National Library of Energy BETA

Sample records for aerobic bacteria microorganisms

  1. Aerobic microorganism for the degradation of chlorinated aliphatic hydrocarbons

    DOE Patents [OSTI]

    Fliermans, Carl B. (Augusta, GA)

    1989-01-01

    A chlorinated aliphatic hydrocarbon-degrading microorganism, having American Type Culture Collection accession numbers ATCC 53570 and 53571, in a biologically pure culture aseptically collected from a deep subsurface habitat and enhanced, mineralizes trichloroethylene and tetrachloroethylene to HCl, H.sub.2 O and Co.sub.2 under aerobic conditions stimulated by methane, acetate, methanol, tryptone-yeast extract, propane and propane-methane.

  2. Expression of Genes Linked to NOx Detoxification in Aerobic Bacteria

    E-Print Network [OSTI]

    Cua, Lynnie

    2010-01-01

    ecology of nitrifying bacteria. In: Biology of the Nitrogennitrogen metabolism in bacteria. Current Opinion in Chemicalin ammonia-oxidizing bacteria. Incomplete oxidation of NH 2

  3. Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide-

    E-Print Network [OSTI]

    Skolnick, Jeff

    Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide uranium [U(VI)] mediated by the intrinsic phosphatase acti- vities of naturally occurring bacteria such as uranium (U), technetium (Tc) and other toxic metals [e.g. cadmium (Cd), lead (Pb), chromium (Cr

  4. Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

    E-Print Network [OSTI]

    Ward, Bess

    -oxidizing bacteria Karen L. Casciotti *,1 , Bess B. Ward Department of Geosciences, Princeton University, Princeton) are climatically important trace gases that are produced by both nitrifying and den- itrifying bacteria-oxidizing bacteria, including Nitrosomonas and Nitrosococcus species (i.e., both b- and c-Proteobacterial ammonia

  5. Use of Disinfectants and Cleaners to Reduce Bacteria on Poultry Transportation Coops with a Compressed Air Foam System 

    E-Print Network [OSTI]

    Hinojosa-Garza, Carolee A.

    2013-05-24

    company?s Hazard Analysis and Critical Control Points (HACCP) because a large amount of this bacteria be an indicator of improper sanitation. Cleaning and disinfection programs for this microorganism are being set by USDA and are being improved upon... Salmonella and aerobic bacteria, which could reduce contamination of carcasses. A recent literature search suggests that there are few procedures on how to clean and sanitize transport coops, this may be because it is currently not a requirement...

  6. Microorganism immobilization

    DOE Patents [OSTI]

    Compere, Alicia L. (Knoxville, TN); Griffith, William L. (Oak Ridge, TN)

    1981-01-01

    Live metabolically active microorganisms are immobilized on a solid support by contacting particles of aggregate material with a water dispersible polyelectrolyte such as gelatin, crosslinking the polyelectrolyte by reacting it with a crosslinking agent such as glutaraldehyde to provide a crosslinked coating on the particles of aggregate material, contacting the coated particles with live microorganisms and incubating the microorganisms in contact with the crosslinked coating to provide a coating of metabolically active microorganisms. The immobilized microorganisms have continued growth and reproduction functions.

  7. Biodegradation of Triclosan by Aerobic Microorganisms 

    E-Print Network [OSTI]

    Lee, Do Gyun

    2012-10-19

    Triclosan, a synthetic antimicrobial agent, is an emerging environmental contaminant. Due to incomplete removal of triclosan by wastewater treatment plants, treated wastewater is one major source of environmental triclosan. Biodegradation...

  8. Engineered microorganisms capable of producing target compounds under anaerobic conditions

    DOE Patents [OSTI]

    Buelter, Thomas (Denver, CO); Meinhold, Peter (Denver, CO); Feldman, Reid M. Renny (San Francisco, CA); Hawkins, Andrew C. (Parker, CO); Urano, Jun (Irvine, CA); Bastian, Sabine (Pasadena, CA); Arnold, Frances (La Canada, CA)

    2012-01-17

    The present invention is generally provides recombinant microorganisms comprising engineered metabolic pathways capable of producing C3-C5 alcohols under aerobic and anaerobic conditions. The invention further provides ketol-acid reductoisomerase enzymes which have been mutated or modified to increase their NADH-dependent activity or to switch the cofactor preference from NADPH to NADH and are expressed in the modified microorganisms. In addition, the invention provides isobutyraldehyde dehydrogenase enzymes expressed in modified microorganisms. Also provided are methods of producing beneficial metabolites under aerobic and anaerobic conditions by contacting a suitable substrate with the modified microorganisms of the present invention.

  9. Aerobic enhanced oil recovery: analysis of the mechanisms and a pilot study 

    E-Print Network [OSTI]

    Eide, Karen

    1998-01-01

    The technique that uses microorganisms to improve oil production in petroleum reservoirs is known as microbial enhanced oil recovery (MEOR). Aerobic microbial enhanced oil recovery is a method which is based on stimulating indigenous oil degrading...

  10. A KINETIC STUDY OF AEROBIC PROPANE UPTAKE AND COMETABOLIC DEGRADATION OF CHLOROFORM,

    E-Print Network [OSTI]

    Semprini, Lewis

    A KINETIC STUDY OF AEROBIC PROPANE UPTAKE AND COMETABOLIC DEGRADATION OF CHLOROFORM, CIS the behavior of different consortiums of aerobic propane-utilizing microorganisms, with respect to both the lag time for growth after exposure to propane, and their ability to transform three chlorinated aliphatic

  11. Mechanisms Regulating Mercury Bioavailability for Methylating Microorganisms in the Aquatic Environment: A Critical Review

    E-Print Network [OSTI]

    Mechanisms Regulating Mercury Bioavailability for Methylating Microorganisms in the Aquatic by anaerobic bacteria. In this Review, we evaluate the current state of knowledge regarding the mechanisms the uptake of inorganic mercury to these microorganisms. Our understanding of the mechanisms behind

  12. RESEARCH ARTICLE Fluid dynamics of self-propelled microorganisms,

    E-Print Network [OSTI]

    Goldstein, Raymond E.

    RESEARCH ARTICLE Fluid dynamics of self-propelled microorganisms, from individuals to concentrated non-pathogenic soil bacteria are rod-shaped (Fig. 1). Their length ranges from 2 to 8 lm, depending

  13. RESEARCH ARTICLE Fluid dynamics of self-propelled microorganisms,

    E-Print Network [OSTI]

    Cortez, Ricardo

    RESEARCH ARTICLE Fluid dynamics of self-propelled microorganisms, from individuals to concentrated00348-007-0387-y #12;Individual cells of these generally non-pathogenic soil bacteria are rod

  14. Cellulolytic Microorganisms from Thermal Environments

    SciTech Connect (OSTI)

    Vishnivetskaya, Tatiana A [ORNL; Raman, Babu [ORNL; Phelps, Tommy Joe [ORNL; Podar, Mircea [ORNL; Elkins, James G [ORNL

    2012-01-01

    Thermal, anaerobic environments rich in decaying plant material are a potential source of novel cellulolytic bacteria. Samples collected from geothermal aquifers in the Yellowstone National Park (YNP) were used to select for cellulolytic thermophiles. Laboratory enrichments on dilute-acid pretreated plant biomass (switchgrass, Populus), and crystalline cellulose (Avicel) resulted in the isolation of 247 environmental clones. The majority of individual clones were affiliated with the cellulolytic bacteria of phylum Firmicutes, followed by xylanolytic and saccharolytic members of the phylum Dictyoglomi. Among the Firmicutes, the clones were affiliated with the genera Caldicellulosiruptor (54.4%), Caloramator (11.5%), Thermoanaerobacter (8.8%), Thermovenabulum (4.1%), and Clostridium (2.0%). From established anaerobic thermophilic enrichments a total of 81 single strains of the genera Caldicellulosiruptor (57%) and Thermoanaerobacter (43%) were isolated. With continuous flow enrichment on Avicel, increases in the relative abundance of Caloramator sp. was observed over clones detected from the Caldicellulosiruptor. Complex communities of interacting microorganisms bring about cellulose decomposition in nature, therefore using up-to-date approaches may yield novel cellulolytic microorganisms with high activity and a rapid rate of biomass conversion to biofuels.

  15. Bacteria recovered from endometritis and pyometra in the beef cow 

    E-Print Network [OSTI]

    Mikulec, Rashel Thi

    1999-01-01

    One hundred and one uteri from beef cows with pyometra were collected from a slaughterhouse. Samples of uterine exudate were cultured for aerobic, microaerophilic, and anaerobic bacteria, and also tested for Trichomonas spp. A section of uterine...

  16. Aerobic landfill bioreactor

    DOE Patents [OSTI]

    Hudgins, Mark P (Aiken, SC); Bessette, Bernard J (Aiken, SC); March, John C (Winterville, GA); McComb, Scott T. (Andersonville, SC)

    2002-01-01

    The present invention includes a system of decomposing municipal solid waste (MSW) within a landfill by converting the landfill to aerobic degradation in the following manner: (1) injecting air via the landfill leachate collection system (2) injecting air via vertical air injection wells installed within the waste mass; (3) applying leachate to the waste mass using a pressurized drip irrigation system; (4) allowing landfill gases to vent; and (5) adjusting air injection and recirculated leachate to achieve a 40% to 60% moisture level and a temperature between 120.degree. F. and 140.degree. F. in steady state.

  17. Aerobic landfill bioreactor

    DOE Patents [OSTI]

    Hudgins, Mark P (Aiken, SC); Bessette, Bernard J (Aiken, SC); March, John (Winterville, GA); McComb, Scott T. (Andersonville, SC)

    2000-01-01

    The present invention includes a method of decomposing municipal solid waste (MSW) within a landfill by converting the landfill to aerobic degradation in the following manner: (1) injecting air via the landfill leachate collection system (2) injecting air via vertical air injection wells installed within the waste mass; (3) applying leachate to the waste mass using a pressurized drip irrigation system; (4) allowing landfill gases to vent; and (5) adjusting air injection and recirculated leachate to achieve a 40% to 60% moisture level and a temperature between 120.degree. F. and 140.degree. F. in steady state.

  18. What is compost? Composting refers to biological decomposition and stabilization of organic materials by microorganisms under

    E-Print Network [OSTI]

    Mukhtar, Saqib

    What is compost? Composting refers to biological decomposition and stabilization of organic materials by microorganisms under aerobic conditions (in the presence of oxygen). During the composting is production of good-quality compost that is biologically stable, relatively uniform in appearance, free

  19. Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria

    E-Print Network [OSTI]

    Sher, Daniel

    Interactions between microorganisms shape microbial ecosystems. Systematic studies of mixed microbes in co-culture have revealed widespread potential for growth inhibition among marine heterotrophic bacteria, but similar ...

  20. Microorganisms for producing organic acids

    DOE Patents [OSTI]

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-09-30

    Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

  1. Ferric hydroxide and ferric hydroxysulfate precipitation by bacteria in an acid mine drainage lagoon

    E-Print Network [OSTI]

    Konhauser, Kurt

    Ferric hydroxide and ferric hydroxysulfate precipitation by bacteria in an acid mine drainage communities growing in an acid mine drainage lagoon sediment has confirmed that microorganisms were also: Ferrihydrite; Ferric hydroxysulfate; Bacteria; Biomineralization; Acid mine drainage Contents 1. Introduction

  2. Expression of Genes Linked to NOx Detoxification in Aerobic Bacteria

    E-Print Network [OSTI]

    Cua, Lynnie

    2010-01-01

    on polychlorinated dibenzo-p-dioxins and dibenzofurans whichdibenzofuran and dibenzo-p-dioxin as well as nitrodiphenylGenetic analysis of dioxin dioxygenase of Sphingomonas sp.

  3. Proteolysis in hyperthermophilic microorganisms

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; Levy, Ryan D.; Michel, Joshua K.; Conners, Shannon B.; Kelly, Robert M.

    2002-01-01

    Proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. Genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. In this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genusPyrococcus, the crenarchaeoteSulfolobus solfataricus, and the bacteriumThermotoga maritima. An overview of the proteases in these organisms is given based on those proteases that have been characterized and on putative proteases that have been identified from genomicmore »sequences, but have yet to be characterized. The analysis revealed both similarities and differences in the mechanisms utilized for proteolysis by each of these hyperthermophiles and indicated how these mechanisms relate to proteolysis in less thermophilic cells and organisms.« less

  4. WHAT IS COMPOST? Composting refers to the biological decomposition and stabilization of organic materials by microorganisms under

    E-Print Network [OSTI]

    Mukhtar, Saqib

    WHAT IS COMPOST? Composting refers to the biological decomposition and stabilization of organic materials by microorganisms under aerobic (in the presence of oxygen) conditions. During the composting, good quality compost is produced that is biologically stable, relatively uniform in appearance, free

  5. Onsite Wastewater Treatment Systems: Aerobic Treatment Unit 

    E-Print Network [OSTI]

    Lesikar, Bruce J.

    2008-10-31

    Aerobic units treat wastewater using the same process, only scaled down, as municipal wastewater treatment systems. This publication explains how aerobic units work, what their design requirements are, and how to maintain them....

  6. Chemosensing in microorganisms to practical biosensors

    E-Print Network [OSTI]

    Surya K. Ghosh; Tapanendu Kundu; Anirban Sain

    2012-10-25

    Microorganisms like bacteria can sense concentration of chemo-attractants in its medium very accurately. They achieve this through interaction between the receptors on their cell surface and the chemo-attractant molecules (like sugar). But the physical processes like diffusion set some limits on the accuracy of detection which was discussed by Berg and Purcell in the late seventies. We have a re-look at their work in order to assess what insight it may offer towards making efficient, practical biosensors. We model the functioning of a typical biosensor as a reaction-diffusion process in a confined geometry. Using available data first we characterize the system by estimating the kinetic constants for the binding/unbinding reactions between the chemo-attractants and the receptors. Then we compute the binding flux for this system which Berg and Purcell had discussed. But unlike in microorganisms where the interval between successive measurements determines the efficiency of the nutrient searching process, it turns out that biosensors depend on long time properties like signal saturation time which we study in detail. We also develop a mean field description of the kinetics of the system.

  7. Digital holographic imaging of microorganisms

    E-Print Network [OSTI]

    Wolf, Michael Trevor

    2006-01-01

    Imaging aquatic microorganisms in 3D space is of interest to biologists and ocean scientists seeking to understand the behavior of these organisms in their natural environments. In this research, digital holographic imaging ...

  8. 1529-6466/03/0054-0004$05.00 Biologically Induced Mineralization by Bacteria

    E-Print Network [OSTI]

    Dove, Patricia M.

    1529-6466/03/0054-0004$05.00 Biologically Induced Mineralization by Bacteria Richard B. Frankel 50011 U.S.A. INTRODUCTION Bacteria are small, prokaryotic, microorganisms that are ubiquitous in surface) in the biological taxonomic hierarchy, the Bacteria and the Archaea. They exhibit remarkable diversity both

  9. Immunology Taught by Bacteria

    E-Print Network [OSTI]

    Vance, Russell E.

    2010-01-01

    purified PAMPs or killed bacteria. Cytosolic RNA sensors do2 Immunology Taught by Bacteria Russell E. Vance Received:multiple pathogenic bacteria. Conclusion Thus, immunology

  10. Engineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms

    SciTech Connect (OSTI)

    James C. Liao

    2012-05-22

    This project is a collaboration with F. R. Tabita of Ohio State. Our major goal is to understand the factors and regulatory mechanisms that influence hydrogen production. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Our part of the project was to develop a modeling technique to investigate the metabolic network in connection to hydrogen production and regulation. Organisms must balance the pathways that generate and consume reducing power in order to maintain redox homeostasis to achieve growth. Maintaining this homeostasis in the nonsulfur purple photosynthetic bacteria is a complex feat with many avenues that can lead to balance, as these organisms possess versatile metabolic capabilities including anoxygenic photosynthesis, aerobic or anaerobic respiration, and fermentation. Growth is achieved by using H{sub 2} as an electron donor and CO{sub 2} as a carbon source during photoautotrophic and chemoautotrophic growth, where CO{sub 2} is fixed via the Calvin-Benson-Bassham (CBB) cycle. Photoheterotrophic growth can also occur when alternative organic carbon compounds are utilized as both the carbon source and electron donor. Regardless of the growth mode, excess reducing equivalents generated as a result of oxidative processes, must be transferred to terminal electron acceptors, thus insuring that redox homeostasis is maintained in the cell. Possible terminal acceptors include O{sub 2}, CO{sub 2}, organic carbon, or various oxyanions. Cells possess regulatory mechanisms to balance the activity of the pathways which supply energy, such as photosynthesis, and those that consume energy, such as CO{sub 2} assimilation or N{sub 2} fixation. The major route for CO{sub 2} assimilation is the CBB reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.

  11. Leachability of salmonella and fecal pollution indicator bacteria through soil 

    E-Print Network [OSTI]

    Fehrmann, Robert Clinton

    1977-01-01

    of Department (Member) / /. ' Member) August 1977 74M3- ABSTRACT Leachability of Salmonella and Fecal Pollution Indicator Bacteria through Soil. (August 1977) Robert Clinton Fehrmann, B. S. , Texas AM University Chairman of Advisory Committee: Dr... microorganisms to be leached through soil, columns :ere filled with different soils and inoculs. ted with suspensions of fecal bacteria. Dif er ences in bacterial movement within a particular sni I, and bacterial movement between different types of soils...

  12. Cellulase producing microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1997-12-30

    Bacteria which produce large amounts of cellulase--containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualifies for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  13. Cellulase producing microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1997-01-01

    Bacteria which produce large amounts of cellulase--containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualifies for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  14. Contribution of microorganisms to corrosion

    SciTech Connect (OSTI)

    Thorp, K.E.G.; Crasto, A.S. [Univ. of Dayton Research Inst., OH (United States); Gu, J.D.; Mitchell, R. [Harvard Univ., Cambridge, MA (United States). Div. of Applied Sciences

    1997-08-01

    Current metal primers utilized by the US Air Force contain chromates to inhibit corrosion of the underlying metal. These chromates are both highly toxic and carcinogenic and pose a severe health risk to personnel involved in their application, stripping and disposal. Environmentally-friendly primers with chromate replacements have historically performed poorly with respect to corrosion inhibition. The purpose of this study was to investigate the interaction of chromates with microorganisms in an environment not traditionally associated with biologically-enhanced corrosion to determine if corrosion inhibition by a chromate pigment is, in part, through its action as a biocide. Inoculation of panels which had been coated with a nonchromated primer prior to salt fog exposure and storage in humid conditions resulted in a significant growth of filiform corrosion around a scribe mark. The presence of chromate in the primer severely limited the formation of this corrosion. Likewise, in the absence of the inoculation procedure, the extent of corrosion was strongly diminished. These results suggest that the chromate may be acting as a biocide to limit corrosion which is enhanced by the presence of biological activity.

  15. Bacteria isolated from amoebae/bacteria consortium

    DOE Patents [OSTI]

    Tyndall, R.L.

    1995-05-30

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  16. Bacteria isolated from amoebae/bacteria consortium

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1995-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  17. Variable carbon isotope fractionation expressed by aerobic CH4-oxidizing bacteria

    E-Print Network [OSTI]

    Chu, Kung-Hui "Bella"

    in biomass carbon isotopes is primarily due to differences in the fraction- ation effect at the formaldehyde in the production and consumption of CH4 oc- cur (e.g., Bergamaschi, 1997; Conrad et al., 1999; Avery and Martens

  18. Bacteria TMDL Projects 

    E-Print Network [OSTI]

    Wythe, Kathy

    2007-01-01

    stream_source_info Bacteria TMDL projects.pdf.txt stream_content_type text/plain stream_size 2550 Content-Encoding ISO-8859-1 stream_name Bacteria TMDL projects.pdf.txt Content-Type text/plain; charset=ISO-8859-1 tx H2O... of the projects are listed below. ? Peach CreekWater Quality Improvement Project ? Monitoring and Educational Programs Focused on Bacteria and Nutrient Runoff on Dairy Operations in the LeonWatershed ? Development of the Plum CreekWPP ? Impact of Proper...

  19. Bacteria in shear flow

    E-Print Network [OSTI]

    Marcos, Ph.D. Massachusetts Institute of Technology

    2011-01-01

    Bacteria are ubiquitous and play a critical role in many contexts. Their environment is nearly always dynamic due to the prevalence of fluid flow: creeping flow in soil, highly sheared flow in bodily conduits, and turbulent ...

  20. Quantification of the Antimicrobial Substances Produced by Lactic Acid Bacteria used as an Intervention to Inhibit Escherichia coli O157:H7 and Salmonella in vitro and on Fresh Spinach (Spinacia oleracea) 

    E-Print Network [OSTI]

    Calix Lara, Thelma

    2012-02-14

    The metabolic activity of bacterial microorganisms may influence the growth and metabolic activities of other microbes that are present in any specific niche. Lactic acid bacteria (LAB) are antagonistic to some microbial ...

  1. Electrosynthesis of Organic Compounds from Carbon Dioxide Is Catalyzed by a Diversity of Acetogenic Microorganisms

    SciTech Connect (OSTI)

    Nevin, KP; Hensley, SA; Franks, AE; Summers, ZM; Ou, JH; Woodard, TL; Snoeyenbos-West, OL; Lovley, DR

    2011-04-20

    Microbial electrosynthesis, a process in which microorganisms use electrons derived from electrodes to reduce carbon dioxide to multicarbon, extracellular organic compounds, is a potential strategy for capturing electrical energy in carbon-carbon bonds of readily stored and easily distributed products, such as transportation fuels. To date, only one organism, the acetogen Sporomusa ovata, has been shown to be capable of electrosynthesis. The purpose of this study was to determine if a wider range of microorganisms is capable of this process. Several other acetogenic bacteria, including two other Sporomusa species, Clostridium ljungdahlii, Clostridium aceticum, and Moorella thermoacetica, consumed current with the production of organic acids. In general acetate was the primary product, but 2-oxobutyrate and formate also were formed, with 2-oxobutyrate being the predominant identified product of electrosynthesis by C. aceticum. S. sphaeroides, C. ljungdahlii, and M. thermoacetica had high (> 80%) efficiencies of electrons consumed and recovered in identified products. The acetogen Acetobacterium woodii was unable to consume current. These results expand the known range of microorganisms capable of electrosynthesis, providing multiple options for the further optimization of this process.

  2. Aerobic Glycolysis: Meeting the Metabolic Requirements of Cell Proliferation

    E-Print Network [OSTI]

    Vander Heiden, Matthew G.

    Warburg's observation that cancer cells exhibit a high rate of glycolysis even in the presence of oxygen (aerobic glycolysis) sparked debate over the role of glycolysis in normal and cancer cells. Although it has been ...

  3. Apparatus and method for the desulfurization of petroleum by bacteria

    DOE Patents [OSTI]

    Lizama, Hector M. (Knoxville, TN); Scott, Timothy C. (Knoxville, TN); Scott, Charles D. (Oak Ridge, TN)

    1995-01-01

    A method for treating petroleum with anaerobic microorganisms acting as biocatalysts that can remove sulfur atoms from hydrocarbon molecules, under anaerobic conditions, and then convert the sulfur atoms to hydrogen sulfide. The microorganisms utilized are from the family known as the "Sulfate Reducing Bacteria." These bacteria generate metabolic energy from the oxidation of organic compounds, but use oxidized forms of sulfur as an electron acceptor. Because the biocatalyst is present in the form of bacteria in an aqueous suspension, whereas the reacting substrate consists of hydrocarbon molecules in an organic phase, the actual desulfurization reaction takes place at the aqueous-organic interphase. To ensure adequate interfacial contacting and mass transfer, a biphasic electrostatic bioreactor system is utilized. The bioreactor is utilized to disperse and recoalesce a biocatalyst contained in the aqueous liquid phase into the organic liquid phase containing the sulfur. High-intensity electrical fields rupture the aqueous drops into a plurality of microdroplets and induce continuous coalescence and redispersion as the microdroplets travel through the organic phase, thus increasing surface area. As the aqueous microdroplets progress through the organic phase, the biocatalyst then reacts with the sulfur to produce hydrogen sulfide which is then removed from the bioreactor. The organic liquid, now free of the sulfur, is ready for immediate use or further processing.

  4. Apparatus and method for the desulfurization of petroleum by bacteria

    DOE Patents [OSTI]

    Lizama, H.M.; Scott, T.C.; Scott, C.D.

    1995-10-17

    A method is described for treating petroleum with anaerobic microorganisms acting as biocatalysts that can remove sulfur atoms from hydrocarbon molecules, under anaerobic conditions, and then convert the sulfur atoms to hydrogen sulfide. The microorganisms utilized are from the family known as the ``Sulfate Reducing Bacteria``. These bacteria generate metabolic energy from the oxidation of organic compounds, but use oxidized forms of sulfur as an electron acceptor. Because the biocatalyst is present in the form of bacteria in an aqueous suspension, whereas the reacting substrate consists of hydrocarbon molecules in an organic phase, the actual desulfurization reaction takes place at the aqueous-organic interphase. To ensure adequate interfacial contacting and mass transfer, a biphasic electrostatic bioreactor system is utilized. The bioreactor is utilized to disperse and recoalesce a biocatalyst contained in the aqueous liquid phase into the organic liquid phase containing the sulfur. High-intensity electrical fields rupture the aqueous drops into a plurality of microdroplets and induce continuous coalescence and redispersion as the microdroplets travel through the organic phase, thus increasing surface area. As the aqueous microdroplets progress through the organic phase, the biocatalyst then reacts with the sulfur to produce hydrogen sulfide which is then removed from the bioreactor. The organic liquid, now free of the sulfur, is ready for immediate use or further processing. 5 figs.

  5. Culture of Bacteria 

    E-Print Network [OSTI]

    Unknown

    2011-08-17

    site located in the lungs of an animal model, thereby enabling detection of fluorescent bacteria during the early stages of infection. In this thesis, I present a contact probe fiber bundle fluorescence micro-endoscope with a range of LED based...

  6. Bioprocessing of lignite coals using reductive microorganisms

    SciTech Connect (OSTI)

    Crawford, D.L.

    1992-03-29

    In order to convert lignite coals into liquid fuels, gases or chemical feedstock, the macromolecular structure of the coal must be broken down into low molecular weight fractions prior to further modification. Our research focused on this aspect of coal bioprocessing. We isolated, characterized and studied the lignite coal-depolymerizing organisms Streptomyces viridosporus T7A, Pseudomonas sp. DLC-62, unidentified bacterial strain DLC-BB2 and Gram-positive Bacillus megaterium strain DLC-21. In this research we showed that these bacteria are able to solubilize and depolymerize lignite coals using a combination of biological mechanisms including the excretion of coal solublizing basic chemical metabolites and extracellular coal depolymerizing enzymes.

  7. Non-indigenous microorganisms in the Antarctic: assessing the risks

    E-Print Network [OSTI]

    Vincent, Warwick F.

    Non-indigenous microorganisms in the Antarctic: assessing the risks Don A. Cowan1 , Steven L. Chown wastes at these sites, little has been done to prevent the introduction of non-indigenous microorganisms largely restricted to the impacts of human and animal pathogens (including viruses) [7,8,13] and organisms

  8. Self-engineering capabilities of bacteria

    E-Print Network [OSTI]

    Ben-Jacob, Eshel; Levine, Herbert

    2006-01-01

    Hellingwerf, K. J. 2005 Bacteria observations: a rudimentaryCommunication among oral bacteria. Microbiol. Mol. Biol.A. & Dworkin, M. 1997 Bacteria as multicellular organisms.

  9. Genomic potential for polysaccharide deconstruction in bacteria

    E-Print Network [OSTI]

    Berlemont, R; Martiny, AC; Martiny, AC

    2015-01-01

    Identification of cellulolytic bacteria in soil by stablepotential cellulases in bacteria. Appl Environ Microbiol 79:chitin catabolism in marine bacteria. Biochim Biophys Acta

  10. Phylogenetic Distribution of Potential Cellulases in Bacteria

    E-Print Network [OSTI]

    Berlemont, R.; Martiny, A. C

    2012-01-01

    cellulose production in bacteria. Res. Microbiol. 153:205–carbohydrate metabo- lism in bacteria. Microbiol. Mol. Biol.2006. Interac- tions of bacteria and fungi on decomposing

  11. STORMWATER MANAGEMENT MEASURES AND FECAL INDICATOR BACTERIA

    E-Print Network [OSTI]

    STORMWATER MANAGEMENT MEASURES AND FECAL INDICATOR BACTERIA BY ROBERT A. WILDEY BA, New College............................................................................................................. 1 Regulatory Limits for Indicator Bacteria................................................................ 2 Indicator Bacteria in the Environment

  12. News and Research Good Bacteria

    E-Print Network [OSTI]

    West, Stuart

    News and Research Good Bacteria Part 2 Article 13 Click here for Probiotics Basics Cooperation Is A No-brainer For Symbiotic Bacteria 9-4-2003 Humans may learn cooperation in kindergarten, but what about bacteria, whose behavior is preprogrammed by their DNA? Some legume plants, which rely

  13. The Resolution of Important Pharmaceutical Building Blocks by Palladium-Catalyzed Aerobic Oxidation of Secondary Alcohols

    E-Print Network [OSTI]

    Stoltz, Brian M.

    The Resolution of Important Pharmaceutical Building Blocks by Palladium-Catalyzed Aerobic Oxidation. Abstract: The palladium-catalyzed aerobic oxidative kinetic resolution of key pharmaceutical building resolution; oxidation; oxygen; palladium; pharmaceutical sub- stance As part of a general program initiated

  14. Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis

    E-Print Network [OSTI]

    Slavov, Nikolai

    Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting ...

  15. Strategies for the aerobic co-metabolism of chlorinated solvents CURRENT OPINION IN BIOTECHNOLOGY

    E-Print Network [OSTI]

    Semprini, Lewis

    Strategies for the aerobic co-metabolism of chlorinated solvents Semprini L CURRENT OPINION for aerobic co- metabolism of chlorinated solvents. Different co-metabolic substrates and different methods

  16. Potential of Diazorphic, Endophytic Bacteria Associated with...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Diazorphic, Endophytic Bacteria Associated with Sugarcane for Energycane Production Potential of Diazorphic, Endophytic Bacteria Associated with Sugarcane for Energycane...

  17. Clostridiumm ljungdahlii, an anaerobic ethanol and acetate producing microorganism

    DOE Patents [OSTI]

    Gaddy, James L. (Fayetteville, AR); Clausen, Edgar C. (Fayetteville, AR)

    1992-01-01

    A newly discovered microorganism was isolated in a biologically pure culture and designated Clostridium ljungdahlii, having the identifying characteristics of ATCC No. 49587. Cultured in an aqueous nutrient medium under anaerobic conditions, this microorganism is capable of producing ethanol and acetate from CO and H.sub.2 O and/or CO.sub.2 and H.sub.2 in synthesis gas. Under optimal growth conditions, the microorganism produces acetate in preference to ethanol. Conversely, under non-growth conditions, ethanol production is favored over acetate.

  18. Clostridiumm ljungdahlii, an anaerobic ethanol and acetate producing microorganism

    DOE Patents [OSTI]

    Gaddy, J.L.; Clausen, E.C.

    1992-12-22

    A newly discovered microorganism was isolated in a biologically pure culture and designated Clostridium ljungdahlii, having the identifying characteristics of ATCC No. 49587. Cultured in an aqueous nutrient medium under anaerobic conditions, this microorganism is capable of producing ethanol and acetate from CO and H[sub 2]O and/or CO[sub 2] and H[sub 2] in synthesis gas. Under optimal growth conditions, the microorganism produces acetate in preference to ethanol. Conversely, under non-growth conditions, ethanol production is favored over acetate. 3 figs.

  19. Biofuels from Solar Energy and Bacteria: Electrofuels Via Direct Electron Transfer from Electrodes to Microbes

    SciTech Connect (OSTI)

    2010-07-01

    Electrofuels Project: UMass is feeding renewable electricity to bacteria to provide the microorganisms with the energy they need to turn carbon dioxide (CO2) directly into liquid fuels. UMass’ energy-to-fuels conversion process is anticipated to be more efficient than current biofuels approaches in part because this process will leverage the high efficiency of photovoltaics to convert solar energy into electricity. UMass is using bacteria already known to produce biofuel from electric current and CO2 and working to increase the amount of electric current those microorganisms will accept and use for biofuels production. In collaboration with scientists at University of California, San Diego, the UMass team is also investigating the use of hydrogen sulfide as a source of energy to power biofuel production.

  20. Selective microorganism concentration using a dielectrophoresis-based microfabricated device

    E-Print Network [OSTI]

    Pucha?a, Katarzyna Anna

    2007-01-01

    Detection of pathogenic microorganisms is a significant challenge in medicine, environmental protection and biological threat safety because samples are often contaminated. This work presents a method of separating bacterial ...

  1. Electrical characterization of micro-organisms using microfabricated devices

    E-Print Network [OSTI]

    Bashir, Rashid

    . Kosari and G. Vasmatzis Mayo Clinic, Rochester, Minnesota 55905 A. Bhunia Department of Food Sciences by the micro-organisms when traversing through the pore. © 2002 American Vacuum Society. DOI: 10

  2. Microorganisms having enhanced tolerance to inhibitors and stress

    DOE Patents [OSTI]

    Brown, Steven D.; Yang, Shihui

    2014-07-29

    The present invention provides genetically modified strains of microorganisms that display enhanced tolerance to stress and/or inhibitors such as sodium acetate and vanillin. The enhanced tolerance can be achieved by increasing the expression of a protein of the Sm-like superfamily such as a bacterial Hfq protein and a fungal Sm or Lsm protein. Further, the present invention provides methods of producing alcohol from biomass materials by using the genetically modified microorganisms of the present invention.

  3. Microorganisms having enhanced resistance to acetate and methods of use

    DOE Patents [OSTI]

    Brown, Steven D; Yang, Shihui

    2014-10-21

    The present invention provides isolated or genetically modified strains of microorganisms that display enhanced resistance to acetate as a result of increased expression of a sodium proton antiporter. The present invention also provides methods for producing such microbial strains, as well as related promoter sequences and expression vectors. Further, the present invention provides methods of producing alcohol from biomass materials by using microorganisms with enhanced resistance to acetate.

  4. Can entropy save bacteria?

    E-Print Network [OSTI]

    Suckjoon Jun

    2008-08-29

    This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the organization of two athermal chains confined in a closed geometry characterized by two length scales (length and width). When applied to rod-shaped bacteria such as Escherichia coli, this phase diagram predicts that, despite strong confinement, duplicated chromosomes will demix, i.e., there exists a primordial physical driving force for chromosome segregation. The author discusses segregation of duplicating chromosomes using the concentric-shell model, which predicts that newly synthesized DNA will be found in the periphery of the chromosome during replication. In contrast to chromosomes, these results suggest that most plasmids will be randomly distributed inside the cell because of their small sizes. An active partitioning system is therefore required for accurate segregation of low-copy number plasmids. Implications of these results are also sketched, e.g., on the role of proteins, segregation mechanisms for bacteria of diverse shapes, cell cycle of an artificial cell, and evolution.

  5. Bioengineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms

    SciTech Connect (OSTI)

    Tabita, F. Robert [The Ohio State University] [The Ohio State University

    2013-07-30

    In this study, the Principal Investigator, F.R. Tabita has teemed up with J. C. Liao from UCLA. This project's main goal is to manipulate regulatory networks in phototrophic bacteria to affect and maximize the production of large amounts of hydrogen gas under conditions where wild-type organisms are constrained by inherent regulatory mechanisms from allowing this to occur. Unrestrained production of hydrogen has been achieved and this will allow for the potential utilization of waste materials as a feed stock to support hydrogen production. By further understanding the means by which regulatory networks interact, this study will seek to maximize the ability of currently available “unrestrained” organisms to produce hydrogen. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Moreover, due to their great metabolic versatility, such organisms highly regulate these processes in the cell and since virtually all such capabilities are dispensable, excellent experimental systems to study aspects of molecular control and biochemistry/physiology are available.

  6. Physical and Chemical Factors Influencing the Transport and Fate of Microorganisms in Soils With Preferential Flow

    E-Print Network [OSTI]

    Wang, Yusong

    2013-01-01

    water resources from pathogenic microorganisms and contaminants associated with the colloidal phase, and to optimize bioremediation

  7. Expansion of the Genomic Encyclopedia of Bacteria and Archaea

    SciTech Connect (OSTI)

    Rinke, Christian; Sczyrba, Alex; Malfatti, Stephanie; Lee, Janye; Cheng, Jan-Fang; Stepanauskas, Ramunas; Eisen, Jonathan A.; Hallam, Steven; Inskeep, William P.; Hedlund, Brian P.; Sievert, Stefan M.; Liu, Wen-Tso; Tsiamis, George; Hugenholtz, Philip; Woyke, Tanja

    2011-03-20

    To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed to systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

  8. Expansion of the Genomic Encyclopedia of Bacteria and Archaea

    SciTech Connect (OSTI)

    Rinke, Christian; Sczyrba, Alex; Malfatti, Stephanie; Lee, Janey; Cheng, Jan-Fang; Stepanauskas, Ramunas; Eisen, Jonathan A.; Hallam, Steven; Inskeep, William P.; Hedlund, Brian P.; Sievert, Stefan M.; Liu, Wen-Tso; Tsiamis, George; Hugenholtz, Philip; Woyke, Tanja

    2011-06-02

    To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed at systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99 percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

  9. Magnetic Microstructure of Magnetotactic Bacteria by

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Magnetic Microstructure of Magnetotactic Bacteria by Electron Holography Rafal E. Dunin microstructure of magnetite nanocrys- tals in magnetotactic bacteria. The magnetite crystals were all single). For example, magnetotactic bacteria contain magnetosomes, which are intracellular, ferri- magnetic crystals

  10. Deciphering Active Estrogen-Degrading Microorganisms in Bioreactors 

    E-Print Network [OSTI]

    Roh, Hyung Keun

    2010-10-12

    degraders (strains KC8 and ammonia-oxidizing bacteria (AOB)) and amoA gene (associated with ammonia oxidation) to total bacteria decreased as SRT increased in SBRs. These observations correspond to the decreasing percentages of 17 beta-estradiol biodegraded...

  11. TSSWCB Bacteria-Related Projects 

    E-Print Network [OSTI]

    Wythe, Kathy

    2007-01-01

    stream_source_info TSSWCB bacteria-related projects.pdf.txt stream_content_type text/plain stream_size 2550 Content-Encoding ISO-8859-1 stream_name TSSWCB bacteria-related projects.pdf.txt Content-Type text/plain; charset=ISO-8859... of the projects are listed below. ? Peach CreekWater Quality Improvement Project ? Monitoring and Educational Programs Focused on Bacteria and Nutrient Runoff on Dairy Operations in the LeonWatershed ? Development of the Plum CreekWPP ? Impact of Proper...

  12. Synthesis of poly-(P-aryleneethynylene)s in neat water under aerobic conditions

    DOE Patents [OSTI]

    Kang, Youn K; Deria, Pravas; Therien, Michael J

    2012-10-16

    Provided are ethyne synthons comprising boron and related methods. Also provided are related water-soluble arylethynylene polymers capable of being synthesized in neat water under aerobic conditions.

  13. Geobiology of marine magnetotactic bacteria

    E-Print Network [OSTI]

    Simmons, Sheri Lynn

    2006-01-01

    Magnetotactic bacteria (MTB) biomineralize intracellular membrane-bound crystals of magnetite (Fe3O4) or greigite (Fe3S4), and are abundant in the suboxic to anoxic zones of stratified marine environments worldwide. Their ...

  14. In Situ Survival of Genetically Engineered Microorganisms in a Tropical

    E-Print Network [OSTI]

    Hazen, Terry

    . Alvarez, G. M. Yumet, and C. L. Santiago Department of Biology, P.O. Box 23360, University of Puerto Rico, Rio Piedras, Puerto Rico 00931-3360 T. C. Hazen Savannah River Laboratory, Environmental Sciences microorganisms (GEMs) and their interactions with the environmental microbiota of a tropical river

  15. Effects of voluntary activity and genetic selection on aerobic capacity in house mice (Mus domesticus)

    E-Print Network [OSTI]

    Saltzman, Wendy

    Effects of voluntary activity and genetic selection on aerobic capacity in house mice (Mus of voluntary activity and genetic selection on aerobic capacity in house mice (Mus domesticus). J. Appl. Physiol. 84(1): 69­76, 1998.--An animal model was developed to study effects on components of exercise

  16. Use of Stable Isotopes in Forensic Analysis of Microorganisms

    SciTech Connect (OSTI)

    Kreuzer-Martin, Helen W.; Hegg, Eric L.

    2012-01-18

    The use of isotopic signatures for forensic analysis of biological materials is well-established, and the same general principles that apply to interpretation of stable isotope content of C, N, O, and H apply to the analysis of microorganisms. Heterotrophic microorganisms derive their isotopic content from their growth substrates, which are largely plant and animal products, and the water in their culture medium. Thus the isotope signatures of microbes are tied to their growth environment. The C, N, O, and H isotope ratios of spores have been demonstrated to constitute highly discriminating signatures for sample matching. They can rule out specific samples of media and/or water as possible production media, and can predict isotope ratio ranges of the culture media and water used to produce a given sample. These applications have been developed and tested through analyses of approximately 250 samples of Bacillus subtilis spores and over 500 samples of culture media, providing a strong statistical basis for data interpretation. A Bayesian statistical framework for integrating stable isotope data with other types of signatures derived from microorganisms has been able to characterize the culture medium used to produce spores of various Bacillus species, leveraging isotopic differences in different medium types and demonstrating the power of data integration for forensic investigations.

  17. ORIGINAL PAPER Characterization of multiple novel aerobic polychlorinated

    E-Print Network [OSTI]

    Craft, Christopher B.

    sites in Lagos, Nigeria were screened for the presence of chlorobiphenyl-degrading bacteria the strains readily utilized a broad spectrum of xenobiotics as sole sources of carbon and energy. Growth, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria e-mail: sadebusoye@yahoo.com S. A

  18. Structural conservation of chemotaxis machinery across Archaea and Bacteria

    E-Print Network [OSTI]

    Briegel, A; Ortega, DR; Huang, AN; Oikonomou, CM; Gunsalus, RP; Jensen, GJ

    2015-01-01

    J. (1966) Chemotaxis in Bacteria. Science 153: 708-716.gene transfer between bacteria and archaea. J Mol MicrobiolProtein Localization in Bacteria. J Bacteriol 183: 3261-

  19. High-throughput comparison of gene fitness among related bacteria

    E-Print Network [OSTI]

    2012-01-01

    5096–5108. 36. Macnab RM: How bacteria assemble. Annu Revgene fitness among related bacteria. BMC Genomics 2012 13:gene fitness among related bacteria Rocio Canals 1 , Xiao-

  20. S. aureus bacteria : a new target of serum calcification activity

    E-Print Network [OSTI]

    Dy, Diane Jazmin

    2009-01-01

    and Antibiotics in Gram-Positive Bacteria and Mycobacteria.If mineralization of live bacteria is possible, differentof mineralization of live bacteria as a leukocyte response

  1. Bacteria Associated With Colitis and Inflammatory Bowel Disease

    E-Print Network [OSTI]

    Ye, Jingxiao

    2009-01-01

    M. and J. M. Rhodes (2000). "Bacteria and inflammatory boweltwo different commensal bacteria." Gastroenterology 128(4):M. and J. M. Rhodes (2000). "Bacteria and inflammatory bowel

  2. Revisiting Modes of energy generation in sulfate reducing bacteria

    E-Print Network [OSTI]

    Joachimiak, Marcin

    2010-01-01

    generation in sulfate reducing bacteria 1. Lawrence BerkeleyAbstract Sulfate reducing bacteria (SRB) play an importantin the sulfate-reducing bacteria Desulfovibrio sp." FEMS

  3. Genomic analysis of high pressure adaptation in deep sea bacteria

    E-Print Network [OSTI]

    Stratton, Taylor Kristen

    2008-01-01

    of proteins in halophilic bacteria. J Mol Bacteriol. 327:Phylogenetic analysis of bacteria preserved in a permafrostof piezophilic bacteria isolated from intestinal contents of

  4. Re-engineering bacteria for ethanol production

    DOE Patents [OSTI]

    Yomano, Lorraine P; York, Sean W; Zhou, Shengde; Shanmugam, Keelnatham; Ingram, Lonnie O

    2014-05-06

    The invention provides recombinant bacteria, which comprise a full complement of heterologous ethanol production genes. Expression of the full complement of heterologous ethanol production genes causes the recombinant bacteria to produce ethanol as the primary fermentation product when grown in mineral salts medium, without the addition of complex nutrients. Methods for producing the recombinant bacteria and methods for producing ethanol using the recombinant bacteria are also disclosed.

  5. Microorganisms to Speed Production of Biofuels - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass map shines light on darkMicroorganisms to Speed Production of Biofuels Oak Ridge

  6. RESEARCH ARTICLE Functional Characterization of Bacteria

    E-Print Network [OSTI]

    Desai, Michael

    resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers bacteria conferred lower levels of resis- tance against clinically relevant antibiotics than resistance) Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance

  7. Drosophila lifespan enhancement by exogenous bacteria

    E-Print Network [OSTI]

    Seroude, Laurent

    Drosophila lifespan enhancement by exogenous bacteria Ted Brummel*, Alisa Ching*, Laurent Seroude with customary procedure. The experiments revealed that the presence of bacteria during the first week of adult life can enhance lifespan, despite unchanged food intake. Later in life, the presence of bacteria can

  8. MicroReview Bistability in bacteria

    E-Print Network [OSTI]

    Mekalanos, John

    MicroReview Bistability in bacteria David Dubnau1 * and Richard Losick2,3 * 1 Public Health 94720, USA. Summary Gene expression in bacteria is traditionally studied from the average behaviour expression in individual cells reveals, however, that populations of genetically identical bacteria

  9. Luminal Bacteria Recruit CD103+ Dendritic Cells

    E-Print Network [OSTI]

    Immunity Article Luminal Bacteria Recruit CD103+ Dendritic Cells into the Intestinal Epithelium@weizmann.ac.il http://dx.doi.org/10.1016/j.immuni.2013.01.009 SUMMARY CD103+ dendritic cells (DCs) carry bacteria from bacteria or presenting bacterial antigens in mesen- tery lymph nodes. We used 2-photon microscopy in live

  10. Mechanism of Transcriptional Bursting in Bacteria

    E-Print Network [OSTI]

    Li, Tiejun

    Mechanism of Transcriptional Bursting in Bacteria Shasha Chong,1,5 Chongyi Chen,1,2,5 Hao Ge,3 phenomenon has not been understood. Here, we present the mechanism in bacteria. We developed a high. Together, these findings prove that transcriptional bursting of highly ex- pressed genes in bacteria

  11. Metagenomic and Cultivation-Based Analysis of Novel Microorganisms and Functions in Metal-Contaminated Environments

    E-Print Network [OSTI]

    Yelton, Alexis Pepper

    2012-01-01

    of copper resistance and accumulation in bacteria. FEMSresistance in addition to energy conservation. Here we report the isolation of a bacteria

  12. Aerobic capacities in the heart, kidneys, and splanchnic organs of harbor seals: adaptations to diving hypoxia 

    E-Print Network [OSTI]

    Fuson, Amanda Lynn

    2002-01-01

    Pinnipeds (seals and sea lions) have an elevated mitochondrial volume density [Vv(mt)] and citrate synthase (CS) and ?-hydroxyacyl-CoA dehydrogenase (HOAD) activity in their swimming muscles, to maintain aerobic metabolism, as an adaptation...

  13. Effects of remediation amendments on vadose zone microorganisms

    SciTech Connect (OSTI)

    Miller, Hannah M.; Tilton, Fred A.

    2012-08-10

    Surfactant-based foam delivery technology has been studied to remediate Hanford 200 area deep vadose zone sediment. However, the surfactants and remediation amendments have an unknown effect on indigenous subsurface microorganisms. Microbial populations are important factors to consider in remediation efforts due to their potential to alter soil geochemistry. This project focuses on measuring microbial metabolic responses to remediation amendments in batch and column studies using Deep Vadose Zone Sediments. Initial studies of the microbes from Hanford 200 area deep vadose zone sediment showed surfactants sodium dodecyl sulfate (SDS) and cocamidopropyl betaine (CAPB) and remediation amendment calcium polysulfide (CPS) had no affect on microbial growth using BiologTM Ecoplates. To move towards a more realistic field analog, soil columns were packed with Hanford 200 Area sediment. Once microbial growth in the column was verified by observing growth of the effluent solution on tryptic soy agar plates, remedial surfactants were injected into the columns, and the resulting metabolic diversity was measured. Results suggest surfactant sodium dodecyl sulfate (SDS) stimulates microbial growth. The soil columns were also visualized using X-ray microtomography to inspect soil packing and possibly probe for evidence of biofilms. Overall, BiologTM Ecoplates provide a rapid assay to predict effects of remediation amendments on Hanford 200 area deep vadose zone microorganisms.

  14. Quantitative and qualitative evaluation of the aerobic and facultative bacterial flora of voided canine urine 

    E-Print Network [OSTI]

    Biggerstaff, Jane

    1978-01-01

    QUANTITATIVE AND QUALITATIVE EVALUATION OF THE AEROBIC AND FACULTATIVE BACTERIAL FLORA OF VOIDED CANINE URINE A Thesis by JANE BIGGERSTAFF Submitted to the Graduate College of Texas ARM University in partial fulfillment of the requirements... and content by Chairman of gs}mmittoe) (Head of Department) (Nember (Nember) August 1978 443163 ABSTRACT Quantitative and Qualitative Evaluation of the Aerobic and Facultative Bacterial Flora of Voided Canine Urine. (August, 1978) Jane Biggerstaff, B...

  15. Protein signaling via type III secretion pathways in phytopathogenic bacteria

    E-Print Network [OSTI]

    109 Protein signaling via type III secretion pathways in phytopathogenic bacteria Mary Beth Mudgett secretion pathway has revealed new mechanisms by which phytopathogenic bacteria infect plants are continually exposed to a number of potentially pathogenic bacteria. Phytopathogenic bacteria, in general

  16. Correlative Electron and Fluorescence Microscopy of Magnetotactic Bacteria in Liquid: Toward In Vivo Imaging

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Woehl, Taylor J.; Kashyap, Sanjay; Firlar, Emre; Perez-Gonzalez, Teresa; Faivre, Damien; Trubitsyn, Denis; Bazylinski, Dennis A.; Prozorov, Tanya

    2014-10-31

    Magnetotactic bacteria biomineralize ordered chains of uniform, membrane-bound magnetite or greigite nanocrystals that exhibit nearly perfect crystal structures and species-specific morphologies. Transmission electron microscopy (TEM) is a critical technique for providing information regarding the organization of cellular and magnetite structures in these microorganisms. However, conventional TEM can only be used to image air-dried or vitrified bacteria removed from their natural environment. Here we present a correlative scanning TEM (STEM) and fluorescence microscopy technique for imaging viable cells of Magnetospirillum magneticum strain AMB-1 in liquid using an in situ fluid cell TEM holder. Fluorescently labeled cells were immobilized on microchip windowmore »surfaces and visualized in a fluid cell with STEM, followed by correlative fluorescence imaging to verify their membrane integrity. Notably, the post-STEM fluorescence imaging indicated that the bacterial cell wall membrane did not sustain radiation damage during STEM imaging at low electron dose conditions. We investigated the effects of radiation damage and sample preparation on the bacteria viability and found that approximately 50% of the bacterial membranes remained intact after an hour in the fluid cell, decreasing to ~30% after two hours. These results represent a first step toward in vivo studies of magnetite biomineralization in magnetotactic bacteria.« less

  17. Correlative Electron and Fluorescence Microscopy of Magnetotactic Bacteria in Liquid: Toward In Vivo Imaging

    SciTech Connect (OSTI)

    Woehl, Taylor J.; Kashyap, Sanjay; Firlar, Emre; Perez-Gonzalez, Teresa; Faivre, Damien; Trubitsyn, Denis; Bazylinski, Dennis A.; Prozorov, Tanya

    2014-10-31

    Magnetotactic bacteria biomineralize ordered chains of uniform, membrane-bound magnetite or greigite nanocrystals that exhibit nearly perfect crystal structures and species-specific morphologies. Transmission electron microscopy (TEM) is a critical technique for providing information regarding the organization of cellular and magnetite structures in these microorganisms. However, conventional TEM can only be used to image air-dried or vitrified bacteria removed from their natural environment. Here we present a correlative scanning TEM (STEM) and fluorescence microscopy technique for imaging viable cells of Magnetospirillum magneticum strain AMB-1 in liquid using an in situ fluid cell TEM holder. Fluorescently labeled cells were immobilized on microchip window surfaces and visualized in a fluid cell with STEM, followed by correlative fluorescence imaging to verify their membrane integrity. Notably, the post-STEM fluorescence imaging indicated that the bacterial cell wall membrane did not sustain radiation damage during STEM imaging at low electron dose conditions. We investigated the effects of radiation damage and sample preparation on the bacteria viability and found that approximately 50% of the bacterial membranes remained intact after an hour in the fluid cell, decreasing to ~30% after two hours. These results represent a first step toward in vivo studies of magnetite biomineralization in magnetotactic bacteria.

  18. Organic acid-tolerant microorganisms and uses thereof for producing organic acids

    DOE Patents [OSTI]

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-05-06

    Organic acid-tolerant microorganisms and methods of using same. The organic acid-tolerant microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid (3HP), acrylic acid, and propionic acid. Further modifications to the microorganisms such as increasing expression of malonyl-CoA reductase and/or acetyl-CoA carboxylase provide or increase the ability of the microorganisms to produce 3HP. Methods of generating an organic acid with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers include replacing acsA or homologs thereof in cells with genes of interest and selecting for the cells comprising the genes of interest with amounts of organic acids effective to inhibit growth of cells harboring acsA or the homologs.

  19. Methods for identifying an essential gene in a prokaryotic microorganism

    DOE Patents [OSTI]

    Shizuya, Hiroaki

    2006-01-31

    Methods are provided for the rapid identification of essential or conditionally essential DNA segments in any species of haploid cell (one copy chromosome per cell) that is capable of being transformed by artificial means and is capable of undergoing DNA recombination. This system offers an enhanced means of identifying essential function genes in diploid pathogens, such as gram-negative and gram-positive bacteria.

  20. Sensory Transduction in Microorganisms 2008 Gordon Research Conference (January 2008)

    SciTech Connect (OSTI)

    Ann M. Stock

    2009-04-08

    Research into the mechanisms involved in the sensing and responses of microorganisms to changes in their environments is currently very active in a large number of laboratories worldwide. An increasingly wide range of prokaryotic and eukaryotic species are being studied with regard to their sensing of diverse chemical and physical stimuli, including nutrients, toxins, intercellular signaling molecules, redox indicators, light, pressure, magnetic fields, and surface contact, leading to adaptive responses affecting motile behavior, gene expression and/or development. The ease of manipulation of microorganisms has facilitated application of a broad range of techniques that have provided comprehensive descriptions of cellular behavior and its underlying molecular mechanisms. Systems and their molecular components have been probed at levels ranging from the whole organism down to atomic resolution using behavioral analyses; electrophysiology; genetics; molecular biology; biochemical and biophysical characterization; structural biology; single molecule, fluorescence and cryo-electron microscopy; computational modeling; bioinformatics and genomic analyses. Several model systems such as bacterial chemotaxis and motility, fruiting body formation in Myxococcus xanthus, and motility and development in Dictyostelium discoideum have traditionally been a focus of this meeting. By providing a basis for assessment of similarities and differences in mechanisms, understanding of these pathways has advanced the study of many other microbial sensing systems. This conference aims to bring together researchers investigating different prokaryotic and eukaryotic microbial systems using diverse approaches to compare data, share methodologies and ideas, and seek to understand the fundamental principles underlying sensory responses. Topic areas include: (1) Receptor Sensing and Signaling; (2) Intracellular Signaling (two-component, c-di-GMP, c-AMP, etc.); (3) Intracellular Localization and the Cytoskeleton; (4) Motors and Motility; (5) Differentiation and Development; (6) Host/Pathogen and Host/Symbiont Interactions; (7) Intercellular Communication; (8) Microbes and the Environment; and (9) Modeling Signaling Pathways.

  1. Transformation of gram positive bacteria by sonoporation

    DOE Patents [OSTI]

    Yang, Yunfeng; Li, Yongchao

    2014-03-11

    The present invention provides a sonoporation-based method that can be universally applied for delivery of compounds into Gram positive bacteria. Gram positive bacteria which can be transformed by sonoporation include, for example, Bacillus, Streptococcus, Acetobacterium, and Clostridium. Compounds which can be delivered into Gram positive bacteria via sonoporation include nucleic acids (DNA or RNA), proteins, lipids, carbohydrates, viruses, small organic and inorganic molecules, and nano-particles.

  2. Managing Bacteria Pollution in Texas Waters 

    E-Print Network [OSTI]

    Wythe, Kathy

    2007-01-01

    Wythe tx H2O | pg. 2 BACTERIA MANAGING tx H2O | pg. 3 IN TEXAS WATERS POLLUTION Managing Bacteria Pollution in Texas Waters tx H2O | pg. 4 W ith 310 water bodies in Texas failing to meetwater quality standards because of bacteria,managing bacteria... pollution is commanding the attention of water agencies, researchers and stake- holders across Texas. These water bodies are listed in the 2006 Texas Water Quality Inventory and 303(d) List for failing to meet the standards designed to protect...

  3. Spectroscopic diagnostics for bacteria in biologic sample

    DOE Patents [OSTI]

    El-Sayed, Mostafa A. (Atlanta, GA); El-Sayed, Ivan H. (Somerville, MA)

    2002-01-01

    A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

  4. Aerobic treatability of waste effluent from the leather finishing industry. Master's thesis

    SciTech Connect (OSTI)

    Vinger, J.A.

    1993-12-01

    The Seton Company supplies finished leather products exclusively for the automotive industry. In the process of finishing leather, two types of wastewaters are generated. The majority of the wastewater is composed of water-based paint residuals while the remainder is composed of solvent-based coating residuals. Aerobic treatability studies were conducted using water-based and solvent-based waste recirculatory waters from the Seton Company's Saxton, Pennsylvania processing plant. The specific objective was to determine the potential for using aerobic biological processes to biodegrade the industry's wastes and determine the potential for joint treatment at the local publicly owned treatment works (POTW). This study was accomplished in two phases. Phase I was conducted during the Spring Semester 1993 and consisted of aerobic respirometer tests of the raw wastes and mass balance analysis. The results of Phase I were published in a report to the Seton Company as Environmental Resources Research Institute project number 92C.II40R-1. Phase II was conducted during the Summer Semester 1993 and consisted of bench-scale reactor tests and additional aerobic respirometer tests. The aerobic respirometer batch tests and bench-scale reactor tests were used to assess the treatability of solvent-based and water-based wastewaters and determine the degree of biodegradability of the wastewaters. Mass balance calculations were made using measured characteristics.

  5. RESEARCH ARTICLE Adaptive Resistance in Bacteria Requires

    E-Print Network [OSTI]

    Cluzel, Philippe

    RESEARCH ARTICLE Adaptive Resistance in Bacteria Requires Epigenetic Inheritance, Genetic Noise Resistance in Bacteria Requires Epigenetic Inheritance, Genetic Noise, and Cost of Efflux Pumps. PLoS ONE 10, Cambridge, Massachusetts, United States of America * max@fis.unam.mx Abstract Adaptive resistance emerges

  6. Method of dispersing a hydrocarbon using bacteria

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1996-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  7. Method of dispersing a hydrocarbon using bacteria

    DOE Patents [OSTI]

    Tyndall, R.L.

    1996-09-24

    A new protozoan derived microbial consortia and method for their isolation are provided. The isolated consortia and bacteria are useful for treating wastes such as trichloroethylene and trinitrotoluene. The isolated consortia, bacteria, and dispersants are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  8. Chemotactic selection of pollutant degrading soil bacteria

    DOE Patents [OSTI]

    Hazen, T.C.

    1991-03-04

    A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  9. Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

    SciTech Connect (OSTI)

    Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

    2013-09-28

    Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and the formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studie

  10. Metabolic Engineering and Modeling of Metabolic Pathways to Improve Hydrogen Production by Photosynthetic Bacteria

    SciTech Connect (OSTI)

    Jiao, Y.; Navid, A.

    2014-12-19

    Rising energy demands and the imperative to reduce carbon dioxide (CO2) emissions are driving research on biofuels development. Hydrogen gas (H2) is one of the most promising biofuels and is seen as a future energy carrier by virtue of the fact that 1) it is renewable, 2) does not evolve the “greenhouse gas” CO2 in combustion, 3) liberates large amounts of energy per unit weight in combustion (having about 3 times the energy content of gasoline), and 4) is easily converted to electricity by fuel cells. Among the various bioenergy strategies, environmental groups and others say that the concept of the direct manufacture of alternative fuels, such as H2, by photosynthetic organisms is the only biofuel alternative without significant negative criticism [1]. Biological H2 production by photosynthetic microorganisms requires the use of a simple solar reactor such as a transparent closed box, with low energy requirements, and is considered as an attractive system to develop as a biocatalyst for H2 production [2]. Various purple bacteria including Rhodopseudomonas palustris, can utilize organic substrates as electron donors to produce H2 at the expense of solar energy. Because of the elimination of energy cost used for H2O oxidation and the prevention of the production of O2 that inhibits the H2-producing enzymes, the efficiency of light energy conversion to H2 by anoxygenic photosynthetic bacteria is in principle much higher than that by green algae or cyanobacteria, and is regarded as one of the most promising cultures for biological H2 production [3]. Here implemented a simple and relatively straightforward strategy for hydrogen production by photosynthetic microorganisms using sunlight, sulfur- or iron-based inorganic substrates, and CO2 as the feedstock. Carefully selected microorganisms with bioengineered beneficial traits act as the biocatalysts of the process designed to both enhance the system efficiency of CO2 fixation and the net hydrogen production rate. Additionally we applied metabolic engineering approaches guided by computational modeling for the chosen model microorganisms to enable efficient hydrogen production.

  11. Reduction and Immobilization of Radionuclides and Toxic Metal Ions Using Combined Zero Valent Iron and Anaerobic Bacteria

    SciTech Connect (OSTI)

    Lenly J. Weathers; Lynn E. Katz

    2002-05-29

    The use of zero valent iron, permeable reactive barriers (PRBs) for groundwater remediation continues to increase. AN exciting variation of this technology involves introducing anaerobic bacteria into these barriers so that both biological and abiotic pollutant removal processes are functional. This work evaluated the hypothesis that a system combining a mixed culture of sulfate reducing bacteria (SRB) with zero valent iron would have a greater cr(VI) removal efficiency and a greater total Cr(VI) removal capacity than a zero valent iron system without the microorganisms. Hence, the overall goal of this research was to compare the performance of these types of systems with regard to their Cr(VI) removal efficiency and total Cr(VI) removal capacity. Both batch and continuous flow reactor systems were evaluated.

  12. Evidence of aerobic utilization of di-ortho-substituted trichlorobiphenyls as growth substrates by

    E-Print Network [OSTI]

    Craft, Christopher B.

    and Olukayode O. Amund1 1 Department of Botany and Microbiology, University of Lagos, Lagos, Nigeria. 2 and energy source has never been demonstrated for any natural or engineered microorganisms. Such isolates may

  13. Magnetic Bacteria: A Future in Industry and Medicine

    E-Print Network [OSTI]

    Low, Emily

    2011-01-01

    http://www.eoearth.org/article/Bacteria? topic=49480 http://day be able to use these bacteria and magnetosomes on largeUsing Magnetotactic Bacteria. IEEE Transactions on Magnetics

  14. Bacteria-Phytoplankton Competition Bacterial immobilization or remineralization of N.

    E-Print Network [OSTI]

    Vallino, Joseph J.

    Bacteria-Phytoplankton Competition Overview: · Bacterial immobilization or remineralization of N. · Competition between bacteria and phytoplankton for DIN. · Experimentally examine how dissolved organic carbon (DOC) affects the competition between bacteria and phytoplankton for limiting nutrients. · Demonstrate

  15. Assessing the transport and fate of bioengineered microorganisms in the environment

    SciTech Connect (OSTI)

    Barnthouse, L.W.; Palumbo, A.V.

    1985-01-01

    We review the methods currently available for quantifying the transport and fate of microbes in atmospheric and aqueous media and assess their adequacy for purposes of risk assessment. We review the literature on transport and fate of microorganisms, including studies of: (1) pathways of migration, (2) the survival of microorganisms during transport and fate. In addition, we review the transport and fate models that have been used in environmental risk assessments for radionuclides and toxic chemicals and evaluate their applicability to the problem of assessing environmental risks of bioengineered microorganisms.

  16. Assessing the Efficacy of the Aerobic Methanotrophic Biofilter in Methane Hydrate Environments

    SciTech Connect (OSTI)

    Valentine, David

    2012-09-30

    In October 2008 the University of California at Santa Barbara (UCSB) initiated investigations of water column methane oxidation in methane hydrate environments, through a project funded by the National Energy Technology Laboratory (NETL) entitled: assessing the efficacy of the aerobic methanotrophic biofilter in methane hydrate environments. This Final Report describes the scientific advances and discoveries made under this award as well as the importance of these discoveries in the broader context of the research area. Benthic microbial mats inhabit the sea floor in areas where reduced chemicals such as sulfide reach the more oxidizing water that overlies the sediment. We set out to investigate the role that methanotrophs play in such mats at locations where methane reaches the sea floor along with sulfide. Mats were sampled from several seep environments and multiple sets were grown in-situ at a hydrocarbon seep in the Santa Barbara Basin. Mats grown in-situ were returned to the laboratory and used to perform stable isotope probing experiments in which they were treated with 13C-enriched methane. The microbial community was analyzed, demonstrating that three or more microbial groups became enriched in methane?s carbon: methanotrophs that presumably utilize methane directly, methylotrophs that presumably consume methanol excreted by the methanotrophs, and sulfide oxidizers that presumably consume carbon dioxide released by the methanotrophs and methylotrophs. Methanotrophs reached high relative abundance in mats grown on methane, but other bacterial processes include sulfide oxidation appeared to dominate mats, indicating that methanotrophy is not a dominant process in sustaining these benthic mats, but rather a secondary function modulated by methane availability. Methane that escapes the sediment in the deep ocean typically dissolved into the overlying water where it is available to methanotrophic bacteria. We set out to better understand the efficacy of this process as a biofilter by studying the distribution of methane oxidation and disposition of methanotrophic populations in the Pacific Ocean. We investigated several environments including the basins offshore California, the continental margin off Central America, and the shallow waters around gas seeps. We succeeded in identifying the distributions of activity in these environments, identified potential physical and chemical controls on methanotrophic activity, we further revealed details about the methanotrophic communities active in these settings, and we developed new approaches to study methanotrophic communities. These findings should improve our capacity to predict the methanotrophic response in ocean waters, and further our ability to generate specific hypotheses as to the ecology and efficacy of pelagic methanotrophic communites. The discharge of methane and other hydrocarbons to Gulf of Mexico that followed the sinking of the Deepwater Horizon provided a unique opportunity to study the methanotorphic biofilter in the deep ocean environment. We set out to understand the consumption of methane and the bloom of methanotrophs resulting from this event, as a window into the regional scale release of gas hydrate under rapid warming scenarios. We found that other hydrocarbon gases, notably propane and ethane, were preferred for consumption over methane, but that methane consumption accelerated rapidly and drove the depletion of methane within a matter of months after initial release. These results revealed the identity of the responsible community, and point to the importance of the seed population in determining the rate at which a methanotrophic community is able to respond to an input of methane. Collectively, these results provide a significant advance in our understanding of the marine methanotrohic biofilter, and further provide direction and context for future investigations of this important phenomenon. This project has resulted in fourteen publications to date, with five more circulating in draft form, and several others planned.

  17. Motility fractionation of bacteria by centrifugation

    E-Print Network [OSTI]

    Claudio Maggi; Alessia Lepore; Jacopo Solari; Alessandro Rizzo; Roberto Di Leonardo

    2013-10-10

    Centrifugation is a widespread laboratory technique used to separate mixtures into fractions characterized by a specific size, weight or density. We demonstrate that centrifugation can be also used to separate swimming cells having different motility. To do this we study self-propelled bacteria under the influence of an external centrifugal field. Using dynamic image correlation spectroscopy we measure the spatially resolved motility of bacteria after centrifugation. A significant gradient in swimming-speeds is observed for increasing centrifugal speeds. Our results can be reproduced by a model that treats bacteria as "hot" colloidal particles having a diffusion coefficient that depends on the swimming speed.

  18. The Effect of Slowly Biodegradable Carbon on the Morphology, Integrity and Performance of Aerobic Granular Sludge

    E-Print Network [OSTI]

    Faraj, Rasha Attwan

    2014-08-31

    and phosphorus. For both experimental phases, the hydraulic loading rate was 1.32 kg COD/m3/day. For the 1st phase, the three reactors were fed soluble organic matter (sodium acetate) as the sole carbon source with an anaerobic-aerobic SBR cycle. To achieve...

  19. Palladium Catalyzed Aerobic Dehydrogenation: From Alcohols to Indoles and Asymmetric Catalysis

    E-Print Network [OSTI]

    Stoltz, Brian M.

    of asymmetric catalytic dehydrogenations is the latest advance in a long line of catalytic asymmetric oxidation reactions. Ç Introduction Asymmetric catalytic oxidation chemistry has profoundly impacted organic synthesis Brian M. Stoltz (Received February 12, 2004; CL-048001) Abstract Catalytic aerobic dehydrogenation

  20. Genome Sequence of "Pedosphaera parvula" Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil

    SciTech Connect (OSTI)

    Kant, Ravi [University of Helsinki; Van Passel, Mark W.J. [Wageningen University and Research Centre, The Netherlands; Palva, Airi [University of Helsinki; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brettin, Thomas S [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); De Vos, Willem M. [Wageningen University and Research Centre, The Netherlands; Janssen, Peter H. [AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand; Smidt, Hauke [Wageningen University and Research Centre, The Netherlands

    2011-01-01

    Pedosphaera parvula Ellin514 is an aerobically grown verrucomicrobial isolate from pasture soil. In contrast to the high abundance of members of Verrucomicrobia subdivision 3 based on molecular surveys in terrestrial environments, Ellin514 is one of the few cultured representatives of this group.

  1. Methane and Methanotrophic Bacteria as a Biotechnological Platform...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Methane and Methanotrophic Bacteria as a Biotechnological Platform Methane and Methanotrophic Bacteria as a Biotechnological Platform Breakout Session 2-B: NewEmerging Pathways...

  2. Bacteria resist! INRA MIMA2 Imaging Center

    E-Print Network [OSTI]

    Ribot, Magali

    Biofilms: Bacteria resist! #12;INRA MIMA2 Imaging Center #12;#12;Biofilms everywhere ! #12 to biocides #12;MicrocoloniesBiofilm mature Détachement D.Davis, 2007. PLOS àEmergence of resistant mutants

  3. Methods for dispersing hydrocarbons using autoclaved bacteria

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1996-01-01

    A method of dispersing a hydrocarbon includes the steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; autoclaving the bacterium to derive a dispersant solution therefrom; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; and autoclaving the bacterium to derive a dispersant solution therefrom.

  4. Reverse and flick: Hybrid locomotion in bacteria

    E-Print Network [OSTI]

    Stocker, Roman

    Many bacteria are motile. They use one or more helical flagella as propellers, rotating them like the corkscrew on a wine bottle opener. Despite the limited morphological repertoire of the propulsive system, radically ...

  5. Methods for dispersing hydrocarbons using autoclaved bacteria

    DOE Patents [OSTI]

    Tyndall, R.L.

    1996-11-26

    A method of dispersing a hydrocarbon includes the following steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; autoclaving the bacterium to derive a dispersant solution; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; and autoclaving the bacterium to derive a dispersant solution.

  6. How Bacteria Make Magnets | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Bacteria Make Magnets For a number of animals, including birds, fish and mammals, there is evidence that magnets are used for orientation. However, little is known about how...

  7. Probiotic Bacteria Induce a ‘Glow of Health’

    E-Print Network [OSTI]

    Levkovich, Tatiana

    Radiant skin and hair are universally recognized as indications of good health. However, this ‘glow of health’ display remains poorly understood. We found that feeding of probiotic bacteria to aged mice induced integumentary ...

  8. Fuel from Bacteria: Bioconversion of Carbon Dioxide to Biofuels by Facultatively Autotrophic Hydrogen Bacteria

    SciTech Connect (OSTI)

    None

    2010-07-01

    Electrofuels Project: Ohio State is genetically modifying bacteria to efficiently convert carbon dioxide directly into butanol, an alcohol that can be used directly as a fuel blend or converted to a hydrocarbon, which closely resembles a gasoline. Bacteria are typically capable of producing a certain amount of butanol before it becomes too toxic for the bacteria to survive. Ohio State is engineering a new strain of the bacteria that could produce up to 50% more butanol before it becomes too toxic for the bacteria to survive. Finding a way to produce more butanol more efficiently would significantly cut down on biofuel production costs and help make butanol cost competitive with gasoline. Ohio State is also engineering large tanks, or bioreactors, to grow the biofuel-producing bacteria in, and they are developing ways to efficiently recover biofuel from the tanks.

  9. Agencies Approve Bacteria TMDL Task Force Recommendations 

    E-Print Network [OSTI]

    Wythe, Kathy

    2007-01-01

    tx H2O | pg. 10 In June 2007 the Texas Commission onEnvironmental Quality (TCEQ) and the TexasState Soil and Water Conservation Board (TSSW- CB) approved the recommendations of the Bacteria Total Maximum Daily Load (TMDL) Task Force and asked... their agencies to update their TMDL guidance documents to reflect these recommendations. They also authorized establishing a multi-agency bacteria TMDL work group to examine the research and development needs identified in the task force report. Both TCEQ...

  10. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    DOE Patents [OSTI]

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  11. Beating bacteria: Scientists work to understand and track bacteria in water 

    E-Print Network [OSTI]

    Wythe, Kathy

    2010-01-01

    stream_source_info Beating Bacteria.pdf.txt stream_content_type text/plain stream_size 24959 Content-Encoding ISO-8859-1 stream_name Beating Bacteria.pdf.txt Content-Type text/plain; charset=ISO-8859-1 tx H2O | pg. 11... Story by Kathy Wythe Bacteria Task Force Recommendations Acknowledging the enormity of the bacteria problem within the state, in September 2006, TCEQ and the Texas State Soil and Water Conservation Board (TSSWCB) established a joint Task Force...

  12. Analysis of Antibiotic Resistant Genes in Aquacultural Bacteria

    E-Print Network [OSTI]

    Kane, Andrew S.

    1 Analysis of Antibiotic Resistant Genes in Aquacultural Bacteria JY Wang* YJ Geng RX Wang J Feng in the selection pressure, retained the resistant strains, spread among the same or different species of bacteria also increased #12;3 2.Potential Hazards of Resistant Bacteria · Resistant bacteria · Resistant gene

  13. MIGHTY BACTERIA IN A CIVILISED WORLD Prepared by Amy Wooding

    E-Print Network [OSTI]

    MIGHTY BACTERIA IN A CIVILISED WORLD Prepared by Amy Wooding The 2013 FABI/ CTHB UPwith of antibacterial products being advertised. The aim was to explore the idea created by these products that bacteria this by testing whether all bacteria can survive in every environment; will bacteria isolated from the UP

  14. Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site

    SciTech Connect (OSTI)

    Kerkhoff, Lee; Williams, Kenneth H.; Long, Philip E.; McGuinness, L.

    2011-02-15

    Uranium contaminated groundwaters are a legacy concern for the U.S. Department of Energy. Previous experiments at the Rifle, Colorado Integrated Field Challenge (IFC) site have demonstrated that field-scale addition of acetate to groundwater reduces the ambient soluable uranium concentration, sequestering the radionuclide as uraninite. However, questions remain regarding which microorganism(s) are consuming this acetate and if active groundwater microorganisms are different from active particle-associated bacteria. In this report, 13-C acetate was used to assess the active microbes that synthesize DNA on 3 size fractions [coarse sand, fines (8-approximately 150 micron), groundwater (0.2-8 micron)] over a 24 -day time frame. Results indicated a stronger signal from 13-C acetate associated with the “fines” fraction compared with smaller amounts of 13-C uptake on the sand fraction and groundwater samples during the SIP incubations. TRFLP analysis of this 13-C-labeled DNA, indicated 31+ 9 OTU's with 6 peaks dominating the active profiles (166, 187, 210, 212, and 277 bp peaks using MnlI). Cloning/sequencing of the amplification products indicated a Geobacter-like group (187, 210, 212 bp) primarily synthesized DNA from acetate in the groundwater phase, an alpha Proteobacterium (166 bp) primarily grew on the fines/sands, and an Acinetobacter sp. (277 bp) utilized much of the 13C acetate in both groundwater and particle-associated phases. These findings will help to delineate the acetate utilization patterns of bacteria during field-scale acetate addition and can lead to improved methods for stimulating distinct microbial populations in situ.

  15. Carbon Flow of Heliobacteria Is Related More to Clostridia than to the Green Sulfur Bacteria*S

    E-Print Network [OSTI]

    Alvarez-Cohen, Lisa

    Carbon Flow of Heliobacteria Is Related More to Clostridia than to the Green Sulfur Bacteria*S, California 94720 The recently discovered heliobacteria are the only Gram-pos- itive photosynthetic bacteria the photosynthetic green sulfur bacteria (containing the type I reaction center) and Clostridia (forming heat

  16. Chemotactic selection of pollutant degrading soil bacteria

    DOE Patents [OSTI]

    Hazen, Terry C. (Augusta, GA)

    1994-01-01

    A method for identifying soil microbial strains which may be bacterial degraders of pollutants comprising the steps of placing a concentration of a pollutant in a substantially closed container, placing the container in a sample of soil for a period of time ranging from one minute to several hours, retrieving the container, collecting the contents of the container, and microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to inoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  17. Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms

    E-Print Network [OSTI]

    Vallino, Joseph J.

    - phologically distinctive, uncultivated bacteria; an important biotechnological process (wastewater treatment the definition of the major lineages (phyla or divisions [132]) within the three primary domains. This not only

  18. Metagenomic and Cultivation-Based Analysis of Novel Microorganisms and Functions in Metal-Contaminated Environments

    E-Print Network [OSTI]

    Yelton, Alexis Pepper

    2012-01-01

    acidophile important in acid mine drainage. Science 2000,III) Bacteria in Acid Mine Drainage Biofilms. Appl EnvironMicrobial communities in acid mine drainage. FEMS Microbiol

  19. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

    SciTech Connect (OSTI)

    Green, Stefan [Florida State University; Prakash, Om [Florida State University; Jasrotia, Puja [Florida State University; Overholt, Will [Florida State University; Cardenas, Erick [Michigan State University, East Lansing; Hubbard, Daniela [Florida State University; Tiedje, James M. [Michigan State University, East Lansing; Watson, David B [ORNL; Schadt, Christopher Warren [ORNL; Brooks, Scott C [ORNL; Kostka, Joel [Florida State University

    2011-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of ribosomal RNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure, and denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as concentration of nitrogen species, oxygen and sampling season did not appear to strongly influence the distribution of Rhodanobacter. Results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  20. Human Occupancy as a Source of Indoor Airborne Bacteria

    E-Print Network [OSTI]

    Hospodsky, Denina

    Exposure to specific airborne bacteria indoors is linked to infectious and noninfectious adverse health outcomes. However, the sources and origins of bacteria suspended in indoor air are not well understood. This study ...

  1. ELECTRON HOLOGRAPHY OF NANOMAGNETS IN ROCKS AND BACTERIA

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    ELECTRON HOLOGRAPHY OF NANOMAGNETS IN ROCKS AND BACTERIA Rafal E. Dunin-Borkowski1 , Richard J-reversed thermo-remanent magnetization. #12;Magnetotactic bacteria provide the simplest example of the use

  2. Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes in Feedlot Dust

    E-Print Network [OSTI]

    Rock, Chris

    Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes in Feedlot Dust :: Texas Tech Today http://today.ttu.edu/2015/01/environmental-scientists-find-antibiotics Print Email + Font - Font Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes

  3. Total synthesis of lysobactin : a natural product antibiotic active against methicillin and vancomycin resistant bacteria

    E-Print Network [OSTI]

    Guzman-Martinez, Aikomari

    2007-01-01

    has led bacteria to evolve and develop resistance toantibiotic resistance in many different kinds of bacteria.is a resistance mechanism utilized by MRSA and VRE bacteria.

  4. CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea.

    E-Print Network [OSTI]

    Fenner, Marsha W

    2007-01-01

    confers acquired phage resistance in Bacteria and Archaea. Aacquired resistance against phages in bacteria and archaeaof phage resistance into sensitive industrial bacteria.

  5. The Structure of Fitness Landscapes in Antibiotic Resistant Bacteria : : Molecular Origins and Evolutionary Consequences

    E-Print Network [OSTI]

    Deris, John Barrett

    generically when bacteria exhibit resistance to translation-Mediated Drug Resistance in Bacteria: an Update. Drugs, 69(more antibiotics. Drug resistance in bacteria is genetically

  6. Selection against spurious promoter motifs correlates with translational efficiency across bacteria

    E-Print Network [OSTI]

    Froula, Jeffrey L.; Francino, M. Pilar

    2008-01-01

    translational efficiency across bacteria. Jeffrey L. Froulaof Eukarya, Archaea, and Bacteria reveals anticodon-sparingrachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A

  7. When Bacteria Get Good: Progress, Purity, and the Making of Probiotics

    E-Print Network [OSTI]

    Yates, Allison

    2013-01-01

    45 Latour (1987). When Bacteria Get Good Bickler, S. W. , J.When Bacteria GetGood WHEN BACTERIA GET GOOD Progress, Purity, and the Making

  8. Computational prediction of type III secreted proteins from gram-negative bacteria

    E-Print Network [OSTI]

    Yang, Yang; Zhao, Jiayuan; Morgan, Robyn L; Ma, Wenbo; Jiang, Tao

    2010-01-01

    source Compared with other bacteria, Pseudomonas syringaeproteins from gram-negative bacteria Yang Yang 1 , Jiayuansystem in gram- negative bacteria that injects proteins (

  9. Selective Association Between the Free-Living Nematode Acrobeloides maximus and Soil Bacteria

    E-Print Network [OSTI]

    Sedky, Sammy Farid

    2013-01-01

    from intracellular bacteria to multicellular eukaryotes.gene transfer between bacteria and animals. Trends inof the symbiotic-pathogenic bacteria Xenorhabdus spp. and

  10. The effect of statin therapy on innate immune clearance of bacteria

    E-Print Network [OSTI]

    Chow, Ohn Aaron

    2010-01-01

    extracellular traps kill bacteria. Science 303, 1532-1535.extracellular traps to ensnare bacteria in septic blood. Natdigestion of Escherichia coli bacteria. J Immunol 169, 3172-

  11. Total synthesis of lysobactin : a natural product antibiotic active against methicillin and vancomycin resistant bacteria

    E-Print Network [OSTI]

    Guzman-Martinez, Aikomari

    2007-01-01

    Gram-Positive Resistant Bacteria. (IN PREPARATION. ) xxVancomycin Resistant Bacteria by Aikomarí Guzmán-Martíneznew strains of harmful bacteria that are resistant to

  12. Bioelectrical Perchlorate Reduction and Characterization of Novel Dissimilatory Perchlorate Reducing Bacteria

    E-Print Network [OSTI]

    Thrash, James Cameron

    2009-01-01

    per)chlorate-reducing bacteria and their phylogeneticper)chlorate- reducing bacteria. Appl. Environ. Microbiol.perchlorate-reducing bacteria Dechlorobacter hydrogenophilus

  13. To establish infection, pathogenic microorganisms have evolved many strategies to circumvent host defences and

    E-Print Network [OSTI]

    Nizet, Victor

    To establish infection, pathogenic microorganisms have evolved many strategies to circumvent host trafficking pathways to and from the host cell surface, which promotes pathogen entry, replication or escape of proteins such as Toll-like receptor 4 (TLR4) to phagosomes for receptor-mediated phagocytosis of pathogens8

  14. Emerging and opportunistic diseases are caused by a microorganism invading a new

    E-Print Network [OSTI]

    Gomulkiewicz, Richard

    Emerging and opportunistic diseases are caused by a microorganism invading a new habitat, either meningitis). Often, the pathogen can live for many generations in the new habitat and, as natural selection be applied to most bacterial pathogens and suggest a phylogeny-based method to search for genes undergoing

  15. RESPONSES OF BENTHIC MICROORGANISMS (THECAMOEBIANS) TO OIL SANDS PROCESS-AFFECTED MATERIALS; PROVIDING

    E-Print Network [OSTI]

    Patterson, Timothy

    RESPONSES OF BENTHIC MICROORGANISMS (THECAMOEBIANS) TO OIL SANDS PROCESS-AFFECTED MATERIALS an important role in reclamation options for fluid tailings (OSPW/M) at surface oil sands operations. Through of oil sands operation have been compared. An index of response to stress has been compiled with the goal

  16. INTRODUCTION The contribution of micro-organisms to amorphous silica precipitation in modern

    E-Print Network [OSTI]

    Benning, Liane G.

    INTRODUCTION The contribution of micro-organisms to amorphous silica precipitation in modern, University of Guelph, Canada 3 Institute of Geological and Nuclear Sciences, Wairakei Research Centre, Taupo as geothermal energy sources and as a proxy to understanding the formation of epithermal ore deposits, which

  17. The impact of soil microorganisms on the global budget of 18

    E-Print Network [OSTI]

    sizes for CA- containing soil microorganisms. Including accelerated soil hydra- tion in global model Biotechnologie, Service de Biologie Ve´ge´tale et de Microbiologie Environnementale, Commissariat a` l'EnergieDepartment of Environmental Sciences and Energy Research, Weizmann Institute of Science, Rehovot, 76100, Israel; h

  18. Evidence That Mutation Is Universally Biased towards AT in Bacteria

    E-Print Network [OSTI]

    Petrov, Dmitri

    Evidence That Mutation Is Universally Biased towards AT in Bacteria Ruth Hershberg*, Dmitri A under severely relaxed selection are uniquely suitable for studying mutational biases in bacteria. We: Hershberg R, Petrov DA (2010) Evidence That Mutation Is Universally Biased towards AT in Bacteria. PLo

  19. A latitudinal diversity gradient in planktonic marine bacteria

    E-Print Network [OSTI]

    Brown, James H.

    A latitudinal diversity gradient in planktonic marine bacteria Jed A. Fuhrman* , Joshua A. Steele and attribute this to their high abundance and dispersal capabilities would suggest that bacteria, the smallest. Despite the high abundance and potentially high dispersal of bacteria, they exhibit geographic patterns

  20. Bacteria Marinobacter aquaeolei. Community Living. Microbes living in coral provide

    E-Print Network [OSTI]

    Bacteria Marinobacter aquaeolei. Community Living. Microbes living in coral provide nutrients Cleaning up. Bacteria are being tested for use as cleaning agents of toxic chemicals and pollutants in our.The big red and green dots (numbering about 1,000) are bacteria, and the very small background dots (about

  1. Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis

    E-Print Network [OSTI]

    Ismagilov, Rustem F.

    Article Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis Graphical Abstract Highlights d Gut microbes regulate levels of 5-HT in the colon and blood d Spore-forming bacteria.cell.2015.02.047 #12;Article Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin

  2. Ancient bacteria show evidence of DNA repair Sarah Stewart Johnson*

    E-Print Network [OSTI]

    Nielsen, Rasmus

    Ancient bacteria show evidence of DNA repair Sarah Stewart Johnson* , Martin B. Hebsgaard , Torben for review June 14, 2007) Recent claims of cultivable ancient bacteria within sealed environ- ments highlight-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence

  3. A new process using a strain of Clostridium bacteria can

    E-Print Network [OSTI]

    Langendoen, Koen

    A new process using a strain of Clostridium bacteria can successfully convert biomass into butyl pipelines, facilitating transport and storage. Clostridium bacteria On the production side biobutanol has several disadvantages. It can be produced by fermentation using Clostridium bacteria, but this process

  4. Bacteria, Biofilms and Fluid Dynamics: Elementary Flows and Unexpected Phenomena

    E-Print Network [OSTI]

    Fisher, Frank

    Bacteria, Biofilms and Fluid Dynamics: Elementary Flows and Unexpected Phenomena Wednesday February the migration of bacteria along surfaces when exposed to a shear flow. In particular, we identify an unusual response where flow produces a directed motion of twitching bacteria in the upstream direction. (ii) We

  5. CHARACTERIZATION OF MAGNETIC NANOCRYSTALS FORMED BY MAGNETOTACTIC BACTERIA

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    CHARACTERIZATION OF MAGNETIC NANOCRYSTALS FORMED BY MAGNETOTACTIC BACTERIA M. Pósfai1 , T. Kasama2 fields remains poorly understood. Magnetotactic bacteria are the simplest organisms that use magnetite fields of iron oxide and iron sulfide nanoparticles in magnetotactic bacteria in order to understand

  6. BACTERIA-FILTERS: PERSISTENT PARTICLE FILTERS FOR BACKGROUND SUBTRACTION

    E-Print Network [OSTI]

    Peleg, Shmuel

    BACTERIA-FILTERS: PERSISTENT PARTICLE FILTERS FOR BACKGROUND SUBTRACTION Yair Movshovitz switch of bacteria between two states: A normal growing cell and a dormant but persistent cell after the stress is over, bacterial growth continues. Similar to bacteria, particles will switch between

  7. Physics 6, 61 (2013) The Aquatic Dance of Bacteria

    E-Print Network [OSTI]

    Goldstein, Raymond E.

    2013-01-01

    Physics 6, 61 (2013) Viewpoint The Aquatic Dance of Bacteria Igor Aranson Materials Science ­ Published May 28, 2013 Bacteria are among the oldest and most abundant liv- ing species on Earth maintain soil structure, ma- rine bacteria control the biochemistry and photosynthetic productivity

  8. Screening genomes of Gram-positive bacteria for

    E-Print Network [OSTI]

    Screening genomes of Gram-positive bacteria for double-glycine-motif- containing peptides Secreted-positive bacteria, the double-glycine (GG) motif plays a key role in many peptide secretion systems involved Microbiology Comment #12;peptides and class II bacteriocins, produced by streptococci and lactic acid bacteria

  9. TRITIUM INCORPORATION STUDIES IN PHOTO-SYNTHETIC BACTERIA

    E-Print Network [OSTI]

    Dehner, Thomas R.; Chan, W.-S.; Caple, Marianne B.; Calvin, M.

    2008-01-01

    STUDIES IN PHOTOSYN- s BACTERIA Thomas R. Dehner, H e n r ySTUDIES I N PHOTOSYNTmI"1C BACTERIA' BY Thomas R. ~ehner,'*rubm a f t e r the bacteria have been illuminated i n growth

  10. BACTERIA, FUNGI, AND UNICELLULAR ALGAE Blank page retained for pagination

    E-Print Network [OSTI]

    CHAPTER VI BACTERIA, FUNGI, AND UNICELLULAR ALGAE #12;Blank page retained for pagination #12;MARINE BACTERIA AND FUNGI IN THE GULF OF MEXICO I By CLAUDE E. ZOBELL, Scripps lrutitution of Oceano; Bavendamm 1932), there are very few published reports on bacteria and fungi in the nearby Gulf of Mexico

  11. Measurement of chlorite dismutase activities in perchlorate respiring bacteria

    E-Print Network [OSTI]

    Measurement of chlorite dismutase activities in perchlorate respiring bacteria Jianlin Xu*, Bruce E to chloride (ClO2 À ! ClÀ + O2) and is present in bacteria capable of cell respiration using perchlorate concentration (0.6 mM) to four other perchlorate respiring bacteria (PRB), and to one non-PRB (Pseudomonas

  12. The identification and biogeochemical interpretation of fossil magnetotactic bacteria

    E-Print Network [OSTI]

    Kirschvink, Joseph L.

    The identification and biogeochemical interpretation of fossil magnetotactic bacteria Robert E. Available online 14 August 2007. Abstract Magnetotactic bacteria, which most commonly live within the oxic, specifically magnetite or greigite. The crystals cause the bacteria to orient themselves passively with respect

  13. Controlled Bacteria -Gold Nanorod Interactions for Enhancement of Optoacoustic Contrast

    E-Print Network [OSTI]

    Natelson, Douglas

    Controlled Bacteria - Gold Nanorod Interactions for Enhancement of Optoacoustic Contrast Anton as a model of positively charged gold surface for quantitative optoacoustic sensing in GNR-bacteria controlled agglomeration of contrast agents with the bacteria E.Coli and Vibrio Cholerae. For bacterial

  14. Microbiol Monogr (3) D. Schler: Magnetoreception and Magnetosomes in Bacteria

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Microbiol Monogr (3) D. Schüler: Magnetoreception and Magnetosomes in Bacteria DOI 10 Abstract Magnetotactic bacteria can be regarded as model systems for studying the struc- tural, chemical Introduction Magnetotactic bacteria contain intracellular ferrimagnetic crystals that are typically 30­120 nm

  15. Biomineralization of carbonate and phosphate by moderately halophilic bacteria

    E-Print Network [OSTI]

    Gilli, Adrian

    Biomineralization of carbonate and phosphate by moderately halophilic bacteria M ´onica S-calcite; coprecipitated; moderately halophilic bacteria. Abstract We investigated the precipitation of carbonate and phosphate minerals by 19 species of moderately halophilic bacteria using media with variable Mg21 /Ca21

  16. Substrata Mechanical Stiffness Can Regulate Adhesion of Viable Bacteria

    E-Print Network [OSTI]

    Van Vliet, Krystyn J.

    Substrata Mechanical Stiffness Can Regulate Adhesion of Viable Bacteria Jenny A. Lichter,, M. Todd, 2008 The competing mechanisms that regulate adhesion of bacteria to surfaces and subsequent biofilm and hospital-acquired infections due to bacteria, there is considerable interest in better understanding

  17. Response of Free-Living Nitrogen-Fixing Microorganisms to Land Use Change in the Amazon Rainforest

    E-Print Network [OSTI]

    Bohannan, Brendan

    ) of this greenhouse gas annually (1, 2). To absorb this enormous amount of CO2, a sig- nificant input of nitrogen (NResponse of Free-Living Nitrogen-Fixing Microorganisms to Land Use Change in the Amazon Rainforest-living nitrogen-fixing microorganisms (di- azotrophs) respond to deforestation in the Amazon rainforest, using

  18. 27/05/2012 21:13Fighting bacteria?s strength in numbers | Britney Spears New Video Page 1 of 2http://britneyspearsnewvideo.fruntrunnazproductions.com/194/fighting-bacterias-strength-in-numbers/

    E-Print Network [OSTI]

    West, Stuart

    27/05/2012 21:13Fighting bacteria?s strength in numbers | Britney Spears New Video Page 1 of 2http://britneyspearsnewvideo.fruntrunnazproductions.com/194/fighting-bacterias-strength-in-numbers/ Home Britney Spears New Video Fighting bacteria?s strength of Nottingham have opened the way for more accurate research into new ways to fight dangerous bacterial

  19. Comparative study of four fluorinated quinolones in susceptibility factors on microorganisms 

    E-Print Network [OSTI]

    Patel, Ketul R

    2013-02-22

    . This study hopes to prove an equal effectiveness of enrofloxacin and ciprofloxacin. Microbial susceptibility to drugs is measured by determining the MIC (Minimum Inhibitory Concentration). The MIC is measured based on the growth of the targeted bacteria...

  20. Biochemistry and physiology of anaerobic bacteria

    SciTech Connect (OSTI)

    2000-05-18

    We welcome you to The Power of Anaerobes. This conference serves two purposes. One is to celebrate the life of Harry D. Peck, Jr.,who was born May 18, 1927 and would have celebrated his 73rd birthday at this conference. He died November 20, 1998. The second is to gather investigators to exchange views within the realm of anaerobic microbiology, an area in which tremendous progress has been seen during recent years. It is sufficient to mention discoveries of a new form of life (the archaea), hyper or extreme thermophiles, thermophilic alkaliphiles and anaerobic fungi. With these discoveries has come a new realization about physiological and metabolic properties of microorganisms, and this in turn has demonstrated their importance for the development, maintenance and sustenance of life on Earth.

  1. Natural Oil Production from Microorganisms: Bioprocess and Microbe Engineering for Total Carbon Utilization in Biofuel Production

    SciTech Connect (OSTI)

    2010-07-15

    Electrofuels Project: MIT is using carbon dioxide (CO2) and hydrogen generated from electricity to produce natural oils that can be upgraded to hydrocarbon fuels. MIT has designed a 2-stage biofuel production system. In the first stage, hydrogen and CO2 are fed to a microorganism capable of converting these feedstocks to a 2-carbon compound called acetate. In the second stage, acetate is delivered to a different microorganism that can use the acetate to grow and produce oil. The oil can be removed from the reactor tank and chemically converted to various hydrocarbons. The electricity for the process could be supplied from novel means currently in development, or more proven methods such as the combustion of municipal waste, which would also generate the required CO2 and enhance the overall efficiency of MIT’s biofuel-production system.

  2. Quantum superposition, entanglement, and state teleportation of a microorganism on an electromechanical oscillator

    E-Print Network [OSTI]

    Li, Tongcang

    2015-01-01

    Schr\\"odinger's thought experiment to prepare a cat in a superposition of both alive and dead states reveals profound consequences of quantum mechanics and has attracted enormous interests. Here we propose a straightforward method to create quantum superposition states of a living microorganism by putting a small bacterium on top of an electromechanical oscillator. Our proposal is based on recent developments that the center-of-mass oscillation of a 15-$\\mu$m-diameter aluminium membrane has been cooled to its quantum ground state [Nature 475, 359 (2011)], and entangled with a microwave field [Science, 342, 710 (2013)]. A microorganism with a mass much smaller than the mass of the electromechanical membrane will not significantly affect the quality factor of the membrane and can be cooled to the quantum ground state together with the membrane. Quantum superposition and teleportation of its center-of-mass motion state can be realized with the help of superconducting microwave circuits. More importantly, the int...

  3. Dynamic Clustering in Suspension of Motile Bacteria

    E-Print Network [OSTI]

    Xiao Chen; Xiang Yang; Mingcheng Yang; Hepeng Zhang

    2015-09-22

    Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counter-clockwise direction; they continuously evolve, merge with others and split into smaller ones. Measurements indicate that long-ranged hydrodynamic interactions have strong influences on cluster properties. Bacterial clusters change material and fluid transport near the interface and hence may have environmental and biological consequences.

  4. Turning bacteria suspensions into a "superfluid"

    E-Print Network [OSTI]

    Héctor Matías López; Jérémie Gachelin; Carine Douarche; Harold Auradou; Eric Clément

    2015-03-18

    The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidences for a low shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semi-dilute regime, for particularly active bacteria, the suspension display a "super-fluid" like transition where the viscous resistance to shear vanishes, thus showing that macroscopically, the activity of pusher swimmers organized by shear, is able to fully overcome the dissipative effects due to viscous loss.

  5. Turning bacteria suspensions into a "superfluid"

    E-Print Network [OSTI]

    López, Héctor Matías; Douarche, Carine; Auradou, Harold; Clément, Eric

    2015-01-01

    The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidences for a low shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semi-dilute regime, for particularly active bacteria, the suspension display a "super-fluid" like transition where the viscous resistance to shear vanishes, thus showing that macroscopically, the activity of pusher swimmers organized by shear, is able to fully overcome the dissipative effects due to viscous loss.

  6. Dynamic Clustering in Suspension of Motile Bacteria

    E-Print Network [OSTI]

    Chen, Xiao; Yang, Mingcheng; Zhang, Hepeng

    2015-01-01

    A bacteria suspension exhibits a wide range of collective phenomena arsing from interactions between individual cells. Here we show that Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counter-clockwise direction; they continuously evolve, merge with others and split into smaller ones. The observed cluster dynamics is qualitatively reproduced by a numerical model of self-propelled particles that interact via pair-wise forces extracted from hydrodynamic calculations. Bacterial clusters change material and fluid transport near the interface and hence may have environmental and biological consequences.

  7. Quantum superposition, entanglement, and state teleportation of a microorganism on an electromechanical oscillator

    E-Print Network [OSTI]

    Tongcang Li; Zhang-Qi Yin

    2015-09-12

    Schr\\"odinger's thought experiment to prepare a cat in a superposition of both alive and dead states reveals profound consequences of quantum mechanics and has attracted enormous interests. Here we propose a straightforward method to create quantum superposition states of a living microorganism by putting a small bacterium on top of an electromechanical oscillator. Our proposal is based on recent developments that the center-of-mass oscillation of a 15-$\\mu$m-diameter aluminium membrane has been cooled to its quantum ground state [Nature 475, 359 (2011)], and entangled with a microwave field [Science, 342, 710 (2013)]. A microorganism with a mass much smaller than the mass of the electromechanical membrane will not significantly affect the quality factor of the membrane and can be cooled to the quantum ground state together with the membrane. Quantum superposition and teleportation of its center-of-mass motion state can be realized with the help of superconducting microwave circuits. More importantly, the internal states of a microorganism, such as the electron spin of a glycine radical, can be prepared in a quantum superposition state and entangled with its center-of-mass motion. Our proposal can be realized with state-of-art technologies. The proposed setup is also a quantum-limited magnetic resonance force microscope (MRFM) that not only can detect the existence of an electron spin, but also can coherently manipulate and detect the quantum state of the spin.

  8. Delayed accumulation of intestinal coliform bacteria enhances life span and stress resistance in Caenorhabditis elegans fed respiratory deficient E. coli

    E-Print Network [OSTI]

    2012-01-01

    coliform bacteria enhances life span and stress resistancecoliform bacteria enhances life span and stress resistance

  9. Biofilter for removal of nitrogen oxides from contaminated gases under aerobic conditions

    DOE Patents [OSTI]

    Apel, William A. (Idaho Falls, ID)

    1998-01-01

    A biofilter for reducing concentrations of gaseous nitrogen oxides in a polluted gas comprises a porous organic filter bed medium disposed in a housing, the filter bed medium including a mixed culture of naturally occurring denitrifying bacteria for converting the nitrogen oxides to nitrogen gas, carbon dioxide, and water. A method of reducing concentrations of nitrogen oxides in polluted gas comprises conducting the polluted gas through the biofilter so that the denitrifying bacteria can degrade the nitrogen oxides. A preferred filter medium is wood compost, however composts of other organic materials are functional. Regulation of pH, moisture content, exogenous carbon sources, and temperature are described.

  10. Biofilter for removal of nitrogen oxides from contaminated gases under aerobic conditions

    DOE Patents [OSTI]

    Apel, W.A.

    1998-08-18

    A biofilter is described for reducing concentrations of gaseous nitrogen oxides in a polluted gas comprises a porous organic filter bed medium disposed in a housing, the filter bed medium including a mixed culture of naturally occurring denitrifying bacteria for converting the nitrogen oxides to nitrogen gas, carbon dioxide, and water. A method is described of reducing concentrations of nitrogen oxides in polluted gas comprises conducting the polluted gas through the biofilter so that the denitrifying bacteria can degrade the nitrogen oxides. A preferred filter medium is wood compost, however composts of other organic materials are functional. Regulation of pH, moisture content, exogenous carbon sources, and temperature are described. 6 figs.

  11. Purple bacteria and quantum Fourier transform

    E-Print Network [OSTI]

    Samir Lipovaca

    2007-02-22

    The LH-II of purple bacteria Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila adopts a highly symmetrical ring shape, with a radius of about 7 nm. In the case of Rps. acidophila the ring has a ninefold symmetry axis, and in LH-II from Rs. molischianum the ring has an eightfold symmetry axis. These rings are found to exibit two bands of excitons. A simplified mathematical description of the exciton states is given in Hu, X. & Schulten, K. (1997) Physics Today 50, 28-34. Using this description, we will show, by suitable labeling of the lowest energy (Qy) excited states of individual BChls, that the resulting exciton states are the quantum Fourier transform of the BChls excited states. For Rs. molischianum ring exciton states will be modeled as the four qubit quantum Fourier transform and the explicit circuit will be derived. Exciton states for Rps. acidophila ring cannot be modeled with an integer number of qubits. Both quantum Fourier transforms are instances of the hidden subgroup problem and this opens up a possibility that both purple bacteria implement an efficient quantum circuit for light harvesting.

  12. Detection of phenols using engineered bacteria

    DOE Patents [OSTI]

    Wise, Arlene A. (Philadelphia, PA); Kuske, Cheryl R. (Los Alamos, NM); Terwilliger, Thomas C. (Santa Fe, NM)

    2007-12-04

    Detection of phenols using engineered bacteria. A biosensor can be created by placing a reporter gene under control of an inducible promoter. The reporter gene produces a signal when a cognate transcriptional activator senses the inducing chemical. Creation of bacterial biosensors is currently restricted by limited knowledge of the genetic systems of bacteria that catabolize xenobiotics. By using mutagenic PCR to change the chemical specificity of the Pseudomonas species CF600 DmpR protein, the potential for engineering novel biosensors for detection of phenols has been demonstrated. DmpR, a well-characterized transcriptional activator of the P. CF600's dmp operon mediates growth on simple phenols. Transcription from Po, the promoter heading the dmp operon, is activated when the sensor domain of DmpR interacts with phenol and mono-substituted phenols. By altering the sensor domain of the DmpR, a group of DmpR derivatives that activate transcription of a Po-lacZ fusion in response to eight of the EPA's eleven priority pollutant phenols has been created. The assays and the sensor domain mutations that alter the chemical specificity of DmpR is described.

  13. Detection of phenols using engineered bacteria

    DOE Patents [OSTI]

    Wise, Arlene A.; Kuske, Cheryl R.; Terwilliger, Thomas C.

    2004-08-10

    Detection of phenols using engineered bacteria. A biosensor can be created by placing a reporter gene under control of an inducible promoter. The reporter gene produces a signal when a cognate transcriptional activator senses the inducing chemical. Creation of bacterial biosensors is currently restricted by limited knowledge of the genetic systems of bacteria that catabolize xenobiotics. By using mutagenic PCR to change the chemical specificity of the Pseudomonas species CF600 DmpR protein, the potential for engineering novel biosensors for detection of phenols has been demonstrated. DmpR, a well-characterized transcriptional activator of the P. CF600's dmp operon mediates growth on simple phenols. Transcription from Po, the promoter heading the dmp operon, is activated when the sensor domain of DmpR interacts with phenol and mono-substituted phenols. By altering the sensor domain of the DmpR, a group of DmpR derivatives that activate transcription of a Po-lacZ fusion in response to eight of the EPA's eleven priority pollutant phenols has been created. The assays and the sensor domain mutations that alter the chemical specificity of DmpR is described.

  14. Starvation-survival of subsurface bacteria

    SciTech Connect (OSTI)

    Magill, N.G.

    1988-01-01

    The ability of four subsurface isolates to survive starvation was examined and the results were compared to survival curves obtained for Escherichia coli B and Serratia marcescens. To examine the starvation-survival phenomenon further, several experimental parameters including nutritional history, initial cell density, growth phase, temperature of growth and starvation, and aeration. Nutritional history, initial cell density, and growth phases of the cells had some effect on the ability of these bacteria to survive whereas temperature and limited aeration had no effect under the conditions tested. No conditions were found where E. coli B or Serratia marcescens died rapidly or where less than 10% of the original cell number of viable cells remained. Because the apparent survival of these bacteria may be due to cryptic growth, cross-feeding experiments with {sup 14}C-labeled cells and unlabeled cells were carried out with E. coli B and Pseudomonas Lula V. Leaked extracellular {sup 14}C-compounds were not used for growth or maintenance energy, and were not taken up by either bacterium. Cryptic growth did not occur; the cells were truly starving under the experimental conditions used.

  15. DNA Strand Cleavage by the Phenazine Di-N-oxide Natural Product Myxin under Both Aerobic and Anaerobic Conditions

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Strand Cleavage by the Phenazine Di-N-oxide Natural Product Myxin under Both Aerobic: Heterocyclic N-oxides are an interesting class of antitumor agents that selectively kill the hypoxic cells found in solid tumors. The hypoxia-selective activity of the lead compound in this class, tirapazamine

  16. Effect of dispersed crude oil exposure upon the aerobic metabolic scope in juvenile golden grey mullet (Liza aurata)

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 Effect of dispersed crude oil exposure upon the aerobic metabolic scope in juvenile golden grey; CD: Chemically Dispersed oil using dispersant; D: Dispersant solution; MD: Mechanically Dispersed oil technique to oil spill. Through an experimental approach with juveniles of Liza aurata, the toxicity of five

  17. Transfer of noncoding DNA drives regulatory rewiring in bacteria

    E-Print Network [OSTI]

    Oren, Yaara

    Understanding the mechanisms that generate variation is a common pursuit unifying the life sciences. Bacteria represent an especially striking puzzle, because closely related strains possess radically different metabolic ...

  18. Rapid quantification of mutant fitness in diverse bacteria by...

    Office of Scientific and Technical Information (OSTI)

    by sequencing randomly bar-coded transposons Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but...

  19. Copy of Synthetic Biology of Novel Thermophilic Bacteria for...

    Office of Scientific and Technical Information (OSTI)

    Copy of Synthetic Biology of Novel Thermophilic Bacteria for Enhanced Production of Ethanol from 5-Carbon Sugars (LDRD %23 105944). Citation Details In-Document Search Title: Copy...

  20. Attachment and detachment of microorganisms as related to sampling carcasses and meat products 

    E-Print Network [OSTI]

    Butler, Jacqueline Love

    1980-01-01

    of Advisory Committee: Dr. C. Vanderzant A model system was developed to study attachment and de- t-chment of' bacteria with pork skin and muscle surfaces of beef and lamb carcasses. The technique involved embedding pork skin and beef and lamb muscle... medium, although in some cases attachment continued to occur over a $0-min period. Gram-negative motile bacteria had greater force of attachment than gram-positive non-motile species. Temperature and pH of the attachment medium had little eff...

  1. Energy conversion in Purple Bacteria Photosynthesis

    E-Print Network [OSTI]

    Caycedo-Soler, Felipe; Quiroga, Luis; Zhao, Guannan; Johnson, Neil F

    2011-01-01

    The study of how photosynthetic organisms convert light offers insight not only into nature's evolutionary process, but may also give clues as to how best to design and manipulate artificial photosynthetic systems -- and also how far we can drive natural photosynthetic systems beyond normal operating conditions, so that they can harvest energy for us under otherwise extreme conditions. In addition to its interest from a basic scientific perspective, therefore, the goal to develop a deep quantitative understanding of photosynthesis offers the potential payoff of enhancing our current arsenal of alternative energy sources for the future. In the following Chapter, we consider the trade-off between dynamics, structure and function of light harvesting membranes in Rps. Photometricum purple bacteria, as a model to highlight the priorities that arise when photosynthetic organisms adapt to deal with the ever-changing natural environment conditions.

  2. Energy conversion in Purple Bacteria Photosynthesis

    E-Print Network [OSTI]

    Felipe Caycedo-Soler; Ferney J. Rodriguez; Luis Quiroga; Guannan Zhao; Neil F. Johnson

    2011-07-01

    The study of how photosynthetic organisms convert light offers insight not only into nature's evolutionary process, but may also give clues as to how best to design and manipulate artificial photosynthetic systems -- and also how far we can drive natural photosynthetic systems beyond normal operating conditions, so that they can harvest energy for us under otherwise extreme conditions. In addition to its interest from a basic scientific perspective, therefore, the goal to develop a deep quantitative understanding of photosynthesis offers the potential payoff of enhancing our current arsenal of alternative energy sources for the future. In the following Chapter, we consider the trade-off between dynamics, structure and function of light harvesting membranes in Rps. Photometricum purple bacteria, as a model to highlight the priorities that arise when photosynthetic organisms adapt to deal with the ever-changing natural environment conditions.

  3. Characteristics of cyclic AMP transport by marine bacteria

    SciTech Connect (OSTI)

    Ammerman, J.W.; Azam, F.

    1987-12-01

    Uptake and autoradiography experiments with natural populations of marine bacteria, sea water cultures, and cultured isolates showed that the high-affinity cyclic AMP transport system in marine bacteria has stringent structural requirements, is found in a minority of cells in mixed bacterial assemblages, and appears to be related to the culture growth state.

  4. Method of separating bacteria from free living amoebae

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1994-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  5. Magnetic minerals produced by magnetotactic bacteria Balzs Arat1

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Magnetic minerals produced by magnetotactic bacteria Balázs Arató1 , Mihály Pósfai1 and Rafal E-controlled mineralization Abstract. Magnetotactic bacteria produce intracellular magnetic minerals that have distinct for studying the biological membrane around the mineral grains. Our goals were to deduce the possible growth

  6. 17 -Estradiol-Degrading Bacteria Isolated from Activated Sludge

    E-Print Network [OSTI]

    Chu, Kung-Hui "Bella"

    17 -Estradiol-Degrading Bacteria Isolated from Activated Sludge C H A N G - P I N G Y U , H Y U N G-degrading bacteria (strains KC1-14) were isolated from activated sludge of a wastewater treatment plant

  7. The Impact of Different Antibiotic Regimens on the Emergence of Antimicrobial-Resistant Bacteria

    E-Print Network [OSTI]

    Ruan, Shigui

    The Impact of Different Antibiotic Regimens on the Emergence of Antimicrobial-Resistant Bacteria-resistant bacteria is a major public health threat. Infections caused by antimicrobial-resistant bacteria by antimicrobial-susceptible bacteria. The emergence and spread of these bacteria is complex and requires

  8. Identification of bacteria synthesizing ribosomal RNA in response to uranium addition during biostimulation at the Rifle, CO Integrated Field Research site

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McGuinness, Lora R.; Wilkins, Michael J.; Williams, Kenneth H.; Long, Philip E.; Kerkhof, Lee J.; Boyanov, Maxim I.

    2015-09-18

    Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this research, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 ?M. Concentrations of U (VI) >2 ?M were generally found to inhibit ribosome synthesis. Two activemore »bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.« less

  9. Detection and quantification of waterborne microorganisms using an image cytometer based on angular spatial frequency processing

    E-Print Network [OSTI]

    Pérez, Juan Miguel; Martínez, Pedro; Pruneri, Valerio

    2015-01-01

    We introduce a new image cytometer design for detection of very small particulate and demonstrate its capability in water analysis. The device is a compact microscope composed of off--the--shelf components, such as a light emitting diode (LED) source, a complementary metal--oxide--semiconductor (CMOS) image sensor, and a specific combination of optical lenses that allow, through an appropriate software, Fourier transform processing of the sample volume. Waterborne microorganisms, such as Escherichia coli (E. coli), Legionella pneumophila (L. pneumophila) and Phytoplankton, are detected by interrogating the volume sample either in a fluorescent or label-free mode, i.e. with or without fluorescein isothiocyanate (FITC) molecules attached to the micro-organisms, respectively. We achieve a sensitivity of 50 CFU/ml, which can be further increased to 0.2 CFU/ml by pre-concentrating an initial sample volume of 500 ml with an ad hoc fluidic system. We also prove the capability of the proposed image cytometer of diffe...

  10. Field application of a genetically engineered microorganism for polycyclic aromatic hydrocarbon bioremediation process monitoring and control

    SciTech Connect (OSTI)

    Sayler, G.S.; Cox, C.D.; Ripp, S.; Nivens, D.E.; Werner, C.; Ahn, Y.; Matrubutham, U.; Burlage, R.

    1998-11-01

    On October 30, 1996, the US Environmental Protection Agency (EPA) commenced the first test release of genetically engineered microorganisms (GEMs) for use in bioremediation. The specific objectives of the investigation were multifaceted and include (1) testing the hypothesis that a GEM can be successfully introduced and maintained in a bioremediation process, (2) testing the concept of using, at the field scale, reporter organisms for direct bioremediation process monitoring and control, and (3) acquiring data that can be used in risk assessment decision making and protocol development for future field release applications of GEMs. The genetically engineered strain under investigation is Pseudomonas fluorescens strain HK44 (King et al., 1990). The original P. fluorescens parent strain was isolated from polycyclic aromatic hydrocarbon (PAH) contaminated manufactured gas plant soil. Thus, this bacterium is able to biodegrade naphthalene (as well as other substituted naphthalenes and other PAHs) and is able to function as a living bioluminescent reporter for the presence of naphthalene contamination, its bioavailability, and the functional process of biodegradation. A unique component of this field investigation was the availability of an array of large subsurface soil lysimeters. This article describes the experience associated with the release of a genetically modified microorganism, the lysimeter facility and its associated instrumentation, as well as representative data collected during the first eighteen months of operation.

  11. Thermodynamic characterization of a tetrahaem cytochrome isolated from a facultative aerobic bacterium, Shewanella frigidimarina : a putative redox model for flavocytochrome c3 

    E-Print Network [OSTI]

    Pessanha, Miguel; Louro, Ricardo O; Correia, Il?dio J; Rothery, Emma L; Pankhurst, Kate L; Reid, Graeme A; Chapman, Stephen K; Turner, David L; Salgueiro, Carlos A

    2003-01-01

    The facultative aerobic bacterium Shewanella frigidimarina produces a small c-type tetrahaem cytochrome (86 residues) under anaerobic growth conditions. This protein is involved in the respiration of iron and shares ...

  12. Bacteria Induced Split Anergy in NK Cells Drive Maturation, Differentiation and Resistance of Healthy and Transformed Stem Cells

    E-Print Network [OSTI]

    Bui, Vickie Tam Doan

    2014-01-01

    of probiotic bacteria in maturation and resistance of Oralwithout probiotic bacteria induced resistance of OSCSCs, MIAof probiotic bacteria in maturation and resistance of Oral

  13. Metal Cycling by Bacteria: Moving Electrons Around

    SciTech Connect (OSTI)

    Nealson, Ken

    2009-07-06

    About 20 years ago, Shewanella oneidensis MR-1 was isolated from a manganese-rich lack in upstate New York, and subsequently shown to utilize solid forms of oxidized manganese or iron as an electron acceptor. Recent studies of metal-reducing bacterial have unveiled a number of unexpected properties of microbes that have enlarged our view of microbes and their role(s) in natural ecosystems. For example, the processes of metal reduction themselves are fundamental to the carbon cycle in many lakes and sediments, where iron and manganese account for the major portion of organic carbon oxidation in many sediments. On more modest spatial scales, iron and manganese reduction can be linked to the oxidation of a wide variety of carbon compounds, many of them recalcitrant and/or toxic. One remarkable property of metal reducers is their ability to reduce solid, often highly crystalline substrates such as iron and manganese oxides and oxyhydroxides. It is now clear that this is done via the utilization of enzymes located on the outer wall of the bacteria - enzymes that apparently interact directly with these solid substrates. Molecular and genomic studies combined have revealed the genes and protoeins responsible for these activities, and many facets of the regulation. This talk focuses on the general features and properties of these remarkable organisms that seem to communicate via electron transfer across a wide variety of soluable, insoluable, and even "inert" substrates, and the way that these processes may be mechanistically linked.

  14. Metal Cycling by Bacteria: Moving Electrons Around

    ScienceCinema (OSTI)

    Nealson, Ken

    2010-01-08

    About 20 years ago, Shewanella oneidensis MR-1 was isolated from a manganese-rich lack in upstate New York, and subsequently shown to utilize solid forms of oxidized manganese or iron as an electron acceptor. Recent studies of metal-reducing bacterial have unveiled a number of unexpected properties of microbes that have enlarged our view of microbes and their role(s) in natural ecosystems. For example, the processes of metal reduction themselves are fundamental to the carbon cycle in many lakes and sediments, where iron and manganese account for the major portion of organic carbon oxidation in many sediments. On more modest spatial scales, iron and manganese reduction can be linked to the oxidation of a wide variety of carbon compounds, many of them recalcitrant and/or toxic. One remarkable property of metal reducers is their ability to reduce solid, often highly crystalline substrates such as iron and manganese oxides and oxyhydroxides. It is now clear that this is done via the utilization of enzymes located on the outer wall of the bacteria - enzymes that apparently interact directly with these solid substrates. Molecular and genomic studies combined have revealed the genes and protoeins responsible for these activities, and many facets of the regulation. This talk focuses on the general features and properties of these remarkable organisms that seem to communicate via electron transfer across a wide variety of soluable, insoluable, and even "inert" substrates, and the way that these processes may be mechanistically linked.

  15. Effects of sodium lactate and sodium propionate on the sensory, microbial, and chemical characteristics of fresh aerobically stored ground beef 

    E-Print Network [OSTI]

    Eckert, Laura Anne

    1995-01-01

    EFFECTS OF SODIUM LACTATE AND SODIUM PROPIONATE ON THE SENSORY, MICROBIAL, AND CHEMICAL CHARACTERISTICS OF FRESH AEROBICALLY STORED GROUND BEEF A Thesis by LAURA ANNE ECKERT Submitted to the Office of Graduate Studies of Texas A&M University... in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 1995 Major Subject: Food Science and Technology EFFECTS OF SODIUM LACTATE AND SODIUM PROPIONATE ON THE SENSORY, MICROBIAL, AND CHEMICAL CHARACTERISTICS OF FRESH...

  16. 1. The derivative of y = mm“ at x = 2. A bacteria culture starts with ...

    E-Print Network [OSTI]

    The derivative of y = mm“ at x = 2. A bacteria culture starts with 200 bacteria and grows at a rate proportional to its size. After 2 hours there were 400 bacteria.

  17. Native California soils are selective reservoirs for multidrug-resistant bacteria

    E-Print Network [OSTI]

    Sachs, Joel

    Native California soils are selective reservoirs for multidrug-resistant bacteria Amanda C of antibiotic resistance in Bradyrhizobium (alphaproteobacteria). Bradyrhizobium are cosmopolitan bacteria bacteria can exhibit extensive antibiotic re- sistomes and act as reservoirs of important antibiotic

  18. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

    E-Print Network [OSTI]

    Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

    2013-01-01

    candidate structured RNAs from bacteria, archaea, and theirT-box regulatory systems in bacteria. RNA 2008, 15. Wels M,and transport genes in bacteria: yet another RNA riboswitch?

  19. Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea

    E-Print Network [OSTI]

    Brocks, Jochen J.

    Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea waters, hostile to eukaryotic algae. Phototrophic purple sulphur bacteria (Chromatiaceae) were detected-existed with communities of green sulphur bacteria (Chlorobiaceae). Collectively, the biomarkers support mounting evidence

  20. Bacteria Total Maximum Daily Load Task Force Final Report 

    E-Print Network [OSTI]

    Jones, C. Allan; Wagner, Kevin; Di Giovanni, George; Hauck, Larry; Mott, Joanna; Rifai, Hanadi; Srinivasan, Raghavan; Ward, George; Wythe, Kathy

    2009-01-01

    stream_source_info TR-341 Bacteria TMDL Task Force Report Draft Four 6.4.07.pdf.txt stream_content_type text/plain stream_size 344770 Content-Encoding ISO-8859-1 stream_name TR-341 Bacteria TMDL Task Force Report Draft Four 6....4.07.pdf.txt Content-Type text/plain; charset=ISO-8859-1 TR-341 2009 Bacteria Total Maximum Daily Load Task Force Final Report By C. Allan Jones and Kevin Wagner, Texas Water Resources...

  1. Process for producing modified microorganisms for oil treatment at high temperatures, pressures and salinity

    DOE Patents [OSTI]

    Premuzic, E.T.; Lin, M.

    1996-02-20

    This invention relates to the preparation of new, modified organisms, through challenge growth processes, that are viable in the extreme temperature, pressure and pH conditions and salt concentrations of an oil reservoir and that are suitable for use in microbial enhanced oil recovery. The modified microorganisms of the present invention are used to enhance oil recovery and remove sulfur compounds and metals from the crude oil. The processes are comprised of steps which successively limit the carbon sources and increase the temperature, pressure and salinity of the media. This is done until microbial strains are obtained that are capable of growing in essentially crude oil as a carbon source and at a temperature range from about 70 C to 90 C, at a pressure range from about 2,000 to 2,500 psi and at a salinity range from about 1.3 to 35%. 68 figs.

  2. Process for producing modified microorganisms for oil treatment at high temperatures, pressures and salinity

    DOE Patents [OSTI]

    Premuzic, Eugene T. (East Moriches, NY); Lin, Mow (Rocky Point, NY)

    1996-02-20

    This invention relates to the preparation of new, modified organisms, through challenge growth processes, that are viable in the extreme temperature, pressure and pH conditions and salt concentrations of an oil reservoir and that are suitable for use in microbial enhanced oil recovery. The modified microorganisms of the present invention are used to enhance oil recovery and remove sulfur compounds and metals from the crude oil. The processes are comprised of steps which successively limit the carbon sources and increase the temperature, pressure and salinity of the media. This is done until microbial strains are obtained that are capable of growing in essentially crude oil as a carbon source and at a temperature range from about 70.degree. C. to 90.degree. C., at a pressure range from about 2,000 to 2,500 psi and at a salinity range from about 1.3 to 35%.

  3. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

    SciTech Connect (OSTI)

    Kuk Lee, Sung; Chou, Howard; Ham, Timothy S.; Soon Lee, Taek; Keasling, Jay D.

    2009-12-02

    The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20 g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and synthetic biology will provide new tools for metabolic engineers to better understand how to rewire the cell in order to create the desired phenotypes for the production of economically viable biofuels.

  4. How sulphate-reducing microorganisms cope with stress: Lessons from systems biology

    SciTech Connect (OSTI)

    Zhou, J.; He, Q.; Hemme, C.L.; Mukhopadhyay, A.; Hillesland, K.; Zhou, A.; He, Z.; Nostrand, J.D. Van; Hazen, T.C.; Stahl, D.A.; Wall, J.D.; Arkin, A.P.

    2011-04-01

    Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.

  5. Micro-scale interactions between chemotactic bacteria and algae

    E-Print Network [OSTI]

    Vahora, Nisha

    2010-01-01

    Traditional views of marine environments describe the ocean pelagic zone as a homogeneous nutrient-poor environment. Heterotrophic marine bacteria that have evolved high-energy mechanisms for swimming abilities and sensing ...

  6. In Vivo Gene Expression Dynamics of Tumor-Targeted Bacteria

    E-Print Network [OSTI]

    Danino, Tal

    The engineering of bacteria to controllably deliver therapeutics is an attractive application for synthetic biology. While most synthetic gene networks have been explored within microbes, there is a need for further ...

  7. Small Talk: Cell-to-Cell Communication in Bacteria

    ScienceCinema (OSTI)

    Bassler, Bonnie [Princeton University, Princeton, New Jersey, United States

    2010-01-08

    Cell-cell communication in bacteria involves the production, release, and subsequent detection of chemical signaling molecules called autoinducers. This process, called quorum sensing, allows bacteria to regulate gene expression on a population-wide scale. Processes controlled by quorum sensing are usually ones that are unproductive when undertaken by an individual bacterium but become effective when undertaken by the group. For example, quorum sensing controls bioluminescence, secretion of virulence factors, biofilm formation, sporulation, and the exchange of DNA. Thus, quorum sensing is a mechanism that allows bacteria to function as multi-cellular organisms. Bacteria make, detect, and integrate information from multiple autoinducers, some of which are used exclusively for intra-species communication while others enable communication between species. Research is now focused on the development of therapies that interfere with quorum sensing to control bacterial virulence.

  8. Top 10 plant pathogenic bacteria in molecular plant pathology.

    E-Print Network [OSTI]

    2012-01-01

    Foster, G.D. (2012) The top 10 fungal pathogens in molecularBLACKWELL PUBLISHING LTD Top 10 plant pathogenic bacteriaC. and Foster, G.D. (2011) Top 10 plant viruses in molecular

  9. Foodborne Sources of Bacteria Associated With Human Obesity 

    E-Print Network [OSTI]

    McElhany, Katherine Grace

    2009-09-30

    Recently published research has suggested that the microbial ecology of the digestive system may play a role in obesity. Obese people have been shown to have a higher proportion of bacteria from the Firmicutes division and ...

  10. Material and method for promoting the growth of anaerobic bacteria

    DOE Patents [OSTI]

    Adler, Howard I. (128 Indian La., Oak Ridge, TN 37830)

    1984-01-01

    A material and method for promoting the growth of anaerobic bacteria which includes a nutrient media containing a hydrogen donor and sterile membrane fragments of bacteria having an electron transfer system which reduces oxygen to water. Dissolved oxygen in the medium is removed by adding the sterile membrane fragments to the nutrient medium and holding the medium at a temperature of about 10.degree. to about 60.degree. C. until the dissolved oxygen is removed.

  11. Global prevalence and distribution of genes and microorganisms involved in mercury methylation

    SciTech Connect (OSTI)

    Podar, Mircea; Gilmour, C C; Brandt, Craig C; Bullock, Allyson L; Brown, Steven D; Crable, Bryan R; Palumbo, Anthony Vito; Somenahally, Anil C; Elias, Dwayne A

    2015-01-01

    Mercury methylation produces the neurotoxic, highly bioaccumulative methylmercury (MeHg). Recent identification of the methylation genes (hgcAB) provides the foundation for broadly evaluating microbial Hg-methylation potential in nature without making explicit rate measurements. We queried hgcAB diversity and distribution in all available microbial metagenomes, encompassing most environments. The genes were found in nearly all anaerobic, but not in aerobic, environments including oxygenated layers of the open ocean. Critically, hgcAB was effectively absent in ~1500 human microbiomes, suggesting a low risk of endogenous MeHg production. New potential methylation habitats were identified, including invertebrate guts, thawing permafrost, coastal dead zones , soils, sediments, and extreme environments, suggesting multiple routes for MeHg entry into food webs. Several new taxonomic groups potentially capable of Hg-methylation emerged, including lineages having no cultured representatives. We begin to address long-standing evolutionary questions about Hg-methylation and ancient carbon fixation mechanisms while generating a new global view of Hg-methylation potential.

  12. Global prevalence and distribution of genes and microorganisms involved in mercury methylation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Podar, Mircea; Gilmour, C C; Brandt, Craig C; Bullock, Allyson L; Brown, Steven D; Crable, Bryan R; Palumbo, Anthony Vito; Somenahally, Anil C; Elias, Dwayne A

    2015-01-01

    Mercury methylation produces the neurotoxic, highly bioaccumulative methylmercury (MeHg). Recent identification of the methylation genes (hgcAB) provides the foundation for broadly evaluating microbial Hg-methylation potential in nature without making explicit rate measurements. We queried hgcAB diversity and distribution in all available microbial metagenomes, encompassing most environments. The genes were found in nearly all anaerobic, but not in aerobic, environments including oxygenated layers of the open ocean. Critically, hgcAB was effectively absent in ~1500 human microbiomes, suggesting a low risk of endogenous MeHg production. New potential methylation habitats were identified, including invertebrate guts, thawing permafrost, coastal dead zones , soils, sediments,more »and extreme environments, suggesting multiple routes for MeHg entry into food webs. Several new taxonomic groups potentially capable of Hg-methylation emerged, including lineages having no cultured representatives. We begin to address long-standing evolutionary questions about Hg-methylation and ancient carbon fixation mechanisms while generating a new global view of Hg-methylation potential.« less

  13. Bioaugmentation of butane-utilizing microorganisms to promote cometabolism of 1,1,1-trichloroethane in groundwater microcosms

    E-Print Network [OSTI]

    Semprini, Lewis

    Bioaugmentation of butane-utilizing microorganisms to promote cometabolism of 1,1,1-trichloroethane. The initial inoculum for bioaugmentation was a butane-utilizing enrichment from the subsurface of the Hanford DOE site. The non-augmented microcosm required 80 days of incubation before butane

  14. Bioprocessing of lignite coals using reductive microorganisms. Final technical report, September 30, 1988--March 29, 1992

    SciTech Connect (OSTI)

    Crawford, D.L.

    1992-03-29

    In order to convert lignite coals into liquid fuels, gases or chemical feedstock, the macromolecular structure of the coal must be broken down into low molecular weight fractions prior to further modification. Our research focused on this aspect of coal bioprocessing. We isolated, characterized and studied the lignite coal-depolymerizing organisms Streptomyces viridosporus T7A, Pseudomonas sp. DLC-62, unidentified bacterial strain DLC-BB2 and Gram-positive Bacillus megaterium strain DLC-21. In this research we showed that these bacteria are able to solubilize and depolymerize lignite coals using a combination of biological mechanisms including the excretion of coal solublizing basic chemical metabolites and extracellular coal depolymerizing enzymes.

  15. Cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1997-12-16

    Bacteria which produce large amounts of cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  16. Method of producing a cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1998-05-26

    Bacteria which produce large amounts of cellulose-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  17. Method of producing a cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01

    Bacteria which produce large amounts of cellulose-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  18. Cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1997-12-16

    Bacteria which produce large amounts of cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  19. Typical College Student Diet Food Derived Microorganisms and Their Relation to the Human Gastrointestinal Microflora 

    E-Print Network [OSTI]

    Haselhorst, Alexandria J.

    2011-08-08

    plates, the results were truly representative of the actual microbial load within the sample. 8 Homogenization was completed by placing 50 g of food product into a sample bag with a filter insert (VWR, West Chester, Penn.). Some products..., such as the drinks, were shaken prior to being weighed to ensure accurate collection of any bacteria present. The filter bag was filled with 450 mL of sterile Butterfield?s phosphate buffer when solid samples were being processed. The stomacher filter bag...

  20. Author's personal copy Arsenic-resistant bacteria solubilized arsenic in the growth media

    E-Print Network [OSTI]

    Ma, Lena

    Author's personal copy Arsenic-resistant bacteria solubilized arsenic in the growth media bacteria As solubilization Plant growth promotion a b s t r a c t The role of arsenic-resistant bacteria was associated with arsenic-induced plant P uptake. Arsenic resistant bacteria may have potential to enhance

  1. Author's personal copy Morts d'amour: mitochondria are bacteria that

    E-Print Network [OSTI]

    Author's personal copy Letters Morts d'amour: mitochondria are bacteria that sometimes become as bacteria, as recently explored in this journal [1], and this highly heuristic viewpoint should also the views of mitochondria as either bacteria or organelles and suggests that some bacteria transmuted

  2. Workshop on Magnetotactic Bacteria 9-11 June 2008, Balatonfred, Hungary The role of iron sulfide crystals in magnetotactic bacteria for

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Workshop on Magnetotactic Bacteria 9-11 June 2008, Balatonfüred, Hungary The role of iron sulfide crystals in magnetotactic bacteria for magnetotaxis: A transmission electron microscopy study Takeshi, Denmark Magnetotactic bacteria comprise a number of aquatic species that orient and migrate along

  3. Factors Affecting Biodefluorination of Fluorotelomer Alcohols (FTOHs): Degradative Microorganisms, Transformation Metabolites and Pathways, and Effects of Co-substrates 

    E-Print Network [OSTI]

    Kim, Myung Hee 1982-

    2012-12-11

    similar microbial community structure. This is the first study reporting that pure strains of alkane- and fluoroacetate-degrading bacteria can bio-transform FTOHs via different or preferred transformation pathways to remove multiple –CF2– groups from...

  4. Natural analogue studies of the role of colloids, natural organics and microorganisms on radionuclide transport

    SciTech Connect (OSTI)

    McCarthy, J.F.

    1994-10-01

    Colloids may be important as a geochemical transport mechanism for radionuclides at geological repositories if they are (1) present in the groundwater, (2) stable with respect to both colloidal and chemical stabilities, (3) capable of adsorbing radionuclides, especially if the sorption is irreversible, and (4) mobile in the subsurface. The available evidence from natural analogue and other field studies relevant to these issues is reviewed, as is the potential role of mobile microorganisms ({open_quotes}biocolloids{close_quotes}) on radionuclide migration. Studies have demonstrated that colloids are ubiquitous in groundwater, although colloid concentrations in deep, geochemically stable systems may be too low to affect radionuclide transport. However, even low colloid populations cannot be dismissed as a potential concern because colloids appear to be stable, and many radionuclides that adsorb to colloids are not readily desorbed over long periods. Field studies offer somewhat equivocal evidence concerning colloid mobility and cannot prove or disprove the significance of colloid transport in the far-field environment. Additional research is needed at new sites to properly represent a repository far-field. Performance assessment would benefit from natural analogue studies to examine colloid behavior at sites encompassing a suite of probable groundwater chemistries and that mimic the types of formations selected for radioactive waste repositories.

  5. Studies of unicellular micro-organisms Saccharomyces cerevisiae by means of Positron Annihilation Lifetime Spectroscopy

    E-Print Network [OSTI]

    Kubicz, E; Zgardzi?ska, B; Bednarski, T; Bia?as, P; Czerwi?ski, E; Gajos, A; Gorgol, M; Kami?ska, D; Kap?on, ?; Kochanowski, A; Korcyl, G; Kowalski, P; Kozik, T; Krzemie?, W; Nied?wiecki, S; Pa?ka, M; Raczy?ski, L; Rajfur, Z; Rudy, Z; Rundel, O; Sharma, N G; Silarski, M; S?omski, A; Strzelecki, A; Wieczorek, A; Wi?licki, W; Zieli?ski, M; Moskal, P

    2015-01-01

    Results of Positron Annihilation Lifetime Spectroscopy (PALS) and microscopic studies on simple microorganisms: brewing yeasts are presented. Lifetime of ortho - positronium (o-Ps) were found to change from 2.4 to 2.9 ns (longer lived component) for lyophilised and aqueous yeasts, respectively. Also hygroscopicity of yeasts in time was examined, allowing to check how water - the main component of the cell - affects PALS parameters, thus lifetime of o-Ps were found to change from 1.2 to 1.4 ns (shorter lived component) for the dried yeasts. The time sufficient to hydrate the cells was found below 10 hours. In the presence of liquid water an indication of reorganization of yeast in the molecular scale was observed. Microscopic images of the lyophilised, dried and wet yeasts with best possible resolution were obtained using Inverted Microscopy (IM) and Environmental Scanning Electron Microscopy (ESEM) methods. As a result visible changes to the surface of the cell membrane were observed in ESEM images.

  6. Computational Chemotaxis in Ants and Bacteria over Dynamic Environments

    E-Print Network [OSTI]

    Ramos, Vitorino; Rosa, A C; Abraham, A

    2007-01-01

    Chemotaxis can be defined as an innate behavioural response by an organism to a directional stimulus, in which bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (e.g., glucose) by swimming towards the highest concentration of food molecules, or to flee from poisons. Based on self-organized computational approaches and similar stigmergic concepts we derive a novel swarm intelligent algorithm. What strikes from these observations is that both eusocial insects as ant colonies and bacteria have similar natural mechanisms based on stigmergy in order to emerge coherent and sophisticated patterns of global collective behaviour. Keeping in mind the above characteristics we will present a simple model to tackle the collective adaptation of a social swarm based on real ant colony behaviors (SSA algorithm) for tracking extrema in dynamic environments and highly multimodal complex functions des...

  7. Rapid identification of bacteria using an umbelliferone fluorescent assay 

    E-Print Network [OSTI]

    Chamblin, Richard Thomas

    1983-01-01

    . Corgnebacterium seudotuberculosis KF which formed hard, dry colonies; or sr 1 11 ~11' LM h1*h f 4 * pt' lly " t"c colonies), 2 loopfulls of' bacteria per ml were estimated. Estimating 2 loopfulls proved to be an acceptable variation in the technique. Wet.... Quarles ( Co-Chairman of Committee) Charles F. Hall ( ember) L. C. Grumbles ( Member) B. G. Foster Head of Depar t) Ian R. Tiz r August 1983 ABSTRACT Rapid Identification of Bacteria Using an Umbelliferone Fluorescent Assay, (August 1983) Richard...

  8. Influence of microorganisms on the oxidation state distribution of multivalent actinides under anoxic conditions

    SciTech Connect (OSTI)

    Reed, Donald Timothy [Los Alamos National Laboratory; Borkowski, Marian [Los Alamos National Laboratory; Lucchini, Jean - Francois [Los Alamos National Laboratory; Ams, David [Los Alamos National Laboratory; Richmann, M. K. [Los Alamos National Laboratory; Khaing, H. [Los Alamos National Laboratory; Swanson, J. S. [Los Alamos National Laboratory

    2010-12-10

    The fate and potential mobility of multivalent actinides in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium, uranium and neptunium are the near-surface multivalent contaminants of concern and are also key contaminants for the deep geologic disposal of nuclear waste. Their mobility is highly dependent on their redox distribution at their contamination source as well as along their potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. Under anoxic conditions, indirect and direct bioreduction mechanisms exist that promote the prevalence of lower-valent species for multivalent actinides. Oxidation-state-specific biosorption is also an important consideration for long-term migration and can influence oxidation state distribution. Results of ongoing studies to explore and establish the oxidation-state specific interactions of soil bacteria (metal reducers and sulfate reducers) as well as halo-tolerant bacteria and Archaea for uranium, neptunium and plutonium will be presented. Enzymatic reduction is a key process in the bioreduction of plutonium and uranium, but co-enzymatic processes predominate in neptunium systems. Strong sorptive interactions can occur for most actinide oxidation states but are likely a factor in the stabilization of lower-valent species when more than one oxidation state can persist under anaerobic microbiologically-active conditions. These results for microbiologically active systems are interpreted in the context of their overall importance in defining the potential migration of multivalent actinides in the subsurface.

  9. 30/04/2009 16:15Quiet Bacteria and Antibiotic Resistance: Scientific American Page 1 of 2http://www.sciam.com/article.cfm?id=bacteria-antibiotic-resistance

    E-Print Network [OSTI]

    West, Stuart

    30/04/2009 16:15Quiet Bacteria and Antibiotic Resistance: Scientific American Page 1 of 2http://www.sciam.com/article.cfm?id=bacteria Bacteria and Antibiotic Resistance Bacteria devoted to growth instead of "quorum sensing" communication could beat antibiotic resistance By Melinda Wenner Despite the rising menace of bacteria--at roughly 19

  10. Biodesulfurization techniques: Application of selected microorganisms for organic sulfur removal from coals. Final report

    SciTech Connect (OSTI)

    Elmore, B.B.

    1993-08-01

    As an alternative to post-combustion desulfurization of coal and pre-combustion desulfurization using physicochemical techniques, the microbial desulfurization of coal may be accomplished through the use of microbial cultures that, in an application of various microbial species, may remove both the pyritic and organic fractions of sulfur found in coal. Organisms have been isolated that readily depyritize coal but often at prohibitively low rates of desulfurization. Microbes have also been isolated that may potentially remove the organic-sulfur fraction present in coal (showing promise when acting on organic sulfur model compounds such as dibenzothiophene). The isolation and study of microorganisms demonstrating a potential for removing organic sulfur from coal has been undertaken in this project. Additionally, the organisms and mechanisms by which coal is microbially depyritized has been investigated. Three cultures were isolated that grew on dibenzothiophene (DBT), a model organic-sulfur compound, as the sole sulfur source. These cultures (UMX3, UMX9, and IGTS8) also grew on coal samples as the sole sulfur source. Numerous techniques for pretreating and ``cotreating`` coal for depyritization were also evaluated for the ability to improve the rate or extent of microbial depyritization. These include prewashing the coal with various solvents and adding surfactants to the culture broth. Using a bituminous coal containing 0.61% (w/w) pyrite washed with organic solvents at low slurry concentrations (2% w/v), the extent of depyritization was increased approximately 25% in two weeks as compared to controls. At slurry concentrations of 20% w/v, a tetrachloroethylene treatment of the coal followed by depyritization with Thiobacillus ferrooxidans increased both the rate and extent of depyritization by approximately 10%.

  11. Modelling of bacteria leaching through porous Graham HORGAN

    E-Print Network [OSTI]

    Molchanov, Ilya

    leaching of bacteria through complex soils, the researcher has to employ numerical methods as the known of statistical stability as the diffusion times vary dramatically between different realisations and soil samples of Mathematics and Mechanics, Moscow State University, 119992, Moscow, Russia. 1 #12;In addition, we have shown

  12. Methods for targetted mutagenesis in gram-positive bacteria

    SciTech Connect (OSTI)

    Yang, Yunfeng

    2014-05-27

    The present invention provides a method of targeted mutagenesis in Gram-positive bacteria. In particular, the present invention provides a method that effectively integrates a suicide integrative vector into a target gene in the chromosome of a Gram-positive bacterium, resulting in inactivation of the target gene.

  13. Method for establishing the presence of salmonella bacteria in eggs

    DOE Patents [OSTI]

    Johnston, Roger G. (Los Alamos, NM); Sinha, Dipen N. (Los Alamos, NM)

    1995-01-01

    Measurement of the acoustical resonances in eggs is shown to provide a rapid, noninvasive technique for establishing the presence of Salmonella bacteria. The technique is also sensitive to yolk puncture, shell cracks, and may be sensitive to other yolk properties and to egg freshness. Remote characterization, potentially useful for characterizing large numbers of eggs, has been demonstrated.

  14. Films of bacteria at interfaces: three stages of behaviour

    E-Print Network [OSTI]

    Liana Vaccari; Daniel Allan; Nima Sharifi-Mood; Aayush Singh; Robert Leheny; Kathleen Stebe

    2015-03-25

    Bacterial attachment to a fluid interface can lead to the formation of a film with physicochemical properties that evolve with time. We study the time evolution of interface (micro)mechanics for interfaces between oil and bacterial suspensions by following the motion of colloidal probes trapped by capillarity to determine the interface microrheology. Initially, active bacteria at and near the interface drive superdiffusive motion of the colloidal probes. Over timescales of minutes, the bacteria form a viscoelastic film which we discuss as a quasi-two-dimensional, active, glassy system. To study late stage mechanics of the film, we use pendant drop elastometry. The films, grown over tens of hours on oil drops, are expanded and compressed by changing the drop volume. For small strains, by modeling the films as 2D Hookean solids, we estimate the film elastic moduli, finding values similar to those reported in the literature for the bacteria themselves. For large strains, the films are highly hysteretic. Finally, from wrinkles formed on highly compressed drops, we estimate film bending energies. The dramatic restructuring of the interface by such robust films has broad implications, e.g. in the study of active colloids, in understanding the community dynamics of bacteria, and in applied settings including bioremediation.

  15. Biodegradation potential of wastewater micropollutants by ammonia-oxidizing bacteria

    E-Print Network [OSTI]

    Chu, Kung-Hui "Bella"

    Available online xxxx Keywords: Triclosan Bisphenol A Ibuprofen Ammonia-oxidizing bacteria Nitrosomonas of three wastewater micropollutants (triclosan, bisphenol A, and ibuprofen) by Nitrosomonas europaea and bisphenol A, but not ibuprofen. The degra- dation was observed only in the absence of allylthiourea (an

  16. Introduction The use of immobilized bacteria for ex situ bioremedi-

    E-Print Network [OSTI]

    Hazen, Terry

    , to immobilize degradative bacteria (Radway et al., 1996). The latter study demonstrated that biomass in a Waring blender. Final biomass concentra- tion was 8­17% (dry weight). Degradation experiments B. cepacia G4 cells were induced by adding phenol at 2 mM for 2 h prior to centrifugation (Shields et al., 1989

  17. Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization

    SciTech Connect (OSTI)

    Lancaster, Andrew [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Menon, Angeli [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Scott, Israel [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Poole, Farris [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Vaccaro, Brian [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Thorgersen, Michael P [ORNL] [ORNL; Geller, Jil [Lawrence Berkeley National Laboratory (LBNL)] [Lawrence Berkeley National Laboratory (LBNL); Hazen, Terry C [ORNL] [ORNL; Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL] [ORNL; Elias, Dwayne A [ORNL] [ORNL; Adams, Michael W. W. [University of Georgia, Athens, GA] [University of Georgia, Athens, GA

    2014-01-01

    Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strain Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.

  18. Measuring Metabolism Using O2 and CO2 Class note readings: Review the section on aerobic metabolism. Be sure that you understand

    E-Print Network [OSTI]

    Prestwich, Ken

    Principle of Respiratory Gas Measurements: When using gas fraction respirometry, V · O2 and V · CO21 Measuring Metabolism Using O2 and CO2 1 Class note readings: Review the section on aerobic of oxygen used per unit time or M · O2 which is the number of mols of oxygen used per unit time or · V · CO2

  19. Magnetic microstructures of chains and clusters of iron oxide and sulfide nanocrystals in bacteria

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Magnetic microstructures of chains and clusters of iron oxide and sulfide nanocrystals in bacteria of intracellular ferrimagnetic magnetite (Fe3O4) and greigite (Fe3S4) nanocrystals inside magnetotactic bacteria

  20. Biofilms as sources of fecal bacteria contamination in the stormwater drainage system in Singapore

    E-Print Network [OSTI]

    Burkhart, Tsung Hwa (Tsung Hwa Sophia)

    2013-01-01

    A study was performed to examine a possible source of fecal bacteria contamination originating from within the stormwater drainage system in Singapore. The extent of fecal bacteria presence in storm drain biofilms was ...

  1. The Association of Virulent Vibrio Spp. Bacteria on Gafftopsail and Hardhead Catfish in Galveston Bay 

    E-Print Network [OSTI]

    Gilbert, Leslie Deanne

    2011-10-21

    Vibrio vulnificus (Vv) and V. parahaemolyticus (Vp) are gram negative, halophilic bacteria that occur naturally in estuarine waters of Galveston Bay. Both bacteria have the potential to cause infections in humans either via consumption or direct...

  2. Aerobic degradation of 2,4,6-trinitrotoluene by Enterobacter cloacae PB2 and by pentaerythritol tetranitrate reductase

    SciTech Connect (OSTI)

    French, C.E.; Bruce, N.C.; Nicklin, S.

    1998-08-01

    Enterobacter cloacae PB2 was originally isolated on the basis of its ability to utilize nitrate esters, such as pentaerythritol tetranitrate (PETN) and glycerol trinitrate, as the sole nitrogen source for growth. The enzyme responsible is an NADPH-dependent reductase designated PETN reductase. E. cloacae PB2 was found to be capable of slow aerobic growth with 2,4,6-trinitrotoluene (TNT) as the sole nitrogen source. Dinitrotoluenes were not produced and could not be used as nitrogen sources. Purified PETN reductase was found to reduce TNT to its hydride-Meisenheimer complex, which was further reduced to the dihydride-Meisenheimer complex. Purified PETN reductase and recombinant Escherichia coli expressing PETN reductase were able to liberate nitrogen as nitrite from TNT. The ability to remove nitrogen from TNT suggests that PB2 or recombinant organisms expressing PETN reductase may be useful for bioremediation of TNT-contaminated soil and water.

  3. The calcification of Staphylococcus aureus bacteria : a potential defense mechanism against infections

    E-Print Network [OSTI]

    Arellano, Catherine Krystle

    2010-01-01

    in Serum: A Possible Mechanism for Biomineralization. J.Bacteria: A Potential Defense Mechanism Against Infections Amechanism

  4. Chemical biology and bacteria: not simply a matter of life or death

    E-Print Network [OSTI]

    Mekalanos, John

    Chemical biology and bacteria: not simply a matter of life or death Deborah T Hung1,3 and Eric J Rubin2,3 Chemical biological approaches to understanding bacteria have largely been confined and that combining chemical biologic and genetic approaches to studying bacteria brings new power to old problems

  5. Characterization of arsenic-resistant bacteria from the rhizosphere of arsenic hyperaccumulator

    E-Print Network [OSTI]

    Ma, Lena

    Characterization of arsenic-resistant bacteria from the rhizosphere of arsenic hyperaccumulator that these arsenic-resistant bacteria are met- abolically adapted to arsenic-induced osmotic or oxidative stresses to the high arsenic resistance in the bacterial isolates. Key words: arsenic-resistant bacteria, Pteris

  6. Source tracking fecal bacteria in water: a critical review of current methods

    E-Print Network [OSTI]

    Mazumder, Asit

    source tracking; E. coli; Fecal bacteria; Water quality; Ribotyping; Antibiotic resistance analysis (ARAReview Source tracking fecal bacteria in water: a critical review of current methods Cynthia L and techniques are being developed to track sources of bacteria in water and food. Currently

  7. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

    E-Print Network [OSTI]

    Handelsman, Jo

    Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization Nikolina­ resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria of antibiotic- resistant bacteria, antibiotic-resistance genes (collectively known as the "resistome

  8. Combating Drug-Resistant Bacteria: Small Molecule Mimics of Plasmid Incompatibility as Antiplasmid Compounds

    E-Print Network [OSTI]

    Hergenrother, Paul J.

    Combating Drug-Resistant Bacteria: Small Molecule Mimics of Plasmid Incompatibility as Antiplasmid, 2004; E-mail: hergenro@uiuc.edu Multidrug resistant bacteria are now ubiquitous in both hospital to vancomycin.2 Due to this prevalence of drug-resistant bacteria, there is a pressing need for novel classes

  9. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)

    E-Print Network [OSTI]

    Quake, Stephen R.

    resistance has hindered characterization of these enigmatic bacteria. In the present study, we isolated five bacteria (SFB) Su¨nje J. Pamp,1 Eoghan D. Harrington,1 Stephen R. Quake,2,3,4 David A. Relman,1 94304, USA Segmented filamentous bacteria (SFB) are host-specific intestinal symbionts that comprise

  10. Mathematical Analysis of a model describing the invasion of bacteria in burn wounds #

    E-Print Network [OSTI]

    Eindhoven, Technische Universiteit

    and references). The rapid development of antibiotic resistance among bacteria has added urgency to the taskMathematical Analysis of a model describing the invasion of bacteria in burn wounds # D. Hilhorst arises as a model for host tissue degradation by bacteria and involves a parameter describing

  11. Mathematical Analysis of a model describing the invasion of bacteria in burn wounds

    E-Print Network [OSTI]

    Eindhoven, Technische Universiteit

    and references). The rapid development of antibiotic resistance among bacteria has added urgency to the taskMathematical Analysis of a model describing the invasion of bacteria in burn wounds D. Hilhorst arises as a model for host tissue degradation by bacteria and involves a parameter describing

  12. Physica A 359 (2006) 495524 Seeking the foundations of cognition in bacteria

    E-Print Network [OSTI]

    Jacob, Eshel Ben

    2006-01-01

    Physica A 359 (2006) 495­524 Seeking the foundations of cognition in bacteria: From Schro¨ dinger fundamental requirement of Life. In other words, all organisms, including bacteria, the most primitive that by acting together, bacteria can perform this most elementary cognitive function more efficiently as can

  13. When Bacteria Talk: Time Elapse Communication for Super-Slow Networks

    E-Print Network [OSTI]

    Sivakumar, Raghupathy

    When Bacteria Talk: Time Elapse Communication for Super-Slow Networks Bhuvana Krishnaswamy a Escherichia coli bacteria serving as the communication receiver that a simple modulation like on-off keying- ically bio-inspired) for use in biological applications [3]­[5]. In recent years, bacteria have emerged

  14. Magnetic microstructure of chains and clusters of iron oxide and sulfide nanocrystals in bacteria

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Magnetic microstructure of chains and clusters of iron oxide and sulfide nanocrystals in bacteria M Magnetotactic bacteria contain intracellular, membrane-bound ferrimagnetic nanocrystals (magnetosomes) that have of magnetotactic bacteria provide a natural laboratory in which the magnetic properties of nanometer

  15. BACTERIA TMDL IMPLEMENTATION CONTROL STRATEGIES OF THE SOUTHEAST: RECOMMENDATIONS FOR GEORGIA

    E-Print Network [OSTI]

    Radcliffe, David

    BACTERIA TMDL IMPLEMENTATION CONTROL STRATEGIES OF THE SOUTHEAST: RECOMMENDATIONS FOR GEORGIA implementation plans for bacteria in the state of Georgia. Methods include reviewing relevant literature, policy bacteria TMDL implementation plans; 2) showing control strategies in other states that could be implemented

  16. A simple bioclogging model that accounts for spatial spreading of bacteria

    E-Print Network [OSTI]

    Demaret, Laurent

    A simple bioclogging model that accounts for spatial spreading of bacteria HJ Eberla , L Demaretb is presented that accounts for spatial expansion of the bacterial popu- lation in the soil. The bacteria move harmful environ- mental factors and mechanical washout. Naturally occurring bacteria are a major

  17. Label-free bacteria detection using evanescent mode of a suspended core terahertz fiber

    E-Print Network [OSTI]

    Skorobogatiy, Maksim

    Label-free bacteria detection using evanescent mode of a suspended core terahertz fiber Anna time an E. coli bacteria sensor based on the evanescent field of the fundamental mode of a suspended\\ SKDJHV DQG WKHQ GHVWUR\\HG ZLWK a P-size fragments remaining bound to the fiber surface. The bacteria

  18. Under consideration for publication in J. Fluid Mech. 1 The wiggling trajectories of bacteria

    E-Print Network [OSTI]

    Hyon, YunKyong

    Under consideration for publication in J. Fluid Mech. 1 The wiggling trajectories of bacteria Y U N) Many motile bacteria display wiggling trajectories, which correspond to helical swimming paths and orientations relative to the cell body for peritrichously flagellated bacteria. Modeling the bundle as a rigid

  19. Bacteria Targeted By Human Natural Antibodies Using -Gal Conjugated Receptor-specic Glycopolymers

    E-Print Network [OSTI]

    Chen, Xi

    Bacteria Targeted By Human Natural Antibodies Using -Gal Conjugated Receptor-speci®c Glycopolymers as speci®c ligands for bacterial cells. The binding of the resulting multivalent glycopolymer to bacteria and infectious disease. However, many bacteria undergo genetic changes to eschew the host immune system. In spite

  20. Physical Channel Characterization for Medium-Range Nano-Networks using Flagellated Bacteria

    E-Print Network [OSTI]

    Politècnica de Catalunya, Universitat

    Physical Channel Characterization for Medium-Range Nano-Networks using Flagellated Bacteria Maria-µm): flagellated bacteria. This tech- nique is based on the transport of DNA-encoded information between emit- ters-machines. Keywords: Nano-networks; Molecular Communication; Flagellated Bacteria; DNA Packet; Propagation delay

  1. AOML Keynotes July-August 2004 Students Discover Microscopic World of Marine Bacteria

    E-Print Network [OSTI]

    Goodwin, Kelly D.

    AOML Keynotes July-August 2004 Students Discover Microscopic World of Marine Bacteria AOML microbiologist Kelly Goodwin helped teach young girls about the invisible world of marine bacteria at a recent support the growth of marine bacteria, microscopic life forms living in the ocean. They were taught how

  2. Bacteria adds to fly lifespan Calgary Herald Calgary, Alta.:Aug 17, 2004. p. A4

    E-Print Network [OSTI]

    Seroude, Laurent

    Bacteria adds to fly lifespan Calgary Herald Calgary, Alta.:Aug 17, 2004. p. A4 Abstract (Article Summary) Exposing the insect drosophila to bacteria at various moments of its notoriously short existence, the researchers found if bacteria were successful in latching onto a host fly within the first four to seven days

  3. Nano-optical Trapping of Rayleigh Particles and Escherichia coli Bacteria

    E-Print Network [OSTI]

    Nano-optical Trapping of Rayleigh Particles and Escherichia coli Bacteria with Resonant Optical demonstrate a novel optical trapping scheme that allows us to hold living Escherichia coli bacteria bacteria are trapped simultaneously with their orientation fixed by the asymmetry of the antennas

  4. 788 NATURE PHYSICS | VOL 10 | NOVEMBER 2014 | www.nature.com/naturephysics Sizing up bacteria

    E-Print Network [OSTI]

    Loss, Daniel

    bacteria Chances are you've never seen a bacterium with your naked eye. The largest physical dimension smaller than the width of a human hair. We've all seen bacteria, but only with the aid of a microscope. You may wonder -- why aren't some bacteria a lot bigger? Well, there's a fairly obvious answer

  5. Phosphorus solubilization and plant growth enhancement by arsenic-resistant bacteria

    E-Print Network [OSTI]

    Ma, Lena

    Phosphorus solubilization and plant growth enhancement by arsenic-resistant bacteria Piyasa Ghosh a, University of Florida, Gainesville, FL 32611, United States h i g h l i g h t s Arsenic-resistant bacteria 2015 Accepted 23 March 2015 Handling Editor: J. de Boer Keywords: Arsenic-resistant bacteria FePO4

  6. Surface-Enhanced Infrared Absorption-Reflectance (SEIRA) Microspectroscopy A Chemical/Biological Probe for Bacteria

    E-Print Network [OSTI]

    /Biological Probe for Bacteria Localization in Geologic Materials Hoi-Ying N. Holman, Dale L. Perry, Michael C and the possibility of using the intrinsic endolithic (rock/mineral-inhabiting) bacteria to either detoxify or immobilize the pollutants have stimulated new interests in the exploration of endolithic bacteria

  7. Development of a simple and sensitive fluorimetric method for isolation of coumaphos-hydrolysing bacteria

    E-Print Network [OSTI]

    Hammock, Bruce D.

    -hydrolysing bacteria R.L. Harcourt*, I. Horne, T.D. Sutherland, B.D. Hammock1 , R.J. Russell and J.G. Oakeshott . Incorporation of coumaphos into agar plates allowed the rapid detection of coumaphos-hydrolysing bacteria when tool to screen for bacteria possessing phosphotriesterase activity. INTRODUCTION Organophosphorus (OP

  8. Magnetic Microstructure of Closely-Spaced Ferrimagnetic Crystals in Magnetotactic Bacteria

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Magnetic Microstructure of Closely-Spaced Ferrimagnetic Crystals in Magnetotactic Bacteria R. E of Cambridge, Pembroke Street, Cambridge CB2 3QZ, United Kingdom Magnetotactic bacteria migrate along of magnetite and greigite crystals in air-dried cells of magnetotactic bacteria, with sub-10-nm spatial

  9. Polar features in the flagellar propulsion of E. coli bacteria

    E-Print Network [OSTI]

    Bianchi, S; Lepore, A; Di Leonardo, R

    2015-01-01

    E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the bundle unwinds and the cell randomizes its orientation. This basic picture represents an idealization of a much more complex dynamical problem. Although it has been shown that bundle formation can occur at either pole of the cell, it is still unclear whether this two run states correspond to asymmetric propulsion features. Using holographic microscopy we record the 3D motions of individual bacteria swimming in optical traps. We find that most cells possess two run states characterised by different propulsion forces, total torque and bundle conformations. We analyse the statistical properties of bundle reversal and compare the hydrodynamic features of forward and backward running states. Our method is naturally multi-particle and opens up the way towards controlled hydrodynam...

  10. Effective run-and-tumble dynamics of bacteria baths

    E-Print Network [OSTI]

    M. Paoluzzi; R. Di Leonardo; L. Angelani

    2013-07-30

    {\\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles or equivalently of very low concentrations. However, in situations of practical interest, the concentration of bacteria is always large enough to make interactions an important factor. Using molecular dynamics simulations, we study the dynamic structure factor of a model bacterial bath for increasing values of densities. We show that it is possible to reproduce the dynamics of density fluctuations in the system using a free run-and-tumble model with effective fitting parameters. We discuss the dependence of these parameters, e.g., the tumbling rate, tumbling time and self-propulsion velocity, on the density of the bath.

  11. Reduction of trichloroethylene in a model aquifer with methanotrophic bacteria 

    E-Print Network [OSTI]

    Hicks, Duane Dee

    1990-01-01

    REDUCTION OF TRICHLOROETHYLENE IN A MODEL AQUIFER WITH METHANOTROPHIC BACTERIA A Thesis by Duane Dee Hicks Submitted to the Office of Graduate Studies of Texas ARM University in partial fullfillment of the requirements for thc degree... of MASTER OF SCIENCE December 1990 Major Subject: Civil Engineering REDUCTION OF TRICHLOROETHYLENE IN A MODEL AQUIFER WITH METHANOTROPHIC BACTEPslA A Thesis by Duane Dec Hicks Approved as to style and content by Bill Batchclor (Chair of Committee...

  12. Petroleum hydrocarbon-degrading bacteria in the Galveston Bay system 

    E-Print Network [OSTI]

    Schropp, Steven James

    1979-01-01

    activities and shipping may all release petroleum hydrocarbons into the marine environment (83), which are potentially detrimental to the estuarine system. Estuaries have been found to be one of the most active types of water in terms of microbial... bacteria to oil inpiit might be used as an indicator or petroleuin pollution (6, 43, 44). To evaluate the effects of ) vllutant hydrocarbons ozi the bacterial populations of estuarine systems, information on the distribution and abundance...

  13. Copy of Synthetic Biology of Novel Thermophilic Bacteria for Enhanced

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing BacteriaConnect Collider Testspolycarbonate and

  14. Degradation of Staphylococcus aureus bacteria by neutral oxygen atoms

    SciTech Connect (OSTI)

    Cvelbar, U.; Mozetic, M. [Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); Hauptman, N.; Klanjsek-Gunde, M. [National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)

    2009-11-15

    The degradation of Staphylococcus aureus bacteria during treatment with neutral oxygen atoms was monitored by scanning electron microscopy. Experiments were performed in an afterglow chamber made from borosilicate glass. The source of oxygen atoms was remote inductively coupled radiofrequency oxygen plasma. The density of atoms at the samples was 8x10{sup 20} m{sup -3}. The treatment was performed at room temperature. The first effect was the removal of dried capsule. Capsule on exposed parts of bacteria was removed after receiving the dose of 6x10{sup 23} at./m{sup 2}, while the parts of capsule filling the gaps between bacteria were removed after receiving the dose of 2.4x10{sup 24} m{sup -2}. After removing the capsule, degradation continued as etching of bacterial cell wall. The etching was rather nonuniform as holes with diameter of several 10 nm were observed. The cell wall was removed after receiving the dose of about 7x10{sup 24} m{sup -2}. The etching probabilities were about 2x10{sup -5} for the capsule and 2x10{sup -6} for the cell wall. The results were explained by different compositions of capsule and the cell wall.

  15. Differential Dynamic Microscopy to characterize Brownian motion and bacteria motility

    E-Print Network [OSTI]

    David Germain; Mathieu Leocmach; Thomas Gibaud

    2015-11-03

    We have developed a lab work module where we teach undergraduate students how to quantify the dynamics of a suspension of microscopic particles, measuring and analyzing the motion of those particles at the individual level or as a group. Differential Dynamic Microscopy (DDM) is a relatively recent technique that precisely does that and constitutes an alternative method to more classical techniques such as dynamics light scattering (DLS) or video particle tracking (VPT). DDM consists in imaging a particle dispersion with a standard light microscope and a camera. The image analysis requires the students to code and relies on digital Fourier transform to obtain the intermediate scattering function, an autocorrelation function that characterizes the dynamics of the dispersion. We first illustrate DDM on the textbook case of colloids where we measure the diffusion coefficient. Then we show that DDM is a pertinent tool to characterize biologic systems such as motile bacteria i.e.bacteria that can self propel, where we not only determine the diffusion coefficient but also the velocity and the fraction of motile bacteria. Finally, so that our paper can be used as a tutorial to the DDM technique, we have joined to this article movies of the colloidal and bacterial suspensions and the DDM algorithm in both Matlab and Python to analyze the movies.

  16. Conducting Nanosponge Electroporation for Affordable and High-Efficiency Disinfection of Bacteria and Viruses in Water

    E-Print Network [OSTI]

    Cui, Yi

    byproducts formation, energy and time intensiveness, and pathogen recovery. Here, we report an innovative more than 3 logs (99.9%) of microorganism removal, voltages as high as 103 to 105 volts are required

  17. Emergent patterns of diversity and dynamics in natural populations of planktonic Vibrio bacteria

    E-Print Network [OSTI]

    Thompson, Janelle Renée, 1976-

    2005-01-01

    Despite the importance of microorganisms for global and engineering processes, currently lacking is a theoretical framework to describe how the structure of a microbial assemblage translates an environmental condition into ...

  18. The future is now: single-cell genomics of bacteria and archaea

    E-Print Network [OSTI]

    Blainey, Paul C.

    Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation ...

  19. Fuel from Bacteria, CO2, Water, and Solar Energy: Engineering a Bacterial Reverse Fuel Cell

    SciTech Connect (OSTI)

    2010-07-01

    Electrofuels Project: Harvard is engineering a self-contained, scalable Electrofuels production system that can directly generate liquid fuels from bacteria, carbon dioxide (CO2), water, and sunlight. Harvard is genetically engineering bacteria called Shewanella, so the bacteria can sit directly on electrical conductors and absorb electrical current. This current, which is powered by solar panels, gives the bacteria the energy they need to process CO2 into liquid fuels. The Harvard team pumps this CO2 into the system, in addition to water and other nutrients needed to grow the bacteria. Harvard is also engineering the bacteria to produce fuel molecules that have properties similar to gasoline or diesel fuel—making them easier to incorporate into the existing fuel infrastructure. These molecules are designed to spontaneously separate from the water-based culture that the bacteria live in and to be used directly as fuel without further chemical processing once they’re pumped out of the tank.

  20. Aerobic and Anaerobic Metabolism Aerobic = oxidative metabolism

    E-Print Network [OSTI]

    Jodice, Patrick

    and lizards · Anaerobic metabolism may supply 50-90% of energy during activity · As with many other processes high rates of gas exchange or efficient circulation · Has low thermal dependence ­ that is, it is not dependent on extensive generation of heat/energy which may be advantageous in poikilotherms (esp. small ones

  1. Influence of inorganic and organic nutrients on aerobic biodegradation and on the adaptation response of subsurface microbial communities

    SciTech Connect (OSTI)

    Swindoll, C.M.; Aelion, C.M.; Pfaender, F.K.

    1988-01-01

    The influence of inorganic and organic amendments on the mineralization of ethylene dibromide, rho-nitrophenol, phenol, and toluene was examined in subsurface soil samples from a pristine aquifer near Lula, Oklahoma. The responses indicate that the metabolic abilities and nutrient requirements of ground water microorganisms vary substantially within an aquifer. In some samples, additions of inorganic nutrients resulted in a more rapid adaptation to the test substrate and a higher rate of metabolism, indicating that metabolism may have been limited by these nutrients. In other samples from the same aquifer layer, inorganic amendments had little or no influence on mineralization. In general, the addition of multiple inorganic nutrients resulted in a greater enhancement of degradation than did the addition of single substances. Additions of alternate carbon sources, such as glucose or amino acids, inhibited the mineralization of the xenobiotic substrates. This inhibition appears to be the result of the preferential utilization of the more easily degradable carbon amendments.

  2. Stress reduction as a link between aerobic activity and academic performance experienced by undergraduate women through the use of the Student Recreation Center at Texas A&M University 

    E-Print Network [OSTI]

    Brennan, Martha

    2007-09-17

    of electrochemical messages between and among neurons (cells specialized for conducting electrochemical impulses) (Gagne et al., 1993). An increase in serotonin may be one of the mechanisms that results from physical activity and potentially linked to improved... by looking at the biochemical make-up in the body and how aerobic activity affects it. Serotonin, a chief ingredient produced by the body and used in antidepressants, increased as a result of physical activity (Nash, 1996). Aerobic activity helps...

  3. Polar features in the flagellar propulsion of E. coli bacteria

    E-Print Network [OSTI]

    S. Bianchi; F. Saglimbeni; A. Lepore; R. Di Leonardo

    2015-06-30

    E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the bundle unwinds and the cell randomizes its orientation. This basic picture represents an idealization of a much more complex dynamical problem. Although it has been shown that bundle formation can occur at either pole of the cell, it is still unclear whether this two run states correspond to asymmetric propulsion features. Using holographic microscopy we record the 3D motions of individual bacteria swimming in optical traps. We find that most cells possess two run states characterised by different propulsion forces, total torque and bundle conformations. We analyse the statistical properties of bundle reversal and compare the hydrodynamic features of forward and backward running states. Our method is naturally multi-particle and opens up the way towards controlled hydrodynamic studies of interacting swimming cells.

  4. Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria

    DOE Patents [OSTI]

    Ooteghem, Suellen Van (Morgantown, WV)

    2005-09-13

    A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

  5. Purple Bacteria Develops Its Own Form of Sunscreen | U.S. DOE...

    Office of Science (SC) Website

    Home Centers Research Science Highlights Highlight Archives News & Events Publications History Contact BES Home 05.03.12 Purple Bacteria Develops Its Own Form of "Sunscreen" Print...

  6. Contribution of Iron-Reducing Bacteria to Mercury Methylation in Marine Sediments

    E-Print Network [OSTI]

    Fleming, Emily J.; Nelson, D C

    2006-01-01

    in continental margin sediments off central Chile. Limnologyof microbial iron reduction in sediments of the Baltic-Northreducing bacteria from sediments of an acid stressed lake.

  7. Mechanism for collective cell alignment in Myxococcus xanthus bacteria

    E-Print Network [OSTI]

    Balagam, Rajesh

    2015-01-01

    M. xanthus cells self-organize into clusters, aligned cell groups, at various stages of its lifecycle. Formation of these clusters is crucial for complex dynamic multi-cellular behavior of these bacteria. However the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework where each agent is based on biophysical model of individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce observed ability of cells to lay and follow slime trails, we show that effective trail following leads to clusters in reversing cells. Furthermore, we conclude th...

  8. Bioaugmentation with butane-utilizing microorganisms to promote in situ cometabolic treatment of 1,1,1-trichloroethane and 1,1-dichloroethene

    E-Print Network [OSTI]

    Semprini, Lewis

    Bioaugmentation with butane-utilizing microorganisms to promote in situ cometabolic treatment of 1) through bioaugmentation with a butane enrichment culture containing predominantly two Rhodococcus sp of butane and dissolved oxygen and or hydrogen peroxide as sources of dissolved oxygen, about 70% removal

  9. Marine microorganisms dominate the ocean ecosystem and sustain planetary habitability. The scientists and educators on the C-MORE Team --women and

    E-Print Network [OSTI]

    Marine microorganisms dominate the ocean ecosystem and sustain planetary habitability to a unique partnership aimed at exploring and understanding how the marine microbial world is structured`i Partnership #12;Marine Microbiology Initiative VIA SEA MAIL SCHOOL OF OCEAN AND EARTH SCIENCE AND TECHNOLOGY U

  10. Detergent composition comprising a cellulase containing cell-free fermentate produced from microorganism ATCC 55702 or mutant thereof

    DOE Patents [OSTI]

    Dees, H.C.

    1998-07-14

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  11. Detergent composition comprising a cellulase containing cell-free fermentate produced from microorganism ATCC 55702 or mutant thereof

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  12. In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria

    E-Print Network [OSTI]

    Gent, Universiteit

    In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria Dirk Gevers a;Ã , Geert Huys a , Jean Swings a;b a Laboratory of Microbiology, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium b BCCM1/LMG Bacteria Collection, Faculty of Sciences, Ghent

  13. Spatial arrangements and magnetic properties of oxide and sulfide magnetosomes in magnetotactic bacteria

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    bacteria M. Pósfai1 , T. Kasama2,3 , E.T. Simpson3 , R.K.K. Chong3 , I. Kósa1 , A. Scheffel4 , D. Schüler4 of intracellular ferrimagnetic magnetite (Fe3O4) and greigite (Fe3S4) crystals in magnetotactic bacteria

  14. Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

    DOE Patents [OSTI]

    Apel, William A.; Dugan, Patrick R.

    1995-04-04

    An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

  15. Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

    DOE Patents [OSTI]

    Apel, William A. (Idaho Falls, ID); Dugan, Patrick R. (Idaho Falls, ID)

    1995-01-01

    An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

  16. Microbial Grazers Lab Objective: Measure the rate at which bacteria are consumed by predators.

    E-Print Network [OSTI]

    Vallino, Joseph J.

    Microbial Grazers Lab Objective: Measure the rate at which bacteria are consumed by predators. Overview ·Size based food webs ·Microbial loop concepts ·Bacterial predators ·Methods to assess microbial bacteria were know to exist, they were not thought to be significant consumers of carbon or energy. #12

  17. Novel Methane, Ethane, and Propane Oxidizing Bacteria at Marine Hydrocarbon Seeps Identified by Stable Isotope Probing

    E-Print Network [OSTI]

    Sessions, Alex L.

    Novel Methane, Ethane, and Propane Oxidizing Bacteria at Marine Hydrocarbon Seeps Identified by Stable Isotope Probing Running Title: Novel Methane, Ethane, and Propane Oxidizing Bacteria Section incubating sediment with 13 C-labeled methane, ethane, or propane, we5 confirmed the incorporation of 13 C

  18. On-line monitoring of aerobic bioremediation with bioluminescent reporter microbes. Final report, July 1991--December 1994

    SciTech Connect (OSTI)

    Sayler, G.S.

    1995-03-01

    A critical issue in the biological characterization of contaminated sites and in the evaluation of relative bioremediation treatment efficiencies is the development of appropriate monitoring methods for the assessment of pollutant bioavailability and microbial in situ activity potential. In nature, pollutants are found dispersed among the solid, liquid and gaseous phases of the complex environments rendering the analytical estimation of their bioavailability and degradation more difficult and irrelevant. Ex situ and extractive analytical techniques have only been misrepresentative of the natural conditions and often resulted in inaccurate estimates of pollutants mass transfer. In this project, the bioluminescent bioreporter bacterium P. Fluorescens HK44 was integrated to an optical device, capable of conducting emitted light, and used as an online biosensor of naphthalene and salicylate. The physiological requirements of the bacteria and the physical limitations of the biosensor were also determined.

  19. Virtual Institute of Microbial Stress and Survival: Deduction of Stress Response Pathways in Metal and Radionuclide Reducing Microorganisms

    SciTech Connect (OSTI)

    2004-04-17

    The projects application goals are to: (1) To understand bacterial stress-response to the unique stressors in metal/radionuclide contamination sites; (2) To turn this understanding into a quantitative, data-driven model for exploring policies for natural and biostimulatory bioremediation; (3) To implement proposed policies in the field and compare results to model predictions; and (4) Close the experimental/computation cycle by using discrepancies between models and predictions to drive new measurements and construction of new models. The projects science goals are to: (1) Compare physiological and molecular response of three target microorganisms to environmental perturbation; (2) Deduce the underlying regulatory pathways that control these responses through analysis of phenotype, functional genomic, and molecular interaction data; (3) Use differences in the cellular responses among the target organisms to understand niche specific adaptations of the stress and metal reduction pathways; (4) From this analysis derive an understanding of the mechanisms of pathway evolution in the environment; and (5) Ultimately, derive dynamical models for the control of these pathways to predict how natural stimulation can optimize growth and metal reduction efficiency at field sites.

  20. 16/11/2007 08:48The bacteria can cheat on their mates (11/16/2007) Page 1 of 3http://www.geneticarchaeology.com/Research/The_bacteria_can_cheat_on_their_mates.asp

    E-Print Network [OSTI]

    West, Stuart

    16/11/2007 08:48The bacteria can cheat on their mates (11/16/2007) Page 1 of 3http://www.geneticarchaeology.com/Research/The_bacteria_can_cheat_on_their_mates.asp www.Affinity- CareTraining.co.uk Ads Dental Qualified & Latest Technol www.StyleSmileClinics.co.uk The bacteria can cheat on their mates (11

  1. 11/17/2007 05:21 PMCooperating bacteria are vulnerable to slackers Not Exactly Rocket Science Page 1 of 5http://notexactlyrocketscience.wordpress.com/2007/11/15/cooperating-bacteria-are-vulnerable-to-slackers/#comment-8042

    E-Print Network [OSTI]

    West, Stuart

    11/17/2007 05:21 PMCooperating bacteria are vulnerable to slackers « Not Exactly Rocket Science Page 1 of 5http://notexactlyrocketscience.wordpress.com/2007/11/15/cooperating-bacteria-NonCommercial- ShareAlike 2.5 License. Carnivals #12;11/17/2007 05:21 PMCooperating bacteria are vulnerable to slackers

  2. Simultaneous regulation of cell size and chromosome replication in bacteria

    E-Print Network [OSTI]

    Po-Yi Ho; Ariel Amir

    2015-07-24

    Bacteria are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, cells divide much faster than their chromosomes replicate. This implies that cells maintain multiple rounds of chromosome replication per cell division by regulating the timing of chromosome replications. Here, we show that both cell size and chromosome replication may be simultaneously regulated by the long-standing initiator accumulation strategy. The strategy proposes that initiators are produced in proportion to the volume increase and is accumulated at each origin of replication, and chromosome replication is initiated when a critical amount per origin has accumulated. We show that this model maps to the incremental model of size control, which was previously shown to reproduce experimentally observed correlations between various events in the cell cycle and explains the exponential dependence of cell size on the growth rate of the cell. Furthermore, we show that this model also leads to the efficient regulation of the timing of initiation and the number of origins consistent with existing experimental results.

  3. Fermentation of aqueous plant seed extracts by lactic acid bacteria

    SciTech Connect (OSTI)

    Schafner, D.W.; Beuchat, R.L.

    1986-05-01

    The effects of lactic acid bacterial fermentation on chemical and physical changes in aqueous extracts of cowpea (Vigna unguiculata), peanut (Arachis hypogea), soybean (Glycine max), and sorghum (Sorghum vulgare) were studied. The bacteria investigated were Lactobacillus helveticus, L. delbrueckii, L. casei, L. bulgaricus, L. acidophilus, and Streptococcus thermophilus. Organisms were inoculated individually into all of the seed extracts; L. bulgaricus and S. thermophilus were also evaluated together as inocula for fermenting the legume extracts. During fermentation, bacterial population and changes in titratable acidity, pH, viscosity, and color were measured over a 72 h period at 37 degrees C. Maximum bacterial populations, titratable acidity, pH, and viscosity varied depending upon the type of extract and bacterial strain. The maximum population of each organism was influenced by fermentable carbohydrates, which, in turn, influenced acid production and change in pH. Change in viscosity was correlated with the amount of protein and titratable acidity of products. Color was affected by pasteurization treatment and fermentation as well as the source of extract. In the extracts inoculated simultaneously with L. bulgaricus and S. thermophilus, a synergistic effect resulted in increased bacterial populations, titratable acidity, and viscosity, and decreased pH in all the legume extracts when compared to the extracts fermented with either of these organisms individually. Fermented extracts offer potential as substitutes for cultured dairy products. 24 references.

  4. Application of Stable Isotope Probing to Identify RDX-degrading Bacteria in Groundwater 

    E-Print Network [OSTI]

    Cho, Kun-Ching

    2013-12-09

    - and fully-labeled ^(15)N-RDX to identify microorganisms capable of utilizing RDX and its metabolites as carbon and/or nitrogen sources in groundwater microcosms, and to associate active RDX-degrading microbial communities in responding to engineered...

  5. Dynamic estimation of specific growth rates and concentrations of bacteria for the anaerobic digestion

    E-Print Network [OSTI]

    Boyer, Edmond

    measured quantities ­ the dilution rate and the flow rates of methane and carbon dioxide in the biogas by microorganisms into biogas (methane and carbon dioxide) and digestate (natural manure) in the absence of oxygen [1, 2, 6]. The biogas is an additional energy source and the methane is a greenhouse gas

  6. Bacteria may hold key to longevity Sarah Staples. Times -Colonist Victoria, B.C.:Aug 17, 2004. p. C11

    E-Print Network [OSTI]

    Seroude, Laurent

    Bacteria may hold key to longevity Sarah Staples. Times - Colonist Victoria, B.C.:Aug 17, 2004. p between infant fruit flies and the bacteria that live on them, have found some of the strongest evidence yet that a dose of bacteria early in life, far from harming babies, may actually help them live longer

  7. Potential Role of Nitrite for Abiotic Fe(II) Oxidation and Cell Encrustation during Nitrate Reduction by Denitrifying Bacteria

    E-Print Network [OSTI]

    Konhauser, Kurt

    Reduction by Denitrifying Bacteria Nicole Klueglein,a Fabian Zeitvogel,b York-Dieter Stierhof,c Matthias and microoxic conditions. While most of the mix- otrophic nitrate-reducing Fe(II)-oxidizing bacteria become assemblage of Fe(II)-oxidizing bacteria in nature and compli- cates our ability to delineate microbial Fe

  8. Bacteria will help baby make 80 Sarah Staples. The Ottawa Citizen Ottawa, Ont.:Aug 17, 2004. p. A3

    E-Print Network [OSTI]

    Seroude, Laurent

    Bacteria will help baby make 80 Sarah Staples. The Ottawa Citizen Ottawa, Ont.:Aug 17, 2004. p. A3 Abstract (Article Summary) Exposing the insect dro-sophila to bacteria at various moments of its notoriously short existence, the researchers found if bacteria were successful in latching onto a host fly

  9. Layer-by-layer carbon nanotube bio-templates for in situ monitoring of the metabolic activity of nitrifying bacteria

    E-Print Network [OSTI]

    Lynch, Jerome P.

    of nitrifying bacteria Kenneth J. Loh*a , Jeremy S. Guestb , Genevieve Hob , Jerome P. Lynchb , Nancy G. Loveb of nitrifying bacteria in wastewater effluent environments (i.e., to monitor the nitrification process). Using1 . In short, nitrification utilizes autotrophic bacteria to oxidize ammonia present in wastewater

  10. An extension of generalized Taylor dispersion in unbounded homogeneous shear flows to run-and-tumble chemotactic bacteria

    E-Print Network [OSTI]

    Bearon, Rachel

    -and-tumble chemotactic bacteria R. N. Bearon School of Oceanography, Box 357940, University of Washington, Seattle of flow, the biased random walk of bacteria such as Escherichia coli is modeled by straight runs. In the well-studied situation of weak bias in tumble rate, bacteria disperse over a diffusive time scale

  11. JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS: Vol. 115, No. 3, pp. 603628, December 2002 ( 2002) Biomimicry of Social Foraging Bacteria

    E-Print Network [OSTI]

    ) Biomimicry of Social Foraging Bacteria for Distributed Optimization: Models, Principles, and Emergent the social foraging behavior of E. coli and M. xanthus bacteria and develop simulation models based that the models of both species of bacteria exhibit the property identified by Grunbaum that postulates

  12. Available online at www.sciencedirect.com Exposing plasmids as the Achilles' heel of drug-resistant bacteria

    E-Print Network [OSTI]

    Hergenrother, Paul J.

    -resistant bacteria Julia J Williams1 and Paul J Hergenrother2 Many multidrug-resistant bacterial pathogens harbor of these plasmids often enables bacteria to survive in the presence of antibiotics, it is possible that plasmids highlights three recently described strategies designed to specifically combat bacteria harboring

  13. Bacteria with tiny projections can make efficient fuel cells September 7th, 2009 -3:52 pm ICT by ANI -

    E-Print Network [OSTI]

    Lovley, Derek

    Bacteria with tiny projections can make efficient fuel cells September 7th, 2009 - 3:52 pm ICT in fuel cells than bacteria with a smooth surface. The team was led by Professor Derek Lovley from they called KN400 that grew prolifically on the graphite anodes of fuel cells. The bacteria formed a thick

  14. The battle of bacteria: Agencies, stakeholders focusing on restoring water quality 

    E-Print Network [OSTI]

    Foust, Margaret

    2010-01-01

    stream_source_info The battle of bacteria.pdf.txt stream_content_type text/plain stream_size 5899 Content-Encoding ISO-8859-1 stream_name The battle of bacteria.pdf.txt Content-Type text/plain; charset=ISO-8859-1 txH2O... | pg. 20 Story by Margaret Foust Bacteria is the No. 1 pollutant of water in Texas, causing many of the state?s water bodies to be placed on the Texas Water Quality Inventory and 303(d) List for failing to meet contact recreation use standards...

  15. The battle of bacteria: Agencies, stakeholders focusing on restoring water quality 

    E-Print Network [OSTI]

    Foust, Margaret

    2011-01-01

    stream_source_info The battle of bacteria.pdf.txt stream_content_type text/plain stream_size 5899 Content-Encoding ISO-8859-1 stream_name The battle of bacteria.pdf.txt Content-Type text/plain; charset=ISO-8859-1 txH2O... | pg. 20 Story by Margaret Foust Bacteria is the No. 1 pollutant of water in Texas, causing many of the state?s water bodies to be placed on the Texas Water Quality Inventory and 303(d) List for failing to meet contact recreation use standards...

  16. Final technical report for project titled Quantitative Characterization of Cell Aggregation/Adhesion as Predictor for Distribution and Transport of Microorganisms in Subsurface Environment

    SciTech Connect (OSTI)

    Gu, April Z; Wan, Kai-tak

    2014-09-02

    This project aims to explore and develop enabling methodology and techniques for nano-scale characterization of microbe cell surface contact mechanics, interactions and adhesion quantities that allow for identification and quantification of indicative properties related to microorganism migration and transport behavior in porous media and in subsurface environments. Microbe transport has wide impact and therefore is of great interest in various environmental applications such as in situ or enhanced subsurface bioremediation,filtration processes for water and wastewater treatments and protection of drinking water supplies. Although great progress has been made towards understanding the identities and activities of these microorganisms in the subsurface, to date, little is known of the mechanisms that govern the mobility and transport of microorganisms in DOE’s contaminated sites, making the outcomes of in situ natural attenuation or contaminant stability enhancement unpredictable. Conventionally, movement of microorganisms was believed to follows the rules governing solute (particle) transport. However, recent studies revealed that cell surface properties, especially those pertaining to cell attachment/adhesion and aggregation behavior, can cause the microbe behavior to deviate from non-viable particles and hence greatly influence the mobility and distribution of microorganisms in porous media.This complexity highlights the need to obtain detailed information of cell-cell and cell-surface interactions in order to improve and refine the conceptual and quantitative model development for fate and transport of microorganisms and contaminant in subsurface. Traditional cell surface characterization methods are not sufficient to fully predict the deposition rates and transport behaviors of microorganism observed. A breakthrough of methodology that would allow for quantitative and molecular-level description of intrinsic cell surface properties indicative for cell-surface interactions is essential for the field. To tackle this, we have developed a number of new Bio-nanomechanical techniques, including reflection interference contrast microscopy (RICM) and bio-AFM (Atomic Force Microscopy), for cell adhesion-detachment measurement of the long-range surface interactions, in combination with mathematical modeling, which would allow us to characterize the mechanical behavior from single cell to multi-cell aggregate, critical thresholds for large scale coaggregation and transportation of cells and aggregates in the presence of long range inter-surface forces etc. Although some technical and mathematical challenges remain, the preliminary results promise great breakthrough potential. In this study, we investigated the cellular surface characteristics of representative bio-remediating microorganisms relevant to DOE IFRC (Integrated Field-Scale Subsurface Research Challenges) sites and their transport behaviors in porous media, aiming to draw a groundbreaking correlation between the micro-scale genetic and biological origin-based cell surface properties, the consequent mechanical adhesion and aggregation behaviors, and the macro-scale microbial mobility and retention in porous media, which are unavailable in the literature. The long-term goal is to significantly improve the mechanistic and quantitative understanding of microbial mobility, sorption, and transport within reactive transport models as needed to manipulate subsurface contaminant fate and transport predictions.

  17. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekov, Andrei D. (Moscow, RU)

    2007-10-30

    The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  18. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekova, legal representative, Natalia V. (Westmont, IL); Mirzabekov, deceased, Andrei D. (Westmont, IL)

    2007-12-04

    The present invention relates to methods and compositions for using nucleotide sequence variations of 16S and 23S rRNA within the B. cereus group to discriminate a highly infectious bacterium B. anthracis from closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations and discriminate B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed samples, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  19. Liquid Fuel from Heat-Loving Microorganisms: H2-Dependent Conversion of CO2 to Liquid Electrofuels by Extremely Thermophilic Archaea

    SciTech Connect (OSTI)

    None

    2010-07-01

    Electrofuels Project: NC State is working with the University of Georgia to create Electrofuels from primitive organisms called extremophiles that evolved before photosynthetic organisms and live in extreme, hot water environments with temperatures ranging from 167-212 degrees Fahrenheit The team is genetically engineering these microorganisms so they can use hydrogen to turn carbon dioxide directly into alcohol-based fuels. High temperatures are required to distill the biofuels from the water where the organisms live, but the heat-tolerant organisms will continue to thrive even as the biofuels are being distilled—making the fuel-production process more efficient. The microorganisms don’t require light, so they can be grown anywhere—inside a dark reactor or even in an underground facility.

  20. Growth-rate dependent partitioning of RNA polymerases in bacteria

    E-Print Network [OSTI]

    Stefan Klumpp; Terence Hwa

    2008-12-11

    Physiological changes which result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Since the availability of RNA polymerase (RNAP) in cells is dependent on the growth rate, transcriptional control involves not only the regulation of promoters, but also depends on the available (or free) RNAP concentration which is difficult to quantify directly. Here we develop a simple physical model describing the partitioning of cellular RNAP into different classes: RNAPs transcribing mRNA and ribosomal RNA (rRNA), RNAPs non-specifically bound to DNA, free RNAP, and immature RNAP. Available experimental data for E. coli allow us to determine the two unknown parameters of the model and hence deduce the free RNAP concentration at different growth rates. The results allow us to predict the growth-rate dependence of the activities of constitutive (unregulated) promoters, and to disentangle the growth-rate dependent regulation of promoters (e.g., the promoters of rRNA operons) from changes in transcription due to changes in the free RNAP concentration at different growth rates. Our model can quantitatively account for the observed changes in gene expression patterns in mutant E. coli strains with altered levels of RNAP expression without invoking additional parameters. Applying our model to the case of the stringent response following amino acid starvation, we can evaluate the plausibility of various scenarios of passive transcriptional control proposed to account for the observed changes in the expression of rRNA and biosynthetic operons.

  1. Genetically modified microorganisms for

    E-Print Network [OSTI]

    Angenent, Lars T.

    of our understanding of microbial reactions in microbial fuel cells (MFCs), or more generally to tailor these microbial reactions to optimize the desired functionality. We are still in the infancy

  2. Radiation-resistant microorganism

    DOE Patents [OSTI]

    Fliermans, Carl B.

    2010-06-15

    An isolated and purified bacterium is provided which was isolated from a high-level radioactive waste site of mixed waste. The isolate has the ability to degrade a wide variety of organic contaminants while demonstrating high tolerance to ionizing radiation. The organism is uniquely suited to bioremediation of a variety or organic contaminants while in the presence of ionizing radiation.

  3. Reduction of Antibiotic-Resistant Bacteria Present in Food Animal Manures by Composting and Anaerobic Digestion

    E-Print Network [OSTI]

    Jones, Michelle

    Reduction of Antibiotic-Resistant Bacteria Present in Food Animal Manures by Composting digestion and composting at mesophilic or moderate temperature significantly reduced the antimicrobial resistance in animal manure. The most effective treatment was composting at thermophilic or high temperature

  4. Cargo delivery into gram-negative bacteria via enterobactin uptake machinery

    E-Print Network [OSTI]

    Zheng, Tengfei

    2014-01-01

    Chapter 1. Introduction to Iron Homeostasis and Siderophores Iron is an essential nutrient for almost all living organisms. This Chapter presents an overview of iron homeostasis in human and bacteria, as well as the biology ...

  5. The YopJ superfamily in plant-associated bacteria JENNIFER D. LEWIS1,2

    E-Print Network [OSTI]

    Review The YopJ superfamily in plant-associated bacteria JENNIFER D. LEWIS1,2 , AMY LEE1,2 , WENBO). ETI relies on resistance (R) proteins, which characteristically have either a coiled-coil (CC) or toll

  6. Reassessment of the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria

    E-Print Network [OSTI]

    Swithers, Kristen S.

    In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria (Nature 460: 967–971). The presented data supported the Gram-negative ...

  7. Geek-Up[09.24.10] -- Magical BEANs, Combating Bacteria's Resistance...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    are comprised of crystal structures in the membrane, remove heavy-metal toxins from bacteria cells. Team lead Edward Yu of Iowa State explains, "We want to understand the...

  8. Caenorhabditis elegans NPR-1–mediated behaviors are suppressed in the presence of mucoid bacteria

    E-Print Network [OSTI]

    Reddy, Kirthi C.

    Caenorhabditis elegans exhibits a diverse range of behaviors in response to bacteria. The presence of bacterial food influences C. elegans aerotaxis, aggregation, locomotion, and pathogen avoidance behaviors through the ...

  9. Amoebae/bacteria consortia and uses for degrading wastes and contaminants

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1996-01-01

    A method of altering trinitrotoluene includes the steps of: providing an amoeba/bacteria consortium, particularly ATCC 40908 or a mutant thereof possessing all the identifying characteristics thereof; and contacting the consortium with trinitrotoluene to alter the trinitrotoluene.

  10. Nano scale devices for plasmonic nanolithography and rapid sensing of bacteria 

    E-Print Network [OSTI]

    Seo, Sungkyu

    2009-05-15

    This dissertation contains two different research topics. One is a ‘Nano Scale Device for Plasmonic Nanolithography – Optical Antenna’ and the other is a ‘Nano Scale Device for Rapid Sensing of Bacteria – SEPTIC’. Since these two different research...

  11. Development of Methodology and Characterization of Ruminal Lipase-Producing Bacteria In Vitro 

    E-Print Network [OSTI]

    Edwards, Holly Danielle

    2012-07-16

    .................................................................................................... xi CHAPTER I INTRODUCTION ................................................................................ 1 II LITERATURE REVIEW ..................................................................... 3 Digestion and Health Effects... Effects of Amide Protected Lipids and Lipid Encapsulation ...... 24 III DEVELOPMENT OF NON FORAGE BASED INCUBATION SYSTEMS FOR CULTURING ANAEROBIC RUMINAL LIPASE- PRODUCING BACTERIA IN VITRO...

  12. Population Genomics of Early Events in the Ecological Differentiation of Bacteria

    E-Print Network [OSTI]

    Shapiro, B. J.

    Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal ...

  13. Bacteria can help convert waste to power IANS 7 September 2009, 02:59pm IST

    E-Print Network [OSTI]

    Lovley, Derek

    they called KN400 that grew prolifically on the graphite anodes of fuel cells. The bacteria formed a thick bio batteries if they fail but to be successful they need to have an efficient and long lasting source of power

  14. Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics

    E-Print Network [OSTI]

    Ding, Huiming

    New therapeutic strategies are needed to treat infections caused by drug-resistant bacteria, which constitute a major growing threat to human health. Here, we use a high-throughput technology to identify combinatorial ...

  15. The incidence and significance of anaerobic bacteria in the equine uterus 

    E-Print Network [OSTI]

    Bolinger, Dean Roger

    1987-01-01

    THE INCIDENCE AND SIGNIFICANCE OF ANAEROBIC BACTERIA IN THE EQUINE UTERUS A Thesis by DEAN ROGER BOLINGER Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements of the degree of MASTER OF SCIENCF.... December I 987 Major Subject: Veterinary Medical Sciences THE INCIDENCE AND SIGNIFICANCE OF ANAEROBIC BACTERIA IN THE EQUINE UTERUS A Thesis by DEAN ROGER BOLINGER Approved as to style and content by: Ronnie G. Elmore (Chairman of Committee...

  16. Effects of marine sulfate-reducing bacteria on the electrochemical behavior of galvanic cells 

    E-Print Network [OSTI]

    Bradley, William Gordon

    1954-01-01

    oirouit side arm connecting the two half~la. Ths left half~oil, which conts1ned sterilised sea waterx was provided with aexmt1on tubes. This established the relative oxygen tension in the right and left halfmelis. In subsequent discussions, these halfme... preparation of the "H4 cells arm listed secusntially. Letter" in parentheses refer to labels on Mi?. ~ 1. l. riltsrs (A) nmre filled with cotton, wrapped in paper and sterilised. 2. The side arm and mouth of the aerobic half-cell were plugged with cotton...

  17. L\\'evy Fluctuations and Tracer Diffusion in Dilute Suspensions of Algae and Bacteria

    E-Print Network [OSTI]

    Zaid, Irwin M; Yeomans, Julia M

    2010-01-01

    Swimming microorganisms rely on effective mixing strategies to achieve efficient nutrient influx. Recent experiments, probing the mixing capability of unicellular biflagellates, revealed that passive tracer particles exhibit anomalous non-Gaussian diffusion when immersed in a dilute suspension of self-motile Chlamydomonas reinhardtii algae. Qualitatively, this observation can be explained by the fact that the algae induce a fluid flow that may occasionally accelerate the colloidal tracers to relatively large velocities. A satisfactory quantitative theory of enhanced mixing in dilute active suspensions, however, is lacking at present. In particular, it is unclear how non-Gaussian signatures in the tracers' position distribution are linked to the self-propulsion mechanism of a microorganism. Here, we develop a systematic theoretical description of anomalous tracer diffusion in active suspensions, based on a simplified tracer-swimmer interaction model that captures the typical distance scaling of a microswimmer'...

  18. A dose of bacteria early in life may help babies to live longer Sarah Staples. The Vancouver Sun Vancouver, B.C.:Aug 17, 2004. p. A6

    E-Print Network [OSTI]

    Seroude, Laurent

    A dose of bacteria early in life may help babies to live longer Sarah Staples. The Vancouver Sun Vancouver, B.C.:Aug 17, 2004. p. A6 Abstract (Article Summary) "We derive nutrients from bacteria, and many systems and organisms need bacteria to properly develop. Exposure to [bacteria] is required to train

  19. Turning Bacteria into Biofuel: Development of an Integrated Microbial Electrocatalytic (MEC) System for Liquid Biofuel Production from CO2

    SciTech Connect (OSTI)

    2010-08-01

    Electrofuels Project: LBNL is improving the natural ability of a common soil bacteria called Ralstonia eutropha to use hydrogen and carbon dioxide for biofuel production. First, LBNL is genetically modifying the bacteria to produce biofuel at higher concentrations. Then, LBNL is using renewable electricity obtained from solar, wind, or wave power to produce high amounts of hydrogen in the presence of the bacteria—increasing the organism’s access to its energy source and improving the efficiency of the biofuel-creation process. Finally, LBNL is tethering electrocatalysts to the bacteria’s surface which will further accelerate the rate at which the organism creates biofuel. LBNL is also developing a chemical method to transform the biofuel that the bacteria produce into ready-to-use jet fuel.

  20. Liquid Fuel From Renewable Electricity and Bacteria: Electro-Autotrophic Synthesis of Higher Alcohols

    SciTech Connect (OSTI)

    None

    2010-07-01

    Electrofuels Project: UCLA is utilizing renewable electricity to power direct liquid fuel production in genetically engineered Ralstonia eutropha bacteria. UCLA is using renewable electricity to convert carbon dioxide into formic acid, a liquid soluble compound that delivers both carbon and energy to the bacteria. The bacteria are genetically engineered to convert the formic acid into liquid fuel—in this case alcohols such as butanol. The electricity required for the process can be generated from sunlight, wind, or other renewable energy sources. In fact, UCLA’s electricity-to-fuel system could be a more efficient way to utilize these renewable energy sources considering the energy density of liquid fuel is much higher than the energy density of other renewable energy storage options, such as batteries.

  1. Inoculation of beef with lactic-acid bacteria prior to vacuum packaging 

    E-Print Network [OSTI]

    Hall, Lester Cedric

    1978-01-01

    August 1978 Major Subject: Animal Science INOCULATION OF BEEF WITH LACTIC-ACID BACTERIA PRIOR TO VACUUM PACKAGING A Thesis by LESTER CEDRIC HALL Approved as to style and content by: 1 ( (Co- hairman of C mmittee) (Co-Chakrm 'g of Committee) (He... d of Department ) (Member) August 1978 ABSTRACT Inoculation of Beef with Lactic-Acid Bacteria Prior to Vacuum Packaging. (August 1978) Lester Cedric Hall, B. S. , Texas A&M University Co-Chairmen of Advisory Committee: Dr. G. C. Smith and Dr Z...

  2. Genetically Modified Bacteria for Fuel Production: Development of Rhodobacteria as a Versatile Platform for Fuels Production

    SciTech Connect (OSTI)

    None

    2010-07-01

    Electrofuels Project: Penn State is genetically engineering bacteria called Rhodobacter to use electricity or electrically generated hydrogen to convert carbon dioxide into liquid fuels. Penn State is taking genes from oil-producing algae called Botryococcus braunii and putting them into Rhodobacter to produce hydrocarbon molecules, which closely resemble gasoline. Penn State is developing engineered tanks to support microbial fuel production and determining the most economical way to feed the electricity or hydrogen to the bacteria, including using renewable sources of power like solar energy.

  3. Investigation of anaerobic bacteria associated with mortality in grey mullet (Mugil cephalus) and redfish (Sciaenops ocellatus) 

    E-Print Network [OSTI]

    Henley, Michael Waite

    1976-01-01

    INVEST1GATION OF ANAEROBIC BACTERIA ASSOCIATED WITH NDRTALITY IN GREY MULLET t~N' I ~*h I ) AND REDYIRH (~H' o ll t A Thesis MICHAEL WAITE HENLEY f Submitted to the Graduate College of Texas ARM University in partial fulfillment... of the requirement for the degree of MASTER OF SCIENCE August 1976 Major Subject: Veterinary Microbiology INVESTIGATION OF ANAEROBIC BACTERIA ASSOCIATED NITH liIIH NDR IlDIIY IN GREY NUDE EI 1M~I ~ll END REDPI H l~R' ll t 1 A Thesis !G!ICHAEL WAITE HENLEY...

  4. Factors affecting the recovery of bacteria in freeze-dried model systems 

    E-Print Network [OSTI]

    Custer, Carl Steven

    1970-01-01

    FACTORS AFFECTING THE RECOVERY OF BACTERIA IN FREEZE-DRIED NODEL SYSTENS A Thesis by CARL STEVEN CUSTER Submitted to the Graduate College of Texas A&N University in partial fulfillment of the requirement for tbe degree of MASTER OF SCIENCE... December 1970' Najor Subject: Food Technology FACTORS AFFECTING THE RECOVERY OF BACTERIA IN FREEZE-DRIED MODEL SYSTEMS A Thesis CARL STEVEN CUSTER Approved as to sty1e and content by: Chairman of Com tee) Head of Departme (Member) (Member) (Member...

  5. ENZYME ACTIVITY PROBE AND GEOCHEMICAL ASSESSMENT FOR POTENTIAL AEROBIC COMETABOLISM OF TRICHLOROETHENE IN GROUNDWATER OF THE NORTHWEST PLUME, PADUCAH GASEOUS DIFFUSION PLANT, KENTUCKY

    SciTech Connect (OSTI)

    Looney, B; M. Hope Lee, M; S. K. Hampson, S

    2008-06-27

    The overarching objective of the Paducah Gaseous Diffusion Plant (PGDP) enzyme activity probe (EAP) effort is to determine if aerobic cometabolism is contributing to the attenuation of trichloroethene (TCE) and other chlorinated solvents in the contaminated groundwater beneath PGDP. The site-specific objective for the EAP assessment is to identify if key metabolic pathways are present and expressed in the microbial community--namely the pathways that are responsible for degradation of methane and aromatic (e.g. toluene, benzene, phenol) substrates. The enzymes produced to degrade methane and aromatic compounds also break down TCE through a process known as cometabolism. EAPs directly measure if methane and/or aromatic enzyme production pathways are operating and, for the aromatic pathways, provide an estimate of the number of active organisms in the sampled groundwater. This study in the groundwater plumes at PGDP is a major part of a larger scientific effort being conducted by Interstate Technology and Regulatory Council (ITRC), U.S. Department of Energy (DOE) Office of Environmental Management (EM), Savannah River National Laboratory (SRNL), and North Wind Inc. in which EAPs are being applied to contaminated groundwater from diverse hydrogeologic and plume settings throughout the U.S. to help standardize their application as well as their interpretation. While EAP data provide key information to support the site specific objective for PGDP, several additional lines of evidence are being evaluated to increase confidence in the determination of the occurrence of biodegradation and the rate and sustainability of aerobic cometabolism. These complementary efforts include: (1) Examination of plume flowpaths and comparison of TCE behavior to 'conservative' tracers in the plume (e.g., {sup 99}Tc); (2) Evaluation of geochemical conditions throughout the plume; and (3) Evaluation of stable isotopes in the contaminants and their daughter products throughout the plume. If the multiple lines of evidence support the occurrence of cometabolism and the potential for the process to contribute to temporal and spatial attenuation of TCE in PGDP groundwater, then a follow-up enzyme probe microcosm study to better estimate biological degradation rate(s) is warranted.

  6. Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Reeve, Wayne [Murdoch University

    2013-03-01

    Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  7. Relative Susceptibility and Transcriptional Response of Nitrogen Cycling Bacteria to Quantum Dots

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    -100 nm) consisting of a metalloid crystalline core, such as CdSe or CdTe, and an encapsulating ZnS or Cd and photostability, which are useful for biomedical imaging, therapeutic applications, and solar cells.4-11 QDs can be toxic to bacteria,12,13 invertebrates,14 and to animal15 and human cells,16 and can damage

  8. in-house windrow composting Many of the water bodies that are impaired by bacteria

    E-Print Network [OSTI]

    in-house windrow composting Many of the water bodies that are impaired by bacteria throughout from new and existing facilities. One such BMP is in-house windrow composting (IWC) of poultry litter. The Environmental Effects of In-House Windrow Composting of Poultry Litter project is demonstrating

  9. ABSTRACTABSTRACT Microbial fuel cells (MFCs) are devices that utilize bacteria to

    E-Print Network [OSTI]

    ) applications are becoming a popular means of power generation within our society and Microbial fuel cells (MFCsABSTRACTABSTRACT Microbial fuel cells (MFCs) are devices that utilize bacteria to generate efficiencies in comparison to varying fuel cell components and structures. Seven single chamber MFCs were

  10. Structure-based Inhibitor Discovery against Adenylyl Cyclase Toxins from Pathogenic Bacteria That Cause Anthrax and

    E-Print Network [OSTI]

    Mrksich, Milan

    That Cause Anthrax and Whooping Cough* Received for publication, February 4, 2003, and in revised form, March bacteria that cause anthrax and whooping cough, respectively. Using the structure of the catalytic site pathogenesis and to fight against anthrax and whooping cough. The 2001 anthrax attacks in the United States

  11. Characterization of arsenic-resistant endophytic bacteria from hyperaccumulators Pteris vittata and Pteris multifida

    E-Print Network [OSTI]

    Ma, Lena

    Characterization of arsenic-resistant endophytic bacteria from hyperaccumulators Pteris vittata i g h l i g h t s 74 As-resistant endophytes from two As-hyperaccumulators were identified AsV reduction and AsIII oxidation. Endophytes from Pteris multifida were more resistant to arsenite

  12. Association with pathogenic bacteria affects life-history traits and population growth in Caenorhabditis elegans.

    E-Print Network [OSTI]

    Diaz, S. Anaid; Mooring, Eric Q.; Rens, Elisabeth G.; Restif, Olivier

    2015-03-23

    with respect to its association with pathogenic bacteria. In order to start filling the gap between the two areas, we conducted a series of experiments aiming at measuring life-history traits as well as population growth of C. elegans in response to three...

  13. Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria

    DOE Patents [OSTI]

    DiSpirito, Alan A. (Ames, IA); Zahn, James A. (Harbor Beach, MI); Graham, David W. (Lawrence, KS); Kim, Hyung J. (St. Paul, MN); Alterman, Michail (Lawrence, KS); Larive, Cynthia (Lawrence, KS)

    2007-04-03

    A means and method for treating bacterial infection, providing antioxidant activity, and chelating copper using a copper binding compound produced by methanotrophic bacteria is described. The compound, known as methanobactin, is the first of a new class of antibiotics having gram-positive activity. Methanobactin has been sequenced, and its structural formula determined.

  14. Protein elemental sparing and codon usage bias are correlated among bacteria

    E-Print Network [OSTI]

    Wagner, Andreas

    Protein elemental sparing and codon usage bias are correlated among bacteria JASON G. BRAGG, in terms of the quantities of carbon (C), nitrogen (N) or sulphur (S) atoms they contain. This `elemental sparing' probably reflects selection to reduce the quantities of potentially growth- limiting elements

  15. Microbial Grazers Lab Objective: Measure the rate at which bacteria are consumed by predators.

    E-Print Network [OSTI]

    Vallino, Joseph J.

    Microbial Grazers Lab Objective: Measure the rate at which bacteria are consumed by predators. Overview ·Size based food webs ·Microbial loop concepts ·Bacterial predators ·Methods to assess microbial, they were not thought to be significant consumers of carbon or energy. microPlankton mesoPlankton #12

  16. Microfluidic capture and release of bacteria in a conical nanopore array Peng Guo,ab

    E-Print Network [OSTI]

    Zare, Richard N.

    Microfluidic capture and release of bacteria in a conical nanopore array Peng Guo,ab Eric W. Hall a microfluidic device. As an example, we demonstrate that cyanobacteria can be captured, one bacterium per pore, in a conical nanoporous membrane (CNM) integrated into a microfluidic chip. This study, to our knowledge

  17. Growth and Survival of Immature Haematobia irritans (Diptera: Muscidae) is Influenced by Bacteria Isolated from Cattle

    E-Print Network [OSTI]

    Selinger, Brent

    by Bacteria Isolated from Cattle Manure and Conspecific Larvae M. A. PEROTTI, T. J. LYSYK, L. D. KALISCHUK from cattle manure and seven species were isolated from the gut of larval horn ßy Hematobia irritans (L bacterial species were evaluated by rearing larvae in sterilized cattle manure that was inoculated

  18. Cross-stress protection in bacteria: an evolutionary perspective Ilias Tagkopoulos

    E-Print Network [OSTI]

    Tagkopoulos, Ilias

    Cross-stress protection in bacteria: an evolutionary perspective Ilias Tagkopoulos Department parameters constantly fluctuate. "Stress" is the term used when these fluctuations vary severely from optimum, and the ability of microbes to sense and respond to environmental stress is critical to their survival. Due

  19. Amoebae/bacteria consortia and uses for degrading wastes and contaminants

    DOE Patents [OSTI]

    Tyndall, R.L.

    1996-05-21

    A method is disclosed of altering trinitrotoluene. The steps include the following: providing an amoeba/bacteria consortium, particularly ATCC 40908 or a mutant which possesses all the identifying characteristics thereof; and contacting the consortium with trinitrotoluene to alter the trinitrotoluene.

  20. Memory-Assisted Exciton Diffusion in the Chlorosome Light-Harvesting Antenna of Green Sulfur Bacteria

    E-Print Network [OSTI]

    Saikin, Semion

    Memory-Assisted Exciton Diffusion in the Chlorosome Light- Harvesting Antenna of Green Sulfur of bacteriochlorophylls (BChls) enclosed by a lipid monolayer.1-4 They can capture light and transfer it in a form. In green sulfur bacteria, light energy absorbed by the rolls is transferred via a baseplate9 to the Fenna

  1. In bacteria, the two defining processes of the cell cycle, chromosome replication and segre

    E-Print Network [OSTI]

    Mekalanos, John

    In bacteria, the two defining processes of the cell cycle, chromosome replication and segre gation and Hunt in 1993 (REF. 2) as "among the most mysterious" events during the bacterial cell cycle, and its segregation. In the first part of this Opinion article, we consider when entropy will drive segrega tion

  2. Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining

    E-Print Network [OSTI]

    Wagner, Andreas

    Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic.wagner@ieu.uzh.ch; nsabath@gmail.com. Accepted: March 25, 2013 Abstract Prokaryotic genomes are small and compact. Either this feature is caused by neutral evolution or by natural selection favoring small genomes--genome streamlining

  3. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

    E-Print Network [OSTI]

    de la Torre, José R.

    LETTERS Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role or their contribution to nitrification8 . Here we report oligotrophic ammonia oxidation kinetics and cellular

  4. Digestion of milk protein and methanol-grown bacteria protein in the preruminant calf. II. Amino acid composition of

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Digestion of milk protein and methanol-grown bacteria protein in the preruminant calf. II. Amino of milk and of methanol-grown bacteria in the terminal small intestine and the hindgut of the preruminant exclusively by skim-milk powder ; 50.5 p. 100 of the protein of the bacte- ria diet was supplied by methanol

  5. Elucidate the mechanism(s) of Hg uptake in methylating bacteria and effects on Hg methylation in nature.

    E-Print Network [OSTI]

    Post, Wilfred M.

    Objective · Elucidate the mechanism(s) of Hg uptake in methylating bacteria and effects on Hg, suggesting a possible detoxification mechanism for the formation and export of methylmercury. 1 BER Overview A New Mechanism of Mercury Uptake and Methylation in Anaerobic Bacteria Contact: Jeffra Schaefer

  6. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.; Lamson, Jacob S.; He, Jennifer; Hoover, Cindi A.; Blow, Matthew J.; Bristow, James; Butland, Gareth; Arkin, Adam P.; et al

    2015-05-12

    Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with anymore »transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative D-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data.« less

  7. Lévy Fluctuations and Tracer Diffusion in Dilute Suspensions of Algae and Bacteria

    E-Print Network [OSTI]

    Irwin M. Zaid; Jörn Dunkel; Julia M. Yeomans

    2010-09-20

    Swimming microorganisms rely on effective mixing strategies to achieve efficient nutrient influx. Recent experiments, probing the mixing capability of unicellular biflagellates, revealed that passive tracer particles exhibit anomalous non-Gaussian diffusion when immersed in a dilute suspension of self-motile Chlamydomonas reinhardtii algae. Qualitatively, this observation can be explained by the fact that the algae induce a fluid flow that may occasionally accelerate the colloidal tracers to relatively large velocities. A satisfactory quantitative theory of enhanced mixing in dilute active suspensions, however, is lacking at present. In particular, it is unclear how non-Gaussian signatures in the tracers' position distribution are linked to the self-propulsion mechanism of a microorganism. Here, we develop a systematic theoretical description of anomalous tracer diffusion in active suspensions, based on a simplified tracer-swimmer interaction model that captures the typical distance scaling of a microswimmer's flow field. We show that the experimentally observed non-Gaussian tails are generic and arise due to a combination of truncated L\\'evy statistics for the velocity field and algebraically decaying time correlations in the fluid. Our analytical considerations are illustrated through extensive simulations, implemented on graphics processing units to achieve the large sample sizes required for analyzing the tails of the tracer distributions.

  8. From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

    SciTech Connect (OSTI)

    REGUERA, GEMMA [Michigan State University

    2014-01-16

    One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilms than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.

  9. ORGANIC GEOCHEMICAL STUDIES. II. THE DISTRIBUTION OF ALIPHATIC HYDROCARBONS IN ALGAE, BACTERIA, AND IN A RECENT LAKE SEDIMENT: A PRELIMINARY REPORT

    E-Print Network [OSTI]

    Han, Jerry; McCarthy, E.D.; Van Hoeven Jr., William; Calvin, Melvin; Bradley, W. H.

    2008-01-01

    ALIPHATIC HYDROCARBONS IN ALGAE, BACTERIA, AND IN A RECENTH F A PRELIMINARY REPORT IN ALGAE, BACTERIA, AKD IN A RECENTrests on the finding that algae have less cellulose and a

  10. A reliable method for the selection and confirmation of transconjugants of plant growth-promoting bacteria especially plant-associated Burkholderia spp.

    E-Print Network [OSTI]

    2015-01-01

    pUTgfp2x on LB. D. Agrobacterium tumefaciens Ca18 carryingtools for tagging Gram-negative bacteria with mCherry fora marker for detection of bacteria in environmental samples.

  11. Transport of bacteria and colloids in intermittent sand filters Maria Auset1, Arturo A. Keller1, Franois Brissaud2, Valentina Lazarova3

    E-Print Network [OSTI]

    Keller, Arturo A.

    Transport of bacteria and colloids in intermittent sand filters Maria Auset1, Arturo A. Keller1 of bacteria, the effects of cyclic infiltration and draining events (transient unsaturated flow) were percolating in a single pass through the unsaturated porous medium. Bacteria suspension Wastewater solution

  12. Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria

    E-Print Network [OSTI]

    Gilli, Adrian

    of phototrophic sulfur bacteria in the sediments of Lake Cadagno D. F. RAVASI,1 S. PEDUZZI,1 , 2 V. GUIDI,2 , 3 R sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S r sulfur bacteria populations from sediment samples. We detected fossil 16S rDNA of nine populations

  13. Turning Bacteria into Fuel: Cyanobacteria Designed for Solar-Powered Highly Efficient Production of Biofuels

    SciTech Connect (OSTI)

    None

    2010-01-01

    Broad Funding Opportunity Announcement Project: ASU is engineering a type of photosynthetic bacteria that efficiently produce fatty acids—a fuel precursor for biofuels. This type of bacteria, called Synechocystis, is already good at converting solar energy and carbon dioxide (CO2) into a type of fatty acid called lauric acid. ASU has modified the organism so it continuously converts sunlight and CO2 into fatty acids—overriding its natural tendency to use solar energy solely for cell growth and maximizing the solar-to-fuel conversion process. ASU’s approach is different because most biofuels research focuses on increasing cellular biomass and not on excreting fatty acids. The project has also identified a unique way to convert the harvested lauric acid into a fuel that can be easily blended with existing transportation fuels.

  14. Collective motion and nonequilibrium cluster formation in colonies of gliding bacteria

    E-Print Network [OSTI]

    Fernando Peruani; Joern Starruss; Vladimir Jakovljevic; Lotte Sogaard-Andersen; Andreas Deutsch; Markus Bar

    2013-02-01

    We characterize cell motion in experiments and show that the transition to collective motion in colonies of gliding bacterial cells confined to a monolayer appears through the organization of cells into larger moving clusters. Collective motion by non-equilibrium cluster formation is detected for a critical cell packing fraction around 17%. This transition is characterized by a scale-free power-law cluster size distribution, with an exponent $0.88\\pm0.07$, and the appearance of giant number fluctuations. Our findings are in quantitative agreement with simulations of self-propelled rods. This suggests that the interplay of self-propulsion of bacteria and the rod-shape of bacteria is sufficient to induce collective motion.

  15. Biofuel from Bacteria and Sunlight: Shewanella as an Ideal Platform for Producing Hydrocarbons

    SciTech Connect (OSTI)

    None

    2010-01-01

    Broad Funding Opportunity Announcement Project: The University of Minnesota is developing clean-burning, liquid hydrocarbon fuels from bacteria. The University is finding ways to continuously harvest hydrocarbons from a type of bacteria called Shewanella by using a photosynthetic organism to constantly feed Shewanella the sugar it needs for energy and hydrocarbon production. The two organisms live and work together as a system. Using Shewanella to produce hydrocarbon fuels offers several advantages over traditional biofuel production methods. First, it eliminates many of the time-consuming and costly steps involved in growing plants and harvesting biomass. Second, hydrocarbon biofuels resemble current petroleum-based fuels and would therefore require few changes to the existing fuel refining and distribution infrastructure in the U.S.

  16. Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

    SciTech Connect (OSTI)

    He, Q.; He, Z.; Joyner, D.C.; Joachimiak, M.; Price, M.N.; Yang, Z.K.; Yen, H.-C. B.; Hemme, C. L.; Chen, W.; Fields, M.; Stahl, D. A.; Keasling, J. D.; Keller, M.; Arkin, A. P.; Hazen, T. C.; Wall, J. D.; Zhou, J.

    2010-07-15

    Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

  17. Effects of UV Light Disinfection on Tetracycline Resistant Bacteria in Wastewater Effluents 

    E-Print Network [OSTI]

    Childress, Hannah

    2011-10-21

    species can utilize the mechanisms of photoreactivation or dark repair to become reactivated. Photoreactivation occurs in UV- A or visible light; it is hypothesized that pyrimidine dimers form a complex with a photoreactivating enzyme which can... OF UV LIGHT DISINFECTION ON TETRACYCLINE RESISTANT BACTERIA IN WASTEWATER EFFLUENTS A Thesis by HANNAH CHILDRESS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements...

  18. Cycling of DOC and DON by Novel Heterotrophic and Photoheterotrophic Bacteria in the Ocean: Final Report

    SciTech Connect (OSTI)

    Kirchman, David L

    2008-12-09

    The flux of dissolved organic matter (DOM) through aquatic bacterial communities is a major process in carbon cycling in the oceans and other aquatic systems. Our work addressed the general hypothesis that the phylogenetic make-up of bacterial communities and the abundances of key types of bacteria are important factors influencing the processing of DOM in aquatic ecosystems. Since most bacteria are not easily cultivated, the phylogenetic diversity of these microbes has to be assessed using culture-independent approaches. Even if the relevant bacteria were cultivated, their activity in the lab would likely differ from that under environmental conditions. This project found variation in DOM uptake by the major bacterial groups found in coastal waters. In brief, the data suggest substantial differences among groups in the use of high and molecular weight DOM components. It also made key discoveries about the role of light in affecting this uptake especially by cyanobacteria. In the North Atlantic Ocean, for example, over half of the light-stimulated uptake was by the coccoid cyanobacterium, Prochlorococcus, with the remaining uptake due to Synechococcus and other photoheterotrophic bacteria. The project also examined in detail the degradation of one organic matter component, chitin, which is often said to be the second most abundant compound in the biosphere. The findings of this project contribute to our understanding of DOM fluxes and microbial dynamics supported by those fluxes. It is possible that these findings will lead to improvements in models of the carbon cycle that have compartments for dissolved organic carbon (DOC), the largest pool of organic carbon in the oceans.

  19. A Scanning Auger Microprobe analysis of corrosion products associated with sulfate reducing bacteria

    SciTech Connect (OSTI)

    Sadowski, R.A.; Chen, G.; Clayton, C.R.; Kearns, J.R.; Gillow, J.B.; Francis, A.J.

    1995-03-01

    A Scanning Auger Microprobe analysis was performed on the corrosion products of an austenitic AISI type 304 SS after a potentiostatic polarization of one volt for ten minutes in a modified Postgate`s C media containing sulfate reducing bacteria. The corrosion products were characterized and mapped in local regions where pitting was observed. A critical evaluation of the applicability of this technique for the examination of microbially influenced corrosion (MIC) is presented.

  20. Environmental diagnostic analysis of ground water bacteria and their involvement in utilization of aromatic compounds

    SciTech Connect (OSTI)

    Wear, J.E. Jr.

    1993-05-01

    The objective of this study was to examine the hypothesis that select functional groups of bacteria from pristine sites have an innate ability to degrade synthetic aromatics that often contaminate groundwater environments,due to exposure to naturally occurring recalcitrant aromatics in their environment. This study demonstrates that subsurface microbial communities are capable of utilizing lignin and humic acid breakdown products. Utilizers of these compounds were found to be present in most all the wells tested. Even the deepest aquifer tested had utilizers present for all six of the aromatics tested. Highest counts for the aromatics tested were observed with the naturally occurring breakdown products of either lignin or humic acid. Carboxylic acids were found to be an important sole carbon source for groundwater bacteria possibly explained by the fact that they are produced by the oxidative cleavage of aromatic ring structures. The carbohydrate sole carbon sources that demonstrated the greatest densities were ones commonly associated with humics. This study indicates that utilization of naturally occurring aromatic compounds in the subsurface is an important nutritional source for groundwater bacteria. In addition, it suggests that adaptation to naturally occurring recalcitrant substrates is the origin of degradative pathways for xenobiotic compounds with analogous structure. This work has important implications for in situ bioremediation as a method of environmental cleanup.

  1. Liquid Fuel From Bacteria: Engineering Ralstonia eutropha for Production of Isobutanol (IBT) Motor Fuel from CO2, Hydrogen, and Oxygen

    SciTech Connect (OSTI)

    2010-07-15

    Electrofuels Project: MIT is using solar-derived hydrogen and common soil bacteria called Ralstonia eutropha to turn carbon dioxide (CO2) directly into biofuel. This bacteria already has the natural ability to use hydrogen and CO2 for growth. MIT is engineering the bacteria to use hydrogen to convert CO2 directly into liquid transportation fuels. Hydrogen is a flammable gas, so the MIT team is building an innovative reactor system that will safely house the bacteria and gas mixture during the fuel-creation process. The system will pump in precise mixtures of hydrogen, oxygen, and CO2, and the online fuel-recovery system will continuously capture and remove the biofuel product.

  2. Studies of multiheme proteins from the disimilatory metal reducing bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens 

    E-Print Network [OSTI]

    Atkinson, Sally

    2009-01-01

    Genomic analysis of the dissimilatory metal-reducing bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA has shown that both are capable of expressing an unprecedented number of multiheme cytochromes. ...

  3. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gallivan, Justin [Emory University

    2013-01-22

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  4. Bacteria in Ballast Water: The Shipping Industry's Contributions to the Transport and Distribution of Microbial Species in Texas 

    E-Print Network [OSTI]

    Neyland, Elizabeth B.

    2010-10-12

    The transportation of organisms in the ballast water of cargo ships has been recognized as a source of invasive species despite current control measures. Pathogenic bacteria in the ballast tank have been studied but the total diversity...

  5. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gallivan, Justin [Emory University] [Emory University

    2012-03-21

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  6. Patterns of antimicrobial resistance among enteric bacteria found in multi-site group-level cohorts of humans and swine 

    E-Print Network [OSTI]

    Campbell, Linda Diane

    2006-04-12

    -1 PATTERNS OF ANTIMICROBIAL RESISTANCE AMONG ENTERIC BACTERIA FOUND IN MULTI-SITE GROUP-LEVEL COHORTS OF HUMANS AND SWINE A Thesis by LINDA DIANE CAMPBELL Submitted to the Office of Graduate Studies of Texas A&M University in partial... fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2004 Major Subject: Epidemiology PATTERNS OF ANTIMICROBIAL RESISTANCE AMONG ENTERIC BACTERIA FOUND IN MULTI-SITE GROUP-LEVEL COHORTS OF HUMANS AND SWINE A Thesis...

  7. Hormetic effect of ionic liquid 1-ethyl-3-methylimidazolium acetate on bacteria

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nancharaiah, Y. V. [Bhabha Atomic Research Center, Kalpakkam (India). Biofouling and Biofilm Processes Sect.; Francis, A. J. [Brookhaven National Laboratory (BNL), Upton, NY (United States). Environmental Sciences Dept.; POSTECH, Pohang (Korea, Rep. of). Div. of Advanced Nuclear Engineering

    2015-06-01

    The biological effect of ionic liquids (ILs) is one of the highly debated topics as they are being contemplated for various industrial applications. 1-ethyl-2-methylimidazolium acetate ([EMIM][Ac]) showed remarkable hormesis on anaerobic Clostridium sp. and aerobic Psueudomonas putida. Bacterial growth was stimulated at up to 2.5 g L-1 and inhibited at > 2.5 g L-1 of ([EMIM][Ac]). The growth of Clostridium sp. and P. putida were higher by 0.4 and 4-fold respectively, in the presense of 0.5 g L-1 of ([EMIM][Ac]). Assessment of the effect of [EMIM][Ac] under different growth conditions showed that the hormesis of [EMIM][Ac] was mediated via regulation of medium pH. Hormetic effect of [EMIM][Ac] was evident only in medium with poor buffering capacity and in the presence of a fermentable substrate as the carbon source. The hormetic effect of [EMIM][Ac] on bacterial growth is most likely associated with the buffering capacity of acetate anion. These observations have implications in ILs toxicity studies and ecological risk assessment.

  8. Hormetic effect of ionic liquid 1-ethyl-3-methylimidazolium acetate on bacteria

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nancharaiah, Y. V.; Francis, A. J.

    2015-02-19

    The biological effect of ionic liquids (ILs) is one of the highly debated topics as they are being contemplated for various industrial applications. 1-ethyl-2-methylimidazolium acetate ([EMIM][Ac]) showed remarkable hormesis on anaerobic Clostridium sp. and aerobic Psueudomonas putida. Bacterial growth was stimulated at up to 2.5 g L-1 and inhibited at > 2.5 g L-1 of ([EMIM][Ac]). The growth of Clostridium sp. and P. putida were higher by 0.4 and 4-fold respectively, in the presense of 0.5 g L-1 of ([EMIM][Ac]). Assessment of the effect of [EMIM][Ac] under different growth conditions showed that the hormesis of [EMIM][Ac] was mediated via regulationmore »of medium pH. Hormetic effect of [EMIM][Ac] was evident only in medium with poor buffering capacity and in the presence of a fermentable substrate as the carbon source. The hormetic effect of [EMIM][Ac] on bacterial growth is most likely associated with the buffering capacity of acetate anion. These observations have implications in ILs toxicity studies and ecological risk assessment.« less

  9. Experimental test of whether electrostatically charged micro-organisms and their spores contribute to the onset of arcs across vacuum gaps

    SciTech Connect (OSTI)

    Grisham, L. R.; Halle, A. von; Carpe, A. F.; Gilton, K. R.; Rossi, Guy; Stevenson, T. N.

    2013-12-15

    Recently it was proposed [L. R. Grisham et al. Phys. Plasmas 19, 023107 (2012)] that one of the initiators of vacuum voltage breakdown between conducting electrodes might be micro-organisms and their spores, previously deposited during exposure to air, which then become electrostatically charged when an electric potential is applied across the vacuum gap. This note describes a simple experiment to compare the number of voltage-conditioning pulses required to reach the nominal maximum operating voltage across a gap between two metallic conductors in a vacuum, comparing cases in which biological cleaning was done just prior to pump-down with cases where this was not done, with each case preceded by exposure to ambient air for three days. Based upon these results, it does not appear that air-deposited microbes and their spores constitute a major pathway for arc initiation, at least for exposure periods of a few days, and for vacuum gaps of a few millimeters, in the regime where voltage holding is usually observed to vary linearly with gap distance.

  10. Experimental Test Of Whether Electrostatically Charged Micro-organisms And Their Spores Contribute To The Onset Of Arcs Across Vacuum Gaps

    SciTech Connect (OSTI)

    none,; Grisham, Larry R.

    2014-02-24

    Recently it was proposed [L.R. Grisham, A. vonHalle, A.F. Carpe, Guy Rossi, K.R. Gilton, E.D. McBride, E.P. Gilson, A. Stepanov, T.N. Stevenson, Physics of Plasma 19 023107 (2012)] that one of the initiators of vacuum voltage breakdown between condu cting electrodes might be micro-organisms and their spores, previously deposited during exposure to air, which tnen become electrostatically charged when an electric potential is applied across the vacuum gap. The note describes a simple experiment to compare the number of voltage-conditioning pulses required to reach the nominal maxium operating voltage across a gap between two metallic conductors in a vacuum, comparing cases in which biological cleaning was done just prior to pump-down with cases where this was not done, with each preceded by exposure to ambient air for three days. Based upon these results, it does not appear that air-deposited microbes and their spores constitute a major pathway for arc initiation, at least for exposure periods of a few days, and for vacuum gaps of a few millimeters, in the regime where voltage holding is usually observed to vary linearly with gap distance

  11. MOLECULAR APPROACHES FOR IN SITU IDENTIFCIATION OF NITRATE UTILIZATION BY MARINE BACTERIA AND PHYTOPLANKTON

    SciTech Connect (OSTI)

    Frischer, Marc E.; Verity, Peter G.; Gilligan, Mathew R.; Bronk, Deborah A.; Zehr, Jonathan P.; Booth, Melissa G.

    2013-09-12

    Traditionally, the importance of inorganic nitrogen (N) for the nutrition and growth of marine phytoplankton has been recognized, while inorganic N utilization by bacteria has received less attention. Likewise, organic N has been thought to be important for heterotrophic organisms but not for phytoplankton. However, accumulating evidence suggests that bacteria compete with phytoplankton for nitrate (NO3-) and other N species. The consequences of this competition may have a profound effect on the flux of N, and therefore carbon (C), in ocean margins. Because it has been difficult to differentiate between N uptake by heterotrophic bacterioplankton versus autotrophic phytoplankton, the processes that control N utilization, and the consequences of these competitive interactions, have traditionally been difficult to study. Significant bacterial utilization of DIN may have a profound effect on the flux of N and C in the water column because sinks for dissolved N that do not incorporate inorganic C represent mechanisms that reduce the atmospheric CO2 drawdown via the ?biological pump? and limit the flux of POC from the euphotic zone. This project was active over the period of 1998-2007 with support from the DOE Biotechnology Investigations ? Ocean Margins Program (BI-OMP). Over this period we developed a tool kit of molecular methods (PCR, RT-PCR, Q-PCR, QRT-PCR, and TRFLP) and combined isotope mass spectrometry and flow-cytometric approaches that allow selective isolation, characterization, and study of the diversity and genetic expression (mRNA) of the structural gene responsible for the assimilation of NO3- by heterotrophic bacteria (nasA). As a result of these studies we discovered that bacteria capable of assimilating NO3- are ubiquitous in marine waters, that the nasA gene is expressed in these environments, that heterotrophic bacteria can account for a significant fraction of total DIN uptake in different ocean margin systems, that the expression of nasA is differentially regulated in genetically distinct NO3- assimilating bacteria, and that the best predictors of nasA gene expression are either NO3- concentration or NO3- uptake rates. These studies provide convincing evidence of the importance of bacterial utilization of NO3-, insight into controlling processes, and provide a rich dataset that are being used to develop linked C and N modeling components necessary to evaluate the significance of bacterial DIN utilization to global C cycling. Furthermore, as a result of BI-OMP funding we made exciting strides towards institutionalizing a research and education based collaboration between the Skidaway Institute of Oceanography (SkIO) and Savannah State University (SSU), an historically black university within the University System of Georgia with undergraduate and now graduate programs in marine science. The BI-OMP program, in addition to supporting undergraduate (24) graduate (10) and postdoctoral (2) students, contributed to the development of a new graduate program in Marine Sciences at SSU that remains an important legacy of this project. The long-term goals of these collaborations are to increase the capacity for marine biotechnology research and to increase representation of minorities in marine, environmental and biotechnological sciences.

  12. Soft inertial microfluidics for high throughput separation of bacteria from human blood cells

    SciTech Connect (OSTI)

    Wu, Zhigang; Willing, Ben; Bjerketorp, Joakim; Jansson, Janet K.; Hjort, Klas

    2009-01-05

    We developed a new approach to separate bacteria from human blood cells based on soft inertial force induced migration with flow defined curved and focused sample flow inside a microfluidic device. This approach relies on a combination of an asymmetrical sheath flow and proper channel geometry to generate a soft inertial force on the sample fluid in the curved and focused sample flow segment to deflect larger particles away while the smaller ones are kept on or near the original flow streamline. The curved and focused sample flow and inertial effect were visualized and verified using a fluorescent dye primed in the device. First the particle behavior was studied in detail using 9.9 and 1.0 {micro}m particles with a polymer-based prototype. The prototype device is compact with an active size of 3 mm{sup 2}. The soft inertial effect and deflection distance were proportional to the fluid Reynolds number (Re) and particle Reynolds number (Re{sub p}), respectively. We successfully demonstrated separation of bacteria (Escherichia coli) from human red blood cells at high cell concentrations (above 10{sup 8}/mL), using a sample flow rate of up to 18 {micro}L/min. This resulted in at least a 300-fold enrichment of bacteria at a wide range of flow rates with a controlled flow spreading. The separated cells were proven to be viable. Proteins from fractions before and after cell separation were analyzed by gel electrophoresis and staining to verify the removal of red blood cell proteins from the bacterial cell fraction. This novel microfluidic process is robust, reproducible, simple to perform, and has a high throughput compared to other cell sorting systems. Microfluidic systems based on these principles could easily be manufactured for clinical laboratory and biomedical applications.

  13. Palladium nanoparticles produced by fermentatively cultivated bacteria as catalyst for diatrizoate removal with biogenic hydrogen

    SciTech Connect (OSTI)

    Hennebel, T.; Fitts, J.; Nevel, S. V.; Verschuere, S.; De Corte, S.; De Gusseme, B.; Cuvelier, C.; van der Lelie, D.; Boon, N.; Verstraete, W.

    2011-05-17

    A new biological inspired method to produce nanopalladium is the precipitation of Pd on a bacterium, i.e., bio-Pd. This bio-Pd can be applied as catalyst in dehalogenation reactions. However, large amounts of hydrogen are required as electron donor in these reactions resulting in considerable costs. This study demonstrates how bacteria, cultivated under fermentative conditions, can be used to reductively precipitate bio-Pd catalysts and generate the electron donor hydrogen. In this way, one could avoid the costs coupled to hydrogen supply. The catalytic activities of Pd(0) nanoparticles produced by different strains of bacteria (bio-Pd) cultivated under fermentative conditions were compared in terms of their ability to dehalogenate the recalcitrant aqueous pollutants diatrizoate and trichloroethylene. While all of the fermentative bio-Pd preparations followed first order kinetics in the dehalogenation of diatrizoate, the catalytic activity differed systematically according to hydrogen production and starting Pd(II) concentration in solution. Batch reactors with nanoparticles formed by Citrobacter braakii showed the highest diatrizoate dehalogenation activity with first order constants of 0.45 {+-} 0.02 h{sup -1} and 5.58 {+-} 0.6 h{sup -1} in batches with initial concentrations of 10 and 50 mg L{sup -1} Pd, respectively. Nanoparticles on C. braakii, used in a membrane bioreactor treating influent containing 20 mg L{sup -1} diatrizoate, were capable of dehalogenating 22 mg diatrizoate mg{sup -1} Pd over a period of 19 days before bio-Pd catalytic activity was exhausted. This study demonstrates the possibility to use the combination of Pd(II), a carbon source and bacteria under fermentative conditions for the abatement of environmental halogenated contaminants.

  14. 30/07/2011 00:22Exploding Bacteria, Self-Fertilizing Bugs and Other Cool Critters -Ecocentric -TIME.com Page 1 of 5http://ecocentric.blogs.time.com/2011/07/29/exploding-bacteria-self-fertilizing-bugs-and-other-cool-critters/

    E-Print Network [OSTI]

    Obbard, Darren

    30/07/2011 00:22Exploding Bacteria, Self-Fertilizing Bugs and Other Cool Critters - Ecocentric - TIME.com Page 1 of 5http://ecocentric.blogs.time.com/2011/07/29/exploding-bacteria for Obama on Auto Efficiency Exploding Bacteria, Self-Fertilizing Bugs and Other Cool Critters Add a Comment

  15. A quantum-theoretical approach to the phenomenon of directed mutations in bacteria

    E-Print Network [OSTI]

    Vasily Ogryzko

    2007-01-30

    The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative scheme of biological adaptation. It is based on appreciation of limits of what we can observe considering an individual biological object. This leads to a possibility for the adaptation process to occur on the level of a single object, as a 'selection among virtual states of the organism'. I discuss the application of this idea to the phenomenon of adaptive mutations in bacteria.

  16. Fiber Optic Micro-endoscopy for Detection of Bacteria in Early Stages of Infection 

    E-Print Network [OSTI]

    Mufti, Nooman Sadat

    2012-02-14

    . have built a wide field Light Emitting Diode (LED) illumination based, 1 mm diameter fiber bundle micro-endoscope capable of sub-cellular resolution imaging (4 ?m resolution with 750 ?m field of view) for pre-cancer detection in the oral mucosa [16... to tissue absorption and scattering of photons emitted by the low numbers of bacteria deep in tissue. Fiber optic micro-endoscopy is uniquely suited to provide a novel solution to this problem by delivering light excitation directly to and collecting...

  17. Light-harvesting in bacteria exploits a critical interplay between transport and trapping dynamics

    E-Print Network [OSTI]

    Felipe Caycedo-Soler; Ferney J. Rodriguez; Luis Quiroga; Neil F. Johnson

    2010-03-11

    Light-harvesting bacteria Rhodospirillum Photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes (HLIM) exploit dissipation as a photo-protective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes (LLIM) efficiently process unused illumination intensity by channelling it to open reaction centers. More generally, our analysis elucidates and quantifies the trade-offs in natural network design for solar energy conversion.

  18. A technique for quantitative and qualitative viewing of aquatic bacteria using scanning electron microscopy 

    E-Print Network [OSTI]

    Dreier, Thomas Michael

    1977-01-01

    microscopic enumeration techniques. Water samples are concentrated on pre-wetted (Triton X-100) Nuclepore filters (0. 2 um pore size) to prov1de a uniform distri- bution of bacteria on the filter surface and vacuum filtered (660 Torr). The filter... is transferred to a petri dish containing filter paper soaked 1n 2% glutaraldehyde and the bacter1a are fixed for one hour. Dehydration 1s performed by transferr1ng the filters through a series of petri dishes conta1ning filter paper saturated with 25, 50, 75...

  19. Isolation of indole-producing bacteria from white shrimp (Penaeus setiferus) 

    E-Print Network [OSTI]

    Smith, Rodney Lee

    1981-01-01

    . 26 5. 40 &3. 0 &3. 0 7. 20 5. 04 7. 36 &3. 0 &3. 0 9. 04 4. 38 8. 57 &3. 0 &3. 0 9. 80 4. 20 9. 04 &3, Q &3. 0 10. 43 12 8+ C 8+ D 8+ I 8+ CDT 8 NT NT NT NT NT 4. 98 5. 23 &3, 0 &3. 0 6. 94 4. 48 6. 49 &3. 0 &3. 0 8... (Member) (Head of Departm nt) December 1981 1804861 ABSTRACT Isolation of Indole-producing Bacteria from White Shrimp (Penaeus setiferus). (December 1981) Rodney Lee Smith, B. S. , Texas A&M University Chairman of Advisory Committee: Dr. Ranzell...

  20. Bacteria mix it up at the microscopic level | Argonne National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 OutreachProductswsicloudwsiclouddenDVA N C E D B L O OLaura BeaneCardwell,Production - Energy InnovationBacteria

  1. Toxin-eating bacteria and bioremediation (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaon and PionExperiments (Journallithium ionToxin-eating bacteria and

  2. Lubricating bacteria model for the growth of bacterial colonies exposed to ultraviolet radiation

    SciTech Connect (OSTI)

    Zhang Shengli; Zhang Lei; Liang Run; Zhang Erhu; Liu Yachao; Zhao Shumin

    2005-11-01

    In this paper, we study the morphological transition of bacterial colonies exposed to ultraviolet radiation by modifying the bacteria model proposed by Delprato et al. Our model considers four factors: the lubricant fluid generated by bacterial colonies, a chemotaxis initiated by the ultraviolet radiation, the intensity of the ultraviolet radiation, and the bacteria's two-stage destruction rate with given radiation intensities. Using this modified model, we simulate the ringlike pattern formation of the bacterial colony exposed to uniform ultraviolet radiation. The following is shown. (1) Without the UV radiation the colony forms a disklike pattern and reaches a constant front velocity. (2) After the radiation is switched on, the bacterial population migrates to the edge of the colony and forms a ringlike pattern. As the intensity of the UV radiation is increased the ring forms faster and the outer velocity of the colony decreases. (3) For higher radiation intensities the total population decreases, while for lower intensities the total population increases initially at a small rate and then decreases. (4) After the UV radiation is switched off, the bacterial population grows both outward as well as into the inner region, and the colony's outer front velocity recovers to a constant value. All these results agree well with the experimental observations [Phys. Rev. Lett. 87, 158102 (2001)]. Along with the chemotaxis, we find that lubricant fluid and the two-stage destruction rate are critical to the dynamics of the growth of the bacterial colony when exposed to UV radiation, and these were not previously considered.

  3. Interplay between excitation kinetics and reaction-center dynamics in purple bacteria

    E-Print Network [OSTI]

    Felipe Caycedo-Soler; Ferney J. Rodríguez; Luis Quiroga; Neil F. Johnson

    2010-08-31

    Photosynthesis is arguably the fundamental process of Life, since it enables energy from the Sun to enter the food-chain on Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations which traverse a complex biomolecular membrane, getting captured and fueling chemical reactions within a reaction-center in order to produce nutrients. The precise nature of these dynamical processes -- which lie at the interface between quantum and classical behaviour, and involve both noise and coordination -- are still being explored. Here we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of {\\it Rsp. Photometricum} purple bacteria. Using stochastic realisations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the reaction center dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.

  4. Thiol-facilitated cell export and desorption of methylmercury by anaerobic bacteria

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lin, Hui; Lu, Xia; Liang, Liyuan; Gu, Baohua

    2015-09-04

    Neurotoxic methylmercury (MeHg), formed by anaerobic bacteria, is shown to be rapidly excreted from the cell, but the mechanism of this process is unclear. Using both Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 strains, we investigated the factors affecting export and distribution of MeHg in mercury methylation and MeHg sorption-desorption assays. Thiols, such as cysteine, were found to greatly facilitate desorption and export of MeHg, particularly by PCA cells. However, in cysteine-free assays (4 h) >90% of the synthesized MeHg was associated with PCA, among which ~73% was sorbed on the cell surface and 19% remained inside the cells. Inmore »comparison, a majority of the MeHg (70%) was exported by ND132, leaving ~20% of the MeHg sorbed on the surface and 10% inside the cells. When MeHg was added directly to the cell suspensions, ND132 adsorbed much lower MeHg but took up more MeHg inside cells than PCA did. These results demonstrate that MeHg export is bacteria strain-specific, time dependent, and is influenced by thiols, implicating important roles of ligand complexation in facilitating MeHg production and mobilization in the environment.« less

  5. Size tunable elemental copper nanoparticles: extracellular synthesis by thermoanaerobic bacteria and capping molecules

    SciTech Connect (OSTI)

    Jang, Gyoung Gug; Jacobs, Christopher B; Gresback, Ryan G; Ivanov, Ilia N; Meyer III, Harry M; Kidder, Michelle; Joshi, Pooran C; Jellison Jr, Gerald Earle; Phelps, Tommy Joe; Graham, David E; Moon, Ji Won

    2015-01-01

    Bimodal sized elemental copper (Cu) nanoparticles (NPs) were synthesized from inexpensive oxidized copper salts by an extracellular metal-reduction process using anaerobic Thermoanaerobacter sp. X513 bacteria in aqueous solution. The bacteria nucleate NPs outside of the cell, and they control the Cu2+ reduction rate to form uniform crystallites with an average diameter of 1.75 0.46 m after 3-day incubation. To control the size and enhance air stability of Cu NPs, the reaction mixtures were supplemented with nitrilotriacetic acid as a chelator, and the surfactant capping agents oleic acid, oleylamine, ascorbic acid, or L-cysteine. Time-dependent UV-visible absorption measurements and XPS studies indicated well-suspended, bimodal colloidal Cu NPs (70 150 and 5 10 nm) with extended air-stability up to 300 min and stable Cu NP films surfaces with 14% oxidation after 20 days. FTIR spectroscopy suggested that these capping agents were effectively adsorbed on the NP surface providing oxidation resistance in aqueous and dry conditions. Compared to previously reported Cu NP syntheses, this biological process substantially reduced the requirement for hazardous organic solvents and chemical reducing agents, while reducing the levels of Cu oxide impurities in the product. This process was highly reproducible and scalable from 0.01 to 1-L batches.

  6. Chemotactic behavior of deep subsurface bacteria toward carbohydrates, amino acids and a chlorinated alkene

    SciTech Connect (OSTI)

    Lopez de Victoria, G. (Puerto Rico Univ., Rio Piedras (Puerto Rico). Dept. of Biology)

    1989-02-01

    The chemotactic behavior of deep terrestrial subsurface bacteria toward amino acids, carbohydrates and trichloroethylene was assayed using a modification of the capillary method and bacterial enumeration by acridine orange direct counts. Eleven isolates of bacteria isolated from six different geological formations were investigated. A bimodal response rather than an absolute positive or negative response was observed in most assays. Most of the isolates were positively chemotactic to low concentrations of substrates and were repelled by high concentrations of the same substrate. However, this was not the case for trichloroethylene (TCE) which was mostly an attractant and elicited the highest responses in all the isolates when compared with amino acids and carbohydrates. The movement rates of these isolates in aseptic subsurface sediments in the absence and presence of TCE were also determined using a laboratory model. All of the isolates showed distinct response range, peak, and threshold concentrations when exposed to the same substrates suggesting that they are possibly different species as has been inferred from DNA homology studies. 101 refs., 4 figs., 57 tabs.

  7. ORGANIC GEOCHEMICAL STUDIES. II. THE DISTRIBUTION OF ALIPHATIC HYDROCARBONS IN ALGAE, BACTERIA, AND IN A RECENT LAKE SEDIMENT: A PRELIMINARY REPORT

    E-Print Network [OSTI]

    Han, Jerry; McCarthy, E.D.; Van Hoeven Jr., William; Calvin, Melvin; Bradley, W. H.

    2008-01-01

    significantly to the hydrocarbons of higher molecular weightDISTRIBUTION OF ALIPHATIC HYDROCARBONS IN ALGAE, BACTERIA,T E DISTRIBUTION O ALIPHATIC HYDROCARBONS H F A PRELIMINARY

  8. Steady-state MreB helices inside bacteria: dynamics without motors

    E-Print Network [OSTI]

    Jun F. Allard; Andrew D. Rutenberg

    2007-08-03

    Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasi-static evolution of the helical pitch with cell growth, as well as timescales of helix turnover and denovo establishment. We find that while the body of a polarized MreB helix treadmills towards its slow-growing end, the fast-growing tips of laterally associated protofilaments move towards the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.

  9. Label-free identification of individual bacteria using Fourier transform light scattering

    E-Print Network [OSTI]

    Jo, YoungJu; Kim, Min-hyeok; Park, HyunJoo; Kang, Suk-Jo; Park, YongKeun

    2015-01-01

    Rapid identification of bacterial species is crucial in medicine and food hygiene. In order to achieve rapid and label-free identification of bacterial species at the single bacterium level, we propose and experimentally demonstrate an optical method based on Fourier transform light scattering (FTLS) measurements and statistical classification. For individual rod-shaped bacteria belonging to four bacterial species (Listeria monocytogenes, Escherichia coli, Lactobacillus casei, and Bacillus subtilis), two-dimensional angle-resolved light scattering maps are precisely measured using FTLS technique. The scattering maps are then systematically analyzed, employing statistical classification in order to extract the unique fingerprint patterns for each species, so that a new unidentified bacterium can be identified by a single light scattering measurement. The single-bacterial and label-free nature of our method suggests wide applicability for rapid point-of-care bacterial diagnosis.

  10. Bacteria and Surface Water Quality Standards Section 303(d) of the Clean Water Act requires that each state set

    E-Print Network [OSTI]

    bodies that support oyster harvesting, called oyster waters, have four clas- sifications which determineBacteria and Surface Water Quality Standards Section 303(d) of the Clean Water Act requires that each state set water quality standards to ensure all uses of a water body have the ap- propriate water

  11. Novel Thermo-Acidophilic Bacteria Isolated from Geothermal Sites in Yellowstone National Park: Physiological and Phylogenetic Characteristics

    SciTech Connect (OSTI)

    D. B. Johnson; N. Okibe; F. F. Roberto

    2003-07-01

    Moderately thermophilic acidophilic bacteria were isolated from geothermal (30–83 °C) acidic (pH 2.7– 3.7) sites in Yellowstone National Park. The temperature maxima and pH minima of the isolates ranged from 50 to 65 °C, and pH 1.0–1.9. Eight of the bacteria were able to catalyze the dissimilatory oxidation of ferrous iron, and eleven could reduce ferric iron to ferrous iron in anaerobic cultures. Several of the isolates could also oxidize tetrathionate. Six of the iron-oxidizing isolates, and one obligate heterotroph, were low G+C gram-positive bacteria (Firmicutes). The former included three Sulfobacillus-like isolates (two closely related to a previously isolated Yellowstone strain, and the third to a mesophilic bacterium isolated from Montserrat), while the other three appeared to belong to a different genus. The other two iron-oxidizers were an Actinobacterium (related to Acidimicrobium ferrooxidans) and a Methylobacterium-like isolate (a genus within the a-Proteobacteria that has not previously been found to contain either iron-oxidizers or acidophiles). The other three (heterotrophic) isolates were also a-Proteobacteria and appeared be a novel thermophilic Acidisphaera sp. An ARDREA protocol was developed to discriminate between the iron-oxidizing isolates. Digestion of amplified rRNA genes with two restriction enzymes (SnaBI and BsaAI) separated these bacteria into five distinct groups; this result was confirmed by analysis of sequenced rRNA genes.

  12. Population Changes in a Community of Alkaliphilic Iron-Reducing Bacteria Due to Changes in the Electron

    E-Print Network [OSTI]

    Burke, Ian

    in the Electron Acceptor: Implications for Bioremediation at Alkaline Cr(VI)-Contaminated Sites Samuel J. Fuller the bacterial community. Keywords COPR . Bacteria . Alkaliphile . Chromium . Iron . Bioremediation 1. 2001; Jankowski et al. 2006; Mayes and Younger 2006). Until recently, these Water Air Soil Pollut (2015

  13. Bacteria that are resistant to current antibiotics have wreaked havoc in the clinic and are a primary cause of

    E-Print Network [OSTI]

    Marshall, Garland R.

    Bacteria that are resistant to current antibiotics have wreaked havoc in the clinic resistant, and up to 50% are resistant to stronger drugs, such as meticillin3 . Meticillin-resistant S of weeks. Moreover, as most bacterial strains are becoming resistant to multiple antibiotics, including

  14. When fish die, bacteria or the enzymes they produce invade the flesh of fish. This process produces toxic

    E-Print Network [OSTI]

    Michel, Howard E.

    ABSTRACT When fish die, bacteria or the enzymes they produce invade the flesh of fish. This process produces toxic compounds in the fish and the fish becomes spoiled. Fourier Transform Infrared spectroscopy neural network (ANN) for the development of an ANN based FT-IR Screening System for fish

  15. Bacteria that generate significant amounts of electricity could be used in microbial fuel cells to provide power in remote environments or to convert

    E-Print Network [OSTI]

    Lovley, Derek

    Bacteria that generate significant amounts of electricity could be used in microbial fuel cells to provide power in remote environments or to convert waste to electricity. Professor Derek Lovley from the University of Massachusetts, USA isolated bacteria with large numbers of tiny projections called pili which

  16. Protecting Our Water: Tracking Sources of Bacterial Contamination Numerous surface waterbodies in Texas are classified as having high levels of fecal coliform bacteria, an indicator of fecal pollution.

    E-Print Network [OSTI]

    in Texas are classified as having high levels of fecal coliform bacteria, an indicator of fecal pollution. coli and other fecal coliform bacteria do not provide information on whether the source of pollution of pollution need to be identified to implement effective pollution control strategies to improve water quality

  17. How do microbial fuel cells (MFCs) work? Bacteria need energy to survive, in the same way that humans need food to

    E-Print Network [OSTI]

    Lee, Dongwon

    How do microbial fuel cells (MFCs) work? Bacteria need energy to survive, in the same way that humans need food to live. Bacteria get this energy in a two-step process. The first step requires are receiving more attention because they are a potential part of the solution to our energy demands and could

  18. Detecting bacteria and Determining Their Susceptibility to Antibiotics by Stochastic Confinement in Nanoliter Droplets using Plug-Based Microfluidics

    SciTech Connect (OSTI)

    Boedicker, J.; Li, L; Kline, T; Ismagilov, R

    2008-01-01

    This article describes plug-based microfluidic technology that enables rapid detection and drug susceptibility screening of bacteria in samples, including complex biological matrices, without pre-incubation. Unlike conventional bacterial culture and detection methods, which rely on incubation of a sample to increase the concentration of bacteria to detectable levels, this method confines individual bacteria into droplets nanoliters in volume. When single cells are confined into plugs of small volume such that the loading is less than one bacterium per plug, the detection time is proportional to plug volume. Confinement increases cell density and allows released molecules to accumulate around the cell, eliminating the pre-incubation step and reducing the time required to detect the bacteria. We refer to this approach as stochastic confinement. Using the microfluidic hybrid method, this technology was used to determine the antibiogram - or chart of antibiotic sensitivity - of methicillin-resistant Staphylococcus aureus (MRSA) to many antibiotics in a single experiment and to measure the minimal inhibitory concentration (MIC) of the drug cefoxitin (CFX) against this strain. In addition, this technology was used to distinguish between sensitive and resistant strains of S. aureus in samples of human blood plasma. High-throughput microfluidic techniques combined with single-cell measurements also enable multiple tests to be performed simultaneously on a single sample containing bacteria. This technology may provide a method of rapid and effective patient-specific treatment of bacterial infections and could be extended to a variety of applications that require multiple functional tests of bacterial samples on reduced timescales.

  19. Impact of bacteria and bacterial components on osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells

    SciTech Connect (OSTI)

    Fiedler, Tomas; Salamon, Achim; Adam, Stefanie; Herzmann, Nicole; Taubenheim, Jan; Peters, Kirsten

    2013-11-01

    Adult mesenchymal stem cells (MSC) are present in several tissues, e.g. bone marrow, heart muscle, brain and subcutaneous adipose tissue. In invasive infections MSC get in contact with bacteria and bacterial components. Not much is known about how bacterial pathogens interact with MSC and how contact to bacteria influences MSC viability and differentiation potential. In this study we investigated the impact of three different wound infection relevant bacteria, Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes, and the cell wall components lipopolysaccharide (LPS; Gram-negative bacteria) and lipoteichoic acid (LTA; Gram-positive bacteria) on viability, proliferation, and osteogenic as well as adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells (adMSC). We show that all three tested species were able to attach to and internalize into adMSC. The heat-inactivated Gram-negative E. coli as well as LPS were able to induce proliferation and osteogenic differentiation but reduce adipogenic differentiation of adMSC. Conspicuously, the heat-inactivated Gram-positive species showed the same effects on proliferation and adipogenic differentiation, while its cell wall component LTA exhibited no significant impact on adMSC. Therefore, our data demonstrate that osteogenic and adipogenic differentiation of adMSC is influenced in an oppositional fashion by bacterial antigens and that MSC-governed regeneration is not necessarily reduced under infectious conditions. - Highlights: • Staphylococcus aureus, Streptococcus pyogenes and Escherichia coli bind to and internalize into adMSC. • Heat-inactivated cells of these bacterial species trigger proliferation of adMSC. • Heat-inactivated E. coli and LPS induce osteogenic differentiation of adMSC. • Heat-inactivated E. coli and LPS reduce adipogenic differentiation of adMSC. • LTA does not influence adipogenic or osteogenic differentiation of adMSC.

  20. Migration of chemotactic bacteria in soft agar: role of gel concentration

    E-Print Network [OSTI]

    O. A. Croze; G. P. Ferguson; M. E. Cates; W. C. K. Poon

    2011-08-06

    We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays.

  1. Active transport, substrate specificity, and methylation of Hg(II) in anaerobic bacteria

    SciTech Connect (OSTI)

    Schasfer, Jeffra [Princeton University; Rocks, Sara [Princeton University; Zheng, Wang [ORNL; Liang, Liyuan [ORNL; Gu, Baohua [ORNL; Morel, Francois M [ORNL

    2011-01-01

    The formation of methylmercury (MeHg), which is biomagnified in aquatic food chains and poses a risk to human health, is effected by some iron- and sulfate-reducing bacteria (FeRB and SRB) in anaerobic environments. However, very little is known regarding the mechanism of uptake of inorganic Hg by these organisms, in part because of the inherent difficulty in measuring the intracellular Hg concentration. By using the FeRB Geobacter sulfurreducens and the SRB Desulfovibrio desulfuricans ND132 as model organisms, we demonstrate that Hg(II) uptake occurs by active transport. We also establish that Hg(II) uptake by G. sulfurreducens is highly dependent on the characteristics of the thiols that bind Hg(II) in the external medium, with some thiols promoting uptake and methylation and others inhibiting both. The Hg(II) uptake system of D. desulfuricans has a higher affinity than that of G. sulfurreducens and promotes Hg methylation in the presence of stronger complexing thiols. We observed a tight coupling between Hg methylation and MeHg export from the cell, suggesting that these two processes may serve to avoid the build up and toxicity of cellular Hg. Our results bring up the question of whether cellular Hg uptake is specific for Hg(II) or accidental, occurring via some essential metal importer. Our data also point at Hg(II) complexation by thiols as an important factor controlling Hg methylation in anaerobic environments.

  2. Genotypic and phenotypic characterization of aerosolized bacteria collected from African dust events

    SciTech Connect (OSTI)

    Wilson, Christina A.; Brigmon, Robin L.; Yeager, Chris; Smith, Garriet W.; Polson, Shawn W.

    2013-07-31

    Twenty-one bacteria were isolated and characterized from air samples collected in Africa and the Caribbean by the United States Geological Survey (USGS). Isolates were selected based on preliminary characterization as possible pathogens. Identification of the bacterial isolates was 25 achieved using 16S rRNA gene sequence analysis, fatty acid methyl esters (FAMEs) profiling, the BIOLOG Microlog® System (carbon substrate assay), and repetitive extragenic palindromic (REP)-PCR analysis. The majority of isolates (18/21) were identified as species of the genus Bacillus. Three isolates were classified within the Bacillus cereus senso lato group, which includes Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus strains. One isolate was identified as a Staphylococcus sp., 30 most closely related to species (i.e Staphylococcus kloosii, Staphylococcus warneri) that are commonly associated with human or animal skin, but can also act as opportunistic pathogen. Another isolate was tentatively identified as Tsukamurella inchonensis, a known respiratory pathogen, and was resistant to the ten antibiotics tested including vancomycin.

  3. Genotypic and phenotypic characterization of aerosolized bacteria collected from African dust events

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wilson, Christina A.; Brigmon, Robin L.; Yeager, Chris; Smith, Garriet W.; Polson, Shawn W.

    2013-07-31

    Twenty-one bacteria were isolated and characterized from air samples collected in Africa and the Caribbean by the United States Geological Survey (USGS). Isolates were selected based on preliminary characterization as possible pathogens. Identification of the bacterial isolates was 25 achieved using 16S rRNA gene sequence analysis, fatty acid methyl esters (FAMEs) profiling, the BIOLOG Microlog® System (carbon substrate assay), and repetitive extragenic palindromic (REP)-PCR analysis. The majority of isolates (18/21) were identified as species of the genus Bacillus. Three isolates were classified within the Bacillus cereus senso lato group, which includes Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus strains. Onemore »isolate was identified as a Staphylococcus sp., 30 most closely related to species (i.e Staphylococcus kloosii, Staphylococcus warneri) that are commonly associated with human or animal skin, but can also act as opportunistic pathogen. Another isolate was tentatively identified as Tsukamurella inchonensis, a known respiratory pathogen, and was resistant to the ten antibiotics tested including vancomycin.« less

  4. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria

    SciTech Connect (OSTI)

    Halavaty, Andrei S. [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States); Kim, Youngchang [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Minasov, George; Shuvalova, Ludmilla; Dubrovska, Ievgeniia; Winsor, James [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States); Zhou, Min [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Onopriyenko, Olena; Skarina, Tatiana [Center for Structural Genomics of Infectious Diseases, (United States); University of Toronto, Toronto, Ontario M5G 1L6 (Canada); Papazisi, Leka; Kwon, Keehwan; Peterson, Scott N. [Center for Structural Genomics of Infectious Diseases, (United States); J. Craig Venter Institute, Rockville, MD 20850 (United States); Joachimiak, Andrzej [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Savchenko, Alexei [Center for Structural Genomics of Infectious Diseases, (United States); University of Toronto, Toronto, Ontario M5G 1L6 (Canada); Anderson, Wayne F., E-mail: wf-anderson@northwestern.edu [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States)

    2012-10-01

    The structural characterization of acyl-carrier-protein synthase (AcpS) from three different pathogenic microorganisms is reported. One interesting finding of the present work is a crystal artifact related to the activity of the enzyme, which fortuitously represents an opportunity for a strategy to design a potential inhibitor of a pathogenic AcpS. Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS{sub SA}), Vibrio cholerae (AcpS{sub VC}) and Bacillus anthracis (AcpS{sub BA}) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS{sub BA} is emphasized because of the two 3?, 5?-adenosine diphosphate (3?, 5?-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3?, 5?-ADP is bound as the 3?, 5?-ADP part of CoA in the known structures of the CoA–AcpS and 3?, 5?-ADP–AcpS binary complexes. The position of the second 3?, 5?-ADP has never been described before. It is in close proximity to the first 3?, 5?-ADP and the ACP-binding site. The coordination of two ADPs in AcpS{sub BA} may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.

  5. VOLUME 75, NUMBER 9 P H Y S I C A L R E V I E W L E T T E R S 28 AUGUST 1995 Aggregation Patterns in Stressed Bacteria

    E-Print Network [OSTI]

    Tsimring, Lev S.

    in Stressed Bacteria Lev Tsimring and Herbert Levine Institute for Nonlinear Science, University of California 1995) We study the formation of spot patterns seen in bacterial colonies when the bacteria aggregating in the face of adversity. Normally, bacteria divide and spread out into regions of initially low

  6. Effect of low po? on growth of bacteria and on loss of soluble carbon from maize roots under hydroponic conditions 

    E-Print Network [OSTI]

    Coker, Dennis Lee

    1992-01-01

    Hydroponic Conditions. (May 1992) Dennis Lee Coker, B. S. , Tarleton State University Chairman of Advisory Committee: Dr. David A. Zuberer In the maize rhizosphere, environmental stress may influence a number of processes mediated by rhizosphere bacteria... of 10 . Upon completion of serial dilutions, 0. 1-mL aliquots of diluted root extract (inoculum) from the three highest dilutions (10 , 10 -8 and 10 ) were transferred to duplicate plates to determine colony forming units (CFU) per gram of root...

  7. Reduction of turkey hatching egg shell contamination with ultraviolet irradiation 

    E-Print Network [OSTI]

    Russo, Rebecca Ann

    2001-01-01

    The effects of ultraviolet light (UV) at 254 nm on indigenous eggshell surface aerobic bacteria, Salmonella, Escherichia coli, gram positive bacteria as well as inoculated Salmonella typhimurium chicken and E. coli O157:H7 were evaluated. Various...

  8. Size-dependent fluorescence of bioaerosols: Mathematical model using fluorescing and absorbing molecules in bacteria

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hill, Steven C.; Williamson, Chatt C.; Doughty, David C.; Pan, Yong-Le; Santarpia, Joshua L.; Hill, Hanna H.

    2015-02-02

    This paper uses a mathematical model of fluorescent biological particles composed of bacteria and/or proteins (mostly as in Hill et al., 2013 [23]) to investigate the size-dependence of the total fluorescence emitted in all directions. The model applies to particles which have negligible reabsorption of fluorescence within the particle. The specific particles modeled here are composed of ovalbumin and of a generic Bacillus. The particles need not be spherical, and in some cases need not be homogeneous. However, the results calculated in this paper are for spherical homogeneous particles. Light absorbing and fluorescing molecules included in the model are aminomore »acids, nucleic acids, and several coenzymes. Here the excitation wavelength is 266 nm. The emission range, 300 to 370 nm, encompasses the fluorescence of tryptophan. The fluorescence cross section (CF) is calculated and compared with one set of published measured values. We investigate power law (Ady) approximations to CF, where d is diameter, and A and y are parameters adjusted to fit the data, and examine how y varies with d and composition, including the fraction as water. The particle's fluorescence efficiency (QF=CF/geometric-cross-section) can be written for homogeneous particles as QabsRF, where Qabs is the absorption efficiency, and RF, the fraction of the absorbed light emitted as fluorescence, is independent of size and shape. When QF is plotted vs. mid or mi(mr-1)d, where m=mr+imi is the complex refractive index, the plots for different fractions of water in the particle tend to overlap.« less

  9. Excitonic energy transfer in light-harvesting complexes in purple bacteria

    E-Print Network [OSTI]

    Jun Ye; Kewei Sun; Yang Zhao; Yunjin Yu; Chee Kong Lee; Jianshu Cao

    2012-07-10

    Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting systems in purple bacteria. It is found that inclusion of long-range dipolar interactions in the two methods results in significant increases in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking caused by the dimerization of BChls and dipolar couplings, such dependence has been largely suppressed. In the studies of coupled-ring systems, both methods reveal interesting role of dipolar interaction in increasing energy transfer efficiency by introducing multiple intra/inter-ring transfer paths. Importantly, the time scale (~4ps) of inter-ring exciton transfer obtained from polaron dynamics is in good agreement with previous studies. In a double-ring LH2 system, dipole-induced symmetry breaking leads to global minima and local minima of the average trapping time when there is a finite value of non-zero dephasing rate, suggesting that environment plays a role in preserving quantum coherent energy transfer. In contrast, dephasing comes into play only when the perfect cylindrical symmetry in the hypothetic system is broken. This study has revealed that dipolar interaction between chromophores may play an important part in the high energy transfer efficiency in the LH2 system and many other natural photosynthetic systems.

  10. Size-dependent fluorescence of bioaerosols: Mathematical model using fluorescing and absorbing molecules in bacteria

    SciTech Connect (OSTI)

    Hill, Steven C.; Williamson, Chatt C.; Doughty, David C.; Pan, Yong-Le; Santarpia, Joshua L.; Hill, Hanna H.

    2015-02-02

    This paper uses a mathematical model of fluorescent biological particles composed of bacteria and/or proteins (mostly as in Hill et al., 2013 [23]) to investigate the size-dependence of the total fluorescence emitted in all directions. The model applies to particles which have negligible reabsorption of fluorescence within the particle. The specific particles modeled here are composed of ovalbumin and of a generic Bacillus. The particles need not be spherical, and in some cases need not be homogeneous. However, the results calculated in this paper are for spherical homogeneous particles. Light absorbing and fluorescing molecules included in the model are amino acids, nucleic acids, and several coenzymes. Here the excitation wavelength is 266 nm. The emission range, 300 to 370 nm, encompasses the fluorescence of tryptophan. The fluorescence cross section (CF) is calculated and compared with one set of published measured values. We investigate power law (Ady) approximations to CF, where d is diameter, and A and y are parameters adjusted to fit the data, and examine how y varies with d and composition, including the fraction as water. The particle's fluorescence efficiency (QF=CF/geometric-cross-section) can be written for homogeneous particles as QabsRF, where Qabs is the absorption efficiency, and RF, the fraction of the absorbed light emitted as fluorescence, is independent of size and shape. When QF is plotted vs. mid or mi(mr-1)d, where m=mr+imi is the complex refractive index, the plots for different fractions of water in the particle tend to overlap.

  11. Effects of Wet and Dry Weather Events on Bacteria (Enterococci) and the Public Health Threat from the Re-Suspension of Sediment Sequestered Enterococci 

    E-Print Network [OSTI]

    Bare, Ryan Michael

    2014-06-04

    Approximately 66% of Texas surface waters are impaired with bacteria from fecal waste, including several tributaries and segments within the Galveston Bay system. This study was conducted in the waters of the Marina Del Sol marina on Clear Lake...

  12. Start | View At a Glance | Author Index 219-5 Coupled Biotic and Abiotic Arsenite Oxidation Kinetics with Heterotrophic Soil Bacteria and a Poorly Crystalline

    E-Print Network [OSTI]

    Sparks, Donald L.

    Kinetics with Heterotrophic Soil Bacteria and a Poorly Crystalline Manganese Oxide. See more from rates in batch experiments with a mixture of poorly crystalline manganese oxide (-MnO2) and four strains

  13. Using the bacteria-2-hybrid system to determine the role of S2 in the equine infectious anemia virus (EIAV) life cycle 

    E-Print Network [OSTI]

    Weidner, Jason Lee

    2013-02-22

    of E. coli to test interactions between fusion products made by fusing S2 with lambda repressor, and random cellular proteins to RNA polymerase (RNAP). Since a reporter strain cassette is contained within the genetically altered bacteria, the lambda...

  14. The relationship between the level of antibiotic use and resistance among enteric bacteria in a multi-site integrated human and swine population 

    E-Print Network [OSTI]

    Christian, Kristi Lynn

    2009-05-15

    The objective of this longitudinal study was to study the relationship between changes in prevalence of resistant enteric bacteria associated with mean monthly doses (MMD) of various antibiotics used in each of two host species. From January 2004...

  15. 13/06/2014 11:11Cooperation and competition in pathogenic bacteria. -F1000Prime Page 1 of 2http://f1000.com/prime/1014932

    E-Print Network [OSTI]

    West, Stuart

    in pathogenic bacteria. Griffin AS, West SA, Buckling A Nature. 2004 Aug 26; 430 RECOMMENDATIONS 1 ABSTRACT COMMENTS Mark Hay F1000 Ecology Georgia Institute of Technology, Atlanta, GA, USA

  16. Excitonic energy transfer in light-harvesting complexes in purple bacteria Jun Ye, Kewei Sun, Yang Zhao, Yunjin Yu, Chee Kong Lee et al.

    E-Print Network [OSTI]

    Cao, Jianshu

    Excitonic energy transfer in light-harvesting complexes in purple bacteria Jun Ye, Kewei Sun, Yang://jcp.aip.org/about/rights_and_permissions #12;THE JOURNAL OF CHEMICAL PHYSICS 136, 245104 (2012) Excitonic energy transfer in light-harvesting complexes in purple bacteria Jun Ye,1 Kewei Sun,1 Yang Zhao,1,a) Yunjin Yu,1,2 Chee Kong Lee,1 and Jianshu

  17. Estimating Bacteria Emissions from Inversion of Atmospheric Transport: Sensitivity to Modelled Particle Characteristics

    SciTech Connect (OSTI)

    Burrows, Susannah M.; Rayner, Perter; Butler, T.; Lawrence, M.

    2013-06-04

    Model-simulated transport of atmospheric trace components can be combined with observed concentrations to obtain estimates of ground-based sources using various inversion techniques. These approaches have been applied in the past primarily to obtain source estimates for long-lived trace gases such as CO2. We consider the application of similar techniques to source estimation for atmospheric aerosols, by using as a case study the estimation of bacteria emissions from different ecosystem regions in the global atmospheric chemistry and climate model ECHAM5/MESSy-Atmospheric Chemistry (EMAC). Simulated particle concentrations in the tropopause region and at high latitudes, as well as transport of particles to tundra and land ice regions are shown to be highly sensitive to scavenging in mixed-phase clouds, which is poorly characterized in most global climate models. This may be a critical uncertainty in correctly simulating the transport of aerosol particles to the Arctic. Source estimation via Monte Carlo Markov Chain is applied to a suite of sensitivity simulations and the global mean emissions are estimated. We present an analysis of the partitioning of uncertainties in the global mean emissions that are attributable to particle size, CCN activity, the ice nucleation scavenging ratios for mixed-phase and cold clouds, and measurement error. Uncertainty due to CCN activity or to a 1 um error in particle size is typically between 10% and 40% of the uncertainty due to data uncertainty, as measured by the 5%-ile to 95%-ile range of the Monte Carlo ensemble. Uncertainty attributable to the ice nucleation scavenging ratio in mized-phase clouds is as high as 10% to 20% of the data uncertainty. Taken together, the four model 20 parameters examined contribute about half as much to the uncertainty in the estimated emissions as do the measurements. This was a surprisingly large contribution from model uncertainty in light of the substantial data uncertainty, which ranges from 81% to 870% for each of ten ecosystems for this case study. The effects of these and other model parameters in contributing to the uncertainties in the transport of atmospheric aerosol particles should be treated explicitly and systematically in both forward and inverse modelling studies.

  18. Biodegradation 13: 7990, 2002. 2002 Kluwer Academic Publishers. Printed in the Netherlands.

    E-Print Network [OSTI]

    Pace, Norman

    mass. Most petroleum-related hydrocarbons are readily biodegraded by aerobic microorganisms (Gibson: aviation gasoline, biodegradation, bioremediation, direct microscopy, petroleum hydrocarbons, radioisotopes-situ bioremediation of petroleum hydrocarbons at one site contaminated with refinery waste and a second site

  19. Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments

    SciTech Connect (OSTI)

    Edlund, A.; Jansson, J.

    2008-05-01

    The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.

  20. EINDHOVEN UNIVERSITY OF TECHNOLOGY Department of Mathematics and Computer Science

    E-Print Network [OSTI]

    Eindhoven, Technische Universiteit

    of sulfates that, in the absence of dissolved oxygen and nitrates, are reduced by bacteria. Such bacteria bacteria ­ metabolizes the H2S gas and oxidize it to sulphuric acid. It is worth noting that Thiobacillus into the headspace environment above the wastewater, a sulfur oxidizing bacteria ­ primarily Thiobacillus aerobic

  1. Water Research 38 (2004) 25292536 The use of isotopic and lipid analysis techniques linking

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    2004-01-01

    toluene degradation to specific microorganisms: applications and limitations Jiasong Fanga, *, Nanh in the subsurface. Intrinsic bioremediation refers to the action of microorganisms to degrade contaminants in situ whether bioremediation candidate bacteria degrade hydrocarbons is a pressing issue in contaminant

  2. Aerobic Biodegradation of N-Nitrosodimethylamine (NDMA)

    E-Print Network [OSTI]

    Wood, Thomas K.

    -mail: alvarez@ce.berkeley.edu 2 Departments of Chemical Engineering and Molecular and Cell Biology, University- ance in the environment is related to the release of rocket fuel and to chlorine-based disinfection, induction of the soluble methane monooxygenase (sMMO) expressed by Methylosinus tri- chosporium OB3b

  3. AEROBIC BIOTRANSFORMATION OF TOXIC ORGANICS IN WASTEWATER

    E-Print Network [OSTI]

    be forwarded to: Technology and Pollution Prevention Section Environment Canada 224 West Esplanade North: Environment Canada Environmental Protection Fraser Pollution Abatement North Vancouver, B.C. Prepared by by Environment Canada under the Environmental Innovation Program and under the Fraser River Action Plan through

  4. Making more efficient fuel cells 08.09.2009 -Bacteria that generate significant amounts of electricity could be used in microbial fuel cells to provide

    E-Print Network [OSTI]

    Lovley, Derek

    to electricity. Professor Derek Lovley from the University of Massachusetts, USA isolated bacteria with large of electricity could be used in microbial fuel cells to provide power in remote environments or to convert waste electricity. The researchers found large quantities of pilin, a protein that makes the tiny fibres

  5. USATODAY.com -Bacteria-powered battery runs on a sweet tooth Page 1 Close|EMAIL THIS|SAVE THIS

    E-Print Network [OSTI]

    Lovley, Derek

    |SAVE THIS Bacteria-powered battery runs on a sweet tooth By Elizabeth Weise USA TODAY Scientists at the University in carbohydrates and turn them into electricity. Previous research has shown it is possible to use microbes to turn organic matter into electricity, but the process required the use of added materials to shuttle

  6. Processing of cellulosic material by a cellulase-containing cell-free fermentate produced from cellulase-producing bacteria, ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1998-08-04

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate, have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase degrading bacterium ATCC 55702, which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic materials. 5 figs.

  7. Phenotypic plasticity of a cooperative behaviour in bacteria R. KU MMERLI, N. JIRICNY, L. S. CLARKE*, S. A. WEST & A. S. GRIFFIN

    E-Print Network [OSTI]

    West, Stuart

    Phenotypic plasticity of a cooperative behaviour in bacteria R. KU¨ MMERLI, N. JIRICNY, L. S to adjust behaviour in response to changes in the environ- ment (phenotypic plasticity), rather than have selection has favoured phenotypic plasticity in a variety of vertebrate and invertebrate species (Charnov

  8. 27/05/2012 21:12Fighting bacteria's strength in numbers Page 1 of 2http://www.sciencedaily.com/releases/2012/05/120517115341.htm

    E-Print Network [OSTI]

    West, Stuart

    27/05/2012 21:12Fighting bacteria's strength in numbers Page 1 of 2http of Nottingham have opened the way for more accurate research into new ways to fight dangerous bacterial at The University of Nottingham, are trying to find other ways of fighting infection. This new work involves using

  9. Isolation and characterization of potential indicator bacteria to be used for validation of Escherichia coli O157:H7 reduction in beef slaughter plant critical control points 

    E-Print Network [OSTI]

    Magana Yepez, Maria Belem

    2005-11-01

    to determine similarity in acid- and heat-resistance characteristics. After evaluation at 2 heating temperatures (55 and 65??C) and 3 pH levels (3.0, 4.0, and 5.0), it was determined that several potential indicator bacteria were slightly more resistant than E...

  10. Processing of cellulosic material by a cellulase-containing cell-free fermentate produced from cellulase-producing bacteria, ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate, have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase degrading bacterium ATCC 55702, which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic materials.

  11. 12/06/2012 09:46Womens T Shirts Environmentally Friendly Gifts Made in USA Eco t shirts Page 1 of 5http://womens-t.com/2012/05/fighting-bacterias-strength-in-numbers/

    E-Print Network [OSTI]

    West, Stuart

    http://womens-t.com/2012/05/fighting-bacterias-strength-in-numbers/ Womens T Shirts Environmentally clothing and Accessories Help to Prevent Global Warming T Shirts Fighting bacteria's strength in numbers The University of Nottingham, are perplexing to find other ways of fighting infection. This new work involves

  12. INFECTION AND IMMUNITY, June 2003, p. 36523656 Vol. 71, No. 6 0019-9567/03/$08.00 0 DOI: 10.1128/IAI.71.6.36523656.2003

    E-Print Network [OSTI]

    Lebendiker, Mario

    -inhibitable coaggregation is a common interaction among oral bacteria, including periodontal microorganisms predominant pathogen in subsequent periodon- tal destruction (4, 13). F. nucleatum strains were shown

  13. Evaluation of five biocarriers as supports for immobilized bacteria: Comparative performance during high chemical loading, acid shocking, drying and heat shocking

    SciTech Connect (OSTI)

    Heitkamp, M.A.; Adams, W.J. (Monsanto Co., St. Louis, MO (United States). Environmental Sciences Center); Camel, V. (Ecole Superieure de Physique et Chimie Industrielle de Paris, (France))

    1993-06-01

    Immobilized bacteria technology (IBT) utilizes inert biocarriers to support high concentrations of chemical-degrading bacteria in reactors designed to provide optimal conditions for microbial activity. This study evaluated IBT performance inpacked bed reactors (PBRs) using a porous inorganic biocarrier (diatomaceous earth), nonporous biocarriers (glass beads), and organic biocarriers having carbon adsorption properties (granular activated carbon) with different porosity. Each reactor was challenged with high chemical loading, acid, dryness, and heat shock conditions. Benchtop PBSs inoculated with a p-nitrophenol (PNP)-degrading Pseudomonas sp. and fed a synthetic waste containing 100 to 1,300 mg/L of PNP showed removal of PNP from effluents within 24 h of start-up. Chemical loading studies showed maximum PNP removal rates of 6.45 to 7.35 kg/m[sup 3]/d for bacteria in PBRs containing diatomaceous earth beads, glass beads, and activated coconut carbon. A lower PNP removal rate of 1.47 kg/m[sup 3]/d was determined for the activated anthracite carbon, and this PBR responded more slowly to increases in chemical loading. The PBR containing bacteria immobilized on activated coconut carbon showed exceptional tolerance to acid shocking, drying, and heat shocking by maintaining PNP removal rates > 85% throughout the entire study. The other biocarriers showed nearly complete loss of PNP degradation during the perturbations, but all recovered high rates of PNP degradation (> 98% removal) within 48 h after an acid shock at pH2, within 8 d after an acid shock at pH 1.0, within 24 h after drying for 72 h, and within 48 h of heat shocking. The resiliency and high chemical removal efficiency demonstrated by immobilized bacteria in this study support the concept of using IBT for the biotreatment of industrial wastes..

  14. Microorganism genomics, compositions and methods related thereto

    DOE Patents [OSTI]

    Handelsman, Jo (Madison, WI); Goodman, Robert M. (Madison, WI); Rondon, Michelle R. (Madison, WI)

    2001-01-01

    The present invention provides methods and compositions for accessing, in a generally unbaised manner, a diverse genetic pool for genes involved in biosynthetic pathways. The invention also provides compounds which can be identified by cloning biosynthetic pathways.

  15. Bacteriocins of Aquatic Microorganisms and Their Potential

    E-Print Network [OSTI]

    Riley, Margaret

    stage (Gillor et al., 2008). The use of bacteriocins in probiotic applications, as preservatives, and promise for use in the creation of probiotic strains for the seafood industry. 2. Bacteriocin basics

  16. METHANE INCORPORATION BY PROCARYOTIC PHOTOSYNTHETIC MICROORGANISMS

    E-Print Network [OSTI]

    Norton, Charles J.; Kirk, Martha; Calvin, Melvin

    1970-01-01

    11. As predicted from Dalton's law, C 14 activities inIN AQ. PHASE FROM DALTON'S LAW,? C ACTIVITY IN LIQUIDconstancy predicted by Dalton's law ll : Pa~ Solubility of

  17. Pentanol isomer synthesis in engineered microorganisms

    E-Print Network [OSTI]

    Cann, Anthony F.; Liao, James C.

    2010-01-01

    For example, current biodiesel production relies mostly onenzymes for in vivo biodiesel production (Kalscheuer et al.292 Gerpen JV (2005) Biodiesel processing and production.

  18. Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy

    E-Print Network [OSTI]

    Ilya Soifer; Lydia Robert; Naama Barkai; Ariel Amir

    2014-10-23

    Unicellular organism from various kingdoms of life face the challenge of regulating their size. Despite decades of research, we still do not have a good understanding of the molecular mechanisms involved in this regulation, and how cells coordinate the different events of the cell cycle, such as growth, division and DNA replication is still unclear. Here, we report on experimental results for the budding yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, showing that, remarkably, they share a common strategy for cell size control. We collected data on single-cell growth and cell cycle progression in S. cerevisiae in several growth media and estimated the distributions of size at birth and interdivision time as well as their correlations throughout cell lineages. We also performed the same analysis on previously collected data on single-cell growth and division in E. coli. The results are in quantitative agreement with the predictions of the incremental model, which leads to the addition of a constant volume (up to fluctuations), independent of size at birth, between birth and division; we show that in both organisms size at birth and size at division exhibit a linear relationship with slope one. This result, together with extended additional analysis supporting the incremental model, argues against the existing "critical size" paradigm for cell size control in bacteria and yeast.

  19. Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria

    SciTech Connect (OSTI)

    Thomas, Dennis G.; Jaramillo Riveri, Sebastian I.; Baxter, Douglas J.; Cannon, William R.

    2014-12-15

    We have applied a new stochastic simulation approach to predict the metabolite levels, energy flow, and material flux in the different oxidative TCA cycles found in E. coli and Synechococcus sp. PCC 7002, and in the reductive TCA cycle typical of chemolithoautotrophs and phototrophic green sulfur bacteria such as Chlorobaculum tepidum. The simulation approach is based on equations of state and employs an assumption similar to that used in transition state theory. The ability to evaluate the thermodynamics of metabolic pathways allows one to understand the relationship between coupling of energy and material gradients in the environment and the selforganization of stable biological systems, and it is shown that each cycle operates in the direction expected due to its environmental niche. The simulations predict changes in metabolite levels and flux in response to changes in cofactor concentrations that would be hard to predict without an elaborate model based on the law of mass action. In fact, we show that a thermodynamically unfavorable reaction can still have flux in the forward direction when it is part of a reaction network. The ability to predict metabolite levels, energy flow and material flux should be significant for understanding the dynamics of natural systems and for understanding principles for engineering organisms for production of specialty chemicals, such as biofuels.

  20. Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site

    SciTech Connect (OSTI)

    Kerkhof, L.; Williams, K.H.; Long, P.E.; McGuinness, L.

    2011-02-21

    Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC) site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via {sup 13}C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 {micro}m), groundwater (0.2-8 {micro}m)] over a 24-day time frame. TRFLP results generally indicated a stronger signal in {sup 13}C-DNA in the 'fines' fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized {sup 13}C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the {sup 13}C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater, while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.

  1. 19/11/2007 10:18Bacteria display human traits like pursuing their own short term inte...s researchers found.But bugs also co-operate for the good of their... Page 1 of 2http://www.thisisnottingham.co.uk/displayNode.jsp?nodeId=133965...entPK=18980737&modul

    E-Print Network [OSTI]

    West, Stuart

    19/11/2007 10:18Bacteria display human traits like pursuing their own short term inte emails Sign up for newsflashes Order a copy of the newspaper back to list BACTERIA LINK TO HUMAN FRAILTIES Be the first reader to comment on this story 09:00 - 16 November 2007 Bacteria display human

  2. In situ capping for size control of monochalcogenides (ZnS, CdS, and SnS) nanocrystals produced by anaerobic metal-reducing bacteria

    SciTech Connect (OSTI)

    Jang, Gyoung Gug; Jacobs, Christopher B; Ivanov, Ilia N; Joshi, Pooran C; Meyer III, Harry M; Kidder, Michelle; Armstrong, Beth L; Datskos, Panos G; Graham, David E; Moon, Ji Won

    2015-01-01

    Metal monochalcogenide quantum dot nanocrystals of ZnS, CdS and SnS were prepared by anaerobic, metal-reducing bacteria using in situ capping by oleic acid or oleylamine. The capping agent preferentially adsorbs on the surface of the nanocrystal, suppressing the growth process in the early stages, thus leading to production of nanocrystals with a diameter of less than 5 nm.

  3. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    SciTech Connect (OSTI)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-01

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­?type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  4. Bacteria mediated heat sinks

    E-Print Network [OSTI]

    Hong, Vu Anh

    2010-01-01

    Many applications, such as laser diode technology, utilize components (eg. resistors) which have performance characteristics heavily dependent on temperature, and therefore, maintaining constant temperature is essential ...

  5. Carotenoid biosynthesis in bacteria: In vitro studies of a crt/bch transcription factor from Rhodobacter capsulatus and carotenoid enzymes from Erwinia herbicola

    SciTech Connect (OSTI)

    O`Brien, D.A.

    1992-11-01

    A putative transcription factor in Rhodobactor capsulatus which binds upstream of the crt and bch pigment biosynthesis operons and appears to play a role in the adaptation of the organism from the aerobic to the anaerobic-photosynthetic growth mode was characterized. Chapter 2 describes the identification of this factor through an in vitro mobility shift assay, as well as the determination of its binding properties and sequence specificity. Chapter 3 focuses on the isolation of this factor. Biochemistry of later carotenoid biosynthesis enzymes derived from the non-photosynthetic bacterium, Erwinia herbicola. Chapter 4 describes the separate overexpression and in vitro analysis of two enzymes involved in the main sequence of the carotenoid biosynthesis pathway, lycopene cyclase and 5-carotene hydroxylase. Chapter 5 examines the overexpression and enzymology of functionally active zeaxanthin glucosyltransferase, an enzyme which carries out a more unusual transformation, converting a carotenoid into its more hydrophilic mono- and diglucoside derivatives. In addition, amino acid homology with other glucosyltransferases suggests a putative binding site for the UDP-activated glucose substrate.

  6. This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research

    E-Print Network [OSTI]

    Ruan, Shigui

    microorganisms. A qualitative analysis about the boundary equilibrium, a state that both microorganisms vanish pathogen and commensal bacteria [4,3]. Alternative methods of combating infection has been considered [5 and toxin sensitivity. A chemostat is a laboratory bio-reactor used to culture microorganisms [11

  7. ECOS Inquiries Series -University of Montana Isolation of Microbes from the

    E-Print Network [OSTI]

    Brewer, Carol

    . 3. Introduce the potential benefits of microorganisms (i.e. not all bacteria are pathogenic). d OF MICROBES FROM THE ENVIRONMENT 3. GOALS AND OBJECTIVES: a. Inquiry Questions: 1. Where do microorganisms grow? 2. Are there areas where microorganisms will not grow? 3. How does the surface of an area

  8. Redox-Linked Changes to the Hydrogen-Bonding Network of Ribonucleotide Reductase ?2

    E-Print Network [OSTI]

    Offenbacher, Adam R.

    Ribonucleotide reductase (RNR) catalyzes conversion of nucleoside diphosphates (NDPs) to 2?-deoxynucleotides, a critical step in DNA replication and repair in all organisms. Class-Ia RNRs, found in aerobic bacteria and all ...

  9. 160 VOLUME 31 NUMBER 2 FEBRUARY 2013 NATURE BIOTECHNOLOGY L E T T E R S

    E-Print Network [OSTI]

    Collins, James J.

    -increasing incidence of antibiotic-resistant infections combined with a weak pipeline of new antibiotics has created this danger, bacteria growing aerobically generate ROS as a metabolic by-product, a risk balanced

  10. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect (OSTI)

    Sobecky, Patricia A.

    2015-04-06

    In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

  11. UPI.com: Bacteria might prove to be energy source http://license.icopyright.net/user/viewFreeUse.act?fuid=Mzk4NDQ= 1 of 1 6/5/2006 12:31 PM

    E-Print Network [OSTI]

    Lovley, Derek

    fuel cells show promise for conversion of organic wastes and renewable biomass to electricity by allowing bacteria in microbial fuel cells to grow on biofilms in the electrodes of a fuel cell. This week, but further optimization is required for most applications," said Derek Lovley of the University

  12. Test of electron beam technology on Savannah River Laboratory low-activity aqueous waste for destruction of benzene, benzene derivatives, and bacteria

    SciTech Connect (OSTI)

    Dougal, R.A.

    1993-08-01

    High energy radiation was studied as a means for destroying hazardous organic chemical wastes. Tests were conducted at bench scale with a {sup 60}Co source, and at full scale (387 l/min) with a 1.5 MV electron beam source. Bench scale tests for both benzene and phenol included 32 permutations of water quality factors. For some water qualities, as much as 99.99% of benzene or 90% of phenol were removed by 775 krads of {sup 60}Co irradiation. Full scale testing for destruction of benzene in a simulated waste-water mix showed loss of 97% of benzene following an 800 krad dose and 88% following a 500 krad dose. At these loss rates, approximately 5 Mrad of electron beam irradiation is required to reduce concentrations from 100 g/l to drinking water quality (5 {mu}g/l). Since many waste streams are also inhabited by bacterial populations which may affect filtering operations, the effect of irradiation on those populations was also studied. {sup 60}Co and electron beam irradiation were both lethal to the bacteria studied at irradiation levels far lower than were necessary to remove organic contaminants.

  13. Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

    SciTech Connect (OSTI)

    Mahony, Jennifer; Ainsworth, Stuart; Stockdale, Stephen; Sinderen, Douwe van

    2012-12-20

    Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

  14. 23/02/2009 16:02Slime cities & bacteria signals -University of Oxford Page 1 of 2http://www.ox.ac.uk/media/science_blog/090223.html

    E-Print Network [OSTI]

    West, Stuart

    23/02/2009 16:02Slime cities & bacteria signals - University of Oxford Page 1 of 2http://www.ox.ac.uk/media/science_blog in humans: OxSciBlog: What are the social interactions that go on between bacterial cells? Stuart West - University of Oxford Page 2 of 2http://www.ox.ac.uk/media/science_blog/090223.html signalling molecules

  15. Bioconversion of natural gas to liquid fuel: Opportunities and challenges

    SciTech Connect (OSTI)

    Fei, Q; Guarnieri, MT; Tao, L; Laurens, LML; Dowe, N; Pienkos, PT

    2014-05-01

    Natural gas is a mixture of low molecular weight hydrocarbon gases that can be generated from either fossil or anthropogenic resources. Although natural gas is used as a transportation fuel, constraints in storage, relatively low energy content (MJ/L), and delivery have limited widespread adoption. Advanced utilization of natural gas has been explored for biofuel production by microorganisms. In recent years, the aerobic bioconversion of natural gas (or primarily the methane content of natural gas) into liquid fuels (Bio-GTL) by biocatalysts (methanotrophs) has gained increasing attention as a promising alternative for drop-in biofuel production. Methanotrophic bacteria are capable of converting methane into microbial lipids, which can in turn be converted into renewable diesel via a hydrotreating process. In this paper, biodiversity, catalytic properties and key enzymes and pathways of these microbes are summarized. Bioprocess technologies are discussed based upon existing literature, including cultivation conditions, fermentation modes, bioreactor design, and lipid extraction and upgrading. This review also outlines the potential of Bio-GTL using methane as an alternative carbon source as well as the major challenges and future research needs of microbial lipid accumulation derived from methane, key performance index, and techno-economic analysis. An analysis of raw material costs suggests that methane-derived diesel fuel has the potential to be competitive with petroleum-derived diesel. (C) 2014 The Authors. Published by Elsevier Inc.

  16. Determination of the specific growth of molds on semi-solid cultures

    SciTech Connect (OSTI)

    Carrizalez, V.; Rodriguez, H.; Sardina, I.

    1981-02-01

    The determination of growth constants of Aspergillus niger were obtained for semisolid cultures on cassava flour, Manihot esculenta, as a sole carbon source. As a consequence, a technique was developed that consisted of the use of a packed-bed microfermentor with a working volume of 16 cubic centimetres. The bed consisted of gelatinized and granulated cassava flour containing material nutrients and mold spores. The carbon dioxide produced during the respiration was drawn off with a current of air and then absorbed in a solution of sodium hydroxide. The absorption of CO/sub 2/, P, was correlated with the specific growth rate mu by means of the equation P equals Kemut, where t is time and K is a constant. Ammonium nitrogen was used as a limiting substrate and its concentration was varied from 0.039 to 2.5% in dry base. The maximum growth rate, mu maximum, and the saturation constant, Ks, were 0.31/hour and 0.065 mmol (N/sub 4/)/sub 2/SO/sub 4//g total dry solids. The proposed method is highly recommended for the evaluation of the semisolid fermentation of molds and for strictly aerobic bacteria and yeasts. It can be used especially in the evaluation of the growth of microorganisms on peanut shells, coffee residues, sugar cane bagasse, and other agricultural wastes.

  17. Assessment of microbial processes on radionuclide mobility in shallow land burial. [West Valley, NY; Beatty, Nevada; Maxey Flats, Kentucky

    SciTech Connect (OSTI)

    Colombo, P.; Tate, R.L. III; Weiss, A.J.

    1982-07-01

    The impact of microbial metabolism of the organic substituents of low level radioactive wastes on radionuclide mobility in disposal sites, the nature of the microbial transformations involved in this metabolism and the effect of the prevailing environmental parameters on the quantities and types of metabolic intermediates accumulated were examined. Since both aerobic and anaerobic periods can occur during trench ecosystem development, oxidation capacities of the microbial community in the presence and absence of oxygen were analyzed. Results of gas studies performed at three commercial low level radioactive waste disposal sites were reviewed. Several deficiencies in available data were determined. Further research needs are suggested. This assessment has demonstrated that the biochemical capabilities expressed within the low level radioactive waste disposal site are common to a wide variety of soil bacteria. Hence, assuming trenches would not be placed in sites with such extreme abiotic conditions that all microbial activity is precluded, the microbial populations needed for colonization and decomposition of the organic waste substances are readily provided from the waste itself and from the soil of existing and any proposed disposal sites. Indeed, considering the ubiquity of occurrence of the microorganisms responsible for waste decomposition and the chemical nature of the organic waste material, long-term prevention of biodecomposition is difficult, if not impossible.

  18. This article was published in the above mentioned Springer issue. The material, including all portions thereof, is protected by copyright;

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    gasoline is likely to interfere with naturally occur- ring microorganisms from fully expressing their aerobic catabolic potential towards hydrocarbons bioremediation. Keywords Bioremediation Á Ethanol Á pollutants can be inhibited or slowed by the presence of easily degradable substrates (Duetz et al. 1994a, b

  19. Study of thermal conductivity in organic solid wastes before composting J. HUET, C. Druilhe, G. Debenest

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Study of thermal conductivity in organic solid wastes before composting J. HUET, C. Druilhe, G. Debenest ORBIT2012 1 STUDY OF THERMAL CONDUCTIVITY IN ORGANIC SOLID WASTES BEFORE COMPOSTING J. Huet and disposal. Composting can be defined as the process whereby aerobic micro-organisms convert organic

  20. Kinetic and Inhibition Studies for the Aerobic Cometabolism of

    E-Print Network [OSTI]

    Semprini, Lewis

    ,1-Dichloroethylene, and 1,1-Dichloroethane by a Butane-Grown Mixed Culture Young Kim,1 Daniel J. Arp,2 Lewis Semprini), and 1,1-dichloroethane (1,1-DCA) by a butane- grown mixed culture. These chlorinated aliphatic hydro. The highest kmax was obtained for butane (2.6 µmol/mg TSS/ h) followed by 1,1-DCE (1.3 µmol/mg TSS/h), 1,1-DCA