Life Sciences Commons^™

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 …

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 …

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

Otto Vogl

No abstract provided.

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.

Recent Insights Into Muscle Fatigue At The Cross-Bridge Level, Edward Debold

Edward P. Debold

The depression in force and/or velocity associated with muscular fatigue can be the result of a failure at any level, from the initial events in the motor cortex of the brain to the formation of an actomyosin cross-bridge in the muscle cell. Since all the force and motion generated by muscle ultimately derives from the cyclical interaction of actin and myosin, researchers have focused heavily on the impact of the accumulation of intracellular metabolites [e.g., Pi, H+ and adenosine diphoshphate (ADP)] on the function these contractile proteins. At saturating Ca++ levels, elevated Pi appears to be the primary cause for …

Solid State Chemical Reactions And Polymerizations: The Initial Synthesis Of Dna?, Otto Vogl, Frank T. Traceski

Otto Vogl

A Proposal for Covering individual Macromolecules with Macromolecules including a Realistic Chiral Synthesis of Nucleic Acids.

Does The Precision Of A Biological Clock Depend Upon Its Period? Effects Of The Duper And Tau Mutations In Syrian Hamsters, Eric L. Bittman

Eric L. Bittman

Mutations which alter the feedback loops that generate circadian rhythms may provide insight into their insensitivity to perturbation robustness) and their consistency of period (precision). I examined relationships between endogenous period, activity and rest (τDD, α and ρ) in Syrian hamsters using two different mutations, duper and tau, both of which speed up the circadian clock. I generated 8 strains of hamsters that are homozygous or heterozygous for the tau, duper, and wild type alleles in all combinations. The endogenous period of activity onsets among these strains ranged from 17.94+0.04 to 24.13±0.04 h. Contrary to predictions, the variability of period …

Paralemmin-1 Is Over-Expressed In Estrogen-Receptor Positive Breast Cancers, Casey M. Turk, Katerina D. Fagan-Solis, Kristin E. Williams, Joseph M. Gozgit, Sallie Smith-Schneider, Sharon A. Marconi, Christopher N. Otis, Giovanna M. Crisi, Douglas L. Anderton, Manfred W. Kilimann, Kathleen Arcaro

Kathleen Arcaro

Background Paralemmin-1 is a phosphoprotein lipid-anchored to the cytoplasmic face of membranes where it functions in membrane dynamics, maintenance of cell shape, and process formation. Expression of paralemmin-1 and its major splice variant (Δ exon 8) as well as the extent of posttranslational modifications are tissue- and development-specific. Paralemmin-1 expression in normal breast and breast cancer tissue has not been described previously. Results Paralemmin-1 mRNA and protein expression was evaluated in ten breast cell lines, 26 primary tumors, and 10 reduction mammoplasty (RM) tissues using real time RT-PCR. Paralemmin-1 splice variants were assessed in tumor and RM tissues using a …

Macondo Crude Oil From The Deepwater Horizon Oil Spill Disrupts Specific Developmental Processes During Zebrafish Embryogenesis, T Yvanka De Soysa, Allison Ulrich, Timo Friedrich, Danielle Pite, Shannon L. Compton, Deborah Ok, Rebecca L. Bernardos, Gerald B. Downes, Shizuka Hsieh, Rachael Stein, M Caterina Lagdameo, Katherine Halvorsen, Lydia-Rose Kesich, Michael Jf Barresi

Gerald B. Downes

Background: The Deepwater Horizon disaster was the largest marine oil spill in history, and total vertical exposure of oil to the water column suggests it could impact an enormous diversity of ecosystems. The most vulnerable organisms are those encountering these pollutants during their early life stages. Water-soluble components of crude oil and specific polycyclic aromatic hydrocarbons have been shown to cause defects in cardiovascular and craniofacial development in a variety of teleost species, but the developmental origins of these defects have yet to be determined. We have adopted zebrafish, Danio rerio, as a model to test whether water accumulated fractions …

Role Of The Nife Hydrogenase Hya In Oxidative Stress Defense In Geobacter Sulfurreducens, Pier-Luc Tremblay, Derek Lovley

Derek Lovley

Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen …

Trace Elements Affect Methanogenic Activity And Diversity In Enrichments From Subsurface Coal Bed Produced Water, B. Unal, V. R. Perry, M. Sheth, V. Gomez-Alvarez, K. J. Chin, Klaus R. Nusslein

Klaus R. Nusslein

Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from …

Identification And Expression Analysis Of Methyl Jasmonate Responsive Ests In Paclitaxel Producing Taxus Cuspidata Suspension Culture Cells, Sangram K. Lenka, Nadia Boutaoui, Bibin Paulose, Kham Vongpaseuth, Jennifer Normanly, Susan C. Roberts, Elsbeth L. Walker

Jennifer Normanly

Background Taxol® (paclitaxel) promotes microtubule assembly and stabilization and therefore is a potent chemotherapeutic agent against wide range of cancers. Methyl jasmonate (MJ) elicited Taxus cell cultures provide a sustainable option to meet the growing market demand for paclitaxel. Despite its increasing pharmaceutical importance, the molecular genetics of paclitaxel biosynthesis is not fully elucidated. This study focuses on identification of MJ responsive transcripts in cultured Taxus cells using PCR-based suppression subtractive hybridization (SSH) to identify genes involved in global pathway control. Results Six separate SSH cDNA libraries of paclitaxel-accumulating Taxus cuspidata P991 cell lines were constructed at three different post-elicitation …

Chlamydia Pneumoniae-Specific Ige Is Prevalent In Asthma And Is Associated With Disease Severity, David L. Hahn, Allison Schure, Katir K. Patel, Tawanna S. Childs, Eduard Drizik, Wilmore C. Webley

Wilmore C Webley

Background: Several Chlamydia pneumoniae (Cp) biomarkers have been associated with asthma but Cp-specific IgE (Cp IgE) has not been investigated extensively. Our objective was to investigate Cp IgE in community adult asthma patients.

Methods: (1) Prevalence of Cp IgE (measured by immunoblotting) and Cp DNA (by polymerase chain reaction) in peripheral blood, and biomarker associations with asthma severity. (2) Case-control studies of Cp IgE association with asthma using healthy blood donor (study 1) and non-asthmatic clinic patient (study 2) controls.

Results: Of 66 asthma subjects (mean age 40.9 years, range 5–75, 59% male, 45% ever-smokers) 33 (50%) were Cp IgE …

Identification And Expression Analysis Of Methyl Jasmonate Responsive Ests In Paclitaxel Producing Taxus Cuspidata Suspension Culture Cells, Sangram K. Lenka, Nadia Boutaoui, Bibin Paulose, Kham Vongpaseuth, Jennifer Normanly, Susan C. Roberts, Elsbeth L. Walker

Elsbeth Walker

Background Taxol(R)(paclitaxel) promotes microtubule assembly and stabilization and therefore is a potent chemotherapeutic agent against wide range of cancers. Methyl jasmonate (MJ) elicited Taxus cell cultures provide a sustainable option to meet the growing market demand for paclitaxel. Despite its increasing pharmaceutical importance, the molecular genetics of paclitaxel biosynthesis is not fully elucidated. This study focuses on identification of MJ responsive transcripts in cultured Taxus cells using PCR-based suppression subtractive hybridization (SSH) to identify genes involved in global pathway control. Results Six separate SSH cDNA libraries of paclitaxel-accumulating Taxus cuspidata P991 cell lines were constructed at three different post-elicitation time …

Transcriptional Regulation Of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up With Arabidopsis Thaliana, Pubudu P. Handakumbura, Samuel P. Hazen

Samuel P Hazen

Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water-conducting vessels and provide structural support. Several transcription factor families regulate genes encoding wall synthesis enzymes. Certain NAC and MYB proteins directly bind to the SNBE and AC elements upstream of structural genes and other transcription factors. The most detailed model of this regulatory network is established predominantly for a eudicot, Arabidopsis thaliana. In grasses, both the patterning and the composition of secondary cell walls are …

The Prevalence And Identity Of Chlamydia-Specific Ige In Children With Asthma And Other Chronic Respiratory Symptoms, Katir K. Patel, Erica A. Anderson, Paul S. Salva, Wilmore C. Webley

Wilmore C Webley

Background Recent studies have confirmed the presence of viable Chlamydia in the bronchoalveolar lavage (BAL) fluid of pediatric patients with airway hyperresponsiveness. While specific IgG and IgM responses to C. pneumoniae are well described, the response and potential contribution of Ag-specific IgE are not known. The current study sought to determine if infection with Chlamydia triggers the production of pathogen-specific IgE in children with chronic respiratory diseases which might contribute to inflammation and pathology. Methods We obtained BAL fluid and serum from pediatric respiratory disease patients who were generally unresponsive to corticosteroid treatment as well as sera from age-matched control …