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Submissions from 2017

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Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium, Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh Mitchell, Matt Gaffrey, Gayla Orr, and Kristen DeAngelis

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Changes in substrate availability drive carbon cycle response to chronic warming, Grace Pold, A. Stuart Grandy, Jerry M. Melillo, and Kristen DeAngelis

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High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp., Hannah L. Woo, Kristen DeAngelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Tracy Erkkila, Lynne Goodwin, Wei Gu, Chien-Chi Lo, Christine Munk, Matthew Scholz, Yan Xu, Patrick Chain, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Blake A. Simmons, and Terry C. Hazen

Submissions from 2016

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Hydrogen Production and Enzyme Activities in the Hyperthermophile Thermococcus paralvinellae Grown on Maltose, Tryptone, and Agricultural Waste, Sarah A. Hensley, Emily Moreira, and James F. Holden

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Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils, Grace Pold, Andrew F. Billings, Jeff L. Blanchard, Daniel B. Burkhardt, Serita D. Frey, Jerry M. Melillo, Julia Schnabel, Linda T.A. van Diepen, and Kristen DeAngelis

Submissions from 2015

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Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov., Andrew F. Billings, Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanya Woyke, and Kristen DeAngelis

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Long-term forest soil warming alters microbial communities in temperate forest soils, Kristen DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T.A. van Diepen, Rebecca M. Varney, Jeffrey L. Blanchard, Jerry Melillo, and Serita D. Frey

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Two decades of warming increases diversity of a potentially lignolytic bacterial community, Grace Pold, Jerry M. Melillo, and Kristen DeAngelis

Submissions from 2014

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Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2, Hannah L. Woo, Nicholas R. Ballor, Terry C. Hazen, Julian L. Fortney, Blake Simmons, Karen Walston Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke, Janet Jansson, Jeff Kimbrell, and Kristen DeAngelis

Submissions from 2013

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Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1, Kristen DeAngelis, Deepak Sharma, Rebecca Varney, Blake Simmons, Nancy G. Isern, Lye Meng Markillie, Carrie Nicora, Angela D. Norbeck, Ronald C. Taylor, Joshua T. Aldrich, and Errol W. Robinson

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When is a microbial culture "pure"? Persistent cryptic contaminant escapes detection even with deep genome sequencing, Pravin Malla, Kelly Nevin, Minita Shrestha, and Derek Lovley

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Aromatic amino acids required for pili conductivity and long-range extracellular electron transport in Geobacter sulfurreducens, Madeline Vargas, Nikhil Malvankar, Pier-Luc Tremblay, Ching Leang, Jessica Smith, Pranav Patel, Oona Synoeyenbos-West, Kelly Nevin, and Derek Lovley

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Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface, Michael Wilkins, Kelly Wrighton, Carrie Nicora, Kenneth Williams, Lee McCue, Kim Handley, Chris Miller, Ludovic Giloteaux, Alison Montogomery, Derek Lovley, Jillian Banfield, Philip Long, and Mary Lipton

Submissions from 2012

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The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features, Muktak Aklujkar, Shelley Haveman, Raymond DiDonato, Olga Chertkov, Cliff Han, Miriam Land, Peter Brown, and Derek Lovley

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Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation, M. Barlett, K. Zhuang, R. Mahadevan, and Derek Lovley

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Analysis of the Genome of the Sexually Transmitted Insect Virus Helicoverpa zea Nudivirus 2, John Burand, Woojin Kim, Claudio Afonso, Edan Tulman, Gerald Kutish, Zhiqiang Lu, and Daniel Rock

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Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production, Jessica Butler, Nelson Young, Muktak Aklujkar, and Derek Lovley

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A Bayesian Model for Pooling Gene Expression Studies That Incorporates Co-Regulation Information, Erin Conlon, Bradley L. Postier, Barbara Methé, Kelly Nevin, and Derek Lovley

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Molecular Analysis of the In Situ Growth Rate of Subsurface Geobacter Species, Dawn Holmes, Ludovic Giloteaux, Melissa Barlett, Milind Chavan, Jessica Smith, Kenneth Williams, Michael Wilkins, Philip Long, and Derek Lovley

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Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction, Yuting Liang, Joy Van Nostrand, Lucie N′Guessan, Aaron Peacock, Ye Deng, Philip Long, Tom Resch, Liyou Wu, Zhili He, Guanghe Li, Terry Hazen, Derek Lovley, and Jizhong Zhoua

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Electrical Conductivity in a Mixed-Species Biofilm, Nikhil Malvankar, Joanne Lau, Kelly Nevin, Ashley Franks, Mark Tuominen, and Derek Lovley

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Role of the NiFe Hydrogenase Hya in Oxidative Stress Defense in Geobacter sulfurreducens, Pier-Luc Tremblay and Derek Lovley

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The Rnf Complex of Clostridium ljungdahlii Is a Proton-Translocating Ferredoxin: NAD+ Oxidoreductase Essential for Autotrophic Growth, Pier-Luc Tremblay, Tian Zhang, Shabir Dar, Ching Leang, and Derek Lovley

Submissions from 2011

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Complete genome sequence of “Enterobacter lignolyticus” SCF1, Kristen DeAngelis, Patrick D'Haeseleer, Dylan Chivian, Julian L. Fortney, Jane Khudyakov, Blake Simmons, Hannah Woo, Adam P. Arkin, Karen Walston Davenport, Lynne Goodwin, Amy Chen, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke, and Terry C. Hazen

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Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus Placidus, Derek Lovley, Dawn Holmes, Carla Risso, and Jessica Smith

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Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates, Masahiko Morita, Nikhil Malvankar, Ashley Franks, Zarath Summers, Ludovic Giloteaux, Amelia Rotaru, Camelia Rotaru, and Derek Lovley

Submissions from 2010

Mitochondrial DNA polymerase POLIB is essential for minicircle DNA replication in African trypanosomes, DF Bruhn, B Mozeleski, L Falkin, and MM Klingbeil

Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes, JE Butler, ND Young, and DR Lovley

Multiple bHLH proteins regulate CIT2 expression in Saccharomyces cerevisiae, LA Chen and JM Lopes

Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms, AE Franks, KP Nevin, RH Glaven, and DR Lovley

Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c-Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens, K Inoue, XL Qian, L Morgado, BC Kim, T Mester, M Izallalen, CA Salgueiro, and DR Lovley

The role of nano-scale heterogeneous electrostatic interactions in initial bacterial adhesion from flow: A case study with Staphylococcus aureus, S Kalasin, J Dabkowski, K Nusslein, and MM Santore

Alignment of the c-Type Cytochrome OmcS along Pili of Geobacter sulfurreducens, C Leang, XL Qian, T Mester, and DR Lovley

RecA4142 Causes SOS Constitutive Expression by Loading onto Reversed Replication Forks in Escherichia coli K-12, JE Long, SC Massoni, and SJ Sandler

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads, H Nagarajan, JE Butler, A Klimes, Y Qiu, K Zengler, J Ward, ND Young, BA Methe, BO Palsson, DR Lovley, and CL Barrett

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer, AL N'Guessan, H Elifantz, KP Nevin, PJ Mouser, B Methe, T LWoodard, K Manley, KH Williams, MJ Wilkins, JT Larsen, PE Long, and DR Lovley

Biotechnological potential of aquatic plant-microbe interactions, L Stout and K Nusslein

Reductive dechlorination of 2-chlorophenol by Anaeromyxobacter dehalogenans with an electrode serving as the electron donor, SM Strycharz, SM Gannon, AR Boles, AE Franks, KP Nevin, and DR Lovley

Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species, T Ueki and DR Lovley

Role of Geobacter sulfurreducens Outer Surface c-Type Cytochromes in Reduction of Soil Humic Acid and Anthraquinone-2,6-Disulfonate, JW Voordeckers, BC Kim, M Izallalen, and DR Lovley

Electrode-Based Approach for Monitoring In Situ Microbial Activity During Subsurface Bioremediation, KH Williams, KP Nevin, A Franks, A Englert, PE Long, and DR Lovley

Electrodic voltages accompanying stimulated bioremediation of a uranium-contaminated aquifer, KH Williams, AL N'Guessan, J Druhan, PE Long, SS Hubbard, DR Lovley, and JF Banfield

Stimulating the anaerobic degradation of aromatic hydrocarbons in contaminated sediments by providing an electrode as the electron acceptor, T Zhang, SM Gannon, KP Nevin, AE Franks, and DR Lovley

Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments, J Zhao, YL Fang, TD Scheibe, DR Lovley, and R Mahadevan

Submissions from 2009

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens, M Aklujkar, J Krushkal, G DiBartolo, A Lapidus, ML Land, and DR Lovley

Microcosm-based Study of the Attenuation of an Acid Mine Drainage-Impacted Site through Biological Sulfate and Iron Reduction, CA Becerra, EL Lopez-Luna, SJ Ergas, and K Nusslein

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Presence and Prevalence of Viruses in Local and Migratory Honeybees (Apis mellifera) in Massachusetts, John Burand, Anna Welch, Francis Drummond, Sunil Tewari, and Anne Averill

Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative genomics of six Geobacteraceae species, JE Butler, ND Young, and DR Lovley

UvrD303, a Hyperhelicase Mutant That Antagonizes RecA-Dependent SOS Expression by a Mechanism That Depends on Its C Terminus, RC Centore, MC Leeson, and SJ Sandler

Hydrophilic Modifications of an Amphiphilic Polynorbornene and the Effects on its Hemolytic and Antibacterial Activity, S Colak, CF Nelson, K Nusslein, and GN Tew

Hierarchical Bayesian meta-analysis models for cross-platform microarray studies, EM Conlon, BL Postier, BA Methe, KP Nevin, and DR Lovley

Novel strategy for three-dimensional real-time imaging of microbial fuel cell communities: monitoring the inhibitory effects of proton accumulation within the anode biofilm, AE Franks, KP Nevin, HF Jia, M Izallalen, TL Woodard, and DR Lovley

Comparison of Facially Amphiphilic versus Segregated Monomers in the Design of Antibacterial Copolymers, GJ Gabriel, JA Maegerlein, CE Nelson, JM Dabkowski, T Eren, K Nusslein, and GN Tew

Single Molecule Analysis of a Red Fluorescent RecA Protein Reveals a Defect in Nucleoprotein Filament Nucleation That Relates to Its Reduced Biological Functions, N Handa, I Amitani, N Gumlaw, SJ Sandler, and SC Kowalczykowski

Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor, DB Hedrick, AD Peacock, DR Lovley, TL Woodard, KP Nevin, PE Long, and DC White

Potential Role of a Novel Psychrotolerant Member of the Family Geobacteraceae, Geopsychrobacter electrodiphilus gen. nov., sp. nov., in Electricity Production by a Marine Sediment Fuel Cell (vol 70, pg 6023, 2004), DE Holmes, JS Nicoll, DR Bond, and DR Lovley

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments, DE Holmes, RA O'Neil, MA Chavan, LA N'Guessan, HA Vrionis, LA Perpetua, MJ Larrahondo, R DiDonato, A Liu, and DR Lovley

Environmental Sequence Data from the Sargasso Sea Reveal That the Characteristics of Genome Reduction in Prochlorococcus Are Not a Harbinger for an Escalation in Genetic Drift, JH Hu and JL Blanchard

Regulated transcription of the Saccharomyces cerevisiae phosphatidylinositol biosynthetic gene, PIS1, yields pleiotropic effects on phospholipid synthesis, NM Jani and JM Lopes

PilR, a Transcriptional Regulator for Pilin and Other Genes Required for Fe(III) Reduction in Geobacter sulfurreducens, K Juarez, BC Kim, K Nevin, L Olvera, G Reguera, DR Lovley, and BA Methe

Unraveling the Secrets of Regulating Mitochondrial DNA Replication, MM Klingbeil and TA Shapiro

Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer, J Krushkal, C Leang, J Barbe, YH Qu, B Yan, M Puljic, R Adkins, and D Lovley

Bioinformatic analysis of gene regulation in Geobacter sulfurreducens, J Krushkal, YH Qu, P Brown, S Sontineni, T Ueki, K Juarez, C Leang, E Merino, J Peeples, JF Barbe, RM Adkins, and DR Lovley

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens, C Leang, J Krushkal, T Ueki, M Puljic, J Sun, K Juarez, C Nunez, G Reguera, R DiDonato, B Postier, RM Adkins, and DR Lovley

"Doubly Selective" Antimicrobial Polymers: How Do They Differentiate between Bacteria?, K Lienkamp, KN Kumar, A Som, K Nusslein, and GN Tew

Antimicrobial Polymers Prepared by Ring-Opening Metathesis Polymerization: Manipulating Antimicrobial Properties by Organic Counterion and Charge Density Variation, K Lienkamp, AE Madkour, KN Kumar, K Nusslein, and GN Tew

Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12, JE Long, N Renzette, and SJ Sandler

Fast Disinfecting Antimicrobial Surfaces, AE Madkour, JA Dabkowski, K Nusslein, and GN Tew

Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation, PJ Mouser, DE Holmes, LA Perpetua, R DiDonato, B Postier, A Liu, and DR Lovley

Influence of Heterogeneous Ammonium Availability on Bacterial Community Structure and the Expression of Nitrogen Fixation and Ammonium Transporter Genes during in Situ Bioremediation of Uranium-Contaminated Groundwater, PJ Mouser, AL N'Guessan, H Elifantz, DE Holmes, KH Williams, MJ Wilkins, PE Long, and DR Lovley

Anode Biofilm Transcriptomics Reveals Outer Surface Components Essential for High Density Current Production in Geobacter sulfurreducens Fuel Cells, KP Nevin, BC Kim, RH Glaven, JP Johnson, TL Woodard, BA Methe, RJ DiDonato, SF Covalla, AE Franks, A Liu, and DR Lovley

GSEL Version 2, an Online Genome-Wide Query System of Operon Organization and Regulatory Sequence Elements of Geobacter sulfurreducens, YH Qu, P Brown, JF Barbe, M Puljic, E Merino, RM Adkins, DR Lovley, and J Krushkal

Cyclic voltammetry of biofilms of wild type and mutant Geobacter sulfurreducens on fuel cell anodes indicates possible roles of OmcB, OmcZ, type IV pili, and protons in extracellular electron transfer, H Richter, KP Nevin, HF Jia, DA Lowy, DR Lovley, and LM Tender

Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens, C Risso, J Sun, K Zhuang, R Mahadevan, R Deboy, W Ismail, S Shrivastava, H Huot, S Kothari, S Daugherty, O Bui, CH Schilling, DR Lovley, and BA Methe

Hydrogenotrophic Denitrification and Perchlorate Reduction in Ion Exchange Brines Using Membrane Biofilm Reactors, AK Sahu, T Conneely, K Nusslein, and SJ Ergas

Biological Perchlorate Reduction in Packed Bed Reactors Using Elemental Sulfur, AK Sahu, T Conneely, KR Nusslein, and SJ Ergas

Genome-scale constraint-based modeling of Geobacter metallireducens, J Sun, B Sayyar, JE Butler, P Pharkya, TR Fahland, I Famili, CH Schilling, DR Lovley, and R Mahadevan

Abundances of Hyperthermophilic Autotrophic Fe(III) Oxide Reducers and Heterotrophs in Hydrothermal Sulfide Chimneys of the Northeastern Pacific Ocean, HC Ver Eecke, DS Kelley, and JF Holden

Occurrence of Chlamydia trachomatis and Chlamydia pneumoniae in paediatric respiratory infections, WC Webley, Y Tilahun, K Lay, K Patel, ES Stuart, C Andrzejewski, and PS Salva

Occurrence of Chlamydia trachomatis and Chlamydia pneumoniae in paediatric respiratory infections, WC Webley, Y Tilahun, K Lay, K Patel, ES Stuart, C Andrzejewski, and PS Salva

Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation, MJ Wilkins, NC VerBerkmoes, KH Williams, SJ Callister, PJ Mouser, H Elifantz, AL N'Guessan, BC Thomas, CD Nicora, MB Shah, P Abraham, MS Lipton, DR Lovley, RL Hettich, PE Long, and JF Banfield

Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells, HN Yi, KP Nevin, BC Kim, AE Franks, A Klimes, LM Tender, and DR Lovley

Submissions from 2008

Investigating the Effect of Increasing Charge Density on the Hemolytic Activity of Synthetic Antimicrobial Polymers, ZM Al-Badri, A Som, S Lyon, CF Nelson, K Nusslein, and GN Tew

Relational learning in children with deafness and cochlear implants, AC Almeida-Verdu, EM Huziwara, DG De Souza, JC De Rose, M Cecilia-Bevilacqua, J Lopes, CO Alves, and WJ McIlvane

XthA (Exonuclease III) regulates loading of RecA onto DNA substrates in log phase Escherichia coli cells, RC Centore, R Lestini, and SJ Sandler

Stem-Loop Silencing Reveals that a Third Mitochondrial DNA Polymerase, POLID, Is Required for Kinetoplast DNA Replication in Trypanosomes, J Chandler, AV Vandoros, B Mozeleski, and MM Klingbeil

Quantifying expression of a dissimilatory (bi) sulfite reductase gene in petroleum-contaminated marine Harbor Sediments, KJ Chin, ML Sharma, LA Russell, KR O'Neill, and DR Lovley

Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor, YHR Ding, KK Hixson, MA Aklujkar, MS Lipton, RD Smith, DR Lovley, and T Mester

Antibacterial and hemolytic activities of quaternary pyridinium functionalized polynorbornenes, T Eren, A Som, JR Rennie, CF Nelson, Y Urgina, K Nusslein, EB Coughlin, and GN Tew

Fluorescent properties of c-type cytochromes reveal their potential role as an extracytoplasmic electron sink in Geobacter sulfurreducens, A Esteve-Nunez, J Sosnik, P Visconti, and DR Lovley

Constraints on anaerobic respiration in the hyperthermophilic archaea Pyrobaculum islandicum and Pyrobaculum aerophilum, LF Feinberg, R Srikanth, RW Vachet, and JF Holden

A new model linking atmospheric methane sources to Pleistocene glaciation via methanogenesis in sedimentary basins, MJ Formolo, JM Salacup, ST Petsch, AM Martini, and K Nusslein

Synthetic Mimic of Antimicrobial Peptide with Nonmembrane-Disrupting Antibacterial Properties, GJ Gabriel, AE Madkour, JM Dabkowski, CF Nelson, K Nusslein, and GN Tew

RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis, MC Gruenig, N Renzette, E Long, S Chitteni-Pattu, RB Inman, MM Cox, and SJ Sandler

Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production, SA Haveman, RJ DiDonato, L Villanueva, ES Shelobolina, BL Postier, B Xu, A Liu, and DR Lovley

Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes, DE Holmes, T Mester, RA O'Neil, LA Perpetua, MJ Larrahondo, R Glaven, ML Sharma, JE Ward, KP Nevin, and DR Lovley

Geobacter sulfurreducens strain engineered for increased rates of respiration, M Izallalen, R Mahadevan, A Burgard, B Postier, R Didonato, J Sun, CH Schilling, and DR Lovley

Transcription regulation of the Saccharomyces cerevisiae PIS1 gene by inositol and the pleiotropic regulator, Ume6p, NM Jani and JM Lopes

Characterization of extracellular minerals produced during dissimilatory Fe(III) and U(VI) reduction at 100 degrees C by Pyrobaculum islandicum, K Kashefi, BM Moskowitz, and DR Lovley

Growth of thermophilic and hyperthermophilic Fe (III)-reducing microorganisms on a ferruginous smectite as the sole electron acceptor, K Kashefi, ES Shelobolina, WC Elliott, and DR Lovley