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Molecular Analysis Of The In Situ Growth Rate Of Subsurface Geobacter Species, Dawn E. Holmes, Ludovic Giloteaux, Melissa Barlett, Milind A. Chavan, Jessica A. Smith, Kenneth H. Williams, Michael Wilkins, Philip Long, Derek Lovley

Derek Lovley

Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole genome microarray analyses of the subsurface isolate, Geobacter uraniireducens, grown under a variety of conditions identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, were further evaluated with quantitative reverse transcription PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r2= 0.90) with specific growth …

The Rnf Complex Of Clostridium Ljungdahlii Is A Proton-Translocating Ferredoxin: Nad+ Oxidoreductase Essential For Autotrophic Growth, Pier-Luc Tremblay, Tian Zhang, Shabir A. Dar, Ching Leang, Derek Lovley

Derek Lovley

It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase which contributes to ATP synthesis by an H+-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H2 as the electron source and CO2 as the electron acceptor. Heterotrophic growth was hindered in …

The Genome Of Pelobacter Carbinolicus Reveals Surprising Metabolic Capabilities And Physiological Features, Muktak Aklujkar, Shelley A. Haveman, Raymond Didonato, Olga Chertkov, Cliff S. Han, Miriam L. Land, Peter Brown, Derek Lovley

Derek Lovley

BackgroundThe bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species.ResultsPathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and …

A Genetic System For Clostridium Ljungdahlii: A Chassis For Autotrophic Production Of Biocommodities And A Model Homoacetogen, Ching Leang, Toshiyuki Ueki, Kelly Nevin, Derek R. Lovley

Kelly Nevin

Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vector …

Improved Cathode Materials For Microbial Electrosynthesis, Tian Zhang, Huarong Nie, Timothy S. Bain, Haiyun Lu, Mengmeng Cui, Oona L. Snoeyenbos-West, Ashley E. Franks, Kelly P. Nevin, Thomas P. Russell, Derek Lovley

Derek Lovley

Microbial electrosynthesis is a promising strategy for the microbial conversion of carbon dioxide to transportation fuels and other organic commodities, but optimization of this process is required for commercialization. Cathodes which enhance electrode–microbe electron transfer might improve rates of product formation. To evaluate this possibility, biofilms of Sporomusa ovata, which are effective in acetate electrosynthesis, were grown on a range of cathode materials and acetate production was monitored over time. Modifications of carbon cloth that resulted in a positive-charge enhanced microbial electrosynthesis. Functionalization with chitosan or cyanuric chloride increased acetate production rates 6–7 fold and modification with 3-aminopropyltriethoxysilane gave rates …

Improved Cathode Materials For Microbial Electrosynthesis, Tian Zhang, Huarong Nie, Timothy S. Bain, Haiyun Lu, Mengmeng Cui, Oona L. Snoeyenbos-West, Ashley E. Franks, Kelly Nevin, Thomas P. Russell, Derek R. Lovley

Kelly Nevin

Microbial electrosynthesis is a promising strategy for the microbial conversion of carbon dioxide to transportation fuels and other organic commodities, but optimization of this process is required for commercialization. Cathodes which enhance electrode–microbe electron transfer might improve rates of product formation. To evaluate this possibility, biofilms of Sporomusa ovata, which are effective in acetate electrosynthesis, were grown on a range of cathode materials and acetate production was monitored over time. Modifications of carbon cloth that resulted in a positive-charge enhanced microbial electrosynthesis. Functionalization with chitosan or cyanuric chloride increased acetate production rates 6–7 fold and modification with 3-aminopropyltriethoxysilane gave rates …

Gene Number Determination And Genetic Polymorphism Of The Gamma Delta T Cell Co-Receptor Wc1 Genes, Chuang Chen, Carolyn Ta Herzig, Leeson J. Alexander, John W. Keele, Tara G. Mcdaneld, Janice C. Telfer, Cynthia Baldwin

Cynthia Baldwin

Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial …

Prelude To A Master Plan: Ware, Massachusetts, Belen Alfaro, Bruno Carneiro, Margaret Engesser, Kathryn E. Fox, Evadne R. Friedman, Timothy Inacio, Anita Lockesmith, Christina Mills, Stephanie Molden, Meagen Mulherin, Russell Pandres, Vinicius Pereira, Brian Reid, Pedro Soto, Jennifer Stromsten

Landscape Architecture & Regional Planning Studio and Student Research and Creative Activity

Prelude to a Master Plan offers ideas, recommendations, and a toolkit to help the town chart its own path towards that future. While the teams and individual students worked to ‘drill down’ into specific topic areas, the Studio defined three basic areas in order to think about how the various assets, challenges and ideas undermine or reinforce one another. The report is loosely organized in those terms: addressing the outlying rural areas and issues specific to these places, considering one of the key growth areas that has extended from town and the conflicts that arise from the many uses occurring …

Crystallization And Polymerization, Otto Vogl, Frank T. Traceski, Eric G. Vogl

Otto Vogl

No abstract provided.

Anaerobic Benzene Oxidation By Geobacter Species, Tian Zhang, Timothy S. Bain, Kelly Nevin, Melissa A. Barlett, Derek R. Lovley

Kelly Nevin

The abundance of Geobacter species in contaminated aquifers in which benzene is anaerobically degraded has led to the suggestion that some Geobacter species might be capable of anaerobic benzene degradation, but this has never been documented. A strain of Geobacter, designated strain Ben, was isolated from sediments from the Fe(III)-reducing zone of a petroleum-contaminated aquifer in which there was significant capacity for anaerobic benzene oxidation. Strain Ben grew in a medium with benzene as the sole electron donor and Fe(III) oxide as the sole electron acceptor. Furthermore, additional evaluation of Geobacter metallireducens demonstrated that it could also grow in benzene-Fe(III) …

Comparative Genomic Analysis Of Geobacter Sulfurreducens Kn400, A Strain With Enhanced Capacity For Extracellular Electron Transfer And Electricity Production, Jessica E. Butler, Nelson D. Young, Muktak Aklujkar, Derek Lovley

Derek Lovley

Background A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved. Results Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in …

Postures For Precision: An Ecological Approach To Marksmanship And The Issue Of Warfighter Load., Christopher Jay Palmer

Open Access Dissertations

The goal of this dissertation was to understand the issue of load in a more operationally realistic way, while examining underlying segmental relations and postural regulation related to functional capability. The ecological approach provides a foundation for this work, as its approach seeks understanding across nested relations and at the level of the Organism-Environment system. First, a landing task was used to examine transitions from movement to upright stance, evaluating the effects of load on changes relevant to prospective control of action. Greater negative head angles, reductions in the field of regard, and reduced variability in orienting coordination (trunk-head relations) …

Identification And Functional Characterization Of The Zebrafish Gene Quetschkommode (Que), Timo Friedrich

Open Access Dissertations

Locomotion in vertebrates depends on proper formation and maintenance of neuronal networks in the hind-brain and spinal cord. Malformation or loss of factors required for proper maintenance of these networks can lead to severe neurodegenerative diseases limiting or preventing locomotion. A powerful tool to investigate the genetic and cellular requirements for development and/or maintenance of these networks is a collection of zebrafish mutants with defects in motility. The zebrafish mutant quetschkommode (que) harbors a previously unknown gene defect leading to abnormal locomotor behavior. Here I show that the que mutants display a seizure-like behavior starting around four days post fertilization …

The Evolutionary Genetics Of Seed Shattering And Flowering Time, Two Weed Adaptive Traits In Us Weedy Rice, Carrie S. Thurber

Open Access Dissertations

Weedy rice is a persistent weed of cultivated rice (Oryza sativa) fields worldwide, which competes with the crop and drastically reduces yields. Within the US, two main populations of genetically differentiated weedy rice exist, the straw-hulled (SH) group and the black-hulled awned (BHA) group. Current research suggests that both groups are derived from Asian cultivated rice. However, the weeds differ from the cultivated groups in various morphological traits. My research focus is on the genetic basis of two such traits: seed shattering ability and differences in flowering time. The persistence of weedy rice has been partly attributed to its ability …

Mechanics And Energetics Of Footfall Patterns In Running, Allison H. Gruber

Open Access Dissertations

The forefoot (FF) running pattern has been recently advocated to improve running economy and prevent overuse injuries compared to the rearfoot (RF) pattern. However, these claims have not been supported by empirical evidence. The purpose of this dissertation was to investigate the potential advantages of RF and FF patterns to improve running economy and reduce injury risk in 20 natural RF and 20 natural FF runners.

The first study found that the RF group was more economical when performing the RF pattern at a slow, medium, and fast speed vs. FF running. Only running at the fast speed resulted in …

Molecular Mechanisms Regulating Complement Receptor 3-Mediated Phagocytosis Of Borrelia Burgdorferi, Kelly Lynn Hawley

Open Access Dissertations

The macrophage receptors that mediate phagocytosis of Borrelia burgdorferi, the Lyme disease spirochete, are unknown despite this cell type's importance in promoting pathogen clearance and inflammation-mediated tissue damage. We now demonstrate that the β2 integrin, Complement Receptor 3 (CR3), mediates the phagocytosis of opsonized and non-opsonized spirochetes by murine macrophages and human monocytes. Although, expression of the surface proteins, CspA and OspE, protects B. burgdorferi from complement-mediated phagocytosis, the versatility of CR3 counteracts the ability of B. burgdorferi to interfere with complement activation and complement-derived opsonins, thus minimizing the bacteria's anti-complement strategy. Interaction of the spirochete with the integrin is …

Refinement, Validation And Application Of A Machine Learning Method For Estimating Physical Activity And Sedentary Behavior In Free-Living People, Kate Lyden

Open Access Dissertations

There is limited knowledge of the dose-response relationship between physical activity (PA), sedentary behavior (SB) and health. Poor measures of free-living PA and SB exposure are major contributing factors to these knowledge gaps. The overall objective of this dissertation was to address these issues by refining, validating and applying a machine-learning methodology for measuring PA and SB for use in free-living people. By combining neural networks and decision tree analyses we developed a method better suited for use in free-living people. Our new method is called the sojourn method and it estimates PA and SB from a single hip mounted …

Strategies To Improve The Performance Of Antioxidants In Oil-In-Water Emulsions, Atikorn Panya

Open Access Dissertations

Due to the limited number of approved antioxidants for food applications, several alternative strategies to improve antioxidant performance have been developed by focusing on synergistic antioxidant interactions. Susceptibility to lipid oxidation in food systems is the result of the summation of antioxidative and prooxidative mechanisms. Understanding the sometimes paradoxical behavior of antioxidants and prooxidants is a vital key to design synergistic antioxidant systems suitable for particular foods. This research focused on 3 main strategies to improve the performance of antioxidant activity in oil-in-water emulsions.

The first part of this research has been focused on inhibition of lipid oxidation by a …

Fabrication, Characterization And Utilization Of Filled Hydrogel Particles As Food Grade Delivery Systems, Alison M. Matalanis

Open Access Dissertations

Filled hydrogel particles consisting of emulsified oil droplets encapsulated within a hydrogel matrix were fabricated based on the phase separation of proteins and polysaccharides through aggregative and segregative mechanisms. A 3% (wt/wt) pectin and 3% (wt/wt) caseinate mixture at pH 7 separated into an upper pectin-rich phase and a lower casein-rich phase. Casein-coated lipid droplets added to this mixture partitioned into the lower casein-rich phase. When shear was applied, an oil-in-water-in-water (O/W1/W2) emulsion consisting of oil droplets (O) contained within a casein-rich dispersed phase (W1) suspended in a pectin-rich continuous phase (W2) was formed. Acidification from pH 7 to 5 …

Biological Control Of The Ambermarked Birch Leafminer (Profenusa Thomsoni) In Alaska, Anna L. Soper

Open Access Dissertations

The ambermarked birch leafminer (AMBLM) (Profenusa thomsoni) is an invasive leafminer native to the Palearctic from the United Kingdom to Turkey to Japan. It was introduced to the eastern United States in 1921 and has since spread to the mid-western U.S. states and Canadian provinces. This leafminer was introduced to Alaska in 1996, where it has since spread over 140,000 acres, from Haines to Fairbanks. The most severe damage is found throughout the Anchorage bowl, which extends south to Girdwood and North to Wasilla. The damage caused by P. thomsoni can be severe, defoliating entire trees. In 2006, it was …

Adsorption Column Studies To Predict The Flow Of Nutrients Through Heterogenous Porous Media Under Equilibrium And Isothermal Conditions, Vijai B. Pandey

Open Access Dissertations

Because of the endangerment of life of the human beings due to the environmental pollution, a serious study of the pollution of the environment is most vital. Because of increasing surface water pollution there is great hazard of ground water pollution. About half the United States of America derives drinking water from aquifers and much of the projected demand is expected to be met from subsurface sources. Therefore, a study was needed to determine the process of ground water contamination due to nutrients, especially Nitrogen, its degree and Length and Time of Travel and factors inhibiting its flow through soil. …

Pictures From My Life With Polymer Science: Album 12, Otto Vogl

Otto Vogl

No abstract provided.

Structural Studies Of Membrane-Assembled Popd And Popb, The Pseudomonas Aeruginosa Type 3 Secretion Translocators, Fabian B Romano Chernac

Doctoral Dissertations 1896 - February 2014

Transport of proteins across membranes is essential during many stages of pathogen infection and colonization of human cells. Many Gram-negative pathogens use a Type 3 Secretion (T3S) system to inject proteins into the target cell during infection. Substantial genetic and biochemical evidence suggest that proteins are translocated across the host plasma membrane through a proteinaceous pore or translocon formed by two bacterial secreted proteins: the T3S translocators. Despite its key role in pathogenesis, virtually nothing is known about the assembly mechanism, structure, and composition of this critical transmembrane complex.

To this end, a cell-free system for the structural and functional …

Interspecies Electron Transfer Via H2 And Formate Rather Than Direct Electrical Connections In Co-Cultures Of Pelobacter Carbinolicus And Geobacter Sulfurreducens, Amelia-Elena Rotaru, Pravin M. Shrestha, Fanghua Liu, Toshiyuki Ueki, Kelly Nevin, Zarath M. Summers, Derek R. Lovley

Kelly Nevin

Direct interspecies electron transfer (DIET) is an alternative to interspecies H2/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with Pelobacter carbinolicus, a close relative of Geobacter metallireducens, which is capable of DIET. P. carbinolicus grew in co-culture with Geobacter sulfurreducens with ethanol as electron donor and fumarate as electron acceptor, conditions under which G. sulfurreducens formed direct electrical connections with G. metallireducens. In contrast to the cell aggregation associated with DIET, P. carbinolicus and G. sulfurreducens did not aggregate. Attempts to initiate …

Design And Baseline Characteristics Of The Short Bouts Of Exercise For Preschoolers (Step) Study, Sofiya Alhassan, Ogechi Nwaokelemeh, Albert Mendoza, Sanyog Shitole, Melicia C. Whitt-Glover, Antronette K. Yancey

Sofiya Alhassan

Background: Most preschool centers provide two 30-min sessions of gross-motor/outdoor playtime per preschool day. Within this time frame, children accumulate most of their activity within the first 10 min. This paper describes the design and baseline participant characteristics of the Short bouTs of Exercise for Preschoolers (STEP) study. The STEP study is a cluster randomized controlled study designed to examine the effects of short bouts of structured physical activity (SBS-PA) implemented within the classroom setting as part of designated gross-motor playtime on during-school physical activity (PA) in preschoolers. Methods/Design: Ten preschool centers serving low-income families were randomized into SBS-PA versus …

Promoting Direct Interspecies Electron Transfer With Activated Carbon, Derek Lovley, Fanghua Liu, Amelia-Elena Rotaru, Pravin M. Shrestha, Nikhil S. Malvankar, Kelly P. Nevin

Derek Lovley

Granular activated carbon (GAC) is added to methanogenic digesters to enhance conversion of wastes to methane, but the mechanism(s) for GAC's stimulatory effect are poorly understood. GAC has high electrical conductivity and thus it was hypothesized that one mechanism for GAC stimulation of methanogenesis might be to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens. Metabolism was substantially accelerated when GAC was added to co-cultures of Geobacter metallireducens and Geobacter sulfurreducens grown under conditions previously shown to require DIET. Cells were attached to GAC, but did not aggregate as they do when making biological electrical connections between cells. …

Promoting Direct Interspecies Electron Transfer With Activated Carbon, Fanghua Liu, Amelia-Elena Rotaru, Pravin M. Shrestha, Nikhil S. Malvankar, Kelly Nevin, Derek R. Lovley

Kelly Nevin

Granular activated carbon (GAC) is added to methanogenic digesters to enhance conversion of wastes to methane, but the mechanism(s) for GAC's stimulatory effect are poorly understood. GAC has high electrical conductivity and thus it was hypothesized that one mechanism for GAC stimulation of methanogenesis might be to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens. Metabolism was substantially accelerated when GAC was added to co-cultures of Geobacter metallireducens and Geobacter sulfurreducens grown under conditions previously shown to require DIET. Cells were attached to GAC, but did not aggregate as they do when making biological electrical connections between cells. …

Transposable Elements In Phytopathogenic Verticillium Spp.: Insights Into Genome Evolution And Inter- And Intra-Specific Diversification, Stefan G. Amyotte, Xiaoping Tan, Kayla Pennerman, Maria Del Mar Jimenez-Gasco, Steven J. Klosterman, Li-Jun Ma, Katherine F. Dobinson, Paola Veronese

Li-Jun Ma

Background Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs) have contributed to the generation of four lineage-specific (LS) regions in VdLs.17. Results We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced …

Lack Of Cytochrome Involvement In Long-Range Electron Transport Through Conductive Biofilms And Nanowires Of Geobacter Sulfurreducens, Nikhil S. Malvankar, Mark T. Tuominen, Derek Lovley

Derek Lovley

Two competing models for long-range electron transport through the conductive biofilms and nanowires of Geobacter sulfurreducens exist. In one model electrons are transported via pili that possess delocalized electronic states to function as protein wires with metallic-like conductivity. In the other model electrons are transported by more traditional electron transfer via electron hopping/tunneling between the c-type cytochromes in G. sulfurreducens biofilms and pili. The cytochrome hypothesis was further examined. Quantifying c-type cytochromes in G. sulfurreducens biofilms and pili indicated that there are insufficient cytochromes to account for electron transport through the bulk of the biofilm or pili and demonstrated that …

Electrical Conductivity In A Mixed-Species Biofilm, Nikhil S. Malvankar, Joanne Lau, Kelly Nevin, Ashley E. Franks, Mark T. Tuominen, Derek R. Lovley

Kelly Nevin

Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community.