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Sample records for rhodopseudomonas palustris regulons

  1. Photometabolism of Heterocyclic Aromatic Compounds by Rhodopseudomonas palustris OU 11

    Science.gov (United States)

    Sasikala, C.; Ramana, C. V.; Rao, P. Raghuveer

    1994-01-01

    Rhodopseudomonas palustris OU 11 (ATCC 51186; DSM 7375) isolated from a pond of chemical industry effluent could anaerobically photometabolize heterocyclic aromatic compounds belonging to the pyridine and pyrazine groups only after a period of adaptation on pyrazinoic acid of 5 to 6 weeks. Growth on heterocyclic compounds was light dependent. The effects of various concentrations of heterocyclic compounds on growth suggest that higher concentrations of these compounds inhibit growth and are toxic. PMID:16349307

  2. Acclimation strategy of Rhodopseudomonas palustris to high light irradiance.

    Science.gov (United States)

    Muzziotti, Dayana; Adessi, Alessandra; Faraloni, Cecilia; Torzillo, Giuseppe; De Philippis, Roberto

    2017-04-01

    The ability of Rhodopseudomonas palustris cells to rapidly acclimate to high light irradiance is an essential issue when cells are grown under sunlight. The aim of this study was to investigate the photo-acclimation process in Rhodopseudomonas palustris 42OL under different culturing conditions: (i) anaerobic (AnG), (ii) aerobic (AG), and (iii) under H 2 -producing (HP) conditions both at low (LL) and high light (HL) irradiances. The results obtained clearly showed that the photosynthetic unit was significantly affected by the light irradiance at which Rp. palustris 42OL was grown. The synthesis of carotenoids was affected by both illumination and culturing conditions. At LL, lycopene was the main carotenoid synthetized under all conditions tested, while at HL under HP conditions, it resulted the predominant carotenoid. Oppositely, under AnG and AG at HL, rhodovibrin was the major carotenoid detected. The increase in light intensity produced a deeper variation in light-harvesting complexes (LHC) ratio. These findings are important for understanding the ecological distribution of PNSB in natural environments, mostly characterized by high light intensities, and for its growth outdoors. Copyright © 2017 Elsevier GmbH. All rights reserved.

  3. Final report: 'Rhodopseudomonas palustris' genome workshop to be held in Spring of 2001; FINAL

    International Nuclear Information System (INIS)

    Harwood, Caroline S.

    2002-01-01

    The 'Rhodopseudomonas palustris' genome workshop took place in Iowa City on April 6-8, 2001. The purpose of the meeting was to instruct members of the annotation working group in approaches to accomplishing the 'human' phase of the 'R. palustris' genome annotation. A partial draft of a paper describing the 'Rhodopseudomonas palustris' genome has been written and a full version of the paper should be ready for submission by the end of the summer 2002

  4. The anaerobic phototrophic metabolism of 3-chlorobenzoate by Rhodopseudomonas palustris

    Energy Technology Data Exchange (ETDEWEB)

    Kamal, V S

    1992-10-09

    The degradation of chlorinated aromatic compounds by anaerobic bacteria is now known to be an important mechanism of bioremediation. In an experimental study, a mixed phototrophic culture was found to metabolize 3-chlorobenzoate in the presence of benzoate following adaptation on a benzoate and 3-chlorobenzoate medium for 7 weeks. The dominant bacterial isolate was identified as Rhodopseudomonas palustris. Radioisotopic studies showed [sup 14]C-3-chlorobenzoate was converted by the isolate to [sup 14]CO[sub 2] and cell biomass in the absence of oxygen and in the presence of a cosubstrate red light. Cyclohexane carboxylate was able to replace the cosubstrate, benzoate. The isolate also metabolized 3-chlorobenzoate in the presence of pimelic acid, sodium acetate, and sodium succinate; however, the metabolic rate was reduced. Gas chromatography mass spectrometry and high pressure liquid chromatography indicated the intracellular presence of 3-chlorobenzoate and benzoyl-CoA. Cell-free extracts produced benzoate and benzoyl-CoA. A probable route of 3-chlorobenzoate metabolism via dehalogenation followed by steps similar to the benzoate reductive ring fission pathway is suggested. Comparison of kinetic coefficients showed a higher affinity of the isolate for benzoate. Isolates from representative samples of various freshwater and wastewater ecosystems indicated widespread ecological distribution of R. palustris and the common occurrence of the 3-chlorobenzoate metabolic phenotype. R. palustris was found to grow in mixed anaerobic cultures and retained its 3-chlorobenzoate degradation property. 91 refs., 25 figs., 14 tabs.

  5. Acquisition of the ability for Rhodopseudomonas palustris to degrade chlorinated benzoic acids as the sole carbon source

    NARCIS (Netherlands)

    Oda, Y; de Vries, YP; Forney, LJ; Gottschal, JC

    2001-01-01

    Three strains of Rhodopseudomonas palustris were isolated from phototrophic enrichment cultures containing 3-chlorobenzoate (3-CBA) and benzoate (BA). These new strains as well as several previously described strains of R. palustris were tested in this study and shown to degrade 3-CBA if grown in

  6. Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach.

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    Chia-Wei Hu

    Full Text Available BACKGROUND: Rhodopseudomonas palustris (R. palustris is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin-Benson-Bassham (CBB cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. METHODOLOGY/PRINCIPAL FINDINGS: By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth

  7. Effects of metal ions on biomass and 5-aminolevulinic acid production in Rhodopseudomonas palustris wastewater treatment.

    Science.gov (United States)

    Liu, Shuli; Zhang, Guangming; Li, Jianzheng; Li, Xiangkun; Zhang, Jie

    2016-01-01

    This work investigated the effects of eight metal ions on Rhodopseudomonas palustris growth and 5-aminolevulinic acid (ALA) yield in wastewater treatment. Results show that metal ions (Mg(2+) of 15 mmol/L, Fe(2+) of 400 μmol/L, Co(2+) of 4 μmol/L, Ni(2+) of 8 μmol/L and Zn(2+) of 4 μmol/L) could effectively improve the chemical oxygen demand (COD) removal, Rp. palustris biomass and ALA yield. The highest ALA yield of 13.1 mg/g-biomass was achieved with Fe(2+) of 400 μmol/L. ALA yields were differentially increased under different metal ions in the following order: Fe(2+) group > Mg(2+) group > Co(2+) group = Ni(2+) group > Zn(2+) group = Mo(2+) group > control. Cu(2+) and Mn(2+) inhibited Rp. palustris growth and ALA production. Mechanism analysis revealed that metal ions changed ALA yields by influencing the activities of ALA synthetase and ALA dehydratase.

  8. Uranium interaction with two multi-resistant environmental bacteria: Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris.

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    Llorens, Isabelle; Untereiner, Guillaume; Jaillard, Danielle; Gouget, Barbara; Chapon, Virginie; Carriere, Marie

    2012-01-01

    Depending on speciation, U environmental contamination may be spread through the environment or inversely restrained to a limited area. Induction of U precipitation via biogenic or non-biogenic processes would reduce the dissemination of U contamination. To this aim U oxidation/reduction processes triggered by bacteria are presently intensively studied. Using X-ray absorption analysis, we describe in the present article the ability of Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris, highly resistant to a variety of metals and metalloids or to organic pollutants, to withstand high concentrations of U and to immobilize it either through biosorption or through reduction to non-uraninite U(IV)-phosphate or U(IV)-carboxylate compounds. These bacterial strains are thus good candidates for U bioremediation strategies, particularly in the context of multi-pollutant or mixed-waste contaminations.

  9. Uranium Interaction with Two Multi-Resistant Environmental Bacteria: Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris

    Science.gov (United States)

    Llorens, Isabelle; Untereiner, Guillaume; Jaillard, Danielle; Gouget, Barbara; Chapon, Virginie; Carriere, Marie

    2012-01-01

    Depending on speciation, U environmental contamination may be spread through the environment or inversely restrained to a limited area. Induction of U precipitation via biogenic or non-biogenic processes would reduce the dissemination of U contamination. To this aim U oxidation/reduction processes triggered by bacteria are presently intensively studied. Using X-ray absorption analysis, we describe in the present article the ability of Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris, highly resistant to a variety of metals and metalloids or to organic pollutants, to withstand high concentrations of U and to immobilize it either through biosorption or through reduction to non-uraninite U(IV)-phosphate or U(IV)-carboxylate compounds. These bacterial strains are thus good candidates for U bioremediation strategies, particularly in the context of multi-pollutant or mixed-waste contaminations. PMID:23251623

  10. How Posttranslational Modification of Nitrogenase Is Circumvented in Rhodopseudomonas palustris Strains That Produce Hydrogen Gas Constitutively

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    Heiniger, Erin K.; Oda, Yasuhiro; Samanta, Sudip K.

    2012-01-01

    Nitrogenase catalyzes the conversion of dinitrogen gas (N2) and protons to ammonia and hydrogen gas (H2). This is a catalytically difficult reaction that requires large amounts of ATP and reducing power. Thus, nitrogenase is not normally expressed or active in bacteria grown with a readily utilized nitrogen source like ammonium. nifA* mutants of the purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris have been described that express nitrogenase genes constitutively and produce H2 when grown with ammonium as a nitrogen source. This raised the regulatory paradox of why these mutants are apparently resistant to a known posttranslational modification system that should switch off the activity of nitrogenase. Microarray, mutation analysis, and gene expression studies showed that posttranslational regulation of nitrogenase activity in R. palustris depends on two proteins: DraT2, an ADP-ribosyltransferase, and GlnK2, an NtrC-regulated PII protein. GlnK2 was not well expressed in ammonium-grown NifA* cells and thus not available to activate the DraT2 nitrogenase modification enzyme. In addition, the NifA* strain had elevated nitrogenase activity due to overexpression of the nif genes, and this increased amount of expression overwhelmed a basal level of activity of DraT2 in ammonium-grown cells. Thus, insufficient levels of both GlnK2 and DraT2 allow H2 production by an nifA* mutant grown with ammonium. Inactivation of the nitrogenase posttranslational modification system by mutation of draT2 resulted in increased H2 production by ammonium-grown NifA* cells. PMID:22179236

  11. Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris

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    Miller, Anthony R.; North, Justin A.; Wildenthal, John A.

    2018-01-01

    ABSTRACT 5′-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments. PMID:29636438

  12. Hydrogen production under salt stress conditions by a freshwater Rhodopseudomonas palustris strain.

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    Adessi, Alessandra; Concato, Margherita; Sanchini, Andrea; Rossi, Federico; De Philippis, Roberto

    2016-03-01

    Hydrogen represents a possible alternative energy carrier to face the growing request for energy and the shortage of fossil fuels. Photofermentation for the production of H2 constitutes a promising way for integrating the production of energy with waste treatments. Many wastes are characterized by high salinity, and polluted seawater can as well be considered as a substrate. Moreover, the application of seawater for bacterial culturing is considered cost-effective. The aims of this study were to assess the capability of the metabolically versatile freshwater Rhodopseudomonas palustris 42OL of producing hydrogen on salt-containing substrates and to investigate its salt stress response strategy, never described before. R. palustris 42OL was able to produce hydrogen in media containing up to 3 % added salt concentration and to grow in media containing up to 4.5 % salinity without the addition of exogenous osmoprotectants. While the hydrogen production performances in absence of sea salts were higher than in their presence, there was no significant difference in performances between 1 and 2 % of added sea salts. Nitrogenase expression levels indicated that the enzyme was not directly inhibited during salt stress, but a regulation of its expression may have occurred in response to salt concentration increase. During cell growth and hydrogen production in the presence of salts, trehalose was accumulated as a compatible solute; it protected the enzymatic functionality against salt stress, thus allowing hydrogen production. The possibility of producing hydrogen on salt-containing substrates widens the range of wastes that can be efficiently used in production processes.

  13. Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

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    Inui, Masayuki; Roh, Jung Hyeob; Zahn, Kenneth; Yukawa, Hideaki

    2000-01-01

    A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria. PMID:10618203

  14. Hydrogen production using Rhodopseudomonas palustris WP 3-5 with hydrogen fermentation reactor effluent

    International Nuclear Information System (INIS)

    Chi-Mei Lee; Kuo-Tsang Hung

    2006-01-01

    The possibility of utilizing the dark hydrogen fermentation stage effluents for photo hydrogen production using purple non-sulfur bacteria should be elucidated. In the previous experiments, Rhodopseudomonas palustris WP3-5 was proven to efficiently produce hydrogen from the effluent of hydrogen fermentation reactors. The highest hydrogen production rate was obtained at a HRT value of 48 h when feeding a 5 fold effluent dilution from anaerobic hydrogen fermentation. Besides, hydrogen production occurred only when the NH 4 + concentration was below 17 mg-NH 4 + /l. Therefore, for successful fermentation effluent utilization, the most important things were to decrease the optimal HRT, increase the optimal substrate concentration and increase the tolerable ammonia concentration. In this study, a lab-scale serial photo-bioreactor was constructed. The reactor overall hydrogen production efficiency with synthetic wastewater exhibiting an organic acid profile identical to that of anaerobic hydrogen fermentation reactor effluent and with effluent from two anaerobic hydrogen fermentation reactors was evaluated. (authors)

  15. Optimization of phototrophic hydrogen production by Rhodopseudomonas palustris PBUM001 via statistical experimental design

    Energy Technology Data Exchange (ETDEWEB)

    Jamil, Zadariana [Department of Civil Engineering, Faculty of Engineering, University of Malaya (Malaysia); Faculty of Civil Engineering, Technology University of MARA (Malaysia); Mohamad Annuar, Mohamad Suffian; Vikineswary, S. [Institute of Biological Sciences, University of Malaya (Malaysia); Ibrahim, Shaliza [Department of Civil Engineering, Faculty of Engineering, University of Malaya (Malaysia)

    2009-09-15

    Phototrophic hydrogen production by indigenous purple non-sulfur bacteria, Rhodopseudomonas palustris PBUM001 from palm oil mill effluent (POME) was optimized using response surface methodology (RSM). The process parameters studied include inoculum sizes (% v/v), POME concentration (% v/v), light intensity (klux), agitation (rpm) and pH. The experimental data on cumulative hydrogen production and COD reduction were fitted into a quadratic polynomial model using response surface regression analysis. The path to optimal process conditions was determined by analyzing response surface three-dimensional surface plot and contour plot. Statistical analysis on experimental data collected following Box-Behnken design showed that 100% (v/v) POME concentration, 10% (v/v) inoculum size, light intensity at 4.0 klux, agitation rate at 250 rpm and pH of 6 were the best conditions. The maximum predicted cumulative hydrogen production and COD reduction obtained under these conditions was 1.05 ml H{sub 2}/ml POME and 31.71% respectively. Subsequent verification experiments at optimal process values gave the maximum yield of cumulative hydrogen at 0.66 {+-} 0.07 ml H{sub 2}/ml POME and COD reduction at 30.54 {+-} 9.85%. (author)

  16. Arsenic-Redox Transformation and Plant Growth Promotion by Purple Nonsulfur Bacteria Rhodopseudomonas palustris CS2 and Rhodopseudomonas faecalis SS5.

    Science.gov (United States)

    Batool, Kanza; Tuz Zahra, Fatima; Rehman, Yasir

    2017-01-01

    Arsenic (As) is a well-known toxic metalloid found naturally and released by different industries, especially in developing countries. Purple nonsulfur bacteria (PNSB) are known for wastewater treatment and plant growth promoting abilities. As-resistant PNSB were isolated from a fish pond. Based on As-resistance and plant growth promoting attributes, 2 isolates CS2 and SS5 were selected and identified as Rhodopseudomonas palustris and Rhodopseudomonas faecalis , respectively, through 16S rRNA gene sequencing. Maximum As(V) resistance shown by R. faecalis SS5 and R. palustris CS2 was up to 150 and 100 mM, respectively. R . palustris CS2 showed highest As(V) reduction up to 62.9% (6.29 ± 0.24 mM), while R. faecalis SS5 showed maximum As(III) oxidation up to 96% (4.8 ± 0.32 mM), respectively. Highest auxin production was observed by R. palustris CS2 and R. faecalis SS, up to 77.18 ± 3.7 and 76.67 ± 2.8  μ g mL -1 , respectively. Effects of these PNSB were tested on the growth of Vigna mungo plants. A statistically significant increase in growth was observed in plants inoculated with isolates compared to uninoculated plants, both in presence and in absence of As. R. palustris CS2 treated plants showed 17% (28.1 ± 0.87 cm) increase in shoot length and 21.7% (7.07 ± 0.42 cm) increase in root length, whereas R. faecalis SS5 treated plants showed 12.8% (27.09 ± 0.81 cm) increase in shoot length and 18.8% (6.9 ± 0.34 cm) increase in root length as compared to the control plants. In presence of As, R. palustris CS2 increased shoot length up to 26.3% (21.0 ± 1.1 cm), while root length increased up to 31.3% (5.3 ± 0.4 cm), whereas R. faecalis SS5 inoculated plants showed 25% (20.7 ± 1.4 cm) increase in shoot length and 33.3% (5.4 ± 0.65 cm) increase in root length as compared to the control plants. Bacteria with such diverse abilities could be ideal for plant growth promotion in As-contaminated sites.

  17. A novel electrophototrophic bacterium Rhodopseudomonas palustris strain RP2, exhibits hydrocarbonoclastic potential in anaerobic environments

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    Krishnaveni Venkidusamy

    2016-07-01

    Full Text Available An electrophototrophic, hydrocarbonoclastic bacterium Rhodopseudomonas palustris stain RP2 was isolated from the anodic biofilms of hydrocarbon fed microbial electrochemical remediation systems (MERS. Salient properties of the strain RP2 were direct electrode respiration, dissimilatory metal oxide reduction, spore formation, anaerobic nitrate reduction, free living diazotrophy and the ability to degrade n-alkane components of petroleum hydrocarbons in anoxic, photic environments. In acetate fed microbial electrochemical cells, a maximum current density of 305±10 mA/m2 (1000Ω was generated (power density 131.65±10 mW/m2 by strain RP2 with a coulombic efficiency of 46.7 ± 1.3%. Cyclic voltammetry studies showed that anaerobically grown cells of strain RP2 is electrochemically active and likely to transfer electrons extracellularly to solid electron acceptors through membrane bound compounds, however, aerobically grown cells lacked the electrochemical activity. The ability of strain RP2 to produce current (maximum current density 21±3 mA/m2; power density 720±7 µW/m2, 1000Ω using petroleum hydrocarbon (PH as a sole energy source was also examined using an initial concentration of 800 mg l-1 of diesel range hydrocarbons (C9- C36 with a concomitant removal of 47.4 ± 2.7% hydrocarbons in MERS. Here, we also report the first study that shows an initial evidence for the existence of a hydrocarbonoclastic behavior in the strain RP2 when grown in different electron accepting and illuminated conditions (anaerobic and MERS degradation. Such observations reveal the importance of photoorganotrophic growth in the utilization of hydrocarbons from contaminated environments. Identification of such novel petrochemical hydrocarbon degrading electricigens, not only expands the knowledge on the range of bacteria known for the hydrocarbon bioremediation but also shows a biotechnological potential that goes well beyond its applications to MERS.

  18. High-throughput transcriptome sequencing analysis provides preliminary insights into the biotransformation mechanism of Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnoside.

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    Bi, Lei; Guan, Chun-jie; Yang, Guan-e; Yang, Fei; Yan, Hong-yu; Li, Qing-shan

    2016-04-01

    The purple photosynthetic bacterium Rhodopseudomonas palustris has been widely applied to enhance the therapeutic effects of traditional Chinese medicine using novel biotransformation technology. However, comprehensive studies of the R. palustris biotransformation mechanism are rare. Therefore, investigation of the expression patterns of genes involved in metabolic pathways that are active during the biotransformation process is essential to elucidate this complicated mechanism. To promote further study of the biotransformation of R. palustris, we assembled all R. palustris transcripts using Trinity software and performed differential expression analysis of the resulting unigenes. A total of 9725, 7341 and 10,963 unigenes were obtained by assembling the alpha-rhamnetin-3-rhamnoside-treated R. palustris (RPB) reads, control R. palustris (RPS) reads and combined RPB&RPS reads, respectively. A total of 9971 unigenes assembled from the RPB&RPS reads were mapped to the nr, nt, Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value biotransformation in R. palustris. Furthermore, we propose two putative ARR biotransformation mechanisms in R. palustris. These analytical results represent a useful genomic resource for in-depth research into the molecular basis of biotransformation and genetic modification in R. palustris. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris.

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    Tatiana V Karpinets

    Full Text Available Anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for efficient degradation of environmental pollutants. In natural environments, the degradation is usually accomplished by syntrophic consortia comprised of different bacterial species. This strategy allows consortium organisms to reduce efforts required for maintenance of the redox homeostasis at each syntrophic level. Cellular mechanisms that maintain the redox homeostasis during the degradation of aromatic compounds by one organism are not fully understood. Here we present a hypothesis that the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris forms its own syntrophic consortia, when it grows anaerobically on p-coumarate or benzoate as a sole carbon source. We have revealed the consortia from large-scale measurements of mRNA and protein expressions under p-coumarate, benzoate and succinate degrading conditions using a novel computational approach referred as phenotype fingerprinting. In this approach, marker genes for known R. palustris phenotypes are employed to determine the relative expression levels of genes and proteins in aromatics versus non-aromatics degrading condition. Subpopulations of the consortia are inferred from the expression of phenotypes and known metabolic modes of the R. palustris growth. We find that p-coumarate degrading conditions may lead to at least three R. palustris subpopulations utilizing p-coumarate, benzoate, and CO2 and H2. Benzoate degrading conditions may also produce at least three subpopulations utilizing benzoate, CO2 and H2, and N2 and formate. Communication among syntrophs and inter-syntrophic dynamics in each consortium are indicated by up-regulation of transporters and genes involved in the curli formation and chemotaxis. The N2-fixing subpopulation in the benzoate degrading consortium has preferential activation of the

  20. Promoting effects of a single Rhodopseudomonas palustris inoculant on plant growth by Brassica rapa chinensis under low fertilizer input.

    Science.gov (United States)

    Wong, Wai-Tak; Tseng, Ching-Han; Hsu, Shu-Hua; Lur, Huu-Sheng; Mo, Chia-Wei; Huang, Chu-Ning; Hsu, Shu-Chiung; Lee, Kung-Ta; Liu, Chi-Te

    2014-09-17

    Several Rhodopseudomonas palustris strains have been isolated from rice paddy fields in Taiwan by combining the Winogradsky column method and molecular marker detection. These isolates were initially screened by employing seed germination and seedling vigor assays to evaluate their potential as inoculants. To fulfill the demand in the present farming system for reducing the application of chemical fertilizers, we assessed the plant growth-promoting effects of the R. palustris YSC3, YSC4, and PS3 inoculants on Brassica rapa chinensis (Chinese cabbage) cultivated under a half quantity of fertilizer. The results obtained showed that supplementation with approximately 4.0×10(6) CFU g(-1) soil of the PS3 inoculant at half the amount of fertilizer consistently produced the same plant growth potential as 100% fertility, and also increased the nitrogen use efficiency of the applied fertilizer nutrients. Furthermore, we noted that the plant growth-promotion rate elicited by PS3 was markedly higher with old seeds than with new seeds, suggesting it has the potential to boost the development of seedlings that were germinated from carry-over seeds of poor quality. These beneficial traits suggest that the PS3 isolate may serve as a potential PGPR inoculant for integrated nutrient management in agriculture.

  1. Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin.

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    Bernstein, Jeffrey R; Bulter, Thomas; Liao, James C

    2008-01-01

    This work demonstrates the transfer of the five-gene cyclohexane carboxylate (CHC) degradation pathway from the high-GC alphaproteobacterium Rhodopseudomonas palustris to Escherichia coli, a gammaproteobacterium. The degradation product of this pathway is pimeloyl-CoA, a key metabolite in E. coli's biotin biosynthetic pathway. This pathway is useful for biotin overproduction in E. coli; however, the expression of GC-rich genes is troublesome in this host. When the native R. palustris CHC degradation pathway is transferred to a DeltabioH pimeloyl-CoA auxotroph of E. coli, it is unable to complement growth in the presence of CHC. To overcome this expression problem we redesigned the operon with decreased GC content and removed stretches of high-GC intergenic DNA which comprise the 5' untranslated region of each gene, replacing these features with shorter low-GC sequences. We show this synthetic construct enables growth of the DeltabioH strain in the presence of CHC. When the synthetic degradation pathway is overexpressed in conjunction with the downstream genes for biotin biosynthesis, we measured significant accumulation of biotin in the growth medium, showing that the pathway transfer is successfully integrated with the host metabolism.

  2. Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex.

    Science.gov (United States)

    Jackson, Philip J; Hitchcock, Andrew; Swainsbury, David J K; Qian, Pu; Martin, Elizabeth C; Farmer, David A; Dickman, Mark J; Canniffe, Daniel P; Hunter, C Neil

    2018-02-01

    The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc 1 complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  3. A two-step fermentation of distillers' grains using Trichoderma viride and Rhodopseudomonas palustris for fish feed.

    Science.gov (United States)

    Zhang, Jian; Zhang, Wen-Xue; Li, Shun-Zhou; You, Ling; Zhang, Chao; Sun, Chuan-Ze; Liu, Xiao-Bin

    2013-10-01

    It is important to provide added value or to make full use of the co-product of grains from ethanol production. In order to convert distillers' grains into a high-quality feed, the Trichoderma viride and Rhodopseudomonas palustris fermentation were combined and investigated in this study. The T. viride fermentation was carried out in an aerobic fermentation installation in favoring of the growth of the fungi and the degradation of the cellulose, and then the fermentation of R. palustris was performed to increase the content of protein with an anaerobic installation. After the two step fermentations, the true protein content of dried distiller' grains increased from 11.4 to 33.6 % (w/w) (the content of crude protein from 14.5 to 39.7 %), the crude fiber content decreased from 21.3 to 7.6 % (w/w), the crude fat content increased from 5.5 to 7.9 % (w/w), the crude ash decreased from 14.6 to 10.2 % (w/w), the total phosphorus content increased from 0.4 to 1.2 % (w/w), and the water content was 11.8 % (w/w). The dried and fermented grains contain the R. palustris viable count of 5.3 × 10¹¹ CFU/g dry matter. The results may support a new application of an active photosynthetic bacteria fish feed in fisheries industry and offer a reference for the further study of lignocellulosic materials as raw materials converting into high-quality feed.

  4. Cloning and characterization of a pyrethroid pesticide decomposing esterase gene, Est3385, from Rhodopseudomonas palustris PSB-S.

    Science.gov (United States)

    Luo, Xiangwen; Zhang, Deyong; Zhou, Xuguo; Du, Jiao; Zhang, Songbai; Liu, Yong

    2018-05-09

    Full length open reading frame of pyrethroid detoxification gene, Est3385, contains 963 nucleotides. This gene was identified and cloned based on the genome sequence of Rhodopseudomonas palustris PSB-S available at the GneBank. The predicted amino acid sequence of Est3385 shared moderate identities (30-46%) with the known homologous esterases. Phylogenetic analysis revealed that Est3385 was a member in the esterase family I. Recombinant Est3385 was heterologous expressed in E. coli, purified and characterized for its substrate specificity, kinetics and stability under various conditions. The optimal temperature and pH for Est3385 were 35 °C and 6.0, respectively. This enzyme could detoxify various pyrethroid pesticides and degrade the optimal substrate fenpropathrin with a Km and Vmax value of 0.734 ± 0.013 mmol·l -1 and 0.918 ± 0.025 U·µg -1 , respectively. No cofactor was found to affect Est3385 activity but substantial reduction of enzymatic activity was observed when metal ions were applied. Taken together, a new pyrethroid degradation esterase was identified and characterized. Modification of Est3385 with protein engineering toolsets should enhance its potential for field application to reduce the pesticide residue from agroecosystems.

  5. Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris.

    Science.gov (United States)

    Kanno, Nanako; Matsuura, Katsumi; Haruta, Shin

    2018-03-29

    Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark. After starvation for 5 d in the light, cells showed increases in the amount of ATP and the NAD + /NADH ratio. Decreases in the amounts of most metabolites related to glycolysis and the TCA cycle in energy-rich starved cells suggest the active utilization of these metabolites for the modification of cellular components. Starvation in the dark induced the consumption of cellular compounds such as amino acids, indicating that the degradation of these cellular components produced ATP in order to maintain viability under energy-poor conditions. The present results suggest that intracellular energy levels alter survival strategies under carbon-starved conditions through metabolism.

  6. Preservation of H2 production activity in nanoporous latex coatings of Rhodopseudomonas palustris CGA009 during dry storage at ambient temperatures: Preservation of R. palustris latex coatings

    Energy Technology Data Exchange (ETDEWEB)

    Piskorska, M. [Univ. of South Carolina, Aiken, SC (United States); Soule, T. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Gosse, J. L. [North Carolina State Univ., Raleigh, NC (United States); Milliken, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Flickinger, M. C. [North Carolina State Univ., Raleigh, NC (United States); Smith, G. W. [Univ. of South Carolina, Aiken, SC (United States); Yeager, C. M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2013-01-21

    To assess the applicability of latex cell coatings as an ‘off-the-shelf’ biocatalyst, the effect of osmoprotectants, temperature, humidity and O2 on preservation of H2 production in Rhodopseudomonas palustris coatings was evaluated. Immediately following latex coating coalescence (24 h) and for up to 2 weeks of dry storage, rehydrated coatings containing different osmoprotectants displayed similar rates of H2 production. Beyond 2 weeks of storage, sorbitol-treated coatings lost all H2 production activity, whereas considerable H2 production was still detected in sucrose- and trehalose-stabilized coatings. The relative humidity level at which the coatings were stored had a significant impact on the recovery and subsequent rates of H2 production. After 4 weeks storage under air at 60% humidity, coatings produced only trace amounts of H2 (0–0.1% headspace accumulation), whereas those stored at < 5% humidity retained 27–53% of their H2 production activity after 8 weeks of storage. In conWhen stored in argon at < 5% humidity and room temperature, R. palustris coatings retained full H2 production activity for 3 months, implicating oxidative damage as a key factor limiting coating storage. Overall, the results demonstrate that biocatalytic latex coatings are an attractive cell immobilization platform for preservation of bioactivity in the dry state.

  7. Single-molecule spectroscopy reveals that individual low-light LH2 complexes from Rhodopseudomonas palustris 2.1.6. have a heterogeneous polypeptide composition.

    Science.gov (United States)

    Brotosudarmo, Tatas H P; Kunz, Ralf; Böhm, Paul; Gardiner, Alastair T; Moulisová, Vladimíra; Cogdell, Richard J; Köhler, Jürgen

    2009-09-02

    Rhodopseudomonas palustris belongs to the group of purple bacteria that have the ability to produce LH2 complexes with unusual absorption spectra when they are grown at low-light intensity. This ability is often related to the presence of multiple genes encoding the antenna apoproteins. Here we report, for the first time to our knowledge, direct evidence that individual low-light LH2 complexes have a heterogeneous alphabeta-apoprotein composition that modulates the site energies of Bchl a molecules, producing absorption bands at 800, 820, and 850 nm. The arrangement of the Bchl a molecules in the "tightly coupled ring" can be modeled by nine alphabeta-Bchls dimers, such that the Bchls bound to six alphabeta-pairs have B820-like site energies and the remaining Bchl a molecules have B850-like site energies. Furthermore, the experimental data can only be satisfactorily modeled when these six alphabeta-pairs with B820 Bchl a molecules are distributed such that the symmetry of the assembly is reduced to C(3). It is also clear from the measured single-molecule spectra that the energies of the electronically excited states in the mixed B820/850 ring are mainly influenced by diagonal disorder.

  8. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A.

    Science.gov (United States)

    Hirakawa, Hidetada; Schaefer, Amy L; Greenberg, E Peter; Harwood, Caroline S

    2012-04-01

    The phenylpropanoid p-coumarate and structurally related aromatic compounds are produced in large amounts by green plants and are excellent carbon sources for many soil bacteria. Aerobic bacteria remove the acyl side chain from phenylpropanoids to leave an aromatic aldehyde, which then enters one of several possible central pathways of benzene ring degradation. We investigated the pathway for the anaerobic degradation of p-coumarate by the phototrophic bacterium Rhodopseudomonas palustris and found that it also follows this metabolic logic. We characterized enzymes for the conversion of p-coumarate to p-hydroxybenzaldehyde and acetyl coenzyme A (acetyl-CoA) encoded by the couAB operon. We also identified a MarR family transcriptional regulator that we named CouR. A couR mutant had elevated couAB expression. In addition, His-tagged CouR bound with high affinity to a DNA fragment encompassing the couAB promoter region, and binding was abrogated by the addition of nanomolar quantities of p-coumaroyl-CoA but not by p-coumarate. Footprinting demonstrated binding of CouR to an inverted repeat sequence that overlaps the -10 region of the couAB promoter. Our results provide evidence for binding of a CoA-modified aromatic compound by a MarR family member. Although the MarR family is widely distributed in bacteria and archaea and includes over 12,000 members, ligands have been identified for relatively few family members. Here we provide biochemical evidence for a new category of MarR ligand.

  9. Hydrogen photo-evolution by Rhodopseudomonas palustris 6A using pre-treated olive mill wastewater and a synthetic medium containing sugars

    International Nuclear Information System (INIS)

    Pintucci, Cristina; Padovani, Giulia; Giovannelli, Alessio; Traversi, Maria Laura; Ena, Alba; Pushparaj, Benjamin; Carlozzi, Pietro

    2015-01-01

    Highlights: • Adsorbent matrices to convert fresh olive mill wastewater (OMW F ) in feedstock. • Dry-Azolla and granular active carbon for adsorbing polyphenols from OMW F . • Photofermentative processes for biohydrogen production. • Culture mixing by means of an impeller or a magnetic stir bar. • A 30% of dephenolised OMW containing medium suits the photofermentative process. - Abstract: Increasing costs of petroleum, associated with the escalating problems of global climate change, require always greater efforts in order to produce an energy carrier as bioH 2 . In this study, bioH 2 production using photofermentative process was investigated. Two culture broths were used: (a) a synthetic medium rich in sugars (glucose and fructose) and (b) a pre-treated fresh olive-mill wastewater (OMW F ) diluted with water (30%, v:v). The pre-treatment was carried out using two different vegetable matrices (dry-Azolla and granular active carbon) to decrease both the content of polyphenols and the dark colour of wastewater. Rhodopseudomonas palustris 6A isolated from soil spread with OMW was utilized for batch growth experiments, carried out indoors under continuous light (200 μE/m 2 /s). When synthetic medium was used, the culture mixing was performed using either (i) a magnetic stir bar, and (ii) an impeller equipped with five turbines. The latter system made it possible to increase the bioH 2 photo-evolution by 1.4 times. The specific hydrogen photo-evolution rate was 13.5 mL/g(dw)/h in the broth containing diluted OMW F and 11.8 mL/g(dw)/h in the synthetic medium containing sugars (glucose and fructose)

  10. Effect of dilution and L-malic acid addition on bio-hydrogen production with Rhodopseudomonas palustris from effluent of an acidogenic anaerobic reactor

    International Nuclear Information System (INIS)

    Azbar, N.; Tuba, F.; Dokgoz, C.

    2009-01-01

    In this study, H 2 was produced in a two-stage biological process: I) first stage; the dark fermentation of cheese whey wastewater, which is rich in lactose, by mixed anaerobic culture grown at thermophilic temperature in a continuously running fermentor and ii) second stage; the photo-fermentation of the residual medium by R. palustris strain (DSM 127) at 31 o C under illumination of 150 W in batch mode, respectively. In the first part of the study, the effluent from the dark fermentation reactor was used either as it is (no dilution) or after dilution with distilled water at varying ratios such as 1/2 , 1/5, 1/10 (1 volume effluent/5 volume distilled water) before used in photo-fermentation experiments. In the second part of the study, L-malic acid at varying amounts was added into the hydrogen production medium in order to have L-malic acid concentrations ranging from 0 to 4 g/l. Non-diluted and pre-diluted mediums with or without L-malic acid addition were also tested for comparison purpose (as controls). Prior to the hydrogen production experiments, all samples were subjected to pH adjustment, (pH 6.7) and sterilized by autoclave at 121 o C for 15 min. In regards to the experiments in which the effect of dilution of the effluent from dark fermentation was studied, it was observed that dilution of the effluent from dark fermentation resulted in much better hydrogen productions. Among the dilution rates used, the experiments operated with 1/5 dilution ratio produced the best hydrogen production (241 ml H 2 / g COD fed ). On the other hand, it was seen that the mixing the effluent with L-malic acid (0 - 4 g/l) at increasing ratios (studied from 0% L-malic acid up to 100% by volume in the mixture) had further positive effect and improved the hydrogen production. The bioreactors containing only L-malic acid media resulted in the best hydrogen production (438 ml H 2 / g COD fed ). It was found that, undiluted raw cheese whey wastewater effluent from dark hydrogen

  11. Effect of dilution and L-malic acid addition on bio-hydrogen production with Rhodopseudomonas palustris from effluent of an acidogenic anaerobic reactor

    Energy Technology Data Exchange (ETDEWEB)

    Azbar, N.; Tuba, F.; Dokgoz, C. [Bioengineering Dept., Faculty of Engineering, Ege Univ., Izmir (Turkey)], E-mail: nuri.azbar@ege.edu.tr

    2009-07-01

    In this study, H{sub 2} was produced in a two-stage biological process: I) first stage; the dark fermentation of cheese whey wastewater, which is rich in lactose, by mixed anaerobic culture grown at thermophilic temperature in a continuously running fermentor and ii) second stage; the photo-fermentation of the residual medium by R. palustris strain (DSM 127) at 31{sup o}C under illumination of 150 W in batch mode, respectively. In the first part of the study, the effluent from the dark fermentation reactor was used either as it is (no dilution) or after dilution with distilled water at varying ratios such as 1/2 , 1/5, 1/10 (1 volume effluent/5 volume distilled water) before used in photo-fermentation experiments. In the second part of the study, L-malic acid at varying amounts was added into the hydrogen production medium in order to have L-malic acid concentrations ranging from 0 to 4 g/l. Non-diluted and pre-diluted mediums with or without L-malic acid addition were also tested for comparison purpose (as controls). Prior to the hydrogen production experiments, all samples were subjected to pH adjustment, (pH 6.7) and sterilized by autoclave at 121{sup o}C for 15 min. In regards to the experiments in which the effect of dilution of the effluent from dark fermentation was studied, it was observed that dilution of the effluent from dark fermentation resulted in much better hydrogen productions. Among the dilution rates used, the experiments operated with 1/5 dilution ratio produced the best hydrogen production (241 ml H{sub 2}/ g COD{sub fed}). On the other hand, it was seen that the mixing the effluent with L-malic acid (0 - 4 g/l) at increasing ratios (studied from 0% L-malic acid up to 100% by volume in the mixture) had further positive effect and improved the hydrogen production. The bioreactors containing only L-malic acid media resulted in the best hydrogen production (438 ml H{sub 2} / g COD{sub fed}). It was found that, undiluted raw cheese whey wastewater

  12. Ecosystem carbon stocks in Pinus palustris forests

    Science.gov (United States)

    Lisa Samuelson; Tom Stokes; John R. Butnor; Kurt H. Johnsen; Carlos A. Gonzalez-Benecke; Pete Anderson; Jason Jackson; Lorenzo Ferrari; Tim A. Martin; Wendell P. Cropper

    2014-01-01

    Longleaf pine (Pinus palustris Mill.) restoration in the southeastern United States offers opportunities for carbon (C) sequestration. Ecosystem C stocks are not well understood in longleaf pine forests, which are typically of low density and maintained by prescribed fire. The objectives of this research were to develop allometric equations for...

  13. The sigma(54) regulon (sigmulon) of Pseudomonas putida

    DEFF Research Database (Denmark)

    Cases, I.; Ussery, David; de Lorenzo, V.

    2003-01-01

    , the sigma(54) regulon has been studied both in Escherichia coli, Salmonella typhimurium and several species of the Rhizobiaceae. Here we present the analysis of the sigma(54) regulon (sigmulon) in the complete genome of Pseudomonas putida KT2440. We have developed an improved method for the prediction...

  14. The cys regulon of Xanthomonas citri

    Energy Technology Data Exchange (ETDEWEB)

    Moutran, A.; Balan, A. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil)

    2012-07-01

    Full text: In Escherichia coli, genes involved in metabolic pathway of sulfate and sulfonate compounds are clustered in a cys regulon, which includes three ABC transport system (operons: sbpcysWUA; ssuABC and tauABC), thirteen genes involved in the sulfur reduction (ssuDE; tauD and cysDNCHIJGK) and two regulatory proteins that belong to LysR transcription family: CysB and Cbl. Notably, a search and comparative analysis of these genes in the genomes of the citrus pathogen Xanthomonas citri and other phylogenetically related Xanthomonas species revealed the presence of genes involved with alkanesulfonate, sulfate ester and taurine, only in X. citri, suggesting that proteins from this regulon might be associated with pathogenicity in citrus. Using the molecular modeling associated with a system biology view, we modeled all the protein structures of the X. citri cys regulon as well as characterized the important residues forming the putative active sites. Comparison with orthologs from different microorganisms was made in order to get a phylogenetic relationships. We showed that proteins that are responsible for the affinity and specificity of the alkanesulfonate, sulfate and taurine transport systems conserved the residues involved in the sulfate coordination but are organized in different branches in evolution. Inside these phylogenetic branches, proteins involved in the sulfate transporter are highly conserved when compared to the others. Moreover, we identified that the taurine-binding protein (TauA) of the X. citri belongs to a different evolutionary branch from that one that described for E. coli. These differences were also noticed for components of the tau operon, including a putative new regulator. The function and mechanism of action of each protein is discussed in order to bring light for the sulfur assimilation processes and their importance for X. citri physiology. (author)

  15. The cys regulon of Xanthomonas citri

    International Nuclear Information System (INIS)

    Moutran, A.; Balan, A.

    2012-01-01

    Full text: In Escherichia coli, genes involved in metabolic pathway of sulfate and sulfonate compounds are clustered in a cys regulon, which includes three ABC transport system (operons: sbpcysWUA; ssuABC and tauABC), thirteen genes involved in the sulfur reduction (ssuDE; tauD and cysDNCHIJGK) and two regulatory proteins that belong to LysR transcription family: CysB and Cbl. Notably, a search and comparative analysis of these genes in the genomes of the citrus pathogen Xanthomonas citri and other phylogenetically related Xanthomonas species revealed the presence of genes involved with alkanesulfonate, sulfate ester and taurine, only in X. citri, suggesting that proteins from this regulon might be associated with pathogenicity in citrus. Using the molecular modeling associated with a system biology view, we modeled all the protein structures of the X. citri cys regulon as well as characterized the important residues forming the putative active sites. Comparison with orthologs from different microorganisms was made in order to get a phylogenetic relationships. We showed that proteins that are responsible for the affinity and specificity of the alkanesulfonate, sulfate and taurine transport systems conserved the residues involved in the sulfate coordination but are organized in different branches in evolution. Inside these phylogenetic branches, proteins involved in the sulfate transporter are highly conserved when compared to the others. Moreover, we identified that the taurine-binding protein (TauA) of the X. citri belongs to a different evolutionary branch from that one that described for E. coli. These differences were also noticed for components of the tau operon, including a putative new regulator. The function and mechanism of action of each protein is discussed in order to bring light for the sulfur assimilation processes and their importance for X. citri physiology. (author)

  16. Moessbauer spectroscopy on the reaction center of Rhodopseudomonas viridis

    International Nuclear Information System (INIS)

    Frolov, E.; Goldanskii, V.I.; Birk, A.; Parak, F.; Fritzsch, G.; Sinning, I.; Michel, H.

    1992-01-01

    Proteins called 'reaction centers' (RC) can be isolated from many photosynthetic bacteria. They have one non-heme iron in a quinone acceptor region. The RC of Rhodopseudomonas viridis contains an additional tightly bound tetra-heme cytochrome c subunit. The electronic configuration of both cytochrome and the non-heme iron has been studied in the crystallized protein by Moessbauer spectroscopy at different redox potentials, pH-values, and with an addition of o-phenanthroline. At high potentials (E h =+500 mV) all heme irons are in the low spin Fe 3+ -state, and at low potential (E h = 1 50 mV) they are low spin Fe 2+ with the same Moessbauer parameters for all hemes independent of pH. Redox titrations change the relative area of the reduced and oxidized states in agreement with other methods. The non-heme iron shows a high spin Fe 2+ configuration independent of E h and pH with parameters comparable to those of Rhodopseudomonas sphaeroides. Surprisingly, there is strong evidence for another non-heme iron species in part of the molecules with a Fe 2+ low spin configuration. Incubation with o-phenanthroline decreases the relative Fe 2+ hs-area and increases the contribution of Fe 2+ ls-area. Above 210 K the mean square displacement, 2 >, of the RC-crystals increases more than linearly with temperature. This may be correlated with the increase of the electron transfer rate and indicates that intramolecular mobility influences the functional activity of a protein. (orig.)

  17. Variability of Caltha palustris L. populations in garden culture

    Directory of Open Access Journals (Sweden)

    Krystyna Falińska

    2014-01-01

    Full Text Available On the basis of studies performed in the experimental garden the character of the variability of Caltha palustris L. populations is described. Individuals were bred under uniform conditions from diaspores of meadow, springwood, flood-plain forest and alder forest populations. The results obtained allow to evaluate the hypothesis concerning the ecological preference of cytotypes (S m i t 1967, 1968 and the somewhat different ecological requirements of two subspecies: C. palustris ssp. palustris and C. palustris ssp. cornuta. It was found that each population includes individuals with different cytotypes. The situation is similar as far as subspecies are concerned, distinguished on the basis of fruit morphology (Fig. 1. It should be stressed, however, that, investigations of many years duration raised serious doubts as to the diagnostic value of fruit morphology (Figs. 2, 3. On the basis of the preserved differences between the populations in shoot habitus, reproduction and phenology in garden culture, a springwood and an alder forest ecotype were distinguished. Meadow and flood-plain populations exhibited a transitional character with certain similarities both to the alder forest and to the springwood populations.

  18. Aberrante Epigynenbildungen bei der Wolfspinne Pardosa palustris (Araneae, Lycosidae

    Directory of Open Access Journals (Sweden)

    Martin, Dieter

    2013-11-01

    Full Text Available Two cases of aberrant epigyne shape in Pardosa palustris (Linnaeus, 1758 are described. Characteristic is the absence of the posterior lateral parts of the septum. Possible causes, such as `genital damage` during mating or the effects of parasite infestation, are discussed.

  19. Fluorescence spectral fluctuations of single LH2 complexes from Rhodopseudomonas acidophila strain 10050

    NARCIS (Netherlands)

    Rutkauskas, D.; Novoderezkhin, V.; Cogdell, R.J.; van Grondelle, R.

    2004-01-01

    We have investigated the energy landscape of the bacterial photosynthetic peripheral light-harvesting complex LH2 of purple bacterium Rhodopseudomonas acidophila by monitoring sequences of fluorescence spectra of single LH2 assemblies, at room temperature, with different excitation intensities as

  20. ?-Oryzanols of North American Wild Rice (Zizania palustris)

    OpenAIRE

    Aladedunye, Felix; Przybylski, Roman; Rudzinska, Magdalena; Klensporf-Pawlik, Dorota

    2013-01-01

    ?-Oryzanol, a natural mixture of ferulic acid esters of triterpene alcohols and sterols, are an important bioactive components present in rice bran oil. In light of the recent increase in the popularity of wild rice among consumers, and the possibility of a direct relationship between ?-oryzanol composition and its bioactivity, the oryzanol profile of major wild rice (Zizania palustris) grown in North America was studied and compared to regular brown rice (Oryza sativa L.). A total of twenty-...

  1. A new marsh plant community of Eleocharito palustris-Alismatetum lanceolati (Eleocharito palustris-Sagittarion sagittifoliae alliance in Slovakia

    Directory of Open Access Journals (Sweden)

    Richard Hrivnák

    2015-10-01

    Full Text Available Open and species-poor stands with a dominance of Alisma lanceolatum were recorded in periodically flooded habitats of the southern part of central Slovakia (Ipeľ River catchment area during the summer of 2013. Phytosociological relevés correspond to the association Eleocharito palustris-Alismatetum lanceolati (alliance Eleocharito palustris-Sagittarion sagittifoliae, which is reported and documented here for the first time from the territory of Slovakia. It inhabits predominantly temporarily flooded depressions on agricultural land – wet arable fields and extensively used pastures. Detrended correspondence analysis showed that the variability in species composition was most significantly influenced by water depth, the presence of arable fields in the contact area and water conductivity. Special attention was paid to a detailed description of the floristic composition, habitat requirements, distribution patterns and nomenclature of the community.

  2. The Flagellar Regulon of Legionella—A Review

    Science.gov (United States)

    Appelt, Sandra; Heuner, Klaus

    2017-01-01

    The Legionella genus comprises more than 60 species. In particular, Legionella pneumophila is known to cause severe illnesses in humans. Legionellaceae are ubiquitous inhabitants of aquatic environments. Some Legionellaceae are motile and their motility is important to move around in habitats. Motility can be considered as a potential virulence factor as already shown for various human pathogens. The genes of the flagellar system, regulator and structural genes, are structured in hierarchical levels described as the flagellar regulon. Their expression is modulated by various environmental factors. For L. pneumophila it was shown that the expression of genes of the flagellar regulon is modulated by the actual growth phase and temperature. Especially, flagellated Legionella are known to express genes during the transmissive phase of growth that are involved in the expression of virulence traits. It has been demonstrated that the alternative sigma-28 factor is part of the link between virulence expression and motility. In the following review, the structure of the flagellar regulon of L. pneumophila is discussed and compared to other flagellar systems of different Legionella species. Recently, it has been described that Legionella micdadei and Legionella fallonii contain a second putative partial flagellar system. Hence, the report will focus on flagellated and non-flagellated Legionella strains, phylogenetic relationships, the role and function of the alternative sigma factor (FliA) and its anti-sigma-28 factor (FlgM). PMID:29104863

  3. Louisiana’s Palustris Experimental Forest: 75 years of research that transformed the South

    Science.gov (United States)

    James P. Barnett; James D. Haywood; Henry A. Pearson

    2011-01-01

    The Palustris Experimental Forest, located on Kisatchie National Forest, has been in existence for 75 years. Research at Palustris has focused on southern pine reforestation technology, including seed production, bareroot nursery production, direct seeding, and planting container seedlings. After establishing pine plantations, researchers developed stand management...

  4. Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

    KAUST Repository

    Permina, Elizaveta A.; Medvedeva, Yulia; Baeck, Pia M.; Hegde, Shubhada R.; Mande, Shekhar C.; Makeev, Vsevolod J.

    2013-01-01

    interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set

  5. Characterization of the YdeO regulon in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Yuki Yamanaka

    Full Text Available Enterobacteria are able to survive under stressful conditions within animals, such as acidic conditions in the stomach, bile salts during transfer to the intestine and anaerobic conditions within the intestine. The glutamate-dependent (GAD system plays a major role in acid resistance in Escherichia coli, and expression of the GAD system is controlled by the regulatory cascade consisting of EvgAS > YdeO > GadE. To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites. All of the seven operons identified by ChIP-chip as being potentially regulated by YdeO were confirmed as being under the direct control of YdeO using RT-qPCR, EMSA, DNaseI-footprinting and reporter assays. Within this YdeO regulon, we identified four stress-response transcription factors, DctR, NhaR, GadE, and GadW and enzymes for anaerobic respiration. Both GadE and GadW are involved in regulation of the GAD system and NhaR is an activator for the sodium/proton antiporter gene. In conjunction with co-transcribed Slp, DctR is involved in protection against metabolic endoproducts under acidic conditions. Taken all together, we suggest that YdeO is a key regulator of E. coli survival in both acidic and anaerobic conditions.

  6. Analysis of the Pho regulon in Streptomyces tsukubaensis.

    Science.gov (United States)

    Ordóñez-Robles, María; Santos-Beneit, Fernando; Rodríguez-García, Antonio; Martín, Juan F

    2017-12-01

    Phosphate regulation of antibiotic biosynthesis in Streptomyces has been studied due to the importance of this genus as a source of secondary metabolites with biological activity. Streptomyces tsukubaensis is the main producer of tacrolimus (or FK506), an immunosuppressant macrolide that generates important benefits for the pharmaceutical market. However, the production of tacrolimus is under a negative control by phosphate and, therefore, is important to know the molecular mechanism of this regulation. Despite its important role, there are no reports about the Pho regulon in S. tsukubaensis. In this work we combined transcriptional studies on the response to phosphate starvation with the search for PHO boxes in the whole genome sequence of S. tsukubaensis. As a result, we identified a set of genes responding to phosphate starvation and containing PHO boxes that include common Pho regulon members but also new species-specific candidates. In addition, we demonstrate for the first time the functional activity of PhoP from S. tsukubaensis through complementation studies in a Streptomyces coelicolor ΔphoP strain. For this purpose, we developed an anhydrotetracycline inducible system that can be applied to the controlled expression of target genes. Copyright © 2017 Elsevier GmbH. All rights reserved.

  7. Isoprenoid hydrocarbons produced by thermal alteration of Nostoc muscorum and Rhodopseudomonas spheroides

    Science.gov (United States)

    Philp, R. P.; Brown, S.; Calvin, M.

    1978-01-01

    The potential of algae and photosynthetic bacteria to serve as precursors of kerogen was studied to determine what factors affect the relative rates of formation of precursor hydrocarbons. Cells of Nostoc muscorum and Rhodopseudomonas spheroides were subjected to thermal alteration (by heating samples in glass tubes sealed under nitrogen) for two, four, and twelve weeks. Both unextracted and extracted cells in the absence and presence of montmorillonite were investigated, and the isoprenoid hydrocarbons produced in these experiments were determined. Phytane and five isomeric phytenes were the main hydrocarbons observed; their relative rates of formation in the different experimental conditions are described. No phytadienes, pristane, or pristenes were detected.

  8. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

    2010-05-26

    RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

  9. Computational analysis of LexA regulons in Cyanobacteria

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2010-09-01

    Full Text Available Abstract Background The transcription factor LexA plays an important role in the SOS response in Escherichia coli and many other bacterial species studied. Although the lexA gene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown that lexA genes in two cyanobacterial genomes Nostoc sp. PCC 7120 and Synechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study. Results Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a

  10. Bradyrhizobium elkanii nod regulon: insights through genomic analysis

    Directory of Open Access Journals (Sweden)

    Luciane M. P. Passaglia

    2017-07-01

    Full Text Available Abstract A successful symbiotic relationship between soybean [Glycine max (L. Merr.] and Bradyrhizobium species requires expression of the bacterial structural nod genes that encode for the synthesis of lipochitooligosaccharide nodulation signal molecules, known as Nod factors (NFs. Bradyrhizobium diazoefficiens USDA 110 possesses a wide nodulation gene repertoire that allows NF assembly and modification, with transcription of the nodYABCSUIJnolMNOnodZ operon depending upon specific activators, i.e., products of regulatory nod genes that are responsive to signaling molecules such as flavonoid compounds exuded by host plant roots. Central to this regulatory circuit of nod gene expression are NodD proteins, members of the LysR-type regulator family. In this study, publicly available Bradyrhizobium elkanii sequenced genomes were compared with the closely related B. diazoefficiens USDA 110 reference genome to determine the similarities between those genomes, especially with regards to the nod operon and nod regulon. Bioinformatics analyses revealed a correlation between functional mechanisms and key elements that play an essential role in the regulation of nod gene expression. These analyses also revealed new genomic features that had not been clearly explored before, some of which were unique for some B. elkanii genomes.

  11. RpfF-dependent regulon of Xylella fastidiosa.

    Science.gov (United States)

    Wang, Nian; Li, Jian-Liang; Lindow, Steven E

    2012-11-01

    ABSTRACT Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF. Although X. fastidiosa rpfF mutants exhibit increased virulence to plants, they are unable to be spread from plant to plant by insect vectors. To gain more insight into the traits that contribute to these processes, a whole-genome Agilent DNA microarray for this species was developed and used to determine the RpfF-dependent regulon by transcriptional profiling. In total, 446 protein coding genes whose expression was significantly different between the wild type and an rpfF mutant (false discovery rate genes were downregulated in the rpfF mutant compared with the wild-type strain whereas 281 genes were over-expressed. RpfF function was required for regulation of 11 regulatory and σ factors, including rpfE, yybA, PD1177, glnB, rpfG, PD0954, PD0199, PD2050, colR, rpoH, and rpoD. In general, RpfF is required for regulation of genes involved in attachment and biofilm formation, enhancing expression of hemagglutinin genes hxfA and hxfB, and suppressing most type IV pili and gum genes. A large number of other RpfF-dependent genes that might contribute to virulence or insect colonization were also identified such as those encoding hemolysin and colicin V, as well as genes with unknown functions.

  12. Reconstruction of the core and extended regulons of global transcription factors.

    Directory of Open Access Journals (Sweden)

    Yann S Dufour

    2010-07-01

    Full Text Available The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across alpha-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual alpha-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 alpha-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator in the alpha-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other

  13. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

    Science.gov (United States)

    Krin, Evelyne; Pierlé, Sebastian Aguilar; Sismeiro, Odile; Jagla, Bernd; Dillies, Marie-Agnès; Varet, Hugo; Irazoki, Oihane; Campoy, Susana; Rouy, Zoé; Cruveiller, Stéphane; Médigue, Claudine; Coppée, Jean-Yves; Mazel, Didier

    2018-05-21

    The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is

  14. Mortalidade em florestas de Pinus palustris causada por tempestade de raios

    Science.gov (United States)

    Kenneth W. Outcalt; Jorge Paladino Corrêa de Lima; Jose Américo de Mello Filho

    2002-01-01

    The importance of lightning as an ignition source for the fire driven Pinus palustris ecosystem is widely recognized. Lightning also impacts this system on a smaller scale by causing individual tree mortality. The objective of this study was to determine the level of mortality due to lightning activity at the Department of Energy's Savannah...

  15. Population Genetic Structure of Cochliobolus miyabeanus on Cultivated Wild Rice (Zizania palustris L.) in Minnesota

    Science.gov (United States)

    Cochliobolus miyabeanus (Bipolaris oryzae) is the causal agent of fungal brown spot (FBS) in wild rice (Zizania palustris L.), an aquatic grass, endemic in Minnesota, Wisconsin, and parts of Canada. Grain yield losses can reach up to 74% when the disease starts at the boot stage and continues until ...

  16. Forest floor depth mediates understory vigor in xeric Pinus palustris ecosystems

    Science.gov (United States)

    J. Kevin Hiers; Joseph J. O' Brien; Rodney E. Will; Robert J. Mitchell

    2007-01-01

    Longleaf pine (Pinus palustris) woodlands and savannas are among the most frequently burned ecosystems in the world with fire return intervals of 1–10 years. This fire regime has maintained high levels of biodiversity in terms of both species richness and endemism. Land use changes have reduced the area of this ecosystem by .95%, and inadequate fire...

  17. Assessing longleaf pine (Pinus palustris) restoration after southern pine beetle kill using a compact experimental design

    Science.gov (United States)

    J.-P. Berrill; C.M. Dagley

    2010-01-01

    A compact experimental design and analysis is presented of longleaf pine (Pinus palustris) survival and growth in a restoration project in the Piedmont region of Georgia, USA. Longleaf pine seedlings were planted after salvage logging and broadcast burning in areas of catastrophic southern pine beetle (Dendroctonus frontalis) attacks on even-aged mixed pine-hardwood...

  18. Nursery response of container Pinus palustris seedlings to nitrogen supply and subsequent effects on outplanting performance

    Science.gov (United States)

    D. Paul Jackson; R. Kasten Dumroese; James P. Barnett

    2012-01-01

    Container longleaf pine (Pinus palustris) seedlings often survive and grow better after outplanting than bareroot seedlings. Because of this, most longleaf pine are now produced in containers. Little is known about nursery fertilization effects on the quality of container longleaf pine seedlings and how that influences outplanting performance. We compared various...

  19. The BvgAS Regulon of Bordetella pertussis

    Directory of Open Access Journals (Sweden)

    Kyung Moon

    2017-10-01

    Full Text Available Nearly all virulence factors in Bordetella pertussis are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated (BvgA~P, and virulence-activated genes (vags are expressed [Bvg(+ mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (vrgs are induced [Bvg(− mode]. Here, we have used transcriptome sequencing (RNA-seq and reverse transcription-quantitative PCR (RT-qPCR to define the BvgAS-dependent regulon of B. pertussis Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as kdpED, multiple other transcriptional regulators, and the extracytoplasmic function (ECF sigma factor brpL, which is needed for type 3 secretion system (T3SS expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using in vitro transcription, we demonstrate that the promoter for brpL is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions −41.5 and −63.5 in bprL. Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the B. pertussis Bvg(− mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(− mode may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new vrgs that can be tested for function.

  20. Definition of the sigma(W) Regulon of Bacillus subtilis in the Absence of Stress

    NARCIS (Netherlands)

    Zweers, Jessica C.; Nicolas, Pierre; Wiegert, Thomas; van Dijl, Jan Maarten; Denham, Emma L.

    2012-01-01

    Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that

  1. The response of Bacillus licheniformis to heat and ethanol stress and the role of the SigB regulon.

    Science.gov (United States)

    Voigt, Birgit; Schroeter, Rebecca; Jürgen, Britta; Albrecht, Dirk; Evers, Stefan; Bongaerts, Johannes; Maurer, Karl-Heinz; Schweder, Thomas; Hecker, Michael

    2013-07-01

    The heat and ethanol stress response of Bacillus licheniformis DSM13 was analyzed at the transcriptional and/or translational level. During heat shock, regulons known to be heat-induced in Bacillus subtilis 168 are upregulated in B. licheniformis, such as the HrcA, SigB, CtsR, and CssRS regulon. Upregulation of the SigY regulon and of genes controlled by other extracytoplasmic function (ECF) sigma factors indicates a cell-wall stress triggered by the heat shock. Furthermore, tryptophan synthesis enzymes were upregulated in heat stressed cells as well as regulons involved in usage of alternative carbon and nitrogen sources. Ethanol stress led to an induction of the SigB, HrcA, and CtsR regulons. As indicated by the upregulation of a SigM-dependent protein, ethanol also triggered a cell wall stress. To characterize the SigB regulon of B. licheniformis, we analyzed the heat stress response of a sigB mutant. It is shown that the B. licheniformis SigB regulon comprises additional genes, some of which do not exist in B. subtilis, such as BLi03885, encoding a hypothetical protein, the Na/solute symporter gene BLi02212, the arginase homolog-encoding gene BLi00198 and mcrA, encoding a protein with endonuclease activity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Assembly and structural organization of pigment-protein complexes in membranes of Rhodopseudomonas sphaeroides

    International Nuclear Information System (INIS)

    Hunter, C.N.; Pennoyer, J.D.; Niederman, R.A.

    1982-01-01

    The B875 and B800-850 light-harvesting pigment-protein complexes of Rhodopseudomonas sphaeroides are characterized further by lithium dodecyl sulfate/polyacrylamide gel electrophoresis at 4 degrees C. Bacteriochlorophyll a was shown in reconstruction studies to remain complexed with its respective binding proteins during this procedure. From distributions in these gels, a quantitative description for the arrangement of the complexes is proposed. Assembly of the complexes was examined in delta-aminolevulinate-requiring mutant H-5 after a shift from high- to low-light intensity. After 10 h of delta-[ 3 H]aminolevulinate labeling, the specific radioactivity of bacteriochlorophyll in a fraction containing putative membrane invaginations reached the maximal level, while that of the mature photosynthetic membrane was at only one-third this level. This suggests that membrane invaginations are sites of preferential bacteriochlorophyll synthesis in which completed pigment-proteins exist transiently. Analysis of the 3 H distribution after electrophoretic separation further suggests that photosynthetic membranes grow mainly by addition of B800-850 to preformed membrane consisting largely of B875 and photochemical reaction centers. These results corroborate the above model for the structural organization of the light-harvesting system and indicate that the structurally and functionally discrete B800-850 pool is not completely assembled until all B875 sites for B800-850 interactions are occupied

  3. Ferrochelatase from Rhodopseudomonas sphaeroides: substrate specificity and role of sulfhydryl and arginyl residues

    International Nuclear Information System (INIS)

    Dailey, H.A.; Fleming, J.E.; Harbin, B.M.

    1986-01-01

    Purified ferrochelatase from the bacterium Rhodopseudomonas sphaeroides was examined to determine the roles of cationic and sulfhydryl residues in substrate binding. Reaction of the enzyme sulfhydryl residues with N-ethylmaleimide or monobromobimane resulted in a rapid loss of enzyme activity. Ferrous iron, but not porphyrin substrate, had a protective effect against inactivation by these two reagents. Quantitation with 3 H-labeled N-ethylmaleimide revealed that inactivation required one to two sulfhydryl groups to be modified. Modification of arginyl residues with either 2,3-butanedione or camphorquinone 10-sulfonate resulted in a loss of ferrochelatase activity. A kinetic analysis of the modified enzyme showed that the K/sub m/ for ferrous iron was not altered but that the K/sub m/ for the prophyrin substrate was increased. These data suggested that arginyl residues may be involved in porphyrin binding, possibly via charge pair interactions between the arginyl residue and the anionic porphyrin propionate side chain. Modification of lysyl residues had no effect on enzyme activity. The authors also examined the ability of bacterial ferrochelatase to use various 2,4-disubstituted porphyrins as substrates. The authors found that 2,4-bis-acetal- and 2,4-disulfonate deuteroporphyrins were effective substrates for the purified bacterial enzyme and that N-methylprotoporphyrin was an effective inhibitor of the enzyme. Data for the ferrochelatase of R. sphaeroides are compared with previously published data for the eucaryotic enzyme

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

    Science.gov (United States)

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

    2013-09-02

    In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome

  5. Cholinesterase inhibitory activity and chemical constituents of Stenochlaena palustris fronds at two different stages of maturity

    Directory of Open Access Journals (Sweden)

    Nelson Jeng-Yeou Chear

    2016-04-01

    Full Text Available Stenochlaena palustris fronds are popular as a vegetable in Southeast Asia. The objectives of this study were to evaluate the anticholinesterase properties and phytochemical profiles of the young and mature fronds of this plant. Both types of fronds were found to have selective inhibitory effect against butyrylcholinesterase compared with acetylcholinesterase. However, different sets of compounds were responsible for their activity. In young fronds, an antibutyrylcholinesterase effect was observed in the hexane extract, which was comprised of a variety of aliphatic hydrocarbons, fatty acids, and phytosterols. In the mature fronds, inhibitory activity was observed in the methanol extract, which contained a series of kaempferol glycosides. Our results provided novel information concerning the ability of S. palustris to inhibit cholinesterase and its phytochemical profile. Further research to investigate the potential use of this plant against Alzheimer's disease is warranted, however, young and mature fronds should be distinguished due to their phytochemical differences.

  6. Molar extinction coefficients and other properties of an improved reaction center preparation from Rhodopseudomonas viridis

    Energy Technology Data Exchange (ETDEWEB)

    Clayton, R.K.; Clayton, B.J.

    1978-01-01

    Reaction centers have been purified from chromatophores of Rhodopseudomonas viridis by treatment with lauryl dimethyl amine oxide followed by hydroxyapatite chromatography and precipitation with ammonium sulfate. The absorption spectrum at low temperature shows bands at 531 and 543 nm, assigned to two molecules of bacteriopheophytin b. The 600 nm band of bacteriochlorophyll b is resolved at low temperature into components at 601 and 606.5 nm. At room temperature the light-induced difference spectrum shows a negative band centered at 615 nm, where the absorption spectrum shows only a week shoulder adjacent to the 600 nm band. The fluorescence spectrum shows a band at 1000 nm and no fluorescence corresponding to the 830 nm absorption band. Two molecules of cytochrome 558 and three of cytochrome 552 accompany each reaction center. The differential extinction coefficient (reduced minus oxidized) of cytochrome 558 nm was estimated as 20 +- 2 mM/sup -1/.cm/sup -1/ through a coupled reaction with equine cytochrome c. The extinction coefficient of reaction centers at 960 nm was determined to be 123 +- 25 mM/sup -1/.cm/sup -1/ by measuring the light-induced bleaching of P-960 and the coupled oxidation of cytochrome 558. The corresponding extinction coefficient at 830 nm is 300 +- 65 mM/sup -1/.cm/sup -1/. The absorbance ratio ..cap alpha../sub 280nm/..cap alpha../sub 830nm/ in our preparations was 2.1, and there was 190 kg protein per mol of reaction centers. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed three major components of apparent molecular weights 31,000, 37,000, and 41,000.

  7. The usage of sulfide and thiosulfate ions by purple non-sulfur bacteria Rhodopseudomonas yavorovii

    Directory of Open Access Journals (Sweden)

    O. V. Tarabas

    2017-07-01

    Full Text Available This article covers the patterns of oxidation of sulfide and thiosulfate ions by bacteria Rhodopseudomonas yavorovii Ya-2016 under different cultivation conditions. In the environments with 1.4–5.6 мМ Na2S2O3, R. yavorovii Ya-2016 bacteria accumulated biomass of 1.4–1.6 g/l, which was higher than biomass (1.2-0.6 g/l accumulated by the bacteria with the same concentrations of Na2S × 9H2O. The efficiency of oxidation of 1.4, 2.8, 5.6 мМ sulfide- and thiosulfate-ions as donors of electrons by the bacteria equaled 97.4, 42.6, 18.7 and 68.8, 28.0, 3.7%, respectively. As a result of bacterial oxidation of 1.4 мМ hydrogen sulfide and sodium thiosulphate in the environment accumulation of 0.13–1.30 мМ sulfate-ions occurs, and the element sulfur becomes an intermediate metabolite in the environment with Na2S×9H2O. R. yavorovii Ya-2016 bacteria are capable of using sulfate-ions as a single source of sulfate at increase in photptrophs. In the environment with 2.5 мМ sulfate-ions concentration the bacteria biomass was 1.4 g/l, the bacteria assimilated 17.7% of sulfates. Because purple non-sulfur bacteria R. yavorovii Ya-2016 are capable of using sulfide-ions as donors of electrons of anoxygenic photosynthesis and using sulfate-ions as a single source of sulfate, they could be successfully used in the technologies of remediating the environment from compounds of sulfur.

  8. The GlnR Regulon in Streptococcus mutans Is Differentially Regulated by GlnR and PmrA.

    Directory of Open Access Journals (Sweden)

    Yi-Ywan M Chen

    Full Text Available GlnR-mediated repression of the GlnR regulon at acidic pH is required for optimal acid tolerance in Streptococcus mutans, the etiologic agent for dental caries. Unlike most streptococci, the GlnR regulon is also regulated by newly identified PmrA (SMUGS5_RS05810 at the transcriptional level in S. mutans GS5. Results from gel mobility shift assays confirmed that both GlnR and PmrA recognized the putative GlnR box in the promoter regions of the GlnR regulon genes. By using a chemostat culture system, we found that PmrA activated the expression of the GlnR regulon at pH 7, and that this activation was enhanced by excess glucose. Deletion of pmrA (strain ΔPmrA reduced the survival rate of S. mutans GS5 at pH 3 moderately, whereas the GlnR mutant (strain ΔGlnR exhibited an acid-sensitive phenotype in the acid killing experiments. Elevated biofilm formation in both ΔGlnR and ΔPmrA mutant strains is likely a result of indirect regulation of the GlnR regulon since GlnR and PmrA regulate the regulon differently. Taken together, it is suggested that activation of the GlnR regulon by PmrA at pH 7 ensures adequate biosynthesis of amino acid precursor, whereas repression by GlnR at acidic pH allows greater ATP generation for acid tolerance. The tight regulation of the GlnR regulon in response to pH provides an advantage for S. mutans to better survive in its primary niche, the oral cavity.

  9. The role of oxalic acid in tolerance to N’N-napthaloylhydroxylamine in Tyromyces palustris

    Science.gov (United States)

    R.A. Arango; C.A. Clausen; Frederick Green

    2006-01-01

    Certain wood decay fungi exhibit tolerance to one or more wood preservatives. Copper tolerance of brown-rot fungi has been studied in our laboratory for the past six years. We have observed some degree of tolerance to N’N-naphthaloylhydroxamine (NHA), a recently patented termite bait, by the brown-rot fungus Tyromyces palustris TYP-6137. In an effort to try and confirm...

  10. Development of antioxidative effect in ice cream with Kalakai (Stenochlaena palustris) water extract

    Science.gov (United States)

    Hadhiwaluyo, Kristania; Rahmawati, Della; Gunawan Puteri, Maria D. P. T.

    2017-11-01

    Kalakai (Stenochlaena. palustris) extract was used to develop the ice cream. The antioxidant activity of the extracts and its stability over process and storage were evaluated through various antioxidant assay including DPPH assay, Folin-Ciocalteau assay and aluminum chloride colorimetric method. In general, the leaves of S. palustris had a significantly higher antioxidant activity (p ice cream without affecting the sensory properties of the ice cream. In addition, the high phenolic and flavonoid content also suggest the more compounds that were capable to act as an antioxidant. The result of the stability test also suggested the ability low temperature storage and processing in maintaining the stability of the antioxidant activity of the extract (p > 0.05) over processing and storage. Thus, this strengthen the feasibility of S. palustris to be used as a potential functional food ingredient that is low cost and easily accessible with an antioxidant activity and safe iron content that is beneficial to increase the quality of food produced including in ice cream.

  11. Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

    KAUST Repository

    Permina, Elizaveta A.

    2013-01-01

    Identification of bacterial modulons from series of gene expression measurements on microarrays is a principal problem, especially relevant for inadequately studied but practically important species. Usage of a priori information on regulatory interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set of genes essential for a regulon is used to control modulon updating. Essential genes for a regulon were selected as a subset of regulon genes highly related by different measures to each other. Using Escherichia coli as a model, we studied how modulon identification depends on the data, including the microarray experiments set, the adopted relevance measure and the regulon itself. We have found that results of modulon identification are highly dependent on all parameters studied and thus the resulting modulon varies substantially depending on the identification procedure. Yet, modulons that were identified correctly displayed higher stability during iterations, which allows developing a procedure for reliable modulon identification in the case of less studied species where the known regulatory interactions are sparse. Copyright © 2013 Taylor & Francis.

  12. Involvement and necessity of the Cpx regulon in the event of aberrant β-barrel outer membrane protein assembly

    Science.gov (United States)

    Gerken, Henri; Leiser, Owen P.; Bennion, Drew; Misra, Rajeev

    2010-01-01

    Summary The Cpx and σE regulons help maintain outer membrane integrity; the Cpx pathway monitors the biogenesis of cell surface structures, such as pili, while the σE pathway monitors the biogenesis of β-barrel outer membrane proteins (OMPs). In this study we revealed the importance of the Cpx regulon in the event of β-barrel OMP mis-assembly, by utilizing mutants expressing either a defective β-barrel OMP assembly machinery (Bam) or assembly defective β-barrel OMPs. Analysis of specific mRNAs showed that ΔcpxR bam double mutants failed to induce degP expression beyond the wild type level, despite activation of the σE pathway. The synthetic conditional lethal phenotype of ΔcpxR in mutant Bam or β-barrel OMP backgrounds was reversed by wild type DegP expressed from a heterologous plasmid promoter. Consistent with the involvement of the Cpx regulon in the event of aberrant β-barrel OMP assembly, the expression of cpxP, the archetypal member of the cpx regulon, was upregulated in defective Bam backgrounds or in cells expressing a single assembly-defective β-barrel OMP species. Together, these results showed that both the Cpx and σE regulons are required to reduce envelope stress caused by aberrant β-barrel OMP assembly, with the Cpx regulon principally contributing by controlling degP expression. PMID:20487295

  13. A model for evolution and regulation of nicotine biosynthesis regulon in tobacco.

    Science.gov (United States)

    Kajikawa, Masataka; Sierro, Nicolas; Hashimoto, Takashi; Shoji, Tsubasa

    2017-06-03

    In tobacco, the defense alkaloid nicotine is produced in roots and accumulates mainly in leaves. Signaling mediated by jasmonates (JAs) induces the formation of nicotine via a series of structural genes that constitute a regulon and are coordinated by JA-responsive transcription factors of the ethylene response factor (ERF) family. Early steps in the pyrrolidine and pyridine biosynthesis pathways likely arose through duplication of the polyamine and nicotinamide adenine dinucleotide (NAD) biosynthetic pathways, respectively, followed by recruitment of duplicated primary metabolic genes into the nicotine biosynthesis regulon. Transcriptional regulation of nicotine biosynthesis by ERF and cooperatively-acting MYC2 transcription factors is implied by the frequency of cognate cis-regulatory elements for these factors in the promoter regions of the downstream structural genes. Indeed, a mutant tobacco with low nicotine content was found to have a large chromosomal deletion in a cluster of closely related ERF genes at the nicotine-controlling NICOTINE2 (NIC2) locus.

  14. The Streptococcus sanguinis Competence Regulon Is Not Required for Infective Endocarditis Virulence in a Rabbit Model

    OpenAIRE

    Callahan, Jill E.; Munro, Cindy L.; Kitten, Todd

    2011-01-01

    Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility i...

  15. Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis.

    Directory of Open Access Journals (Sweden)

    Robert Antonius Gerhardus Huis in 't Veld

    Full Text Available Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. Specific response genes that are regulated by a subset of alternative σ(70-like transcription factors have evolved in order to respond to this changing environment. Recently, we have described the existence of a σ(E regulon including the anti-σ-factor MseR in the obligate human bacterial pathogen Neisseria meningitidis. To unravel the complete σ(E regulon in N. meningitidis, we sequenced total RNA transcriptional content of wild type meningococci and compared it with that of mseR mutant cells (ΔmseR in which σ(E is highly expressed. Eleven coding genes and one non-coding gene were found to be differentially expressed between H44/76 wildtype and H44/76ΔmseR cells. Five of the 6 genes of the σ(E operon, msrA/msrB, and the gene encoding a pepSY-associated TM helix family protein showed enhanced transcription, whilst aniA encoding a nitrite reductase and nspA encoding the vaccine candidate Neisserial surface protein A showed decreased transcription. Analysis of differential expression in IGRs showed enhanced transcription of a non-coding RNA molecule, identifying a σ(E dependent small non-coding RNA. Together this constitutes the first complete exploration of an alternative σ-factor regulon in N. meningitidis. The results direct to a relatively small regulon indicative for a strictly defined response consistent with a relatively stable niche, the human throat, where N. meningitidis resides.

  16. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.

    Science.gov (United States)

    Lemmens, Karen; De Bie, Tijl; Dhollander, Thomas; De Keersmaecker, Sigrid C; Thijs, Inge M; Schoofs, Geert; De Weerdt, Ami; De Moor, Bart; Vanderleyden, Jos; Collado-Vides, Julio; Engelen, Kristof; Marchal, Kathleen

    2009-01-01

    We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.

  17. Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons

    DEFF Research Database (Denmark)

    Larsen, Rasmus; van Hijum, Sacha A. F. T.; Martinussen, Jan

    2008-01-01

    In previous studies, we have shown that direct protein-protein. interaction between the two regulators ArgR and AhrC in Lactococcus lactis is required for arginine-dependent repression of the biosynthetic argC promoter and the activation of the catabolic arcA promoter. Here, we establish the global...... ArgR and AhrC regulons by transcriptome analyses and show that both regulators are dedicated to the control of arginine metabolism in L. lactis....

  18. The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

    Directory of Open Access Journals (Sweden)

    Jill E Callahan

    Full Text Available Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

  19. The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

    Science.gov (United States)

    Callahan, Jill E; Munro, Cindy L; Kitten, Todd

    2011-01-01

    Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

  20. Evidence for a Very Early Intermediate in Bacterial Photosynthesis. A Photon-Echo and Hole-Burning Study of the Primary Donor Band in Rhodopseudomonas Sphaeroides

    NARCIS (Netherlands)

    Meech, S.R.; Hoff, A.J.

    1985-01-01

    Two coherent spectroscopic methods, accumulated photon echo and population bottleneck hole-burning, have been employed in a study of the decay rate of the primary donor (P) of Rhodopseudomonas sphaeroides at 1.5 K. The decay rate is instrument-limited in the photon-echo experiment, implying a

  1. Phosphoenolpyruvate-Dependent Fructose Phosphotransferase System of Rhodopseudomonas sphaeroides : Purification and Physicochemical and Immunochemical Characterization of a Membrane-Associated Enzyme I

    NARCIS (Netherlands)

    Brouwer, Marius; Elferink, Marieke G.L.; Robillard, George T.

    1982-01-01

    The phosphotransferase system (PTS) of the phototrophic bacterium Rhodopseudomonas sphaeroides consists of a component located in the cytoplasmic membrane and a membrane-associated enzyme called “soluble factor” (SF). SF has been partially purified by a combination of hydrophobic interaction and

  2. Muscle senescence in short-lived wild mammals, the soricine shrews Blarina brevicauda and Sorex palustris.

    Science.gov (United States)

    Hindle, Allyson G; Lawler, John M; Campbell, Kevin L; Horning, Markus

    2009-06-01

    Red-toothed (soricine) shrews are consummate predators exhibiting the highest energy turnovers and shortest life spans (ca. 18 months) of any mammal, yet virtually nothing is known regarding their physiological aging. We assessed the emerging pattern of skeletal muscle senescence (contractile/connective tissue components) in sympatric species, the semi-aquatic water shrew (WS), Sorex palustris, and the terrestrial short-tailed shrew (STS), Blarina brevicauda, to determine if muscle aging occurs in wild, short-lived mammals (H(0): shrews do not survive to an age where senescence occurs), and if so, whether these alterations are species-specific. Gracilis muscles were collected from first-year (n=17) and second-year (n=17) field-caught shrews. Consistent with typical mammalian aging, collagen content (% area) increased with age in both species (S. palustris: approximately 50%; B. brevicauda: approximately 60%). Muscle was dominated by stiffer Type I collagen, and the ratio of collagen Type I:Type III more than doubled with age. The area ratio of muscle:collagen decreased with age in both species, but was considerably lower in adult STS, suggesting species-specificity of senescence. Extracellular space was age-elevated in B. brevicauda, but was preserved in S. palustris ( approximately 50 vs. 10% elevation). Though juvenile interspecific comparisons revealed no significance, adult WS myocytes had 68% larger cross-sectional area and occurred at 28% lower fibers/area than those of adult STS. We demonstrate that age-related muscle senescence does occur in wild-caught, short-lived mammals, and we therefore reject this classic aging theory tenet. Our findings moreover illustrate that differential age adjustments in contractile/connective tissue components of muscle occur in the two species of wild-caught shrews. (c) 2009 Wiley-Liss, Inc.

  3. Muscle Senescence in Short-Lived Wild Mammals, the Soricine Shrews Blarina brevicauda and Sorex palustris

    Science.gov (United States)

    HINDLE, ALLYSON G.; LAWLER, JOHN M.; CAMPBELL, KEVIN L.; HORNING, MARKUS

    2015-01-01

    Red-toothed (soricine) shrews are consummate predators exhibiting the highest energy turnovers and shortest life spans (ca. 18 months) of any mammal, yet virtually nothing is known regarding their physiological aging. We assessed the emerging pattern of skeletal muscle senescence (contractile/connective tissue components) in sympatric species, the semi-aquatic water shrew (WS), Sorex palustris, and the terrestrial short-tailed shrew (STS), Blarina brevicauda, to determine if muscle aging occurs in wild, short-lived mammals (H0: shrews do not survive to an age where senescence occurs), and if so, whether these alterations are species-specific. Gracilis muscles were collected from first-year (n = 17) and second-year (n = 17) field-caught shrews. Consistent with typical mammalian aging, collagen content (% area) increased with age in both species (S. palustris: ~50%; B. brevicauda: ~60%). Muscle was dominated by stiffer Type I collagen, and the ratio of collagen Type I:Type III more than doubled with age. The area ratio of muscle:collagen decreased with age in both species, but was considerably lower in adult STS, suggesting species-specificity of senescence. Extracellular space was age-elevated in B. brevicauda, but was preserved in S. palustris (~50 vs. 10% elevation). Though juvenile interspecific comparisons revealed no significance, adult WS myocytes had 68% larger cross-sectional area and occurred at 28% lower fibers/area than those of adult STS. We demonstrate that age-related muscle senescence does occur in wild-caught, short-lived mammals, and we therefore reject this classic aging theory tenet. Our findings moreover illustrate that differential age adjustments in contractile/connective tissue components of muscle occur in the two species of wild-caught shrews. PMID:19296507

  4. Endemic Marsh Mongoose Herpestes palustris (Carnivora: Herpestidae of East Kolkata Wetlands, India: a status report

    Directory of Open Access Journals (Sweden)

    J.K. Mallick

    2009-04-01

    Full Text Available Marsh Mongoose Herpestes palustris is the only extant endemic mammal of the East Kolkata wetlands, which has been declared a RAMSAR site in 2002. Since its first description by the scientists of the Zoological Survey of India, the population of this species has dwindled to an alarming state due to reclamation of the Salt Lake City and Rajarhat expansion, as well as from other anthropogenic causes. Recently, during a field survey only a small population of this endangered mongoose was found in a single location. Immediate conservation measures are required to be taken by the concerned authorities to stop its probable extinction in the near future.

  5. The SOS and RpoS Regulons Contribute to Bacterial Cell Robustness to Genotoxic Stress by Synergistically Regulating DNA Polymerase Pol II.

    Science.gov (United States)

    Dapa, Tanja; Fleurier, Sébastien; Bredeche, Marie-Florence; Matic, Ivan

    2017-07-01

    Mitomycin C (MMC) is a genotoxic agent that induces DNA cross-links, DNA alkylation, and the production of reactive oxygen species (ROS). MMC induces the SOS response and RpoS regulons in Escherichia coli SOS-encoded functions are required for DNA repair, whereas the RpoS regulon is typically induced by metabolic stresses that slow growth. Thus, induction of the RpoS regulon by MMC may be coincidental, because DNA damage slows growth; alternatively, the RpoS regulon may be an adaptive response contributing to cell survival. In this study, we show that the RpoS regulon is primarily induced by MMC-induced ROS production. We also show that RpoS regulon induction is required for the survival of MMC-treated growing cells. The major contributor to RpoS-dependent resistance to MMC treatment is DNA polymerase Pol II, which is encoded by the polB gene belonging to the SOS regulon. The observation that polB gene expression is controlled by the two major stress response regulons that are required to maximize survival and fitness further emphasizes the key role of this DNA polymerase as an important factor in genome stability. Copyright © 2017 by the Genetics Society of America.

  6. Definition of the σ(W) regulon of Bacillus subtilis in the absence of stress.

    Science.gov (United States)

    Zweers, Jessica C; Nicolas, Pierre; Wiegert, Thomas; van Dijl, Jan Maarten; Denham, Emma L

    2012-01-01

    Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σ(W) regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σ(X), σ(Y), and σ(M) regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σ(W)-regulated. Under these conditions, σ(W) exhibits a basal level of activity. Subsequently, we verified the σ(W)-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σ(W) anti-sigma factor RsiW and subsequent activation of the σ(W)-regulon. Taken together, our studies identify 89 genes as being strictly σ(W)-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σ(W)-dependent genes were relatively mild, which implies that σ(W)-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σ(W), but that this membrane protease also exerts other important post-transcriptional regulatory

  7. The potential of Thelypteris palustris and Asparagus sprengeri in phytoremediation of arsenic contamination.

    Science.gov (United States)

    Anderson, LaShunda L; Walsh, Maud; Roy, Amitava; Bianchetti, Christopher M; Merchan, Gregory

    2011-02-01

    The potential of two plants, Thelypteris palustris (marsh fern) and Asparagus sprengeri (asparagus fern), for phytoremediation of arsenic contamination was evaluated. The plants were chosen for this study because of the discovery of the arsenic hyperaccumulating fern, Pteris vittata (Ma et al., 2001) and previous research indicating asparagus fern's ability to tolerate > 1200 ppm soil arsenic. Objectives were (1) to assess if selected plants are arsenic hyperaccumulators; and (2) to assess changes in the species of arsenic upon accumulation in selected plants. Greenhouse hydroponic experiments arsenic treatment levels were established by adding potassium arsenate to solution. All plants were placed into the hydroponic experiments while still potted in their growth media. Marsh fern and Asparagus fern can both accumulate arsenic. Marsh fern bioaccumulation factors (> 10) are in the range of known hyperaccumulator, Pteris vittata Therefore, Thelypteris palustris is may be a good candidate for remediation of arsenic soil contamination levels of arsenic. Total oxidation of As (III) to As (V) does not occur in asparagus fern. The asparagus fern is arsenic tolerant (bioaccumulation factors phytoremediation candidate.

  8. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Query: 350 RNEMTARRIVTADHTILVSGSGYVPKGDLTVDGKDNPEAVSSAMQLVRSALLCNDAQLRP 409 ... RNEMTARRIVTADHT...ILVSGSGYVPKGDLTVDGKDNPEAVSSAMQLVRSALLCNDAQLRP Sbjct: 1 ... RNEMTARRIVTADHTILVSGSGYVPKGDL... ... cation-transporting P-type ATPase [Rhodopseudomonas ... palustris CGA009] ... Length = 203 ...

  9. ORF Alignment: NC_004757 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Rhodopseudomonas palustris CGA009] ... Length = 102 ... Query: 14 ... ...MRDGEFLVSKTTAKGVITYINEPFIRMSGFTEQELVGQAHNIIRHPDMPPEAFADFWNTL 73 ... + DG ++VSKT ... KG +TY NE F++ SGF+EQ

  10. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Rhodopseudomonas palustris CGA009] ... Length = 150 ... Query: 1 ... MRIALFQPDIPQNTGTILRFCACLNVEAHIIEPAGFPTSD...RHFRRSGMDYLDQVSIVRHD 60 ... MRIALFQPDIPQNTGTILRFCACLNVEAHIIEPAGFPTSD...RHFRRSGMDYLDQVSIVRHD Sbjct: 1 ... MRIALFQPDIPQNTGTILRFCACLNVEAHIIEPAGFPTSDRHFRRSGMDYLDQVSIVRHD 60 ... Qu

  11. In silico discovery of the dormancy regulons in a number of Actinobacteria genomes

    Energy Technology Data Exchange (ETDEWEB)

    Gerasimova, Anna; Dubchak, Inna; Arkin, Adam; Gelfand, Mikhail

    2010-11-16

    Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.

  12. Ethylene regulates fast apoplastic acidification and expansin A transcription during submergence-induced petiole elongation in Rumex palustris

    NARCIS (Netherlands)

    Vreeburg, RAM; Benschop, JJ; Peeters, AJM; Colmer, TD; Ammerlaan, AHM; Staal, M; Elzenga, TM; Staals, RHJ; Darley, CP; McQueen-Mason, SJ; Voesenek, LACJ

    The semi-aquatic dicot Rumex palustris responds to complete submergence by enhanced elongation of young petioles. This elongation of petiole cells brings leaf blades above the water surface, thus reinstating gas exchange with the atmosphere and increasing survival in flood-prone environments. We

  13. Modeling silviculture after natural disturbance to sustain biodiversity in the longleaf pine (Pinus palustris) ecosystem : balancing complexity and implementation

    Science.gov (United States)

    Brian J. Palik; Robert J. Mitchell; J. Kevin Hiers

    2002-01-01

    Modeling silviculture after natural disturbance to maintain biodiversity is a popular concept, yet its application remains elusive. We discuss difficulties inherent to this idea, and suggest approaches to facilitate implementation, using longleaf pine (Pinus palustris) as an example. Natural disturbance regimes are spatially and temporally variable. Variability...

  14. Influence of residual basal area on longleaf pine (Pinus palustris Mill.) first year germination and establishment under selection silviculture

    Science.gov (United States)

    Ferhat Kara; Edward F. Loewenstein

    2015-01-01

    Even-aged silvicultural methods have been successfully used to manage longleaf pine (Pinus palustris Mill.) forests for wood production; however, successful use of uneven-aged methods to manage this ecosystem is less well documented. In this study, the effects of varying levels of residual basal area (RBA) (9.2, 13.8, and 18.4 m2...

  15. Phytodesalinization potential of Typha angustifolia, Juncus maritimus, and Eleocharis palustris for removal of de-icing salts from runoff water.

    Science.gov (United States)

    Guesdon, Gaëlle; de Santiago-Martín, Ana; Galvez-Cloutier, Rosa

    2016-10-01

    Typha angustifolia, Juncus maritimus, and Eleocharis palustris were evaluated for de-icing salt removal from runoff water. Plants were exposed to a range of de-icing salt levels (0.2, 0.7, 4, 8, and 13 dS m(-1)) in laboratory-scale subsurface constructed wetlands (CWs) for 2 months under greenhouse conditions. Effluent characteristics, plant height, biomass, and Cl and Na removal rates and uptake were monitored. More water volume was retained in CWs of T. angustifolia (∼60 %) than of J. maritimus and E. palustris (∼37.5 %), which accounted for the electrical conductivity increase in effluents (1.3-1.9-fold). Based on the NaCl removal rate, T. angustifolia showed the greatest phytodesalinization ability (31-60 %) with the highest removal at the lowest salt levels (0.2-0.7 dS m(-1)), followed by J. maritimus (22-36 %) without differences in removal among levels, and E. palustris (3-26 %) presenting a removal rate highly decreased with increasing salt levels. Plant height and biomass were stimulated at low de-icing salt levels, but, at higher levels, T. angustifolia and E. palustris growth was inhibited (tolerance index ∼67 and 10 %, respectively, in the worst cases). Salt amounts in aboveground biomass in g m(-2) differed among levels and ranged as follows: 13.6-29.1 (Cl), 4.2-9.3 (Na; T. angustifolia); 7.0-12.0 (Cl), 2.7-6.4 (Na; J. maritimus); and 0.9-7.6 (Cl), 0.3-1.6 (Na; E. palustris). Chloride and Na translocation decreased with de-icing salt increase in T. angustifolia, while no significant differences were found in J. maritimus, which is interesting for harvesting purposes.

  16. Experiments on accumulation of phosphorus in the plants Myosotis palustris, Glyceria maxima and Nasturtium officinale

    Directory of Open Access Journals (Sweden)

    O. Prokopchuk

    2016-10-01

    Full Text Available The problem of availability of quality water is highly relevant today, so the technologies of prediction and prevention of water pollution and purification are very important. Biological methods of cleaning, in paticular cleaning water by the so-called method of biosorption, have been increasingly used in the last decade. This method means the removal of dangerous substances and improvement of water condition by using aquatic organisms, in particular plants. Therefore, in view of the rich experience of research conducted in the biosorption sphere, we decided to predict the effectiveness of this method by using the cumulative ability of higher water plants to absorb phosphorus compounds. For this purpose, we selected water and plant samples (Glyceria maxima (C. Hartm. Holmb., Nasturtium officinale R. Br., Myosotis palustris (L. L. from the river Seret (Ternopil, Ukraine. The plants were placed into sterilized glass jars filled with 3 liters of water from the river Seret (control samples and still tap water with addition of sodium phosphate with phosphorus concentration of 3.5 mg/dm³ (research sample, which were cultured in laboratory conditions for four months. We determined the content of phosphates, permanganate and dichromate oxidation in the water and the total content of phosphorus in the plants. We traced the dynamic of organic substances and the content of phosphates in the water, the accumulation of phosphorus in plants and the rate of accumulation of phosphorus in the plants and in the water. We calculated correlation coefficients to detect the dependence between phosphorus indicators in the aquatic plants and the concentration of phosphate ions in the water. We found that M. palustris had the greatest capacity to accumulate phosphorus and the highest rate of phosphorus accumulation from water, which allows us to consider it the most effective aquatic plant for absorption of elements and decreasing water pollution. We also established

  17. Current status of Marsh Crocodiles Crocodylus palustris (Reptilia: Crocodylidae in Vishwamitri River, Vadodara City, Gujarat, India

    Directory of Open Access Journals (Sweden)

    R. Vyas

    2012-11-01

    Full Text Available Data presented here is based on a three year study (2008-2010 on a population of Mugger Crocodylus palustris inhabiting Vishwamitri River near Vadodara City, Gujarat State, India. In total, 155 Muggers were counted in the 25km river stretch during 2010. In all, 40 burrows were observed along the river bank, and the same were clumped in certain sections of the river. Muggers fed eight species of birds, and domestic livestock in addition to scavenging. Eight instances of human-crocodile conflicts were observed including four human causalities. A total 90 Muggers were rescued from the urban areas and the same were relocated elsewhere in the river system. Various types of threats to Mugger were also noticed including habitat loss, alteration and soil erosion and mortality due to rail traffic. The present study suggests further research to propose strategies to conserve this population.

  18. Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica.

    Science.gov (United States)

    Jacquemyn, Hans; Waud, Michael; Lievens, Bart; Brys, Rein

    2016-07-01

    In orchid species that have populations occurring in strongly contrasting habitats, mycorrhizal divergence and other habitat-specific adaptations may lead to the formation of reproductively isolated taxa and ultimately to species formation. However, little is known about the mycorrhizal communities associated with recently diverged sister taxa that occupy different habitats. In this study, 454 amplicon pyrosequencing was used to investigate mycorrhizal communities associating with Epipactis helleborine in its typical forest habitat and with its presumed sister species E. neerlandica that almost exclusively occurs in coastal dune habitats. Samples of the phylogenetically more distant E. palustris, which co-occurred with E. neerlandica, were also included to investigate the role of habitat-specific conditions on mycorrhizal communities. A total of 105 operational taxonomic units (OTUs) of putative orchid mycorrhizal fungi were observed in the three studied species. The majority of these fungi were endophytic fungi of Helotiales and ectomycorrhizal fungi belonging to Thelephoraceae, Sebacinaceae and Inocybaceae. In addition, a large number of other ectomycorrhizal taxa were detected, including Cortinarius, Cenococcum, Tuber, Geopora, Wilcoxina, Meliniomyces, Hebeloma, Tricholoma, Russula and Peziza Mycorrhizal communities differed significantly between the three species, but differences were most pronounced between the forest species (E. helleborine) and the two dune slack species (E. neerlandica and E. palustris). The results clearly showed that recently diverged orchid species that occupy different habitats were characterized by significantly different mycorrhizal communities and call for more detailed experiments that aim at elucidating the contribution of habitat-specific adaptations in general and mycorrhizal divergence in particular to the process of speciation in orchids. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany

  19. Characterization of the SOS meta-regulon in the human gut microbiome.

    Science.gov (United States)

    Cornish, Joseph P; Sanchez-Alberola, Neus; O'Neill, Patrick K; O'Keefe, Ronald; Gheba, Jameel; Erill, Ivan

    2014-05-01

    Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.

  20. Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

    Directory of Open Access Journals (Sweden)

    Núñez Cinthia

    2009-07-01

    Full Text Available Abstract Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III, which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT. Conclusion The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of

  1. Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

    Directory of Open Access Journals (Sweden)

    da Silva Neto José F

    2010-08-01

    Full Text Available Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase, was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

  2. Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Engelmann Susanne

    2009-05-01

    Full Text Available Abstract Background The catabolite control protein A (CcpA is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram-positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in Staphylococcus aureus, focussing on short-time effects of glucose under stable pH conditions. Results The addition of glucose to exponentially growing S. aureus increased the expression of genes and enzymes of the glycolytic pathway, while genes and proteins of the tricarboxylic acid (TCA cycle, required for the complete oxidation of glucose, were repressed via CcpA. Phosphotransacetylase and acetate kinase, converting acetyl-CoA to acetate with a concomitant substrate-level phosphorylation, were neither regulated by glucose nor by CcpA. CcpA directly repressed genes involved in utilization of amino acids as secondary carbon sources. Interestingly, the expression of a larger number of genes was found to be affected by ccpA inactivation in the absence of glucose than after glucose addition, suggesting that glucose-independent effects due to CcpA may have a particular impact in S. aureus. In the presence of glucose, CcpA was found to regulate the expression of genes involved in metabolism, but also that of genes coding for virulence determinants. Conclusion This study describes the CcpA regulon of exponentially growing S. aureus cells. As in other bacteria, CcpA of S. aureus seems to control a large regulon that comprises metabolic genes as well as virulence determinants that are affected in their expression by CcpA in a glucose-dependent as well as -independent manner.

  3. R-prime site-directed transposon Tn7 mutagenesis of the photosynthetic apparatus in Rhodopseudomonas capsulata

    Energy Technology Data Exchange (ETDEWEB)

    Youvan, D C [Univ. of California, Berkeley; Elder, J T; Sandlin, D E; Zsebo, K; Alder, D P; Panopoulos, N J; Marrs, B L; Hearst, J E

    1982-01-01

    Site-directed mutagenesis of the photosynthetic apparatus (PSA) genes in Rhodopseudomonas capsulata is presented utilizing a transposon Tn7 mutagenized R-prime. The R-prime, pRPS404, bears most of the genes necessary for the differentiation of the photosynthetic apparatus. Mutagenesis of the R-prime with Tn7 in Escherichia coli, conjugation into R. capsulata, and homologous recombination with the wild-type alleles efficiently generates photosynthetic apparatus lesions. Wild-type alleles are lost spontaneously and the Tn7-induced lesions are revealed by subsequent intramolecular recombination between IS21 insertion elements that bracket the prime sequences in direct repeat. The molecular nature of the intermediates involved in the transposition, recombination and deletion have been investigated by Southern hybridization analysis. The spontaneous loss of wild-type alleles after homologous recombination with the chromosome may be of general use to other prokaryotic site-directed transposon mutagenesis schemes. The IS21-mediated deletion of the prime DNA is dependent on the RecA protein in E. coli, generating the parental R-factor bearing one IS21 element. A genetic-physical map exists for a portion of the prime photosynthetic apparatus DNA. When Tn7 is inserted into a bacteriochlorophyll gene in the R-prime and then crossed into R. capsulata, mutants are produced that accumulate a bacteriochlorophyll precursor, which is in excellent agreement with the existing genetic-physical map. This corroborates the mutagenesis scheme.

  4. Traffic-emitted metal status and uptake by Carex meyeriana Kunth and Thelypteris palustris var. pubescens Fernald growing in roadside turfy swamp in the Changbai Mountain area, China.

    Science.gov (United States)

    Wang, Hong; Nie, Lei; Xu, Yan; Li, Miao; Lv, Yan

    2018-04-26

    Six traffic-emitted metals (Cr, Zn, Cu, Cd, Pb, and Ni) were determined in soil and plants for below- and aboveground parts along different distances from highway to evaluate their behavior and uptake by Carex meyeriana Kunth and Thelypteris palustris var. pubescens Fernald growing in turfy swamps. The results indicated that the different plant tissues showed significantly different levels of metal content. Nonlinear regression analysis indicated that metal contents leveled off at constant values before they decreased as the distance from the roadside increased. The high R 2 values of the regression model indicated good fit of the exponential function applied to depict the distribution pattern of the metal elements. It was deduced that Cr, Cu, and Cd in Thelypteris palustris var. pubescens Fernald were mainly derived from the soil; Carex meyeriana Kunth and Thelypteris palustris var. pubescens Fernald absorbed Pb mainly through the stomata from atmospheric depositions; Cr, Cu, and Cd in Carex meyeriana Kunth and Zn in Thelypteris palustris var. pubescens Fernald were mainly affected by soil and atmospheric depositions. After excluding the effects of traffic, only the bioaccumulation factor of Cd (1.34) in Carex meyeriana Kunth and the translocation factor of Zn (1.13) in Thelypteris palustris var. pubescens Fernald were greater than 1, suggesting that Carex meyeriana Kunth could be a good candidate for assimilating Cd from soils and Thelypteris palustris var. pubescens Fernald could be suitable for the phytoextraction of Zn.

  5. A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana

    OpenAIRE

    Carvallo, Marcela A.; Pino, María-Teresa; Jeknić, Zoran; Zou, Cheng; Doherty, Colleen J.; Shiu, Shin-Han; Chen, Tony H. H.; Thomashow, Michael F.

    2011-01-01

    Solanum commersonii and Solanum tuberosum are closely related plant species that differ in their abilities to cold acclimate; whereas S. commersonii increases in freezing tolerance in response to low temperature, S. tuberosum does not. In Arabidopsis thaliana, cold-regulated genes have been shown to contribute to freezing tolerance, including those that comprise the CBF regulon, genes that are controlled by the CBF transcription factors. The low temperature transcriptomes and CBF regulons of ...

  6. Correlation between oxalic acid production and tolerance of Tyromyces palustris strain TYP-6137 to N',N-naphthaloylhydroxamine

    Science.gov (United States)

    Rachel A. Arango; Patricia K. Lebow; Frederick III Green

    2009-01-01

    Eleven strains of T. palustris were evaluated for mass loss and production of phosphate buffer soluble oxalic acid on pine wood blocks treated with 0.5% N’,N-naphthaloylhydroxamine (NHA) in a soil-block test. After 12 weeks higher percentage mass loss was observed in control groups for 10 strains, while TYP-6137 was shown to be tolerant with no difference between the...

  7. Toxicity of sulfide to early life stages of wild rice (Zizania palustris).

    Science.gov (United States)

    Fort, Douglas J; Todhunter, Kevin; Fort, Troy D; Mathis, Michael B; Walker, Rachel; Hansel, Mike; Hall, Scott; Richards, Robin; Anderson, Kurt

    2017-08-01

    The sensitivity of wild rice (Zizania palustris) to sulfide is not well understood. Because sulfate in surface waters is reduced to sulfide by anaerobic bacteria in sediments and historical information indicated that 10 mg/L sulfate in Minnesota (USA) surface water reduced Z. palustris abundance, the Minnesota Pollution Control Agency established 10 mg/L sulfate as a water quality criterion in 1973. A 21-d daily-renewal hydroponic study was conducted to evaluate sulfide toxicity to wild rice and the potential mitigation of sulfide toxicity by iron (Fe). The hydroponic design used hypoxic test media for seed and root exposure and aerobic headspace for the vegetative portion of the plant. Test concentrations were 0.3, 1.6, 3.1, 7.8, and 12.5 mg/L sulfide in test media with 0.8, 2.8, and 10.8 mg/L total Fe used to evaluate the impact of iron on sulfide toxicity. Visual assessments (i.e., no plants harvested) of seed activation, mesocotyl emergence, seedling survival, and phytoxicity were conducted 10 d after dark-phase exposure. Each treatment was also evaluated for time to 30% emergence (ET30), total plant biomass, root and shoot lengths, and signs of phytotoxicity at study conclusion (21 d). The results indicate that exposure of developing wild rice to sulfide at ≥3.1 mg sulfide/L in the presence of 0.8 mg/L Fe reduced mesocotyl emergence. Sulfide toxicity was mitigated by the addition of Fe at 2.8 mg/L and 10.8 mg/L relative to the control value of 0.8 mg Fe/L, demonstrating the importance of iron in mitigating sulfide toxicity to wild rice. Ultimately, determination of site-specific sulfate criteria taking into account factors that alter toxicity, including sediment Fe and organic carbon, are necessary. Environ Toxicol Chem 2017;36:2217-2226. © 2017 SETAC. © 2017 SETAC.

  8. Hydrogen gas production by fermentation from various organic wastewater using Clostridium butyricum NCIB 9576 and Rhodopseudomonas sphaeroides E15-1

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Young Sue; Kim, Hyun Kyung; Rye, Hye Yeon; Lee, In Gu; Kim, Mi Sun [Biomass Research Team, Korea Institute of Energy Research, Taejeon (Korea)

    2000-03-01

    Anaerobic fermentation using Clostidium butyricum NCIB 9576, and phto-fermentation using Rhodopseudomonas sphaeroides E15-1 were studied for the production of hydrogen from Makkoli, fruits (orange and apple, watermelon and melon) and Tofu wastewaters. From the Makkoli wastewater, which contained 0.94 g/liter sugars and 2.74 g/liter solubel starch, approximately 49 mM H{sub 2}/liter wastewater was produced during the initial 18h of the anaerobic fermentation with pH control between 6.5-7.0. Several organic acids such as butyric acid, acetic acid, propionic acid, lactic acid and ethanol were also produced. From watermelon and melon wastewater, which contained 43 g/liter sugars, generated about approximately 71 mM H{sub 2}/liter wastewater was produced during the initial 24h of the anaerobic fermentation. Tofu wastewater, pH 6.5, containing 12.6 g/liter soluble starch and 0.74 g/liter sugars, generated about 30mM H{sub 2}/liter wastewater, along with some organic acids, during the initial 24 h of anaerobic fermentation. Makkoli and Tofu wastewaters as substrates for the photo-fermentation by Rhodopseudomonas sphaeroides E15-1 produced approximately 37.9 and 22.2 {mu}M H{sub 2}/ml wastewaters, respectively for 9 days of incubation under the average of 9,000010,000 lux illumination at the surface of reactor using tungsten halogen lamps. Orange and apple wastewater, which contained 93.4 g/l produced approximately 13.1 {mu}M H{sub 2}/ml wastewater only for 2 days of photo-fermentation and the growth of Rhodopseudomonas spnaeroides E15-1 and hydrogen production were stopped. 22 refs, 4 figs., 2 tabs.

  9. Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon.

    Science.gov (United States)

    Kelley, William L

    2006-12-01

    The SOS response that responds to DNA damage induces many genes that are under LexA repression. A detailed examination of LexA regulons using genome-wide techniques has recently been undertaken in both Escherichia coli and Bacillus subtilis. These extensive and elegant studies have now charted the extent of the LexA regulons, uncovered many new genes, and exposed a limited overlap in the LexA regulon between the two bacteria. As more bacterial genomes are analysed, more curiosities in LexA regulons arise. Several notable examples include the discovery of a LexA-like protein, HdiR, in Lactococcus lactis, organisms with two lexA genes, and small DNA damage-inducible cassettes under LexA control. In the cyanobacterium Synechocystis, genetic and microarray studies demonstrated that a LexA paralogue exerts control over an entirely different set of carbon-controlled genes and is crucial to cells facing carbon starvation. An examination of SOS induction evoked by common therapeutic drugs has shed new light on unsuspected consequences of drug exposure. Certain antibiotics, most notably fluoroquinolones such as ciprofloxacin, can induce an SOS response and can modulate the spread of virulence factors and drug resistance. SOS induction by beta-lactams in E. coli triggers a novel form of antibiotic defence that involves cell wall stress and signal transduction by the DpiAB two-component system. In this review, we provide an overview of these new directions in SOS and LexA research with emphasis on a few themes: identification of genes under LexA control, the identification of new endogenous triggers, and antibiotic-induced SOS response and its consequences.

  10. Synchrotron small-angle x-ray scattering investigation on integral membrane protein light-harvesting complex LH2 from photosynthetic bacterium rhodopseudomonas acidophila

    International Nuclear Information System (INIS)

    Du Luchao; Weng Yuxiang; Hong Xinguo; Xian Dingchang; Kobayashi Katsumi

    2006-01-01

    Structures of membrane protein in solution are different from that in crystal phase. We present the primary results of small angle x-ray scattering (SAXS) resolved topological structures of a light harvesting antenna membrane protein complex LH2 from photosynthetic bacteria Rhodopseudomonas acidophila in detergent solution for the first time. Our results show that the elliptical shape of the LH2 complex in solution clearly deviates from its circular structure in crystal phase determined by x-ray diffraction. This result provides an insight into the structure and function interplay in LH2. (authors)

  11. The components of the unique Zur regulon of Cupriavidus metallidurans mediate cytoplasmic zinc handling.

    Science.gov (United States)

    Bütof, Lucy; Schmidt-Vogler, Christopher; Herzberg, Martin; Große, Cornelia; Nies, Dietrich H

    2017-08-14

    Zinc is an essential trace element and at the same time it is toxic at high concentrations. In the beta-proteobacterium Cupriavidus metallidurans the highly efficient removal of surplus zinc from the periplasm is responsible for its outstanding metal resistance. Rather than having a typical Zur-dependent, high-affinity ATP-binding cassette transporter of the ABC protein superfamily for zinc uptake at low concentrations, C. metallidurans instead has the secondary zinc importer ZupT of the ZRT/IRT (ZIP) family. It is important to understand, therefore, how this zinc-resistant bacterium copes when it is exposed to low zinc concentrations. Members of the Zur regulon in C. metallidurans were identified by comparing the transcriptomes of a Δ zur mutant and its parent strain. The consensus sequence of the Zur-binding box was derived for the zupTp promoter-regulatory region using a truncation assay. The motif was used to predict possible Zur-boxes upstream of Zur regulon members. Binding of Zur to these boxes was confirmed. Two Zur-boxes upstream of the cobW 1 gene, encoding a putative zinc chaperone, proved to be required for complete repression of cobW 1 and its downstream genes in cells cultivated in mineral salts medium. A Zur box upstream of each of zur-cobW 2 , cobW 3 and zupT permitted low-expression level of these genes plus their up-regulation under zinc starvation conditions. This demonstrates a compartmentalization of zinc homeostasis in C. metallidurans with the periplasm being responsible for removal of surplus zinc and cytoplasmic components for management of zinc as an essential co-factor, with both compartments connected by ZupT. Importance Elucidating zinc homeostasis is necessary to understand both host-pathogen interactions and performance of free-living bacteria in their natural environment. Escherichia coli acquires zinc under low zinc concentrations by the Zur-controlled ZnuABC importer of the ABC superfamily, and this was also the paradigm for other

  12. The Rcs regulon in Proteus mirabilis: implications for motility, biofilm formation, and virulence.

    Science.gov (United States)

    Howery, Kristen E; Clemmer, Katy M; Rather, Philip N

    2016-11-01

    The overall role of the Rcs phosphorelay in Proteus mirabilis is largely unknown. Previous work had demonstrated that the Rcs phosphorelay represses the flhDC operon and activates the minCDE cell division inhibition system. To identify additional cellular functions regulated by the Rcs phosphorelay, an analysis of RNA-seq data was undertaken. In this report, the results of the RNA-sequencing are discussed with an emphasis on the predicted roles of the Rcs phosphorelay in swarmer cell differentiation, motility, biofilm formation, and virulence. RcsB is shown to activate genes important for differentiation and fimbriae formation, while repressing the expression of genes important for motility and virulence. Additionally, to follow up on the RNA-Seq data, we demonstrate that an rcsB mutant is deficient in its ability to form biofilm and exhibits enhanced virulence in a Galleria mellonella waxworm model. Overall, these results indicate the Rcs regulon in P. mirabilis extends beyond flagellar genes to include those involved in biofilm formation and virulence. Furthermore, the information presented in this study may provide clues to additional roles of the Rcs phosphorelay in other members of the Enterobacteriaceae.

  13. Optimization of Photosynthetic Productivity in Contrasting Environments by Regulons Controlling Plant Form and Function

    Directory of Open Access Journals (Sweden)

    Barbara Demmig-Adams

    2018-03-01

    Full Text Available We review the role of a family of transcription factors and their regulons in maintaining high photosynthetic performance across a range of challenging environments with a focus on extreme temperatures and water availability. Specifically, these transcription factors include CBFs (C-repeat binding factors and DREBs (dehydration-responsive element-binding, with CBF/DREB1 primarily orchestrating cold adaptation and other DREBs serving in heat, drought, and salinity adaptation. The central role of these modulators in plant performance under challenging environments is based on (i interweaving of these regulators with other key signaling networks (plant hormones and redox signals as well as (ii their function in integrating responses across the whole plant, from light-harvesting and sugar-production in the leaf to foliar sugar export and water import and on to the plant’s sugar-consuming sinks (growth, storage, and reproduction. The example of Arabidopsis thaliana ecotypes from geographic origins with contrasting climates is used to describe the links between natural genetic variation in CBF transcription factors and the differential acclimation of plant anatomical and functional features needed to support superior photosynthetic performance in contrasting environments. Emphasis is placed on considering different temperature environments (hot versus cold and light environments (limiting versus high light, on trade-offs between adaptations to contrasting environments, and on plant lines minimizing such trade-offs.

  14. Aptitude of Lymnaea palustris and L. stagnalis to Fasciola hepatica larval development through the infection of several successive generations of 4-mm-high snails.

    Science.gov (United States)

    Vignoles, P; Rondelaud, D; Dreyfuss, G

    2016-06-01

    Bimiracidial infections of Lymnaea palustris and Lymnaea stagnalis (shell height at exposure, 4 mm) with Fasciola hepatica were carried out during six successive snail generations to determine if prevalence and intensity of snail infection increased over time through descendants issuing from eggs laid by parents already exposed to this digenean. Controls were constituted by a French population of Galba truncatula (a single generation) infected according to the same protocol. In a first experiment performed with the F1 to F5 generations of L. palustris, the prevalence and intensity of F. hepatica infection in snails progressively increased. Immature rediae and a few cercariae-containing rediae of the digenean were observed in L. stagnalis from the F3 generation, but no free cercaria was noted in the bodies of this lymnaeid from the F4 to F6 generations. In another experiment carried out with the F6 generation of L. palustris, the prevalence of F. hepatica infection and the number of shed cercariae were significantly lower in L. palustris than in G. truncatula. This mode of snail infection suggests an explanation for cases of human fasciolosis occurring in central France after the collection of wild watercress from beds where L. palustris was the sole lymnaeid.

  15. Linear-dichroism measurements on the LH2 antenna complex of Rhodopseudomonas Acidophila strain 10050 show that the transition dipole moment of the Carotenoid Rhodopin Glucoside us nit collinair with the long molecular axis

    NARCIS (Netherlands)

    Georgakopoulou, S.; Gogdell, R.J.; Grondelle, van R.; Amerongen, van H.

    2003-01-01

    We have applied linear-dichroism experiments to determine the orientation of the transition dipole moment, corresponding to the main absorption band of the carotenoid, rhodopin glucoside, in the light-harvesting complex LH2 from Rhodopseudomonas acidophila strain 10050. The crystal structure of this

  16. Gnotobiotic cultures of rice plants up to ear stage in the absence of combined nitrogen source but in the presence of free living nitrogen fixing bacteria Azotobacter vinelandii and Rhodopseudomonas capsulata

    International Nuclear Information System (INIS)

    Maudinas, B.; Chemardin, M.; Yovanovitch, E.; Gadal, P.

    1981-01-01

    An all glass tight growth chamber, entirely sterilizable, has been constructed to carry out axenic and gnotobiotic cultures of rice plants (Oryza sativa L.). When grown in liquid medium and in the absence of combined nitrogen but in the presence of the diazotrophs Azotobacter vinelandii and Rhodopseudomonas capsulata, rice plants exhibited a complete biological cycle from germination up to ear stage, during a period of time similiar to the one encountered in French paddy soil of Camargue. In one experiment, mannitol was given to rice culture medium together with Azotobacter vinelandii and Rhodopseudomonas capsulata. In another experiment, mannitol was not given together with Rhodopseudomonas, and still positive nitrogen gain was obtained, although it was less than culture with mannitol. When 15 N labeled cells of Rhodopseudomonas were added in rice culture medium, 15 N was partly transferred to rice plant. Among the nitrogen substances excreted from the bacteria in the rhizosphere medium, large organic molecules were shown to be the most abundant in our experimental conditions. Moreover, the concentration of free ammonia or aminoacids present in the rice rhizosphere were always compatible with a bacterial nitrogenase activity. (orig.)

  17. Hydraulic architecture and tracheid allometry in mature Pinus palustris and Pinus elliottii trees.

    Science.gov (United States)

    Gonzalez-Benecke, C A; Martin, T A; Peter, G F

    2010-03-01

    Pinus palustris Mill. (longleaf pine, LL) and Pinus elliottii Engelm. var. elliottii (slash pine, SL) frequently co-occur in lower coastal plain flatwoods of the USA, with LL typically inhabiting slightly higher and better-drained microsites than SL. The hydraulic architecture and tracheid dimensions of roots, trunk and branches of mature LL and SL trees were compared to understand their role in species microsite occupation. Root xylem had higher sapwood-specific hydraulic conductivity (k(s)) and was less resistant to cavitation compared with branches and trunk sapwood. Root k(s) of LL was significantly higher than SL, whereas branch and trunk k(s) did not differ between species. No differences in vulnerability to cavitation were observed in any of the organs between species. Across all organs, there was a significant but weak trade-off between water conduction efficiency and safety. Tracheid hydraulic diameter (D(h)) was strongly correlated with k(s) across all organs, explaining >73% of the variation in k(s). In contrast, tracheid length (L(t)) explained only 2.4% of the variability. Nevertheless, for trunk xylem, k(s) was 39.5% higher at 20 m compared with 1.8 m; this increase in k(s) was uncorrelated with D(h) and cell-wall thickness but was strongly correlated with the difference in L(t). Tracheid allometry markedly changed between sapwood of roots, trunks and branches, possibly reflecting different mechanical constraints. Even though vulnerability to cavitation was not different for sapwood of roots, branches or the trunks of LL and SL, higher sapwood to leaf area ratio and higher maximum sapwood-specific hydraulic conductivity in roots of LL are functional traits that may provide LL with a competitive advantage on drier soil microsites.

  18. A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli.

    Science.gov (United States)

    Zhu, Y; Lin, E C

    1988-05-01

    L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose.

  19. Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus

    Directory of Open Access Journals (Sweden)

    Du Zongmin

    2008-03-01

    Full Text Available Abstract Background The transcription regulator PhoP has been shown to be important for Y. pestis survival in macrophages and under various in vitro stresses. However, the mechanism by which PhoP promotes bacterial intracellular survival is not fully understood. Our previous microarray analysis suggested that PhoP governed a wide set of cellular pathways in Y. pestis. A series of biochemical experiments were done herein to study members of the PhoP regulon of Y. pestis biovar Microtus. Results By using gel mobility shift assay and quantitative RT-PCR, a total of 30 putative transcription units were characterized as direct PhoP targets. The primer extension assay was further used to determine the transcription start sites of 18 PhoP-dependent promoters and to localize the -10 and -35 elements. The DNase I footprinting was used to identify the PhoP-binding sites within 17 PhoP-dependent promoters, enabling the identification of PhoP box and matrix that both represented the conserved signals for PhoP recognition in Y. pestis. Data presented here providing a good basis for modeling PhoP-promoter DNA interactions that is crucial to the PhoP-mediated transcriptional regulation. Conclusion The proven direct PhoP targets include nine genes encoding regulators and 21 genes or operons with functions of detoxification, protection against DNA damages, resistance to antimicrobial peptides, and adaptation to magnesium limitation. We can presume that PhoP is a global regulator that controls a complex regulatory cascade by a mechanism of not only directly controlling the expression of specific genes, but also indirectly regulating various cellular pathways by acting on a set of dedicated regulators. These results help us gain insights into the PhoP-dependent mechanisms by which Y. pestis survives the antibacterial strategies employed by host macrophages.

  20. Transcriptome analysis of the Dickeya dadantii PecS regulon during the early stages of interaction with Arabidopsis thaliana.

    Science.gov (United States)

    Pédron, Jacques; Chapelle, Emilie; Alunni, Benoît; Van Gijsegem, Frédérique

    2018-03-01

    PecS is one of the major global regulators controlling the virulence of Dickeya dadantii, a broad-host-range phytopathogenic bacterium causing soft rot on several plant families. To define the PecS regulon during plant colonization, we analysed the global transcriptome profiles in wild-type and pecS mutant strains during the early colonization of the leaf surfaces and in leaf tissue just before the onset of symptoms, and found that the PecS regulon consists of more than 600 genes. About one-half of these genes are down-regulated in the pecS mutant; therefore, PecS has both positive and negative regulatory roles that may be direct or indirect. Indeed, PecS also controls the regulation of a few dozen regulatory genes, demonstrating that this global regulator is at or near the top of a major regulatory cascade governing adaptation to growth in planta. Notably, PecS acts mainly at the very beginning of infection, not only to prevent virulence gene induction, but also playing an active role in the adaptation of the bacterium to the epiphytic habitat. Comparison of the patterns of gene expression inside leaf tissues and during early colonization of leaf surfaces in the wild-type bacterium revealed 637 genes modulated between these two environments. More than 40% of these modulated genes are part of the PecS regulon, emphasizing the prominent role of PecS during plant colonization. © 2017 BSPP AND JOHN WILEY & SONS LTD.

  1. Ecosystem engineering potential of the gastropod Terebralia palustris (Linnaeus, 1767) in mangrove wastewater wetlands - A controlled mesocosm experiment

    Energy Technology Data Exchange (ETDEWEB)

    Penha-Lopes, Gil, E-mail: gil.penha-lopes@biology-research.co [Centro de Oceanografia - Laboratorio Maritimo da Guia, Departamento de Biologia Animal, Faculdade de Ciencias da Universidade de Lisboa, Avenida Na, Senhora do Cabo 939, 2750-374 Cascais (Portugal); Department of Analytical and Environmental Chemistry, Vrije Universiteit Brussels, Brussels (Belgium); Bartolini, Fabrizio [Dipartimento di Biologia Evoluzionistica, Universita degli Studi di Firenze, via Romana 17, I-50125 Firenze (Italy); Limbu, Samwel [University of Dar es Salaam, Department of Aquatic Sciences and Fisheries, P.O. Box 35064, Dar es Salaam (Tanzania, United Republic of); Cannicci, Stefano [Dipartimento di Biologia Evoluzionistica, Universita degli Studi di Firenze, via Romana 17, I-50125 Firenze (Italy); Mgaya, Yunus [University of Dar es Salaam, Department of Aquatic Sciences and Fisheries, P.O. Box 35064, Dar es Salaam (Tanzania, United Republic of); Kristensen, Erik [Institute of Biology, University of Southern Denmark, DK-5230 Odense M (Denmark); Paula, Jose [Centro de Oceanografia - Laboratorio Maritimo da Guia, Departamento de Biologia Animal, Faculdade de Ciencias da Universidade de Lisboa, Avenida Na, Senhora do Cabo 939, 2750-374 Cascais (Portugal)

    2010-01-15

    The effect of different sewage concentrations (0, 20, 60 and 100%), vegetation (Bare, Avicennia marina or Rhizophora mucronata) and immersion periods (immersion/emersion period of 12/12 h or 3/3 days just for 100%) conditions were studied for 6 months on survival and growth rates of Terebralia palustris (Linnaeus, 1767). Gastropods' activity and ecosystem engineering preformed at bare and A. marina planted cells and 3 sewage conditions (0, 20 and 60%) were determined. Survival rates were higher than 70% in all treatments. Growth rate decreased significantly with increasing sewage concentrations (mainly at unplanted conditions) and longer immersion periods. A complete shift (from immersion to emersion periods) and a significant decrease in mobility and consequently its engineer potential, due to sewage contamination, lead to a 3-4 fold decrease in the amount of sediment disturbed. Sewage contamination, primary producers' abundance and environmental conditions may have influenced the gastropods survival, growth and its ecosystem engineering potential. - Terebralia palustris high ecosystem engineering potential in constructed mangrove wetlands.

  2. Differential responses of the freshwater wetland species Juncus effusus L. and Caltha palustris L. to iron supply in sulfidic environments

    International Nuclear Information System (INIS)

    Welle, Marlies E.W. van der; Niggebrugge, Karla; Lamers, Leon P.M.; Roelofs, Jan G.M.

    2007-01-01

    Sulfur pollution can lead to serious problems in freshwater wetlands, including phosphorus eutrophication and sulfide toxicity. We tested the effects of anaerobic iron-rich groundwater discharge in fens, simulated by iron injection, on two characteristic species (Juncus effusus and Caltha palustris) in a sulfidic environment. Biomass production of C. palustris roots showed an optimum response to the combined addition of iron and sulfide, with highest values at intermediate concentrations of both substances. Iron deficiency apparently occurred at low iron concentrations, while at high iron concentrations, growth was decreased. For J. effusus, in contrast, no toxic effects were found of both iron and sulfide. This could be explained by larger radial oxygen loss (ROL) of J. effusus and could not be explained by differences in phosphorous concentrations. The results of our experiments confirm that iron-rich groundwater discharge has the potential to affect vegetation composition through toxicity modification in sulfidic environments. - Toxicity of iron and sulfide are interacting with each other and have the potential to affect vegetation composition

  3. Fluorescence-excitation and emission spectra from LH2 antenna complexes of Rhodopseudomonas acidophila as a function of the sample preparation conditions.

    Science.gov (United States)

    Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J; Köhler, Jürgen; Freiberg, Arvi

    2013-10-10

    The high sensitivity of optical spectra of pigment-protein complexes to temperature and pressure is well known. In the present study, we have demonstrated the significant influence of the environments commonly used in bulk and single-molecule spectroscopic studies at low temperatures on the LH2 photosynthetic antenna complex from Rhodopseudomonas acidophila. A transfer of this LH2 complex from a bulk-buffer solution into a spin-coated polymer film results in a 189 cm(-1) blue shift of the B850 excitonic absorption band at 5 K. Within the molecular exciton model, the origin of this shift could be disentangled into three parts, namely to an increase of the local site energies, a contraction of the exciton band, and a decrease of the displacement energy.

  4. Correlation of paramagnetic states and molecular structure in bacterial photosynthetic reaction centers: The symmetry of the primary electron donor in Rhodopseudomonas viridis and Rhodobacter sphaeroides R-26

    International Nuclear Information System (INIS)

    Norris, J.R.; Budil, D.E.; Gast, P.; Chang, C.H.; El-Kabbani, O.; Schiffer, M.

    1989-01-01

    The orientation of the principal axes of the primary electron donor triplet state measured in single crystals of photosynthetic reaction centers is compared to the x-ray structures of the bacteria Rhodobacter (Rb.) sphaeroides R-26 and Rhodopseudomonas (Rps.) viridis. The primary donor of Rps. viridis is significantly different from that of Rb. sphaeroides. The measured directions of the axes indicate that triplet excitation is almost completely localized on the L-subunit half of the dimer in Rps. viridis but is more symmetrically distributed on the dimeric donor in Rb. sphaeroides R-26. The large reduction of the zero field splitting parameters relative to monomeric bacteriochlorophyll triplet in vitro suggests significant participation of asymmetrical charge transfer electronic configurations in the special pair triplet state of both organisms

  5. Streptococcus mutans NADH oxidase lies at the intersection of overlapping regulons controlled by oxygen and NAD+ levels.

    Science.gov (United States)

    Baker, J L; Derr, A M; Karuppaiah, K; MacGilvray, M E; Kajfasz, J K; Faustoferri, R C; Rivera-Ramos, I; Bitoun, J P; Lemos, J A; Wen, Z T; Quivey, R G

    2014-06-01

    NADH oxidase (Nox, encoded by nox) is a flavin-containing enzyme used by the oral pathogen Streptococcus mutans to reduce diatomic oxygen to water while oxidizing NADH to NAD(+). The critical nature of Nox is 2-fold: it serves to regenerate NAD(+), a carbon cycle metabolite, and to reduce intracellular oxygen, preventing formation of destructive reactive oxygen species (ROS). As oxygen and NAD(+) have been shown to modulate the activity of the global transcription factors Spx and Rex, respectively, Nox is potentially poised at a critical junction of two stress regulons. In this study, microarray data showed that either addition of oxygen or loss of nox resulted in altered expression of genes involved in energy metabolism and transport and the upregulation of genes encoding ROS-metabolizing enzymes. Loss of nox also resulted in upregulation of several genes encoding transcription factors and signaling molecules, including the redox-sensing regulator gene rex. Characterization of the nox promoter revealed that nox was regulated by oxygen, through SpxA, and by Rex. These data suggest a regulatory loop in which the roles of nox in reduction of oxygen and regeneration of NAD(+) affect the activity levels of Spx and Rex, respectively, and their regulons, which control several genes, including nox, crucial to growth of S. mutans under conditions of oxidative stress. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  6. Cross-species comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei quorum-sensing regulons.

    Science.gov (United States)

    Majerczyk, Charlotte D; Brittnacher, Mitchell J; Jacobs, Michael A; Armour, Christopher D; Radey, Matthew C; Bunt, Richard; Hayden, Hillary S; Bydalek, Ryland; Greenberg, E Peter

    2014-11-01

    Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei (the Bptm group) are close relatives with very different lifestyles: B. pseudomallei is an opportunistic pathogen, B. thailandensis is a nonpathogenic saprophyte, and B. mallei is a host-restricted pathogen. The acyl-homoserine lactone quorum-sensing (QS) systems of these three species show a high level of conservation. We used transcriptome sequencing (RNA-seq) to define the quorum-sensing regulon in each species, and we performed a cross-species analysis of the QS-controlled orthologs. Our analysis revealed a core set of QS-regulated genes in all three species, as well as QS-controlled factors shared by only two species or unique to a given species. This global survey of the QS regulons of B. pseudomallei, B. thailandensis, and B. mallei serves as a platform for predicting which QS-controlled processes might be important in different bacterial niches and contribute to the pathogenesis of B. pseudomallei and B. mallei. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  7. Cross-Species Comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei Quorum-Sensing Regulons

    Science.gov (United States)

    Majerczyk, Charlotte D.; Brittnacher, Mitchell J.; Jacobs, Michael A.; Armour, Christopher D.; Radey, Matthew C.; Bunt, Richard; Hayden, Hillary S.; Bydalek, Ryland

    2014-01-01

    Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei (the Bptm group) are close relatives with very different lifestyles: B. pseudomallei is an opportunistic pathogen, B. thailandensis is a nonpathogenic saprophyte, and B. mallei is a host-restricted pathogen. The acyl-homoserine lactone quorum-sensing (QS) systems of these three species show a high level of conservation. We used transcriptome sequencing (RNA-seq) to define the quorum-sensing regulon in each species, and we performed a cross-species analysis of the QS-controlled orthologs. Our analysis revealed a core set of QS-regulated genes in all three species, as well as QS-controlled factors shared by only two species or unique to a given species. This global survey of the QS regulons of B. pseudomallei, B. thailandensis, and B. mallei serves as a platform for predicting which QS-controlled processes might be important in different bacterial niches and contribute to the pathogenesis of B. pseudomallei and B. mallei. PMID:25182491

  8. Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wild rice (Zizania palustris L.)

    Science.gov (United States)

    Cochliobolus miyabeanus causes a severe, yield-reducing leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of the pathogen in wildrice, little is known about mechanisms of p...

  9. Long-term effects of fire and fire-return interval on population structure and growth of longleaf pine (Pinus palustris)

    Science.gov (United States)

    Chelcy R. Ford; Emily S. Minor; Gordon A. Fox

    2010-01-01

    We investigated the effect of fire and fire frequency on stand structure and longleaf pine (Pinus palustris P. Mill.) growth and population demography in an experimental research area in a southwest Florida sandhill community. Data were collected from replicated plots that had prescribed fire-return intervals of 1, 2, 5, or 7 years or were left...

  10. Effects of site preparation treatments on early growth and survival of planted longleaf pine (Pinus palustris Mill.) seedlings in North Carolina

    Science.gov (United States)

    Benjamin O. Knapp; G. Geoff Wang; Joan L. Walker; Susan Cohen

    2006-01-01

    We tested the effects of eight site preparation treatments on early growth and survival of container-grown longleaf pine (Pinus palustris Mill.) seedlings. Treatments included an untreated check, six combinations of two initial vegetation control treatments (chopping or herbicide) with three planting site conditions (flat [no additional treatment],...

  11. High-resolution bioactivity profiling combined with HPLC-HRMS-SPE-NMR: α-glucosidase inhibitors and acetylated ellagic acid rhamnosides from Myrcia palustris DC. (Myrtaceae)

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Moresco, Henrique H.; Tahtah, Yousof

    2015-01-01

    , and therefore improved drug leads or functional foods containing α-glucosidase inhibitors are needed for management of blood glucose. In this study, leaves of Myrcia palustris were investigated by high-resolution α-glucosidase inhibition profiling combined with HPLC–HRMS–SPE–NMR. This led to identification...

  12. Purification, molecular cloning, and enzymatic properties of a family 12 endoglucanase (EG-II) from fomitopsis palustris: role of EG-II in larch holocellulose hydrolysis.

    Science.gov (United States)

    Shimokawa, Tomoko; Shibuya, Hajime; Nojiri, Masanobu; Yoshida, Shigeki; Ishihara, Mitsuro

    2008-09-01

    A family 12 endoglucanase with a molecular mass of 23,926 Da (EG-II) from the brown-rot basidiomycete Fomitopsis palustris was purified and characterized. One of the roles of EG-II in wood degradation is thought to be to loosen the polysaccharide network in cell walls by disentangling hemicelluloses that are associated with cellulose.

  13. Comparison of red-cockaded woodpecker (Picoides borealis) nestling diet in old-growth and old-field longleaf pine (Pinus palustris) habitats

    Science.gov (United States)

    James L. Hanula; R. Todd Engstrom

    2000-01-01

    Automatic cameras were used to record adult red-cockaded woodpecker (Picoides borealis) nest visits with food for nestlings. Diet of nestlings on or near an old-growth longleaf pine (Pinus palustris) remnant in southern Georgia was compared to that in longleaf pine stands established on old farm fields in western South Carolina....

  14. Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium

    Directory of Open Access Journals (Sweden)

    Porwollik Steffen

    2011-03-01

    Full Text Available Abstract Background Salmonella enterica serovar Typhimurium (S. Typhimurium is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium. Results We compared the transcriptional profiles of the virulent wild-type (WT strain (ATCC 14028s and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome; of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV, Gifsy-1 prophage genes, and three SPI-3 genes (mgtBC, slsA, STM3784. In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Additionally, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr. Conclusion(s We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella

  15. Phosphoribosyl diphosphate synthetase-independent NAD de novo synthesis in Escherichia coli: a new phenotype of phosphate regulon mutants

    DEFF Research Database (Denmark)

    Hove-Jensen, Bjarne

    1996-01-01

    Phosphoribosyl diphosphate-lacking (Δprs) mutant strains of Escherichia coli require NAD, guanosine, uridine, histidine, and tryptophan for growth. NAD is required by phosphoribosyl diphosphate-lacking mutants because of lack of one of the substrates for the quinolinate phosphoribosyltransferase...... reaction, an enzyme of the NAD de novo pathway. Several NAD-independent mutants of a host from which prs had been deleted were isolated; all of them were shown to have lesions in the pstSCAB-phoU operon, in which mutations lead to derepression of the Pho regulon. In addition NAD-independent growth...... was dependent on a functional quinolinate phosphoribosyltransferase. The prs suppressor mutations led to the synthesis of a new phosphoryl compound that may act as a precursor for a new NAD biosynthetic pathway. This compound may be synthesized by the product of an unknown phosphate starvation-inducible gene...

  16. Size-dependent distribution and feeding habits of Terebralia palustris in mangrove habitats of Gazi Bay, Kenya

    Science.gov (United States)

    Pape, Ellen; Muthumbi, Agnes; Kamanu, Chomba Peter; Vanreusel, Ann

    2008-03-01

    The gastropod Terebralia palustris often dominates the surface of muddy to sandy substrates of intertidal mudflats and mangrove forests, where they clearly destabilize the sediment. In the present study, it was investigated whether and to what extent the behaviour of juvenile and adult snails differs among habitats (mudflat vs. mangrove stand) in a Sonneratia alba mangal at Gazi Bay, Kenya. For this purpose we: (1) examined their distribution along three land-sea transects; and (2) applied stable isotope analysis to determine the feeding patterns of different-sized snails from the mangrove and mudflat habitats. Additionally, we investigated if these gastropods exert an impact on microphytobenthic (diatom) biomass, and whether this is size-dependent. The latter objective was met by either enclosing or excluding different-sized snails from experimental cages on the intertidal mudflat and the subsequent assessment of a change in pigment concentration of the sediment surface. In agreement with several previous studies conducted in other mangroves and geographical locations, a spatial segregation was demonstrated between juveniles (more common on the mudflat) and adults (more common in the mangrove forest). On the intertidal mudflat juveniles avoided sediment patches characterized by highly saline water in intertidal pools and a high mud content, while adults tended to dwell on substrates covered by a high amount of leaf litter. Stable carbon isotope analysis of the foot tissue of snails sampled from the S. alba stand and the mudflat indicated a transition in food source when a shell length of 51 mm is reached. Considering the δ13C value of juveniles, it seems they might be selecting for microphytobenthos, which might explain their preference for the mudflat. The diet of size classes found in both habitats did not differ significantly, although juveniles inhabiting the mangrove forest were slightly more depleted in 13C compared to those residing on the mudflat

  17. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.

    Directory of Open Access Journals (Sweden)

    Catherine Cheng

    Full Text Available The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein and the tad focus (which encodes type IVb pili in Yersinia enterocolitica. Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized

  18. Differentiation of epipactis palustris (l.) crantz (orchidaceae) in habitats altered by man based on species populations within poznan city (poland)

    International Nuclear Information System (INIS)

    Wieloch, M.K.; Raszewska, M.W.; Drapikowska, M.

    2017-01-01

    The aim of the study was to compare two populations of Epipactis palustris (Orchidaceae) growing in the valley of Junikowski Stream, in the south-western part of the Poznan city (square of ATPOL BD08) and to compare current results to data on the species described in the literature. Group characteristics of both populations, such as population size, average density and congestion factor, as well as the average coefficient of dispersion, were defined. Specimen variability was determined by measuring 250 generative ramets in each population. The following plant traits were included: stem length, inflorescence length, number of flowers per inflorescence, number of leaves per stem and length and width of the largest leaf. Obtained data were subjected to statistical analyses. Descriptive statistics were calculated (arithmetic average, standard deviation, minimum and maximum). The variation coefficient (V) was established to determine the variation degree of each trait. In order to determine statistical significance of average values of traits of the samples in question, the factor variance ANOVA F-statistics was used. The significance degree was examined with Scheffe's test. Principal component analysis (PCA) enabled the examination of mutual relations between the samples in the system of two first principal components. This work confirmed previous information about low variability of marsh helleborine. Individual traits in both populations were very similar. The differences concerned the group characteristics. The plants were in good condition irrespective of occupied habitat. (author)

  19. An evaluation of memory accuracy in food hoarding marsh tits Poecile palustris--how accurate are they compared to humans?

    Science.gov (United States)

    Brodin, Anders; Urhan, A Utku

    2013-07-01

    Laboratory studies of scatter hoarding birds have become a model system for spatial memory studies. Considering that such birds are known to have a good spatial memory, recovery success in lab studies seems low. In parids (titmice and chickadees) typically ranging between 25 and 60% if five seeds are cached in 50-128 available caching sites. Since these birds store many thousands of food items in nature in one autumn one might expect that they should easily retrieve five seeds in a laboratory where they know the environment with its caching sites in detail. We designed a laboratory set up to be as similar as possible with previous studies and trained wild caught marsh tits Poecile palustris to store and retrieve in this set up. Our results agree closely with earlier studies, of the first ten looks around 40% were correct when the birds had stored five seeds in 100 available sites both 5 and 24h after storing. The cumulative success curve suggests high success during the first 15 looks where after it declines. Humans performed much better, in the first five looks most subjects were 100% correct. We discuss possible reasons for why the birds were not doing better. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions

    Science.gov (United States)

    Atack, John M; Yang, Yuedong; Jennings, Michael P

    2018-01-01

    Abstract Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on and off. This process is called phase variation. Several phase-variable N6-adenine DNA-methyltransferases from Type III restriction-modification systems have been reported in bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA methylation pattern, leading to changes in gene expression. These epigenetic regulatory systems are called phasevarions — phase-variable regulons. The extent of these phase-variable genes in the bacterial kingdom is unknown. Here, we interrogated a database of restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been previously identified. The newly discovered examples are widely distributed and include many examples in opportunistic pathogens as well as in environmental species. In many cases, multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions in some species. We found several new types of phase-variable mod genes, including the first example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic bacteria. PMID:29554328

  1. Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons.

    Science.gov (United States)

    Garmyn, Dominique; Augagneur, Yoann; Gal, Laurent; Vivant, Anne-Laure; Piveteau, Pascal

    2012-01-01

    Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

  2. Divergent regulation of CBF regulon on cold tolerance and plant phenotype in cassava overexpressing Arabidopsis CBF3 gene

    Directory of Open Access Journals (Sweden)

    Dong An

    2016-12-01

    Full Text Available Cassava is a tropical origin plant that is sensitive to chilling stress. In order to understand the CBF cold response pathway, a well-recognized regulatory mechanism in temperate plants, in cassava, overexpression of an Arabidopsis CBF3 gene is studied. This gene renders cassava increasingly tolerant to cold and drought stresses but is associated with retarded plant growth, leaf curling, reduced storage root yield, and reduced anthocyanin accumulation in a transcript abundance-dependent manner. Physiological analysis revealed that the transgenic cassava increased proline accumulation, reduced malondialdehyde production, and electrolyte leakage under cold stress. These transgenic lines also showed high relative water content when faced with drought. The expression of partial CBF-targeted genes in response to cold displayed temporal and spatial variations in the wild-type and transgenic plants: highly inducible in leaves and less altered in apical buds. In addition, anthocyanin accumulation was inhibited by downregulating the expression of genes involved in its biosynthesis and by interplaying between the CBF3 and the endogenous transcription factors. Thus, the heterologous CBF3 modulates the expression of stress-related genes and carries out a series of physiological adjustments under stressful conditions, showing a varied regulation pattern of CBF regulon from that of cassava CBFs.

  3. Eficiencia de pseudomonas sp, rhodopseudomonas sp, micrococcus sp y bacillus sp empleados como cultivos individuales y en consorcio, en la degradación de petróleo diesel ii

    OpenAIRE

    Otiniano García, Nélida Milly Esther

    2010-01-01

    In order to evaluate the efficiency of Pseudomonas sp, Rhodopseudomonas sp, Micrococcus sp, Bacillus sp, and the consortium formed by these four microorganisms in the diesel II petroleum degradation, it was worked in 5 bioreactors of aerated and shaken tank of 1.5 litters of capacity, with speed agitation of 120 rpm, and air flow of 0.5 vvm; in which were placed; 940 mL of Minimum Broth of Davies pH 7.0; 50 mL of diesel II petroleum as source of carbon and 10 mL of a suspension of approx...

  4. The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. II. Homo-arrays of LH2 complexes reconstituted into phospholipid model membranes.

    Science.gov (United States)

    Pflock, Tobias J; Oellerich, Silke; Krapf, Lisa; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

    2011-07-21

    We performed time-resolved spectroscopy on homoarrays of LH2 complexes from the photosynthetic purple bacterium Rhodopseudomonas acidophila. Variations of the fluorescence transients were monitored as a function of the excitation fluence and the repetition rate of the excitation. These parameters are directly related to the excitation density within the array and to the number of LH2 complexes that still carry a triplet state prior to the next excitation. Comparison of the experimental observations with results from dynamic Monte Carlo simulations for a model cluster of LH2 complexes yields qualitative agreement without the need for any free parameter and reveals the mutual relationship between energy transfer and annihilation processes.

  5. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available clase ... (GGDEF) [Rhodopseudomonas palustris CGA009] ... Length = 124 ... Query: 353 PDILWHETYACGEPTIDAQHRELFDLANVILGPEI...EMLEPARLSELVELLLTRVAEHFQY 412 ... PDILWHETYACGEPTIDAQHRELFDLANVILGPEI...EMLEPARLSELVELLLTRVAEHFQY Sbjct: 1 ... PDILWHETYACGEPTIDAQHRELFDLANVILGPEIEMLEPARLSELVELLLTRVAEHFQY 60 ... Query: 473 DRRF 476 ... DRRF Sbjct: 121 DRRF 124

  6. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005296 gi|39936477 >1kmoA 7 661 92 753 2e-72 ... emb|CAE28855.1| putative hydroxamate-type ferris... ... putative hydroxamate-type ferrisiderophore receptor ... [Rhodopseudomonas palustris CGA009] ...

  7. Magnitude and direction of the change in dipole moment associated with excitation of the primary electron donor in Rhodopseudomonas sphaeroides reaction centers

    Energy Technology Data Exchange (ETDEWEB)

    Lockhart, D.J.; Boxer, S.G.

    1987-02-10

    The magnitude and direction of the change in dipole moment, ..delta mu.., associated with the Q/sub y/ transition of the dimeric primary electron donor (special pair or P870) in Rhodopseudomonas sphaeroides reaction centers have been measured by Stark spectroscopy at 20 /sup 0/C. The magnitude of ..delta mu.. is found to be f/sup -1/ (10.3 +/- 0.7) D, where f is a correction factor for the local dielectric properties of the protein matrix. With the spherical cavity approximation and an effective local dielectric constant of 2, f = 1.2, and absolute value of ..delta mu.. is 8.6 +/- 0.6 D. Absolute value of ..delta mu.. for the Q/sub y/ transition of the special pair is approximately a factor of 3.4 and 2 greater than for the monomeric bacteriochlorophylls and bacteriopheophytins, respectively, in the reaction center. The angle between ..delta mu.. and the transition dipole moment for excitation of the first singlet electron state of the special pair was found to be 24 +/- 2/sup 0/. The measured values are combined to suggest a physical model in which the lowest excited singlet state of the special pair has substantial charge-transfer character and where charge is separated between the two monomers comprising the dimeric special pair. This leads to the hypothesis that the first charge-separated state in bacterial photosynthesis is formed directly upon photoexcitation. These data provide stringent values for comparison with theoretical calculations of the electronic structure of the chromophores in the reaction center.

  8. Proposed megakaryocytic regulon of p53: the genes engaged to control cell cycle and apoptosis during megakaryocytic differentiation

    Science.gov (United States)

    Apostolidis, Pani A.; Lindsey, Stephan; Miller, William M.

    2012-01-01

    During endomitosis, megakaryocytes undergo several rounds of DNA synthesis without division leading to polyploidization. In primary megakaryocytes and in the megakaryocytic cell line CHRF, loss or knock-down of p53 enhances cell cycling and inhibits apoptosis, leading to increased polyploidization. To support the hypothesis that p53 suppresses megakaryocytic polyploidization, we show that stable expression of wild-type p53 in K562 cells (a p53-null cell line) attenuates the cells' ability to undergo polyploidization during megakaryocytic differentiation due to diminished DNA synthesis and greater apoptosis. This suggested that p53's effects during megakaryopoiesis are mediated through cell cycle- and apoptosis-related target genes, possibly by arresting DNA synthesis and promoting apoptosis. To identify candidate genes through which p53 mediates these effects, gene expression was compared between p53 knock-down (p53-KD) and control CHRF cells induced to undergo terminal megakaryocytic differentiation using microarray analysis. Among substantially downregulated p53 targets in p53-KD megakaryocytes were cell cycle regulators CDKN1A (p21) and PLK2, proapoptotic FAS, TNFRSF10B, CASP8, NOTCH1, TP53INP1, TP53I3, DRAM1, ZMAT3 and PHLDA3, DNA-damage-related RRM2B and SESN1, and actin component ACTA2, while antiapoptotic CKS1B, BCL2, GTSE1, and p53 family member TP63 were upregulated in p53-KD cells. Additionally, a number of cell cycle-related, proapoptotic, and cytoskeleton-related genes with known functions in megakaryocytes but not known to carry p53-responsive elements were differentially expressed between p53-KD and control CHRF cells. Our data support a model whereby p53 expression during megakaryopoiesis serves to control polyploidization and the transition from endomitosis to apoptosis by impeding cell cycling and promoting apoptosis. Furthermore, we identify a putative p53 regulon that is proposed to orchestrate these effects. PMID:22548738

  9. The new pLAI (lux regulon based auto-inducible expression system for recombinant protein production in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Nocadello Salvatore

    2012-01-01

    Full Text Available Abstract Background After many years of intensive research, it is generally assumed that no universal expression system can exist for high-level production of a given recombinant protein. Among the different expression systems, the inducible systems are the most popular for their tight regulation. However, induction is in many cases less favorable due to the high cost and/or toxicity of inducers, incompatibilities with industrial scale-up or detrimental growth conditions. Expression systems using autoinduction (or self-induction prove to be extremely versatile allowing growth and induction of recombinant proteins without the need to monitor cell density or add inducer. Unfortunately, almost all the actual auto inducible expression systems need endogenous or induced metabolic changes during the growth to trigger induction, both frequently linked to detrimental condition to cell growth. In this context, we use a simple modular approach for a cell density-based genetic regulation in order to assemble an autoinducible recombinant protein expression system in E. coli. Result The newly designed pLAI expression system places the expression of recombinant proteins in Escherichia coli under control of the regulatory genes of the lux regulon of Vibrio fischeri's Quorum Sensing (QS system. The pLAI system allows a tight regulation of the recombinant gene allowing a negligible basal expression and expression only at high cell density. Sequence optimization of regulative genes of QS of V. fischeri for expression in E. coli upgraded the system to high level expression. Moreover, partition of regulative genes between the plasmid and the host genome and introduction of a molecular safety lock permitted tighter control of gene expression. Conclusion Coupling gene expression to cell density using cell-to-cell communication provides a promising approach for recombinant protein production. The system allows the control of expression of the target recombinant gene

  10. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Directory of Open Access Journals (Sweden)

    Jared D Sharp

    Full Text Available Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  11. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Science.gov (United States)

    Sharp, Jared D; Singh, Atul K; Park, Sang Tae; Lyubetskaya, Anna; Peterson, Matthew W; Gomes, Antonio L C; Potluri, Lakshmi-Prasad; Raman, Sahadevan; Galagan, James E; Husson, Robert N

    2016-01-01

    Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  12. Diverse Genetic Regulon of the Virulence-Associated Transcriptional Regulator MucR in Brucella abortus 2308

    Science.gov (United States)

    Caswell, Clayton C.; Elhassanny, Ahmed E. M.; Planchin, Emilie E.; Roux, Christelle M.; Weeks-Gorospe, Jenni N.; Ficht, Thomas A.; Dunman, Paul M.

    2013-01-01

    The Ros-type regulator MucR is one of the few transcriptional regulators that have been linked to virulence in Brucella. Here, we show that a Brucella abortus in-frame mucR deletion strain exhibits a pronounced growth defect during in vitro cultivation and, more importantly, that the mucR mutant is attenuated in cultured macrophages and in mice. The genetic basis for the attenuation of Brucella mucR mutants has not been defined previously, but in the present study the genes regulated by MucR in B. abortus have been elucidated using microarray analysis and real-time reverse transcription-PCR (RT-PCR). In B. abortus 2308, MucR regulates a wide variety of genes whose products may function in establishing and maintaining cell envelope integrity, polysaccharide biosynthesis, iron homeostasis, genome plasticity, and transcriptional regulation. Particularly notable among the MucR-regulated genes identified is arsR6 (nolR), which encodes a transcriptional regulator previously linked to virulence in Brucella melitensis 16 M. Importantly, electrophoretic mobility shift assays (EMSAs) determined that a recombinant MucR protein binds directly to the promoter regions of several genes repressed by MucR (including arsR6 [nolR]), and in Brucella, as in other alphaproteobacteria, MucR binds to its own promoter to repress expression of the gene that encodes it. Overall, these studies have uncovered the diverse genetic regulon of MucR in Brucella, and in doing so this work has begun to define the MucR-controlled genetic circuitry whose misregulation contributes to the virulence defect of Brucella mucR mutants. PMID:23319565

  13. Conformational heterogeneity of the bacteriopheophytin electron acceptor HA in reaction centers from Rhodopseudomonas viridis revealed by Fourier transform infrared spectroscopy and site-directed mutagenesis.

    Science.gov (United States)

    Breton, J; Bibikova, M; Oesterhelt, D; Nabedryk, E

    1999-08-31

    The light-induced Fourier transform infrared (FTIR) difference spectra corresponding to the photoreduction of either the HA bacteriopheophytin electron acceptor (HA-/HA spectrum) or the QA primary quinone (QA-/QA spectrum) in photosynthetic reaction centers (RCs) of Rhodopseudomonas viridis are reported. These spectra have been compared for wild-type (WT) RCs and for two site-directed mutants in which the proposed interactions between the carbonyls on ring V of HA and the RC protein have been altered. In the mutant EQ(L104), the putative hydrogen bond between the protein and the 9-keto C=O of HA should be affected by changing Glu L104 to a Gln. In the mutant WF(M250), the van der Waals interactions between Trp M250 and the 10a-ester C=O of HA should be modified. The characteristic effects of both mutations on the FTIR spectra support the proposed interactions and allow the IR modes of the 9-keto and 10a-ester C=O of HA and HA- to be assigned. Comparison of the HA-/HA and QA-/QA spectra leads us to conclude that the QA-/QA IR signals in the spectral range above 1700 cm-1 are largely dominated by contributions from the electrostatic response of the 10a-ester C=O mode of HA upon QA photoreduction. A heterogeneity in the conformation of the 10a-ester C=O mode of HA in WT RCs, leading to three distinct populations of HA, appears to be related to differences in the hydrogen-bonding interactions between the carbonyls of ring V of HA and the RC protein. The possibility that this structural heterogeneity is related to the observed multiexponential kinetics of electron transfer and the implications for primary processes are discussed. The effect of 1H/2H exchange on the QA-/QA spectra of the WT and mutant RCs shows that neither Glu L104 nor any other exchangeable carboxylic residue changes appreciably its protonation state upon QA reduction.

  14. A Tribal Story Written in Silica: Using Phytoliths to Research the Effects of Mining on Past Wild Rice (Zizania palustris) Abundance in Sandy Lake, Minnesota

    Science.gov (United States)

    Clarke, I. R.; Jones, M. A.; Yost, C. L.; Drake, C.; Ladwig, J. L.; Myrbo, A.; Howes, T.

    2014-12-01

    Wild rice (Zizania palustris, manoomin) is an emergent aquatic plant that grows annually in the northern Great Lakes region of North America. This region is also rich in iron ore deposits and correspondingly has an extensive history of mining activities. Wild rice no longer grows in some areas where it was previously abundant. Sandy Lake, located in St. Louis County on federally protected lands that are ceded territory of the Fond du Lac Band of Lake Superior Chippewa in Minnesota and downstream of the nearby U.S. Steel Minntac mine, was selected as a test site. This lake has a history of ricing activities by the Ojibwe (Chippewa) People, for whom manoomin has cultural importance. Lake cores were taken on June 17, 2014 by LacCore and FDLRM staff and samples were obtained. This project used phytolith analysis to answer the question of past wild rice presence and abundance in Sandy Lake. Phytoliths are microscopic opal silica deposits produced in some plants. Zizania palustris produces phytolith morphotypes that are unequivocally diagnostic of this species in this region. Microscopic slides were prepared and analyzed for wild rice phytoliths. Concentration values ranged from 25 to 4379 phytoliths per cm3/year, and wild rice accumulation figures ranged from 7 to 789 phytoliths/cm2/year, the maximum values of which occurred in the 1920s and generally declined to the current lowest levels observed. Mining has likely impacted wild rice populations by causing increased sulfate levels and possibly contributing to higher lake levels.

  15. Allodaposuchus palustris sp. nov. from the upper cretaceous of Fumanya (South-Eastern Pyrenees, Iberian Peninsula: systematics, palaeoecology and palaeobiogeography of the enigmatic allodaposuchian crocodylians.

    Directory of Open Access Journals (Sweden)

    Alejandro Blanco

    Full Text Available The controversial European genus Allodaposuchus is currently composed of two species (A. precedens, A. subjuniperus and it has been traditionally considered a basal eusuchian clade of crocodylomorphs. In the present work, the new species A. palustris is erected on the base of cranial and postcranial remains from the lower Maastrichtian of the southern Pyrenees. Phylogenetic analyses here including both cranial and postcranial data support the hypothesis that Allodaposuchus is included within Crocodylia. The studied specimen suggests little change in postcranial skeleton along the evolutionary history of crocodylians, except for some bone elements such as the axis, the first caudal vertebra and the ilium. The specimen was found in an organic mudstone corresponding to a coastal wetland environment. Thus, A. palustris from Fumanya is the first Allodaposuchus reported in lacustrine-palustrine settings that expand the ecological range for this genus. The S-DIVA palaeobiogeographic reconstruction of ancestral area suggests that early members of Crocodylia rapidly widespread for the Northern Hemisphere landmasses no later than the Campanian, leading the apparition of endemic groups. In that way "Allodaposuchia" represents an endemic European clade probably originated in the Ibero-Armorican domain in the late Campanian and dispersed by the Southern European archipelago prior to the early Maastrichtian.

  16. Action of sulfurous acid on pollen. [Hepatica triloba; Helleborus orientalis; Vinca minor; Viola tricolor; Primula officinalis; Lilium candidum; Petunia; Pisum; Helleborus viridus; Galanthus nivealis; Vinca major; Convallaria maialis; Narcissus poeticus; Caltha palustris; Cystisus laburnum; Orchis maculata; Bilbergia; Eranthus; Crocus

    Energy Technology Data Exchange (ETDEWEB)

    Sabachnikoff, V

    1912-01-23

    The following ornamental plants: Hepatica triloba, Helleborus orientalis, Vinca minor, Viola tricolor, Primula officinalis, Lilium candidum, Petunia, Pisum, Helleborus viridus, Galanthus nivealis, Vinca major, Convallaria maialis, Narcissus poeticus, Caltha palustris, Cystisus laburnum, Orchis maculata, Bilbergia, Eranthus, and Crocus were tested for seed production. Exposure to sulfuric acid ranged from three to forty-eight hours. Responses were noted for varying concentrations.

  17. Scheuchzeria palustris L

    Czech Academy of Sciences Publication Activity Database

    Šída, O.; Štěpánková, Jitka

    2015-01-01

    Roč. 50, č. 1 (2015), s. 100-101 ISSN 1211-5258 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : floristics * distribution * endangered species Subject RIV: EF - Botanics

  18. The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. I. Isolated, non-interacting LH2 complexes.

    Science.gov (United States)

    Pflock, Tobias J; Oellerich, Silke; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

    2011-07-21

    We have employed time-resolved spectroscopy on the picosecond time scale in combination with dynamic Monte Carlo simulations to investigate the photophysical properties of light-harvesting 2 (LH2) complexes from the purple photosynthetic bacterium Rhodopseudomonas acidophila. The variations of the fluorescence transients were studied as a function of the excitation fluence, the repetition rate of the excitation and the sample preparation conditions. Here we present the results obtained on detergent solubilized LH2 complexes, i.e., avoiding intercomplex interactions, and show that a simple four-state model is sufficient to grasp the experimental observations quantitatively without the need for any free parameters. This approach allows us to obtain a quantitative measure for the singlet-triplet annihilation rate in isolated, noninteracting LH2 complexes.

  19. The Listeria monocytogenes Bile Stimulon under Acidic Conditions Is Characterized by Strain-Specific Patterns and the Upregulation of Motility, Cell Wall Modification Functions, and the PrfA Regulon

    Science.gov (United States)

    Guariglia-Oropeza, Veronica; Orsi, Renato H.; Guldimann, Claudia; Wiedmann, Martin; Boor, Kathryn J.

    2018-01-01

    Listeria monocytogenes uses a variety of transcriptional regulation strategies to adapt to the extra-host environment, the gastrointestinal tract, and the intracellular host environment. While the alternative sigma factor SigB has been proposed to be a key transcriptional regulator that facilitates L. monocytogenes adaptation to the gastrointestinal environment, the L. monocytogenes' transcriptional response to bile exposure is not well-understood. RNA-seq characterization of the bile stimulon was performed in two L. monocytogenes strains representing lineages I and II. Exposure to bile at pH 5.5 elicited a large transcriptomic response with ~16 and 23% of genes showing differential transcription in 10403S and H7858, respectively. The bile stimulon includes genes involved in motility and cell wall modification mechanisms, as well as genes in the PrfA regulon, which likely facilitate survival during the gastrointestinal stages of infection that follow bile exposure. The fact that bile exposure induced the PrfA regulon, but did not induce further upregulation of the SigB regulon (beyond that expected by exposure to pH 5.5), suggests a model where at the earlier stages of gastrointestinal infection (e.g., acid exposure in the stomach), SigB-dependent gene expression plays an important role. Subsequent exposure to bile induces the PrfA regulon, potentially priming L. monocytogenes for subsequent intracellular infection stages. Some members of the bile stimulon showed lineage- or strain-specific distribution when 27 Listeria genomes were analyzed. Even though sigB null mutants showed increased sensitivity to bile, the SigB regulon was not found to be upregulated in response to bile beyond levels expected by exposure to pH 5.5. Comparison of wildtype and corresponding ΔsigB strains newly identified 26 SigB-dependent genes, all with upstream putative SigB-dependent promoters. PMID:29467736

  20. Humoral Responses to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR Regulon-Encoded Proteins of Mycobacterium tuberculosis in Individuals with Latent Tuberculosis Infection

    Directory of Open Access Journals (Sweden)

    Simon G. Kimuda

    2017-01-01

    Full Text Available Latent tuberculosis infection (LTBI is evidence of immunological control of tuberculosis. Dormancy survival regulator (DosR regulon-encoded proteins may have a role in the maintenance of LTBI. T cell responses to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins were found to be most frequent among household contacts of TB cases from Uganda compared to other DosR proteins, but antibody responses were not described. We characterized antibody responses to these proteins in individuals from Uganda. Antibodies to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins were measured in 68 uninfected individuals, 62 with LTBI, and 107 with active pulmonary tuberculosis (APTB cases. There were no differences in the concentrations of antibodies to Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins between individuals with LTBI and APTB and those who were uninfected. LTBI was associated with higher concentrations of antibodies to Rv1733c in female participants [adjusted geometric mean ratio: 1.812, 95% confidence interval (CI: 1.105 2.973, and p=0.019] but not in males (p value for interaction = 0.060. Antibodies to the four DosR regulon-encoded proteins investigated may not serve as good biomarkers of LTBI in the general population. More of the M.tb proteome needs to be screened to identify proteins that induce strong antibody responses in LTBI.

  1. Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus

    Directory of Open Access Journals (Sweden)

    Hakenbeck Regine

    2010-11-01

    Full Text Available Abstract Background Post-transcriptional regulation by small RNAs (sRNAs in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system. Results Genes for csRNAs were predicted in streptococcal genomes and data base entries other than S. pneumoniae by searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions, S. mitis, S. oralis, and S. sanguinis were subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene from S. thermophilus plasmid pST0 introduced into S. pneumoniae was also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision. Conclusions The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of

  2. Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris.

    Science.gov (United States)

    Dedysh, S N; Derakshani, M; Liesack, W

    2001-10-01

    Two 16S rRNA-targeted oligonucleotide probes, Mcell-1026 and Mcell-181, were developed for specific detection of the acidophilic methanotroph Methylocella palustris using fluorescence in situ hybridization (FISH). The fluorescence signal of probe Mcell-181 was enhanced by its combined application with the oligonucleotide helper probe H158. Mcell-1026 and Mcell-181, as well as 16S rRNA oligonucleotide probes with reported group specificity for either type I methanotrophs (probes M-84 and M-705) or the Methylosinus/Methylocystis group of type II methanotrophs (probes MA-221 and M-450), were used in FISH to determine the abundance of distinct methanotroph groups in a Sphagnum peat sample of pH 4.2. M. palustris was enumerated at greater than 10(6) cells per g of peat (wet weight), while the detectable population size of type I methanotrophs was three orders of magnitude below the population level of M. palustris. The cell counts with probe MA-221 suggested that only 10(4) type II methanotrophs per g of peat (wet weight) were present, while the use of probe M-450 revealed more than 10(6) type II methanotroph cells per g of the same samples. This discrepancy was due to the fact that probe M-450 targets almost all currently known strains of Methylosinus and Methylocystis, whereas probe MA-221, originally described as group specific, does not detect a large proportion of Methylocystis strains. The total number of methanotrophic bacteria detected by FISH was 3.0 (+/-0.2) x 10(6) cells per g (wet weight) of peat. This was about 0.8% of the total bacterial cell number. Thus, our study clearly suggests that M. palustris and a defined population of Methylocystis spp. were the predominant methanotrophs detectable by FISH in an acidic Sphagnum peat bog.

  3. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

    Science.gov (United States)

    Dedysh, S N; Liesack, W; Khmelenina, V N; Suzina, N E; Trotsenko, Y A; Semrau, J D; Bares, A M; Panikov, N S; Tiedje, J M

    2000-05-01

    A new genus, Methylocella, and a new species, Methylocella palustris, are proposed for three strains of methane-oxidizing bacteria isolated from acidic Sphagnum peat bogs. These bacteria are aerobic, Gram-negative, colourless, non-motile, straight and curved rods that utilize the serine pathway for carbon assimilation, multiply by normal cell division and contain intracellular poly-beta-hydroxybutyrate granules (one at each pole). These strains use methane and methanol as sole sources of carbon and energy and are moderately acidophilic organisms with growth between pH 4.5 and pH 7.0, the optimum being at pH 5.0-5.5. The temperature range for growth is 10-28 degrees C with the optimum at 15-20 degrees C. The intracytoplasmic membrane system is different from those of type I and II methanotrophs. Cells contain an extensive periplasmic space and a vesicular membrane system connected to the cytoplasmic membrane. The strains grew only on media with a low salt content (0.2-0.5 g l(-1)). All three strains were found to possess soluble methane monooxygenase and are able to fix atmospheric nitrogen via an oxygen-sensitive nitrogenase. No products were observed in a PCR with particulate methane monooxygenase-targeted primers; hybridization with a pmoA probe was also negative. The major phospholipid fatty acids are 18:1 acids. The G+C content of the DNA is 61.2 mol%. The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. The three strains are most closely related to the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica (96.5% 16S rDNA sequence similarity). Collectively, these strains comprise a new species and genus Methylocella palustris gen. nov., sp. nov.; strain KT (= ATCC 700799T) is the type strain.

  4. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)

    DEFF Research Database (Denmark)

    Johansen, L.E.; Nygaard, P.; Lassen, C.

    2003-01-01

    In Bacillus subtilis expression of genes or operons encoding enzymes and other proteins involved in purine synthesis is affected by purine bases and nucleosides in the growth medium. The genes belonging to the PurR regulon (purR, purA, glyA, guaC, pbuO, pbuG, and the pur, yqhZ-folD, and xpt...

  5. Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

    Science.gov (United States)

    Zarrineh, Peyman; Sánchez-Rodríguez, Aminael; Hosseinkhan, Nazanin; Narimani, Zahra; Marchal, Kathleen; Masoudi-Nejad, Ali

    2014-01-01

    Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica. PMID:25101984

  6. Sulfide Generated by Sulfate Reduction is a Primary Controller of the Occurrence of Wild Rice (Zizania palustris) in Shallow Aquatic Ecosystems

    Science.gov (United States)

    Myrbo, A.; Swain, E. B.; Engstrom, D. R.; Coleman Wasik, J.; Brenner, J.; Dykhuizen Shore, M.; Peters, E. B.; Blaha, G.

    2017-11-01

    Field observations suggest that surface water sulfate concentrations control the distribution of wild rice, an aquatic grass (Zizania palustris). However, hydroponic studies show that sulfate is not toxic to wild rice at even unrealistically high concentrations. To determine how sulfate might directly or indirectly affect wild rice, potential wild rice habitat was characterized for 64 chemical and physical variables in over 100 sites spanning a relatively steep climatic and geological gradient in Minnesota. Habitat suitability was assessed by comparing the occurrence of wild rice with the field variables, through binary logistic regression. This analysis demonstrated that sulfide in sediment pore water, generated by the microbial reduction of sulfate that diffuses or advects into the sediment, is the primary control of wild rice occurrence. Water temperature and water transparency independently control the suitability of habitat for wild rice. In addition to generating phytotoxic sulfide, sulfate reduction also supports anaerobic decomposition of organic matter, releasing nutrients that can compound the harm of direct sulfide toxicity. These results are important because they show that increases in sulfate loading to surface water can have multiple negative consequences for ecosystems, even though sulfate itself is relatively benign.

  7. Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).

    Science.gov (United States)

    Kovács, G; Burghardt, J; Pradella, S; Schumann, P; Stackebrandt, E; Màrialigeti, K

    1999-01-01

    Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T.

  8. High-resolution bioactivity profiling combined with HPLC-HRMS-SPE-NMR: α-Glucosidase inhibitors and acetylated ellagic acid rhamnosides from Myrcia palustris DC. (Myrtaceae).

    Science.gov (United States)

    Wubshet, Sileshi G; Moresco, Henrique H; Tahtah, Yousof; Brighente, Inês M C; Staerk, Dan

    2015-08-01

    Type 2 diabetes (T2D) is an endocrine metabolic disease with a worldwide prevalence of more than 8%, and an expected increase close to 50% in the next 15-20years. T2D is associated with severe and life-threatening complications like retinopathy, neuropathy, nephropathy, and cardiovascular diseases, and therefore improved drug leads or functional foods containing α-glucosidase inhibitors are needed for management of blood glucose. In this study, leaves of Myrcia palustris were investigated by high-resolution α-glucosidase inhibition profiling combined with HPLC-HRMS-SPE-NMR. This led to identification of casuarinin, myricetin 3-O-β-d-(6″-galloyl)galactopyranoside, kaempferol 3-O-β-d-galactopyranoside, myricetin, and quercetin as α-glucosidase inhibitors. In addition, four acetylated ellagic acid rhamnosides, i.e., 4-O-(2″,4″-O-diacetyl-α-l-rhamnopyranosyl)ellagic acid, 4-O-(2″,3″-O-diacetyl-α-l-rhamnopyranosyl)ellagic acid, 4-O-(3″,4″-O-diacetyl-α-l-rhamnopyranosyl)ellagic acid, and 4-O-(2″,3″,4″-O-triacetyl-α-l-rhamnopyranosyl)ellagic acid were identified. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme.

    Science.gov (United States)

    Bell, Nicole; Lee, Jamie J; Summers, Michael L

    2017-04-01

    Based on primary sequence comparisons and genomic context, Npun_F4153 (SigG)/Npun_F4154 (SapG) of the cyanobacterium Nostoc punctiforme were hypothesized to encode an ECF sigma factor/anti-sigma factor pair. Transcription of sigG increased in heterocysts and akinetes, and after EDTA treatment. Interaction between SigG and the predicted cytoplasmic domain of SapG was observed in vitro. A SigG-GFP translational fusion protein localized to the periphery of vegetative cells in vivo, but lost this association following heat stress. A sigG mutant was unable to survive envelope damage caused by heat or EDTA, but was able to form functional heterocysts. Akinetes in the mutant strain appeared normal, but these cultures were less resistant to lysozyme and cold treatments than those of the wild-type strain. The SigG in vivo regulon was determined before and during akinete differentiation using DNA microarray analysis, and found to include multiple genes with putative association to the cell envelope. Mapped promoters common to both arrays enabled identification of a SigG promoter-binding motif that was supported in vivo by reporter studies, and in vitro by run-off transcription experiments. These findings support SigG/SapG as a sigma/anti-sigma pair involved in repair of envelope damage resulting from exogenous sources or cellular differentiation. © 2017 John Wiley & Sons Ltd.

  10. The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning.

    Science.gov (United States)

    Chen, Y M; Zhu, Y; Lin, E C

    1987-12-01

    In Escherichia coli the six known genes specifying the utilization of L-fucose as carbon and energy source cluster at 60.2 min and constitute a regulon. These genes include fucP (encoding L-fucose permease), fucI (encoding L-fucose isomerase), fucK (encoding L-fuculose kinase), fucA (encoding L-fuculose 1-phosphate aldolase), fucO (encoding L-1,2-propanediol oxidoreductase), and fucR (encoding the regulatory protein). In this study the fuc genes were cloned and their positions on the chromosome were established by restriction endonuclease and complementation analyses. Clockwise, the gene order is: fucO-fucA-fucP-fucI-fucK-fucR. The operons comprising the structural genes and the direction of transcription were determined by complementation analysis and Southern blot hybridization. The fucPIK and fucA operons are transcribed clockwise. The fucO operon is transcribed counterclockwise. The fucR gene product activates the three structural operons in trans.

  11. Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L..

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    Claudia V Castell-Miller

    Full Text Available The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa and two North American specialty crops, American wildrice (Zizania palustris and switchgrass (Panicum virgatum. Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.

  12. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

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    O'Gara Fergal

    2010-11-01

    Full Text Available Abstract Background Catabolite repression control (CRC is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas

  13. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    Science.gov (United States)

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  14. The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus.

    Science.gov (United States)

    Zhan, Lingjun; Han, Yanping; Yang, Lei; Geng, Jing; Li, Yingli; Gao, He; Guo, Zhaobiao; Fan, Wei; Li, Gang; Zhang, Lianfeng; Qin, Chuan; Zhou, Dongsheng; Yang, Ruifu

    2008-11-01

    The cyclic AMP receptor protein (CRP) is a bacterial regulator that controls more than 100 promoters, including those involved in catabolite repression. In the present study, a null deletion of the crp gene was constructed for Yersinia pestis bv. microtus strain 201. Microarray expression analysis disclosed that at least 6% of Y. pestis genes were affected by this mutation. Further reverse transcription-PCR and electrophoretic mobility shift assay analyses disclosed a set of 37 genes or putative operons to be the direct targets of CRP, and thus they constitute the minimal CRP regulon in Y. pestis. Subsequent primer extension and DNase I footprinting assays mapped transcriptional start sites, core promoter elements, and CRP binding sites within the DNA regions upstream of pla and pst, revealing positive and direct control of these two laterally acquired plasmid genes by CRP. The crp disruption affected both in vitro and in vivo growth of the mutant and led to a >15,000-fold loss of virulence after subcutaneous infection but a pestis and, particularly, is more important for infection by subcutaneous inoculation. It can further be concluded that the reduced in vivo growth phenotype of the crp mutant should contribute, at least partially, to its attenuation of virulence by both routes of infection. Consistent with a previous study of Y. pestis bv. medievalis, lacZ reporter fusion analysis indicated that the crp deletion resulted in the almost absolute loss of pla promoter activity. The plasminogen activator encoded by pla was previously shown to specifically promote Y. pestis dissemination from peripheral infection routes (subcutaneous infection [flea bite] or inhalation). The above evidence supports the notion that in addition to the reduced in vivo growth phenotype, the defect of pla expression in the crp mutant will greatly contribute to the huge loss of virulence of this mutant strain in subcutaneous infection.

  15. A proteomic analysis of the regulon of the NarP two-component regulatory system response regulator in the bovine pathogen Mannheimia haemolytica A1

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    Inamoto Ichiro

    2011-11-01

    Full Text Available Abstract Background The response of the NarQP two-component signal transduction system regulon in response to the presence of nitrate for the bovine pathogen Mannheimia haemolytica A1 was investigated by proteomic analysis. Total proteins from a narP mutant and the parent SH1217 grown with or without NaNO3 supplement were examined by ISO-DALT 2D electrophoresis and liquid chromatography-mass spectrometry. Results Seventeen proteins were differentially expressed in the parent strain SH1217 in response to the addition of NaNO3 to the growth media. These responses were absent in the narP mutant, indicating that the altered production of these proteins is mediated by NarPMh. Interestingly, NarPMh mediated the increased production of some proteins which are not generally associated with nitrate respiration, such as the iron transporters FbpA and YfeA. The increased production of proteins such as superoxide dismutase, SodA, and GAPDH were also observed. The increased production of these iron-regulated proteins by NarPMh is thought to enhance the swift establishment of the nitrate respiration mechanism of M. haemolytica during pathogenesis. Conclusion The data suggested NarPMh acts as an important regulator which regulates the expression of a small set of proteins in response to nitrate availability. This may contribute to the prevalence of M. haemolytica A1 in its host during pathogenesis of BPP, through enhancing the effectiveness of nitrate respiration either directly or indirectly.

  16. Intracellular Zn(II) Intoxication Leads to Dysregulation of the PerR Regulon Resulting in Heme Toxicity in Bacillus subtilis

    Science.gov (United States)

    2016-01-01

    Transition metal ions (Zn(II), Cu(II)/(I), Fe(III)/(II), Mn(II)) are essential for life and participate in a wide range of biological functions. Cellular Zn(II) levels must be high enough to ensure that it can perform its essential roles. Yet, since Zn(II) binds to ligands with high avidity, excess Zn(II) can lead to protein mismetallation. The major targets of mismetallation, and the underlying causes of Zn(II) intoxication, are not well understood. Here, we use a forward genetic selection to identify targets of Zn(II) toxicity. In wild-type cells, in which Zn(II) efflux prevents intoxication of the cytoplasm, extracellular Zn(II) inhibits the electron transport chain due to the inactivation of the major aerobic cytochrome oxidase. This toxicity can be ameliorated by depression of an alternate oxidase or by mutations that restrict access of Zn(II) to the cell surface. Conversely, efflux deficient cells are sensitive to low levels of Zn(II) that do not inhibit the respiratory chain. Under these conditions, intracellular Zn(II) accumulates and leads to heme toxicity. Heme accumulation results from dysregulation of the regulon controlled by PerR, a metal-dependent repressor of peroxide stress genes. When metallated with Fe(II) or Mn(II), PerR represses both heme biosynthesis (hemAXCDBL operon) and the abundant heme protein catalase (katA). Metallation of PerR with Zn(II) disrupts this coordination, resulting in depression of heme biosynthesis but continued repression of catalase. Our results support a model in which excess heme partitions to the membrane and undergoes redox cycling catalyzed by reduced menaquinone thereby resulting in oxidative stress. PMID:27935957

  17. Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR.

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    Imane El Meouche

    Full Text Available Clostridium difficile intestinal disease is mediated largely by the actions of toxins A (TcdA and B (TcdB, whose production occurs after the initial steps of colonization involving different surface or flagellar proteins. In B. subtilis, the sigma factor SigD controls flagellar synthesis, motility, and vegetative autolysins. A homolog of SigD encoding gene is present in the C.difficile 630 genome. We constructed a sigD mutant in C. difficile 630 ∆erm to analyze the regulon of SigD using a global transcriptomic approach. A total of 103 genes were differentially expressed between the wild-type and the sigD mutant, including genes involved in motility, metabolism and regulation. In addition, the sigD mutant displayed decreased expression of genes involved in flagellar biosynthesis, and also of genes encoding TcdA and TcdB as well as TcdR, the positive regulator of the toxins. Genomic analysis and RACE-PCR experiments allowed us to characterize promoter sequences of direct target genes of SigD including tcdR and to identify the SigD consensus. We then established that SigD positively regulates toxin expression via direct control of tcdR transcription. Interestingly, the overexpression of FlgM, a putative anti-SigD factor, inhibited the positive regulation of motility and toxin synthesis by SigD. Thus, SigD appears to be the first positive regulator of the toxin synthesis in C. difficile.

  18. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  19. Listeria-vectored vaccine expressing the Mycobacterium tuberculosis 30 kDa major secretory protein via the constitutively active prfA* regulon boosts BCG efficacy against tuberculosis.

    Science.gov (United States)

    Jia, Qingmei; Dillon, Barbara Jane; Masleša-Galić, Saša; Horwitz, Marcus A

    2017-06-19

    A potent vaccine against tuberculosis, one of the world's deadliest diseases, is needed to enhance the immunity of people worldwide, most of whom have been vaccinated with the partially effective BCG vaccine. Here we investigate novel live attenuated recombinant Listeria monocytogenes (rLm) vaccines expressing the Mycobacterium tuberculosis (Mtb) 30 kDa major secretory protein (r30/Ag85B) (rLm30) as heterologous booster vaccines in animals primed with BCG. Using three attenuated Lm vectors, rLm Δ actA (LmI), rLm Δ actA Δ inlB (LmII), and rLm Δ actA Δ inlB prfA * (LmIII), we constructed five rLm30 vaccine candidates expressing the r30 linked in-frame to the Lm Listeriolycin O signal sequence and driven by the hly promoter (h30) or linked in-frame to the ActA N-terminus and driven by the actA promoter (a30). All five rLm30 vaccines secreted r30 in broth and macrophages; while rLm expressing r30 via a constitutively active prfA * regulon (rLmIII/a30) expressed the greatest amount of r30 in broth culture, all five rLm vaccines expressed equivalent amounts of r30 in infected macrophages. In comparative studies, boosting BCG-immunized mice with rLmIII/a30 induced the strongest antigen-specific T-cell responses, including splenic and lung polyfunctional CD4+ T-cells expressing the three cytokines of interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-2 (IL-2) ( P vaccines were generally more potent booster vaccines than r30 in adjuvant and a recombinant adenovirus vaccine expressing r30. In a setting in which BCG alone was highly immunoprotective, boosting mice with rLmIII/a30, the most potent of the vaccines, significantly enhanced protection against aerosolized Mtb ( P <0.01). Copyright © 2017 American Society for Microbiology.

  20. The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator.

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    John T Sullivan

    Full Text Available Mesorhizobium loti is the microsymbiont of Lotus species, including the model legume L. japonicus. M. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifA, nifA1 and nifA2, both of which are located on the symbiosis island ICEMlSym(R7A. M. loti R7A also contains two rpoN genes, rpoN1 located on the chromosome outside of ICEMlSym(R7A and rpoN2 that is located on ICEMlSym(R7A. The aims of the current work were to establish how nifA expression was activated in M. loti and to characterise the NifA-RpoN regulon. The nifA2 and rpoN2 genes were essential for nitrogen fixation whereas nifA1 and rpoN1 were dispensable. Expression of nifA2 was activated, possibly in response to an inositol derivative, by a novel regulator of the LacI/GalR family encoded by the fixV gene located upstream of nifA2. Other than the well-characterized nif/fix genes, most NifA2-regulated genes were not required for nitrogen fixation although they were strongly expressed in nodules. The NifA-regulated nifZ and fixU genes, along with nifQ which was not NifA-regulated, were required in M. loti for a fully effective symbiosis although they are not present in some other rhizobia. The NifA-regulated gene msi158 that encodes a porin was also required for a fully effective symbiosis. Several metabolic genes that lacked NifA-regulated promoters were strongly expressed in nodules in a NifA2-dependent manner but again mutants did not have an overt symbiotic phenotype. In summary, many genes encoded on ICEMlSym(R7A were strongly expressed in nodules but not free-living rhizobia, but were not essential for symbiotic nitrogen fixation. It seems likely that some of these genes have functional homologues elsewhere in the genome and that bacteroid metabolism may be sufficiently plastic to adapt to loss of certain enzymatic functions.

  1. The Role of OmpR in the Expression of Genes of the KdgR Regulon Involved in the Uptake and Depolymerization of Oligogalacturonides in Yersinia enterocolitica

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    Marta Nieckarz

    2017-08-01

    Full Text Available Oligogalacturonide (OGA-specific porins of the KdgM family have previously been identified and characterized in enterobacterial plant pathogens. We found that deletion of the gene encoding response regulator OmpR causes the porin KdgM2 to become one of the most abundant proteins in the outer membrane of the human enteropathogen Yersinia enterocolitica. Reporter gene fusion and real-time PCR analysis confirmed that the expression of kdgM2 is repressed by OmpR. We also found that kdgM2 expression is subject to negative regulation by KdgR, a specific repressor of genes involved in the uptake and metabolism of pectin derivatives in plant pathogens. The additive effect of kdgR and ompR mutations suggested that KdgR and OmpR regulate kdgM2 expression independently. We confirmed that kdgM2 occurs in an operon with the pelP gene, encoding the periplasmic pectate lyase PelP. A pectinolytic assay showed strong upregulation of PelP production/activity in a Y. enterocolitica strain lacking OmpR and KdgR, which corroborates the repression exerted by these regulators on kdgM2. In addition, our data showed that OmpR is responsible for up regulation of the kdgM1 gene encoding the second specific oligogalacturonide porin KdgM1. This indicates the involvement of OmpR in the reciprocal regulation of both KdgM1 and KdgM2. Moreover, we demonstrated the negative impact of OmpR on kdgR transcription, which might positively affect the expression of genes of the KdgR regulon. Binding of OmpR to the promoter regions of the kdgM2-pelP-sghX operon, and kdgM1 and kdgR genes was confirmed using the electrophoretic mobility shift assay, suggesting that OmpR can directly regulate their transcription. We also found that the overexpression of porin KdgM2 increases outer membrane permeability. Thus, OmpR-mediated regulation of the KdgM porins may contribute to the fitness of Y. enterocolitica in particular local environments.

  2. The Vibrio cholerae var regulon encodes a metallo-β-lactamase and an antibiotic efflux pump, which are regulated by VarR, a LysR-type transcription factor.

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    Hong-Ting Victor Lin

    Full Text Available The genome sequence of V. cholerae O1 Biovar Eltor strain N16961 has revealed a putative antibiotic resistance (var regulon that is predicted to encode a transcriptional activator (VarR, which is divergently transcribed relative to the putative resistance genes for both a metallo-β-lactamase (VarG and an antibiotic efflux-pump (VarABCDEF. We sought to test whether these genes could confer antibiotic resistance and are organised as a regulon under the control of VarR. VarG was overexpressed and purified and shown to have β-lactamase activity against penicillins, cephalosporins and carbapenems, having the highest activity against meropenem. The expression of VarABCDEF in the Escherichia coli (ΔacrAB strain KAM3 conferred resistance to a range of drugs, but most significant resistance was to the macrolide spiramycin. A gel-shift analysis was used to determine if VarR bound to the promoter regions of the resistance genes. Consistent with the regulation of these resistance genes, VarR binds to three distinct intergenic regions, varRG, varGA and varBC located upstream and adjacent to varG, varA and varC, respectively. VarR can act as a repressor at the varRG promoter region; whilst this repression was relieved upon addition of β-lactams, these did not dissociate the VarR/varRG-DNA complex, indicating that the de-repression of varR by β-lactams is indirect. Considering that the genomic arrangement of VarR-VarG is strikingly similar to that of AmpR-AmpC system, it is possible that V. cholerae has evolved a system for resistance to the newer β-lactams that would prove more beneficial to the bacterium in light of current selective pressures.

  3. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005296 gi|39936538 >1u07A 13 88 186 259 1e-09 ... emb|CAE28917.1| possible energy ...transducer TonB [Rhodopseudomonas palustris CGA009] ... ref|NP_948814.1| possible energy transducer T

  4. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005296 gi|39935198 >1u07A 9 88 204 283 1e-12 ... emb|CAE27570.1| possible energy t...ransducer TonB, C-terminal region ... [Rhodopseudomonas palustris CGA009] ref|NP_947474.1| ... possible energy

  5. ORF Alignment: NC_002939 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002939 gi|39995137 >1u07A 13 88 186 259 1e-09 ... emb|CAE28917.1| possible energy ...transducer TonB [Rhodopseudomonas palustris CGA009] ... ref|NP_948814.1| possible energy transducer T

  6. ORF Alignment: NC_002939 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002939 gi|39996799 >1u07A 9 88 204 283 1e-12 ... emb|CAE27570.1| possible energy t...ransducer TonB, C-terminal region ... [Rhodopseudomonas palustris CGA009] ref|NP_947474.1| ... possible energy

  7. ORF Alignment: NC_002678 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002678 gi|13471241 >1u07A 13 88 186 259 1e-09 ... emb|CAE28917.1| possible energy ...transducer TonB [Rhodopseudomonas palustris ... CGA009] ref|NP_948814.1| possible energy transducer ...

  8. ORF Alignment: NC_004463 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004463 gi|27379019 >1u07A 13 88 186 259 1e-09 ... emb|CAE28917.1| possible energy ...transducer TonB [Rhodopseudomonas palustris CGA009] ... ref|NP_948814.1| possible energy transducer T

  9. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005296 gi|39933548 >1v7zA 10 254 14 256 2e-44 ... emb|CAE25915.1| putative creatin...e amidohydrolase [Rhodopseudomonas palustris ... CGA009] ref|NP_945824.1| putative creatine ...

  10. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005296 gi|39933534 >1rkd0 3 296 29 346 6e-36 ... emb|CAE25901.1| possible cabohydr...ate kinases [Rhodopseudomonas palustris CGA009] ... ref|NP_945810.1| possible cabohydrate kinases ...

  11. In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS Genes

    Directory of Open Access Journals (Sweden)

    Csengele E. Barta

    2017-10-01

    Full Text Available Mature oak (Quercus spp. leaves, although abundantly available during the plants’ developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS from pin oak (Quercus palustris, whose full genome has not yet been sequenced.

  12. Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD.

    Science.gov (United States)

    Martínez, Luary C; Yakhnin, Helen; Camacho, Martha I; Georgellis, Dimitris; Babitzke, Paul; Puente, José L; Bustamante, Víctor H

    2011-06-01

    Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) play key roles in the pathogenesis of Salmonella enterica. Previously, we showed that when Salmonella grows in Luria-Bertani medium, HilD, encoded in SPI-1, first induces the expression of hilA, located in SPI-1, and subsequently of the ssrAB operon, located in SPI-2. These genes code for HilA and the SsrA/B two-component system, the positive regulators of the SPI-1 and SPI-2 regulons respectively. In this study, we demonstrate that CsrA, a global regulatory RNA binding protein, post-transcriptionally regulates hilD expression by directly binding near the Shine-Dalgarno and translation initiation codon sequences of the hilD mRNA, preventing its translation and leading to its accelerated turnover. Negative regulation is counteracted by the global SirA/BarA two-component system, which directly activates the expression of CsrB and CsrC, two non-coding regulatory RNAs that sequester CsrA, thereby preventing it from binding to its target mRNAs. Our results illustrate the integration of global and specific regulators into a multifactorial regulatory cascade controlling the expression of virulence genes acquired by horizontal transfer events. © 2011 Blackwell Publishing Ltd.

  13. A 400-year phytolith-based reconstruction of wild rice (Zizania palustris) abundance from Mud Lake core sediments, Fond du Lac Band of Lake Superior Chippewa Reservation, Minnesota, USA.

    Science.gov (United States)

    Munoz, R.; Caylor, E.; Yost, C. L.; Drake, C.; Ladwig, J. L.; Myrbo, A.; Howes, T.

    2014-12-01

    Wild rice (Zizania palustris L.) is an aquatic grass with spiritual and subsistence significance to Native people of the Great Lakes region of North America. Mud Lake (Mashkiigwaagamaag), located on the Fond du Lac Band of Lake Superior Chippewa Reservation in Carlton County, Minnesota, USA, once supported an extensive population of wild rice (manoomin). However, early 20th century attempts to ditch and drain surrounding wetlands for landuse intensification severely altered the natural hydrological system that supports wild rice. Fond du Lac Resource Management (FDLRM) technicians are currently working to increase the wild rice population in Mud Lake. As part of these efforts, this phytolith study was undertaken to better understand how wild rice abundance has fluctuated over the past 400 years, with particular emphasis on the 19th and 20th centuries. Phytoliths are microscopic opal silica plant remains that are incorporated into soils and lake sediments after the plant-parts that contain them decay. Wild rice produces phytolith morphotypes that are unequivocally diagnostic. Mud Lake core MNMN-MUD11-1C-1P-1 (46°43'38.39"N, 92°42'2.45"W) was piston cored by LacCore (National Lacustrine Core Facility) and FDLRM technicians on 24 May 2011. Initial core descriptions, multi-sensor core logging, phytolith sampling and phytolith extractions were completed during the summer of 2014 at LacCore. Wild rice phytolith identification and quantification was conducted on twelve samples using brightfield microscopy at 400x magnification. Wild rice phytolith concentration values ranged from 68 to 2,300 phytoliths/cm3. Wild rice accumulation rates ranged from 9 to 383 phytoliths/ cm2/yr, peaking in 1952 AD. Wild rice abundance in Mud Lake appears to be influenced by a complex set of variables that include anthropogenic disturbance, climatic events and aquatic plant community succession.

  14. Development of a Novel Escherichia coli–Kocuria Shuttle Vector Using the Cryptic pKPAL3 Plasmid from K. palustris IPUFS-1 and Its Utilization in Producing Enantiopure (S-Styrene Oxide

    Directory of Open Access Journals (Sweden)

    Hiroshi Toda

    2017-11-01

    Full Text Available The novel cryptic pKPAL3 plasmid was isolated from the Gram-positive microorganism Kocuria palustris IPUFS-1 and characterized in detail. pKPAL3 is a circular plasmid that is 4,443 bp in length. Open reading frame (ORF and homology search analyses indicated that pKPAL3 possesses four ORFs; however, there were no replication protein coding genes predicted in the plasmid. Instead, there were two nucleotide sequence regions that showed significant identities with untranslated regions of K. rhizophila DC2201 (NBRC 103217 genomic sequences, and these sequences were essential for autonomous replication of pKPAL3 in Kocuria cells. Based on these findings, we constructed the novel Escherichia coli–Kocuria shuttle vectors pKITE301 (kanamycin resistant and pKITE303 (thiostrepton resistant from pKPAL3. The copy numbers of the constructed shuttle vectors were estimated to be 20 per cell, and they exhibited low segregation stability in Kocuria transformant cells in the absence of antibiotics. Moreover, constructed vectors showed compatibility with the other K. rhizophila shuttle vector pKITE103. We successfully expressed multiple heterologous genes, including the styrene monooxygenase gene from Rhodococcus sp. ST-10 (rhsmo and alcohol dehydrogenase gene from Leifsonia sp. S749 (lsadh, in K. rhizophila DC2201 using the pKITE301P and pKITE103P vectors under the control of the glyceraldehyde 3-phosphate dehydrogenase (gapdh promotor. The RhSMO–LSADH co-expressing K. rhizophila was used as a biocatalyst in an organic solvent–water biphasic reaction system to efficiently convert styrene into (S-styrene oxide with 99% ee in the presence of 2-propanol as a hydrogen donor. The product concentration of the reaction in the organic solvent reached 235 mM after 30 h under optimum conditions. Thus, we demonstrated that this novel shuttle vector is useful for developing biocatalysts based on organic solvent-tolerant Kocuria cells.

  15. Molecular Regulation of Photosynthetic Carbon Dioxide Fixation in Nonsulfur Purple Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Tabita, Fred Robert [The Ohio State Univ., Columbus, OH (United States)

    2015-12-01

    The overall objective of this project is to determine the mechanism by which a transcriptional activator protein affects CO2 fixation (cbb) gene expression in nonsulfur purple photosynthetic bacteria, with special emphasis to Rhodobacter sphaeroides and with comparison to Rhodopseudomonas palustris. These studies culminated in several publications which indicated that additional regulators interact with the master regulator CbbR in both R. sphaeroides and R. palustris. In addition, the interactive control of the carbon and nitrogen assimilatory pathways was studied and unique regulatory signals were discovered.

  16. Integrating large-scale functional genomics data to dissect metabolic networks for hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline S

    2012-12-17

    The goal of this project is to identify gene networks that are critical for efficient biohydrogen production by leveraging variation in gene content and gene expression in independently isolated Rhodopseudomonas palustris strains. Coexpression methods were applied to large data sets that we have collected to define probabilistic causal gene networks. To our knowledge this a first systems level approach that takes advantage of strain-to strain variability to computationally define networks critical for a particular bacterial phenotypic trait.

  17. Characteristics of purple nonsulfur bacteria grown under Stevia residue extractions.

    Science.gov (United States)

    Xu, J; Feng, Y; Wang, Y; Lin, X

    2013-11-01

    As a consequence of the large-scale cultivation of Stevia plants, releases of plant residues, the byproduct after sweetener extraction, to the environment are inevitable. Stevia residue and its effluent after batching up contain large amounts of organic matters with small molecular weight, which therefore are a potential pollution source. Meanwhile, they are favourite substrates for micro-organism growths. This investigation was aimed to utilize the simulated effluent of Stevia residue to enrich the representative purple nonsulfur bacterium (PNSB), Rhodopseudomonas palustris (Rps. palustris), which has important economic values. The growth profile and quality of Rps. palustris were characterized by spectrophotometry, compared to those grown in common PNSB mineral synthetic medium. Our results revealed that the simulated effluent of Stevia residue not only stimulated Rps. palustris growth to a greater extent, but also increased its physiologically active cytochrome concentrations and excreted indole-3-acetic acid (IAA) content. This variation in phenotype of Rps. palustris could result from the shift in its genotype, further revealed by the repetitive sequence-based PCR (rep-PCR) fingerprinting analysis. Our results showed that the effluent of Stevia residue was a promising substrate for microbial growth. © 2013 The Society for Applied Microbiology.

  18. Identification and growth conditions of purple non-sulfur photosynthetic bacteria isolated from palm oil mill effluent

    International Nuclear Information System (INIS)

    Radziah Ariffin

    2004-01-01

    An indigenous strain of the purple non-sulphur photosynthetic bacterium, isolated from palm oil mill effluent was presumably identified as species of Rhodopseudomonas palustris. Cultivation in synthetic medium under different conditions indicated that it gave maximum carotenoid and bacteriophyll synthesis under anaerobic conditions in the light with values of 12.6 and 108.1 mg/g dry cell weight respectively. These values were significantly higher than the pigment content obtained from aerobic cultivation. The specific growth rates in anaerobic was twice those in aerobic conditions in the light. Growth was not occurred in anaerobic or aerobic conditions in the dark. (Author)

  19. Carbon Dynamics of Pinus palustris Ecosystems Following Drought

    Directory of Open Access Journals (Sweden)

    Gregory Starr

    2016-04-01

    Full Text Available Drought can affect forest structure and function at various spatial and temporal scales. Forest response and recovery from drought may be a result of position within landscape. Longleaf pine forests in the United States have been observed to reduce their carbon sequestration capacity during drought. We collected eddy covariance data at the ends of an edaphic longleaf pine gradient (xeric and mesic sites over seven years; two years of normal rainfall were followed by 2.5 years of drought, then 2.5 years of normal or slightly above-average rainfall. Drought played a significant role in reducing the physiological capacity of the sites and was compounded when prescribed fire occurred during the same periods. The mesic site has a 40% greater basal area then the xeric site, which accounts for its larger sequestration capacity; however, both sites show the same range of variance in fluxes over the course of the study. Following drought, both sites became carbon sinks. However, the xeric site had a longer carry-over effect and never returned to pre-drought function. Although this study encompassed seven years, we argue that longer studies with greater spatial variance must be undertaken to develop a more comprehensive understanding of forest response to changing climate.

  20. Adiciones a las haloragaceae de Colombia: Proserpinaca palustris

    Directory of Open Access Journals (Sweden)

    Schmidt Mumm Udo

    2000-07-01

    Full Text Available Las especies colombianas de la familia Haloragaceae se han asignado a dos subfamilias y tres géneros. Según Mora-Osejo (1984, quién comparte la opinión de Schindler (1905 en incluir el género Gunnera L. en la sub familia terrestre Gunneroideae, la sub familia Haloragoideae distingue las plantas acuáticas y semiacuáticas de tallos herbáceos, raras veces subleñosos, hojas opuestas o verticiladas e inflorescencias terminales. Inicialmente se designaron dos especies del género Myriophyllum L. a esta subfamilia y poco después se señaló también el hallazgo del género Laurembergia Berg. (Mora-Osejo et al. 1988. En la actualidad, sin embargo, se ha generalizado la tendencia a considerar el género Gunnera separadamente en la familia Gunneraceae (Cronquist 1988, L. E. Mora-Osejo, como pers., con lo cual las Haloragaceae de Colombia se encuentran representadas por tres especies de los géneros Myriophyllum y Laurembergia.

  1. Adiciones a las haloragaceae de Colombia: Proserpinaca palustris

    OpenAIRE

    Schmidt Mumm Udo; Posada José Andrés

    2000-01-01

    Las especies colombianas de la familia Haloragaceae se han asignado a dos subfamilias y tres géneros. Según Mora-Osejo (1984), quién comparte la opinión de Schindler (1905) en incluir el género Gunnera L. en la sub familia terrestre Gunneroideae, la sub familia Haloragoideae distingue las plantas acuáticas y semiacuáticas de tallos herbáceos, raras veces subleñosos, hojas opuestas o verticiladas e inflorescencias terminales. Inicialmente se designaron dos especies del género Myriophyllum L. a...

  2. Identification of the ClpX Regulon in Staphylococcus aureus

    DEFF Research Database (Denmark)

    Jelsbak, Lotte; Thomsen, Line Elnif; Ingmer, Hanne

    Staphyloccous aureus is a major human pathogen capable of causing a wide spectrum of infections ranging from superficial wound infections to life-threatening endocarditis and toxic shock syndrome. Essential for S. aureus virulence is a large number of cell-surface-associated proteins and secreted...... we show here that almost 400 genes (15%) are influenced by the clpX deletion. Furthermore, ClpX not only regulates many virulence factors, but rather serves as a global regulator of central functions for S. aureus lifestyle and pathogenicity....

  3. Enhanced photo-H2 production by Rhodopseudomonas faecalis RLD-53 immobilization on activated carbon fibers

    International Nuclear Information System (INIS)

    Xie, Guo-Jun; Liu, Bing-Feng; Ding, Jie; Xing, De-Feng; Ren, Hong-Yu; Guo, Wan-Qian; Ren, Nan-Qi

    2012-01-01

    Activated carbon fibers (ACFs) were firstly applied as fluidized solid carrier to immobilize photo-fermentative bacteria (PFB) for H 2 production in batch culture. The observations by scanning electronic microscopy (SEM) demonstrated the close interaction between ACFs and PFB. The amount of immobilized bacteria and the performance of H 2 production were strongly affected by specific surface area, length and amount of ACFs, respectively. Large specific surface area provided more surface attachment sites and more PFB were immobilized. ACFs with proper length avoided intertwining with each other and better fluidized during reactor operation. Excessive amount of ACFs not only limited the light conversion efficiency, but also increased biofilm detachment, resulting in low H 2 yield. The maximum yield (3.08 mol H 2 mol −1 acetate) and rate (32.85 ml l −1 h −1 ) of H 2 production were obtained, using specific surface area (1500 m 2 g −1 ), length (1 mm) and amount (0.8 g l −1 ) of ACFs. Compared with the conventional solid carriers, ACFs were effective solid carriers to immobilize PFB for improving H 2 production, due to bacteria immobilized on the external surface of fluidized ACFs and formed a layer of dense biofilm. -- Highlights: ► ACFs were firstly used to immobilize photo-fermentative bacteria for H 2 production. ► ACFs were fluidized in the reactor during the operation. ► Bacteria covered on the external surface of ACFs and formed dense biofilm. ► Each bacterium on the ACFs could absorb the light and convert substrate into H 2 .

  4. AFM imaging of bacteria in liquid media immobilized on gelatin coated mica surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Doktycz, M.J.; Sullivan, C.J.; Hoyt, P.R.; Pelletier, D.A.; Wu, S.; Allison, D.P

    2003-10-15

    Immobilization of particulates, especially biomolecules and cells, onto surfaces is critical for imaging with the atomic force microscope (AFM). In this paper, gelatin coated mica surfaces are shown to be suitable for immobilizing and imaging both gram positive, Staphylococcus aureus, and gram negative, Escherichia coli, bacteria in both air and liquid environments. Gelatin coated surfaces are shown to be superior to poly-L-lysine coated surfaces that are commonly used for the immobilization of cells. This cell immobilization technique is being developed primarily for live cell imaging of Rhodopseudomonas palustris. The genome of R. palustris has been sequenced and the organism is the target of intensive studies aimed at understanding genome function. Images of R. palustris grown both aerobically and anaerobically in liquid media are presented. Images in liquid media show the bacteria is rod shaped and smooth while images in air show marked irregularity and folding of the surface. Significant differences in the vertical dimension are also apparent with the height of the bacteria in liquid being substantially greater than images taken in air. In air immobilized bacterial flagella are clearly seen while in liquid this structure is not visible. Additionally, significant morphological differences are observed that depend on the method of bacterial growth.

  5. Towards understanding the biological function of hopanoids (Invited)

    Science.gov (United States)

    Doughty, D. M.; Hunter, R.; Summons, R. E.; Newman, D. K.

    2010-12-01

    Rhodopseudomonas palustris TIE-1 expresses bacterial hopanoid lipids that are structurally similar and evolutionarily related to eukaryotic sterols. The genome of R. palustris TIE-1 contains two copies of the hpnN gene (hpnN1 and hpnN2) that are orthologs of genes encoding eukaryotic sterol and lipid transporters. Hopanoid localization to the outer membrane was found to be dependent upon hpnN1. Since the cell cycle of R. palustris TIE-1 is obligately bimodal with each cell division resulting in the generation of one mother and one swarmer cell, evidence was obtained that hopanoids where specifically localized to the outer membrane of mother cells. The sequestration of hopanoids to the mother cells was also disrupted by the deletion of the hpnN1 gene. Mutants lacking the hopanoid transporters were able to grow normally at 30 °C but showed decreased growth at 38 °C. The hopanoid transporter mutant formed cellular filaments when grown at elevated temperature. Because sedimentary steranes and hopanes comprise some of the earliest evidence for the emergence of distinct bacteria and eukaryotic phyla, a better appreciation of the function of hopanoids will improve our ability to interpret the evolution of life on Earth.

  6. [Construction and Characterization of B850-Only LH2 Energy Transfer System in Purple Bacteria].

    Science.gov (United States)

    Li, Kai; Zhao, Chun-gui; Yue, Hui-ying; Yang, Su-ping; Qu, Yin-bo; Jiao, Nian-zhi

    2015-04-01

    To seek microscopic molecular mechanism of energy transfer and complex reconstitution in the photosynthesis, the conditions for construction of B850-only peripheral light-harvesting complex (LH2) and their properties were investigated using absorption, fluorescence spectroscopy, molecular sieve chromatography, ultrafiltration and sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) from the purple bacteria. The results indicated that bacteriochlorophylls (BChl) of B800 incubated in 10 mmo · L(-1) Tris-HCl (pH 8.0) buffer are selectively released from their binding sites of LH2 of Rhodobacter azotoformans (A-LH2) by 0.08% (W/V) SDS. B850-only A-LH2 was constructed after removing free BChl mixing with 10% methyl alcohol by ultrafiltration. B850 BChl was released after A-LH2 was incubated for 240 min in dark at room temperature (RT). While BChl of B800 incubated in pH 1.9 buffer were selectively released from their binding sites of LH2 of Rhodopseudomonas palustris (P-LH2). The authors acquired two components using molecular sieve chromatography. Free BChl of one component was not removed and self-assembled to P-LH2. The other removed free BChl and B850-only P-LH2 was constructed. B850 unchanged after P-LH2 was incubated. P-LH2 α and β subunits have different molecular weights, but those of A-LH2 are in the contrary. It is concluded that B850-only P-LH2 is more stable than A-LH2. The enigmatic split of the B800 absorption band was not observed in these LH2, but we acquired two kinds of B800-released LH2 from Rhodopseudomonas palustris. The authors' results may provide a new light to separate homogeneous Apoprotein LH2.

  7. Genes essential for phototrophic growth by a purple alphaproteobacterium: Genes for phototrophic growth

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jianming [Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao Shandong Province People' s Republic of China; Department of Microbiology, University of Washington, Seattle WA USA; Yin, Liang [Department of Microbiology, University of Washington, Seattle WA USA; Lessner, Faith H. [Department of Biological Sciences, University of Arkansas, Fayetteville AR USA; Nakayasu, Ernesto S. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Payne, Samuel H. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Fixen, Kathryn R. [Department of Microbiology, University of Washington, Seattle WA USA; Gallagher, Larry [Department of Genome Sciences, University of Washington, Seattle WA USA; Harwood, Caroline S. [Department of Microbiology, University of Washington, Seattle WA USA

    2017-07-24

    Anoxygenic purple phototrophic bacteria have served as important models for studies of photophosphorylation. The pigment-protein complexes responsible for converting light energy to ATP are relatively simple and these bacteria can grow heterotrophically under aerobic conditions, thus allowing for the study of mutants defective in photophosphorylation. In the past, genes responsible for anoxygenic phototrophic growth have been identified in a number of different bacterial species. Here we systematically studied the genetic basis for this metabolism by using Tn-seq to identify genes essential for the anaerobic growth of the purple bacterium Rhodopseudomonas palustris on acetate in light. We identified 171 genes required for growth in this condition, 35 of which are annotated as photosynthesis genes. Among these are a few new genes not previously shown to be essential for phototrophic growth. We verified the essentiality of many of the genes we identified by analyzing the phenotypes of mutants we generated by Tn mutagenesis that had altered pigmentation. We used directed mutagenesis to verify that the R. palustris NADH:quinone oxidoreductase complex IE is essential for phototrophic growth. As a complement to the genetic data, we carried out proteomics experiments in which we found that 429 proteins were present in significantly higher amounts in cells grown anaerobically in light compared to aerobically. Among these were proteins encoded by subset of the phototrophic growth-essential genes.

  8. The ecological classification of coastal wet longleaf pine (pinus palustris) of Florida from reference conditions

    Science.gov (United States)

    George L. McCaskill; Jose. Shibu

    2012-01-01

    Tropical storms, fire, and urbanization have produced a heavily fragmented forested landscape along Florida’s Gulf coast. The longleaf pine forest, one of the most threatened ecosystems in the US, makes up a major part of this fragmented landscape. These three disturbance regimes have produced a mosaic of differently-aged pine patches of single or two cohort structures...

  9. Factors Affecting the Distribution of Wild Rice (Zizania palustris) and the Surrounding Macrophyte Community.

    Science.gov (United States)

    Pillsbury, R. W.; McGuire, M.

    2005-05-01

    A recent decline in wild rice wetlands is cause for concern due to its importance as a food source, refuge for wildlife, and cultural significance. Sixty wetlands in Wisconsin and Minnesota (USA) were sampled, with approximately equal numbers displaying dense, moderate and sparse wild rice production. Chemical, physical, and watershed parameters were measured as well as macrophyte densities. Data were analyzed using multivariate statistics (CCA). Moderate levels of phosphorus appear beneficial to the overall success of wild rice, while free-floating macrophytes show an overwhelming positive response to higher levels of P. The distribution of macrophytes bordering wild rice beds is correlated to pH,with Potamogeton robbinsii and filamentous green algae responding most strongly to its increase. Healthy stands of wild rice exhibit a narrow circum-neutral range of pH (6.1-8.0)which is significantly different from the greater range exhibited by sparse wild rice wetlands (6.5-8.5). This pattern was paralleled when considering depth which suggests that deeper wetlands may be more susceptible to wild rice loss. Management of existing wild rice wetlands should focus monitoring on pH, depth, phosphorus concentrations and shore development. We are currently using this data base to locate the best reintroduction sites for wild rice.

  10. Moulting and wintering grounds of Marsh Warblers Acrocephalus palustris: evidence from stable isotopes and ring recoveries

    Czech Academy of Sciences Publication Activity Database

    Procházka, Petr; Kralj, J.; Pearson, D. J.; Yohannes, E.

    2014-01-01

    Roč. 49, č. 2 (2014), s. 193-200 ISSN 0001-6454 R&D Projects: GA ČR GA13-06451S Institutional support: RVO:68081766 Keywords : bird migration * feather stable isotopes * ring recoveries * stopover * migratory connectivity * δ13C * δ15N Subject RIV: EG - Zoology Impact factor: 0.745, year: 2014

  11. Resprouting after disturbance in the short-lived herb Rorippa palustris (Brassicaceae): an experiment with juveniles

    Czech Academy of Sciences Publication Activity Database

    Martínková, Jana; Kočvarová, Marie; Klimešová, Jitka

    2004-01-01

    Roč. 25, č. 3 (2004), s. 143-150 ISSN 1146-609X R&D Projects: GA AV ČR KSK6005114; GA ČR GD206/03/H034; GA ČR GA206/01/1039 Institutional research plan: CEZ:AV0Z6005908 Keywords : root-sprouting * bud bank * disturbance Subject RIV: EF - Botanics Impact factor: 1.034, year: 2004

  12. Photosynthetic consequences of phenotypic plasticity in response to submergence: Rumex palustris as a case study

    NARCIS (Netherlands)

    Mommer, L.; Pons, T.L.; Visser, E.J.W.

    2006-01-01

    Survival and growth of terrestrial plants is negatively affected by complete submergence. This is mainly the result of hampered gas exchange between plants and their environment, since gas diffusion is severely reduced in water compared with air, resulting in O2 deficits which limit aerobic

  13. Time series analysis of forest carbon dynamics: recovery of Pinus palustris physiology following a prescribed fire

    Science.gov (United States)

    G. Starr; C. L. Staudhammer; H. W. Loescher; R. Mitchell; A. Whelan; J. K. Hiers; J. J. O’Brien

    2015-01-01

    Frequency and intensity of fire determines the structure and regulates the function of savanna ecosystems worldwide, yet our understanding of prescribed fire impacts on carbon in these systems is rudimentary. We combined eddy covariance (EC) techniques and fuel consumption plots to examine the short-term response of longleaf pine forest carbon dynamics to one...

  14. Spatial patterns of longleaf pine (Pinus palustris) seedling eastablishment on the croatan national forest, North Carolina

    Science.gov (United States)

    Chadwick R. Avery; Susan Cohen; Kathleen C. Parker; John S. Kush

    2004-01-01

    Ecological research aimed at determining optimal conditions for longleaf pine regeneration has become increasingly important in efforts @ restore the longleaf pine ecosystem. Numerous authors have concluded that a negative relationship exists between the occurrence of seedlings and the occurrence of mature trees; however, observed field conditions in several North...

  15. Spatial and Temporal Analyses of Environmental Affects on Zizania Palustris and Its Natural Cycles

    Science.gov (United States)

    Rickman, Douglas L.; Greensky, Wayne; Al-Hamdan, M. Z.; Estes, M. G.; Crosson, W. L.; Estes, Sue M.

    2017-01-01

    As part of a joint education and research effort funded by NASA, research studies were initiated involving students associated with the Ojibwe and researchers at Marshall Space Flight Center. Topics were chosen that satisfied the nature of the work proposed and were tractable, given the student's constraints (abilities, interests, and time). One of the studies, which spanned two summers, examined some potential environmental effects on northern wild rice in northern Wisconsin. The rice of interest is naturally occurring ('wild' wild rice), as opposed to cultivated wild rice ('paddy' wild rice).

  16. Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica

    OpenAIRE

    Jacquemyn, Hans; Waud, Michael; Lievens, Bart; Brys, Rein

    2016-01-01

    Background and Aims In orchid species that have populations occurring in strongly contrasting habitats, mycorrhizal divergence and other habitat-specific adaptations may lead to the formation of reproductively isolated taxa and ultimately to species formation. However, little is known about the mycorrhizal communities associated with recently diverged sister taxa that occupy different habitats.

  17. Phosphoenolpyruvate-dependent fructose phosphotransferase system in Rhodopseudomonas sphaeroides : The coupling between transport and phosphorylation in inside-out vesicles

    NARCIS (Netherlands)

    Lolkema, Juke S.; Robillard, George T.

    The bacterial phosphotransferase systems are believed to catalyze the concomitant transport and phosphorylation of hexoses and hexitols. The transport is from the outside to the inside of the cell. An absolute coupling between transport and phosphorylation has however been questioned in the

  18. Cysteine-mediated gene expression and characterization of the CmbR regulon in Streptococcus pneumoniae

    Directory of Open Access Journals (Sweden)

    Muhammad Afzal

    2016-12-01

    Full Text Available In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to cysteine. Transcriptome comparison of the D39 wild-type strain grown at a restricted concentration of cysteine (0.03 mM to one grown at a high concentration of cysteine (50 mM in chemically-define medium (CDM revealed elevated expression of various genes/operons, i.e. spd-0150, metQ, spd-0431, metEF, gshT, spd-0618, fhs, tcyB, metB-csd, metA, spd-1898, yvdE, and cysK, likely to be involved in the transport and utilization of cysteine and/or methionine. Microarray-based data were further confirmed by quantitative RT-PCR. Promoter lacZ-fusion studies and quantitative RT-PCR data showed that the transcriptional regulator CmbR acts as a transcriptional repressor of spd-0150, metEF, gshT, spd-0618, tcyB, metA, and yvdE, putatively involved in cysteine uptake and utilization. The operator site of CmbR in the promoter regions of CmbR-regulated genes is predicted and confirmed by mutating or deleting CmbR operator sites from the promoter regions of these genes.

  19. Role of the Fur regulon in iron transport in Bacillus subtilis.

    Science.gov (United States)

    Ollinger, Juliane; Song, Kyung-Bok; Antelmann, Haike; Hecker, Michael; Helmann, John D

    2006-05-01

    The Bacillus subtilis ferric uptake regulator (Fur) protein mediates the iron-dependent repression of at least 20 operons encoding approximately 40 genes. We investigated the physiological roles of Fur-regulated genes by the construction of null mutations in 14 transcription units known or predicted to function in siderophore biosynthesis or iron uptake. We demonstrate that ywbLMN, encoding an elemental iron uptake system orthologous to the copper oxidase-dependent Fe(III) uptake system of Saccharomyces cerevisiae, is essential for growth in low iron minimal medium lacking citric acid. 2,3-Dihydroxybenzoyl-glycine (Itoic acid), the siderophore precursor produced by laboratory strains of B. subtilis, is of secondary importance. In the presence of citrate, the YfmCDEF ABC transporter is required for optimal growth. B. subtilis is unable to grow in minimal medium containing the iron chelator EDDHA unless the ability to synthesize the intact bacillibactin siderophore is restored (by the introduction of a functional sfp gene) or exogenous siderophores are provided. Utilization of the catecholate siderophores bacillibactin and enterobactin requires the FeuABC importer and the YusV ATPase. Utilization of hydroxamate siderophores requires the FhuBGC ABC transporter together with the FhuD (ferrichrome) or YxeB (ferrioxamine) substrate-binding proteins. Growth with schizokinen or arthrobactin is at least partially dependent on the YfhA YfiYZ importer and the YusV ATPase. We have also investigated the effects of a fur mutation on the proteome and documented the derepression of 11 Fur-regulated proteins, including a newly identified thioredoxin reductase homolog, YcgT.

  20. PePPER : a webserver for prediction of prokaryote promoter elements and regulons

    NARCIS (Netherlands)

    de Jong, Anne; Pietersma, Hilco; Cordes, Martijn; Kuipers, Oscar P.; Kok, Jan

    2012-01-01

    Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison

  1. Activation of silent gal genes in the lac-gal regulon of Streptococcus thermophilus

    NARCIS (Netherlands)

    Vaughan, E.E.; Bogaard, van den P.T.C.; Catzeddu, P.; Kuipers, O.P.; Vos, de W.M.

    2001-01-01

    Streptococcus thermophilus strain CNRZ 302 is unable to ferment galactose, neither that generated intracellularly by lactose hydrolysis nor the free sugar. Nevertheless, sequence analysis and complementation studies with Escherichia coli demonstrated that strain CNRZ 302 contained structurally

  2. Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

    Science.gov (United States)

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D.; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard

    2014-01-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei. PMID:24464461

  3. Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli▿ †

    Science.gov (United States)

    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-01-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism. PMID:21115656

  4. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli.

    Science.gov (United States)

    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-02-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.

  5. Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon.

    Science.gov (United States)

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E Peter

    2014-04-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei.

  6. Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

    OpenAIRE

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D.; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E. Peter

    2014-01-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that gene...

  7. Fire Frequency Effects on Longleaf Pine (Pinus palustris P. Miller) Vegetation in South Carolina and Northeast Florida, USA

    Science.gov (United States)

    Jeff S. Glitzenstein; Donna R. Streng; Dale D. Wade

    2003-01-01

    Southeastern United States habitats dominated by longleaf pine (Pinus pulutris P. Miller) have declined precipitously in area and extent. Conservation of diverse ground-layer vegetation in these endangered habitats depends on prescribed fire. While the need for prescribed fire is now generally accepted, there is disagreement concerning the most...

  8. The effect of flooding and injury on vegetative regeneration from roots: a case study with Rorippa palustris

    Czech Academy of Sciences Publication Activity Database

    Sosnová, Monika; Klimešová, Jitka

    2013-01-01

    Roč. 214, č. 8 (2013), 999-1006 ISSN 1385-0237 R&D Projects: GA ČR GA526/09/0963 Institutional support: RVO:67985939 Keywords : root buds * submergence * disturbance Subject RIV: EH - Ecology, Behaviour Impact factor: 1.640, year: 2013

  9. LONG-TERM TRENDS IN GROWTH OF PINUS PALUSTRIS AND PINUS ELLIOTTII GROWING ALONG A HYDROLOGICAL GRADIENT IN CENTRAL FLORIDA

    Science.gov (United States)

    Land-use change and urbanization has led to changes in the hydrologic regime in wet central Florida, with a trend toward lowered water table levels. These hydrologic changes are having environmental consequences in wetlands, where shifts in species composition and fire frequency...

  10. Imputation of individual longleaf pine (Pinus palustris Mill.) tree attributes from field and LiDAR data

    Science.gov (United States)

    Carlos A. Silva; Andrew T. Hudak; Lee A. Vierling; E. Louise Loudermilk; Joseph J. O' Brien; J. Kevin Hiers; Steve B. Jack; Carlos Gonzalez-Benecke; Heezin Lee; Michael J. Falkowski; Anahita Khosravipour

    2016-01-01

    Light Detection and Ranging (LiDAR) has demonstrated potential for forest inventory at the individual-tree level. The aim in this study was to predict individual-tree height (Ht; m), basal area (BA; m2), and stem volume (V; m3...

  11. Study of Feasibility Integrated Agroindustry Development Unit Black Grass Jelly Powder (Mesona palustris in Province of East Java

    Directory of Open Access Journals (Sweden)

    Irvan Adhin Cholilie

    2017-01-01

    Full Text Available Potential of black grass jelly plant in Indonesia is very prospective. These plants grow in areas such as Malang East Java, Pacitan, Magetan and Ponorogo. In 2010 the production of dried black grass jelly of 568 tons with a total productivity of 8.6 tons / year.  Location selection of the plant with a score weighting method produces the highest value of 4,16 for the city of Surabaya, so the establishment of the plant will be held in Surabaya. Therefore, it is necessary the application of a suitable drying models for this factory that is tunnel dryer based on the results of research and with the highest value is 4,281. To ensure the availability of black grass jelly dried leaves as raw materials of black grass jelly powder it is necessary to establish a partnership between farmers and companies. The partnership pattern that works best for black grass jelly powder factory is a partnership “inti plasma”. It is based on research with the results of the assessment and weighting by using pairwise comparison and rating scale, the value of the highest weight in the “inti plasma” partnership with a value of 4,893. By implementing this partnership will allow the factory to obtain raw materials easily and is more economical and can always be available throughout the year for partnering with farmers.    Keywords: black grass jelly powder, drying method, financial feasibility analysis, partnership patterns

  12. Life-history variation in the short-lived herb Rorippa palustris: effects of germination date and injury timing

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Sosnová, Monika; Martínková, Jana

    2007-01-01

    Roč. 189, - (2007), s. 237-246 ISSN 1385-0237 R&D Projects: GA ČR GD206/03/H034 Institutional research plan: CEZ:AV0Z60050516 Keywords : Bud bank * Cohorts * Life history Subject RIV: EF - Botanics Impact factor: 1.236, year: 2007

  13. No evidence for memory interference across sessions in food hoarding marsh tits Poecile palustris under laboratory conditions.

    Science.gov (United States)

    Urhan, A Utku; Brodin, Anders

    2015-05-01

    Scatter hoarding birds are known for their accurate spatial memory. In a previous experiment, we tested the retrieval accuracy in marsh tits in a typical laboratory set-up for this species. We also tested the performance of humans in this experimental set-up. Somewhat unexpectedly, humans performed much better than marsh tits. In the first five attempts, humans relocated almost 90 % of the caches they had hidden 5 h earlier. Marsh tits only relocated 25 % in the first five attempts and just above 40 % in the first ten attempts. Typically, in this type of experiment, the birds will be caching and retrieving many times in the same sites in the same experimental room. This is very different from the conditions in nature where hoarding parids only cache once in a caching site. Hence, it is possible that memories from previous sessions will disturb the formation of new memories. If there is such proactive interference, the prediction is that success should decay over sessions. Here, we have designed an experiment to investigate whether there is such memory interference in this type of experiment. We allowed marsh tits and humans to cache and retrieve in three repeated sessions without prior experience of the arena. The performance did not change over sessions, and on average, marsh tits correctly visited around 25 % of the caches in the first five attempts. The corresponding success in humans was constant across sessions, and it was around 90 % on average. We conclude that the somewhat poor performance of the marsh tits did not depend on proactive memory interference. We also discuss other possible reasons for why marsh tits in general do not perform better in laboratory experiments.

  14. Structural features of PhoX, one of the phosphate-binding proteins from Pho regulon of Xanthomonas citri

    Science.gov (United States)

    Pegos, Vanessa R.; Santos, Rodrigo M. L.; Medrano, Francisco J.

    2017-01-01

    In Escherichia coli, the ATP-Binding Cassette transporter for phosphate is encoded by the pstSCAB operon. PstS is the periplasmic component responsible for affinity and specificity of the system and has also been related to a regulatory role and chemotaxis during depletion of phosphate. Xanthomonas citri has two phosphate-binding proteins: PstS and PhoX, which are differentially expressed under phosphate limitation. In this work, we focused on PhoX characterization and comparison with PstS. The PhoX three-dimensional structure was solved in a closed conformation with a phosphate engulfed in the binding site pocket between two domains. Comparison between PhoX and PstS revealed that they originated from gene duplication, but despite their similarities they show significant differences in the region that interacts with the permeases. PMID:28542513

  15. Dehydrogenase GRD1 Represents a Novel Component of the Cellulase Regulon in Trichoderma reesei (Hypocrea jecorina) ▿ † §

    Science.gov (United States)

    Schuster, André; Kubicek, Christian P.; Schmoll, Monika

    2011-01-01

    Trichoderma reesei (Hypocrea jecorina) is nowadays the most important industrial producer of cellulase and hemicellulase enzymes, which are used for pretreatment of cellulosic biomass for biofuel production. In this study, we introduce a novel component, GRD1 (glucose-ribitol dehydrogenase 1), which shows enzymatic activity on cellobiose and positively influences cellulase gene transcription, expression, and extracellular endo-1,4-β-d-glucanase activity. grd1 is differentially transcribed upon growth on cellulose and the induction of cellulase gene expression by sophorose. The transcription of grd1 is coregulated with that of cel7a (cbh1) under inducing conditions. GRD1 is further involved in carbon source utilization on several carbon sources, such as those involved in lactose and d-galactose catabolism, in several cases in a light-dependent manner. We conclude that GRD1 represents a novel enhancer of cellulase gene expression, which by coregulation with the major cellulase may act via optimization of inducing mechanisms. PMID:21602376

  16. Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae

    Directory of Open Access Journals (Sweden)

    Hasnain Seyed

    2004-09-01

    Full Text Available Abstract Background The diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae. Result Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG, an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin. Conclusions We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase, a potential vaccine candidate and proteins of secretory system.

  17. MMSET deregulation affects cell cycle progression and adhesion regulons in t(4;14) myeloma plasma cells

    Science.gov (United States)

    Brito, Jose L.R.; Walker, Brian; Jenner, Matthew; Dickens, Nicholas J.; Brown, Nicola J.M.; Ross, Fiona M.; Avramidou, Athanasia; Irving, Julie A.E.; Gonzalez, David; Davies, Faith E.; Morgan, Gareth J.

    2009-01-01

    Background The recurrent immunoglobulin translocation, t(4;14)(p16;q32) occurs in 15% of multiple myeloma patients and is associated with poor prognosis, through an unknown mechanism. The t(4;14) up-regulates fibroblast growth factor receptor 3 (FGFR3) and multiple myeloma SET domain (MMSET) genes. The involvement of MMSET in the pathogenesis of t(4;14) multiple myeloma and the mechanism or genes deregulated by MMSET upregulation are still unclear. Design and Methods The expression of MMSET was analyzed using a novel antibody. The involvement of MMSET in t(4;14) myelomagenesis was assessed by small interfering RNA mediated knockdown combined with several biological assays. In addition, the differential gene expression of MMSET-induced knockdown was analyzed with expression microarrays. MMSET gene targets in primary patient material was analyzed by expression microarrays. Results We found that MMSET isoforms are expressed in multiple myeloma cell lines, being exclusively up-regulated in t(4;14)-positive cells. Suppression of MMSET expression affected cell proliferation by both decreasing cell viability and cell cycle progression of cells with the t(4;14) translocation. These findings were associated with reduced expression of genes involved in the regulation of cell cycle progression (e.g. CCND2, CCNG1, BRCA1, AURKA and CHEK1), apoptosis (CASP1, CASP4 and FOXO3A) and cell adhesion (ADAM9 and DSG2). Furthermore, we identified genes involved in the latter processes that were differentially expressed in t(4;14) multiple myeloma patient samples. Conclusions In conclusion, dysregulation of MMSET affects the expression of several genes involved in the regulation of cell cycle progression, cell adhesion and survival. PMID:19059936

  18. Evolution of the miR5200-FLOWERING LOCUS T flowering time regulon in the temperate grass subfamily Pooideae.

    Science.gov (United States)

    McKeown, Meghan; Schubert, Marian; Preston, Jill C; Fjellheim, Siri

    2017-09-01

    Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition. We hypothesize that miR5200 photoperiod-sensitive regulation of Pooideae flowering time networks assisted their transition into northern seasonal environments. Here, we test predictions derived from this hypothesis that miR5200, originally found in bread wheat and later identified in Brachypodium distachyon, (1) was present in the genome of the Pooideae common ancestor, (2) is transcriptionally regulated by photoperiod, and (3) is negatively correlated with FT transcript abundance, indicative of miR5200 regulating FT. Our results demonstrate that miR5200 did evolve at or around the base of Pooideae, but only acquired photoperiod-regulated transcription within the Brachypodium lineage. Based on expression profiles and previous data, we posit that the progenitor of miR5200 was co-regulated with FT by an unknown mechanism. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. MzrA: a novel modulator of the EnvZ/OmpR two-component regulon

    Science.gov (United States)

    Gerken, Henri; Charlson, Emily S; Cicirelli, Elisha M; Kenney, Linda J; Misra, Rajeev

    2009-01-01

    Analysis of suppressors that alleviate the acute envelope stress phenotype of a ΔbamBΔdegP strain of Escherichia coli identified a novel protein MzrA and pleiotropic envZ mutations. Genetic evidence shows that overexpression of MzrA – formerly known as YqjB and EcfM – modulates the activity of EnvZ/OmpR similarly to pleiotropic EnvZ mutants and alter porin expression. However, porin expression in strains devoid of MzrA or overexpressing it is still sensitive to medium osmolarity, pH and procaine, all of which modulate EnvZ/OmpR activities. Thus, MzrA appears to alter the output of the EnvZ/OmpR system but not its ability to receive and respond to various environmental signals. Localization and topology experiments indicate that MzrA is a type II membrane protein, with its N-terminus exposed in the cytoplasm and C-terminus in the periplasm. Bacterial two-hybrid experiments determined that MzrA specifically interacts with EnvZ but not with OmpR or the related membrane sensor kinase, CpxA. This and additional genetic and biochemical evidence suggest that the interaction of MzrA with EnvZ would either enhance EnvZ's kinase activity or reduce its phosphatase activity, thus elevating the steady state levels of OmpR∼P. Furthermore, our data show that MzrA links the two-component envelope stress response regulators, CpxA/CpxR and EnvZ/OmpR. PMID:19432797

  20. Exposure to Glycolytic Carbon Sources Reveals a Novel Layer of Regulation for the MalT Regulon

    Directory of Open Access Journals (Sweden)

    Sylvia A. Reimann

    2011-01-01

    Full Text Available Bacteria adapt to changing environments by means of tightly coordinated regulatory circuits. The use of synthetic lethality, a genetic phenomenon in which the combination of two nonlethal mutations causes cell death, facilitates identification and study of such circuitry. In this study, we show that the E. coli ompR malTcon double mutant exhibits a synthetic lethal phenotype that is environmentally conditional. MalTcon, the constitutively active form of the maltose system regulator MalT, causes elevated expression of the outer membrane porin LamB, which leads to death in the absence of the osmoregulator OmpR. However, the presence and metabolism of glycolytic carbon sources, such as sorbitol, promotes viability and unveils a novel layer of regulation within the complex circuitry that controls maltose transport and metabolism.

  1. Convergent Transcription in the Butyrolactone Regulon in Streptomyces coelicolor Confers a Bistable Genetic Switch for Antibiotic Biosynthesis

    Science.gov (United States)

    Chatterjee, Anushree; Drews, Laurie; Mehra, Sarika; Takano, Eriko; Kaznessis, Yiannis N.; Hu, Wei-Shou

    2011-01-01

    cis-encoded antisense RNAs (cis asRNA) have been reported to participate in gene expression regulation in both eukaryotic and prokaryotic organisms. Its presence in Streptomyces coelicolor has also been reported recently; however, its role has yet to be fully investigated. Using mathematical modeling we explore the role of cis asRNA produced as a result of convergent transcription in scbA-scbR genetic switch. scbA and scbR gene pair, encoding repressor–amplifier proteins respectively, mediates the synthesis of a signaling molecule, the γ-butyrolactone SCB1 and controls the onset of antibiotic production. Our model considers that transcriptional interference caused by convergent transcription of two opposing RNA polymerases results in fatal collision and transcriptional termination, which suppresses transcription efficiency. Additionally, convergent transcription causes sense and antisense interactions between complementary sequences from opposing strands, rendering the full length transcript inaccessible for translation. We evaluated the role of transcriptional interference and the antisense effect conferred by convergent transcription on the behavior of scbA-scbR system. Stability analysis showed that while transcriptional interference affects the system, it is asRNA that confers scbA-scbR system the characteristics of a bistable switch in response to the signaling molecule SCB1. With its critical role of regulating the onset of antibiotic synthesis the bistable behavior offers this two gene system the needed robustness to be a genetic switch. The convergent two gene system with potential of transcriptional interference is a frequent feature in various genomes. The possibility of asRNA regulation in other such gene-pairs is yet to be examined. PMID:21765930

  2. The PurR regulon in Lactococcus lactis – transcriptional regulation of the purine nucleotide metabolism and translational machinery

    DEFF Research Database (Denmark)

    Jendresen, Christian Bille; Martinussen, Jan; Kilstrup, Mogens

    2012-01-01

    Purine nucleotides are either synthesized de novo from 5-phosphoribosyl-1-pyrophosphate (PRPP) or salvaged from the environment. In Lactococcus lactis, transcription of the de novo synthesis operons, purCSQLF and purDEK, has genetically been shown to be activated by the PurR protein when bound to......-related functions. Of special interest is the presence of PurBox motifs in rrn promoters, suggesting a novel connection between nucleotide availability and the translational machinery....

  3. The Redox-Sensitive Transcriptional Activator OxyR Regulates the Peroxide Response Regulon in the Obligate Anaerobe Bacteroides fragilis

    Science.gov (United States)

    Rocha, Edson R.; Owens, Gary; Smith, C. Jeffrey

    2000-01-01

    The peroxide response-inducible genes ahpCF, dps, and katB in the obligate anaerobe Bacteroides fragilis are controlled by the redox-sensitive transcriptional activator OxyR. This is the first functional oxidative stress regulator identified and characterized in anaerobic bacteria. oxyR and dps were found to be divergently transcribed, with an overlap in their respective promoter regulatory regions. B. fragilis OxyR and Dps proteins showed high identity to homologues from a closely related anaerobe, Porphyromonas gingivalis. Northern blot analysis revealed that oxyR was expressed as a monocistronic 1-kb mRNA and that dps mRNA was approximately 500 bases in length. dps mRNA was induced over 500-fold by oxidative stress in the parent strain and was constitutively induced in the peroxide-resistant mutant IB263. The constitutive peroxide response in strain IB263 was shown to have resulted from a missense mutation at codon 202 (GAT to GGT) of the oxyR gene [oxyR(Con)] with a predicted D202G substitution in the OxyR protein. Transcriptional fusion analysis revealed that deletion of oxyR abolished the induction of ahpC and katB following treatment with hydrogen peroxide or oxygen exposure. However, dps expression was induced approximately fourfold by oxygen exposure in ΔoxyR strains but not by hydrogen peroxide. This indicates that dps expression is also under the control of an oxygen-dependent OxyR-independent mechanism. Complementation of ΔoxyR mutant strains with wild-type oxyR and oxyR(Con) restored the inducible peroxide response and the constitutive response of the ahpCF, katB, and dps genes, respectively. However, overexpression of OxyR abolished the catalase activity but not katB expression, suggesting that higher levels of intracellular OxyR may be involved in other physiological processes. Analysis of oxyR expression in the parents and in ΔoxyR and overexpressing oxyR strains by Northern blotting and oxyR′::xylB fusions revealed that B. fragilis OxyR does not control its own expression. PMID:10960088

  4. Adaptation of Rhodopseudomonas acidophila strain 7050 to growth at different light intensities: what are the benefits to changing the type of LH2?

    Science.gov (United States)

    Gardiner, A T; Niedzwiedzki, D M; Cogdell, R J

    2018-04-01

    Typical purple bacterial photosynthetic units consist of light harvesting one/reaction centre 'core' complexes surrounded by light harvesting two complexes. Factors such as the number and size of photosynthetic units per cell, as well as the type of light harvesting two complex that is produced, are controlled by environmental factors. In this paper, the change in the type of LH2 present in the Rhodopsuedomonas acidophila strain 7050 is described when cells are grown at a range of different light intensities. This species contains multiple pucBA genes that encode the apoproteins that form light-harvesting complex two, and a more complex mixture of spectroscopic forms of this complex has been found than was previously thought to be the case. Femto-second time resolved absorption has been used to investigate how the energy transfer properties in the membranes of high-light and low-light adapted cells change as the composition of the LH2 complexes varies.

  5. A pilot-scale study of biohydrogen production from distillery effluent using defined bacterial co-culture

    Energy Technology Data Exchange (ETDEWEB)

    Vatsala, T.M.; Raj, S. Mohan; Manimaran, A. (Shri AMM Murugappa Chettiar Research Centre, Photosynthesis and Energy Division, Tharamani, Chennai, India, 600)

    2008-10-15

    We evaluated the feasibility of improving the scale of hydrogen (H{sub 2}) production from sugar cane distillery effluent using co-cultures of Citrobacter freundii 01, Enterobacter aerogenes E10 and Rhodopseudomonas palustris P2 at 100 m{sup 3} scale. The culture conditions at 100 ml and 2 L scales were optimized in minimal medium and we observed that the co-culture of the above three strains enhanced H{sub 2} productivity significantly. Results at the 100 m{sup 3} scale revealed a maximum of 21.38 kg of H{sub 2}, corresponding to 10692.6 mol, which was obtained through batch method at 40 h from reducing sugar (3862.3 mol) as glucose. The average yield of H{sub 2} was 2.76 mol mol{sup -1} glucose, and the rate of H{sub 2} production was estimated as 0.53 kg/100 m{sup 3}/h. Our results demonstrate the utility of distillery effluent as a source of clean alternative energy and provide insights into treatment for industrial exploitation. (author)

  6. Effects of probiotics on the growth performance and intestinal micro flora of broiler chickens.

    Science.gov (United States)

    Li, Yin-bo; Xu, Qian-qian; Yang, Cun-jin; Yang, Xin; Lv, Le; Yin, Chun-hua; Liu, Xiao-lu; Yan, Hai

    2014-05-01

    Antibiotics have been used in poultry industry for decades to promote growth and protect animals from diseases, followed by various side effects. In efforts of searching for a better alternative, probiotic is of extensive attention. We investigated the effects of Bacillus subtitles, Rhodopseudomonas palustris, Candida utilis and Lactobacillus acidophilus as 0.1% (W/W) feed additives on broiler growth performance and intestinal microflora. The results showed the probiotics treatments significantly improved growth of broilers. Broilers supplemented with B. subtilis and L. acidophilus weighed 18.4% and 10.1% more than birds in control group at 42 days of age. Furthermore the feed conversion ratios of the birds in the two groups were also improved, decreasing 9.1% and 12.9%, respectively. Further study indicated a significant increase of cecal Lactobacilli concentration in briolers supplemented with probiotics, expecially in L. acidophilus treatment group. Meanwhile, the count of cecal Actinomyces in birds treated with probiotics was significantly lower compared with the control group. In conclusion, probiotics such as B. subtitles and L. acidophilus are good alternatives to antibiotics in promoting growth resulting from a beneficial modulation of the intestinal micro flora, which leads to increased efficiency of intestinal digestion in the host animal.

  7. Development of bacteria-based bioassays for arsenic detection in natural waters.

    Science.gov (United States)

    Diesel, Elizabeth; Schreiber, Madeline; van der Meer, Jan Roelof

    2009-06-01

    Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.

  8. Bioaugmentation for Electricity Generation from Corn Stover Biomass Using Microbial Fuel Cells

    KAUST Repository

    Wang, Xin

    2009-08-01

    Corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. However, it is possible to directly generate electricity from corn stover in microbial fuel cells (MFCs) through the addition of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to singlechamber, air-cathode MFCs acclimated for power production using glucose. The MFC produced a maximum power of 331 mW/ m 2 with the bioaugmented mixed culture and corn stover, compared to 510 mW/m2 using glucose. Denaturing gradient gel electrophoresis (DGGE) showed the communities continued to evolve on both the anode and corn stover biomass over 60 days, with several bacteria identified including Rhodopseudomonas palustris. The use of residual solids from the steam exploded corn stover produced 8% more power (406 mW/m2) than the raw corn stover. These results show that it is possible to directly generate electricity from waste corn stover in MFCs through bioaugmentation using naturally occurring bacteria. © 2009 American Chemical Society.

  9. Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

    KAUST Repository

    Xing, Defeng

    2009-09-01

    Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8-10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs. © 2009 Elsevier B.V. All rights reserved.

  10. Introducing capnophilic lactic fermentation in a combined dark-photo fermentation process: a route to unparalleled H2 yields.

    Science.gov (United States)

    Dipasquale, L; Adessi, A; d'Ippolito, G; Rossi, F; Fontana, A; De Philippis, R

    2015-01-01

    Two-stage process based on photofermentation of dark fermentation effluents is widely recognized as the most effective method for biological production of hydrogen from organic substrates. Recently, it was described an alternative mechanism, named capnophilic lactic fermentation, for sugar fermentation by the hyperthermophilic bacterium Thermotoga neapolitana in CO2-rich atmosphere. Here, we report the first application of this novel process to two-stage biological production of hydrogen. The microbial system based on T. neapolitana DSM 4359(T) and Rhodopseudomonas palustris 42OL gave 9.4 mol of hydrogen per mole of glucose consumed during the anaerobic process, which is the best production yield so far reported for conventional two-stage batch cultivations. The improvement of hydrogen yield correlates with the increase in lactic production during capnophilic lactic fermentation and takes also advantage of the introduction of original conditions for culturing both microorganisms in minimal media based on diluted sea water. The use of CO2 during the first step of the combined process establishes a novel strategy for biohydrogen technology. Moreover, this study opens the way to cost reduction and use of salt-rich waste as feedstock.

  11. Electron uptake by iron-oxidizing phototrophic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Bose, A; Gardel, EJ; Vidoudez, C; Parra, EA; Girguis, PR

    2014-02-26

    Oxidation-reduction reactions underlie energy generation in nearly all life forms. Although most organisms use soluble oxidants and reductants, some microbes can access solid-phase materials as electron-acceptors or -donors via extracellular electron transfer. Many studies have focused on the reduction of solid-phase oxidants. Far less is known about electron uptake via microbial extracellular electron transfer, and almost nothing is known about the associated mechanisms. Here we show that the iron-oxidizing photoautotroph Rhodopseudomonas palustris TIE-1 accepts electrons from a poised electrode, with carbon dioxide as the sole carbon source/electron acceptor. Both electron uptake and ruBisCo form I expression are stimulated by light. Electron uptake also occurs in the dark, uncoupled from photosynthesis. Notably, the pioABC operon, which encodes a protein system essential for photoautotrophic growth by ferrous iron oxidation, influences electron uptake. These data reveal a previously unknown metabolic versatility of photoferrotrophs to use extracellular electron transfer for electron uptake.

  12. Development of bacteria-based bioassays for arsenic detection in natural waters

    Energy Technology Data Exchange (ETDEWEB)

    Diesel, Elizabeth; Schreiber, Madeline [Virginia Tech, Department of Geosciences, Blacksburg, VA (United States); Meer, Jan Roelof van der [University of Lausanne, Department of Fundamental Microbiology, Lausanne (Switzerland)

    2009-06-15

    Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams. (orig.)

  13. Phylogenetic diversity of hpnP, the hopanoid methylase, and its implications for 2-methylhopanoids as biomarkers

    Science.gov (United States)

    Ricci, J. N.; Coleman, M. L.; Osburn, M. R.; Sessions, A. L.; Spear, J. R.; Newman, D. K.

    2011-12-01

    Hopanoids are a class of sterols produced by bacteria. Their hydrocarbon skeletons are resistant to degradation making their diagenetic products, hopanes, attractive biomarkers. Particular attention has been paid to 2-methylhopanes, which have been found at discrete times and locations in Earth history as far back as 2,500 Myr. Previously, they were inferred to be markers of oxygenic photosynthesis in cyanobacteria, but the discovery of an anoxygenic phototroph, Rhodopseudomonas palustris TIE-1, capable of producing significant quantities of 2-methylbacteriohopanetetrol, the parent molecule of the fossil 2-methylhopane, challenged this interpretation. In this study, we sought to determine the diversity and origin of the enzyme responsible for methylating hopanoids, HpnP. To accomplish this task, we surveyed a diversity of Yellowstone hot springs using degenerate PCR primers and searched publically available metagenomic databases for hpnP-like sequences. The Yellowstone hot spring samples were dominated by cyanobacterial-like hpnP sequences, while the metagenomic data contained many hpnP-like sequences from a diversity of environments that grouped with all known hpnP-containing phyla. With these additional hpnP sequences, we will report updated phylogenetic trees that attempt to determine the origin of hpnP. Understanding the distribution of 2-methylhopanoid production throughout the tree of life and its origin is important to be able to use 2-methylhopanes as biomarkers for any particular taxonomic group.

  14. Arsenic biotransformation and volatilization in transgenic rice

    Science.gov (United States)

    Meng, Xiang-Yan; Qin, Jie; Wang, Li-Hong; Duan, Gui-Lan; Sun, Guo-Xin; Wu, Hui-Lan; Chu, Cheng-Cai; Ling, Hong-Qing; Rosen, Barry P.; Zhu, Yong-Guan

    2011-01-01

    Summary Biotransformation of arsenic includes oxidation, reduction, methylation and conversion to more complex organic arsenicals. Members of the class of arsenite [As(III)] S-adenosylmethyltransferase enzymes catalyze As(III) methylation to a variety of mono-, di- and trimethylated species, some of which are less toxic than As(III) itself. However, no methyltransferase gene has been identified in plants. Here, an arsM gene from the soil bacterium Rhodopseudomonas palustris was expressed in Japonica rice (Oryza sativa L.) cultivar Nipponbare, and the transgenic rice produced methylated arsenic species, which were measured by inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS). Both monomethylarsenate [MAs(V)] and dimethylarsenate [DMAs(V)] were detected in the root and shoot of transgenic rice. After 12-d exposure to As(III), the transgenic rice gave off 10-fold more volatile arsenicals. The present study demonstrates that expression of an arsM gene in rice induces arsenic methylation and volatilization, providing a potential stratagem for phytoremediation theoretically. PMID:21517874

  15. Effect of light-dark cycles on hydrogen and poly-β-hydroxybutyrate production by a photoheterotrophic culture and Rhodobacter capsulatus using a dark fermentation effluent as substrate.

    Science.gov (United States)

    Montiel Corona, Virginia; Le Borgne, Sylvie; Revah, Sergio; Morales, Marcia

    2017-02-01

    A Rhodobacter capsulatus strain and a photoheterotrophic culture (IZT) were cultivated to produce hydrogen under different light-dark cycles. A dark fermentation effluent (DFE) was used as substrate. It was found that IZT culture had an average cumulative hydrogen production (Paccum H 2 ) of 1300±43mLH 2 L -1 under continuous illumination and light-dark cycles of 30 or 60min. In contrast, R. capsulatus reduced its Paccum H 2 by 20% under 30:30min light-dark cycles, but tripled its poly-β-hydroxybutyrate (PHB) content (308±2mgPHB gdw -1 ) compared to continuous illumination. The highest PHB content by IZT culture was 178±10mgPHB gdw -1 under 15:15min light-dark cycles. PCR-DGGE analysis revealed that the IZT culture was mainly composed of Rhodopseudomonas palustris identified with high nucleotide similarity (99%). The evaluated cultures might be used for hydrogen and PHB production. They might provide energy savings by using light-dark cycles and DFE valorization. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Beneficial effects of Ectothiorhodospira shaposhnikovii WF on larval cultivation of Litopenaeus vannamei.

    Science.gov (United States)

    Wen, C Q; Xue, M; Liang, H F; Wu, Y; Li, X

    2015-01-01

    To develop high quality probiotics for shrimp larviculture, the effects of a photosynthetic purple sulphur bacterium WF identified as Ectothiorhodospira shaposhnikovii on survival and development of Litopenaeus vannamei larvae were evaluated in vivo. The larvae exhibited a better survival rate after administration of strain WF compared to the probiotic Rhodopseudomonas palustris. To investigate the effect of dose and dosing frequency, strain WF was added to larvae, stages nauplius 6 to zoea 3, at three different doses and dosing frequencies. Larval treatment with strain WF twice at 10(6) cfu/ml exhibited significantly higher survival compared to the other doses and dosing frequencies as well as the control. The effect on water quality was assessed by applying strain WF to larvae, stages nauplius 6 to postlarvae 1, under conditions of zero water exchange and one-third water exchange. The larvae exhibited higher survival and faster growth when treated under conditions of zero water exchange. No significant difference was detected in the levels of three water quality parameters and in vibrio counts between these two conditions. Therefore, E. shaposhnikovii WF acts both as a bioremediation agent and nutrient source and can benefit shrimp larvae if given at an appropriate dose and dosing frequency. Strain WF, a moderate halophile, shows great promise as a water additive in improving water quality and providing nutrition for shrimp larviculture.

  17. Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

    KAUST Repository

    Xing, Defeng; Cheng, Shaoan; Regan, John M.; Logan, Bruce E.

    2009-01-01

    Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8-10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs. © 2009 Elsevier B.V. All rights reserved.

  18. Performance, carotenoids yield and microbial population dynamics in a photobioreactor system treating acidic wastewater: Effect of hydraulic retention time (HRT) and organic loading rate (OLR).

    Science.gov (United States)

    Liu, Shuli; Zhang, Guangming; Zhang, Jie; Li, Xiangkun; Li, Jianzheng

    2016-01-01

    Effects of hydraulic retention time (HRT) and influent organic loading rate (OLR) were investigated in a photobioreactor containing PNSB (Rhodopseudomonas palustris)-chemoheterotrophic bacteria to treat volatile fatty acid wastewater. Pollutants removal, biomass production and carotenoids yield in different phases were investigated in together with functional microbial population dynamics. The results indicated that properly decreasing HRT and increasing OLR improved the nutrient removal performance as well as the biomass and carotenoids productions. 85.7% COD, 89.9% TN and 91.8% TP removals were achieved under the optimal HRT of 48h and OLR of 2.51g/L/d. Meanwhile, the highest biomass production and carotenoids yield were 2719.3mg/L and 3.91mg/g-biomass respectively. In addition, HRT and OLR have obvious impacts on PNSB and total bacteria dynamics. Statistical analyses indicated that the COD removal exhibited a positive relationship with OLR, biomass and carotenoids production. PNSB/total bacteria ratio had a positive correlation with the carotenoids yield. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists.

    Science.gov (United States)

    McCully, Alexandra L; LaSarre, Breah; McKinlay, James B

    2017-11-28

    Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer's waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris In return, R. palustris cross-feeds E. coli ammonium (NH 4 + ), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH 4 + in each species. The model predicted that interpartner competition for NH 4 + could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH 4 + transporters in both NH 4 + competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH 4 + to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. IMPORTANCE Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical

  20. Soil nitrogen availability and in situ nitrogen uptake by Acer rubrum L. and Pinus palustris Mill. in the southeastern U.S. Coastal Plain

    Science.gov (United States)

    Plant uptake of soil organic N in addition to inorganic N could play an important role in ecosystem N cycling as well as plant nutrition. We measured in situ plant uptake of organic and inorganic N by the dominant canopy species in two contrasting temperate forest ecosystems (bottomland floodplain ...

  1. Comparison of Red-Cockaded Woodpecker (Piciodes borealis) Nestling Diet in Old-Growth and Old-Field Longleaf Pine (Pinus palustris)

    Energy Technology Data Exchange (ETDEWEB)

    Hanula, J.L.; Engstrom, R.T.

    1999-10-01

    Automatic cameras were used to record adult woodpecker diets in old-growth and old-field longleaf pine in the South. Roaches were the number one prey for the woodpeckers based on either biomass or numbers. The latter ranged from 37% to 57% of the prey numbers and 55%-73% of the biomass. Morisita's index of similarity between old-field and old growth varied from 0.89 to 0.95. The authors conclude that the prey base is similar in both conditions and that old-growth provides similar foraging habitat.

  2. Weeds that can do both tricks: vegetative versus generative regeneration of short-lived root-sprouting herbs Rorippa palustris and Barbarea vulgaris

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Kociánová, Alena; Martínková, Jana

    2008-01-01

    Roč. 48, č. 2 (2008), s. 131-135 ISSN 0043-1737 R&D Projects: GA ČR GD206/03/H034 Institutional research plan: CEZ:AV0Z60050516 Keywords : Adventitious sprouting * disturbance * Brassicaceae Subject RIV: EF - Botanics Impact factor: 1.793, year: 2008

  3. Effects of dormant and growing season burning on surface fuels and potential fire behavior in northern Florida longleaf pine (Pinus palustris) flatwoods

    Science.gov (United States)

    James B. Cronan; Clinton S. Wright; Maria Petrova

    2015-01-01

    Prescribed fire is widely used to manage fuels in high-frequency, low-severity fire regimes including pine flatwoods of the southeastern USA where prescribed burning during the growing season (the frost-free period during the calendar year) has become more common in recent decades. Growing season prescribed fires address ecological management objectives that focus on...

  4. Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-a-1-pyrophosphate during purine depletion in Lactococcus lactis

    DEFF Research Database (Denmark)

    Jendresen, Christian Bille; Dimitrov, Peter; Gautier, Laurent

    2014-01-01

    Short-term adaptation to changing environments relies on regulatory elements translating shifting metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecu...

  5. Contributions of the σ(W) , σ(M) and σ(X) regulons to the lantibiotic resistome of Bacillus subtilis.

    Science.gov (United States)

    Kingston, Anthony W; Liao, Xiaojie; Helmann, John D

    2013-11-01

    In Bacillus subtilis, the extracytoplasmic function (ECF) σ factors σ(M) , σ(W) and σ(X) all contribute to resistance against lantibiotics. Nisin, a model lantibiotic, has a dual mode of action: it inhibits cell wall synthesis by binding lipid II, and this complex also forms pores in the cytoplasmic membrane. These activities can be separated in a nisin hinge-region variant (N20P M21P) that binds lipid II, but no longer permeabilizes membranes. The major contribution of σ(M) to nisin resistance is expression of ltaSa, encoding a stress-activated lipoteichoic acid synthase, and σ(X) functions primarily by activation of the dlt operon controlling d-alanylation of teichoic acids. Together, σ(M) and σ(X) regulate cell envelope structure to decrease access of nisin to its lipid II target. In contrast, σ(W) is principally involved in protection against membrane permeabilization as it provides little protection against the nisin hinge region variant. σ(W) contributes to nisin resistance by regulation of a signal peptide peptidase (SppA), phage shock proteins (PspA and YvlC, a PspC homologue) and tellurite resistance related proteins (YceGHI). These defensive mechanisms are also effective against other lantibiotics such as mersacidin, gallidermin and subtilin and comprise an important subset of the intrinsic antibiotic resistome of B. subtilis. © 2013 John Wiley & Sons Ltd.

  6. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analogue

    Directory of Open Access Journals (Sweden)

    Sigde Mamani

    2016-09-01

    Full Text Available While a functional quorum sensing system has been identified in the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans ATCC 23270T and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in At. ferrooxidansT, the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL analogue has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analogue, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy experiments. A faster adherence of At. ferrooxidansT cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signalling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the At. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that QS network represents at least 4.5 % (141 genes of the ATCC 23270T genome of which 42.5 % (60 genes are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of At. ferrooxidans to quorum sensing and on biofilm biogenesis, opening new biological/chemical alternatives for bioleaching development and managing acid Mine/Rock drainage environmental damages.

  7. GlnR-Mediated Regulation of ectABCD Transcription Expands the Role of the GlnR Regulon to Osmotic Stress Management.

    Science.gov (United States)

    Shao, ZhiHui; Deng, WanXin; Li, ShiYuan; He, JuanMei; Ren, ShuangXi; Huang, WeiRen; Lu, YinHua; Zhao, GuoPing; Cai, ZhiMing; Wang, Jin

    2015-10-01

    Ectoine and hydroxyectoine are excellent compatible solutes for bacteria to deal with environmental osmotic stress and temperature damages. The biosynthesis cluster of ectoine and hydroxyectoine is widespread among microorganisms, and its expression is activated by high salinity and temperature changes. So far, little is known about the mechanism of the regulation of the transcription of ect genes and only two MarR family regulators (EctR1 in methylobacteria and the EctR1-related regulator CosR in Vibrio cholerae) have been found to negatively regulate the expression of ect genes. Here, we characterize GlnR, the global regulator for nitrogen metabolism in actinomycetes, as a negative regulator for the transcription of ectoine/hydroxyectoine biosynthetic genes (ect operon) in Streptomyces coelicolor. The physiological role of this transcriptional repression by GlnR is proposed to protect the intracellular glutamate pool, which acts as a key nitrogen donor for both the nitrogen metabolism and the ectoine/hydroxyectoine biosynthesis. High salinity is deleterious, and cells must evolve sophisticated mechanisms to cope with this osmotic stress. Although production of ectoine and hydroxyectoine is one of the most frequently adopted strategies, the in-depth mechanism of regulation of their biosynthesis is less understood. So far, only two MarR family negative regulators, EctR1 and CosR, have been identified in methylobacteria and Vibrio, respectively. Here, our work demonstrates that GlnR, the global regulator for nitrogen metabolism, is a negative transcriptional regulator for ect genes in Streptomyces coelicolor. Moreover, a close relationship is found between nitrogen metabolism and osmotic resistance, and GlnR-mediated regulation of ect transcription is proposed to protect the intracellular glutamate pool. Meanwhile, the work reveals the multiple roles of GlnR in bacterial physiology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. GlnR-Mediated Regulation of ectABCD Transcription Expands the Role of the GlnR Regulon to Osmotic Stress Management

    OpenAIRE

    Shao, ZhiHui; Deng, WanXin; Li, ShiYuan; He, JuanMei; Ren, ShuangXi; Huang, WeiRen; Lu, YinHua; Zhao, GuoPing; Cai, ZhiMing; Wang, Jin

    2015-01-01

    Ectoine and hydroxyectoine are excellent compatible solutes for bacteria to deal with environmental osmotic stress and temperature damages. The biosynthesis cluster of ectoine and hydroxyectoine is widespread among microorganisms, and its expression is activated by high salinity and temperature changes. So far, little is known about the mechanism of the regulation of the transcription of ect genes and only two MarR family regulators (EctR1 in methylobacteria and the EctR1-related regulator Co...

  9. Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator

    DEFF Research Database (Denmark)

    Schultz, Anna Charlotte; Nygaard, P.; Saxild, Hans Henrik

    2001-01-01

    The soil bacterium Bacillus subtilis has developed a highly controlled system for the utilization of a diverse array of low molecular-weight compounds as a nitrogen source when the preferred nitrogen sources, e.g., glutamate plus ammonia, are exhausted. We have identified such a system...... for the utilization of purines as nitrogen source in B. subtilis. Based on growth studies of strains with knockout mutations in genes, complemented with enzyme analysis, we could ascribe functions to 14 genes encoding enzymes or proteins of the purine degradation pathway. A functional xanthine dehydrogenase requires......ABCDE unit was decreased 16-fold, while expression of pucR was decreased 4-fold in the presence of allantoin. We have identified genes of the purine degradation pathway in B. subtilis and showed that their expression is subject to both general nitrogen catabolite control and pathway-specific control....

  10. Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria

    NARCIS (Netherlands)

    Schaik, van W.; Voort, van der M.; Molenaar, D.; Moezelaar, R.; Vos, de W.M.; Abee, T.

    2007-01-01

    The alternative sigma factor B has an important role in the acquisition of stress resistance in many gram-positive bacteria, including the food-borne pathogen Bacillus cereus. Here, we describe the identification of the set of B-regulated genes in B. cereus by DNA microarray analysis of the

  11. Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach

    Directory of Open Access Journals (Sweden)

    Kirti Pandey

    2016-01-01

    Conclusion: Our study has generated several promiscuous antigenic peptides capable of binding to major histocompatibility complex class I with high affinity. These epitopes can become part of a postexposure multivalent subunit vaccine upon experimental validation.

  12. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    International Nuclear Information System (INIS)

    Svintradze, David V.; Peterson, Darrell L.; Collazo-Santiago, Evys A.; Lewis, Janina P.; Wright, H. Tonie

    2013-01-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each

  13. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    Energy Technology Data Exchange (ETDEWEB)

    Svintradze, David V. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Peterson, Darrell L. [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Collazo-Santiago, Evys A.; Lewis, Janina P. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Wright, H. Tonie, E-mail: xrdproc@vcu.edu [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Virginia Commonwealth University, Richmond, VA 23298-0566 (United States)

    2013-10-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

  14. Truncation of Gal4p explains the inactivation of the GAL/MEL regulon in both Saccharomyces bayanus and some Saccharomyces cerevisiae wine strains.

    Science.gov (United States)

    Dulermo, Rémi; Legras, Jean-Luc; Brunel, François; Devillers, Hugo; Sarilar, Véronique; Neuvéglise, Cécile; Nguyen, Huu-Vang

    2016-09-01

    In the past, the galactose-negative (Gal(-)) phenotype was a key physiological character used to distinguish Saccharomyces bayanus from S. cerevisiae In this work, we investigated the inactivation of GAL gene networks in S. bayanus, which is an S. uvarum/S. eubayanus hybrid, and in S. cerevisiae wine strains erroneously labelled 'S. bayanus'. We made an inventory of their GAL genes using genomes that were either available publicly, re-sequenced by us, or assembled from public data and completed with targeted sequencing. In the S. eubayanus/S. uvarum CBS 380(T) hybrid, the GAL/MEL network is composed of genes from both parents: from S. uvarum, an otherwise complete set that lacks GAL4, and from S. eubayanus, a truncated version of GAL4 and an additional copy of GAL3 and GAL80 Similarly, two different truncated GAL4 alleles were found in S. cerevisiae wine strains EC1118 and LalvinQA23. The lack of GAL4 activity in these strains was corrected by introducing a full-length copy of S. cerevisiae GAL4 on a CEN4/ARS plasmid. Transformation with this plasmid restored galactose utilisation in Gal(-) strains, and melibiose fermentation in strain CBS 380(T) The melibiose fermentation phenotype, formerly regarded as characteristic of S. uvarum, turned out to be widespread among Saccharomyces species. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Enhancer-binding proteins with a forkhead-associated domain and the sigma(54) regulon in Myxococcus xanthus fruiting body development

    DEFF Research Database (Denmark)

    Jelsbak, Lars; Givskov, Michael Christian; Kaiser, D.

    2005-01-01

    -binding proteins. Here we report the finding of an unusual group of 12 genes encoding sigma(54)-dependent enhancer-binding proteins containing a forkhead-associated (FHA) domain as their N-terminal sensory domain. FHA domains in other proteins recognize phosphothreonine residues. An insertion mutation in one...... donor cell. Because FHA domains respond to phosphothreonine-containing proteins, these results suggest a regulatory link to the abundant Ser/Thr protein kinases in M. xanthus....

  16. Contributions of the σW, σM, and σX Regulons to the Lantibiotic Resistome of Bacillus subtilis

    Science.gov (United States)

    Kingston, Anthony W.; Liao, Xiaojie; Helmann, John D.

    2014-01-01

    Summary In Bacillus subtilis, the extracytoplasmic function (ECF) σ factors σM, σW, and σX all contribute to resistance against lantibiotics. Nisin, a model lantibiotic, has a dual mode of action: it inhibits cell wall synthesis by binding lipid II, and this complex also forms pores in the cytoplasmic membrane. These activities can be separated in a nisin hinge-region variant (N20P M21P) that binds lipid II, but no longer permeabilizes membranes. The major contribution of σM to nisin resistance is expression of ltaSa, encoding a stress-activated lipoteichoic acid synthase, and σX functions primarily by activation of the dlt operon controlling D-alanylation of teichoic acids. Together, σM and σX regulate cell envelope structure to decrease access of nisin to its lipid II target. In contrast, σW is principally involved in protection against membrane permeabilization as it provides little protection against the nisin hinge region variant. σW contributes to nisin resistance by regulation of a signal peptide peptidase (SppA), phage shock proteins (PspA and YvlC, a PspC homolog), and tellurite resistance related proteins (YceGHI). These defensive mechanisms are also effective against other lantibiotics such as mersacidin, gallidermin, and subtilin and comprise an important subset of the intrinsic antibiotic resistome of B. subtilis. PMID:23980836

  17. A direct link between the global regulator PhoP and the Csr regulon in Y. pseudotuberculosis through the small regulatory RNA CsrC.

    Science.gov (United States)

    Nuss, Aaron M; Schuster, Franziska; Kathrin Heroven, Ann; Heine, Wiebke; Pisano, Fabio; Dersch, Petra

    2014-01-01

    In this study we investigated the influence of the global response regulator PhoP on the complex regulatory cascade controlling expression of early stage virulence genes of Yersinia pseudotuberculosis via the virulence regulator RovA. Our analysis revealed the following novel features: (1) PhoP activates expression of the CsrC RNA in Y. pseudotuberculosis, leading to activation of RovA synthesis through the CsrABC-RovM cascade, (2) activation of csrC transcription is direct and PhoP is shown to bind to two separate PhoP box-like sites, (3) PhoP-mediated activation results in transcription from two different promoters closely downstream of the PhoP binding sites, leading to two distinct CsrC RNAs, and (4) the stability of the CsrC RNAs differs significantly between the Y. pseudotuberculosis strains YPIII and IP32953 due to a 20 nucleotides insertion in CsrC(IP32953), which renders the transcript more susceptible to degradation. In summary, our study showed that PhoP-mediated influence on the regulatory cascade controlling the Csr system and RovA in Y. pseudotuberculosis varies within the species, suggesting that the Csr system is a focal point to readjust and adapt the genus to different hosts and reservoirs.

  18. GenBank blastx search result: AK288454 [KOME

    Lifescience Database Archive (English)

    Full Text Available protein, putative response regulator of the competence regulon ComE1, putative histidine kinase of the competence regulon ComD1, comp...in, putative histidine kinase of the competence regulon ComD2, putative histidine kinase of the competence... regulon ComD3, putative response regulator of the competence regulon ComE2, putati...etence stimulating protein precursor, hypothetical protein, putative immunity prote

  19. Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.

    Science.gov (United States)

    Fonseca, Jose Pedro; Hoffmann, Luisa; Cabral, Bianca Catarina Azeredo; Dias, Victor Hugo Giordano; Miranda, Marcio Rodrigues; de Azevedo Martins, Allan Cezar; Boschiero, Clarissa; Bastos, Wanderley Rodrigues; Silva, Rosane

    2018-02-05

    Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon

  20. Energy transfer and clustering of photosynthetic light-harvesting complexes in reconstituted lipid membranes

    International Nuclear Information System (INIS)

    Dewa, Takehisa; Sumino, Ayumi; Watanabe, Natsuko; Noji, Tomoyasu; Nango, Mamoru

    2013-01-01

    Highlights: ► Photosynthetic light-harvesting complexes were reconstituted into lipid membranes. ► Energy transfers between light-harvesting complexes were examined. ► Atomic force microscopy indicated cluster formation of light-harvesting complexes. ► Efficient energy transfer was observed for the clustered complexes in the membranes. - Abstract: In purple photosynthetic bacteria, light-harvesting complex 2 (LH2) and light harvesting/reaction centre core complex (LH1-RC) play the key roles of capturing and transferring light energy and subsequent charge separation. These photosynthetic apparatuses form a supramolecular assembly; however, how the assembly influences the efficiency of energy conversion is not yet clear. We addressed this issue by evaluating the energy transfer in reconstituted photosynthetic protein complexes LH2 and LH1-RC and studying the structures and the membrane environment of the LH2/LH1-RC assemblies, which had been embedded into various lipid bilayers. Thus, LH2 and LH1-RC from Rhodopseudomonas palustris 2.1.6 were reconstituted in phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE)/PG/cardiolipin (CL). Efficient energy transfer from LH2 to LH1-RC was observed in the PC and PE/PG/CL membranes. Atomic force microscopy revealed that LH2 and LH1-RC were heterogeneously distributed to form clusters in the PC and PE/PG/CL membranes. The results indicated that the phospholipid species influenced the cluster formation of LH2 and LH1-RC as well as the energy transfer efficiency

  1. Energy transfer and clustering of photosynthetic light-harvesting complexes in reconstituted lipid membranes

    Energy Technology Data Exchange (ETDEWEB)

    Dewa, Takehisa, E-mail: takedewa@nitech.ac.jp [Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Japan Science and Technology, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan); Sumino, Ayumi; Watanabe, Natsuko; Noji, Tomoyasu [Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Nango, Mamoru, E-mail: nango@nitech.ac.jp [Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan)

    2013-06-20

    Highlights: ► Photosynthetic light-harvesting complexes were reconstituted into lipid membranes. ► Energy transfers between light-harvesting complexes were examined. ► Atomic force microscopy indicated cluster formation of light-harvesting complexes. ► Efficient energy transfer was observed for the clustered complexes in the membranes. - Abstract: In purple photosynthetic bacteria, light-harvesting complex 2 (LH2) and light harvesting/reaction centre core complex (LH1-RC) play the key roles of capturing and transferring light energy and subsequent charge separation. These photosynthetic apparatuses form a supramolecular assembly; however, how the assembly influences the efficiency of energy conversion is not yet clear. We addressed this issue by evaluating the energy transfer in reconstituted photosynthetic protein complexes LH2 and LH1-RC and studying the structures and the membrane environment of the LH2/LH1-RC assemblies, which had been embedded into various lipid bilayers. Thus, LH2 and LH1-RC from Rhodopseudomonas palustris 2.1.6 were reconstituted in phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE)/PG/cardiolipin (CL). Efficient energy transfer from LH2 to LH1-RC was observed in the PC and PE/PG/CL membranes. Atomic force microscopy revealed that LH2 and LH1-RC were heterogeneously distributed to form clusters in the PC and PE/PG/CL membranes. The results indicated that the phospholipid species influenced the cluster formation of LH2 and LH1-RC as well as the energy transfer efficiency.

  2. Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'.

    Science.gov (United States)

    Danielson, Travis A; Bowler, Bruce E

    2018-01-23

    Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c' from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c'. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c'. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. Expressed Peptide Tags: An additional layer of data for genome annotation

    Energy Technology Data Exchange (ETDEWEB)

    Savidor, Alon [ORNL; Donahoo, Ryan S [ORNL; Hurtado-Gonzales, Oscar [University of Tennessee, Knoxville (UTK); Verberkmoes, Nathan C [ORNL; Shah, Manesh B [ORNL; Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL

    2006-01-01

    While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller sub-databases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While ~77% of Phytophthora EPTs supported the current annotation, a portion of them (7.2% and 12.6% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.

  4. Bioremediation of trace cobalt from simulated spent decontamination solutions of nuclear power reactors using E. coli expressing NiCoT genes

    International Nuclear Information System (INIS)

    Raghu, G.; Maruthi Mohan, P.; Balaji, V.; Venkateswaran, G.; Rodrigue, A.; Lyon 1 Univ., 69

    2008-01-01

    Removal of radioactive cobalt at trace levels (∼nM) in the presence of large excess (10 6 -fold) of corrosion product ions of complexed Fe, Cr, and Ni in spent chemical decontamination formulations (simulated effluent) of nuclear reactors is currently done by using synthetic organic ion exchangers. A large volume of solid waste is generated due to the nonspecific nature of ion sorption. Our earlier work using various fungi and bacteria, with the aim of nuclear waste volume reduction, realized up to 30% of Co removal with specific capacities calculated up to 1 μg/g in 6-24 h. In the present study using engineered Escherichia coli expressing NiCoT genes from Rhodopseudomonas palustris CGA009 (RP) and Novosphingobium aromaticivorans F-199 (NA), we report a significant increase in the specific capacity for Co removal (12 μg/g) in 1-h exposure to simulated effluent. About 85% of Co removal was achieved in a two-cycle treatment with the cloned bacteria. Expression of NiCoT genes in the E. coli knockout mutant of NiCoT efflux gene (rcnA) was more efficient as compared to expression in wild-type E. coli MC4100, JM109 and BL21 (DE3) hosts. The viability of the E. coli strains in the formulation as well as at different doses of gamma rays exposure and the effect of gamma dose on their cobalt removal capacity are determined. The potential application scheme of the above process of bioremediation of cobalt from nuclear power reactor chemical decontamination effluents is discussed. (orig.)

  5. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparisons with Other Methods

    International Nuclear Information System (INIS)

    Wu, Liyou; Yi, T.Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-01-01

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site (Hanford Reach of the Columbia River (HRCR), 11 strains), Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  6. Apo-bacteriophytochromes modulate bacterial photosynthesis in response to low light.

    Science.gov (United States)

    Fixen, Kathryn R; Baker, Anna W; Stojkovic, Emina A; Beatty, J Thomas; Harwood, Caroline S

    2014-01-14

    Bacteriophytochromes (BphPs) are light-sensing regulatory proteins encoded by photosynthetic and nonphotosynthetic bacteria. This protein class has been characterized structurally, but its biological activities remain relatively unexplored. Two BphPs in the anoxygenic photosynthetic bacterium Rhodopseudomonas palustris, designated regulatory proteins RpBphP2 and RpBphP3, are configured as light-regulated histidine kinases, which initiate a signal transduction system that controls expression of genes for the low light harvesting 4 (LH4) antenna complex. In vitro, RpBphP2 and RpBphP3 respond to light quality by reversible photoconversion, a property that requires the light-absorbing chromophore biliverdin. In vivo, RpBphP2 and RpBphP3 are both required for the expression of the LH4 antenna complex under anaerobic conditions, but biliverdin requires oxygen for its synthesis by heme oxygenase. On further investigation, we found that the apo-bacteriophytochrome forms of RpBphP2 and RpBphP3 are necessary and sufficient to control LH4 expression in response to light intensity in conjunction with other signal transduction proteins. One possibility is that the system senses a reduced quinone pool generated when light energy is absorbed by bacteriochlorophyll. The biliverdin-bound forms of the BphPs have the additional property of being able to fine-tune LH4 expression in response to light quality. These observations support the concept that some bacteriophytochromes can function with or without a chromophore and may be involved in regulating physiological processes not directly related to light sensing.

  7. Engineering strategies for the enhanced photo-H{sub 2} production using effluents of dark fermentation processes as substrate

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chun-Yen; Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan (China); Sustainable Environment Research Center, National Cheng Kung University, Tainan (China); Yeh, Kuei-Ling; Lo, Yung-Chung [Department of Chemical Engineering, National Cheng Kung University, Tainan (China); Wang, Hui-Min [Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung (China)

    2010-12-15

    The major obstacle of combining dark and photo fermentation for high-yield biohydrogen production is substrate inhibition while using dark fermentation effluent as the sole substrate. To solve this problem, the dark fermentation broth was diluted with different dilution ratio to improve photo-H{sub 2} production performance of an indigenous purple nonsulfur bacterium Rhodopseudomonas palustris WP3-5. The best photo-H{sub 2} production performance occurred at a dilution ratio of 1:2, giving a highest overall H{sub 2} production rate of 10.72 ml/l/h and a higher overall H{sub 2} yield of 6.14 mol H{sub 2}/mol sucrose. The maximum H{sub 2} content was about 88.1% during the dilution ratio of 1:2. The photo-H{sub 2} production performance was further improved by supplying yeast extract and glutamic acid as the nutrient. The results indicate that the overall H{sub 2} production rate and H{sub 2} yield increased to 17.02 ml/l/h and 10.25 mol H{sub 2}/mol sucrose, respectively. Using a novel solar-energy-excited optical fiber photobioreactor (SEEOFP) with supplementing tungsten filament lamp (TL) irradiation, the overall H{sub 2} production rate was improved to 17.86 ml/l/h. Meanwhile, the power consumption by combining SEEOFP and TL was about 37.1% lower than using TL alone. This study demonstrates that using optimal light sources and proper dilution of dark fermentation effluent, the performance of photo-H{sub 2} production can be markedly enhanced along with a reduction of power consumption. (author)

  8. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-05-17

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  9. Redox thermodynamics of the native and alkaline forms of eukaryotic and bacterial class I cytochromes c.

    Science.gov (United States)

    Battistuzzi, G; Borsari, M; Sola, M; Francia, F

    1997-12-23

    The reduction potentials of beef heart cytochrome c and cytochromes c2 from Rhodopseudomonas palustris, Rhodobacter sphaeroides, and Rhodobacter capsulatus were measured through direct electrochemistry at a surface-modified gold electrode as a function of temperature in nonisothermal experiments carried out at neutral and alkaline pH values. The thermodynamic parameters for protein reduction (DeltaS degrees rc and DeltaH degrees rc) were determined for the native and alkaline conformers. Enthalpy and entropy terms underlying species-dependent differences in E degrees and pH- and temperature-induced E degrees changes for a given cytochrome were analyzed. The difference of about +0.1 V in E degrees between cytochromes c2 and the eukaryotic species can be separated into an enthalpic term (-DeltaDeltaH degrees rc/F) of +0.130 V and an entropic term (TDeltaDeltaS degrees rc/F) of -0.040 V. Hence, the higher potential of the bacterial species appears to be determined entirely by a greater enthalpic stabilization of the reduced state. Analogously, the much lower potential of the alkaline conformer(s) as compared to the native species is by far enthalpic in origin for both protein families, and is largely determined by the substitution of Met for Lys in axial heme ligation. Instead, the biphasic E degrees /temperature profile for the native cytochromes is due to a difference in reduction entropy between the conformers at low and high temperatures. Temperature-dependent 1H NMR experiments suggest that the temperature-induced transition also involves a change in orientation of the axial methionine ligand with respect to the heme plane.

  10. Characterizations of purple non-sulfur bacteria isolated from paddy fields, and identification of strains with potential for plant growth-promotion, greenhouse gas mitigation and heavy metal bioremediation.

    Science.gov (United States)

    Sakpirom, Jakkapan; Kantachote, Duangporn; Nunkaew, Tomorn; Khan, Eakalak

    2017-04-01

    This study was aimed at selecting purple non-sulfur bacteria (PNSB) isolated from various paddy fields, including Cd- and Zn-contaminated paddy fields, based on their biofertilizer properties. Among 235 PNSB isolates, strain TN110 was most effective in plant growth-promoting substance (PGPS) production, releasing 3.2 mg/L of [Formula: see text] , 4.11 mg/L of 5-aminolevulinic acid (ALA) and 3.62 mg/L of indole-3-acetic acid (IAA), and reducing methane emission up to 80%. This strain had nifH, vnfG and anfG, which are the Mo, V and Fe nitrogenase genes encoded for key enzymes in nitrogen fixation under different conditions. This strain provided 84% and 55% removal of Cd and Zn, respectively. Another isolate, TN414, not only produced PGPS (1.30 mg/L of [Formula: see text] , 0.94 mg/L of ALA and 0.65 mg/L of IAA), but was also efficient in removing both Cd and Zn at 72% and 74%, respectively. Based on 16S rDNA sequencing, strain TN110 was identified as Rhodopseudomonas palustris, while strain TN414 was Rubrivivax gelatinosus. A combination of TN110 and TN414 could potentially provide a biofertilizer, which is a greener alternative to commercial/chemical fertilizers and an agent for bioremediation of heavy metals and greenhouse gas mitigation in paddy fields. Copyright © 2016 Institut Pasteur. All rights reserved.

  11. Structural characterization of core-bradavidin in complex with biotin

    Science.gov (United States)

    Agrawal, Nitin; Määttä, Juha A. E.; Kulomaa, Markku S.; Hytönen, Vesa P.; Johnson, Mark S.; Airenne, Tomi T.

    2017-01-01

    Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 (“Brad-tag”) act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin–Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin. PMID:28426764

  12. CHAR ACTERIZA T ION OF THR EE BENZO A TE DEG RADING ANOX YGENIC PH OTOSYNTHETIC BA CTERI A ISO LA TED F RO M THE ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    DWI SURYANTO

    2001-01-01

    Full Text Available Three anoxygenic photosyn thetic bacter ia, DS-1, DS-4 and Cas-13, have been exam in ated for their morphological and physiolog ical propert ies. All s trains were rod-sh ape ce lls with a swollen terminal end, Gram nega tive , motile, non-hal ophilic, non-alkal ophilic a n d non- acid ophilic , a nd capable of utilizing benzoate aerobically and photo-anaerobically. Sequ ence analysis of part of 16S rRNA genes showed that DS-1 and Cas- 13 we re cl osel y relate d to Rhodopseudomonas palustris Stra in 7 w ith a simila ri ty of 97%, where a s DS-4 ma y not be c losel y rela te d t o the former t wo str ai ns wit h a si milarit y of 78% based on t he constr ucte d phyloge nic tree . Sp ec tral anal ys is ind ica te d that the thr ee ba cter ia ha d ba cter io ch lorophyl a and norm al sp ir il loxa nthi n ser ies. Growth in med ium enriched with vitamin and supplemen ted with ben zoa te as their s ole C-s ources wa s bette r t han in me di um witho ut vita min. Benz oate deg ra dati on in me di u m with vita min was ac ce lerated. The ab ility to grow on benzoate withou t added vitam ins ind icated that the bacteria were able to s ynthesize th eir own vitamins.

  13. Study on improvement of continuous hydrogen production by photosynthetic biofilm in interior illuminant reactor.

    Science.gov (United States)

    Liu, Wenhui; Yuan, Linjiang; Wei, Bo

    2016-09-01

    In the present study, a new type of interior optical fiber illuminating reactor was developed for H2 production to solve the problem of luminous intensity attenuation at the center portion of a reactor, and an immobilization technique was used to enhance the stability of a continuous hydrogen production process with attached photosynthetic bacteria, using glucose as a sole carbon substrate for the indigenous photosynthetic bacteria (PSB) Rhodopseudomonas palustris SP-6. Results of the experiments showed that the interior optical fiber illuminating reactor produces H2 more efficiently and productively than the exterior light source reactor, with the cumulative H2 production, the maximum H2 production rate and H2 yield increased by 813ml, 11.3ml l-1 h-1 and 22.3%, respectively. The stability of the product of continuous hydrogen was realized by immobilizing PSB on the surface of powder active carbon(PAC). After adding the dosage of 2.0g l-1 PAC, the continuous steady operation of H2 production gave a high H2 yield of 1.398 mol H2 mol-1 glucose and an average H2 production rate of 35.1ml l-1 h-1 illuminating with a single interior optical fiber light source. Meanwhile, a higher H2 yield of 1.495 mol H2 mol-1 glucose and an average H2 production rate of 38.7ml l-1 h-1 were attained illuminating with a compound lamp in the continuous H2 production for 20 days.

  14. Structural characterization of core-bradavidin in complex with biotin.

    Directory of Open Access Journals (Sweden)

    Nitin Agrawal

    Full Text Available Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 ("Brad-tag" act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala of core-bradavidin (CC mutant. Our data help us to further engineer the core-bradavidin-Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin.

  15. Comparison normal composting with composting using effective microorganisms for poultry carcasses disposal in poultry farms

    Directory of Open Access Journals (Sweden)

    D. M. Taher

    2009-01-01

    Full Text Available Composting offers a convenient and environmentally acceptable safe, effective method for the disposal of carcasses as an alternative method to burning, burial and rendering. This study was conducted to evaluate the effects of a natural biological products containing an effective microorganisms namily; Lactic acid bacill (Lactobacillus plantarum; L. casei Streptococcus Lactis., Photosynthetic bacteria (Rhodopseudomonas palustris; Rhodobacter sphaeroides,Yeast (Saccharomyces cerevisiae; Candida utilis Toula, Pichia Jadinii, Actinomycetes (Streptomyces albus; S. griseus., and Fermenting fungi (Aspergillus oryzae; Mucor hiemalis in the composting activity of poultry carcasses. The composting stacks constitute multi alternative layers of wood shaves, hay, poultry carcasses and then wood shaves and so on. The layers have been bypassed with plastic tubes for oxygen supply. Moreover, a petri dishes of salmonella and E. coli colonies were introduced within poultry carcasses layer. After 8 days of the experimental period this study follows the physical properties of the composting process according to its odor intesity, color and pH level as well as the bacterial reisolation from the stored colonies. Results indicate that the biological products increase the temperature of the composting stack (66-68° C with a minimal odors as the pH meters recording 5.4 as compared to the control composting stack (52-64° C and pH 6.8 with offender odors. On the other hand ,the biological product inhibit the bacterial reisolation offers since the 10the day of the experiment, however, in the normal composting stack that periods will prolonged till the 17 days of the experiment. Interestingly, the biological product induce high and rapid digestable rate for the poultry carcasses which shown within 25 days of the experiment, in comparison to the normal composting stack which induce that effects in 60 days. In conclusion, the addition of effective microorganism to the

  16. Study of the impact of environmental bacteria ob uranium speciation in order to engage bioremediation process

    International Nuclear Information System (INIS)

    Untereiner, G.

    2008-11-01

    Uranium is both a radiological and a chemical toxic. Its concentration in the environment is low except when human activities have caused pollution. Uranium is a heavy reactive element, and thus it is easily complexed with soil component like minerals or organic molecules. These different complexes can be more or less bioavailable for microorganisms and plants, and then get in the human food chain. The knowledge and the understanding of transfer mechanisms and also the fate of toxic elements in the biosphere are a key issue to estimate health and ecological hazards. The knowledge of the speciation is very important for bioremediation processes. Here, we focused on the microorganisms effects onto uranium speciation in environment. Bacteria can accumulate and/or transform uranium depending on the initial form of the element. Thus, its bioavailability could be changed. The species used in this work are Cupriavidus metallidurans CH34, which is an environmental bacteria with a high resistance to heavy metal, Deinococcus radiodurans R1, which is known for his radiological resistance, and Rhodopseudomonas palustris, which is a purple photo-trophic bacteria capable of degrading aromatic compounds. Two forms of uranium were used with these bacteria, a mineral one, uranyl carbonate, and an organic one, uranyl citrate. In a first step, the growth media were modified in order to stabilize uranium complexes thanks to a simulation program. Then, the capacity of the bacteria to accumulate or transform uranium was studied. We saw a difference between minimal inhibition concentrations of these two speciation which is due to a difference between phosphate bioavailability. No accumulation was observed with environmental pH but uranium precipitation was observed with acidic pH (pH 1). Uranium speciation seemed to be well controlled in the growth media and the precipitates were uranyl phosphate. (author)

  17. Atomic force microscopy studies of native photosynthetic membranes.

    Science.gov (United States)

    Sturgis, James N; Tucker, Jaimey D; Olsen, John D; Hunter, C Neil; Niederman, Robert A

    2009-05-05

    In addition to providing the earliest surface images of a native photosynthetic membrane at submolecular resolution, examination of the intracytoplasmic membrane (ICM) of purple bacteria by atomic force microscopy (AFM) has revealed a wide diversity of species-dependent arrangements of closely packed light-harvesting (LH) antennae, capable of fulfilling the basic requirements for efficient collection, transmission, and trapping of radiant energy. A highly organized architecture was observed with fused preparations of the pseudocrystalline ICM of Blastochloris viridis, consiting of hexagonally packed monomeric reaction center light-harvesting 1 (RC-LH1) core complexes. Among strains which also form a peripheral LH2 antenna, images of ICM patches from Rhodobacter sphaeroides exhibited well-ordered, interconnected networks of dimeric RC-LH1 core complexes intercalated by rows of LH2, coexisting with LH2-only domains. Other peripheral antenna-containing species, notably Rhodospirillum photometricum and Rhodopseudomonas palustris, showed a less regular organization, with mixed regions of LH2 and RC-LH1 cores, intermingled with large, paracrystalline domains. The ATP synthase and cytochrome bc(1) complex were not observed in any of these topographs and are thought to be localized in the adjacent cytoplasmic membrane or in inaccessible ICM regions separated from the flat regions imaged by AFM. The AFM images have served as a basis for atomic-resolution modeling of the ICM vesicle surface, as well as forces driving segregation of photosynthetic complexes into distinct domains. Docking of atomic-resolution molecular structures into AFM topographs of Rsp. photometricum membranes generated precise in situ structural models of the core complex surrounded by LH2 rings and a region of tightly packed LH2 complexes. A similar approach has generated a model of the highly curved LH2-only membranes of Rba. sphaeroides which predicts that sufficient space exists between LH2 complexes

  18. Could photosynthesis function on Proxima Centauri b?

    Science.gov (United States)

    Ritchie, Raymond J.; Larkum, Anthony W. D.; Ribas, Ignasi

    2018-04-01

    Could oxygenic and/or anoxygenic photosynthesis exist on planet Proxima Centauri b? Proxima Centauri (spectral type - M5.5 V, 3050 K) is a red dwarf, whereas the Sun is type G2 V (5780 K). The light regimes on Earth and Proxima Centauri b are compared with estimates of the planet's suitability for Chlorophyll a (Chl a) and Chl d-based oxygenic photosynthesis and for bacteriochlorophyll (BChl)-based anoxygenic photosynthesis. Proxima Centauri b has low irradiance in the oxygenic photosynthesis range (400-749 nm: 64-132 µmol quanta m-2 s-1). Much larger amounts of light would be available for BChl-based anoxygenic photosynthesis (350-1100 nm: 724-1538 µmol quanta m-2 s-1). We estimated primary production under these light regimes. We used the oxygenic algae Synechocystis PCC6803, Prochlorothrix hollandica, Acaryochloris marina, Chlorella vulgaris, Rhodomonas sp. and Phaeodactylum tricornutum and the anoxygenic photosynthetic bacteria Rhodopseudomonas palustris (BChl a), Afifella marina (BChl a), Thermochromatium tepidum (BChl a), Chlorobaculum tepidum (BChl a + c) and Blastochloris viridis (BChl b) as representative photosynthetic organisms. Proxima Centauri b has only ~3% of the PAR (400-700 nm) of Earth irradiance, but we found that potential gross photosynthesis (P g) on Proxima Centauri b could be surprisingly high (oxygenic photosynthesis: earth ~0.8 gC m-2 h-1 Proxima Centauri b ~0.14 gC m-2 h-1). The proportion of PAR irradiance useable by oxygenic photosynthetic organisms (the sum of Blue + Red irradiance) is similar for the Earth and Proxima Centauri b. The oxygenic photic zone would be only ~10 m deep in water compared with ~200 m on Earth. The P g of an anoxic Earth (gC m-2 h-1) is ~0.34-0.59 (land) and could be as high as ~0.29-0.44 on Proxima Centauri b. 1 m of water does not affect oxygenic or anoxygenic photosynthesis on Earth, but on Proxima Centauri b oxygenic P g is reduced by ~50%. Effective elimination of near IR limits P g by photosynthetic

  19. Improving hydrogen production from cassava starch by combination of dark and photo fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Su, Huibo; Cheng, Jun; Zhou, Junhu; Song, Wenlu; Cen, Kefa [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)

    2009-02-15

    The combination of dark and photo fermentation was studied with cassava starch as the substrate to increase the hydrogen yield and alleviate the environmental pollution. The different raw cassava starch concentrations of 10-25 g/l give different hydrogen yields in the dark fermentation inoculated with the mixed hydrogen-producing bacteria derived from the preheated activated sludge. The maximum hydrogen yield (HY) of 240.4 ml H{sub 2}/g starch is obtained at the starch concentration of 10 g/l and the maximum hydrogen production rate (HPR) of 84.4 ml H{sub 2}/l/h is obtained at the starch concentration of 25 g/l. When the cassava starch, which is gelatinized by heating or hydrolyzed with {alpha}-amylase and glucoamylase, is used as the substrate to produce hydrogen, the maximum HY respectively increases to 258.5 and 276.1 ml H{sub 2}/g starch, and the maximum HPR respectively increases to 172 and 262.4 ml H{sub 2}/l/h. Meanwhile, the lag time ({lambda}) for hydrogen production decreases from 11 h to 8 h and 5 h respectively, and the fermentation duration decreases from 75-110 h to 44-68 h. The metabolite byproducts in the dark fermentation, which are mainly acetate and butyrate, are reused as the substrates in the photo fermentation inoculated with the Rhodopseudomonas palustris bacteria. The maximum HY and HPR are respectively 131.9 ml H{sub 2}/g starch and 16.4 ml H{sub 2}/l/h in the photo fermentation, and the highest utilization ratios of acetate and butyrate are respectively 89.3% and 98.5%. The maximum HY dramatically increases from 240.4 ml H{sub 2}/g starch only in the dark fermentation to 402.3 ml H{sub 2}/g starch in the combined dark and photo fermentation, while the energy conversion efficiency increases from 17.5-18.6% to 26.4-27.1% if only the heat value of cassava starch is considered as the input energy. When the input light energy in the photo fermentation is also taken into account, the whole energy conversion efficiency is 4.46-6.04%. (author)

  20. In vitro kinetic studies on the mechanism of oxygen-dependent cellular uptake of copper radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Holland, Jason P; Bell, Stephen G; Wong, Luet-Lok; Dilworth, Jonathan R [Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA (United Kingdom); Giansiracusa, Jeffrey H [Department of Mathematics, Mathematical Institute, University of Oxford, 24-29 St Giles' , Oxford, OX1 3LB (United Kingdom)], E-mail: hollanj3@mskcc.org, E-mail: jasonpholland@gmail.com

    2009-04-07

    The development of hypoxia-selective radiopharmaceuticals for use as therapeutic and/or imaging agents is of vital importance for both early identification and treatment of cancer and in the design of new drugs. Radiotracers based on copper for use in positron emission tomography have received great attention due to the successful application of copper(II) bis(thiosemicarbazonato) complexes, such as [{sup 60/62/64}Cu(II)ATSM] and [{sup 60/62/64}Cu(II)PTSM], as markers for tumour hypoxia and blood perfusion, respectively. Recent work has led to the proposal of a revised mechanism of hypoxia-selective cellular uptake and retention of [Cu(II)ATSM]. The work presented here describes non-steady-state kinetic simulations in which the reported pO{sub 2}-dependent in vitro cellular uptake and retention of [{sup 64}Cu(II)ATSM] in EMT6 murine carcinoma cells has been modelled by using the revised mechanistic scheme. Non-steady-state (NSS) kinetic analysis reveals that the model is in very good agreement with the reported experimental data with a root-mean-squared error of less than 6% between the simulated and experimental cellular uptake profiles. Estimated rate constants are derived for the cellular uptake and washout (k{sub 1} = 9.8 {+-} 0.59 x 10{sup -4} s{sup -1} and k{sub 2} = 2.9 {+-} 0.17 x 10{sup -3} s{sup -1}), intracellular reduction (k{sub 3} = 5.2 {+-} 0.31 x 10{sup -2} s{sup -1}), reoxidation (k{sub 4} = 2.2 {+-} 0.13 mol{sup -1} dm{sup 3} s{sup -1}) and proton-mediated ligand dissociation (k{sub 5} = 9.0 {+-} 0.54 x 10{sup -5} s{sup -1}). Previous mechanisms focused on the reduction and reoxidation steps. However, the data suggest that the origins of hypoxia-selective retention may reside with the stability of the copper(I) anion with respect to protonation and ligand dissociation. In vitro kinetic studies using the nicotimamide adenine dinucleotide (NADH)-dependent ferredoxin reductase enzyme PuR isolated from the bacterium Rhodopseudomonas palustris have

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

    Energy Technology Data Exchange (ETDEWEB)

    Jiao, Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Navid, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    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

  2. 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes.

    Science.gov (United States)

    Kuntze, Kevin; Shinoda, Yoshifumi; Moutakki, Housna; McInerney, Michael J; Vogt, Carsten; Richnow, Hans-Hermann; Boll, Matthias

    2008-06-01

    In anaerobic bacteria, most aromatic growth substrates are channelled into the benzoyl-coenzyme A (CoA) degradation pathway where the aromatic ring is dearomatized and cleaved into an aliphatic thiol ester. The initial step of this pathway is catalysed by dearomatizing benzoyl-CoA reductases yielding the two electron-reduction product, cyclohexa-1,5-diene-1-carbonyl-CoA, to which water is subsequently added by a hydratase. The next two steps have so far only been studied in facultative anaerobes and comprise the oxidation of the 6-hydroxyl-group to 6-oxocyclohex-1-ene-1-carbonyl-CoA (6-OCH-CoA), the addition of water and hydrolytic ring cleavage yielding 3-hydroxypimelyl-CoA. In this work, two benzoate-induced genes from the obligately anaerobic bacteria, Geobacter metallireducens (bamA(Geo)) and Syntrophus aciditrophicus (bamA(Syn)), were heterologously expressed in Escherichia coli, purified and characterized as 6-OCH-CoA hydrolases. Both enzymes consisted of a single 43 kDa subunit. Some properties of the enzymes are presented and compared with homologues from facultative anaerobes. An alignment of the nucleotide sequences of bamA(Geo) and bamA(Syn) with the corresponding genes from facultative anaerobes identified highly conserved DNA regions, which enabled the discrimination of genes coding for 6-OCH-CoA hydrolases from those coding for related enzymes. A degenerate oligonucleotide primer pair was deduced from conserved regions and applied in polymerase chain reaction reactions. Using these primers, the expected DNA fragment of the 6-OCH-CoA hydrolase genes was specifically amplified from the DNA of nearly all known facultative and obligate anaerobes that use aromatic growth substrates. The only exception was the aromatic compound-degrading Rhodopseudomonas palustris, which uniquely uses a modified benzoyl-CoA degradation pathway. Using the oligonucleotide primers, the expected DNA fragment was also amplified in a toluene-degrading and a m

  3. The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size

    DEFF Research Database (Denmark)

    Nygaard, P.; Saxild, Hans Henrik

    2005-01-01

    a functional PbuE pump. In a mutant defective in the metabolism of adenine, the ade apt mutant, we found a high intracellular level of adenine and constitutive high levels of PbuE. A growth test using a purine auxotroph provided further evidence for the role of PbuE in lowering the intracellular concentration...

  4. Identification of VceA and VceC, two members of the VjbR regulon that are translocated into macrophages by the Brucella type IV secretion system

    NARCIS (Netherlands)

    de Jong, Maarten F.; Sun, Yao-Hui; den Hartigh, Andreas B.; van Dijl, Jan Maarten; Tsolis, Renee M.

    2008-01-01

    Survival and replication inside host cells by Brucella spp. requires a type IV secretion system (T4SS), encoded by the virB locus. However, the identity of the molecules secreted by the T4SS has remained elusive. We hypothesized that proteins translocated by the T4SS would be co-regulated with the

  5. Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon.

    Science.gov (United States)

    Rouanet, Carine; Reverchon, Sylvie; Rodionov, Dmitry A; Nasser, William

    2004-07-16

    In Erwinia chrysanthemi, production of pectic enzymes is modulated by a complex network involving several regulators. One of them, PecS, which belongs to the MarR family, also controls the synthesis of various other virulence factors, such as cellulases and indigoidine. Here, the PecS consensus-binding site is defined by combining a systematic evolution of ligands by an exponential enrichment approach and mutational analyses. The consensus consists of a 23-base pair palindromic-like sequence (C(-11)G(-10)A(-9)N(-8)W(-7)T(-6)C(-5)G(-4)T(-3)A(-2))T(-1)A(0)T(1)(T(2)A(3)C(4)G(5)A(6)N(7)N(8)N(9)C(10)G(11)). Mutational experiments revealed that (i) the palindromic organization is required for the binding of PecS, (ii) the very conserved part of the consensus (-6 to 6) allows for a specific interaction with PecS, but the presence of the relatively degenerated bases located apart significantly increases PecS affinity, (iii) the four bases G, A, T, and C are required for efficient binding of PecS, and (iv) the presence of several binding sites on the same promoter increases the affinity of PecS. This consensus is detected in the regions involved in PecS binding on the previously characterized target genes. This variable consensus is in agreement with the observation that the members of the MarR family are able to bind various DNA targets as dimers by means of a winged helix DNA-binding motif. Binding of PecS on a promoter region containing the defined consensus results in a repression of gene transcription in vitro. Preliminary scanning of the E. chrysanthemi genome sequence with the consensus revealed the presence of strong PecS-binding sites in the intergenic region between fliE and fliFGHIJKLMNOPQR which encode proteins involved in the biogenesis of flagellum. Accordingly, PecS directly represses fliE expression. Thus, PecS seems to control the synthesis of virulence factors required for the key steps of plant infection.

  6. Biofilm Formation by a Metabolically Versatile Bacterium

    National Research Council Canada - National Science Library

    Harwood, Caroline S

    2005-01-01

    .... The goal of this project is to conduct basic studies that will facilitate the development of a process wherein Rhodopseudomonas cells grown on surfaces as biofilms, produce hydrogen with energy...

  7. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... palustris CGA009] ... Length = 77 ... Query: 195 NRRKVYPESARQTRQQGTASLSFAIGASGEVISYKITRSTGSDALDRAIDS...MMKTARPPP 254 ... NRRKVYPESARQTRQQGTASLSFAIGASGEVISYKITRSTGSDALDRAIDSMMKTA...RPPP Sbjct: 1 ... NRRKVYPESARQTRQQGTASLSFAIGASGEVISYKITRSTGSDALDRAIDSMMKTARPPP 60 ...

  8. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... palustris CGA009] ... Length = 157 ... Query: 95 ... YLQTAIDCHSRYAFARLYSSKLPVTAVHLMNNDVLPTFEAHDA...KIETVLSDNGREFCGRP 154 ... YLQTAIDCHSRYAFARLYSSKLPVTAVHLMNNDVLPTFEAHDAKIETV...LSDNGREFCGRP Sbjct: 1 ... YLQTAIDCHSRYAFARLYSSKLPVTAVHLMNNDVLPTFEAHDAKIETVLSDNGREFCGRP 60 ... Query: 215 LDDYLVGY

  9. ORF Alignment: NC_005296 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available LGETGSGKDVFARRVHAESARRNKPFVPVNCAALPEGLIES 387 ... MAQLSRTVRLVEAGIPVLLLGETGSGKDVFARRVHAESARRNKPFVPVNCA...ALPEGLIES Sbjct: 1 ... MAQLSRTVRLVEAGIPVLLLGETGSGKDVFARRVHAESARRNKPFVPVNCAALPEGLIES 60 ... Query: 448 GRPVPVDFALI...domonas palustris CGA009] ... Length = 229 ... Query: 328 MAQLSRTVRLVEAGIPVLL

  10. City of Freeport, Florida, State Road 20 Water Main Installation, Final Environmental Assessment, Eglin Air Force Base, Florida

    Science.gov (United States)

    2010-07-01

    If contamination, drought or natural disaster, such as a hurricane, impacted one water supply, an interconnection with neighboring municipalities...Scientific Name Sandhills Ecological Association Longleaf Pine Pinus palustris Red-cockaded Woodpecker Picoides borealis Turkey Oak Quercus laevis...canadensis Flatwoods Ecological Association Longleaf Pine Pinus palustris Wood Duck Aix sponsa Runner Oak Quercus pumila Red-winged Blackbird Agelaius

  11. sigma54-Mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

    NARCIS (Netherlands)

    Stevens, M.J.A.; Molenaar, D.; Jong, de A.; Vos, de W.M.; Kleerebezem, M.

    2010-01-01

    Sigma factors direct specific binding of the bacterial RNA polymerase to the promoter. Here we present the elucidation of the sigma(54 ) regulon in Lactobacillus plantarum. A sequence-based regulon prediction of sigma(54)-dependent promoters revealed an operon encoding a mannose phosphotransferase

  12. sigma(54)-mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

    NARCIS (Netherlands)

    Stevens, Marc J. A.; Molenaar, Douwe; de Jong, Anne; De Vos, Willem M.; Kleerebezem, Michiel

    Sigma factors direct specific binding of the bacterial RNA polymerase to the promoter. Here we present the elucidation of the sigma(54) regulon in Lactobacillus plantarum. A sequence-based regulon prediction of sigma(54)-dependent promoters revealed an operon encoding a mannose phosphotransferase

  13. Gclust Server: 85869 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available equence length 496 Representative annotation D-lactate dehydrogenase, part of the retrograde regulon which c...rograde regulon which consists of genes whose expression is stimulated by damage to...85869 SCE_YEL071W=DLD3 Cluster Sequences Related Sequences(271) 496 D-lactate dehydrogenase, part of the ret

  14. Cloning, sequence analysis, and characterization of the genes involved in isoprimeverose metabolism in Lactobacillus pentosus

    NARCIS (Netherlands)

    Chaillou, S.; Lokman, B.C.; Leer, R.J.; Posthuma, C.; Postma, P.W.; Pouwels, P.H.

    1998-01-01

    Two genes, xylP and xylQ, from the xylose regulon of Lactobacillus pentosus were cloned and sequenced. Together with the repressor gene of the regulon, xylR, the xylPQ genes form an operon which is inducible by xylose and which is transcribed from a promoter located 145 bp upstream of xylP. A

  15. Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO

    DEFF Research Database (Denmark)

    Saxild, Hans Henrik; Brunstedt, K.; Nielsen, K.I.

    2001-01-01

    The expression of the pur operon, which encodes enzymes of the purine biosynthetic pathway in Bacillus subtilis, is subject to control by the purR gene product (PurR) and phosphoribosylpyrophosphate. This control is also exerted on the purA and purR genes. A consensus sequence for the binding...... of PurR, named the PurBox, has been suggested (M. Kilstrup, S.G. Jessing, S.B. Wichmand-Jorgensen, M. Madsen, and D. Nilsson, J. Bacteriol. 180:3900-3906, 1998). To determine whether the expression of other genes might be regulated by PurR, we performed a search for PurBox sequences in the B. subtilis...

  16. Spectral diffusion and electron-phonon coupling of the B800 BChl a molecules in LH2 complexes from three different species of purple bacteria.

    Science.gov (United States)

    Baier, J; Gabrielsen, M; Oellerich, S; Michel, H; van Heel, M; Cogdell, R J; Köhler, J

    2009-11-04

    We have investigated the spectral diffusion and the electron-phonon coupling of B800 bacteriochlorophyll a molecules in the peripheral light-harvesting complex LH2 for three different species of purple bacteria, Rhodobacter sphaeroides, Rhodospirillum molischianum, and Rhodopseudomonas acidophila. We come to the conclusion that B800 binding pockets for Rhodobacter sphaeroides and Rhodopseudomonas acidophila are rather similar with respect to the polarity of the protein environment but that the packaging of the alphabeta-polypeptides seems to be less tight in Rb. sphaeroides with respect to the other two species.

  17. Rare, threatened and relict species in flora of SNR Zasavica

    Directory of Open Access Journals (Sweden)

    Stanković, M.

    2011-09-01

    Full Text Available In group of biodiversity important plant species there are 23 taxa. 20 taxa are mentioned in „Preliminary Red List of flora of Serbia and Montenegro with IUCN 2001 Conservation Statuses“ in following categories: two as critically endangered (Aldrovanda vesiculosa L. and Hottonia palustris L., four as endangered (Hippuris vulgaris L., Lindernia palustris Hartm., Ranunculus lingua L. and Urtica kioviensis Rogow., five as vulnerable (Achillea aspleniifolia Vent., Dryopteris carthusiana (Vill. H. P. Fuchs, Leucojum aestivum L. subsp. aestivum, Stratiotes aloides L. and Thelypteris palustris (Schott subsp.palustris, while 9 are with indefinite categories (CR-VU, due to data deficient (DD. Special Nature Reserve „Zasavica“ is the only habitat in Serbia for Aldrovanda vesiculosa L., which was until 2005. considered as extinct from Serbia.

  18. Variation in manuka oil lure efficacy for capturing Xyleborus glabratus (Coleoptera: Curculionidae: Scholytinae), and Cubeb oil as an alternative attractant

    Science.gov (United States)

    James Hanula; Brian Sullivan; David Wakarchuk

    2013-01-01

    Redbay ambrosia beetle, Xyleborus glabratus Eichoff, is an exotic species to North America vectoring a deadly vascular wilt disease of redbay [Persea borbonia (L.) Spreng], swampbay [P. palustris (Raf.) Sarg.], avocado (P. americana Mill.), and sassafras [Sassafras albidum (...

  19. Soil Fungi Respond More Strongly Than Fine Roots to Elevated CO2 in a Model Regenerating Longleaf Pine-Wiregrass Ecosystem

    Science.gov (United States)

    Increasing atmospheric CO2 will have significant effects on belowground processes which will affect forest structure and function. A model regenerating longleaf pine-wiregrass community [consisting of longleaf pine (Pinus palustris), wiregrass (Aristida stricta), sand post oak (Quescus margaretta),...

  20. Bioregional Planning in Central Georgia, USA

    National Research Council Canada - National Science Library

    Dale, Virginia; Aldridge, Matthew; Arthur, Taryn; Baskaran, Latha; Berry, Michael; Chang, Michael; Efroymson, Rebecca; Garten, Chuck; Stewart, Catherine; Washington-Allen, Robert

    2005-01-01

    ...% of the native longleaf pine (Pinus palustris) forest remains intact. Besides the loss of species, habitats, and ecosystem services associated with longleaf pine forests, the environmental concerns of the region include air, water, and noise pollution...

  1. Formalized classification of European fen vegetation at the alliance level

    DEFF Research Database (Denmark)

    Peterka, Tomáš; Hájek, Michal; Jiroušek, Martin

    2017-01-01

    Aims Phytosociological classification of fen vegetation (Scheuchzerio palustris-Caricetea fuscae class) differs among European countries. Here we propose a unified vegetation classification of European fens at the alliance level, provide unequivocal assignment rules for individual vegetation plot...

  2. Las Haloragaceae de Cuba

    Directory of Open Access Journals (Sweden)

    Betancourt Gandul, Martha

    1999-12-01

    Full Text Available A study of the Haloragaceae in Cuba is presented. The presence of Proserpinaca palustris, P. pectinata. Myriophyllum laxum and M. pinnatum is confirmed, and the possible extinction of M. sparsiflorum is suggestedEstudio de la familia Haloragaceae en Cuba. Se confirma la existencia de Proserpinaca palustris, P. pectinata. Myriophyllum laxum y M, pinnatum, y se plantea la posible extinción de M. sparsiflorum.

  3. Fort Bragg Old Post Historic District Landscape Report

    Science.gov (United States)

    2011-01-01

    proved to be of substantial economic value (Lefler and Powell 1973). Lon- gleaf pines ( Pinus palustris) produce higher quality pine resin/crude gum than...plants that have the same characteristics as the historic varieties; na- tive plants require relatively little upkeep, are drought tolerant, and can... Pinus palustris Longleaf Pine 1933/IDG 2009 Native Quercus alba White Oak Large Evergreen Trees 1933/IDG 2009 Native Magnolia grandiflora Southern

  4. Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR‐type transcriptional regulator NunF

    OpenAIRE

    Hennessy, Rosanna C.; Phippen, Christopher B. W.; Nielsen, Kristian F.; Olsson, Stefan; Stougaard, Peter

    2017-01-01

    Abstract Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun–nup regulon. Organization of the regulon is similar to clusters found in other CLP‐producing pseudomonads except for the border regions where putative LuxR‐type regulators are located. This study focuses on understanding the regulatory role of the LuxR‐type‐encoding gene nun...

  5. Fluorescence spectroscopy of conformational changes of single LH2 complexes

    NARCIS (Netherlands)

    Rutkauskas, D.; Novoderezhkin, V.; Cogdell, R.J.; van Grondelle, R.

    2005-01-01

    We have investigated the energy landscape of the bacterial photosynthetic peripheral light-harvesting complex LH2 of purple bacterium Rhodopseudomonas acidophila by monitoring sequences of fluorescence spectra of single LH2 assemblies, at room temperature, with different excitation intensities as

  6. Role of charge-transfer states in bacterial photosynthesis

    NARCIS (Netherlands)

    Meech, S.R.; Hoff, A.J.

    1986-01-01

    Photon echo, photon-echo excitation, and "hole-burning" data recorded in the 800-990 nm region of Rhodobacter sphaeroides R26 and Rhodopseudomonas viridis reaction centers are reported. The primary process in these reaction centers, following excitation, was found to occur in ≈25 fsec; the

  7. Direct interaction between linear electron transfer chains and solute transport systems in bacteria

    NARCIS (Netherlands)

    Elferink, Marieke G.L.; Hellingwerf, Klaas J.; Belkum, Marco J. van; Poolman, Bert; Konings, Wil N.

    1984-01-01

    In studies on alanine and lactose transport in Rhodopseudomonas sphaeroides we have demonstrated that the rate of solute uptake in this phototrophic bacterium is regulated by the rate of light-induced cyclic electron transfer. In the present paper the interaction between linear electron transfer

  8. RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

    Science.gov (United States)

    Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

    2013-11-01

    Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in

  9. Integrated Approach to Reconstruction of Microbial Regulatory Networks

    Energy Technology Data Exchange (ETDEWEB)

    Rodionov, Dmitry A [Sanford-Burnham Medical Research Institute; Novichkov, Pavel S [Lawrence Berkeley National Laboratory

    2013-11-04

    This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated in RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.

  10. Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR-type transcriptional regulator NunF

    DEFF Research Database (Denmark)

    Hennessy, Rosanna Catherine; Phippen, Christopher; Nielsen, Kristian Fog

    2017-01-01

    -producing pseudomonads except for the border regions where putative LuxR-type regulators are located. This study focuses on understanding the regulatory role of the LuxR-type-encoding gene nunF in CLP production of P. fluorescens In5. Functional analysis of nunF coupled with liquid chromatography-high-resolution mass......Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun-nup regulon. Organization of the regulon is similar to clusters found in other CLP...... spectrometry (LC-HRMS) showed that CLP biosynthesis is regulated by nunF. Quantitative real-time PCR analysis indicated that transcription of the NRPS genes catalyzing CLP production is strongly reduced when nunF is mutated indicating that nunF is part of the nun-nup regulon. Swarming and biofilm formation...

  11. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

    Directory of Open Access Journals (Sweden)

    Kovaleva Galina

    2011-06-01

    Full Text Available Abstract Background Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria. Results To explore conservation and variations in the Shewanella transcriptional networks we analyzed the repertoire of transcription factors and performed genomics-based reconstruction and comparative analysis of regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors and their DNA binding sites, 8 riboswitches and 6 translational attenuators. Forty five regulons were newly inferred from the genome context analysis, whereas others were propagated from previously characterized regulons in the Enterobacteria and Pseudomonas spp.. Multiple variations in regulatory strategies between the Shewanella spp. and E. coli include regulon contraction and expansion (as in the case of PdhR, HexR, FadR, numerous cases of recruiting non-orthologous regulators to control equivalent pathways (e.g. PsrA for fatty acid degradation and, conversely, orthologous regulators to control distinct pathways (e.g. TyrR, ArgR, Crp. Conclusions We tentatively defined the first reference collection of ~100 transcriptional regulons in 16 Shewanella genomes. The resulting regulatory network contains ~600 regulated genes per genome that are mostly involved in metabolism of carbohydrates, amino acids, fatty acids, vitamins, metals, and stress responses. Several reconstructed regulons including NagR for N-acetylglucosamine catabolism were experimentally validated in S

  12. Integrated Genome-Based Studies of Shewanella Ecophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Andrei L. Osterman, Ph.D.

    2012-12-17

    Integration of bioinformatics and experimental techniques was applied to mapping and characterization of the key components (pathways, enzymes, transporters, regulators) of the core metabolic machinery in Shewanella oneidensis and related species with main focus was on metabolic and regulatory pathways involved in utilization of various carbon and energy sources. Among the main accomplishments reflected in ten joint publications with other participants of Shewanella Federation are: (i) A systems-level reconstruction of carbohydrate utilization pathways in the genus of Shewanella (19 species). This analysis yielded reconstruction of 18 sugar utilization pathways including 10 novel pathway variants and prediction of > 60 novel protein families of enzymes, transporters and regulators involved in these pathways. Selected functional predictions were verified by focused biochemical and genetic experiments. Observed growth phenotypes were consistent with bioinformatic predictions providing strong validation of the technology and (ii) Global genomic reconstruction of transcriptional regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors, 8 riboswitches and 6 translational attenuators. Of those, 45 regulons were inferred directly from the genome context analysis, whereas others were propagated from previously characterized regulons in other species. Selected regulatory predictions were experimentally tested. Integration of this analysis with microarray data revealed overall consistency and provided additional layer of interactions between regulons. All the results were captured in the new database RegPrecise, which is a joint development with the LBNL team. A more detailed analysis of the individual subsystems, pathways and regulons in Shewanella spp included bioinfiormatics-based prediction and experimental characterization of: (i) N-Acetylglucosamine catabolic pathway; (ii)Lactate utilization machinery; (iii) Novel Nrt

  13. Ontogenesis peculiarities species of genus Rorippa Scopoli (Cruciferae in the subzone of the southern taiga

    Directory of Open Access Journals (Sweden)

    Svetlana Shabalkina

    2014-04-01

    Full Text Available Latent, pregenerative and generative periods in the ontogeny of Rorippa amphibia (L. Bess., R. palustris (L. Bess. and R. ×anceps (Wahlenb. Reichenb. were described. Skipping of a postgenerative stage, and some of ontogenetic states demonstrates the dynamic multiplicity of individual development; while the combination of seed and vegetative reproductions – multiplicity of the ways of reproduction and generation. The ontogeny of R. palustris individuals corresponds to A-type, R. amphibia and R. ×anceps – to G-type, and R. ×anceps – to D-type.

  14. Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s

    OpenAIRE

    Chandler, Danielle E.; Gumbart, James; Stack, John D.; Chipot, Christophe; Schulten, Klaus

    2009-01-01

    The photosynthetic apparatus of purple bacteria is contained within organelles called chromatophores, which form as extensions of the cytoplasmic membrane. The shape of these chromatophores can be spherical (as in Rhodobacter sphaeroides), lamellar (as in Rhodopseudomonas acidophila and Phaeospirillum molischianum), or tubular (as in certain Rb. sphaeroides mutants). Chromatophore shape is thought to be influenced by the integral membrane proteins Light Harvesting Complexes I and II (LH1 and ...

  15. Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

    1990-01-01

    A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

  16. 8.3 Microbiology and Biodegradation: A New Bacterial Communication System

    Science.gov (United States)

    2014-04-09

    Approved for Public Release; Distribution Unlimited 8.3 Microbiology and Biodegradation: A new bacterial communication system The views, opinions and...JB.01479-10 Federico E. Rey, Caroline S. Harwood. FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas...Quorum sensing is a term used to describe bacterial cell-to-cell communication that allows cell-density-dependent gene expression. There are many

  17. Appendix 1

    African Journals Online (AJOL)

    Blyth's Reed Warbler x Marsh Warbler hybrid Acrocephalus dumetorum x A. palustris ............1. Number of .... in May 2009 when the finding date was given as “in December. 2005” ...... worn, brown wing feathers would not be replaced until the ...

  18. A whole stand growth and yield system for young longleaf pine plantations in Southwest Georgia

    Science.gov (United States)

    John R. Brooks; Steven B. Jack

    2006-01-01

    A whole stand growth and yield system for planted longleaf pine (Pinus palustris Mill.) was developed from permanent plot data collected annually over an 8 year period. The dataset consists of 12 intensively-managed longleaf pine plantations that are located in Lee, Worth, Mitchell, and Baker counties in southwest Georgia. Stand survival, dominant...

  19. 7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

    Science.gov (United States)

    2010-01-01

    ... reinsured policies: Cultivated Wild Rice Crop Provisions. 1. Definitions Approved laboratory. A testing.... Cultivated Wild Rice. A member of the grass family Zizania Palustris L., adapted for growing in man-made... for the crop year. Planted acreage. In addition to the definition contained in the Basic Provisions...

  20. Evaluation of Fungal Deterioration in Liquidambar orientalis Mill. heartwood by FT-IR and light microscopy.

    Science.gov (United States)

    Nural Yilgor; Dilek Dogu; Roderquita Moore; Evren Terzi; S. Nami Kartal

    2013-01-01

    The chemical and morphological changes in heartwood specimens of Liquidambar orientalis Mill. caused by the white-rot fungus Trametes versicolor and the brown-rot fungi Tyromyces palustris and Gloeophyllum trabeum were studied by wet chemistry, FT-IR, GC-MS analyses, and photo-...

  1. Final Environmental Assessment for Aircraft Maintenance Operations Center

    Science.gov (United States)

    2014-06-01

    lies within the Southern Mixed Forest Province that is typically characterized by forests of broadleaf deciduous and needleleaf evergreen trees ...virginiana), pin oak (Q. palustris), and southern magnolia (Magnolia grandiflora). Small tree and shrub species include the eastern red cedar, eastern ...this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden, to Washington

  2. Introducing close-range photogrammetry for characterizing forest understory plant diversity and surface fuel structure at fine scales

    Science.gov (United States)

    Benjamin C. Bright; E. Louise Loudermilk; Scott M. Pokswinski; Andrew T. Hudak; Joseph J. O' Brien

    2016-01-01

    Methods characterizing fine-scale fuels and plant diversity can advance understanding of plant-fire interactions across scales and help in efforts to monitor important ecosystems such as longleaf pine (Pinus palustris Mill.) forests of the southeastern United States. Here, we evaluate the utility of close-range photogrammetry for measuring fuels and plant...

  3. Long-term effects of biennial prescribed fires on the growth of longleaf pine

    Science.gov (United States)

    William D. Boyer

    2000-01-01

    The effects of several hardwood control treatments on understory succession and overstory growth have been followed for 22 years on a Coastal Plain site in southwest Alabama. The study began in 1973, with 12 treatment combinations in 14-year-old naturally established longleaf pine (Pinus palustris) thinned to about 1,236 stems per hectare (500 stems...

  4. First report of laurel wilt, caused by Raffaelea lauricola, on sassafras (Sassafras albidum) in Alabama

    Science.gov (United States)

    C.A. Bates; Stephen Fraedrich; T.C. Harrington; R.S. Cameron; R.D. Menard; Susan Best

    2013-01-01

    Laurel wilt, caused by Raffaelea lauricola, a fungal symbiont of the redbay ambrosia beetle, Xyleborus glabratus, is responsible for extensive mortality of native redbays (Persea borbonia and P. Palustris) in the coastal plains of the southeastern United States. The wilt also affect the more...

  5. Typhaceae

    NARCIS (Netherlands)

    Backer, C.A.

    1948-01-01

    Perennial, palustrial or aquatic herbs with a creeping rhizome; stems erect, solid, submerged at the base. Leaves biseriate, partly radical or subradical, partly cauline, lower congested, higher remote, elongate-linear, rather thick and spongy, bluntmargined; their sheathing bases excreting slime on

  6. Restoration of the Native Plant Communities in Longleaf Pine Landscapes on the Kisatchie National Forest, Louisiana

    Science.gov (United States)

    James D. Haywood; Alton Martin; Finis L. Harris; Michael L. Elliott-Smith

    1998-01-01

    In January 1993, the Kisatchie National Forest and Southern Research Station began monitoring the effects of various management practices on overstory and midstory trees, shrubs, and understory woody and herbaceous vegetation in several longleaf pine (Pinus palustris Mill.) stands. The monitoring of these stands is part of several Ecosystem...

  7. Disturbance from southern pine beetle, suppression, and wildfire affects vegetation composition in central Louisiana: a case study

    Science.gov (United States)

    T.W. Coleman; Alton Martin; J.R. Meeker

    2010-01-01

    We assessed plant composition and forest succession following tree mortality from infestation of southern pine beetle (Dendroctonus frontalis), associated suppression, and wildfire in two forest types, pine (Pinus spp.) with mixed hardwood and longleaf pine (P. palustris). In this case study, vegetation was...

  8. Protecting and restoring longleaf pine forests on the Kisatchie National Forest in Louisiana

    Science.gov (United States)

    James D. Haywood; Michael Elliot-Smith; Finis Harris; Alton Martin

    2000-01-01

    Longleaf pine (Pinus palustris Mill.) forests once constituted a major ecosystem in the Southern United States stretching from southeastern Virginia south to central Florida and west into East Texas. These forests covered a wide range of site conditions, from wet pine flatwoods to dry mountain slopes. Intensive exploitation reduced the extent of old-...

  9. Ecological restoration of an old-growth longleaf pine stand utilizing prescribed fire

    Science.gov (United States)

    J. Morgan Varner; John S. Kush; Ralph S. Meldahl

    2000-01-01

    Ecological restoration using prescribed fire has been underway for 3 years in an uncut, old-growth longleaf pine (Pinus palustris) stand located in south Alabama. The longleaf pine ecosystem requires frequent (once every 1-10 years) surface fire to prevent succesion to later several stages. Before this study began, this stand had not burned in >...

  10. Fungicide sensitivity in the wild rice pathogen Bipolaris oryzae

    Science.gov (United States)

    In recent years the occurrence of fungal brown spot, caused by Bipolaris oryzae has increased in cultivated wild rice (Zizania palustris) paddies in spite of the use of fungicides. To implement an efficient integrated disease management system, we are exploring whether field isolates have developed ...

  11. Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

    Science.gov (United States)

    The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

  12. Site Index Curves for Direct-Seeded Loblolly and Longleaf Pines in Louisiana

    Science.gov (United States)

    Quang V. Cao; V. Clark Baldwin; Richard E. Lohrey

    1995-01-01

    Site index equations were developed for direct-seeded loblollypine (Pinus taeda L.) and longleaf pine (Pinus palustris Mill.) based on data from 148 and 75 permanent plots, respectively. These plots varied from 0.053 to 0.119 ac in size, and were established in broadcast, row, and spot seeded stands throughout Louisiana. The Bailey and Clutter (1974) model was...

  13. Analyzing the complexity of cone production in longleaf pine by multiscale entropy

    Science.gov (United States)

    Xiongwen Chen; Qinfeng Guo; Dale G. Brockway

    2016-01-01

    The longleaf pine (Pinus palustris Mill.) forests are important ecosystems in the southeastern USA because of their ecological and economic value. Since European settlement, longleaf pine ecosystems have dramatically declined in extent, to the degree that they are now listed as endangered ecosystems. Its sporadic seed production, which...

  14. Fire in longleaf pine stand management: an economic analysis

    Science.gov (United States)

    Rodney L. Busby; Donald G. Hodges

    1999-01-01

    A simulation analysis of the economics of using prescribed fire as a forest management tool in the management of longleaf pine (Pinus palustris Mill.) plantations was conducted. A management regime using frequent prescribed fire was compared to management regimes involving fertilization and chemical release, chemical control, and mechanical control. Determining the...

  15. Air lateral root pruning affects longleaf pine seedling root system morphology

    Science.gov (United States)

    Shi-Jean Susana Sung; Dave Haywood

    2016-01-01

    Longleaf pine (Pinus palustris) seedlings were cultured with air lateral root pruning (side-vented containers, VT) or without (solid-walled containers, SW). Seedling root system morphology and growth were assessed before planting and 8 and 14 months after planting. Although VT seedlings had greater root collar diameter than the SW before planting,...

  16. Understory fuel variation at the Carolina Sandhills National Wildlife Refuge: a description of chemical and physical properties

    Science.gov (United States)

    Evelyn S. Wenk; G. Geoff Wang; Joan L. Walker

    2013-01-01

    Upland forest in the Carolina Sandhills National Wildlife Refuge is characterized by a longleaf pine (Pinus palustris) canopy with a variable understory and ground-layer species composition. The system was historically maintained by fire and has been managed with prescribed fire in recent decades. A management goal is to reduce turkey oak (...

  17. Early growth of planted longleaf pine seedlings in relation to light, soil moisture, and soil temperature

    Science.gov (United States)

    Benjamin O. Knapp; G. Geoff Wang; Joan L. Walker

    2006-01-01

    Drastic reductions in longleaf pine (Pinus palustris Mill.) acreage have led to an increased focus on regeneration of the longleaf pine ecosystem. Many areas require artificial regeneration for establishment, and site preparation techniques may be implemented to increase regeneration success. The objectives of this study were to determine differences...

  18. Using existing growth models to predict RCW habitat development following site preparation: pitfalls of the process and potential growth response

    Science.gov (United States)

    Benjamin O. Knapp; Joan L. Walker

    2013-01-01

    Land managers throughout the Southeast are interested in restoring the longleaf pine (Pinus palustris Mill.) ecosystem, due in part to its value as habitat for the endangered red-cockaded woodpecker (Picoides borealis). In 2003, we established a study at Camp Lejeune, NC, to determine the effects of common site preparation...

  19. The health of loblolly pine stands at Fort Benning, GA

    Science.gov (United States)

    Soung-Ryoul Ryu; G. Geoff Wang; Joan L. Walker

    2013-01-01

    Approximately two-thirds of the red-cockaded woodpecker (Picoides borealis) (RCW) groups at Fort Benning, GA, depend on loblolly pine (Pinus taeda) stands for nesting or foraging. However, loblolly pine stands are suspected to decline. Forest managers want to replace loblolly pine with longleaf pine (P. palustris...

  20. Silvicultural treatments for converting loblolly pine to longleaf pine dominance: Effects on planted longleaf pine seedlings

    Science.gov (United States)

    Huifeng Hu; G.Geoff Wang; Joan L. Walker; Benjamin O. Knapp

    2012-01-01

    A field study was installed to test silvicultural treatments for establishing longleaf pine (Pinus palustris Mill) in loblolly pine (P. taeda L.) stands. Harvesting was used to create seven canopy treatments, four with uniformly distributed canopies at different residual basal areas [Control (16.2 m2/ha),...

  1. Effects of canopy treatments on early growth of planted longleaf pine seedlings and ground vegetation in North Carolina: a preliminary study

    Science.gov (United States)

    Huifeng Hu; Benjamin O. Knapp; G. Geoff Wang; Joan L. Walker

    2013-01-01

    We installed a field experiment to support the development of protocols to restore longleaf pine (Pinus palustris Mill.) to existing mature loblolly pine (P. taeda L.) stands at Camp Lejeune, NC. Seven canopy treatments included four uniform and three gap treatments. The four uniform treatments were defined by target residual basal...

  2. Silvicultural treatments for converting loblolly pine to longleaf pine dominance: Effects on resource availability and their relationships with planted longleaf pine seedlings

    Science.gov (United States)

    Huifeng Hu; G.Geoff Wang; Joan L. Walker; Benjamin O. Knapp

    2012-01-01

    Throughout the southeastern United States, land managers are currently interested in converting loblolly pine (Pinus taeda L.) plantations to species rich longleaf pine (Pinus palustris Mill.) ecosystems. In a 3-year study on moderately well- to well-drained soils of the Lower Coastal Plain in North Carolina, we examined the...

  3. Effects of spring prescribed fire on short-term, leaf-level photosynthesis and water use efficiency in longleaf pine

    Science.gov (United States)

    John K. Jackson; Dylan N. Dillaway; Michael C. Tyree; Mary Anne Sword Sayer

    2015-01-01

    Fire is a natural and important environmental disturbance influencing the structure, function, and composition of longleaf pine (Pinus palustris Mill.) ecosystems. However, recovery of young pines to leaf scorch may involve changes in leaf physiology, which could influence leaf water-use efficiency (WUE). This work is part of a larger seasonal...

  4. Measured and modelled leaf and stand-scale productivity across a soil moisture gradient and a severe drought.

    Science.gov (United States)

    Wright, J K; Williams, M; Starr, G; McGee, J; Mitchell, R J

    2013-02-01

    Environmental controls on carbon dynamics operate at a range of interacting scales from the leaf to landscape. The key questions of this study addressed the influence of water and nitrogen (N) availability on Pinus palustris (Mill.) physiology and primary productivity across leaf and canopy scales, linking the soil-plant-atmosphere (SPA) model to leaf and stand-scale flux and leaf trait/canopy data. We present previously unreported ecophysiological parameters (e.g. V(cmax) and J(max)) for P. palustris and the first modelled estimates of its annual gross primary productivity (GPP) across xeric and mesic sites and under extreme drought. Annual mesic site P. palustris GPP was ∼23% greater than at the xeric site. However, at the leaf level, xeric trees had higher net photosynthetic rates, and water and light use efficiency. At the canopy scale, GPP was limited by light interception (canopy level), but co-limited by nitrogen and water at the leaf level. Contrary to expectations, the impacts of an intense growing season drought were greater at the mesic site. Modelling indicated a 10% greater decrease in mesic GPP compared with the xeric site. Xeric P. palustris trees exhibited drought-tolerant behaviour that contrasted with mesic trees' drought-avoidance behaviour. © 2012 Blackwell Publishing Ltd.

  5. 75 FR 31387 - Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for Mississippi...

    Science.gov (United States)

    2010-06-03

    ...-- historically forest dominated by longleaf pine (Pinus palustris) --and isolated temporary wetland breeding... frequency and duration of severe storms and droughts (McLauglin et al. 2002, p. 6074; Golladay et al. 2004, p. 504; Seager et al. 2009, p. 5043). During a period of drought from 2004 to 2007, rainfall during...

  6. Preliminary Feasibility Report (Stage 2), Review of Reports on Lorain Harbor, Ohio. Volume 2. Appendices. Revision

    Science.gov (United States)

    1981-05-01

    casts for iron ore within the GL/SLS region. A recent downturn in the economic health of the domestic steel industry has probably deferred any major...emergents: Swamp rose mallow Hibiscus palustris Nettle Urtica sp. Nightshade Solanum dulcamara Hedge bindweed Convolvulus sepium Peppermint Mentha arvensis

  7. Chesapeake Bay Low Freshwater Inflow Study. Biota Assessment. Phase I. Appendices.

    Science.gov (United States)

    1980-08-01

    Resources Coastal Resources Power Plant Siting Maryland Geological Survey Maryland Environmental Health Administration university of Maryland Marine...are very common: Acorus calamus Polygonum spp. Hibiscus palustris Pontederia cordata Leersia spp. Sagittaria latifolia Nuphar leiteum Typha... Hibiscus ) penetrate to mesohaline salinities. In general, the fresh water marsh associations are limited to areas upstream of 3 - 50Xsalinity

  8. Individual tree diameter, height, and volume functions for longleaf pine

    Science.gov (United States)

    Carlos A. Gonzalez-Benecke; Salvador A. Gezan; Timothy A. Martin; Wendell P. Cropper; Lisa J. Samuelson; Daniel J. Leduc

    2014-01-01

    Currently, little information is available to estimate individual tree attributes for longleaf pine (Pinus palustris Mill.), an important tree species of the southeastern United States. The majority of available models are local, relying on stem diameter outside bark at breast height (dbh, cm) and not including stand-level parameters. We developed...

  9. Environmental Impact Study of the Northern Section of the Upper Mississippi River, St. Croix River Pool.

    Science.gov (United States)

    1973-11-01

    Poa palustris Fowl meadow-grass P Poa pratensis Blue grass Setaria viridis Green foxtail P P P P D Setaria sp. Bristly foxtail P Spartina pectinata...Juneberry) Crataegus spp. (Thorn-Apple) Fragaria vesca (Wild Strawberry) Geum canadense (White Avens) Geum laciniatum (Avens) Geum triflorum (Three

  10. A decision tree approach using silvics to guide planning for forest restoration

    Science.gov (United States)

    Sharon M. Hermann; John S. Kush; John C. Gilbert

    2013-01-01

    We created a decision tree based on silvics of longleaf pine (Pinus palustris) and historical descriptions to develop approaches for restoration management at Horseshoe Bend National Military Park located in central Alabama. A National Park Service goal is to promote structure and composition of a forest that likely surrounded the 1814 battlefield....

  11. Are we over-managing longleaf pine?

    Science.gov (United States)

    John S. Kush; Rebecca J. Barlow; John C. Gilbert

    2012-01-01

    Longleaf pine (Pinus palustris Mill.) is not loblolly (Pinus taeda L.) or slash pine (Pinus elliottii L.). There is the need for a paradigmatic shift in our thinking about longleaf pine. All too often we think of longleaf as an intolerant species, slow-grower, difficult to regenerate, and yet it dominated the pre...

  12. Analysis of seasonal, diurnal, and noctural growth patterns of young longleaf pine

    Science.gov (United States)

    John C. Gilbert; Ralph S. Meldahl; John S. Kush; William D. Boyer

    2006-01-01

    Forty longleaf pine (Pinus palustris Mill.) trees initially ranging from 1 to 1.5 m in height were measured on the Escambia Experimental Forest from 1969 through 1980. The trees were evenly divided between two soil types. From 1969 through 1970, height and diameter measurements were recorded one to four times weekly during the growing seasons and...

  13. What 45 years of RLGS data has to say about longleaf pine mortality - not much

    Science.gov (United States)

    John S. Kush; John C. Gilbert; Rebecca J. Barlow

    2015-01-01

    The original longleaf pine (Pinus palustris Mill.) forest was self-perpetuating where seedlings always had to be present. It reproduced itself in openings in the overstory where dense young stands developed. These openings would range from a few tenths of an acre to large openings of several thousand acres. Regardless of the event size, longleaf...

  14. Overhead shading and growth of young longleaf pine

    Science.gov (United States)

    John C. Gilbert; John S. Kush; Ralph S. Meldahl; William D. Boyer; Dean H. Gjerstad

    2014-01-01

    A study to determine the effects of environmental conditions on the growth of longleaf pine (Pinus palustris Mill.) was initiated in 1969 on the Escambia Experimental Forest near Brewton, Alabama, USA. This study sample consisted of forty young naturally regenerated, even aged longleaf pine seedlings evenly divided between two soil types. At the beginning of the study...

  15. Spatial analysis of longleaf pine stand dynamics after 60 years of management

    Science.gov (United States)

    John C. Gilbert; John S. Kush; Rebecca J. Barlow

    2012-01-01

    There are still many questions and misconceptions about the stand dynamics of naturally-regenerated longleaf pine (Pinus palustris Mill.). Since 1948, the “Farm Forty,” a forty-acre tract located on the USDA Forest Service Escambia Experimental Forest near Brewton, Alabama, has been managed to create high quality wood products, to successfully...

  16. Prescribed fire effects in a longleaf pine ecosystem--are winter fires working?

    Science.gov (United States)

    Rebecca J. Barlow; John S. Kush; John C. Gilbert; Sharon M. Hermann

    2015-01-01

    Longleaf pine (Pinus palustris Mill.) ecosystems once dominated 60 to 90 million acres and supported one of the most diverse floras in North America. It is well-known that longleaf pine ecosystems must burn frequently to maintain natural structure and function. This vegetation type ranks as one of the most fire-dependent in the country and must...

  17. Impact of fire in two old-growth montane longleaf pine stands

    Science.gov (United States)

    John S. Kush; John C. Gilbert; Crystal Lupo; Na Zhou; Becky Barlow

    2013-01-01

    The structure of longleaf pine (Pinus palustris Mill.) forests of the Southeastern United States Coastal Plains has been the focus of numerous studies. By comparison, the forests in the mountains of Alabama and Georgia are not well understood. Less than 1 percent of longleaf pine stands found in the montane portion of longleaf’s range are considered...

  18. Longleaf Pine: An Updated Bibliography

    Science.gov (United States)

    John S. Kush; Ralph S. Meldahl; William D. Boyer; Charles K. McMahon

    1996-01-01

    The longleaf pine (Pinus palustris Mill.) forest figured prominently in the cultural and economic development of the South. What was once one of the most extensive forest ecosystems in North America has now become critically endangered (6). At the time of European settlement, this ecosystem dominated as much as 92 million acres throughout the...

  19. WATER-USE ALONG A HYDROLOGICAL GRADIENT IN CENTRAL FLORIDA: A TALE OF TWO PINUS SPECIES

    Science.gov (United States)

    Although central Florida is relatively flat, the distribution of species on the landscape is controlled by subtle changes in elevation. Along a four-meter elevation gradient, xeric sandhill vegetation dominated by Pinus palustris (Longleaf pine) gives way to mesic pine flatwoods...

  20. Surfing the Koehler Curve: revisiting a method for the identification of longleaf pine stumps and logs

    Science.gov (United States)

    Thomas L. Eberhardt; Philip M. Sheridan; Karen G. Reed

    2009-01-01

    Measurements of pith and second growth ring diameters were used by Koehler in 1932 to separate longleaf pine (Pinus palustris Mill.) timbers from those of several southern pines (e.g., loblolly, shortleaf). In the current study, measurements were taken from plantation-grown longleaf, loblolly and shortleaf pine trees, as well as old growth longleaf pine, lightwood, and...

  1. The quest for methods to identify longleaf pine stump relicts in Southeastern Virginia

    Science.gov (United States)

    Thomas L. Eberhardt; Philip M. Sheridan; Chi-Leung So; Arvind A.R. Bhuta; Karen G. Reed

    2015-01-01

    The discovery of lightwood and turpentine stumps in southeastern Virginia raised questions about the true historical range for longleaf pine (Pinus palustris Mill.). Several investigative studies were therefore carried out to develop a method to determine the taxa of these relicts. Chemical approaches included the use of near infrared (NIR) spectroscopy coupled with...

  2. Revivification of a method for identifying longleaf pine timber and its application to southern pine relicts in southeastern Virginia

    Science.gov (United States)

    Thomas L. Eberhardt; Philip M. Sheridan; Arvind A.R. Bhuta

    2011-01-01

    Abstract: Longleaf pine (Pinus palustris Mill.) cannot be distinguished from the other southern pines based on wood anatomy alone. A method that involves measuring pith and second annual ring diameters, reported by Arthur Koehler in 1932 (The Southern Lumberman, 145: 36–37), was revisited as an option for identifying longleaf pine timbers and stumps. Cross-section...

  3. The influence of canopy, sky condition, and solar angle on light quality in a longleaf pine woodland

    Science.gov (United States)

    Stephen D. Pecot; Stephen B. Horsley; Michael A. Battaglia; Robert J. Mitchell

    2005-01-01

    Light transmittance estimates under open, heterogeneous woodland canopies such as those of longleaf pine (Pinus palustris Mill.) forests report high spatial and temporal variation in the quantity of the light environment. In addition, light quality, that is, the ratio of red to far-red light (R:FR), regulates important aspects of plant...

  4. Competitive responses of seedlings and understory plants in longleaf pine woodlands: separating canopy influences above and below ground

    Science.gov (United States)

    Stephen D. Pecot; Robert J. Mitchell; Brian J. Palik; Barry Moser; J. Kevin Hiers

    2007-01-01

    A trenching study was used to investigate above- and below-ground competition in a longleaf pine (Pinus palustris P. Mill.) woodland. Trenched and nontrenched plots were replicated in the woodland matrix, at gap edges, and in gap centers representing a range of overstory stocking. One-half of each plot received a herbicide treatment to remove the...

  5. Structure and composition of historical longleaf pine ccosystems in Mississippi, USA

    Science.gov (United States)

    Brice B. Hanberry; Keith Coursey; John S. Kush

    2018-01-01

    Longleaf pine (Pinus palustris) historically was a widespread ecosystem composed of a simple tree canopy and grasslands ground layer. After widespread loss of this ecosystem due to logging and fire exclusion, little quantitative information exists about historical structure for restoration goals. We identified composition in De Soto National Forest and Pearl River...

  6. The social and economic drivers of the southeastern forest landscape

    Science.gov (United States)

    R. Kevin McIntyre; Barrett B. McCall; David N. Wear

    2018-01-01

    The last quarter century has witnessed an unprecedented resurgence of interest in the management of longleaf pine (Pinus palustris) forests, a phenomenon that has been coupled with increased understanding of the ecology, management, and restoration of these ecosystems. As interest in longleaf pine becomes more mainstream among landowners and the...

  7. Fertilizer responses of longleaf pine trees within a loblolly pine plantation: separating direct effects from competition effects

    Science.gov (United States)

    Peter H Anderson; Kurt H. Johnsen

    2009-01-01

    Evidence is mixed on how well longleaf pine (Pinus palustris Mill.) responds to increased soil nitrogen via fertilization. We examined growth and physiological responses of volunteer longleaf pine trees within an intensive loblolly pine (Pinus taeda L.) fertilization experiment. Fertilizer was applied annually following thinning at age 8 years (late 1992) at rates...

  8. Financial performance of loblolly and longleaf pine plantations

    Science.gov (United States)

    Steven D. Mills; Charles T. Stiff

    2013-01-01

    The financial performance of selected management regimes for loblolly (Pinus taeda L.) and longleaf pine (P. palustris Mill.) plantations were compared for four cases, each with low- and high-site productivity levels and each evaluated using 5 and 7 percent real discount rates. In all cases, longleaf pine was considered both with...

  9. Growth and mortality of pin oak and pecan reforestation in a constructed wetland: analysis with management implications

    Science.gov (United States)

    D.E. Henderson; P. Botch; J. Cussimanio; D. Ryan; J. Kabrick; D. Dey

    2009-01-01

    Pin oak (Quercus palustris Muenchh.) and pecan (Carya illinoensis (Wangenh.) K. Koch) trees were planted on reforestation plots at Four Rivers Conservation Area in west-central Missouri. The study was conducted to determine survival and growth rates of the two species under different production methods and environmental variables....

  10. Ecosystem carbon density and allocation across a chronosequence of longleaf pine forests

    Science.gov (United States)

    Lisa J. Samuelson; Thomas A. Stokes; John R. Butnor; Kurt H. Johnsen; Carlos A. Gonzalez-Benecke; Timothy A. Martin; Wendell P. Cropper; Pete H. Anderson; Michael R. Ramirez; John C. Lewis

    2017-01-01

    Forests can partially offset greenhouse gas emissions and contribute to climate change mitigation, mainly through increases in live biomass. We quantified carbon (C) density in 20 managed longleaf pine (Pinus palustris Mill.) forests ranging in age from 5...

  11. North American Lauraceae: terpenoid emissions, relative attraction and boring preferences of redbay ambrosia beetle, Xyleborus glabratus (Coleoptera: Curculionidae: Scolytinae).

    Science.gov (United States)

    Paul E. Kendra; Wayne S. Montgomery; Jerome Niogret; Grechen E. Pruett; Albert (Bud) Mayfield; Martin MacKenzie; Mark A. Deyrup; Gary R. Bauchan; Randy C. Ploetz

    2014-01-01

    Abstract The invasive redbay ambrosia beetle, Xyleborus glabratus, is the primary vector of Raffaelea lauricola, a symbiotic fungus and the etiologic agent of laurel wilt. This lethal disease has caused severe mortality of redbay (Persea borbonia) and swampbay (P. palustris) trees in the southeastern USA, threatens avocado (P. americana) production in Florida, and has...

  12. From loblolly to longleaf: fifth-year results of a longleaf pine restoration study at two ecologically distinct sites

    Science.gov (United States)

    Benjamin O. Knapp; G. Geoff Wang; Joan L. Walker; Huifeng Hu

    2015-01-01

    Historical land-use and management practices in the southeastern United States have resulted in the widespread conversion of many upland sites from dominance of longleaf pine (Pinus palustris Mill.) to loblolly pine (P. taeda L.) in the time following European settlement. Given the ecological, economic, and cultural...

  13. Picloram Movement in Soil Solution and Streamflow from a Coastal Plain Forest

    Science.gov (United States)

    Jerry L. Michael; D.G. Neary; M.J.M. Wells

    1989-01-01

    Picloram (4-amino-3,5,6-trichloropicolinic acid) was aerially applied to P longleaf pine (Pinus palustris L.) site in the upper constnl plain of Alabama to control kudzu [Purraria lobota (Willd.) Ohwi]. Pellets (10% a.i.) were spread at the rate of 56 kg ha-1 on loamy sand Typic Knnhspludult soils....

  14. Korte mededeling

    NARCIS (Netherlands)

    Rensen-Bronkhorst, R.; Spronk, J.

    1983-01-01

    Ludwigia palustris (L.) Elliot weer in Noord-Brabant gevonden. Geïnspireerd door leuke plantevondsten op de ijsbaan van Schijndel werd op 17 augustus 1983 door de plantenwerkgroep van de KNNV-afdeling Eindhoven een bezoek gebracht aan de Nuenense ijsbaan. Door de zeer droge zomer was het terreintje

  15. Cavity size and copper root pruning affect production and establishment of container-grown longleaf pine seedlings

    Science.gov (United States)

    Marry Anne Sword Sayer; James D. Haywood; Shi-Jean Susana Sung

    2009-01-01

    With six container types, we tested the effects of cavity size (i.e., 60, 93, and 170 ml) and copper root pruning on the root system development of longleaf pine (Pinus palustris Mill.) seedlings grown in a greenhouse. We then evaluated root egress during a root growth potential test and assessed seedling morphology and root system development 1 year after planting in...

  16. The role of large container seedlings in afforesting oaks in bottomlands

    Science.gov (United States)

    Daniel C. Dey; John M. Kabrick; Michael Gold

    2006-01-01

    We planted large container (RPM®) and 1-0 bareroot seedlings of pin oak (Quercus palustris Muenchh.) and swamp white oak (Q. bicolor Willd.) in crop fields in the Missouri River floodplain. We also evaluated the benefits of soil mounding and a grass (Agrostis gigantea Roth) cover crop. RPM®) oak seedlings had significantly greater...

  17. Planning for an uncertain future: Restoration to mitigate water scarcity and sustain carbon sequestration

    Science.gov (United States)

    Steven T. Brantley; James M. Vose; David N. Wear; Larry Band

    2018-01-01

    The desired future conditions of longleaf pine (Pinus palustris) can be described by ecosystem structural characteristics as well as by the provision of ecosystem services. Although the desired structural characteristics of restored longleaf pine ecosystems have been described at length, these characteristics deserve a brief review here because...

  18. Arthropod density and biomass in longleaf pines: effects of pine age and hardwood midstory

    Science.gov (United States)

    Richard N. Conner; Christopher S. Collins; Daniel Saenz; Toni Trees; Richard R. Schaefer; D. Craig Rudolph

    2004-01-01

    During a 2-year study we examined arthropod communities (density and biomass) on longleaf pines (Pinus palustris) in eastern Texas during spring, summer, and winter on trees in 3 age classes: 40-50, 60-70, and 130-1 50 years, as a potential food source for the red-cockaded woodpecker (Picoides borealis). We also examined arthropod...

  19. Ground-dwelling arthropod association with coarse woody debris following long-term dormant season prescribed burning in the longleaf pine flatwoods of North Carolina

    Science.gov (United States)

    James L Hanula; Dale Wade; Joseph O' Brien; Susan Loeb

    2009-01-01

    A 5-year study of long-term (40 years) study plots was conducted on the Osceola National Forest in northern Florida to determine how dormant-season fire frequency (annual, biennial, quadrennial, or unburned) affects ground-dwelling macroarthropod use of coarse woody debris in longleaf pine (Pinus palustris Mill.) forests. Pitfall traps were used to sample arthropods...

  20. Thickness and roughness measurements for air-dried longleaf pine bark

    Science.gov (United States)

    Thomas L. Eberhardt

    2015-01-01

    Bark thicknesses for longleaf pine (Pinus palustris Mill.) were investigated using disks collected from trees harvested on a 70-year-old plantation. Maximum inner bark thickness was relatively constant along the tree bole whereas maximum outer bark thickness showed a definite decrease from the base of the tree to the top. The minimum whole bark thickness followed the...

  1. Longleaf pine site response to repeated fertilization and forest floor removal by raking and prescribed burning

    Science.gov (United States)

    Kim Ludovici; Robert Eaton; Stanley Zarnoch

    2018-01-01

    Removal of forest floor litter by pine needle raking and prescribed burning is a common practice in longleaf pine (Pinus palustris Mill.) stands on Coastal Plain sites in the Southeastern United States. Repeated removal of litter by raking and the loss of surface organic matter from controlled burns can affect the...

  2. Journal of Biosciences | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences. Anurag Kumar Mishra. Articles written in Journal of Biosciences. Volume 27 Issue 3 June 2002 pp 251-259 Articles. Cloning and sequencing of complete -crystallin cDNA from embryonic lens of Crocodylus palustris · Raman Agrawal Reena Chandrashekhar Anurag Kumar Mishra ...

  3. On the number of genes controlling the grass stage in longleaf pine

    Science.gov (United States)

    C. Dana Nelson; C. Weng; Thomas L. Kubisiak; M. Stine; C.L. Brown

    2003-01-01

    The grass stage is an inherent and distinctive developmental trait of longleaf pine (Pinus palustris), in which height growth in the first few years after germination is suppressed. In operational forestry practice the grass stage extends for nvo to several years and often plays a role in planting failures and decisions to plant alternative species....

  4. Insect Pollinators of Three Rare Plants in a Florida Longleaf Pine Forest

    Science.gov (United States)

    Theresa Pitts-Singer; James L. Hanula; Joan L. Walker

    2002-01-01

    As a result of human activity, longleaf pine (Pinus palustris Miller) forests in the southern United States have been lost or drastically altered. Many of the plant species that historically occupied those forests now persist only as remnants and are classified as threatened or endangered. In order to safeguard such species, a better understanding of...

  5. Influence of herbicides and felling, fertilization, and prescribed fire on longleaf pine growth and understory vegetation through ten growing seasons and the outcome of an ensuing wildfire

    Science.gov (United States)

    James D. Haywood

    2011-01-01

    Restoring longleaf pine (Pinus palustris Mill.) over much of its original range requires artificial regeneration. In central Louisiana, USA, two fertilization levels - No (NF) or Yes (F-36 kg/ha N and 40 kg/ha P) in combination with three vegetation treatments - Check, four prescribed fires (PF), or multi-year vegetation control by herbicidal and mechanical means (IVM...

  6. Preliminary Guide to the Onsite Identification and Delineation of the Wetlands of the South Atlantic United States.

    Science.gov (United States)

    1982-05-01

    shield) Ceratophyilum demersum (Coontail) Myriophyllum spp. (Watermilfoil) Nelumbo lutea ( American lotus) Nuphar luteum (Spatterdock) Nymphaea odorata...Overcup oak) Quercus palustris (Pin oak) Quercus phelios (Willow oak) Ulmus americana ( American elm) UlmuS rubra (Slippery elm) c. Atlantic White...var. biflora (Swamp black gum) Persea borbonia (Red bay) Pinus serotina (Pond pine) Smilax laurifolia (Bamboo vine) Sphagnum spp. (Sphagnum moss

  7. Feasibility Report and Environmental Impact Statement for Navigation Improvements at Bayou La Batre, Alabama

    Science.gov (United States)

    1988-09-12

    and plant corn. When coastal Alabama was opened to British and American settlers; fishing, livestock and, later, resort hotels became the important...bay (Magnolia virginiana), swamp bay ( Persea palustris), water oak (Quercus nigra), and sweet gum (Liquidambar styraciflua). Bald cypress (Taxodium

  8. Regional Guidebook for Applying the Hydrogeomorphic Approach to Assessing the Functions of Headwater Slope Wetlands on the Mississippi and Alabama Coastal Plans

    Science.gov (United States)

    2007-08-01

    sourwood Bignonia capreolata crossvine Panicum virgatum switchgrass Callicarpa americana American beautyberry Persea borbonia redbay Calystegia sepium...sweetbay (Magnolia virginiana), loblolly-bay (Gordonia lasianthus), redbay ( Persea borbonia), and swamp bay ( Persea palustris) make up a significant...com- munity model. The Society of American Foresters (Eyre 1980) recognizes a “Sweetbay- Swamp Tupelo (Nyssa sylvatica var. biflora)-Redbay” forest

  9. Seed Bank Viability in Disturbed Longleaf Pine Sites

    Science.gov (United States)

    Susan Cohen; Richard Braham; Felipe Sanchez

    2004-01-01

    Some of the most species-rich areas and highest concentrations of threatened and endangered species in the southeastern United States are found in wet savanna and flatwood longleaf pine (Pinus palustris Mill.) communities. Where intensive forestry practices have eliminated much of the natural understory of the longleaf ecosystem, the potential for...

  10. Impacts of pine species, stump removal, cultivation, and fertilization on soil properties half a century after planting

    Science.gov (United States)

    John R. Butnor; Kurt H. Johnsen; Felipe G Sanchez; C. Dana Nelson

    2012-01-01

    To better understand the long-term effects of species selection and forest management practices on soil quality and soil C retention, we analyzed soil samples from an experimental planting of loblolly (Pinus taeda L.), longleaf ((Pinus palustris Mill.), and slash ((Pinus elliottii Engelm.) pines under...

  11. Longleaf and loblolly pine seedlings respond differently to soil compaction, water content, and fertilization

    Science.gov (United States)

    D. Andrew Scott; James A. Burger

    2014-01-01

    Aims Longleaf pine (Pinus palustris Mill.) is being restored across the U.S. South for a multitude of ecological and economic reasons, but our understanding of longleaf pine’s response to soil physical conditions is poor. On the contrary, our understanding of loblolly pine (Pinus taeda L.) root and...

  12. Comparison of arthropod prey of red-cockaded woodpeckers on the boles of long-leaf and loblolly pines

    Science.gov (United States)

    Scott Horn; James L. Hanula

    2002-01-01

    Red-cockaded woodpeckers (Picoides borealis) forage on the boles of most southern pines. Woodpeckers may select trees based on arthropod availability, yet no published studies have evaluated differences in arthropod abundance on different species of pines. We used knockdown insecticides to sample arthropods on longleaf (Pinus palustris...

  13. Modeling survival, yield, volume partitioning and their response to thinning for longleaf pine plantations

    Science.gov (United States)

    Carlos A. Gonzalez-Benecke; Salvador A. Gezan; Daniel J. Leduc; Timothy A. Martin; Wendell P. Cropper Jr; Lisa J Samuelson

    2012-01-01

    Longleaf pine (Pinus palustris Mill.) is an important tree species of the southeast U.S. Currently there is no comprehensive stand-level growth and yield model for the species. The model system described here estimates site index (SI) if dominant height (Hdom) and stand age are known (inversely, the model can project H

  14. Within tree variation of lignin, extractives, and microfibril angle coupled with the theoretical and near infrared modeling of microfibril angle

    Science.gov (United States)

    Brian K. Via; chi L. So; Leslie H. Groom; Todd F. Shupe; michael Stine; Jan. Wikaira

    2007-01-01

    A theoretical model was built predicting the relationship between microfibril angle and lignin content at the Angstrom (A) level. Both theoretical and statistical examination of experimental data supports a square root transformation of lignin to predict microfibril angle. The experimental material used came from 10 longleaf pine (Pinus palustris)...

  15. Comparative serum biochemistry of captive mugger crocodiles ...

    African Journals Online (AJOL)

    Standard serum biochemical parameters were determined for 28 mugger crocodiles (Crocodylus palustris) using Supra-occipital plexus technique and/or Cardiocentesis technique at the Arignar Anna Zoological Park, Vandalur, Chennai, Guindy Snake Park Trust and Amaravathy Crocodile farm, Tamilnadu, India (13° 0´ N; ...

  16. Impacts of logging and prescribed burning in longleaf pine forests managed under uneven-aged silviculture

    Science.gov (United States)

    Ferhat Kara; Edward Francis Loewenstein

    2015-01-01

    The longleaf pine (Pinus palustris Mill.) ecosystem has historically been very important in the southeastern United States due to its extensive area and high biodiversity. Successful regeneration of longleaf pine forests requires an adequate number of well distributed seedlings. Thus, mortality of longleaf pine seedlings during logging operations...

  17. Assessing tolerance of longleaf pine understory herbaceous plants to herbicide applications in a container nursery

    Science.gov (United States)

    D. Paul Jackson; Scott A. Enebak; James West; Drew Hinnant

    2015-01-01

    Renewed efforts in longleaf pine (Pinus palustris Mill.) ecosystem restoration has increased interest in the commercial production of understory herbaceous species. Successful establishment of understory herbaceous species is enhanced when using quality nursery-grown plants that have a better chance of survival after outplanting. Nursery growing practices have not been...

  18. Effects of container cavity size and copper coating on field performance of container-grown longleaf pine seedlings

    Science.gov (United States)

    Shi-Jean Susana Sung; James D. Haywood; Mary A. Sword-Sayer; Kristina F. Connor; D. Andrew Scott

    2010-01-01

    Longleaf pine (Pinus palustris Mill.) seedlings were grown for 27 weeks in 3 container cavity sizes [small (S), medium (M), and large (L)], and half the containers were coated with copper (Cu). In November 2004, we planted 144 seedlings from each of 6 container treatments in each of 4 replications in central LA. All plots were burned in February 2006...

  19. Carbon sequestration and natural longleaf pine ecosystems

    Science.gov (United States)

    Ralph S. Meldahl; John S. Kush

    2006-01-01

    A fire-maintained longleaf pine (Pinus palustris Mill.) ecosystem may offer the best option for carbon (C) sequestration among the southern pines. Longleaf is the longest living of the southern pines, and products from longleaf pine will sequester C longer than most since they are likely to be solid wood products such as structural lumber and poles....

  20. Stand conditions and tree characteristics affect quality of longleaf pine for red-cockaded woodpecker cavity trees

    Science.gov (United States)

    W.G. Ross; D.L. Kulhavy; R.N. Conner

    1997-01-01

    We measured resin flow of longleaf (Pinus palustris Mill.) pines in red-cockaded woodpecker (Picoides borealis Vieillot) clusters in the Angelina National Forest in Texas, and the Apalachicola National Forest in Florida. Sample trees were categorized as active cavity trees, inactive cavity trees and control trees. Sample trees were further...

  1. Red-cockaded woodpecker nestling provisioning and reproduction in two different pine habitats

    Science.gov (United States)

    Richard R. Schaefer; Richard N. Conner; D. Craig Rudolph; Daniel Saenz

    2004-01-01

    We obtained nestling provisioning and rcpntductive data from 24 Red-cockaded Woodpecker (Picoides borealis) groups occupying two different pine habitats-longleaf pine (Pinus palustris) and a mixture of loblolly (P. taeda) and shortleaf pine (P. echinata)--in eastern Texas during 1990 and 1901....

  2. Ecological, political and social challenges of prescribed fire restoration in east Texas pineywoods ecosystems: a case study

    Science.gov (United States)

    Sandra Rideout; Brian P. Oswald; Michael H. Legg

    2003-01-01

    The effectiveness of prescribed fire restoration of forested sites in three state parks in east Texas, USA was studied. Two sites consisted of mixed shortleaf (Pinus echinata Mill.) or loblolly pine (Pinus taeda L.) and broadleaf overstoreys. The third site was a longleaf pine (Pinus palustris Mill.)/little...

  3. A single, specific thymine mutation in the ComK-Binding site severely decreases binding and transcription activation by the competence transcription factor ComK of Bacillus subtilis

    NARCIS (Netherlands)

    Susanna, Kim A.; Mironczuk, Aleksandra M.; Smits, Wiep Klaas; Hamoen, Leendert W.; Kuipers, Oscar P.

    The competence transcription factor ComK plays a central role in competence development in Bacillus subtilis by activating the transcription of the K regulon. ComK-activated genes are characterized by the presence of a specific sequence to which ComK binds, a K-box, in their upstream DNA region.

  4. Expression of Streptococcus pneumoniae Bacteriocins Is Induced by Antibiotics via Regulatory Interplay with the Competence System

    NARCIS (Netherlands)

    Kjos, Morten; Miller, Eric; Slager, Jelle; Lake, Frank B; Gericke, Oliver; Roberts, Ian S; Rozen, Daniel E; Veening, Jan-Willem

    2016-01-01

    Pneumococcal bacteriocins (pneumocins) are antibacterial toxins that mediate intra-species competition within the human host. However, the triggers of pneumocin expression are poorly understood. Using RNA-sequencing, we mapped the regulon of the pneumocin cluster (blp) of Streptococcus pneumoniae

  5. Monitoring the ethanol stress response of a sigM deletion strain of B. cereus ATCC 14579.

    NARCIS (Netherlands)

    Voort, van der M.

    2008-01-01

    Here, the role of σM and its regulon in stress response and survival of B. cereus ATCC 14579 was assessed by comparative transciptome and phenotypic analysis of this strain and its sigM deletion strain. Exposure of B. cereus ATCC 14579 to a wide range of stresses revealed expression of sigM,

  6. Regulated expression of the dinR and recA genes during competence development and SOS induction in Bacillus subtilis

    NARCIS (Netherlands)

    Haijema, BJ; vanSinderen, D; Winterling, K; Kooistra, J; Venema, G; Hamoen, LW

    1996-01-01

    It has been hypothesized that the dinR gene product of Bacillus subtilis acts as a repressor of the SOS regulon by binding to DNA sequences located upstream of SOS genes, including dinR and recA. Following activation as a result of DNA damage, RecA is believed to catalyse DinR-autocleavage, thus

  7. Bacillus subtilis NhaC, an Na+/H+ antiporter, influences expression of the phoPR operon and production of alkaline phosphatases

    NARCIS (Netherlands)

    Pragai, Z; Eschevins, C; Bron, S; Harwood, CR

    When Bacillus subtilis is subjected to phosphate starvation, genes of the Pho regulon are either induced or repressed. Among those induced are genes encoding alkaline phosphatases (APases). A set of isogenic mutants, with a beta -galactosidase gene transcriptionally fused to the inactivated target

  8. The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis

    DEFF Research Database (Denmark)

    Bisicchia, Paola; Noone, David; Lioliou, Efthimia

    2007-01-01

    Adaptation of bacteria to the prevailing environmental and nutritional conditions is often mediated by two-component signal transduction systems (TCS). The Bacillus subtilis YycFG TCS has attracted special attention as it is essential for viability and its regulon is poorly defined. Here we show...

  9. Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

    DEFF Research Database (Denmark)

    Hansen, Heidi Theil; Rasmussen, Simon Horskjær; Adolph, Sidsel Kramshøj

    2015-01-01

    BACKGROUND: Post-transcriptional RNA regulons ensure co-ordinated expression of monocistronic mRNAs encoding functionally related proteins. In this study, we employ a combination of RIP-seq and short- and long-wave individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP...

  10. The YvfTU Two-component System is involved in plcR expression in Bacillus cereus

    Directory of Open Access Journals (Sweden)

    Nguyen-the Christophe

    2008-10-01

    Full Text Available Abstract Background Most extracellular virulence factors produced by Bacillus cereus are regulated by the pleiotropic transcriptional activator PlcR. Among strains belonging to the B. cereus group, the plcR gene is always located in the vicinity of genes encoding the YvfTU two-component system. The putative role of YvfTU in the expression of the PlcR regulon was therefore investigated. Results Expression of the plcR gene was monitored using a transcriptional fusion with a lacZ reporter gene in a yvfTU mutant and in its B. cereus ATCC 14579 parental strain. Two hours after the onset of the stationary phase, a stage at which the PlcR regulon is highly expressed, the plcR expression in the yvfTU mutant was only 50% of that of its parental strain. In addition to the reduced plcR expression in the yvfTU mutant, a few members of the PlcR regulon showed a differential expression, as revealed by transcriptomic and proteomic analyses. The virulence of the yvfTU mutant in a Galleria mellonella insect model was slightly lower than that of the parental strain. Conclusion The YvfTU two-component system is not required for the expression of most of the virulence factors belonging to the PlcR regulon. However, YvfTU is involved in expression of plcR, a major regulator of virulence in B. cereus.

  11. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

    DEFF Research Database (Denmark)

    Seo, Sang Woo; Gao, Ye; Kim, Donghyuk

    2017-01-01

    ) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite...

  12. ORF Alignment: NC_001137 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ograde regulon which ... consists of genes whose expression is stimulated by... NC_001137 gi|6320764 >1wvfA 13 508 29 496 1e-67 ... ref|NP_010843.1| D-lactate dehydrogenase, part of the retr

  13. Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development

    KAUST Repository

    Park, Myoungryoul; Yun, Kilyoung; Mohanty, Bijayalaxmi; Herath, Venura; Xu, Fuyu; Wijaya, Edward; Bajic, Vladimir B.; Yun, Songjoong; De Los Reyes, Benildo G.

    2010-01-01

    acid (JA), salicylic acid (SA), ethylene and reactive oxygen species (ROS) responsive genes. OsMyb4 network is independent of drought response element binding protein/C-repeat binding factor (DREB/CBF) and its sub-regulons operate with possible co

  14. Tarini Shankar Ghosh

    Indian Academy of Sciences (India)

    Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework · VARUN MEHRA TARINI SHANKAR GHOSH SHARMILA S MANDE · More Details Abstract Fulltext PDF. Horizontal Gene Transfer (HGT) events, initially thought to be rare ...

  15. Dual function of the McaS small RNA in controlling biofilm formation

    DEFF Research Database (Denmark)

    Jørgensen, Mikkel Girke; Thomason, Maureen K.; Havelund, Johannes

    2013-01-01

    , and biofilm formation. Moreover, ectopic McaS expression leads to induction of two additional CsrA-repressed genes encoding diguanylate cyclases. Collectively, our study shows that McaS is a dual-function sRNA with roles in the two major post-transcriptional regulons controlled by the RNA-binding proteins Hfq...

  16. Ribosomal dimerization factor YfiA is the major protein synthesized after abrupt glucose depletion in Lactococcus lactis

    DEFF Research Database (Denmark)

    Breuner, Anne; Frees, Dorte; Varmanen, Pekka

    2016-01-01

    R, CcpA, ArgR and AhrC regulons, while protein synthesis stopped due to an extremely low GTP concentration emerging a few minutes after glucose depletion. The yfiA deletion mutant exhibited a longer lag phase upon replenishment of glucose and a faster death rate after prolonged starvation supporting...

  17. The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk

    NARCIS (Netherlands)

    de Jong, Anne; Hansen, Morten E.; Kuipers, Oscar P.; Kilstrup, Mogens; Kok, Jan

    2013-01-01

    In the present study we examine the changes in the expression of genes of Lactococcus lactis subspecies cremoris MG1363 during growth in milk. To reveal which specific classes of genes (pathways, operons, regulons, COGs) are important, we performed a transcriptome time series experiment. Global

  18. An overview on the small heat shock proteins | Mahmood | African ...

    African Journals Online (AJOL)

    In eukaryotes, different heat shock genes are expressed uncoordinatedly, whereas in prokaryote, heat shock genes form a regulon and appear simultaneously. sHSPs are associated with nuclei, cytoskeleton and membranes. They bind partially to denatured proteins, preventing irreversible protein aggregation during stress.

  19. Computational prediction of cAMP receptor protein (CRP binding sites in cyanobacterial genomes

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2009-01-01

    Full Text Available Abstract Background Cyclic AMP receptor protein (CRP, also known as catabolite gene activator protein (CAP, is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The

  20. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

    Directory of Open Access Journals (Sweden)

    2005-10-01

    Full Text Available Bacterial response to nitric oxide (NO is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metabolism, not only in most gamma- and beta-proteobacteria (including well-studied species such as Escherichia coli, but also in Gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding motif. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon also includes two nitrite-responsive loci, nipAB (hcp-hcr and nipC (dnrN, thus confirming the identity of the effector, i.e. nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include

  1. Dissimilatory Metabolism of Nitrogen Oxides in Bacteria:Comparative Reconstruction of Transcriptional Networks

    Energy Technology Data Exchange (ETDEWEB)

    Rodionov, Dmitry A.; Dubchak, Inna L.; Arkin, Adam P.; Alm, EricJ.; Gelfand, Mikhail S.

    2005-09-01

    Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR and NnrR, two-component systems NarXL and NarQP, NO-responsive activator NorR, and nitrite sensitive repressor NsrR. Using comparative genomics approaches we predict DNA-binding signals for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA signal. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria including Clostridia, Thermotogales and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides metabolism not only in most gamma- and beta-proteobacteria (including well-studied species like Escherichia coli), but also in Gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding signal. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon includes also two nitrite-responsive loci, nipAB (hcp-hcr) and nipC(dnrN), thus confirming the identity of the effector, i.e., nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include denitrification genes. As the

  2. Carotenoid stoichiometry in the LH2 crystal: no spectral evidence for the presence of the second molecule in the alpha/beta-apoprotein dimer.

    Science.gov (United States)

    Gall, Andrew; Gardiner, Alastair T; Cogdell, Richard J; Robert, Bruno

    2006-07-10

    In this work we have investigated the carotenoid-protein interactions in LH2 complexes of Rhodopseudomonas acidophila both in "free in solution" mixed-micelles and in three-dimensional crystals by Raman spectroscopy in resonance with the carotenoid (Car) molecules. We show that the Car molecules when bound to their binding pockets show no significant differences when the complexes are "free in solution" or packed in crystalline arrays. Furthermore, there is no significant wavelength dependence in the Raman spectrum of the Car molecules of LH2. This indicates that there is only one Car configuration in LH2 and thus only one molecule per alpha/beta-heterodimer.

  3. Using narrowband excitation to confirm that the S∗ state in carotenoids is not a vibrationally-excited ground state species

    Science.gov (United States)

    Jailaubekov, Askat E.; Song, Sang-Hun; Vengris, Mikas; Cogdell, Richard J.; Larsen, Delmar S.

    2010-02-01

    The hypothesis that S∗ is a vibrationally-excited ground-state population is tested and discarded for two carotenoid samples: β-carotene in solution and rhodopin glucoside embedded in the light harvesting 2 protein from Rhodopseudomonas acidophila. By demonstrating that the transient absorption signals measured in both systems that are induced by broadband (1000 cm -1) and narrowband (50 cm -1) excitation pulses are near identical and hence bandwidth independent, the impulsive stimulated Raman scattering mechanism proposed as the primary source for S∗ generation is discarded. To support this conclusion, previously published multi-pulse pump-dump-probe signals [17] are revisited to discard secondary mechanisms for S∗ formation.

  4. Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope.

    Science.gov (United States)

    Helmann, John D

    2016-04-01

    Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    DEFF Research Database (Denmark)

    Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon

    2013-01-01

    available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about......BACKGROUND: Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking....... RESULTS: In this study, we report genome-scale transcript response diversity of 10 A. thaliana ecotypes originating from different geographical locations to non-freezing cold stress (10°C). To analyze the transcriptional response diversity, we initially compared transcriptome changes in all 10 ecotypes...

  6. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  7. A Guide to the George Palmiter River Restoration Techniques.

    Science.gov (United States)

    1982-03-01

    reduction. The raft is driven by a 35 h.p. ’ outboard engine, weighs 4 tons, and has 1500 lb. of flotation material under it. Additionally, the raft has a...Sycamore (Platanus occidentalis) 4. Red Maple (Acer rubrum) 5. Silver Maple (Acer saccharinum) 6. Pin Oak (Quercus palustris) 7. Red Oak (Quercus...safety goggles 5 - ear protectors 5 - flotation jackets 1, - industrial first aid kit--one that floats and is waterproof 1 - snake bite kit several

  8. Weather effects on the success of longleaf pine cone crops

    Science.gov (United States)

    Daniel J. Leduc; Shi-Jean Susana Sung; Dale G. Brockway; Mary Anne Sword Sayer

    2016-01-01

    We used National Oceanic and Atmospheric Administration weather data and historical records of cone crops from across the South to relate weather conditions to the yield of cones in 10 longleaf pine (Pinus palustris Mill.) stands. Seed development in this species occurs over a three-year time period and weather conditions during any part of this...

  9. Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol.

    Science.gov (United States)

    Dunfield, Peter F; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Dedysh, Svetlana N

    2003-09-01

    Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2(T) and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris K(T). The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2(T) and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.5 and 7 (with an optimum at pH 5.5) and at temperatures between 4 and 30 degrees C. Compared with Methylocella palustris K(T), these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2(T) is most closely related to Methylocella palustris K(T) (97.3 % identity), Beijerinckia indica subsp. indica ATCC 9039(T) (97.1 %) and Methylocapsa acidiphila B2(T) (96.2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1omega7. Strain BL2(T) showed only 21-22 % DNA-DNA hybridization with Methylocella palustris K(T). The data therefore suggest that strains BL2(T) and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2(T) (=DSM 15510(T)=NCIMB 13906(T)) as the type strain.

  10. Fire Science Strategy: Resource Conservation and Climate Change

    Science.gov (United States)

    2014-09-01

    are southern yellow pine ( Pinus spp.; this currently includes over 0.6 million acres of managed longleaf pine [P. palustris], Robert Larimore, pers...Prosopis spp.), pinyon ( Pinus spp.)-juniper (Juniperus spp.), and chaparral-type ecosystems, and 0.7 million acres of annual and perennial grasslands...that meet current and future military land-use and stewardship objectives. Under current conditions, the presence of insects, disease, and drought

  11. Application of Hyperspectal Techniques to Monitoring & Management of Invasive Plant Species Infestation

    Science.gov (United States)

    2008-01-09

    Scirpus olnei, S. robustus, Hibiscus palustris, Eryngium virginianum. 1. Common reed (Phragmites australis) - large cane or bamboo-like grass...Index 2 760 695 R R plant stress status Zarco-Tejada (1998) PI3, Pigment Index 3 690 440 R R vegetation health , based on chlorophyll fluorescence...ratios Lichtenthaler et al. (1996) PI4, Pigment Index 4 740 440 R R vegetation health , based on chlorophyll fluorescence ratios

  12. Impacts of Flooding Regime Modification on Wildlife Habitats of Bottomland Hardwood Forests in the Lower Mississippi Valley.

    Science.gov (United States)

    1981-10-01

    Diospyros virginiana White ash Fraxinus americana Shingle oak Quercus imbricaria Pin oak 0 palustris (Continued) Able to survive deep, prolonged...Mississippi, and found little significant dif- ference in overall capture data. Natural stands almost exclusively sup- ported mice of the genus Peromyscus...frequent wetlands but are not restricted to them. k. Although the cottonmouth is common in wetlands, water snakes of the genus Nerodia are most important in

  13. Destroyed virgin longleaf pine stand lives-on digitally

    Science.gov (United States)

    John C. Gilbert; S. Kush; Rebecca J. Barlow

    2015-01-01

    The Flomaton Natural Area (FNA) once stood as one of the few remnant fragments of virgin, old-growth longleaf pine stands (Pinus palustris Mill.) in the Southeast. This 80-acre stand contained trees over 200 years old. A restoration effort began in 1994 to remove off-site trees and to reintroduce fire to the site after over 40 years of fire suppression. A geographic...

  14. Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia.

    Science.gov (United States)

    Florentín, Javier Elias; Cabaña Fader, Andrea Alejandra; Salas, Roberto Manuel; Janssens, Steven; Dessein, Steven; Cabral, Elsa Leonor

    2017-01-01

    Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia , with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata . In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia . The molecular position within Galianthe , based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe , have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii , from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris , Borreria pterophora has been placed under synonymy of Galianthe palustris , and Galianthe boliviana is reported for the first time from Peru

  15. Contribuciones al conocimiento de la flora de navarra

    Directory of Open Access Journals (Sweden)

    BALDA, Angel

    2002-01-01

    Full Text Available Nuevos datos acerca de 58 táxones de plantas de interés, bien por su rareza en el terrirorio navarro o por la ampliación de área que suponen. De ellos, 12 se citan por primera vez para Navarra : Epilobium angustifolium, Fraxinus pennylvanica, Galinsoga quadriradiata, Gamochaeta falcata, Isatis tinctoria subsp. tinctoria, Ludwigia palustris, Lycopodeilla inundata, Pseudorchis albida, Ramonda myconi, Rynchospora alba, Rynchospora fusca y Spiranthes aestivalis

  16. Modeling the effects of forest management on in situ and ex situ longleaf pine forest carbon stocks

    Science.gov (United States)

    C.A. Gonzalez-Benecke; L.J. Samuelson; T.A. Martin; W.P. Cropper Jr; Kurt Johnsen; T.A. Stokes; John Butnor; P.H. Anderson

    2015-01-01

    Assessment of forest carbon storage dynamics requires a variety of techniques including simulation models. We developed a hybrid model to assess the effects of silvicultural management systems on carbon (C) budgets in longleaf pine (Pinus palustris Mill.) plantations in the southeastern U.S. To simulate in situ C pools, the model integrates a growth and yield model...

  17. Light and electron microscopic study of Pelomyxa binucleata (Gruber, 1884) (Peloflagellatea, Pelobiontida)

    OpenAIRE

    Frolov, Alexander; Chystjakova, Ludmila; Goodkov, Andrew

    2005-01-01

    Morphology of a pelobiont Pelomyxa binucleata (Gruber, 1884) has been studied using light and electron microscopy. The organisation of P. binucleata has been shown to differ from that of P. palustris, P. prima and P. corona. The cell surface of P. binucleata is represented by the plasma membrane with a thin but distinct layer of non structured glycocalyx. The ectoplasm, containing a network of fine fibrils, is separated from the endoplasm with a boundary layer of cisterns and reticulum channe...

  18. Demonstration and Certification of Amphibian Ecological Risk Assessment Protocol

    Science.gov (United States)

    2009-04-01

    pools observed on site persist through the breeding season and long enough for the larvae to metamorphose, suitable amphibian breeding habitat exists in...frog (R. palustris): vocalizations • Fairy shrimp (Eubranchipus sp.): dip net • Isopoda: dip net • Unknown water beetle (Coleoptera): dip net...oxygen-lacking) conditions that favor the growth and regeneration of hydrophytic vegetation)) to amphibians. This test procedure uses larvae of the

  19. Surface-based GPR underestimates below-stump root biomass

    Science.gov (United States)

    John R. Butnor; Lisa J. Samuelson; Thomas A. Stokes; Kurt H. Johnsen; Peter H. Anderson; Carlos A. Gonzalez-Benecke

    2016-01-01

    Aims While lateral root mass is readily detectable with ground penetrating radar (GPR), the roots beneath a tree (below-stump) and overlapping lateral roots near large trees are problematic for surface-based antennas operated in reflection mode. We sought to determine if tree size (DBH) effects GPR root detection proximal to longleaf pine (Pinus palustris Mill) and if...

  20. Accumulation of 226Ra, 238U and 230Th by wetland plants in a vicinity of U-mill tailings at Zirovski vrh (Slovenia)

    International Nuclear Information System (INIS)

    Marko Cerne; Borut Smodis; Marko Strok; Radojko Jacimovic

    2010-01-01

    The impact of a U-mill tailing on radionuclide accumulation by plants was assayed. In particular, a preliminary screening of 226 Ra, 238 U and 230 Th in Marsh marigold (Caltha palustris L.), soft rush (Juncus effusus L.) and Tall Moor grass (Molinia arundinacea (L.) Moench) grown in a marsh habitat is presented. Activity concentrations for the studied radionuclides and their transfer factors for the particular plants are shown and discussed. (author)

  1. Early density management of longleaf pine reduces susceptibility to ice storm damage

    Science.gov (United States)

    Timothy B. Harrington; Thaddeus A. Harrington

    2016-01-01

    The Pax winter storm of February 2014 caused widespread damage to forest stands throughout the southeastern U.S. In a long-term study of savanna plant community restoration at the Savannah River Site, Aiken, SC, precommercial thinning (PCT) of 8- to 11-year-old plantations of longleaf pine (Pinus palustris) in 1994 reduced...

  2. Root system architecture: The invisible trait in container longleaf pine seedlings

    Science.gov (United States)

    Shi-Jean Susana Sung; R. Kasten Dumroese

    2013-01-01

    Longleaf pine (Pinus palustris Mill.) seedlings cultured in four cavity volumes (60 to 336 ml [3.7 to 20.5 cubic inches]), two root pruning treatments (with or without copper coating), and 3 nitrogen levels (low to high) were grown for 29 weeks before they were outplanted into an open area in central Louisiana. Twenty-two months after outplanting, 3 seedlings were...

  3. North American Lauraceae: Terpenoid Emissions, Relative Attraction and Boring Preferences of Redbay Ambrosia Beetle, Xyleborus glabratus (Coleoptera: Curculionidae: Scolytinae)

    OpenAIRE

    Kendra, Paul E.; Montgomery, Wayne S.; Niogret, Jerome; Pruett, Grechen E.; Mayfield, Albert E.; MacKenzie, Martin; Deyrup, Mark A.; Bauchan, Gary R.; Ploetz, Randy C.; Epsky, Nancy D.

    2014-01-01

    The invasive redbay ambrosia beetle, Xyleborus glabratus, is the primary vector of Raffaelea lauricola, a symbiotic fungus and the etiologic agent of laurel wilt. This lethal disease has caused severe mortality of redbay (Persea borbonia) and swampbay (P. palustris) trees in the southeastern USA, threatens avocado (P. americana) production in Florida, and has potential to impact additional New World species. To date, all North American hosts of X. glabratus and suscepts of laurel wilt are mem...

  4. Location and Description of Transects for Ecological Studies in Floodplain Forests of the Lower Suwannee River, Florida

    Science.gov (United States)

    2002-01-01

    Level Datum of 1929. Horizontal datum: In this report, horizontal coordinate information is referenced to the North American Datum of 1927 (NAD27...ileopa Ilex opaca Ait. var. opaca American holly junsil Juniperus silicicola (Small) Bailey 1 southern red cedar liqsty Liquidambar styraciflua L...swamp gum nyssyl Nyssa sylvatica Marsh.1 blackgum ostvir Ostrya virginiana (Mill.) K. Koch eastern hophornbeam perpal Persea palustris (Raf.) Sarg

  5. Deletion analysis of Streptococcus pneumoniae late competence genes distinguishes virulence determinants that are dependent or independent of competence induction

    OpenAIRE

    Zhu, Luchang; Lin, Jingjun; Kuang, Zhizhou; Vidal, Jorge E.; Lau, Gee W.

    2015-01-01

    The competence regulon of Streptococcus pneumoniae (pneumococcus) is crucial for genetic transformation. During competence development, the alternative sigma factor ComX is activated, which in turn, initiates transcription of 80 “late” competence genes. Interestingly, only 16 late genes are essential for genetic transformation. We hypothesized that these late genes that are dispensable for competence are beneficial to pneumococcal fitness during infection. These late genes were systematically...

  6. Induction of a stable sigma factor SigR by translation-inhibiting antibiotics confers resistance to antibiotics

    OpenAIRE

    Yoo, Ji-Sun; Oh, Gyeong-Seok; Ryoo, Sungweon; Roe, Jung-Hye

    2016-01-01

    Antibiotic-producing streptomycetes are rich sources of resistance mechanisms against endogenous and exogenous antibiotics. An ECF sigma factor ?R (SigR) is known to govern the thiol-oxidative stress response in Streptomyces coelicolor. Amplification of this response is achieved by producing an unstable isoform of ?R called ?R?. In this work, we present evidence that antibiotics induce the SigR regulon via a redox-independent pathway, leading to antibiotic resistance. The translation-inhibiti...

  7. Enhancement of L-cysteine production by disruption of yciW in Escherichia coli.

    Science.gov (United States)

    Kawano, Yusuke; Ohtsu, Iwao; Takumi, Kazuhiro; Tamakoshi, Ai; Nonaka, Gen; Funahashi, Eri; Ihara, Masaki; Takagi, Hiroshi

    2015-02-01

    Using in silico analysis, the yciW gene of Escherichia coli was identified as a novel L-cysteine regulon that may be regulated by the transcriptional activator CysB for sulfur metabolic genes. We found that overexpression of yciW conferred tolerance to L-cysteine, but disruption of yciW increased L-cysteine production in E. coli. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  8. Quorum-sensing regulators control virulence gene expression in Vibrio cholerae

    OpenAIRE

    Zhu, Jun; Miller, Melissa B.; Vance, Russell E.; Dziejman, Michelle; Bassler, Bonnie L.; Mekalanos, John J.

    2002-01-01

    The production of virulence factors including cholera toxin and the toxin-coregulated pilus in the human pathogen Vibrio cholerae is strongly influenced by environmental conditions. The well-characterized ToxR signal transduction cascade is responsible for sensing and integrating the environmental information and controlling the virulence regulon. We show here that, in addition to the known components of the ToxR signaling circuit, quorum-sensing regulators are involved in regulation of V. ch...

  9. Clostridium perfringens Antigens Recognized by Broiler Chickens Immune to Necrotic Enteritis▿

    OpenAIRE

    Kulkarni, R. R.; Parreira, V. R.; Sharif, S.; Prescott, J. F.

    2006-01-01

    Little is known about immunity to necrotic enteritis (NE) in chickens. A recent study of broiler chickens showed that protection against NE was associated with infection-immunization with virulent but not with avirulent Clostridium perfringens.In the current study, six secreted antigenic proteins unique to virulent C. perfringens that reacted to serum antibodies from immune birds were identified by mass spectrophotometry; three of these proteins are part of the VirR-VirS regulon.

  10. PecS Is a Global Regulator of the Symptomatic Phase in the Phytopathogenic Bacterium Erwinia chrysanthemi 3937▿ †

    OpenAIRE

    Hommais, Florence; Oger-Desfeux, Christine; Van Gijsegem, Frédérique; Castang, Sandra; Ligori, Sandrine; Expert, Dominique; Nasser, William; Reverchon, Sylvie

    2008-01-01

    Pathogenicity of the enterobacterium Erwinia chrysanthemi (Dickeya dadantii), the causative agent of soft-rot disease in many plants, is a complex process involving several factors whose production is subject to temporal regulation during infection. PecS is a transcriptional regulator that controls production of various virulence factors. Here, we used microarray analysis to define the PecS regulon and demonstrated that PecS notably regulates a wide range of genes that could be linked to path...

  11. Redox-Active Antibiotics Control Gene Expression and Community Behavior in Divergent Bacteria

    OpenAIRE

    Dietrich, Lars E. P.; Teal, Tracy K.; Price-Whelan, Alexa; Newman, Dianne K.

    2008-01-01

    It is thought that bacteria excrete redox-active pigments as antibiotics to inhibit competitors. In Pseudomonas aeruginosa, the endogenous antibiotic pyocyanin activates SoxR, a transcription factor conserved in Proteo- and Actinobacteria. In Escherichia coli, SoxR regulates the superoxide stress response. Bioinformatic analysis coupled with gene expression studies in P. aeruginosa and Streptomyces coelicolor revealed that the majority of SoxR regulons in bacteria lack the genes required for ...

  12. Screening of 18 species for digestate phytodepuration.

    Science.gov (United States)

    Pavan, Francesca; Breschigliaro, Simone; Borin, Maurizio

    2015-02-01

    This experiment assesses the aptitude of 18 species in treating the digestate liquid fraction (DLF) in a floating wetland treatment system. The pilot system was created in NE Italy in 2010 and consists of a surface-flow system with 180 floating elements (Tech-IA®) vegetated with ten halophytes and eight other wetland species. The species were transplanted in July 2011 in basins filled with different proportions of DLF/water (DLF/w); periodic increasing of the DLF/w ratio was imposed after transplanting, reaching the worst conditions for plants in summer 2012 (highest EC value 7.3 mS cm/L and NH4-N content 225 mg/L). It emerged that only Cynodon dactylon, Typha latifolia, Elytrigia atherica, Halimione portulacoides, Salicornia fruticosa, Artemisia caerulescens, Spartina maritima and Puccinellia palustris were able to survive under the system conditions. Halophytes showed higher dry matter production than other plants. The best root development (up to 40-cm depth) was recorded for Calamagrostis epigejos, Phragmites australis, T. latifolia and Juncus maritimus. The highest nitrogen (10-15 g/m(2)) and phosphorus (1-4 g/m(2)) uptakes were obtained with P. palustris, Iris pseudacorus and Aster tripolium. In conclusion, two halophytes, P. palustris and E. atherica, present the highest potential to be used to treat DLF in floating wetlands.

  13. Epigeic spiders of the pastures of northern Wielkopolska

    Directory of Open Access Journals (Sweden)

    Woźny, Marek

    2000-10-01

    Full Text Available The fauna of epigeic spiders (Araneae occurring on three different types of pastures in northern Wielkopolska was analysed. Studies were conducted from May 1992 to October 1993. The 18,995 specimens collected were classified as belonging to 137 species and 17 families. The family Linyphiidae proved the richest in species while Lycosidae was the most abundantly in terms of number of specimens. Zoocenological analysis of spider communities showed their differentiation testifying to differences in the sites studied. The dominants were: 1 Osowo Stare (Site 1: Pardosa palustris, 2 Sycyn Dolny (Site 2: Xerolycosa miniata, P. palustris, Xysticus kochi, 3 Braczewo (Site 3: Erigone dentipalpis, P. palustris. Seasonal changes of dominance of the species at each site were established. A comparison of changes of the species’ dominances in the years 1992 and 1993 disclosed similar values of the individual dominance coefficient at the sites in Osowo Stare and Braczewo. This result indicates the occurrence of the process of stabilization of these biocenoses and a tendency to equilibrium in the environment. The least stable proved to be the site at Sycyn Dolny. Analysis of the seasonal dynamics of epigeic spider communities was also made by determining the mean number of species at each site in the two years of study. The highest number of species was noted in spring. It is interesting to note the appearance of species which are rare or very rare in Poland such as: Lepthyphantes insignis, Ostearius melanopygius, Enoplognatha mordax and Enoplognatha oelandica.

  14. Immunogenicity of 60 novel latency-related antigens of Mycobacterium tuberculosis.

    Science.gov (United States)

    Serra-Vidal, Mᵃdel Mar; Latorre, Irene; Franken, Kees L C M; Díaz, Jéssica; de Souza-Galvão, Maria Luiza; Casas, Irma; Maldonado, José; Milà, Cèlia; Solsona, Jordi; Jimenez-Fuentes, M Ángeles; Altet, Neus; Lacoma, Alícia; Ruiz-Manzano, Juan; Ausina, Vicente; Prat, Cristina; Ottenhoff, Tom H M; Domínguez, José

    2014-01-01

    The aim of our work here was to evaluate the immunogenicity of 60 mycobacterial antigens, some of which have not been previously assessed, notably a novel series of in vivo-expressed Mycobacterium tuberculosis (IVE-TB) antigens. We enrolled 505 subjects and separated them in individuals with and without latent tuberculosis infection (LTBI) vs. patients with active tuberculosis (TB). Following an overnight and 7 days stimulation of whole blood with purified recombinant M. tuberculosis antigens, interferon-γ (IFN-γ) levels were determined by ELISA. Several antigens could statistically significantly differentiate the groups of individuals. We obtained promising antigens from all studied antigen groups [dormancy survival regulon (DosR regulon) encoded antigens; resuscitation-promoting factors (Rpf) antigens; IVE-TB antigens; reactivation associated antigens]. Rv1733, which is a probable conserved transmembrane protein encoded in DosR regulon, turned out to be very immunogenic and able to discriminate between the three defined TB status, thus considered a candidate biomarker. Rv2389 and Rv2435n, belonging to Rpf family and IVE-TB group of antigens, respectively, also stood out as LTBI biomarkers. Although more studies are needed to support our findings, the combined use of these antigens would be an interesting approach to TB immunodiagnosis candidates.

  15. Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR-type transcriptional regulator NunF.

    Science.gov (United States)

    Hennessy, Rosanna C; Phippen, Christopher B W; Nielsen, Kristian F; Olsson, Stefan; Stougaard, Peter

    2017-12-01

    Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun-nup regulon. Organization of the regulon is similar to clusters found in other CLP-producing pseudomonads except for the border regions where putative LuxR-type regulators are located. This study focuses on understanding the regulatory role of the LuxR-type-encoding gene nunF in CLP production of P. fluorescens In5. Functional analysis of nunF coupled with liquid chromatography-high-resolution mass spectrometry (LC-HRMS) showed that CLP biosynthesis is regulated by nunF. Quantitative real-time PCR analysis indicated that transcription of the NRPS genes catalyzing CLP production is strongly reduced when nunF is mutated indicating that nunF is part of the nun-nup regulon. Swarming and biofilm formation was reduced in a nunF knockout mutant suggesting that these CLPs may also play a role in these phenomena as observed in other pseudomonads. Fusion of the nunF promoter region to mCherry showed that nunF is strongly upregulated in response to carbon sources indicating the presence of a fungus suggesting that environmental elicitors may also influence nunF expression which upon activation regulates nunamycin and nunapeptin production required for the growth inhibition of phytopathogens. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  16. Exploring the bZIP transcription factor regulatory network in Neurospora crassa.

    Science.gov (United States)

    Tian, Chaoguang; Li, Jingyi; Glass, N Louise

    2011-03-01

    Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution.

  17. Comparative genomics of CytR, an unusual member of the LacI family of transcription factors.

    Directory of Open Access Journals (Sweden)

    Natalia V Sernova

    Full Text Available CytR is a transcription regulator from the LacI family, present in some gamma-proteobacteria including Escherichia coli and known not only for its cellular role, control of transport and utilization of nucleosides, but for a number of unusual structural properties. The present study addressed three related problems: structure of CytR-binding sites and motifs, their evolutionary conservation, and identification of new members of the CytR regulon. While the majority of CytR-binding sites are imperfect inverted repeats situated between binding sites for another transcription factor, CRP, other architectures were observed, in particular, direct repeats. While the similarity between sites for different genes in one genome is rather low, and hence the consensus motif is weak, there is high conservation of orthologous sites in different genomes (mainly in the Enterobacteriales arguing for the presence of specific CytR-DNA contacts. On larger evolutionary distances candidate CytR sites may migrate but the approximate distance between flanking CRP sites tends to be conserved, which demonstrates that the overall structure of the CRP-CytR-DNA complex is gene-specific. The analysis yielded candidate CytR-binding sites for orthologs of known regulon members in less studied genomes of the Enterobacteriales and Vibrionales and identified a new candidate member of the CytR regulon, encoding a transporter named NupT (YcdZ.

  18. Cth2 Protein Mediates Early Adaptation of Yeast Cells to Oxidative Stress Conditions.

    Directory of Open Access Journals (Sweden)

    Laia Castells-Roca

    Full Text Available Cth2 is an mRNA-binding protein that participates in remodeling yeast cell metabolism in iron starvation conditions by promoting decay of the targeted molecules, in order to avoid excess iron consumption. This study shows that in the absence of Cth2 immediate upregulation of expression of several of the iron regulon genes (involved in high affinity iron uptake and intracellular iron redistribution upon oxidative stress by hydroperoxide is more intense than in wild type conditions where Cth2 is present. The oxidative stress provokes a temporary increase in the levels of Cth2 (itself a member of the iron regulon. In such conditions Cth2 molecules accumulate at P bodies-like structures when the constitutive mRNA decay machinery is compromised. In addition, a null Δcth2 mutant shows defects, in comparison to CTH2 wild type cells, in exit from α factor-induced arrest at the G1 stage of the cell cycle when hydroperoxide treatment is applied. The cell cycle defects are rescued in conditions that compromise uptake of external iron into the cytosol. The observations support a role of Cth2 in modulating expression of diverse iron regulon genes, excluding those specifically involved in the reductive branch of the high-affinity transport. This would result in immediate adaptation of the yeast cells to an oxidative stress, by controlling uptake of oxidant-promoting iron cations.

  19. Semi-solid state fermentation of bagasse for hydrogen production; the cost-effective approach in Indian context

    International Nuclear Information System (INIS)

    Singh, S.P.; Asthana, R.K.; Singh, A.P.

    2006-01-01

    Semi-solid state fermentation route of hydrogen production from agro-waste sugar cane bagasse was tried using the photosynthetic bacterium Rhodopseudomonas (BHU strain-1) and the non-photosynthetic Enterobacter aerogenes MTCC2822. The process seems an alternative to submerged fermentation that requires high volumes of nutrient broth. Bagasse (10 g) pre-hydrolyzed with NaOH (2%, w/v) was coated with Ca-alginate (1.5%, v/v) containing Rhodopseudomonas and E. aerogenes in the co-immobilized state (300 μg bacterial biomass ml -1 ). The fermenting medium was just 150 ml to sustain the moistened bagasse in a 0.5 L fermenter kept in light. A parallel set of free bacterial cells served as control. Hydrogen production by the immobilized sets reached 30 L within 60 h with the average rate of 0.177 L H 2 h -1 . For free cells, the values for hydrogen output (20 L) or the rate 0.1125 L H 2 h -1 were approximately 1.5-fold low. It is proposed that semi-solid fermentation route of hydrogen production from bagasse will be a cost-effective technology in countries generating this agro-waste. (authors)

  20. Semi-solid state fermentation of bagasse for hydrogen production; the cost-effective approach in Indian context

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S.P.; Asthana, R.K.; Singh, A.P. [Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, (India)

    2006-07-01

    Semi-solid state fermentation route of hydrogen production from agro-waste sugar cane bagasse was tried using the photosynthetic bacterium Rhodopseudomonas (BHU strain-1) and the non-photosynthetic Enterobacter aerogenes MTCC2822. The process seems an alternative to submerged fermentation that requires high volumes of nutrient broth. Bagasse (10 g) pre-hydrolyzed with NaOH (2%, w/v) was coated with Ca-alginate (1.5%, v/v) containing Rhodopseudomonas and E. aerogenes in the co-immobilized state (300 {mu}g bacterial biomass ml{sup -1}). The fermenting medium was just 150 ml to sustain the moistened bagasse in a 0.5 L fermenter kept in light. A parallel set of free bacterial cells served as control. Hydrogen production by the immobilized sets reached 30 L within 60 h with the average rate of 0.177 L H{sub 2} h{sup -1}. For free cells, the values for hydrogen output (20 L) or the rate 0.1125 L H{sub 2} h{sup -1} were approximately 1.5-fold low. It is proposed that semi-solid fermentation route of hydrogen production from bagasse will be a cost-effective technology in countries generating this agro-waste. (authors)

  1. Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization

    Directory of Open Access Journals (Sweden)

    Aleksandr A. Arzamasov

    2018-04-01

    Full Text Available Members of the genus Bifidobacterium are common inhabitants of the human gastrointestinal tract. Previously it was shown that arabino-oligosaccharides (AOS might act as prebiotics and stimulate the bifidobacterial growth in the gut. However, despite the rapid accumulation of genomic data, the precise mechanisms by which these sugars are utilized and associated transcription control still remain unclear. In the current study, we used a comparative genomic approach to reconstruct arabinose and AOS utilization pathways in over 40 bacterial species belonging to the Bifidobacteriaceae family. The results indicate that the gene repertoire involved in the catabolism of these sugars is highly diverse, and even phylogenetically close species may differ in their utilization capabilities. Using bioinformatics analysis we identified potential DNA-binding motifs and reconstructed putative regulons for the arabinose and AOS utilization genes in the Bifidobacteriaceae genomes. Six LacI-family transcriptional factors (named AbfR, AauR, AauU1, AauU2, BauR1 and BauR2 and a TetR-family regulator (XsaR presumably act as local repressors for AOS utilization genes encoding various α- or β-L-arabinofuranosidases and predicted AOS transporters. The ROK-family regulator AraU and the LacI-family regulator AraQ control adjacent operons encoding putative arabinose transporters and catabolic enzymes, respectively. However, the AraQ regulator is universally present in all Bifidobacterium species including those lacking the arabinose catabolic genes araBDA, suggesting its control of other genes. Comparative genomic analyses of prospective AraQ-binding sites allowed the reconstruction of AraQ regulons and a proposed binary repression/activation mechanism. The conserved core of reconstructed AraQ regulons in bifidobacteria includes araBDA, as well as genes from the central glycolytic and fermentation pathways (pyk, eno, gap, tkt, tal, galM, ldh. The current study expands the

  2. An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice

    Directory of Open Access Journals (Sweden)

    Jia Yulin

    2007-06-01

    Full Text Available Abstract Background Plants respond to low temperature through an intricately coordinated transcriptional network. The CBF/DREB-regulated network of genes has been shown to play a prominent role in freeze-tolerance of Arabidopsis through the process of cold acclimation (CA. Recent evidence also showed that the CBF/DREB regulon is not unique to CA but evolutionarily conserved between chilling-insensitive (temperate and chilling-sensitive (warm-season plants. In this study, the wide contrast in chilling sensitivity between indica and japonica rice was used as model to identify other regulatory clusters by integrative analysis of promoter architecture (ab initio and gene expression profiles. Results Transcriptome analysis in chilling tolerant japonica rice identified a subset of 121 'early response' genes that were upregulated during the initial 24 hours at 10°C. Among this group were four transcription factors including ROS-bZIP1 and another larger sub-group with a common feature of having as1/ocs-like elements in their promoters. Cold-induction of ROS-bZIP1 preceded the induction of as1/ocs-like element-containing genes and they were also induced by exogenous H2O2 at ambient temperature. Coordinated expression patterns and similar promoter architectures among the 'early response' genes suggest that they belong to a potential regulon (ROS-bZIP – as1/ocs regulatory module that responds to elevated levels of ROS during chilling stress. Cultivar-specific expression signatures of the candidate genes indicate a positive correlation between the activity of the putative regulon and genotypic variation in chilling tolerance. Conclusion A hypothetical model of an ROS-mediated regulon (ROS-bZIP – as1/ocs triggered by chilling stress was assembled in rice. Based on the current results, it appears that this regulon is independent of ABA and CBF/DREB, and that its activation has an important contribution in configuring the rapid responses of rice seedlings

  3. Comparison Of Cd2+ Biosorption And Bioaccumulation By Bacteria – A Radiometric Study

    Directory of Open Access Journals (Sweden)

    Machalová Linda

    2015-12-01

    Full Text Available In this work, bioaccumulation and biosorption characteristics of Cd2+ ions by both dead and living non-growing biomass of gram-positive bacteria Kocuria palustris and Micrococcus luteus isolated from spent nuclear fuel pools were compared. The radioindicator method with radionuclide 109Cd was used to obtain precise and reliable data characterizing Cd compartmentalization in bacterial cells. The following cellular distribution of Cd in living non-growing biomass after 4 h incubation in solutions containing different concentration of Cd2+ ions (100, 250, 500, 750 and 1000 µmol/L spiked with 109CdCl2 under aeration at 30 °C were obtained: in M. luteus almost 85 % of Cd was localized on the cell surface and 15 % in cytoplasm. Similarly, in K. palustris 83 % of Cd was localized on the cell surface and 17 % in cytoplasm. The data were obtained by gamma spectrometry of extracts and solids after sequential extraction of biomass with 5 mM Ca(NO32 and 20 mM EDTA. Biosorption of Cd by non-living bacterial biomass is a rapid process strongly affected by solution pH and as was confirmed by FTIR analysis beside carboxylate ions also other functional groups such as amino and phosphate contribute to Cd binding by bacterial cell surfaces. Maximum sorption capacities Qmax (μmol/g calculated from the Langmuir isotherm were 444 ± 15 μmol/g for M. luteus and 381 ± 1 μmol/g for K. palustris.

  4. Eficiência de um composto de iodo orgânico contra fungos apodrecedores de madeiras e térmitas

    Directory of Open Access Journals (Sweden)

    Alexandre da Costa Florian

    2003-01-01

    Full Text Available The effectiveness of a low toxicity organic compound as fungicide and insecticide was studied by a accelerated laboratory bioassay according to the japanese standard. The compound was evaluated at concentrations of 0,5, 0,75 and 1,0% using ethanol as solvent. The subterraneous termites Coptotermes formosanus Shiraki and the decay fungi Coriolus versicolor (white rot and Tyromyces palustris (brown rot were used in the trials to evaluate the insecticide and fungicide action respectively. The wood specimens with dimensions of 40 x 20 x 5mm were treated by surface coating (brushing method at a rate of 110±10g/m2. The percentage weight loss of the wood blocks and the termite mortality (insecticide action and the weight loss of the wood blocks before and after the fungi attack (fungicide action were determined. The efficiency of the formulations were evaluated according to the Value of Efficiency. Results showed that the compound was of little or no efficient as insecticide against Coptotermes formosanus in the three concentrations analysed. The compound showed a good performance as fungicide against Coriolus versicolor and Tyromyces palustris with a Value of Efficiency higher than 90 in the three concentrations analysed. The best results were obtained with the product at 1,0% concentration in the treated and unleached wood specimens. Tyromyces palustris caused a larger damage in the wood blocks than Coriolus versicolor. The product showed a low capacity of fixation in the wood; therefore, it is not indicated for treating wood that will be in direct contact with the soil or under outdoor conditions.

  5. Vegetation in the Forsmark biotest basin, 1974-1986

    International Nuclear Information System (INIS)

    Renstroem, S.; Svensson, Roger; Wigren-Svensson, M.

    1990-05-01

    Since 1980, Forsmark Power Plants has discharged large amount of cooling water into the Biotest basin. In 1974, before the dam was constructed, and 1980 to 1986, the macrophytic algae and higher vegetation inside and around the basin has been investigated. The observed changes are mainly caused by the increased water temperature causing lack of ice cover during the winter, the embankment reducing the exposition, the heavy water stream through the basin and the reduced light transmission in the water. The macroscopic vegetation in the Biotest basin was originally distributed all over the lake, but is now mainly found in more shallow water. The deepest part, a passage from the input of the cooling water to the output, totally lack vegetation. The reason for this is a combination of the heavy stream, raised temperature and reduced light transmission. The total biomass of macroscopic vegetation in the basin has been reduced from c. 70 metric ton in 1980 to c. 27 ton in 1982 and 1986. Among the most important species, the production of Chara spp. and Potamogeton pectinatus have been strongly reduced, while Cladophora glomerata and Vaucheria sp. have increased. Especially for Vaucheria, the raised temperature has been of vital importance. Among other species, Tolypella nidifica first increased, but has now totally disappeared. Zannichellia palustris was the only phanerogam which increased all the time. It is Z. palustris var. major which stands for the increase, while Z. palustris var. repens has disappeared from the basin. The shore vegetation, mainly reeds, has expanded conspicuously. From 1974 to 1980, the shore vegetation was favoured by the reduced exposition caused by the embankment. Since then, the raised temperature and absence of ice cover have resulted in an accelerating expansion of mainly Phragmites communis. Scirpus tabernaemontani and S. maritimus were first increasing, but do not seem to be able to compete with Phragmites in the long run. (au)

  6. Stable Transmission of Borrelia burgdorferi Sensu Stricto on the Outer Banks of North Carolina.

    Science.gov (United States)

    Levine, J F; Apperson, C S; Levin, M; Kelly, T R; Kakumanu, M L; Ponnusamy, L; Sutton, H; Salger, S A; Caldwell, J M; Szempruch, A J

    2017-08-01

    The spirochaete (Borrelia burgdorferi) associated with Lyme disease was detected in questing ticks and rodents during a period of 18 years, 1991-2009, at five locations on the Outer Banks of North Carolina. The black-legged tick (Ixodes scapularis) was collected at varied intervals between 1991 and 2009 and examined for B. burgdorferi. The white-footed mouse (Peromyscus leucopus), house mouse (Mus musculus) marsh rice rat (Oryzomys palustris), marsh rabbit (Sylvilagus palustris), eastern cottontail (Sylvilagus floridanus) and six-lined racerunner (Cnemidophorus sexlineatus) were live-trapped, and their tissues cultured to isolate spirochaetes. Borrelia burgdorferi isolates were obtained from questing adult I. scapularis and engorged I. scapularis removed from P. leucopus, O. palustris and S. floridanus. The prevalence of B. burgdorferi infection was variable at different times and sites ranging from 7 to 14% of examined questing I. scapularis. Mitochondrial (16S) rRNA gene phylogenetic analysis from 65 adult I. scapularis identified 12 haplotypes in two major clades. Nine haplotypes were associated with northern/Midwestern I. scapularis populations and three with southern I. scapularis populations. Sixteen isolates obtained from tick hosts in 2005 were confirmed to be B. burgdorferi by amplifying and sequencing of 16S rRNA and 5S-23S intergenic spacer fragments. The sequences had 98-99% identity to B. burgdorferi sensu stricto strains B31, JD1 and M11p. Taken together, these studies indicate that B. burgdorferi sensu stricto is endemic in questing I. scapularis and mammalian tick hosts on the Outer Banks of North Carolina. © 2016 Blackwell Verlag GmbH.

  7. Population and coherence dynamics in light harvesting complex II (LH2).

    Science.gov (United States)

    Yeh, Shu-Hao; Zhu, Jing; Kais, Sabre

    2012-08-28

    The electronic excitation population and coherence dynamics in the chromophores of the photosynthetic light harvesting complex 2 (LH2) B850 ring from purple bacteria (Rhodopseudomonas acidophila) have been studied theoretically at both physiological and cryogenic temperatures. Similar to the well-studied Fenna-Matthews-Olson (FMO) protein, oscillations of the excitation population and coherence in the site basis are observed in LH2 by using a scaled hierarchical equation of motion approach. However, this oscillation time (300 fs) is much shorter compared to the FMO protein (650 fs) at cryogenic temperature. Both environment and high temperature are found to enhance the propagation speed of the exciton wave packet yet they shorten the coherence time and suppress the oscillation amplitude of coherence and the population. Our calculations show that a long-lived coherence between chromophore electronic excited states can exist in such a noisy biological environment.

  8. Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

    Science.gov (United States)

    Rancova, Olga; Sulskus, Juozas; Abramavicius, Darius

    2012-07-12

    Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

  9. Photosynthetic antennae systems: energy transport and optical absorption

    International Nuclear Information System (INIS)

    Reineker, P.; Supritz, Ch.; Warns, Ch.; Barvik, I.

    2004-01-01

    The energy transport and the optical line shape of molecular aggregates, modeling bacteria photosynthetic light-harvesting systems (chlorosomes in the case of Chlorobium tepidum or Chloroflexus aurantiacus and LH2 in the case of Rhodopseudomonas acidophila) is investigated theoretically. The molecular units are described by two-level systems with an average excitation energy ε and interacting with each other through nearest-neighbor interactions. For LH2 an elliptical deformation of the ring is also allowed. Furthermore, dynamic and in the case of LH2 also quasi-static fluctuations of the local excitation energies are taken into account, simulating fast molecular vibrations and slow motions of the protein backbone, respectively. The fluctuations are described by Gaussian Markov processes in the case of the chlorosomes and by colored dichotomic Markov processes, with exponentially decaying correlation functions, with small (λ s ) and large (λ) decay constants, in the case of LH2

  10. Theory of Excitonic Delocalization for Robust Vibronic Dynamics in LH2.

    Science.gov (United States)

    Caycedo-Soler, Felipe; Lim, James; Oviedo-Casado, Santiago; van Hulst, Niek F; Huelga, Susana F; Plenio, Martin B

    2018-06-11

    Nonlinear spectroscopy has revealed long-lasting oscillations in the optical response of a variety of photosynthetic complexes. Different theoretical models that involve the coherent coupling of electronic (excitonic) or electronic-vibrational (vibronic) degrees of freedom have been put forward to explain these observations. The ensuing debate concerning the relevance of either mechanism may have obscured their complementarity. To illustrate this balance, we quantify how the excitonic delocalization in the LH2 unit of Rhodopseudomonas acidophila purple bacterium leads to correlations of excitonic energy fluctuations, relevant coherent vibronic coupling, and importantly, a decrease in the excitonic dephasing rates. Combining these effects, we identify a feasible origin for the long-lasting oscillations observed in fluorescent traces from time-delayed two-pulse single-molecule experiments performed on this photosynthetic complex and use this approach to discuss the role of this complementarity in other photosynthetic systems.

  11. Isolation of non-sulphur photosynthetic bacterial strains efficient in hydrogen production at elevated temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S.P.; Srivastava, S.C. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

    1991-01-01

    Four strains of non-sulphur photosynthetic bacteria were isolated from root zone associations of aquatic plants like Azolla, Salvinia and Eichhornia, as well as the deep-water rice. Based on the gross cell morphology and pigmentation, the isolates resembled Rhodopseudomonas sp. and have been designated as BHU strains 1 to 4, respectively. When subjected to elevated temperature (from 33-45{sup o}C), substantial growth/hydrogen production could be observed only in strains 1 and 4. Strains 2 and 3 on the other hand, showed diminished growth and negligible hydrogen photoproduction. The BHU strains 1 and 4 have been selected as the most active (thermostable) hydrogen producing strains of local origin as far as the Indian tropical climate is concerned. (author).

  12. Temperature dependence of the anisotropy of fluorescence in ring molecular systems

    International Nuclear Information System (INIS)

    Herman, Pavel; Barvik, Ivan

    2007-01-01

    The time dependence of the anisotropy of fluorescence after an impulsive excitation in the molecular ring (resembling the B850 ring of the purple bacterium Rhodopseudomonas acidophila) is calculated. Fast fluctuations of the environment are simulated by dynamic disorder and slow fluctuations by uncorrelated static disorder. Without dynamic disorder modest degrees of static disorder are sufficient to cause the experimentally found initial drop of the anisotropy on a sub-100 fs time scale. In the present investigation we are comparing results for the time-dependent optical anisotropy of the molecular ring for four models of the uncorrelated static disorder: Gaussian disorder in the local energies (model A), Gaussian disorder in the transfer integrals (model B), Gaussian disorder in radial positions of molecules (model C) and Gaussian disorder in angular positions of molecules (model D). Both types of disorder-static and dynamic-are taken into account simultaneously

  13. The anisotropy of fluorescence in ring units II: transfer integral fluctuations

    International Nuclear Information System (INIS)

    Herman, Pavel; Barvik, Ivan; Reiter, Michal

    2005-01-01

    The time dependence of the anisotropy of fluorescence after an impulsive excitation in the molecular ring (resembling the B850 ring of the purple bacterium Rhodopseudomonas acidophila) is calculated. Fast fluctuations of the environment are simulated by dynamic disorder and slow fluctuations by static disorder. Without dynamic disorder, modest degrees of static disorder are sufficient to cause the experimentally found initial drop of the anisotropy on a sub-100 fs time scale. In the present investigation we are comparing results for the time-dependent optical anisotropy of the molecular ring for three models of the static disorder: Gaussian disorder in the local energies (Model A), Gaussian disorder in the transfer integrals (Model B) and Gaussian disorder in radial positions of molecules (Model C). Both types of disorder-static and dynamic-are taken into account simultaneously

  14. Some experiments on the primary electron acceptor in reaction centres from Rhodopseudomanas sphaeroides

    Energy Technology Data Exchange (ETDEWEB)

    Wraight, C A; Cogdell, R J; Clayton, R K

    1975-01-01

    The bacterial reaction center absorbance change at 450 nm (A-450), assigned to an anionic semiquinone, has been suggested as a candidate for the reduced form of the primary electron acceptor in bacterial photosynthesis. In reaction centers of Rhodopseudomonas sphaeroides we have found kinetic discrepancies between the decay of A-450 and the recovery of photochemical competence. In addition, no proton uptake is measurable on the first turnover, although subsequent ones elicit one proton bound per electron. These results are taken to indicate that the acceptor reaction after a long dark period may be different for the first turnover than for subsequent ones. It is suggested that A-450 is still a likely candidate for the acceptor function but that in reaction centers, additional quinone may act as an adventitious primary acceptor when the ''true'' primary acceptor is reduced. Alternatively, the primary acceptor may act in a ''ping-pong'' fashion with respect to subsequent photoelectrons.

  15. Transcriptional and physiological changes during Mycobacterium tuberculosis reactivation from non-replicating persistence

    Directory of Open Access Journals (Sweden)

    Peicheng Du

    2016-08-01

    Full Text Available Mycobacterium tuberculosis can persist for years in the hostile environment of the host in a non-replicating or slowly replicating state. While active disease predominantly results from reactivation of a latent infection, the molecular mechanisms of M. tuberculosis reactivation are still poorly understood. We characterized the physiology and global transcriptomic profiles of M. tuberculosis during reactivation from hypoxia-induced non-replicating persistence. We found that M. tuberculosis reactivation upon reaeration was associated with a lag phase, in which the recovery of cellular physiological and metabolic functions preceded the resumption of cell replication. Enrichment analysis of the transcriptomic dynamics revealed changes to many metabolic pathways and transcription regulons/subnetworks that orchestrated the metabolic and physiological transformation in preparation for cell division. In particular, we found that M. tuberculosis reaeration lag phase is associated with down-regulation of persistence-associated regulons/subnetworks, including DosR, MprA, SigH, SigE and ClgR, as well as metabolic pathways including those involved in the uptake of lipids and their catabolism. More importantly, we identified a number of up-regulated transcription regulons and metabolic pathways, including those involved in metal transport and remobilization, second messenger-mediated responses, DNA repair and recombination, and synthesis of major cell wall components. We also found that inactivation of the major alternative sigma factors SigE or SigH disrupted exit from persistence, underscoring the importance of the global transcriptional reprogramming during M. tuberculosis reactivation. Our observations suggest that M. tuberculosis lag phase is associated with a global gene expression reprogramming that defines the initiation of a reactivation process.

  16. PhoB activates Escherichia coli O157:H7 virulence factors in response to inorganic phosphate limitation.

    Directory of Open Access Journals (Sweden)

    Samuel Mohammed Chekabab

    Full Text Available Enterohemorrhagic Escherichia coli (EHEC, an emerging food- and water-borne hazard, is highly pathogenic to humans. In the environment, EHEC must survive phosphate (Pi limitation. The response to such Pi starvation is an induction of the Pho regulon including the Pst system that senses Pi variation. The interplay between the virulence of EHEC, Pho-Pst system and environmental Pi remains unknown. To understand the effects of Pi deprivation on the molecular mechanisms involved in EHEC survival and virulence under Pho regulon control, we undertook transcriptome profiling of the EDL933 wild-type strain grown under high Pi and low Pi conditions and its isogenic ΔphoB mutant grown in low Pi conditions. The differentially expressed genes included 1067 Pi-dependent genes and 603 PhoB-dependent genes. Of these 131 genes were both Pi and PhoB-dependent. Differentially expressed genes that were selected included those involved in Pi homeostasis, cellular metabolism, acid stress, oxidative stress and RpoS-dependent stress responses. Differentially expressed virulence systems included the locus of enterocyte effacement (LEE encoding the type-3 secretion system (T3SS and its effectors, as well as BP-933W prophage encoded Shiga toxin 2 genes. Moreover, PhoB directly regulated LEE and stx2 gene expression through binding to specific Pho boxes. However, in Pi-rich medium, constitutive activation of the Pho regulon decreased LEE gene expression and reduced adherence to HeLa cells. Together, these findings reveal that EHEC has evolved a sophisticated response to Pi limitation involving multiple biochemical strategies that contribute to its ability to respond to variations in environmental Pi and to coordinating the virulence response.

  17. The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

    Directory of Open Access Journals (Sweden)

    Ivan Erill

    2016-07-01

    Full Text Available The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

  18. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

    Science.gov (United States)

    Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi

    2016-01-01

    The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

  19. Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes.

    Science.gov (United States)

    Sanchez-Alberola, Neus; Campoy, Susana; Barbé, Jordi; Erill, Ivan

    2012-02-03

    The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the Vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. Here we combine in silico and in vitro techniques to perform a comparative genomics analysis of the SOS regulon in the Vibrionaceae, and we extend the methodology to map this transcriptional network in other bacterial species harboring multiple chromosomes. Our analysis provides the first comprehensive description of the SOS response in a family (Vibrionaceae) that includes major human pathogens. It also identifies several previously unreported members of the SOS transcriptional network, including two proteins of unknown function. The analysis of the SOS response in other bacterial species with multiple chromosomes uncovers additional regulon members and reveals that there is a conserved core of SOS genes, and that specialized additions to this basic network take place in different phylogenetic groups. Our results also indicate that across all groups the main elements of the SOS response are always found in the large chromosome, whereas specialized additions are found in the smaller chromosomes and plasmids. Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and dissemination of antibiotic resistance, and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an essential role in these organisms and sheds light into the

  20. MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently.

    Science.gov (United States)

    Yun, Choong-Soo; Takahashi, Yurika; Shintani, Masaki; Takeda, Toshiharu; Suzuki-Minakuchi, Chiho; Okada, Kazunori; Yamane, Hisakazu; Nojiri, Hideaki

    2016-02-01

    MvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an mvaT-homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, pmr and the chromosomally carried homologous genes, turA and turB, are transcribed at high levels, and Pmr interacts with TurA and TurB in vitro. In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the P. putida KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage. Copyright © 2016, American Society for Microbiology. All Rights Reserved.