@article {1963,
	title = {Nuclease escape elements protect messenger RNA against cleavage by multiple viral endonucleases},
	journal = {PLOS Pathogens},
	volume = {13},
	year = {2017},
	month = {aug},
	pages = {e1006593},
	doi = {10.1371/journal.ppat.1006593},
	url = {https://doi.org/10.1371/journal.ppat.1006593},
	author = {Mandy Muller and Britt A. Glaunsinger},
	editor = {James R. Smiley}
}
@article {1425,
	title = {Novel mechanisms of controlling the activities of the transcription factors Spo0A and ComA by the plasmid-encoded quorum sensing regulators Rap60-Phr60 in Bacillus subtilis.},
	journal = {Mol Microbiol},
	year = {2015},
	month = {2015 Jan 19},
	abstract = {<p>Bacillus subtilis and its closest relatives have multiple rap-phr quorum sensing gene pairs that coordinate a variety of physiological processes with population density. Extra-chromosomal rap-phr genes are also present on mobile genetic elements, yet relatively little is known about their function. In this work, we demonstrate that Rap60-Phr60 from plasmid pTA1060 coordinates a variety of biological processes with population density including sporulation, cannibalism, biofilm formation and genetic competence. Similar to other Rap proteins that control sporulation, Rap60 modulates phosphorylation of the transcription factor Spo0A by acting as a phosphatase of Spo0F\&sim;P, an intermediate of the sporulation phosphorelay system. Additionally, Rap60 plays a noncanonical role in regulating the autophosphorylation of the sporulation-specific kinase KinA, a novel activity for Rap proteins. In contrast, Rap proteins that modulate genetic competence interfere with DNA binding by the transcription factor ComA. Rap60 regulates the activity of ComA in a unique manner by forming a Rap60-ComA-DNA ternary complex that inhibits transcription of target genes. Taken together, this work provides new insight into two novel mechanisms of regulating Spo0A and ComA by Rap60 and expands our general understanding of how plasmid-encoded quorum sensing pairs regulate important biological processes.</p>
},
	issn = {1365-2958},
	doi = {10.1111/mmi.12939},
	author = {Boguslawski, Kristina M and Hill, Patrick A and Griffith, Kevin L}
}
@article {723,
	title = {New bactericidal surgical suture coating.},
	journal = {Langmuir},
	volume = {28},
	year = {2012},
	month = {2012 Aug 21},
	pages = {12134-9},
	abstract = {This paper demonstrates the effectiveness of a new antimicrobial suture coating. An amphiphilic polymer, poly[(aminoethyl methacrylate)-co-(butyl methacrylate)] (PAMBM), inspired by antimicrobial peptides, was bactericidal against S. aureus in time-kill experiments. PAMBM was then evaluated in a variety of polymer blends using the Japanese Industrial Standard (JIS) method and showed excellent antimicrobial activity at a low concentration (0.5 wt \%). Using a similar antimicrobial coating formula to commercial Vicryl Plus sutures, disk samples of the coating material containing PAMBM effectively killed bacteria (98\% reduction at 0.75 wt \%). Triclosan, the active ingredient in Vicryl Plus coatings, did not kill the bacteria. Further Kirby-Bauer assays of these disk samples showed an increasing zone of inhibition with increasing concentration of PAMBM. Finally, the PAMBM-containing coating was applied to sutures, and the morphology of the coating surface was characterized by SEM, along with Vicryl and uncoated sutures. The PAMBM-containing sutures killed bacteria more effectively (3 log(10) reduction at 2.4 wt \%) than Vicryl Plus sutures (0.5 log(10) reduction).},
	issn = {1520-5827},
	doi = {10.1021/la302732w},
	author = {Li, Yan and Kumar, Kushi N and Dabkowski, Jeffrey M and Corrigan, Meagan and Scott, Richard W and N{\"u}sslein, Klaus and Tew, Gregory N}
}
@article {440,
	title = {Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.},
	journal = {Nucleic Acids Res},
	volume = {38},
	year = {2010},
	month = {2010 Nov},
	pages = {7485-99},
	abstract = {Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of nitrogen-fixation genes and represses a gene encoding glutamate dehydrogenase during nitrogen fixation. The other system whose expression is directly activated by the master regulatory system appears to control by antitermination the expression of a subset of the nitrogen-fixation genes whose transcription is activated by the master regulatory system and whose promoter contains transcription termination signals. This study provides a new paradigm for nitrogen-fixation gene regulation.},
	keywords = {Bacterial Proteins, Binding Sites, DNA-Binding Proteins, Gene Expression Regulation, Bacterial, Geobacter, Nitrogen Fixation, Promoter Regions, Genetic, Protein Kinases, RNA-Binding Proteins, Transcription, Genetic},
	issn = {1362-4962},
	doi = {10.1093/nar/gkq652},
	author = {Ueki, Toshiyuki and Lovley, Derek R}
}
@article {854,
	title = {Notice of duplicate publication.},
	journal = {Am J Respir Crit Care Med},
	volume = {175},
	year = {2007},
	month = {2007 Jan 1},
	pages = {94},
	keywords = {Duplicate Publication as Topic},
	issn = {1073-449X},
	author = {Webley, Wilmore C and Salva, Paul S and Andrzejewski, Chester and Cirino, Frances and West, Corrie A and Tilahun, Yaphet and Stuart, Elizabeth S}
}
@article {819,
	title = {A novel dnaC mutation that suppresses priB rep mutant phenotypes in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {60},
	year = {2006},
	month = {2006 May},
	pages = {973-83},
	abstract = {The loading of a replisome in prokaryotic and eukaryotic cells at an origin of DNA replication and during replication restart is a highly ordered and regulated process. During replication restart in Escherichia coli, the PriA, PriB, PriC, DnaT and Rep proteins form multiple pathways that bind to repaired replication forks. These complexes are then recognized by DnaC as sites to load DnaB, the replicative helicase. Several dnaC mutations have been isolated that suppress phenotypes of some replication restart mutants. A new dnaC mutation (dnaC824) is reported here that efficiently suppresses priB rep mutant phenotypes. Furthermore, it is shown that dnaC824 will suppress phenotypes of priB priA300, rep priA300 and priB priC strains. Unlike other dnaC suppressors, it can only weakly suppress the absence of priA. Others have reported a different type of dnaC mutation, dnaC1331, is able to mimic priB mutant phenotypes. This is supported herein by showing that like dnaC1331, a priB mutation is synthetically lethal with a dam mutation and this can be rescued by a mutH mutation. Furthermore, priB dam lethality can also be suppressed by dnaC824. Like a priB mutation, a dnaC1331 mutation causes a priA2::kan-like phenotype when combined with priA300. Lastly, we show that dnaC824 is dominant to wild type and that dnaC1331 is recessive to wild type. Several models are discussed for the action of these mutant dnaC proteins in replication restart.},
	keywords = {DNA Replication, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Dominant, Genes, Lethal, Genes, Recessive, Mutant Proteins, Mutation, Phenotype, Suppression, Genetic},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2006.05147.x},
	author = {Boonsombat, Ruethairat and Yeh, Su-Ping and Milne, Amy and Sandler, Steven J}
}
@article {534,
	title = {A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens.},
	journal = {BMC Microbiol},
	volume = {5},
	year = {2005},
	month = {2005},
	pages = {41},
	abstract = {BACKGROUND: Metal reduction is thought to take place at or near the bacterial outer membrane and, thus, outer membrane proteins in the model dissimilatory metal-reducing organism Geobacter sulfurreducens are of interest to understand the mechanisms of Fe(III) reduction in the Geobacter species that are the predominant Fe(III) reducers in many environments. Previous studies have implicated periplasmic and outer membrane cytochromes in electron transfer to metals. Here we show that the most abundant outer membrane protein of G. sulfurreducens, OmpJ, is not a cytochrome yet it is required for metal respiration.

RESULTS: When outer membrane proteins of G. sulfurreducens were separated via SDS-PAGE, one protein, designated OmpJ (outer membrane protein J), was particularly abundant. The encoding gene, which was identified from mass spectrometry analysis of peptide fragments, is present in other Geobacteraceae, but not in organisms outside this family. The predicted localization and structure of the OmpJ protein suggested that it was a porin. Deletion of the ompJ gene in G. sulfurreducens produced a strain that grew as well as the wild-type strain with fumarate as the electron acceptor but could not grow with metals, such as soluble or insoluble Fe(III) and insoluble Mn(IV) oxide, as the electron acceptor. The heme c content in the mutant strain was ca. 50\% of the wild-type and there was a widespread loss of multiple cytochromes from soluble and membrane fractions. Transmission electron microscopy analyses of mutant cells revealed an unusually enlarged periplasm, which is likely to trigger extracytoplasmic stress response mechanisms leading to the degradation of periplasmic and/or outer membrane proteins, such as cytochromes, required for metal reduction. Thus, the loss of the capacity for extracellular electron transport in the mutant could be due to the missing c-type cytochromes, or some more direct, but as yet unknown, role of OmpJ in metal reduction.

CONCLUSION: OmpJ is a putative porin found in the outer membrane of the model metal reducer G. sulfurreducens that is required for respiration of extracellular electron acceptors such as soluble and insoluble metals. The effect of OmpJ in extracellular electron transfer is indirect, as OmpJ is required to keep the integrity of the periplasmic space necessary for proper folding and functioning of periplasmic and outer membrane electron transport components. The exclusive presence of ompJ in members of the Geobacteraceae family as well as its role in metal reduction suggest that the ompJ sequence may be useful in tracking the growth or activity of Geobacteraceae in sedimentary environments.},
	keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Base Sequence, Biological Transport, Deltaproteobacteria, DNA Primers, Ferric Compounds, Gene Deletion, Genome, Bacterial, Geobacter, Manganese Compounds, Molecular Sequence Data, Oxides, Peptide Fragments, Phylogeny, Protein Structure, Secondary, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization},
	issn = {1471-2180},
	doi = {10.1186/1471-2180-5-41},
	author = {Afkar, Eman and Reguera, Gemma and Schiffer, Marianne and Lovley, Derek R}
}
@article {604,
	title = {N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species.},
	journal = {Environ Microbiol},
	volume = {2},
	year = {2000},
	month = {2000 Jun},
	pages = {266-73},
	abstract = {Cells of Geobacter metallireducens, Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2-dependent growth, the first anaerobically with Fe(III) as the electron acceptor, and the latter three species microaerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5+/-5.9 nmol C2H4 produced min(-1) mg(-1) cell protein) while growing with Fe(III) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.},
	keywords = {Acetylene, DNA, Bacterial, Ethylenes, Genes, Bacterial, Iron, Nitrogen Fixation, Nitrogenase, Oxidation-Reduction, Oxidoreductases, Proteobacteria, Rhodospirillaceae},
	issn = {1462-2912},
	author = {Bazylinski, D A and Dean, A J and Sch{\"u}ler, D and Phillips, E J and Lovley, D R}
}
@article {44,
	title = {A network of yeast basic helix-loop-helix interactions.},
	journal = {Nucleic Acids Res},
	volume = {28},
	year = {2000},
	month = {2000 Nov 15},
	pages = {4460-6},
	abstract = {The Ino4 protein belongs to the basic helix-loop-helix (bHLH) family of proteins. It is known to form a dimer with Ino2p, which regulates phospholipid biosynthetic genes. Mammalian bHLH proteins have been shown to form multiple dimer combinations. However, this flexibility in dimerization had not been documented for yeast bHLH proteins. Using the yeast two-hybrid assay and a biochemical assay we show that Ino4p dimerizes with the Pho4p, Rtg1p, Rtg3p and Sgc1p bHLH proteins. Screening a yeast cDNA library identified three additional proteins that interact with Ino4p: Bck2p, YLR422W and YNR064C. The interaction with Bck2p prompted us to examine if any of the Bck2p-associated functions affect expression of phospholipid biosynthetic genes. We found that hyperosmotic growth conditions altered the growth phase regulation of a phospholipid biosynthetic gene, CHO1. There are two recent reports of initial whole genome yeast two-hybrid interactions. Interestingly, one of these reports identified five proteins that interact with Ino4p: Ino2p, Hcs1p, Apl2p, YMR317W and YNL279W. Ino2p is the only protein in common with the data presented here. Our finding that Ino4p interacts with five bHLH proteins suggests that Ino4p is likely to be a central player in the coordination of multiple biological processes.},
	keywords = {DNA-Binding Proteins, Fungal Proteins, Gene Expression Regulation, Fungal, Helix-Loop-Helix Motifs, Lac Operon, Methyltransferases, Phosphatidylethanolamine N-Methyltransferase, Plasmids, Protein Binding, Recombinant Fusion Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Trans-Activators, Transcription Factors, Transcriptional Activation, Two-Hybrid System Techniques},
	issn = {1362-4962},
	author = {Robinson, K A and Koepke, J I and Kharodawala, M and Lopes, J M}
}
@article {608,
	title = {Novel forms of anaerobic respiration of environmental relevance.},
	journal = {Curr Opin Microbiol},
	volume = {3},
	year = {2000},
	month = {2000 Jun},
	pages = {252-6},
	abstract = {Novel forms of anaerobic respiration continue to be discovered. Many of these are environmentally significant as they have important impacts on the fate of organic carbon and the cycling of many inorganic compounds. Furthermore, anaerobic respiration is becoming increasing recognized as a strategy for the remediation of organic and metal contaminants in the subsurface.},
	keywords = {Anaerobiosis, Bacteria, Anaerobic, Environment, Industrial Microbiology, Industrial Waste},
	issn = {1369-5274},
	author = {Lovley, D R and Coates, J D}
}
@article {797,
	title = {A new Borrelia infecting Lone Star ticks.},
	journal = {Lancet},
	volume = {347},
	year = {1996},
	month = {1996 Jan 6},
	pages = {67-8},
	keywords = {Animals, Base Sequence, Borrelia, Borrelia Infections, Deer, Disease Vectors, DNA Primers, Maryland, Molecular Sequence Data, Ticks},
	issn = {0140-6736},
	author = {Armstrong, P M and Rich, S M and Smith, R D and Hartl, D L and Spielman, A and Telford, S R}
}
@article {645,
	title = {Novel processes for anaerobic sulfate production from elemental sulfur by sulfate-reducing bacteria.},
	journal = {Appl Environ Microbiol},
	volume = {60},
	year = {1994},
	month = {1994 Jul},
	pages = {2394-9},
	abstract = {Sulfate reducers and related organisms which had previously been found to reduce Fe(III) with H(2) or organic electron donors oxidized S to sulfate when Mn(IV) was provided as an electron acceptor. Organisms catalyzing this reaction in washed cell suspensions included Desulfovibrio desulfuricans, Desulfomicrobium baculatum, Desulfobacterium autotrophicum, Desulfuromonas acetoxidans, and Geobacter metallireducens. These organisms produced little or no sulfate from S with Fe(III) as a potential electron acceptor or in the absence of an electron acceptor. In detailed studies with Desulfovibrio desulfuricans, the stoichiometry of sulfate and Mn(II) production was consistent with the reaction S + 3 MnO(2) + 4H-->SO(4) + 3Mn(II) + 2H(2)O. None of the organisms evaluated could be grown with S as the sole electron donor and Mn(IV) as the electron acceptor. In contrast to the other sulfate reducers evaluated, Desulfobulbus propionicus produced sulfate from S in the absence of an electron acceptor and Fe(III) oxide stimulated sulfate production. Sulfide also accumulated in the absence of Mn(IV) or Fe(III). The stoichiometry of sulfate and sulfide production indicated that Desulfobulbus propionicus disproportionates S as follows: 4S + 4H(2)O-->SO(4) + 3HS + 5 H. Growth of Desulfobulbus propionicus with S as the electron donor and Fe(III) as a sulfide sink and/or electron acceptor was very slow. The S oxidation coupled to Mn(IV) reduction described here provides a potential explanation for the Mn(IV)-dependent sulfate production that previous studies have observed in anoxic marine sediments. Desulfobulbus propionicus is the first example of a pure culture known to disproportionate S.},
	issn = {0099-2240},
	author = {Lovley, D R and Phillips, E J}
}
@article {800,
	title = {Norway rats as reservoir hosts for Lyme disease spirochetes on Monhegan Island, Maine.},
	journal = {J Infect Dis},
	volume = {168},
	year = {1993},
	month = {1993 Sep},
	pages = {687-91},
	abstract = {To determine whether the agent of Lyme disease, Borrelia burgdorferi, may be maintained in the absence of its usual white-footed mouse reservoir host, Ixodes dammini ticks from an island where mice are absent were examined. Prevalence of spirochetal infection was described for ticks removed from mammals, birds, and vegetation on Monhegan Island, Maine. Forty percent of adult I. dammini removed from vegetation were infected. Norway rats were heavily infested with ticks, and > 60\% of such ticks contained spirochetes. Other hosts were less frequently infested by ticks, and few such ticks were infected by spirochetes. The prevalence of antibody to B. burgdorferi was 23\% in dogs and cats; 4\% of island residents had Lyme disease. Thus, rats maintain Lyme disease spirochetes on Monhegan Island, and there may be transmission of this agent by I. dammini to island residents and their pets.},
	keywords = {Animals, Animals, Domestic, Antibodies, Bacterial, Borrelia burgdorferi Group, Cats, Disease Reservoirs, Disease Vectors, Dogs, Geography, Humans, Incidence, Lyme Disease, Maine, Rats, Ticks},
	issn = {0022-1899},
	author = {Smith, R P and Rand, P W and Lacombe, E H and Telford, S R and Rich, S M and Piesman, J and Spielman, A}
}
@article {662,
	title = {Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.},
	journal = {Appl Environ Microbiol},
	volume = {54},
	year = {1988},
	month = {1988 Jun},
	pages = {1472-80},
	abstract = {A dissimilatory Fe(III)- and Mn(IV)-reducing microorganism was isolated from freshwater sediments of the Potomac River, Maryland. The isolate, designated GS-15, grew in defined anaerobic medium with acetate as the sole electron donor and Fe(III), Mn(IV), or nitrate as the sole electron acceptor. GS-15 oxidized acetate to carbon dioxide with the concomitant reduction of amorphic Fe(III) oxide to magnetite (Fe(3)O(4)). When Fe(III) citrate replaced amorphic Fe(III) oxide as the electron acceptor, GS-15 grew faster and reduced all of the added Fe(III) to Fe(II). GS-15 reduced a natural amorphic Fe(III) oxide but did not significantly reduce highly crystalline Fe(III) forms. Fe(III) was reduced optimally at pH 6.7 to 7 and at 30 to 35 degrees C. Ethanol, butyrate, and propionate could also serve as electron donors for Fe(III) reduction. A variety of other organic compounds and hydrogen could not. MnO(2) was completely reduced to Mn(II), which precipitated as rhodochrosite (MnCO(3)). Nitrate was reduced to ammonia. Oxygen could not serve as an electron acceptor, and it inhibited growth with the other electron acceptors. This is the first demonstration that microorganisms can completely oxidize organic compounds with Fe(III) or Mn(IV) as the sole electron acceptor and that oxidation of organic matter coupled to dissimilatory Fe(III) or Mn(IV) reduction can yield energy for microbial growth. GS-15 provides a model for how enzymatically catalyzed reactions can be quantitatively significant mechanisms for the reduction of iron and manganese in anaerobic environments.},
	issn = {0099-2240},
	author = {Lovley, D R and Phillips, E J}
}
