevisiae Rad51 protein is both structurally and functionally similar to the Escherichia coli RecA protein, the RecA paradigm for homologous recombination was extended to the Eucarya. The ubiquitous presence of RecA and Rad51 protein homologs raises the question of whether this archetypal protein exists within the third domain of life, the Archaea. Here we present the isolation of a Rad51/RecA protein homolog from the archaeon Sulfolobus solfataricus, and show that this protein, RadA, possesses the characteristics of a DNA strand exchange protein: The RadA protein is a DNA-dependent ATPase, forms a nucleoprotein filament on DNA, and catalyzes DNA pairing and strand exchange.}, keywords = {Adenosine Triphosphatases, Archaeal Proteins, Bacterial Proteins, DNA Helicases, DNA, Archaeal, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Archaeal, Nucleoproteins, Rad51 Recombinase, Rec A Recombinases, Recombinant Proteins, Recombination, Genetic, Sulfolobus}, issn = {0890-9369}, author = {Seitz, E M and Brockman, J P and Sandler, S J and Clark, A J and Kowalczykowski, S C} } @article {624, title = {Rapid Benzene Degradation in Methanogenic Sediments from a Petroleum-Contaminated Aquifer}, journal = {Appl Environ Microbiol}, volume = {64}, year = {1998}, month = {1998 May 1}, pages = {1937-9}, abstract = {In methanogenic sediments from a petroleum-contaminated aquifer, [14C]benzene was converted to 14CH4 and 14CO2 without an apparent lag. Phenol, acetate, and propionate were intermediates in benzene mineralization. These results suggest that alternative electron acceptors need not be available for there to be significant natural attenuation of benzene in some petroleum-contaminated aquifers.}, issn = {1098-5336}, author = {Weiner, JM and Lovley, D R} } @article {792, title = {The recent origin of allelic variation in antigenic determinants of Plasmodium falciparum.}, journal = {Genetics}, volume = {150}, year = {1998}, month = {1998 Sep}, pages = {515-7}, keywords = {Alleles, Animals, Epitopes, Genetic Variation, Merozoite Surface Protein 1, Plasmodium falciparum, Protozoan Proteins}, issn = {0016-6731}, author = {Rich, S M and Ayala, F J} } @article {625, title = {Recovery of humic-reducing bacteria from a diversity of environments.}, journal = {Appl Environ Microbiol}, volume = {64}, year = {1998}, month = {1998 Apr}, pages = {1504-9}, abstract = {To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments.}, keywords = {Acetic Acid, Anthraquinones, Base Sequence, DNA Primers, Electron Transport, Fresh Water, Gram-Negative Anaerobic Bacteria, Humic Substances, Iron, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial, RNA, Ribosomal, 16S, Seawater, Sulfur-Reducing Bacteria, Water Microbiology}, issn = {0099-2240}, author = {Coates, J D and Ellis, D J and Blunt-Harris, E L and Gaw, C V and Roden, E E and Lovley, D R} } @article {636, title = {Rapid Anaerobic Benzene Oxidation with a Variety of Chelated Fe(III) Forms.}, journal = {Appl Environ Microbiol}, volume = {62}, year = {1996}, month = {1996 Jan}, pages = {288-91}, abstract = {Fe(III) chelated to such compounds as EDTA, N-methyliminodiacetic acid, ethanol diglycine, humic acids, and phosphates stimulated benzene oxidation coupled to Fe(III) reduction in anaerobic sediments from a petroleum-contaminated aquifer as effectively as or more effectively than nitrilotriacetic acid did in a previously demonstrated stimulation experiment. These results indicate that many forms of chelated Fe(III) might be applicable to aquifer remediation.}, issn = {0099-2240}, author = {Lovley, D R and Woodward, J C and Chapelle, F H} } @article {835, title = {recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae.}, journal = {Nucleic Acids Res}, volume = {24}, year = {1996}, month = {1996 Jun 1}, pages = {2125-32}, abstract = {The process of homologous recombination has been documented in bacterial and eucaryotic organisms. The Escherichia coli RecA and Saccharomyces cerevisiae Rad51 proteins are the archetypal members of two related families of proteins that play a central role in this process. Using the PCR process primed by degenerate oligonucleotides designed to encode regions of the proteins showing the greatest degree of identity, we examined DNA from three organisms of a third phylogenetically divergent group, Archaea, for sequences encoding proteins similar to RecA and Rad51. The archaeans examined were a hyperthermophilic acidophile, Sulfolobus sofataricus (Sso); a halophile, Haloferax volcanii (Hvo); and a hyperthermophilic piezophilic methanogen, Methanococcus jannaschii (Mja). The PCR generated DNA was used to clone a larger genomic DNA fragment containing an open reading frame (orf), that we refer to as the radA gene, for each of the three archaeans. As shown by amino acid sequence alignments, percent amino acid identities and phylogenetic analysis, the putative proteins encoded by all three are related to each other and to both the RecA and Rad51 families of proteins. The putative RadA proteins are more similar to the Rad51 family (approximately 40\% identity at the amino acid level) than to the RecA family (approximately 20\%). Conserved sequence motifs, putative tertiary structures and phylogenetic analysis implied by the alignment are discussed. The 5{\textquoteright} ends of mRNA transcripts to the Sso radA were mapped. The levels of radA mRNA do not increase after treatment with UV irradiation as do recA and RAD51 transcripts in E.coli and S.cerevisiae. Hence it is likely that radA in this organism is a constitutively expressed gene and we discuss possible implications of the lack of UV-inducibility.}, keywords = {Amino Acid Sequence, Archaea, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Escherichia coli, Halobacteriaceae, Methanococcus, Models, Molecular, Molecular Sequence Data, Phylogeny, Rad51 Recombinase, Rec A Recombinases, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Alignment, Sulfolobus}, issn = {0305-1048}, author = {Sandler, S J and Satin, L H and Samra, H S and Clark, A J} } @article {838, title = {recO and recR mutations delay induction of the SOS response in Escherichia coli.}, journal = {Mol Gen Genet}, volume = {246}, year = {1995}, month = {1995 Jan 20}, pages = {254-8}, abstract = {RecF, RecO and RecR, three of the important proteins of the RecF pathway of recombination, are also needed for repair of DNA damage due to UV irradiation. recF mutants are not proficient in cleaving LexA repressor in vivo following DNA damage: therefore they show a delay of induction of the SOS response. In this communication, by measuring the in vivo levels of LexA repressor using anti-LexA antibodies, we show that recO and recR mutant strains are also not proficient in LexA cleavage reactions. In addition, we show that recO and recR mutations delay induction of beta-galactosidase activity expressed from a lexA-regulated promoter following exposure of cells to UV, thus further supporting the idea that recF, recO and recR gene products are needed for induction of the SOS response.}, keywords = {Bacterial Proteins, beta-Galactosidase, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Mutation, Promoter Regions, Genetic, Recombinant Fusion Proteins, Repressor Proteins, Serine Endopeptidases, SOS Response (Genetics), Ultraviolet Rays}, issn = {0026-8925}, author = {Hegde, S and Sandler, S J and Clark, A J and Madiraju, M V} } @article {705, title = {Relationship between expression of epidermal growth factor and simian virus 40 T antigen in a line of transgenic mice.}, journal = {Transgenic Res}, volume = {4}, year = {1995}, month = {1995 Sep}, pages = {306-14}, abstract = {The pattern of expression of the simian virus 40 (SV40) T antigen gene and resultant dysplasia were re-examined in a line of transgenic mice in which the T antigen gene was under the control of the SV40 early promoter. We found that T antigen expression in the kidney, and resulting dysplastic lesions, occurred exclusively in the distal convoluted tubules and the ascending limbs of Henle. Epidermal growth factor (EGF) expression in the kidney of normal mice was similarly immunolocalized. The correlation between high EGF immunoreactivity in normal mouse tissues and T antigen expression in the transgenic counterpart was also seen in the choroid plexus epithelium and in the submandibular glands of male mice. T antigen was not found in the submandibular gland of transgenic females. Similarly, EGF was only rarely detected in the normal female submandibular gland. In contrast to the correlation between T antigen expression in the transgenic mice and EGF expression in the corresponding tissues of the normal mice, within the dysplastic lesions of the transgenic mice EGF expression was severely diminished. Adenocarcinomas of the male submandibular gland from another line of transgenic mice that expresses the Int-1 transgene, showed similarly reduced levels of immunostaining for EGF. Thus, reduced expression of EGF might be a general feature of dysplasia and tumorigenesis in those tissues that normally express EGF.}, keywords = {Adenocarcinoma, Animals, Antigens, Viral, Tumor, Cattle, Choroid Plexus, Cricetinae, Epidermal Growth Factor, Female, Gene Expression Regulation, Neoplastic, Kidney, Kidney Tubules, Distal, Male, Mice, Mice, Transgenic, Proto-Oncogene Proteins, Simian virus 40, Submandibular Gland, Submandibular Gland Neoplasms, Wnt Proteins, Wnt1 Protein, Zebrafish Proteins}, issn = {0962-8819}, author = {Lafond, R E and Giammalvo, J T and Norkin, L C} } @article {841, title = {RecOR suppression of recF mutant phenotypes in Escherichia coli K-12.}, journal = {J Bacteriol}, volume = {176}, year = {1994}, month = {1994 Jun}, pages = {3661-72}, abstract = {The recF, recO, and recR genes form the recFOR epistasis group for DNA repair. recF mutants are sensitive to UV irradiation and fail to properly induce the SOS response. Using plasmid derivatives that overexpress combinations of the recO+ and recR+ genes, we tested the hypothesis that high-level expression of recO+ and recR+ (recOR) in vivo will indirectly suppress the recF mutant phenotypes mentioned above. We found that overexpression of just recR+ from the plasmid will partially suppress both phenotypes. Expression of the chromosomal recO+ gene is essential for the recR+ suppression. Hence we call this RecOR suppression of recF mutant phenotypes. RecOR suppression of SOS induction is more efficient with recO+ expression from a plasmid than with recO+ expression from the chromosome. This is not true for RecOR suppression of UV sensitivity (the two are equal). Comparison of RecOR suppression with the suppression caused by recA801 and recA803 shows that RecOR suppression of UV sensitivity is more effective than recA803 suppression and that RecOR suppression of UV sensitivity, like recA801 suppression, requires recJ+. We present a model that explains the data and proposes a function for the recFOR epistasis group in the induction of the SOS response and recombinational DNA repair.}, keywords = {Bacterial Proteins, Base Sequence, DNA Damage, DNA Repair, DNA-Binding Proteins, Epistasis, Genetic, Escherichia coli, Escherichia coli Proteins, Models, Genetic, Molecular Sequence Data, Phenotype, Plasmids, SOS Response (Genetics), Suppression, Genetic, Ultraviolet Rays}, issn = {0021-9193}, author = {Sandler, S J and Clark, A J} } @article {646, title = {Reduction of Chromate by Desulfovibrio vulgaris and Its c(3) Cytochrome.}, journal = {Appl Environ Microbiol}, volume = {60}, year = {1994}, month = {1994 Feb}, pages = {726-8}, abstract = {Washed cell suspensions of Desulfovibrio vulgaris rapidly reduced Cr(VI) to Cr(III) with H(2) as the electron donor. The c(3) cytochrome from this organism functioned as a Cr(VI) reductase. D. vulgaris may have advantages over previously described Cr(VI) reducers for the bioremediation of Cr(VI)-contaminated waters.}, issn = {0099-2240}, author = {Lovley, D R and Phillips, E J} } @article {647, title = {Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris.}, journal = {Appl Environ Microbiol}, volume = {59}, year = {1993}, month = {1993 Nov}, pages = {3572-6}, abstract = {The mechanism for U(VI) reduction by Desulfovibrio vulgaris (Hildenborough) was investigated. The H2-dependent U(VI) reductase activity in the soluble fraction of the cells was lost when the soluble fraction was passed over a cationic exchange column which extracted cytochrome c3. Addition of cytochrome c3 back to the soluble fraction that had been passed over the cationic exchange column restored the U(VI)-reducing capacity. Reduced cytochrome c3 was oxidized by U(VI), as was a c-type cytochrome(s) in whole-cell suspensions. When cytochrome c3 was combined with hydrogenase, its physiological electron donor, U(VI) was reduced in the presence of H2. Hydrogenase alone could not reduce U(VI). Rapid U(VI) reduction was followed by a subsequent slow precipitation of the U(IV) mineral uraninite. Cytochrome c3 reduced U(VI) in a uranium-contaminated surface water and groundwater. Cytochrome c3 provides the first enzyme model for the reduction and biomineralization of uranium in sedimentary environments. Furthermore, the finding that cytochrome c3 can catalyze the reductive precipitation of uranium may aid in the development of fixed-enzyme reactors and/or organisms with enhanced U(VI)-reducing capacity for the bioremediation of uranium-contaminated waters and waste streams.}, keywords = {Biotransformation, Chemical Precipitation, Cytochrome c Group, Desulfovibrio vulgaris, Oxidation-Reduction, Uranium, Water Pollutants, Radioactive}, issn = {0099-2240}, author = {Lovley, D R and Widman, P K and Woodward, J C and Phillips, E J} } @article {655, title = {Reduction of uranium by Desulfovibrio desulfuricans.}, journal = {Appl Environ Microbiol}, volume = {58}, year = {1992}, month = {1992 Mar}, pages = {850-6}, abstract = {The possibility that sulfate-reducing microorganisms contribute to U(VI) reduction in sedimentary environments was investigated. U(VI) was reduced to U(IV) when washed cells of sulfate-grown Desulfovibrio desulfuricans were suspended in a bicarbonate buffer with lactate or H2 as the electron donor. There was no U(VI) reduction in the absence of an electron donor or when the cells were killed by heat prior to the incubation. The rates of U(VI) reduction were comparable to those in respiratory Fe(III)-reducing microorganisms. Azide or prior exposure of the cells to air did not affect the ability of D. desulfuricans to reduce U(VI). Attempts to grow D. desulfuricans with U(VI) as the electron acceptor were unsuccessful. U(VI) reduction resulted in the extracellular precipitation of the U(IV) mineral uraninite. The presence of sulfate had no effect on the rate of U(VI) reduction. Sulfate and U(VI) were reduced simultaneously. Enzymatic reduction of U(VI) by D. desulfuricans was much faster than nonenzymatic reduction of U(VI) by sulfide, even when cells of D. desulfuricans were added to provide a potential catalytic surface for the nonenzymatic reaction. The results indicate that enzymatic U(VI) reduction by sulfate-reducing microorganisms may be responsible for the accumulation of U(IV) in sulfidogenic environments. Furthermore, since the reduction of U(VI) to U(IV) precipitates uranium from solution, D. desulfuricans might be a useful organism for recovering uranium from contaminated waters and waste streams.}, keywords = {Biodegradation, Environmental, Desulfovibrio, Kinetics, Oxidation-Reduction, Sulfates, Uranium, X-Ray Diffraction}, issn = {0099-2240}, author = {Lovley, D R and Phillips, E J} } @article {658, title = {Rates of microbial metabolism in deep coastal plain aquifers.}, journal = {Appl Environ Microbiol}, volume = {56}, year = {1990}, month = {1990 Jun}, pages = {1865-74}, abstract = {Rates of microbial metabolism in deep anaerobic aquifers of the Atlantic coastal plain of South Carolina were investigated by both microbiological and geochemical techniques. Rates of [2-C]acetate and [U-C]glucose oxidation as well as geochemical evidence indicated that metabolic rates were faster in the sandy sediments composing the aquifers than in the clayey sediments of the confining layers. In the sandy aquifer sediments, estimates of the rates of CO(2) production (millimoles of CO(2) per liter per year) based on the oxidation of [2-C] acetate were 9.4 x 10 to 2.4 x 10 for the Black Creek aquifer, 1.1 x 10 for the Middendorf aquifer, and <7 x 10 for the Cape Fear aquifer. These estimates were at least 2 orders of magnitude lower than previously published estimates that were based on the accumulation of CO(2) in laboratory incubations of similar deep subsurface sediments. In contrast, geochemical modeling of groundwater chemistry changes along aquifer flowpaths gave rate estimates that ranged from 10 to 10 mmol of CO(2) per liter per year. The age of these sediments (ca. 80 million years) and their organic carbon content suggest that average rates of CO(2) production could have been no more than 10 mmol per liter per year. Thus, laboratory incubations may greatly overestimate the in situ rates of microbial metabolism in deep subsurface environments. This has important implications for the use of laboratory incubations in attempts to estimate biorestoration capacities of deep aquifers. The rate estimates from geochemical modeling indicate that deep aquifers are among the most oligotrophic aquatic environments in which there is ongoing microbial metabolism.}, issn = {0099-2240}, author = {Chapelle, F H and Lovley, D R} } @article {660, title = {Requirement for a Microbial Consortium To Completely Oxidize Glucose in Fe(III)-Reducing Sediments.}, journal = {Appl Environ Microbiol}, volume = {55}, year = {1989}, month = {1989 Dec}, pages = {3234-6}, abstract = {In various sediments in which Fe(III) reduction was the terminal electron-accepting process, [C]glucose was fermented to C-fatty acids in a manner similar to that observed in methanogenic sediments. These results are consistent with the hypothesis that, in Fe(III)-reducing sediments, fermentable substrates are oxidized to carbon dioxide by the combined activity of fermentative bacteria and fatty acid-oxidizing, Fe(III)-reducing bacteria.}, issn = {0099-2240}, author = {Lovley, D R and Phillips, E J} } @article {664, title = {Rapid assay for microbially reducible ferric iron in aquatic sediments.}, journal = {Appl Environ Microbiol}, volume = {53}, year = {1987}, month = {1987 Jul}, pages = {1536-40}, abstract = {The availability of ferric iron for microbial reduction as directly determined by the activity of iron-reducing organisms was compared with its availability as determined by a newly developed chemical assay for microbially reducible iron. The chemical assay was based on the reduction of poorly crystalline ferric iron by hydroxylamine under acidic conditions. There was a strong correlation between the extent to which hydroxylamine could reduce various synthetic ferric iron forms and the susceptibility of the iron to microbial reduction in an enrichment culture of iron-reducing organisms. When sediments that contained hydroxylamine-reducible ferric iron were incubated under anaerobic conditions, ferrous iron accumulated as the concentration of hydroxylamine-reducible ferric iron declined over time. Ferrous iron production stopped as soon as the hydroxylamine-reducible ferric iron was depleted. In anaerobic incubations of reduced sediments that did not contain hydroxylamine-reducible ferric iron, there was no microbial iron reduction, even though the sediments contained high concentrations of oxalate-extractable ferric iron. A correspondence between the presence of hydroxylamine-reducible ferric iron and the extent of ferric iron reduction in anaerobic incubations was observed in sediments from an aquifer and in fresh- and brackish-water sediments from the Potomac River estuary. The assay is a significant improvement over previously described procedures for the determination of hydroxylamine-reducible ferric iron because it provides a correction for the high concentrations of solid ferrous iron which may also be extracted from sediments with acid. This is a rapid, simple technique to determine whether ferric iron is available for microbial reduction.}, issn = {0099-2240}, author = {Lovley, D R and Phillips, E J} } @article {670, title = {Rapidly growing rumen methanogenic organism that synthesizes coenzyme M and has a high affinity for formate.}, journal = {Appl Environ Microbiol}, volume = {48}, year = {1984}, month = {1984 Jul}, pages = {81-7}, abstract = {Methanogenic bacteria with a coccobacillus morphology similar to Methanobrevibacter ruminantium were isolated from the bovine rumen. One isolate, 10-16B, represented a previously undescribed rumen population that, unlike M. ruminantium, synthesized coenzyme M, grew rapidly (mu = 0.24 h-1) on H2-CO2 in a complex medium, had simple nutritional requirements, and metabolized formate at reported rumen concentrations. H2 was metabolized to partial pressures 10-fold lower than those reported for the rumen. After H2 starvation for 26 h, strain 10-16B rapidly resumed growth when H2 was made available. The minimum concentrations of acetate (6 mM) and ammonia (less than 7 mM) that were required for optimal growth were lower than the reported acetate and ammonia concentrations in the rumen. Isoleucine and leucine stimulated growth, but only at concentrations (greater than 50 microM) higher than those reported for the rumen. Another coccobacillary methanogenic organism that synthesized coenzyme M was isolated from a different animal as were organisms that required an exogenous supply of coenzyme M. In general, methanogenic bacteria that required an exogenous supply of coenzyme M had lower maximum growth rates and more complex nutritional requirements than organisms that synthesized the cofactor. The ability of all isolates to metabolize formate below the detection limit of 10 microM indicated that, in contrast to previous reports, methanogenic bacteria have the potential to directly metabolize formate in the rumen. This study demonstrated that there are physiologically diverse populations of coccobacillary methanogenic bacteria in the rumen that can interact competitively and cooperatively.}, keywords = {Animals, Cattle, Culture Media, Enzyme Induction, Euryarchaeota, Formates, Hydrogen, Male, Mercaptoethanol, Mesna, Rumen, Substrate Specificity}, issn = {0099-2240}, author = {Lovley, D R and Greening, R C and Ferry, J G} } @article {1713, title = {The relative importance of monoamine oxidase and catechol-O-methyl transferase on the physiologic response to administered norepinephrine in the turkey.}, journal = {Comp Biochem Physiol C}, volume = {52}, year = {1975}, month = {1975 Oct 1}, pages = {35-9}, keywords = {Animals, Blood Pressure, Catechol O-Methyltransferase, Chickens, Epinephrine, Heart, Kidney, Kinetics, Liver, Monoamine Oxidase, Myocardium, Norepinephrine, Organ Specificity, Rats, Species Specificity, Turkeys}, issn = {0306-4492}, author = {El Halawani, M E and Waibel, P E} } @article {1732, title = {Relaxation as a factor in semantic desensitization.}, journal = {J Consult Clin Psychol}, volume = {43}, year = {1975}, month = {1975 Dec}, pages = {925}, keywords = {Behavior Therapy, Desensitization, Psychologic, Female, Follow-Up Studies, Humans, Phobic Disorders, Relaxation Therapy, Semantics}, issn = {0022-006X}, author = {Bechtel, J E and McNamara, J R} }