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Sample records for acid bacterium lab

  1. Probiotic spectra of lactic acid bacteria (LAB).

    PubMed

    Naidu, A S; Bidlack, W R; Clemens, R A

    1999-01-01

    Lactic acid bacteria (LAB) and their probio-active cellular substances exert many beneficial effects in the gastrointestinal tract. LAB prevent adherence, establishment, and replication of several enteric mucosal pathogens through several antimicrobial mechanisms. LAB also release various enzymes into the intestinal lumen and exert potential synergistic effects on digestion and alleviate symptoms of intestinal malabsoption. Consumption of LAB fermented dairy products with LAB may elicit antitumor effects. These effects are attributed to the inhibition of mutagenic activity; decrease in several enzymes implicated in the generation of carcinogens, mutagens, or tumor-promoting agents; suppression of tumors; and the epidemiology correlating dietary regimes and cancer. Specific cellular components in LAB strains seem to induce strong adjuvant effects including modulation of cell-mediated immune responses, activation of reticuloendothelial system, augmentation of cytokine pathways and regulation of interleukins, and tumor necrosis factors. Oral administration of LAB is well tolerated and proven to be safe in 143 human clinical trials and no adverse effects were reported in any of the total 7,526 subjects studied during 1961-1998. In an effort to decrease the reliance on synthetic antimicrobials and control the emerging immunocompromised host population, the time has come to carefully explore the prophylactic and therapeutic applications of probiotic LAB.

  2. Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor.

    PubMed

    Hahnke, Sarah; Maus, Irena; Wibberg, Daniel; Tomazetto, Geizecler; Pühler, Alfred; Klocke, Michael; Schlüter, Andreas

    2015-01-10

    In this study, the whole genome sequence of the mesophilic, anaerobic Porphyromonadaceae bacterium strain ING2-E5B (LMG 28429, DSM 28696) is reported. The new isolate belongs to the phylum Bacteroidetes and was obtained from a biogas-producing lab-scale completely stirred tank reactor (CSTR) optimized for anaerobic digestion of maize silage in co-fermentation with pig and cattle manure. The genome of strain ING2-E5B contains numerous genes encoding proteins and enzymes involved in the degradation of complex carbohydrates and proteinaceous compounds. Moreover, it possesses genes catalyzing the production of volatile fatty acids. Hence, this bacterium was predicted to be involved in hydrolysis and acidogenesis during anaerobic digestion and biomethanation.

  3. High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

    PubMed

    Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

    2014-07-01

    Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.

  4. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Xie, Gary; Dalin, Eileen; Tice, Hope; Chertkov, Olga; Land, Miriam L

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  5. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Rhee, Mun Su; Moritz, Brelan E.; Xie, Gary; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Pitluck, Sam; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, Keelnathan T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  6. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    PubMed Central

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  7. Effect of alginic acid decomposing bacterium on the growth of Laminaria japonica (Phaeophyceae).

    PubMed

    Wang, You; Tang, Xue-Xi; Yang, Zhen; Yu, Zhi-Ming

    2006-01-01

    We collected the diseased blades of Laminaria japonica from Yantai Sea Farm from October to December 2002, and the alginic acid decomposing bacterium on the diseased blade was isolated and purified, and was identified as Alteromonas espejiana. This bacterium was applied as the causative pathogen to infect the blades of L. japonica under laboratory conditions. The aim of the present study was to identify the effects of the bacterium on the growth of L. japonica, and to find the possibly effective mechanism. Results showed that: (1) The blades of L. japonica exhibited symptoms of lesion, bleaching and deterioration when infected by the bacterium, and their growth and photosynthesis were dramatically suppressed. At the same time, the reactive oxygen species (ROS) generation enhanced obviously, and the relative membrane permeability increased significantly. The contents of malonaldehyde (MDA) and free fatty acid in the microsomol membrane greatly elevated, but the phospholipid content decreased. Result suggested an obvious peroxidation and deesterrification in the blades of L. japonica when infected by the bacterium. (2) The simultaneous assay on the antioxidant enzyme activities demonstrated that superoxide dismutase (SOD) and catalase (CAT) increased greatly when infected by the bacterium, but glutathione peroxidase (Gpx) and ascorbate peroxidase (APX) did not exhibit active responses to the bacterium throughout the experiment. (3) The histomorphological observations gave a distinctive evidence of the severity of the lesions as well as the relative abundance in the bacterial population on the blades after infection. The bacterium firstly invaded into the endodermis of L. japonica and gathered around there, and then resulted in the membrane damage, cells corruption and ultimately, the death of L. japonica.

  8. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannins are plant-produced organic compounds that are found in soils, are able to sequester iron, and have antimicrobial properties. We studied the effect of tannic acid on the molecular physiology of the soil-inhabiting biocontrol bacterium Pseudomonas protegens Pf-5 (formerly Pseudomonas fluoresce...

  9. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5.

    PubMed

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A; Loper, Joyce E; Paulsen, Ian T

    2013-05-01

    Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and secondary metabolite biosynthesis in the soil- and rhizosphere-inhabiting bacterium Pseudomonas protegens Pf-5.

  10. Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5

    PubMed Central

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A.

    2013-01-01

    Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and secondary metabolite biosynthesis in the soil- and rhizosphere-inhabiting bacterium Pseudomonas protegens Pf-5. PMID:23435890

  11. Catabolism of N-acetylneuraminic acid, a fitness function of the food-borne lactic acid bacterium Lactobacillus sakei, involves two newly characterized proteins.

    PubMed

    Anba-Mondoloni, Jamila; Chaillou, Stéphane; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2013-03-01

    In silico analysis of the genome sequence of the meat-borne lactic acid bacterium (LAB) Lactobacillus sakei 23K has revealed a repertoire of potential functions related to the adaptation of this bacterium to the meat environment. Among these functions, the ability to use N-acetyl-neuraminic acid (NANA) as a carbon source could provide a competitive advantage for growth on meat in which this amino sugar is present. In this work, we proposed to analyze the functionality of a gene cluster encompassing nanTEAR and nanK (nanTEAR-nanK). We established that this cluster encoded a pathway allowing transport and early steps of the catabolism of NANA in this genome. We also demonstrated that this cluster was absent from the genome of other L. sakei strains that were shown to be unable to grow on NANA. Moreover, L. sakei 23K nanA, nanT, nanK, and nanE genes were able to complement Escherichia coli mutants. Construction of different mutants in L. sakei 23K ΔnanR, ΔnanT, and ΔnanK and the double mutant L. sakei 23K Δ(nanA-nanE) made it possible to show that all were impaired for growth on NANA. In addition, two genes located downstream from nanK, lsa1644 and lsa1645, are involved in the catabolism of sialic acid in L. sakei 23K, as a L. sakei 23K Δlsa1645 mutant was no longer able to grow on NANA. All these results demonstrate that the gene cluster nanTEAR-nanK-lsa1644-lsa1645 is indeed involved in the use of NANA as an energy source by L. sakei.

  12. An Oleaginous Bacterium That Intrinsically Accumulates Long-Chain Free Fatty Acids in its Cytoplasm

    PubMed Central

    Katayama, Taiki; Kanno, Manabu; Morita, Naoki; Hori, Tomoyuki; Narihiro, Takashi; Mitani, Yasuo

    2014-01-01

    Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production. PMID:24296497

  13. A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163.

    PubMed

    Mohedano, María de la Luz; Russo, Pasquale; de Los Ríos, Vivian; Capozzi, Vittorio; Fernández de Palencia, Pilar; Spano, Giuseppe; López, Paloma

    2014-02-26

    Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

  14. Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium

    SciTech Connect

    Wada, M.; Fukunaga, N.; Sasaki, S. )

    1989-08-01

    Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

  15. Use of rRNA gene restriction patterns to evaluate lactic acid bacterium contamination of vacuum-packaged sliced cooked whole-meat product in a meat processing plant.

    PubMed Central

    Björkroth, K J; Korkeala, H J

    1997-01-01

    Molecular typing was applied to an in-plant lactic acid bacterium (LAB) contamination analysis of a vacuum-packaged sliced cooked whole-meat product. A total of 982 LAB isolates from the raw mass, product, and the environment at different production stages were screened by restriction endonuclease (EcoRI and HindIII) analysis. rRNA gene restriction patterns were further determined for different strains obtained from each source. These patterns were used for recognizing the spoilage-causing LAB strains from the product on the sell-by day and tracing the sources and sites of spoilage LAB contamination during the manufacture. LAB typing resulted in 71 different ribotypes, of which 27 were associated with contamination routes. Raw material was distinguished as the source of the major spoilage strains. Contamination of the product surfaces after cooking was shown to be airborne. The removal of the product from the cooking forms was localized as a major site of airborne LAB contamination. Food handlers and some surfaces in contact with the product during the manufacture were also contaminated with the spoilage strains. Some LAB strains were also able to resist cooking in the core of the product bar. These strains may have an effect on the product shelf life by contaminating the slicing machine. The air in the slicing department and adjacent cold room contained very few LAB. Surface-mediated contamination was detected during the slicing and packaging stages. Food handlers also carried strains later found in the packaged product. Molecular typing provided useful information revealing the LAB contamination sources and sites of this product. The production line will be reorganized in accordance with these results to reduce spoilage LAB contamination. PMID:9023922

  16. Use of rRNA gene restriction patterns to evaluate lactic acid bacterium contamination of vacuum-packaged sliced cooked whole-meat product in a meat processing plant.

    PubMed

    Björkroth, K J; Korkeala, H J

    1997-02-01

    Molecular typing was applied to an in-plant lactic acid bacterium (LAB) contamination analysis of a vacuum-packaged sliced cooked whole-meat product. A total of 982 LAB isolates from the raw mass, product, and the environment at different production stages were screened by restriction endonuclease (EcoRI and HindIII) analysis. rRNA gene restriction patterns were further determined for different strains obtained from each source. These patterns were used for recognizing the spoilage-causing LAB strains from the product on the sell-by day and tracing the sources and sites of spoilage LAB contamination during the manufacture. LAB typing resulted in 71 different ribotypes, of which 27 were associated with contamination routes. Raw material was distinguished as the source of the major spoilage strains. Contamination of the product surfaces after cooking was shown to be airborne. The removal of the product from the cooking forms was localized as a major site of airborne LAB contamination. Food handlers and some surfaces in contact with the product during the manufacture were also contaminated with the spoilage strains. Some LAB strains were also able to resist cooking in the core of the product bar. These strains may have an effect on the product shelf life by contaminating the slicing machine. The air in the slicing department and adjacent cold room contained very few LAB. Surface-mediated contamination was detected during the slicing and packaging stages. Food handlers also carried strains later found in the packaged product. Molecular typing provided useful information revealing the LAB contamination sources and sites of this product. The production line will be reorganized in accordance with these results to reduce spoilage LAB contamination.

  17. Identification of bisphosphatidic acid and its plasmalogen analogues in the phospholipids of a marine bacterium.

    PubMed

    McAllister, D J; De Siervo, A J

    1975-07-01

    A relatively nonpolar unidentified phospholipid (phospholipid X) , isolated from the gram-negative marine bacterium MB 45, was characterized both chromatographically and by chemical analysis. Phospholipid X was shown to be an acidic phospholipid without vicinal hydroxyl, free-amino, or amide groups. The presence of O-alkenyl groups was indicated by a positive reaction for plasmalogen. Mild alkaline methanolysis of phospholipid X yielded only glycerophosphoryglycerol as the derivative. Acetolysis produced only diacyl-glycerol monoacetate. Clevage of O-alkenyl chains by methanolic hydrochloride resulted in the formation of three lyso derivatives. It was estimated that 18.2% of phospholipid X was plasmalogen. From these data, together with chromatographic comparisons with standards, infrared spectra, a molecular weight estimation, and the determination of the glycerol-phosphate-acyl ester ratio, it was concluded that phospholipid X was bisphosphatidic acid mixed with its plasmalogen analogues. PMID:1141198

  18. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen

    NASA Astrophysics Data System (ADS)

    Sundset, Monica A.; Kohn, Alexandra; Mathiesen, Svein D.; Præsteng, Kirsti E.

    2008-08-01

    Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer ( Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 × 2.0-3.5 μm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

  19. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

    PubMed Central

    Bolotin, Alexander; Wincker, Patrick; Mauger, Stéphane; Jaillon, Olivier; Malarme, Karine; Weissenbach, Jean; Ehrlich, S. Dusko; Sorokin, Alexei

    2001-01-01

    Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group. [The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176.] PMID:11337471

  20. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

    PubMed Central

    Xiao, Jingfa; Hao, Lirui; Crowley, David E.; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

  1. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

    PubMed

    Wang, Xiaoyu; Chen, Meili; Xiao, Jingfa; Hao, Lirui; Crowley, David E; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

  2. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

    PubMed Central

    Meneghel, Julie; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

  3. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

    PubMed

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

  4. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

    PubMed

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-03-03

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

  5. Quantitative analysis of growth and volatile fatty acid production by the anaerobic ruminal bacterium Megasphaera elsdenii T81

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Megaspheara elsdenii T81 grew on either DL-lactate or D-glucose at similar rates (0.85 per h), but displayed major differences in the fermentation of these substrates. Lactate was fermented at up to 210-mM concentration to yield acetic, propionic, butyric, and valeric acids. The bacterium was able t...

  6. Complete genome sequence of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid.

    PubMed

    Kato, Hiroaki; Shiwa, Yuh; Oshima, Kenshiro; Machii, Miki; Araya-Kojima, Tomoko; Zendo, Takeshi; Shimizu-Kadota, Mariko; Hattori, Masahira; Sonomoto, Kenji; Yoshikawa, Hirofumi

    2012-04-01

    We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and produces predominantly L-lactic acid at high xylose concentrations. From ortholog analysis with other five L. lactis strains, IO-1 was identified as L. lactis subsp. lactis.

  7. Proteomic analysis of responses of a new probiotic bacterium Lactobacillus casei Zhang to low acid stress.

    PubMed

    Wu, Rina; Zhang, Wenyi; Sun, Tiansong; Wu, Junrui; Yue, Xiqing; Meng, He; Zhang, Heping

    2011-06-30

    Tolerance to acid is an important feature for probiotic bacteria during transition through the gastrointestinal tract. Proteomics analysis of a new probiotic bacterium, Lactobacillus casei Zhang, was performed upon 30-min exposure to low acid stress (pH 2.5 vs. pH 6.4) using two-dimensional electrophoresis. Out of 33 protein spots that showed changes of expression between the two pHs, 22 showed 1.5-fold higher expression at pH 2.5 than at pH 6.4, whereas five spots had expression decreased by 1.5-fold at pH 2.5. There were also six protein spots that were exclusively present on different pH maps. Further analysis showed that eight of the enhanced proteins, NagA, NagB, PGM, GlmM, LacC, TDP, GALM and PtsI, were involved in carbohydrate catabolism. Moreover, quantitative RT-PCR showed that the mRNA expression levels of dnaK, nagB, galm, estC, tuf and luxS were consistent with changes in protein expression. We postulate that there might be some relationship between differentially expressed proteins and acid tolerance in L. casei Zhang. PMID:21561676

  8. Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs.

    PubMed

    Lhomme, Emilie; Lattanzi, Anna; Dousset, Xavier; Minervini, Fabio; De Angelis, Maria; Lacaze, Guylaine; Onno, Bernard; Gobbetti, Marco

    2015-12-23

    Sixteen sourdoughs (FS1-FS16) used for the manufacture of traditional French breads were characterized by strongly acid conditions (median value of pH 3.5). The concentration of free amino acids (FAA) was highly variable, due to different proteolytic activity of flour used for back slopping and of dominant microorganisms. Median value of cell density of lactic acid bacteria (LAB) was 9.2 log CFU/g. The ratio between LAB and yeasts ranged from 10,000:1 to 10:1. According to the culture-dependent method and 16S metagenetics, Lactobacillus sanfranciscensis was the dominant species in French sourdoughs. FS5 and FS15, propagated according to protocols including one back slopping step at 14 °C, were the only exceptions. High positive correlations were found between L. sanfranciscensis, temperature of back slopping and FAA. The results of this study highlighted the broad adaptability of L. sanfranciscensis to very acid sourdough. Besides species frequently encountered (e.g., Lactobacillus parabrevis/Lactobacillus hammesii, Lactobacillus plantarum and Leuconostoc mesenteroides), first Lactobacillus xiangfangensis (FS5) and Lactobacillus diolivorans (FS15) were found in sourdough. As determined by RAPD-PCR analyses, the sourdough samples showed a different number of strains, ranging from 5 (FS9, FS11 and FS15) to 12 (FS1 and FS13), meaning a highly variable bacterial diversity. Cluster analysis showed that different sourdoughs, especially when propagated in the same bakery, may harbor similar strains. Except for L. plantarum (FS5) and Ln. mesenteroides (FS3), all the dominant species were detected by both 16S metagenetics and culture-dependent method. Yeast diversity was lower than LAB. Except for FS4 (solely dominated by Kazachstania servazzii), yeast microbiota of French sourdoughs was dominated by Saccharomyces cerevisiae. Strains isolated in this study could be a useful base for developing new basic researches on physiology, metabolism, and intraspecific diversity of L

  9. Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.

    PubMed

    Chang, Chi-huan; Chen, Yi-sheng; Lee, Tzu-tai; Chang, Yu-chung; Yu, Bi

    2015-01-01

    A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)).

  10. Application of Lactic Acid Bacteria (LAB) in freshness keeping of tilapia fillets as sashimi

    NASA Astrophysics Data System (ADS)

    Cao, Rong; Liu, Qi; Chen, Shengjun; Yang, Xianqing; Li, Laihao

    2015-08-01

    Aquatic products are extremely perishable food commodities. Developing methods to keep the freshness of fish represents a major task of the fishery processing industry. Application of Lactic Acid Bacteria (LAB) as food preservative is a novel approach. In the present study, the possibility of using lactic acid bacteria in freshness keeping of tilapia fillets as sashimi was examined. Fish fillets were dipped in Lactobacillus plantarum 1.19 (obtained from China General Microbiological Culture Collection Center) suspension as LAB-treated group. Changes in K-value, APC, sensory properties and microbial flora were analyzed. Results showed that LAB treatment slowed the increase of K-value and APC in the earlier storage, and caused a smooth decrease in sensory score. Gram-negative bacteria dominated during refrigerated storage, with Pseudomonas and Aeromonas being relatively abundant. Lactobacillus plantarum 1.19 had no obvious inhibitory effect against these Gram-negatives. However, Lactobacillus plantarum 1.19 changed the composition of Gram-positive bacteria. No Micrococcus were detected and the proportion of Staphylococcus decreased in the spoiled LAB-treated samples. The period that tilapia fillets could be used as sashimi material extended from 24 h to 48 h after LAB treatment. The potential of using LAB in sashimi processing was confirmed.

  11. Fermentation products of solvent tolerant marine bacterium Moraxella spp. MB1 and its biotechnological applications in salicylic acid bioconversion.

    PubMed

    Wahidullah, Solimabi; Naik, Deepak N; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3-8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9-12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment. PMID:24391802

  12. Fermentation products of solvent tolerant marine bacterium Moraxella spp. MB1 and its biotechnological applications in salicylic acid bioconversion.

    PubMed

    Wahidullah, Solimabi; Naik, Deepak N; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3-8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9-12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment.

  13. Fermentation Products of Solvent Tolerant Marine Bacterium Moraxella spp. MB1 and Its Biotechnological Applications in Salicylic Acid Bioconversion

    PubMed Central

    Wahidullah, Solimabi; Naik, Deepak N.; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3–8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9–12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment. PMID:24391802

  14. Methanol and ethanol oxidase respiratory chains of the methylotrophic acetic acid bacterium, Acetobacter methanolicus.

    PubMed

    Matsushita, K; Takahashi, K; Takahashi, M; Ameyama, M; Adachi, O

    1992-06-01

    Acetobacter methanolicus is a unique acetic acid bacterium which has a methanol oxidase respiratory chain, as seen in methylotrophs, in addition to its ethanol oxidase respiratory chain. In this study, the relationship between methanol and ethanol oxidase respiratory chains was investigated. The organism is able to grow by oxidizing several carbon sources, including methanol, glycerol, and glucose. Cells grown on methanol exhibited a high methanol-oxidizing activity and contained large amounts of methanol dehydrogenase and soluble cytochromes c. Cells grown on glycerol showed higher oxygen uptake rate and dehydrogenase activity with ethanol but little methanol-oxidizing activity. Furthermore, two different terminal oxidases, cytochrome c and ubiquinol oxidases, have been shown to be involved in the respiratory chain; cytochrome c oxidase predominates in cells grown on methanol while ubiquinol oxidase predominates in cells grown on glycerol. Both terminal oxidases could be solubilized from the membranes and separated from each other. The cytochrome c oxidase and the ubiquinol oxidase have been shown to be a cytochrome co and a cytochrome bo, respectively. Methanol-oxidizing activity was diminished by several treatments that disrupt the integrity of the cells. The activity of the intact cells was inhibited with NaCl and/or EDTA, which disturbed the interaction between methanol dehydrogenase and cytochrome c. Ethanol-oxidizing activity in the membranes was inhibited with 2-heptyl-4-hydroxyquinoline N-oxide, which inhibited ubiquinol oxidase but not cytochrome c oxidase. Alcohol dehydrogenase has been purified from the membranes of glycerol-grown cells and shown to reduce ubiquinone-10 as well as a short side-chain homologue in detergent solution.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Recycling of carbon dioxide and acetate as lactic acid by the hydrogen-producing bacterium Thermotoga neapolitana.

    PubMed

    d'Ippolito, Giuliana; Dipasquale, Laura; Fontana, Angelo

    2014-09-01

    The heterotrophic bacterium Thermotoga neapolitana produces hydrogen by fermentation of sugars. Under capnophilic (carbon dioxide requiring) conditions, the process is preferentially associated with the production of lactic acid, which, as shown herein, is synthesized by reductive carboxylation of acetyl coenzyme A. The enzymatic coupling is dependent on the carbon dioxide stimulated activity of heterotetrameric pyruvate:ferredoxin oxidoreductase. Under the same culture conditions, T. neapolitana also operates the unfavorable synthesis of lactic acid from an exogenous acetate supply. This process, which requires carbon dioxide (or carbonate) and an unknown electron donor, allows for the conversion of carbon dioxide into added-value chemicals without biomass deconstruction.

  16. Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments.

    PubMed

    Florentino, Anna P; Brienza, Claudio; Stams, Alfons J M; Sánchez-Andrea, Irene

    2016-03-01

    A novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5-2 × 0.5-0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20-52 °C with an optimum close to 50 °C, and a pH range of 3-7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T). PMID:26704766

  17. Identification and Characterization of a New 7-Aminocephalosporanic Acid Deacetylase from Thermophilic Bacterium Alicyclobacillus tengchongensis

    PubMed Central

    Ding, Jun-Mei; Yu, Ting-Ting; Han, Nan-Yu; Yu, Jia-Lin; Li, Jun-Jun; Yang, Yun-Juan; Tang, Xiang-Hua; Xu, Bo; Zhou, Jun-Pei

    2015-01-01

    ABSTRACT Deacetylation of 7-aminocephalosporanic acid (7-ACA) at position C-3 provides valuable starting material for producing semisynthetic β-lactam antibiotics. However, few enzymes have been characterized in this process before now. Comparative analysis of the genome of the thermophilic bacterium Alicyclobacillus tengchongensis revealed a hypothetical protein (EstD1) with typical esterase features. The EstD1 protein was functionally cloned, expressed, and purified from Escherichia coli BL21(DE3). It indeed displayed esterase activity, with optimal activity at around 65°C and pH 8.5, with a preference for esters with short-chain acyl esters (C2 to C4). Sequence alignment revealed that EstD1 is an SGNH hydrolase with the putative catalytic triad Ser15, Asp191, and His194, which belongs to carbohydrate esterase family 12. EstD1 can hydrolyze acetate at the C-3 position of 7-aminocephalosporanic acid (7-ACA) to form deacetyl-7-ACA, which is an important starting material for producing semisynthetic β-lactam antibiotics. EstD1 retained more than 50% of its initial activity when incubated at pH values ranging from 4 to 11 at 65°C for 1 h. To the best of our knowledge, this enzyme is a new SGNH hydrolase identified from thermophiles that is able to hydrolyze 7-ACA. IMPORTANCE Deacetyl cephalosporins are highly valuable building blocks for the industrial production of various kinds of semisynthetic β-lactam antibiotics. These compounds are derived mainly from 7-ACA, which is obtained by chemical or enzymatic processes from cephalosporin C. Enzymatic transformation of 7-ACA is the main method because of the adverse effects chemical deacylation brought to the environment. SGNH hydrolases are widely distributed in plants. However, the tools for identifying and characterizing SGNH hydrolases from bacteria, especially from thermophiles, are rather limited. Here, our work demonstrates that EstD1 belongs to the SGNH family and can hydrolyze acetate at the C-3 position of

  18. Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas

    PubMed Central

    Minervini, Fabio; Lattanzi, Anna; De Angelis, Maria; Gobbetti, Marco

    2012-01-01

    Seven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA band corresponding to Saccharomyces cerevisiae was no longer detectable in several sourdoughs. Twelve species of lactic acid bacteria were variously identified through a culture-dependent approach. All sourdoughs harbored a certain number of species and strains, which were dominant throughout time and, in several cases, varied depending on the environment of propagation. As shown by statistical permutation analysis, the lactic acid bacterium populations differed among sourdoughs propagated at artisan bakery and laboratory levels. Lactobacillus plantarum, Lactobacillus sakei, and Weissella cibaria dominated in only some sourdoughs back-slopped at artisan bakeries, and Leuconostoc citreum seemed to be more persistent under laboratory conditions. Strains of Lactobacillus sanfranciscensis were indifferently found in some sourdoughs. Together with the other stable species and strains, other lactic acid bacteria temporarily contaminated the sourdoughs and largely differed between artisan bakery and laboratory levels. The environment of propagation has an undoubted influence on the composition of sourdough yeast and lactic acid bacterium microbiotas. PMID:22635989

  19. Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions.

    PubMed

    Leong, Lex E X; Denman, Stuart E; Hugenholtz, Philip; McSweeney, Christopher S

    2016-02-01

    Synergistetes strain MFA1 is an asaccharolytic ruminal bacterium isolated based on its ability to degrade fluoroacetate, a plant toxin. The amino acid and peptide requirements of the bacterium were investigated under different culturing conditions. The growth of strain MFA1 and its fluoroacetate degradation rate were enhanced by peptide-rich protein hydrolysates (tryptone and yeast extract) compared to casamino acid, an amino acid-rich protein hydrolysate. Complete utilization and preference for arginine, asparagine, glutamate, glycine, and histidine as free amino acids from yeast extract were observed, while the utilization of serine, threonine, and lysine in free form and peptide-bound glutamate was stimulated during growth on fluoroacetate. A predominant peptide in yeast extract preferentially utilized by strain MFA1 was partially characterized by high-liquid performance chromatography-mass spectrometry as a hepta-glutamate oligopeptide. Similar utilization profiles of amino acids were observed between the co-culture of strain MFA1 with Methanobrevibacter smithii without fluoroacetate and pure strain MFA1 culture with fluoroacetate. This suggests that growth of strain MFA1 could be enhanced by a reduction of hydrogen partial pressure as a result of hydrogen removal by a methanogen or reduction of fluoroacetate.

  20. Spoilage potential of psychrotrophic lactic acid bacteria (LAB) species: Leuconostoc gelidum subsp. gasicomitatum and Lactococcus piscium, on sweet bell pepper (SBP) simulation medium under different gas compositions.

    PubMed

    Pothakos, Vasileios; Nyambi, Clarice; Zhang, Bao-Yu; Papastergiadis, Antonios; De Meulenaer, Bruno; Devlieghere, Frank

    2014-05-16

    Sweet bell peppers are a significant constituent of retail, chilled-stored and packaged food products like fresh salads, marinades and ready-to-eat (RTE) meals. Previously, through general screening of the Belgian market and by means of source tracking analysis in a plant manufacturing minimally processed, vegetable salads the susceptibility of fresh-cut sweet bell peppers to lactic acid bacterium (LAB) contamination was substantiated. The determination of the metabolic profiles of Leuconostoc gelidum subsp. gasicomitatum and Lactococcus piscium, two major psychrotrophic, spoilage-related LAB species, on sweet bell pepper (SBP) simulation medium under different packaging conditions - 1.) vacuum: 100% N2, 2.) air: 21% O2, 79% N2, 3.) MAP1: 30% CO2, 70% N2 and 4.) MAP2: 50% O2, 50% CO2 - facilitated a better understanding of the spoilage potential of these microbes as well as the presumptive contribution of O2 in the spectrum of produced volatile organic compounds (VOCs) associated with poor organoleptic properties of food products. Generally, none of the applied gas compositions inhibited the growth of the 4 L. gelidum subsp. gasicomitatum isolates, however the presence of O2 resulted in buttery off-odors by inducing primarily the accumulation of diacetyl and pungent "vinegar" smell due to acetic acid. The 3 tested isolates of L. piscium varied greatly among their growth dynamics and inhibition at MAP2. They exhibited either weak spoilage profile or very offensive metabolism confirming significant intraspecies diversity.

  1. Spoilage potential of psychrotrophic lactic acid bacteria (LAB) species: Leuconostoc gelidum subsp. gasicomitatum and Lactococcus piscium, on sweet bell pepper (SBP) simulation medium under different gas compositions.

    PubMed

    Pothakos, Vasileios; Nyambi, Clarice; Zhang, Bao-Yu; Papastergiadis, Antonios; De Meulenaer, Bruno; Devlieghere, Frank

    2014-05-16

    Sweet bell peppers are a significant constituent of retail, chilled-stored and packaged food products like fresh salads, marinades and ready-to-eat (RTE) meals. Previously, through general screening of the Belgian market and by means of source tracking analysis in a plant manufacturing minimally processed, vegetable salads the susceptibility of fresh-cut sweet bell peppers to lactic acid bacterium (LAB) contamination was substantiated. The determination of the metabolic profiles of Leuconostoc gelidum subsp. gasicomitatum and Lactococcus piscium, two major psychrotrophic, spoilage-related LAB species, on sweet bell pepper (SBP) simulation medium under different packaging conditions - 1.) vacuum: 100% N2, 2.) air: 21% O2, 79% N2, 3.) MAP1: 30% CO2, 70% N2 and 4.) MAP2: 50% O2, 50% CO2 - facilitated a better understanding of the spoilage potential of these microbes as well as the presumptive contribution of O2 in the spectrum of produced volatile organic compounds (VOCs) associated with poor organoleptic properties of food products. Generally, none of the applied gas compositions inhibited the growth of the 4 L. gelidum subsp. gasicomitatum isolates, however the presence of O2 resulted in buttery off-odors by inducing primarily the accumulation of diacetyl and pungent "vinegar" smell due to acetic acid. The 3 tested isolates of L. piscium varied greatly among their growth dynamics and inhibition at MAP2. They exhibited either weak spoilage profile or very offensive metabolism confirming significant intraspecies diversity. PMID:24690877

  2. Enterococcus faecium QU 50: a novel thermophilic lactic acid bacterium for high-yield l-lactic acid production from xylose.

    PubMed

    Abdel-Rahman, Mohamed Ali; Tashiro, Yukihiro; Zendo, Takeshi; Sakai, Kenji; Sonomoto, Kenji

    2015-01-01

    Production of optically pure lactic acid from lignocellulosic material for commercial purposes is hampered by several difficulties, including heterofermentation of pentose sugars and high energy consumption by mesophilic lactic acid bacteria. Here, we report a novel lactic acid bacterium, strain QU 50, that has the potential to produce optically pure l-lactic acid (≥99.2%) in a homofermentative manner from xylose under thermophilic conditions. Strain QU 50 was isolated from Egyptian fertile soil and identified as Enterococcus faecium QU 50 by analyzing its sugar fermentation pattern and 16S rRNA gene sequence. Enterococcus faecium QU 50 fermented xylose efficiently to produce lactic acid over wide pH (6.0-10.0) and temperature ranges (30-52°C), with a pH of 6.5 and temperature of 50°C being optimal. To our knowledge, this is the first report of homofermentative lactic acid production from xylose by a thermophilic lactic acid bacterium.

  3. Value-added lipid production from brown seaweed biomass by two-stage fermentation using acetic acid bacterium and thraustochytrid.

    PubMed

    Arafiles, Kim Hazel V; Iwasaka, Hiroaki; Eramoto, Yuri; Okamura, Yoshiko; Tajima, Takahisa; Matsumura, Yukihiko; Nakashimada, Yutaka; Aki, Tsunehiro

    2014-11-01

    Thraustochytrid production of polyunsaturated fatty acids and xanthophylls have been generally sourced from crop-derived substrates, making the exploration of alternative feedstocks attractive since they promise increased sustainability and lower production costs. In this study, a distinct two-stage fermentation system was conceptualized for the first time, using the brown seaweed sugar mannitol as substrate for the intermediary biocatalyst Gluconobacter oxydans, an acetic acid bacterium, along with the marine thraustochytrid Aurantiochytrium sp. to produce the value-added lipids and xanthophylls. Jar fermenter culture resulted in seaweed mannitol conversion to fructose with an efficiency of 83 % by G. oxydans and, after bacteriostasis with sea salts, production of astaxanthin and docosahexaenoic acid by Aurantiochytrium sp. KH105. Astaxanthin productivity was high at 3.60 mg/L/day. This new system, therefore, widens possibilities of obtaining more varieties of industrially valuable products including foods, cosmetics, pharmaceuticals, and biofuel precursor lipids from seaweed fermentation upon the use of suitable thraustochytrid strains.

  4. Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium

    PubMed Central

    Ridlon, Jason M.; Hylemon, Phillip B.

    2012-01-01

    The human bile acid pool composition is composed of both primary bile acids (cholic acid and chenodeoxycholic acid) and secondary bile acids (deoxycholic acid and lithocholic acid). Secondary bile acids are formed by the 7α-dehydroxylation of primary bile acids carried out by intestinal anaerobic bacteria. We have previously described a multistep biochemical pathway in Clostridium scindens that is responsible for bile acid 7α-dehydroxylation. We have identified a large (12 kb) bile acid inducible (bai) operon in this bacterium that encodes eight genes involved in bile acid 7α-dehydroxylation. However, the function of the baiF gene product in this operon has not been elucidated. In the current study, we cloned and expressed the baiF gene in E. coli and discovered it has bile acid CoA transferase activity. In addition, we discovered a second bai operon encoding three genes. The baiK gene in this operon was expressed in E. coli and found to encode a second bile acid CoA transferase. Both bile acid CoA transferases were determined to be members of the type III family by amino acid sequence comparisons. Both bile acid CoA transferases had broad substrate specificity, except the baiK gene product, which failed to use lithocholyl-CoA as a CoA donor. Primary bile acids are ligated to CoA via an ATP-dependent mechanism during the initial steps of 7α-dehydroxylation. The bile acid CoA transferases conserve the thioester bond energy, saving the cell ATP molecules during bile acid 7α-dehydroxylation. ATP-dependent CoA ligation is likely quickly supplanted by ATP-independent CoA transfer. PMID:22021638

  5. Identification of an Arachidonic Acid-Producing Bacterium and Description of Kineococcus arachidonicus sp. nov.

    SciTech Connect

    Fliermans, C.B.

    2001-05-15

    The identification of bacterial with the ability to produce polyunsaturated fatty acids as been limited almost exclusively to gram-negative, psychrophilic, marine microorganisms. Here we describe a new gram-type-positive bactgerium, strain SRS30216T, that produces the polyunsaturated fatty acid, arachidonic acid, and is neither psychrophilic nor a marine isolate.

  6. A novel algicide: evidence of the effect of a fatty acid compound from the marine bacterium, Vibrio sp. BS02 on the harmful dinoflagellate, Alexandrium tamarense.

    PubMed

    Li, Dong; Zhang, Huajun; Fu, Lijun; An, Xinli; Zhang, Bangzhou; Li, Yi; Chen, Zhangran; Zheng, Wei; Yi, Lin; Zheng, Tianling

    2014-01-01

    Alexandrium tamarense is a notorious bloom-forming dinoflagellate, which adversely impacts water quality and human health. In this study we present a new algicide against A. tamarense, which was isolated from the marine bacterium Vibrio sp. BS02. MALDI-TOF-MS, NMR and algicidal activity analysis reveal that this compound corresponds to palmitoleic acid, which shows algicidal activity against A. tamarense with an EC50 of 40 μg/mL. The effects of palmitoleic acid on the growth of other algal species were also studied. The results indicate that palmitoleic acid has potential for selective control of the Harmful algal blooms (HABs). Over extended periods of contact, transmission electron microscopy shows severe ultrastructural damage to the algae at 40 μg/mL concentrations of palmitoleic acid. All of these results indicate potential for controlling HABs by using the special algicidal bacterium and its active agent. PMID:24626054

  7. A novel algicide: evidence of the effect of a fatty acid compound from the marine bacterium, Vibrio sp. BS02 on the harmful dinoflagellate, Alexandrium tamarense.

    PubMed

    Li, Dong; Zhang, Huajun; Fu, Lijun; An, Xinli; Zhang, Bangzhou; Li, Yi; Chen, Zhangran; Zheng, Wei; Yi, Lin; Zheng, Tianling

    2014-01-01

    Alexandrium tamarense is a notorious bloom-forming dinoflagellate, which adversely impacts water quality and human health. In this study we present a new algicide against A. tamarense, which was isolated from the marine bacterium Vibrio sp. BS02. MALDI-TOF-MS, NMR and algicidal activity analysis reveal that this compound corresponds to palmitoleic acid, which shows algicidal activity against A. tamarense with an EC50 of 40 μg/mL. The effects of palmitoleic acid on the growth of other algal species were also studied. The results indicate that palmitoleic acid has potential for selective control of the Harmful algal blooms (HABs). Over extended periods of contact, transmission electron microscopy shows severe ultrastructural damage to the algae at 40 μg/mL concentrations of palmitoleic acid. All of these results indicate potential for controlling HABs by using the special algicidal bacterium and its active agent.

  8. A Novel Algicide: Evidence of the Effect of a Fatty Acid Compound from the Marine Bacterium, Vibrio sp. BS02 on the Harmful Dinoflagellate, Alexandrium tamarense

    PubMed Central

    Fu, Lijun; An, Xinli; Zhang, Bangzhou; Li, Yi; Chen, Zhangran; Zheng, Wei; Yi, Lin; Zheng, Tianling

    2014-01-01

    Alexandrium tamarense is a notorious bloom-forming dinoflagellate, which adversely impacts water quality and human health. In this study we present a new algicide against A. tamarense, which was isolated from the marine bacterium Vibrio sp. BS02. MALDI-TOF-MS, NMR and algicidal activity analysis reveal that this compound corresponds to palmitoleic acid, which shows algicidal activity against A. tamarense with an EC50 of 40 μg/mL. The effects of palmitoleic acid on the growth of other algal species were also studied. The results indicate that palmitoleic acid has potential for selective control of the Harmful algal blooms (HABs). Over extended periods of contact, transmission electron microscopy shows severe ultrastructural damage to the algae at 40 μg/mL concentrations of palmitoleic acid. All of these results indicate potential for controlling HABs by using the special algicidal bacterium and its active agent. PMID:24626054

  9. Tryptophan, thiamine and indole-3-acetic acid exchange between Chlorella sorokiniana and the plant growth-promoting bacterium Azospirillum brasilense.

    PubMed

    Palacios, Oskar A; Gomez-Anduro, Gracia; Bashan, Yoav; de-Bashan, Luz E

    2016-06-01

    During synthetic mutualistic interactions between the microalga Chlorella sorokiniana and the plant growth-promoting bacterium (PGPB) Azospirillum brasilense, mutual exchange of resources involved in producing and releasing the phytohormone indole-3-acetic acid (IAA) by the bacterium, using tryptophan and thiamine released by the microalga, were measured. Although increased activities of tryptophan synthase in C. sorokiniana and indole pyruvate decarboxylase (IPDC) in A. brasilense were observed, we could not detect tryptophan or IAA in the culture medium when both organisms were co-immobilized. This indicates that no extra tryptophan or IAA is produced, apart from the quantities required to sustain the interaction. Over-expression of the ipdC gene occurs at different incubation times: after 48 h, when A. brasilense was immobilized alone and grown in exudates of C. sorokiniana and at 96 h, when A. brasilense was co-immobilized with the microalga. When A. brasilense was cultured in exudates of C. sorokiniana, increased expression of the ipdC gene, corresponding increase in activity of IPDC encoded by the ipdC gene, and increase in IAA production were measured during the first 48 h of incubation. IAA production and release by A. brasilense was found only when tryptophan and thiamine were present in a synthetic growth medium (SGM). The absence of thiamine in SGM yielded no detectable IAA. In summary, this study demonstrates that C. sorokiniana can exude sufficient tryptophan and thiamine to allow IAA production by a PGPB during their interaction. Thiamine is essential for IAA production by A. brasilense and these three metabolites are part of a communication between the two microorganisms.

  10. Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium.

    PubMed

    Shiwa, Yuh; Yanase, Hiroaki; Hirose, Yuu; Satomi, Shohei; Araya-Kojima, Tomoko; Watanabe, Satoru; Zendo, Takeshi; Chibazakura, Taku; Shimizu-Kadota, Mariko; Yoshikawa, Hirofumi; Sonomoto, Kenji

    2014-08-01

    Enterococcus mundtii QU 25, a non-dairy bacterial strain of ovine faecal origin, can ferment both cellobiose and xylose to produce l-lactic acid. The use of this strain is highly desirable for economical l-lactate production from renewable biomass substrates. Genome sequence determination is necessary for the genetic improvement of this strain. We report the complete genome sequence of strain QU 25, primarily determined using Pacific Biosciences sequencing technology. The E. mundtii QU 25 genome comprises a 3 022 186-bp single circular chromosome (GC content, 38.6%) and five circular plasmids: pQY182, pQY082, pQY039, pQY024, and pQY003. In all, 2900 protein-coding sequences, 63 tRNA genes, and 6 rRNA operons were predicted in the QU 25 chromosome. Plasmid pQY024 harbours genes for mundticin production. We found that strain QU 25 produces a bacteriocin, suggesting that mundticin-encoded genes on plasmid pQY024 were functional. For lactic acid fermentation, two gene clusters were identified-one involved in the initial metabolism of xylose and uptake of pentose and the second containing genes for the pentose phosphate pathway and uptake of related sugars. This is the first complete genome sequence of an E. mundtii strain. The data provide insights into lactate production in this bacterium and its evolution among enterococci.

  11. Simultaneous saccharification and high titer lactic acid fermentation of corn stover using a newly isolated lactic acid bacterium Pediococcus acidilactici DQ2.

    PubMed

    Zhao, Kai; Qiao, Qingan; Chu, Deqiang; Gu, Hanqi; Dao, Thai Ha; Zhang, Jian; Bao, Jie

    2013-05-01

    A lactic acid bacterium with high tolerance of temperature and lignocellulose derived inhibitor was isolated and characterized as Pediococcus acidilactici DQ2. The strain used in the simultaneous saccharification and fermentation (SSF) for high titer lactic acid production at the high solids loading of corn stover. Corn stover was pretreated using the dry sulphuric acid pretreatment, followed by a biological detoxification to remove the inhibitors produced in the pretreatment. The bioreactor with a novel helical impeller was used to the SSF operation of the pretreated and biodetoxified corn stover. The results show that a typical SSF operation at 48 °C, pH 5.5, and near 30% (w/w) solids loading in both 5 and 50 L bioreactors was demonstrated. The lactic acid titer, yield, and productivity reached 101.9 g/L, 77.2%, and 1.06 g/L/h, respectively. The result provided a practical process option for cellulosic lactic acid production using virgin agriculture lignocellulose residues.

  12. Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications.

    PubMed

    Perez, Rodney H; Zendo, Takeshi; Sonomoto, Kenji

    2014-08-29

    Bacteriocins are heat-stable ribosomally synthesized antimicrobial peptides produced by various bacteria, including food-grade lactic acid bacteria (LAB). These antimicrobial peptides have huge potential as both food preservatives, and as next-generation antibiotics targeting the multiple-drug resistant pathogens. The increasing number of reports of new bacteriocins with unique properties indicates that there is still a lot to learn about this family of peptide antibiotics. In this review, we highlight our system of fast tracking the discovery of novel bacteriocins, belonging to different classes, and isolated from various sources. This system employs molecular mass analysis of supernatant from the candidate strain, coupled with a statistical analysis of their antimicrobial spectra that can even discriminate novel variants of known bacteriocins. This review also discusses current updates regarding the structural characterization, mode of antimicrobial action, and biosynthetic mechanisms of various novel bacteriocins. Future perspectives and potential applications of these novel bacteriocins are also discussed. PMID:25186038

  13. Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications

    PubMed Central

    2014-01-01

    Bacteriocins are heat-stable ribosomally synthesized antimicrobial peptides produced by various bacteria, including food-grade lactic acid bacteria (LAB). These antimicrobial peptides have huge potential as both food preservatives, and as next-generation antibiotics targeting the multiple-drug resistant pathogens. The increasing number of reports of new bacteriocins with unique properties indicates that there is still a lot to learn about this family of peptide antibiotics. In this review, we highlight our system of fast tracking the discovery of novel bacteriocins, belonging to different classes, and isolated from various sources. This system employs molecular mass analysis of supernatant from the candidate strain, coupled with a statistical analysis of their antimicrobial spectra that can even discriminate novel variants of known bacteriocins. This review also discusses current updates regarding the structural characterization, mode of antimicrobial action, and biosynthetic mechanisms of various novel bacteriocins. Future perspectives and potential applications of these novel bacteriocins are also discussed. PMID:25186038

  14. Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications.

    PubMed

    Perez, Rodney H; Zendo, Takeshi; Sonomoto, Kenji

    2014-08-29

    Bacteriocins are heat-stable ribosomally synthesized antimicrobial peptides produced by various bacteria, including food-grade lactic acid bacteria (LAB). These antimicrobial peptides have huge potential as both food preservatives, and as next-generation antibiotics targeting the multiple-drug resistant pathogens. The increasing number of reports of new bacteriocins with unique properties indicates that there is still a lot to learn about this family of peptide antibiotics. In this review, we highlight our system of fast tracking the discovery of novel bacteriocins, belonging to different classes, and isolated from various sources. This system employs molecular mass analysis of supernatant from the candidate strain, coupled with a statistical analysis of their antimicrobial spectra that can even discriminate novel variants of known bacteriocins. This review also discusses current updates regarding the structural characterization, mode of antimicrobial action, and biosynthetic mechanisms of various novel bacteriocins. Future perspectives and potential applications of these novel bacteriocins are also discussed.

  15. [Screening and identification of indoleacetic acid producing endophytic bacterium in Panax ginseng].

    PubMed

    Jiang, Yun; Tian, Lei; Chen, Chang-qing; Zhang, Guan-jun; Li, Tong; Chen, Jing-xiu; Wang, Xue

    2015-01-01

    Endophytic bacteria which was producing indoleacetic acid was screened from Panax ginseng by using the Salkowski method. The active strain was also tested for its ability of nitrogen fixation by using the Ashby agar plates, the PKV plates and quantitative analysis of Mo-Sb-Ascrobiology acid colorimetry was used to measure its ability of phosphate solubilization, for its ability of potassium solubilization the silicate medium and flame spectrophotometry was used, for its ability of producing siderophores the method detecting CAS was used, for its ability of producing ACC deaminase the Alpha ketone butyric acid method was applied. And the effect on promoting growth of seed by active strain was tested. The results showed that the indoleacetic acid producing strain of JJ5-2 was obtained from 118 endophytes, which the content of indoleacetic acid was 10.2 mg x L(-1). The JJ5-2 strain also had characteristics of phosphate and potassium solubilization, nitrogen fixation, producing siderophores traits, and the promoting germination of ginseng seeds. The JJ5-2 strain was identified as Bacillus thuringiensis by analyzing morphology, physiological and biochemical properties and 16S rRNA gene sequences. PMID:26080547

  16. Gluconacetobacter kakiaceti sp. nov., an acetic acid bacterium isolated from a traditional Japanese fruit vinegar.

    PubMed

    Iino, Takao; Suzuki, Rei; Tanaka, Naoto; Kosako, Yoshimasa; Ohkuma, Moriya; Komagata, Kazuo; Uchimura, Tai

    2012-07-01

    Two novel acetic acid bacteria, strains G5-1(T) and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1(T) and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01(T) (99.3% 16S rRNA gene sequence similarity). The isolates showed 96-100% DNA-DNA relatedness with each other, but <53% DNA-DNA relatedness with closely related members of the genus Gluconacetobacter. The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30% (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1(T) and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1(T) and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1(T) (=JCM 25156(T)=NRIC 0798(T)=LMG 26206(T)).

  17. Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum spp.

    NASA Astrophysics Data System (ADS)

    Rodriguez, Hilda; Gonzalez, Tania; Goire, Isabel; Bashan, Yoav

    2004-11-01

    In vitro gluconic acid formation and phosphate solubilization from sparingly soluble phosphorus sources by two strains of the plant growth-promoting bacteria A. brasilense (Cd and 8-I) and one strain of A. lipoferum JA4 were studied. Strains of A. brasilense were capable of producing gluconic acid when grown in sparingly soluble calcium phosphate medium when their usual fructose carbon source is amended with glucose. At the same time, there is a reduction in pH of the medium and release of soluble phosphate. To a greater extent, gluconic acid production and pH reduction were observed for A. lipoferum JA4. For the three strains, clearing halos were detected on solid medium plates with calcium phosphate. This is the first report of in vitro gluconic acid production and direct phosphate solubilization by A. brasilense and the first report of P solubilization by A. lipoferum. This adds to the very broad spectrum of plant growth-promoting abilities of this genus.

  18. Gluconacetobacter maltaceti sp. nov., a novel vinegar producing acetic acid bacterium.

    PubMed

    Slapšak, Nina; Cleenwerck, Ilse; De Vos, Paul; Trček, Janja

    2013-02-01

    Comparison of HaeIII- and HpaII-restriction profiles of PCR-amplified 16S-23S rDNA ITS regions of Gluconacetobacter sp. LMG 1529(T) and SKU 1109 with restriction profiles of reference strains of acetic acid bacteria described by Trček and Teuber [34] revealed the same but unique restriction profiles for LMG 1529(T) and SKU 1109. Further analyses of nearly complete 16S rRNA gene sequences, nearly complete 16S-23S rDNA ITS sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, allocated both strains to a single phylogenetic cluster well separated from the other species of the genus Gluconacetobacter. DNA-DNA hybridizations confirmed their novel species identity by 73% DNA-DNA relatedness between both strains, and values below the species level (<70%) between SKU 1109 and the type strains of the closest phylogenetic neighbors. The classification of strains LMG 1529(T) and SKU 1109 into a single novel species was confirmed also by AFLP and (GTG)(5)-PCR DNA fingerprinting data, as well as by phenotypic data. Strains LMG 1529(T) and SKU 1109 can be differentiated from their closely related Gluconacetobacter species, Gluconacetobacter entanii and Gluconacetobacter hansenii, by their ability to form 2-keto-d-gluconic acid from d-glucose, their ability to use d-mannitol, d-gluconate and glycerol as carbon source and form acid from d-fructose, and their ability to grow without acetic acid. The major fatty acid of LMG 1529(T) and SKU 1109 is C(18:1ω7c) (60.2-64.8%). The DNA G+C content of LMG 1529(T) and SKU 1109 is 62.5 and 63.3mol% respectively. The name Gluconacetobacter maltaceti sp. nov. is proposed. The type strain is LMG 1529(T) (=NBRC 14815(T)=NCIMB 8752(T)).

  19. Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment.

    PubMed

    Lee, Yong-Jin; Romanek, Christopher S; Wiegel, Juergen

    2007-02-01

    An obligately anaerobic, spore-forming, moderately acid-tolerant bacterium, strain JW/YJL-B3T, was isolated from a sediment sample from a constructed wetland system receiving acid sulfate water. Based on 16S rRNA gene sequence analysis, the isolate belonged to the Firmicutes branch with Clostridium drakei SL1T (96.2 % gene sequence similarity) as its closest relative. The G+C content of the genomic DNA was 30.8 mol% (HPLC). Cells were straight to curved rods, 0.5-1.0 microm in diameter and 3.0-9.0 microm in length. The temperature range for growth was 20-45 degrees C, with an optimum around 35 degrees C. Growth was not detected below 18 degrees C or above 47 degrees C. The pH range for growth was broad, pH(25 degrees C) 3.8-8.9, with an optimum at 7.0-7.5. However at pH 4.5, the strain grew at 52 % of the optimal growth rate. The salinity range was 0-1.5 % NaCl (w/v). Strain JW/YJL-B3T utilized beef extract, Casamino acids, peptone, tryptone, arabinose, cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, raffinose, ribose, sucrose, xylose, pyruvate, glutamate and inulin as a carbon and energy source. There were no indications of growth under aerobic or autotrophic conditions. The isolate produced acetate, butyrate and ethanol as fermentation end products from glucose. Based on these characteristics and other physiological properties, the isolate is placed into the novel taxon, Clostridium aciditolerans sp. nov., with strain JW/YJL-B3T (=DSM 17425T=ATCC BAA-1220T) as the type strain.

  20. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species.

  1. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species. PMID:25336723

  2. Diversity of Heteropolysaccharide-Producing Lactic Acid Bacterium Strains and Their Biopolymers

    PubMed Central

    Mozzi, Fernanda; Vaningelgem, Frederik; Hébert, Elvira María; Van der Meulen, Roel; Foulquié Moreno, María Remedios; Font de Valdez, Graciela; De Vuyst, Luc

    2006-01-01

    Thirty-one lactic acid bacterial strains from different species were evaluated for exopolysaccharide (EPS) production in milk. Thermophilic strains produced more EPS than mesophilic ones, but EPS yields were generally low. Ropiness or capsular polysaccharide formation was strain dependent. Six strains produced high-molecular-mass EPS. Polymers were classified into nine groups on the basis of their monomer composition. EPS from Enterococcus strains were isolated and characterized. PMID:16751563

  3. Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum

    SciTech Connect

    David E. Cummings; Scott Fendorf; Rajesh K. Sani; Brent M. Peyton; Timothy S. Magnuson

    2007-01-01

    The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and was inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.

  4. Lactococcus piscium: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food-a review.

    PubMed

    Saraoui, T; Leroi, F; Björkroth, J; Pilet, M F

    2016-10-01

    The genus Lactococcus comprises 12 species, some known for decades and others more recently described. Lactococcus piscium, isolated in 1990 from rainbow trout, is a psychrotrophic lactic acid bacterium, probably disregarded because most of the strains are unable to grow at 30°C. During the last 10 years, this species has been isolated from a large variety of food: meat, seafood and vegetables, mostly packed under vacuum (VP) or modified atmosphere (MAP) and stored at chilled temperature. Recently, culture-independent techniques used for characterization of microbial ecosystems have highlighted the importance of Lc. piscium in food. Its role in food spoilage varies according to the strain and the food matrix. However, most studies have indicated that Lc. piscium spoils meat, whereas it does not degrade the sensory properties of seafood. Lactococcus piscium strains have a large antimicrobial spectrum, including Gram-positive and negative bacteria. In various seafoods, some strains have a protective effect against spoilage and can extend the sensory shelf-life of the products. They can also inhibit the growth of Listeria monocytogenes, by a cell-to-cell contact-dependent. This article reviews the physiological and genomic characteristics of Lc. piscium and discusses its spoilage or protective activities in food.

  5. Lactococcus piscium: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food-a review.

    PubMed

    Saraoui, T; Leroi, F; Björkroth, J; Pilet, M F

    2016-10-01

    The genus Lactococcus comprises 12 species, some known for decades and others more recently described. Lactococcus piscium, isolated in 1990 from rainbow trout, is a psychrotrophic lactic acid bacterium, probably disregarded because most of the strains are unable to grow at 30°C. During the last 10 years, this species has been isolated from a large variety of food: meat, seafood and vegetables, mostly packed under vacuum (VP) or modified atmosphere (MAP) and stored at chilled temperature. Recently, culture-independent techniques used for characterization of microbial ecosystems have highlighted the importance of Lc. piscium in food. Its role in food spoilage varies according to the strain and the food matrix. However, most studies have indicated that Lc. piscium spoils meat, whereas it does not degrade the sensory properties of seafood. Lactococcus piscium strains have a large antimicrobial spectrum, including Gram-positive and negative bacteria. In various seafoods, some strains have a protective effect against spoilage and can extend the sensory shelf-life of the products. They can also inhibit the growth of Listeria monocytogenes, by a cell-to-cell contact-dependent. This article reviews the physiological and genomic characteristics of Lc. piscium and discusses its spoilage or protective activities in food. PMID:27172050

  6. Lactococcus fujiensis sp. nov., a lactic acid bacterium isolated from vegetable matter.

    PubMed

    Cai, Yimin; Yang, Jinsong; Pang, Huili; Kitahara, Maki

    2011-07-01

    Three strains of lactic acid bacteria, designated NJ 317(T), NJ 414 and NJ 415, were isolated from the outer leaves of Chinese cabbages (Brassica rapa L. var. glabra Regel) and characterized taxonomically. The strains were gram-reaction-positive, catalase-negative, facultatively anaerobic cocci that did not produce gas from glucose and formed L-lactic acid. The major fatty acids were C(18 : 1)ω9c, C(16 : 0), C(14 : 0) and summed feature 10. Morphological, physiological and phylogenetic data indicated that the strains belonged to the genus Lactococcus. These strains shared similar phenotypic characteristics and exhibited DNA relatedness values >96.6 % to each other, indicating that they represent a single species. The DNA G+C contents of the three strains were 42.1-42.5 mol%. 16S rRNA gene sequences of the novel strains were determined and aligned with those of other species of the genus Lactococcus. On the basis of phylogenetic analysis the three strains grouped with other members of the genus Lactococcus. Lactococcus lactis and Lactococcus garvieae were the most closely related species, sharing a sequence similarity value of 94.4 % with the three strains. Ribotyping patterns, however, revealed that these strains were well-separated from reference strains of species of the genus Lactococcus and DNA-DNA hybridization studies indicated that the novel strains had low levels (<20.2 %) of DNA relatedness with reference strains of L. lactis, L. garvieae and other type strains of previously described species, showing that they represent a different species. Based on this evidence, strains NJ 317(T), NJ 414 and NJ 415 represent a novel species of the genus Lactococcus, for which the name Lactococcus fujiensis sp. nov. is proposed. The type strain is NJ 317(T) ( = JCM16395(T)  = CGMCC 1.10453(T)).

  7. Asaia siamensis sp. nov., an acetic acid bacterium in the alpha-proteobacteria.

    PubMed

    Katsura, K; Kawasaki, H; Potacharoen, W; Saono, S; Seki, T; Yamada, Y; Uchimura, T; Komagata, K

    2001-03-01

    Five bacterial strains were isolated from tropical flowers collected in Thailand and Indonesia by the enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located within the cluster of the genus Asaia. The isolates constituted a group separate from Asaia bogorensis on the basis of DNA relatedness values. Their DNA G+C contents were 58.6-59.7 mol%, with a range of 1.1 mol%, which were slightly lower than that of A. bogorensis (59.3-61.0 mol%), the type species of the genus Asaia. The isolates had morphological, physiological and biochemical characteristics similar to A. bogorensis strains, but the isolates did not produce acid from dulcitol. On the basis of the results obtained, the name Asaia siamensis sp. nov. is proposed for these isolates. Strain S60-1T, isolated from a flower of crown flower (dok rak, Calotropis gigantea) collected in Bangkok, Thailand, was designated the type strain ( = NRIC 0323T = JCM 10715T = IFO 16457T).

  8. Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicus

    PubMed Central

    Marcellin, Esteban; Gruber, Christian W; Archer, Colin; Craik, David J; Nielsen, Lars K

    2009-01-01

    Background Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is a commensal of horses and an opportunistic pathogen in many animals and humans. Some strains produce copious amounts of hyaluronic acid, making S. zooepidemicus an important industrial microorganism for the production of this valuable biopolymer used in the pharmaceutical and cosmetic industry. Encapsulation by hyaluronic acid is considered an important virulence factor in other streptococci, though the importance in S. zooepidemicus remains poorly understood. Proteomics may provide a better understanding of virulence factors in S. zooepidemicus, facilitate the design of better diagnostics and treatments, and guide engineering of superior production strains. Results Using hyaluronidase to remove the capsule and by optimising cellular lysis, a reference map for S. zooepidemicus was completed. This protocol significantly increased protein recovery, allowing for visualisation of 682 spots and the identification of 86 proteins using mass spectrometry (LC-ESI-MS/MS and MALDI-TOF/TOF); of which 16 were membrane proteins. Conclusion The data presented constitute the first reference map for S. zooepidemicus and provide new information on the identity and characteristics of the more abundantly expressed proteins. PMID:19327162

  9. Biochemical and phylogenetic analyses of a cold-active {beta}-galactosidase from the lactic acid bacterium Carnobacterium piscicola BA

    SciTech Connect

    Coombs, J.M.; Brenchley, J.E.

    1999-12-01

    The authors are investigating glycosyl hydrolases from new psychrophilic isolates to examine the adaptations of enzymes to low temperatures. A {beta}-galactosidase from isolate BA, which they have classified as a strain of the lactic acid bacterium Carnobacterium piscicola, was capable of hydrolyzing the chromogen 5-bromo-4-chloro-3-indolyl {beta}-D-galactopyranoside (X-Gal) at 4 C and possessed higher activity in crude cell lysates at 25 than at 37 C. Sequence analysis of a cloned DNA fragment encoding this activity revealed a gene cluster containing three glycosyl hydrolases with homology to an {alpha}-galactosidase and two {beta}-galactosidases. The larger of the two {beta}-galactosidase genes, bgaB, encoded the 76.9-kDa cold-active enzyme. This gene was homologous to family 42 glycosyl hydrolases, a group which contains several thermophilic enzymes but none from lactic acid bacteria. The bgaB gene from isolate BA was subcloned in Escherichia coli, and its enzyme, BgaB, was purified. The purified enzyme was highly unstable and required 10% glycerol to maintain activity. Its optimal temperature for activity was 30 C, and it was inactivated at 40 C in 10 min. The K{sub m} of freshly purified enzyme at 30 C was 1.7 mM, and the V{sub max} was 450 {micro}mol {sm{underscore}bullet} min{sup {minus}1}{sm{underscore}bullet}mg{sup {minus}1} with o-nitrophenyl {beta}-D-galactopyranoside. This cold-active enzyme is interesting because it is homologous to a thermophilic enzyme from Bacillus stearothermophilus, and comparisons could provide information about structural features important for activity at low temperatures.

  10. Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond.

    PubMed

    Sánchez-Andrea, Irene; Sanz, Jose Luis; Stams, Alfons J M

    2014-12-01

    A novel anaerobic propionigenic bacterium, strain ADRI(T), was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6×1-1.7 µm), non-motile and non-spore-forming rods. Cells possessed a Gram-negative cell-wall structure and were vancomycin-resistant. Strain ADRI(T) utilized yeast extract and various sugars as substrates and formed propionate, lactate and acetate as major fermentation products. The optimum growth temperature was 30 °C and the optimum pH for growth was pH 6.5, but strain ADRI(T) was able to grow at a pH as low as 3.0. Oxidase, indole formation, and urease and catalase activities were negative. Aesculin and gelatin were hydrolysed. The predominant cellular fatty acids of strain ADRI(T) were anteiso-C15 : 0 (30.3 %), iso-C15 : 0 (29.2 %) and iso-C17 : 0 3-OH (14.9 %). Major menaquinones were MK-8 (52 %) and MK-9 (48 %). The genomic DNA G+C content was 39.9 mol%. Phylogenetically, strain ADRI(T) was affiliated to the family Porphyromonadaceae of the phylum Bacteroidetes. The most closely related cultured species were Paludibacter propionicigenes with 16S rRNA gene sequence similarity of 87.5 % and several species of the genus Dysgonomonas (similarities of 83.5-85.4 % to the type strains). Based on the distinctive ecological, phenotypic and phylogenetic characteristics of strain ADRI(T), a novel genus and species, Microbacter margulisiae gen. nov., sp. nov., is proposed. The type strain is ADRI(T) ( = JCM 19374(T) = DSM 27471(T)).

  11. Genome sequence of a food spoilage lactic acid bacterium, Leuconostoc gasicomitatum LMG 18811T, in association with specific spoilage reactions.

    PubMed

    Johansson, Per; Paulin, Lars; Säde, Elina; Salovuori, Noora; Alatalo, Edward R; Björkroth, K Johanna; Auvinen, Petri

    2011-07-01

    Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium causing spoilage of cold-stored, modified-atmosphere-packaged (MAP), nutrient-rich foods. Its role has been verified by challenge tests in gas and slime formation, development of pungent acidic and buttery off odors, and greening of beef. MAP meats have especially been prone to L. gasicomitatum spoilage. In addition, spoilage of vacuum-packaged vegetable sausages and marinated herring has been reported. The genomic sequencing project of L. gasicomitatum LMG 18811T was prompted by a need to understand the growth and spoilage potentials of L. gasicomitatum, to study its phylogeny, and to be able to knock out and overexpress the genes. Comparative genomic analysis was done within L. gasicomitatum LMG 18811T and the three fully assembled Leuconostoc genomes (those of Leuconostoc mesenteroides, Leuconostoc citreum, and Leuconostoc kimchii) available. The genome of L. gasicomitatum LMG 18811T is plasmid-free and contains a 1,954,080-bp circular chromosome with an average GC content of 36.7%. It includes genes for the phosphoketolase pathway and alternative pathways for pyruvate utilization. As interesting features associated with the growth and spoilage potential, LMG 18811T possesses utilization strategies for ribose, external nucleotides, nucleosides, and nucleobases and it has a functional electron transport chain requiring only externally supplied heme for respiration. In respect of the documented specific spoilage reactions, the pathways/genes associated with a buttery off odor, meat greening, and slime formation were recognized. Unexpectedly, genes associated with platelet binding and collagen adhesion were detected, but their functionality and role in food spoilage and processing environment contamination need further study.

  12. Production of L-lactic Acid from Biomass Wastes Using Scallop Crude Enzymes and Novel Lactic Acid Bacterium

    NASA Astrophysics Data System (ADS)

    Yanagisawa, Mitsunori; Nakamura, Kanami; Nakasaki, Kiyohiko

    In the present study, biomass waste raw materials including paper mill sludge, bamboo, sea lettuce, and shochu residue (from a distiller) and crude enzymes derived from inedible and discarded scallop parts were used to produce L-lactic acid for the raw material of biodegradable plastic poly-lactic acid. The activities of cellulase and amylase in the crude enzymes were 22 and 170units/L, respectively, and L-lactic acid was produced from every of the above mentioned biomass wastes, by the method of liquid-state simultaneous saccharification and fermentation (SSF) . The L-lactic acid concentrations produced from sea lettuce and shochu residue, which contain high concentration of starch were 3.6 and 9.3g/L, respectively, and corresponded to greater than 25% of the conversion of glucans contained in these biomass wastes. Furthermore, using the solid state SSF method, concentrations as high as 13g/L of L-lactic acid were obtained from sea lettuce and 26g/L were obtained from shochu residue.

  13. Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments.

    PubMed

    Sánchez-Andrea, Irene; Stams, Alfons J M; Hedrich, Sabrina; Ňancucheo, Ivan; Johnson, D Barrie

    2015-01-01

    Three strains of sulfate-reducing bacteria (M1(T), D, and E) were isolated from acidic sediments (White river and Tinto river) and characterized phylogenetically and physiologically. All three strains were obligately anaerobic, mesophilic, spore-forming straight rods, stained Gram-negative and displayed variable motility during active growth. The pH range for growth was 3.8-7.0, with an optimum at pH 5.5. The temperature range for growth was 15-40 °C, with an optimum at 30 °C. Strains M1(T), D, and E used a wide range of electron donors and acceptors, with certain variability within the different strains. The nominated type strain (M1(T)) used ferric iron, nitrate, sulfate, elemental sulfur, and thiosulfate (but not arsenate, sulfite, or fumarate) as electron acceptors, and organic acids (formate, lactate, butyrate, fumarate, malate, and pyruvate), alcohols (glycerol, methanol, and ethanol), yeast extract, and sugars (xylose, glucose, and fructose) as electron donors. It also fermented some substrates such as pyruvate and formate. Strain M1(T) tolerated up to 50 mM ferrous iron and 10 mM aluminum, but was inhibited by 1 mM copper. On the basis of phenotypic, phylogenetic, and genetic characteristics, strains M1(T), D, and E represent a novel species within the genus Desulfosporosinus, for which the name Desulfosporosinus acididurans sp. nov. is proposed. The type strain is M1(T) (=DSM 27692(T) = JCM 19471(T)). Strain M1(T) was the first acidophilic SRB isolated, and it is the third described species of acidophilic SRB besides Desulfosporosinus acidiphilus and Thermodesulfobium narugense.

  14. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system.

    PubMed

    Kato, Yusuke

    2015-01-01

    Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1-1.8) per 10(5) cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3. PMID:26401457

  15. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

    PubMed Central

    2015-01-01

    Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8) per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3. PMID:26401457

  16. Lab-on-a-chip Strategies for the Analysis of Amino Acids in Mars Analogue Extract Liquid Samples

    NASA Astrophysics Data System (ADS)

    Mora, Maria; Bryant, S.; Greer, F.; Fisher, A.; Willis, P.

    2010-10-01

    Amino acids, as the building blocks of proteins, are essential molecules for life on Earth. Terrestrial organisms synthesize and utilize almost exclusively L amino acids. However, amino acids can also be also synthesized by non-biological means. In order to determine the origin of an amino acid mixture it is necessary to analyze the D/L ratio. Under abiotic conditions, amino acids are made as racemic mixtures while in biological systems one chiral form prevails over the other. This characteristic of amino acids makes them the preferred biomarkers in the search for extraterrestrial life in Mars. Capillary electrophoresis (CE) is a popular technique that has been widely used for the analysis of amino acids. Capillary electrophoresis provides highly efficient separations with short analysis times and minimum sample consumption. In addition, CE can be miniaturized to portable devices (Lab-on-a-chip) that allow us to take the lab to the sample. These characteristics make CE an ideal technique for space exploration applications. In this regard, we have developed a lab-on-a-chip system capable of performing automated labeling, mixing, dilution, and analysis of amino acids by capillary electrophoresis and fluorescence detection. This device allows nanomolar detection of amino acids in aqueous samples. In addition, we are also testing monolithic columns packed inside microfluidic channels to perform chiral separations on amino acids by capillary electrochromatography (CEC). CEC is a hybrid technique combining the best aspects of liquid chromatography (LC) and capillary electrophoresis. These columns will later be incorporated into the automated device to perform a complete analysis of Mars analogue samples.

  17. Lactobacillus vini sp. nov., a wine lactic acid bacterium homofermentative for pentoses.

    PubMed

    Rodas, Ana María; Chenoll, Empar; Macián, M Carmen; Ferrer, Sergi; Pardo, Isabel; Aznar, Rosa

    2006-03-01

    Six strains with more than 99.5 % 16S rRNA gene sequence similarity, identical internal spacer region profiles and restriction analysis of the amplified 16S rRNA gene patterns were isolated from fermenting grape musts during independent studies carried out in France and Spain many years apart. Strains are Gram-positive, motile, facultatively anaerobic rods that do not exhibit catalase activity and have the ability to utilize pentose sugars (ribose and/or l-arabinose), although they are homofermentative bacteria. Strains ferment pentoses exclusively yielding lactic acid as the end product. A broad set of molecular techniques has been applied to characterize these strains and the results show a high degree of genotypical congruence, sharing identical profiles with 16S rRNA-based techniques. Phylogenetic analysis based on 16S rRNA gene sequences placed these strains within the genus Lactobacillus, closely related to Lactobacillus mali, Lactobacillus nagelii and Lactobacillus satsumensis (with approximately 95 % sequence similarity). DNA-DNA hybridization experiments confirmed the independent status at the species level of these fermenting grape-musts strains. Phenotypically they can be distinguished from the closest relatives by several traits such as growth temperatures and fermentation of carbohydrates. The name Lactobacillus vini sp. nov. is proposed, with strain Mont 4T (= DSM 20605T = CECT 5924T) as the type strain.

  18. Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk.

    PubMed

    Kadri, Zaina; Spitaels, Freek; Cnockaert, Margo; Praet, Jessy; El Farricha, Omar; Swings, Jean; Vandamme, Peter

    2015-11-01

    Four lactic acid bacteria isolates obtained from fresh dromedary camel milk produced in Dakhla, a city in southern Morocco, were characterised in order to determine their taxonomic position. The four isolates had highly similar MALDI-TOF MS and RAPD fingerprints and identical 16S rRNA gene sequences. Comparative sequence analysis revealed that the 16S rRNA gene sequence of the four isolates was most similar to that of Enterococcus sulfureus ATCC 49903(T) and Enterococcus italicus DSM 15952(T) (99.33 and 98.59% similarity, respectively). However, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes revealed that the taxon represented by strain LMG 28766(T) was well separated from E. sulfureus LMG 13084(T) and E. italicus LMG 22039(T), which was further confirmed by DNA-DNA hybridization values that were clearly below the species demarcation threshold. The novel taxon was easily differentiated from its nearest neighbour species through sequence analysis of protein encoding genes, MALDI-TOF mass spectrometry and multiple biochemical tests, but had a similar percentage G+C content of about 39%. We therefore propose to formally classify these isolates as Enterococcus bulliens sp. nov., with LMG 28766(T) (=CCMM B1177(T)) as the type strain.

  19. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.

    PubMed

    Yukphan, Pattaraporn; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanticharoen, Morakot; Yamada, Yuzo

    2004-03-01

    Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60.2-60.5 mol% G+C, with a range of 0.3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA-DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q(10). On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08(T) (=BCC 12978(T)=TISTR 1524(T)=NBRC 100057(T)=NRIC 0535(T)), which had a DNA G+C content of 60.3 mol% and was isolated from a heliconia flower ('paksaasawan' in Thai; Heliconia sp.) collected in Bangkok, Thailand.

  20. Genes involved in protein metabolism of the probiotic lactic acid bacterium Lactobacillus delbrueckii UFV H2b20.

    PubMed

    Do Carmo, A P; da Silva, D F; De Oliveira, M N V; Borges, A C; De Carvalho, A F; De Moraes, C A

    2011-09-01

    A basic requirement for the prediction of the potential use of lactic acid bacteria (LAB) in the dairy industry is the identification of specific genes involved in flavour-forming pathways. The probiotic Lactobacillus delbrueckii UFV H2b20 was submitted to a genetic characterisation and phylogenetic analysis of genes involved in protein catabolism. Eight genes belonging to this system were identified, which possess a closely phylogenetic relationship to NCFM strains representative, as it was demonstrated for oppC and oppBII, encoding oligopeptide transport system components. PepC, PepN, and PepX might be essential for growth of LAB, probiotic or not, since the correspondent genes are always present, including in L. delbrueckii UFV H2b20 genome. For pepX gene, a probable link between carbohydrate catabolism and PepX expression may exists, where it is regulated by PepR1/CcpA-like, a common feature between Lactobacillus strains and also in L. delbrueckii UFV H2b20. The well conserved evolutionary history of the ilvE gene is evidence that the pathways leading to branched-chain amino acid degradation, such as isoleucine and valine, are similar among L. delbrueckii subsp. bulgaricus strains and L. delbrueckii UFV H2b20. Thus, the involvement of succinate in flavour formation can be attributed to IlvE activity. The presence of aminopeptidase G in L. delbrueckii UFV H2b20 genome, which is absent in several strains, might improve the proteolytic activity and effectiveness. The nucleotide sequence encoding PepG revealed that it is a cysteine endopeptidase, belonging to Peptidase C1 superfamily; sequence analysis showed 99% identity with L. delbrueckii subsp. bulgaricus ATCC 11842 pepG, whereas protein sequence analysis revealed 100% similarity with PepG from the same organism. The present study proposes a schematic model to explain how the proteolytic system of the probiotic L. delbrueckii UFV H2b20 works, based on the components identified so far.

  1. Soil acidity determines the effectiveness of an organic amendment and a native bacterium for increasing soil stabilisation in semiarid mine tailings.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Roldán, A

    2009-01-01

    Unstable mine tailings are vulnerable to water and air erosion, so it is important to promote their surface stabilisation in order to avoid the spread of heavy metals. In a greenhouse experiment, we assessed the effect of the addition of Aspergillus niger-treated sugar beet waste and inoculation with a native bacterium, Bacillus cereus, on the stabilisation of soil aggregates of two acidic, semiarid mine tailings, with different acidity degree, during watering and drying periods. Organic amendment raised the pH of both the moderately and highly acidic tailings, whereas the bacterial inoculation increased this parameter in the former. Only the amendment addition increased soil water-soluble carbon in both tailings compared with their controls, under either watering or drying conditions. Both the amendment and B. cereus enhanced water-soluble carbohydrates. Both treatments increased dehydrogenase activity and aggregate stability, particularly in the moderately acidic tailing under drying conditions. After soil drying, aggregate stability was increased by the amendment (about 66% higher than the control soil) and by the bacterium (about 45% higher than the control soil) in the moderately acidic tailing. The effectiveness of these treatments as structure-stabilisation methods for degraded, semiarid mine ecosystems appears to be restricted to tailings of moderate acidity. PMID:18954889

  2. Soil acidity determines the effectiveness of an organic amendment and a native bacterium for increasing soil stabilisation in semiarid mine tailings.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Roldán, A

    2009-01-01

    Unstable mine tailings are vulnerable to water and air erosion, so it is important to promote their surface stabilisation in order to avoid the spread of heavy metals. In a greenhouse experiment, we assessed the effect of the addition of Aspergillus niger-treated sugar beet waste and inoculation with a native bacterium, Bacillus cereus, on the stabilisation of soil aggregates of two acidic, semiarid mine tailings, with different acidity degree, during watering and drying periods. Organic amendment raised the pH of both the moderately and highly acidic tailings, whereas the bacterial inoculation increased this parameter in the former. Only the amendment addition increased soil water-soluble carbon in both tailings compared with their controls, under either watering or drying conditions. Both the amendment and B. cereus enhanced water-soluble carbohydrates. Both treatments increased dehydrogenase activity and aggregate stability, particularly in the moderately acidic tailing under drying conditions. After soil drying, aggregate stability was increased by the amendment (about 66% higher than the control soil) and by the bacterium (about 45% higher than the control soil) in the moderately acidic tailing. The effectiveness of these treatments as structure-stabilisation methods for degraded, semiarid mine ecosystems appears to be restricted to tailings of moderate acidity.

  3. Isolation, characterization, and amino acid sequences of auracyanins, blue copper proteins from the green photosynthetic bacterium Chloroflexus aurantiacus

    NASA Technical Reports Server (NTRS)

    McManus, J. D.; Brune, D. C.; Han, J.; Sanders-Loehr, J.; Meyer, T. E.; Cusanovich, M. A.; Tollin, G.; Blankenship, R. E.

    1992-01-01

    Three small blue copper proteins designated auracyanin A, auracyanin B-1, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus. All three auracyanins are peripheral membrane proteins. Auracyanin A was described previously (Trost, J. T., McManus, J. D., Freeman, J. C., Ramakrishna, B. L., and Blankenship, R. E. (1988) Biochemistry 27, 7858-7863) and is not glycosylated. The two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis apparent monomer molecular masses are 14 (A), 18 (B-2), and 22 (B-1) kDa. The amino acid sequences of the B forms are presented. All three proteins have similar absorbance, circular dichroism, and resonance Raman spectra, but the electron spin resonance signals are quite different. Laser flash photolysis kinetic analysis of the reactions of the three forms of auracyanin with lumiflavin and flavin mononucleotide semiquinones indicates that the site of electron transfer is negatively charged and has an accessibility similar to that found in other blue copper proteins. Copper analysis indicates that all three proteins contain 1 mol of copper per mol of protein. All three auracyanins exhibit a midpoint redox potential of +240 mV. Light-induced absorbance changes and electron spin resonance signals suggest that auracyanin A may play a role in photosynthetic electron transfer. Kinetic data indicate that all three proteins can donate electrons to cytochrome c-554, the electron donor to the photosynthetic reaction center.

  4. Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47.

    PubMed

    Andreevskaya, Margarita; Johansson, Per; Laine, Pia; Smolander, Olli-Pekka; Sonck, Matti; Rahkila, Riitta; Jääskeläinen, Elina; Paulin, Lars; Auvinen, Petri; Björkroth, Johanna

    2015-06-01

    Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered. PMID:25819958

  5. Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47.

    PubMed

    Andreevskaya, Margarita; Johansson, Per; Laine, Pia; Smolander, Olli-Pekka; Sonck, Matti; Rahkila, Riitta; Jääskeläinen, Elina; Paulin, Lars; Auvinen, Petri; Björkroth, Johanna

    2015-06-01

    Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered.

  6. Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient.

    PubMed

    Leisner, J J; Vancanneyt, M; Goris, J; Christensen, H; Rusul, G

    2000-01-01

    Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.

  7. Lactic Acid Bacterium and Yeast Microbiotas of 19 Sourdoughs Used for Traditional/Typical Italian Breads: Interactions between Ingredients and Microbial Species Diversity

    PubMed Central

    Minervini, Fabio; Di Cagno, Raffaella; Lattanzi, Anna; Antonielli, Livio; Cardinali, Gianluigi; Cappelle, Stefan; Gobbetti, Marco

    2012-01-01

    The study of the microbiotas of 19 Italian sourdoughs used for the manufacture of traditional/typical breads allowed the identification, through a culture-dependent approach, of 20 and 4 species of lactic acid bacteria (LAB) and yeasts, respectively. Numerically, the most frequent LAB isolates were Lactobacillus sanfranciscensis (ca. 28% of the total LAB isolates), Lactobacillus plantarum (ca. 16%), and Lactobacillus paralimentarius (ca. 14%). Saccharomyces cerevisiae was identified in 16 sourdoughs. Candida humilis, Kazachstania barnettii, and Kazachstania exigua were also identified. As shown by principal component analysis (PCA), a correlation was found between the ingredients, especially the type of flour, the microbial community, and the biochemical features of sourdoughs. Triticum durum flours were characterized by the high level of maltose, glucose, fructose, and free amino acids (FAA) correlated with the sole or main presence of obligately heterofermentative LAB, the lowest number of facultatively heterofermentative strains, and the low cell density of yeasts in the mature sourdoughs. This study highlighted, through a comprehensive and comparative approach, the dominant microbiotas of 19 Italian sourdoughs, which determined some of the peculiarities of the resulting traditional/typical Italian breads. PMID:22156414

  8. [Isolation, identification and oxidizing characterization of an iron-sulfur oxidizing bacterium LY01 from acid mine drainage].

    PubMed

    Liu, Yu-jiao; Yang, Xin-ping; Wang, Shi-mei; Liang, Yin

    2013-05-01

    An acidophilic iron-sulfur oxidizing bacterium LY01 was isolated from acid mine drainage of coal in Guizhou Province, China. Strain LY01 was identified as Acidithiobacillusferrooxidans by morphological and physiological characteristics, and phylogenetic analysis of its 16S rRNA gene sequence. Strain LY01 was able to grow using ferrous ion (Fe2+), elemental sulfur (S0) and pyrite as sole energy source, respectively, but significant differences in oxidation efficiency and bacterial growth were observed when different energy source was used. When strain LY01 was cultured in 9K medium with 44.2 g x L(-1) FeSO4.7H2O as the substrate, the oxidation efficiency of Fe2+ was 100% in 30 h and the cell number of strain LY01 reached to 4.2 x 10(7) cell x mL(-1). When LY01 was cultured in 9K medium with 10 g x L(-1) S0 as the substrate, 6.7% S0 oxidation efficiency, 2001 mg x L(-1) SO4(2-) concentration and 8.9 x 10(7) cell x mL(-1) cell number were observed in 21 d respectively. When LY01 was cultured with 30 g x L(-1) pyrite as the substrate, the oxidation efficiency of pyrite, SO4(2-) concentration and cell number reached 10%, 4443 mg x L(-1) and 3.4 x 10(8) cell x mL(-1) respectively in 20 d. The effects of different heavy metals (Ni2+, Pb2+) on oxidation activity of strain LY01 cultured with pyrite were investigated. Results showed that the oxidation activity of strain LY01 was inhibited to a certain extent with the addition of Ni2+ at 10-100 mg x L(-1) to the medium, but the addition of 10-100 mg x L(-1) Pb2+ had no effect on LY01 activity.

  9. Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum

    SciTech Connect

    Svetlitshnyi, V.; Wiegel, J.; Rainey, F.

    1996-10-01

    Three strains of an anaerobic thermophilic organoheterotrophic lipolytic alkalitolerant bacterium, Thermosyntropha lipolytica gen. nov., sp. nov. (type strain JW/VS-264{sup T}; DSM 11003) were isolated from alkaline hot springs of Lake Bogoria (Kenya). The cells were nonmotile, non-spore forming, straight or slightly curved rods. At 60{degrees}C, the pH range for growth determined at 25{degrees}C [pH{sup 25{degrees}C}] was 7.15 to 9.5, with an optimum between 8.1 and 8.9 (pH{sup 60{degrees}C} of 7.6 and 8.1). At a pH{sup 25{degrees}C} of 8.5 temperature range for growth was from 52 to 70{degrees}C, with an optimum between 60 and 66{degrees}C. The shortest doubling time was around 1 h. In pure culture the bacterium grew in a mineral base medium supplemented with yeast extract, tryptone, Casamino Acids, betaine, and crotonate as carbon sources, producing acetate as a major product and constitutively a lipase. During growth in the presence of olive oil, free long-chain fatty acids were accumulated in the medium but the pure culture syntrophic coculture (Methanobacterium strain JW/VS-M29) the lipolytic bacteria grew on triacylglycerols and linear saturated and unsaturated fatty acids with 4 to 18 carbon atoms, but glycerol was not utilized. Fatty acids with even numbers of carbon atoms were degraded to acetate and methane, while from odd-numbered fatty acids 1 mol of propionate per mol of fatty acid was additionally formed. 16S rDNA sequence analysis identified Syntrophospora and Syntrophomonas spp. as closest phylogenetic neighbors.

  10. Dye-linked D-amino acid dehydrogenase from the thermophilic bacterium Rhodothermus marinus JCM9785: characteristics and role in trans-4-hydroxy-L-proline catabolism.

    PubMed

    Satomura, Takenori; Ishikura, Masaru; Koyanagi, Takashi; Sakuraba, Haruhiko; Ohshima, Toshihisa; Suye, Shin-ichiro

    2015-05-01

    A gene from the thermophilic Gram-negative bacterium Rhodothermus marinus JCM9785, encoding a dye-linked D-amino acid dehydrogenase homologue, was overexpressed in Escherichia coli, and its product was purified and characterized. The expressed enzyme was a highly thermostable dye-linked D-amino acid dehydrogenase that retained more than 80% of its activity after incubation for 10 min at up to 70 °C. When enzyme-catalyzed dehydrogenation of several D-amino acids was carried out using 2,6-dichloroindophenol as the electron acceptor, D-phenylalanine was the most preferable substrate among the D-amino acids tested. Immediately upstream of the dye-linked D-amino acid dehydrogenase gene (dadh) was a gene encoding a 4-hydroxyproline 2-epimerase homologue (hypE). That gene was successfully expressed in E. coli, and the gene product exhibited strong 4-hydroxyproline 2-epimerase activity. Reverse transcription PCR and quantitative real-time PCR showed that the six genes containing the dadh and hypE genes were arranged in an operon and were required for catabolism of trans-4-hydroxy-L-proline in R. marinus. This is the first description of a dye-linked D-amino acid dehydrogenase (Dye-DADH) with broad substrate specificity involved in trans-4-hydroxy-L-proline catabolism. PMID:25472442

  11. Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells.

    PubMed

    Wang, Ling; Wang, Zhouli; Yuan, Yahong; Cai, Rui; Niu, Chen; Yue, Tianli

    2015-01-01

    The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2-4.0, and enhanced significantly at pH 4.0-6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0-6.0).

  12. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti

    PubMed Central

    Draghi, W. O.; Del Papa, M. F.; Hellweg, C.; Watt, S. A.; Watt, T. F.; Barsch, A.; Lozano, M. J.; Lagares, A.; Salas, M. E.; López, J. L.; Albicoro, F. J.; Nilsson, J. F.; Torres Tejerizo, G. A.; Luna, M. F.; Pistorio, M.; Boiardi, J. L.; Pühler, A.; Weidner, S.; Niehaus, K.; Lagares, A.

    2016-01-01

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0–6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia. PMID:27404346

  13. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

    PubMed

    Draghi, W O; Del Papa, M F; Hellweg, C; Watt, S A; Watt, T F; Barsch, A; Lozano, M J; Lagares, A; Salas, M E; López, J L; Albicoro, F J; Nilsson, J F; Torres Tejerizo, G A; Luna, M F; Pistorio, M; Boiardi, J L; Pühler, A; Weidner, S; Niehaus, K; Lagares, A

    2016-07-11

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

  14. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

    PubMed

    Draghi, W O; Del Papa, M F; Hellweg, C; Watt, S A; Watt, T F; Barsch, A; Lozano, M J; Lagares, A; Salas, M E; López, J L; Albicoro, F J; Nilsson, J F; Torres Tejerizo, G A; Luna, M F; Pistorio, M; Boiardi, J L; Pühler, A; Weidner, S; Niehaus, K; Lagares, A

    2016-01-01

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia. PMID:27404346

  15. Preparation and Identification of Benzoic Acids and Benzamides: An Organic "Unknown" Lab

    NASA Astrophysics Data System (ADS)

    Taber, Douglass F.; Nelson, Jade D.; Northrop, John P.

    1999-06-01

    The reaction of an unknown substituted benzene derivative (illustrated by toluene) with oxalyl chloride and aluminum chloride gives the acid chloride. Hydrolysis of the acid chloride gives the acid, and reaction of the acid with concentrated aqueous ammonia gives the benzamide.

    The equivalent weight of the acid can be determined by titration with standardized aqueous sodium hydroxide. Given this information and the melting points of the acid and the benzamide, it is possible to deduce the structure of the initial unknown.

  16. Influence of selected lab cultures on the evolution of free amino acids, free fatty acids and Fiore Sardo cheese microflora during the ripening.

    PubMed

    Mangia, Nicoletta P; Murgia, Marco A; Garau, Giovanni; Sanna, Maria G; Deiana, Pietrino

    2008-04-01

    Fiore Sardo Protected Denomination of Origin is a traditional Sardinian (Italy) hard cheese produced exclusively from whole raw ovine milk and coagulated with lamb rennet paste. Currently, Fiore Sardo is still produced by shepherds at the farmhouse level without the addition of any starter culture and the cheese-making process is characterized by significant waste. The first objective of the present work was to investigate the autochthonous microflora present in milk and Fiore Sardo cheese in order to select lactic acid bacterial (LAB) cultures with suitable cheese-making attributes and, possibly reduce the production waste. Secondly, the ability of selected cultures to guarantee cheese healthiness and quality was tested in experimental cheese-making trials. In this study, we show that the typical lactic microflora of raw ewe's milk and Fiore Sardo cheese is mostly composed of mesophilic LAB such as Lactococcus lactis subsp. lactis, Lactobacillus plantarum and Lactobacillus casei subsp. casei. Moreover, strains belonging to the species were selected for cheese-making attributes and used in experimental cheese-making trials carried out in different farms producing Fiore Sardo. The evolution of the cheese microflora, free amino acids and free fatty acids during the ripening showed that the experimental cheeses were characterized by a balanced ratio of the chemical constituents, by a reduced number of spoilage microorganisms and, remarkably, by the absence of production waste that were significant for the control cheeses.

  17. Leuconostoc gasicomitatum is the dominating lactic acid bacterium in retail modified-atmosphere-packaged marinated broiler meat strips on sell-by-day.

    PubMed

    Susiluoto, Tuija; Korkeala, Hannu; Björkroth, K Johanna

    2003-01-15

    Lactic acid bacteria (LAB) in retail, modified-atmosphere-packaged (MAP), marinated broiler meat strips on sell-by-day were mainly identified as Leuconostoc gasicomitatum. A total of 32 packages, three to five packages of seven differently marinated broiler meat products, were studied at the end of the producer-defined shelf life (at 6 degrees C, 7-9 days depending on the manufacturer). Prior to the microbiological analyses, appearance and smell of the product was checked and pH measured. Bacteria were cultured on MRS and Tomato Juice Agar (TJA), Rogosa SL agar (SLA), Plate Count Agar (PCA) and Streptomycin Thallium Acetate Agar (STAA) for the enumeration of LAB, lactobacilli, total bacterial count and Brochothrix thermosphacta, respectively. The average CFU/g of the 32 packages was 2.3 x 10(8) on PCA. The highest bacterial average, 3.1 x 10(8), was recovered on TJA, the corresponding CFU/g averages on MRS and SLA being 2.3 x 10(8) and 1.3 x 10(8), respectively. Despite the high LAB numbers detected, radical spoilage changes such as unpleasant odor, slime production and formation of gas were not seen. B. thermosphacta did not form a significant part of the bacterial population since none of the levels exceeded the spoilage threshold level of 10(5) CFU/g reported in previous studies for this organism. In order to characterize the dominating LAB population, as many as 85, 85 and 88 colonies from MRS, TJA and SLA, respectively, were randomly picked and cultured pure. LAB were identified to species level using a 16 and 23S rDNA HindIiI RFLP (ribotyping) database. Fifty-six of the 170 isolates picked from the non-selective LAB media (MRS and TJA) were identified as L. gasicomitatum, followed by Carnobacterium divergens (41 isolates), Lactobacillus sakei and Lactobacillus curvatus subsp. melibiosus (31 isolates) and L. curvatus subsp. curvatus (20 isolates) species. SLA proved not to be completely selective for lactobacilli because the growth of Leuconostoc spp. was not

  18. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA).

    PubMed

    Lutz, Sascha; Weber, Patrick; Focke, Max; Faltin, Bernd; Hoffmann, Jochen; Müller, Claas; Mark, Daniel; Roth, Günter; Munday, Peter; Armes, Niall; Piepenburg, Olaf; Zengerle, Roland; von Stetten, Felix

    2010-04-01

    For the first time we demonstrate a self-sufficient lab-on-a-foil system for the fully automated analysis of nucleic acids which is based on the recently available isothermal recombinase polymerase amplification (RPA). The system consists of a novel, foil-based centrifugal microfluidic cartridge including prestored liquid and dry reagents, and a commercially available centrifugal analyzer for incubation at 37 degrees C and real-time fluorescence detection. The system was characterized with an assay for the detection of the antibiotic resistance gene mecA of Staphylococcus aureus. The limit of detection was <10 copies and time-to-result was <20 min. Microfluidic unit operations comprise storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into < or = 30 independent reaction cavities, and mixing of reagents with the DNA samples. The foil-based cartridge was produced by blow-molding and sealed with a self-adhesive tape. The demonstrated system excels existing PCR based lab-on-a-chip platforms in terms of energy efficiency and time-to-result. Applications are suggested in the field of mobile point-of-care analysis, B-detection, or in combination with continuous monitoring systems. PMID:20300675

  19. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA).

    PubMed

    Lutz, Sascha; Weber, Patrick; Focke, Max; Faltin, Bernd; Hoffmann, Jochen; Müller, Claas; Mark, Daniel; Roth, Günter; Munday, Peter; Armes, Niall; Piepenburg, Olaf; Zengerle, Roland; von Stetten, Felix

    2010-04-01

    For the first time we demonstrate a self-sufficient lab-on-a-foil system for the fully automated analysis of nucleic acids which is based on the recently available isothermal recombinase polymerase amplification (RPA). The system consists of a novel, foil-based centrifugal microfluidic cartridge including prestored liquid and dry reagents, and a commercially available centrifugal analyzer for incubation at 37 degrees C and real-time fluorescence detection. The system was characterized with an assay for the detection of the antibiotic resistance gene mecA of Staphylococcus aureus. The limit of detection was <10 copies and time-to-result was <20 min. Microfluidic unit operations comprise storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into < or = 30 independent reaction cavities, and mixing of reagents with the DNA samples. The foil-based cartridge was produced by blow-molding and sealed with a self-adhesive tape. The demonstrated system excels existing PCR based lab-on-a-chip platforms in terms of energy efficiency and time-to-result. Applications are suggested in the field of mobile point-of-care analysis, B-detection, or in combination with continuous monitoring systems.

  20. Pre-storage of gelified reagents in a lab-on-a-foil system for rapid nucleic acid analysis.

    PubMed

    Sun, Yi; Høgberg, Jonas; Christine, Thanner; Florian, Laouenan; Monsalve, Lisandro G; Rodriguez, Sonia; Cao, Cuong; Wolff, Anders; Ruano-Lopez, Jesus M; Bang, Dang Duong

    2013-04-21

    Reagent pre-storage in a microfluidic chip can enhance operator convenience, simplify the system design, reduce the cost of storage and shipment, and avoid the risk of cross-contamination. Although dry reagents have long been used in lateral flow immunoassays, they have rarely been used for nucleic acid-based point-of-care (POC) assays due to the lack of reliable techniques to dehydrate and store fragile molecules involved in the reaction. In this study, we describe a simple and efficient method for prolonged on-chip storage of PCR reagents. The method is based on gelification of all reagents required for PCR as a ready-to-use product. The approach was successfully implemented in a lab-on-a-foil system, and the gelification process was automated for mass production. Integration of reagents on-chip by gelification greatly facilitated the development of easy-to-use lab-on-a-chip (LOC) devices for fast and cost-effective POC analysis.

  1. Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms

    NASA Technical Reports Server (NTRS)

    Jackson, B. E.; Bhupathiraju, V. K.; Tanner, R. S.; Woese, C. R.; McInerney, M. J.

    1999-01-01

    Strain SBT is a new, strictly anaerobic, gram-negative, nonmotile, non-sporeforming, rod-shaped bacterium that degrades benzoate and certain fatty acids in syntrophic association with hydrogen/formate-using microorganisms. Strain SBT produced approximately 3 mol of acetate and 0.6 mol of methane per mol of benzoate in coculture with Methanospirillum hungatei strain JF1. Saturated fatty acids, some unsaturated fatty acids, and methyl esters of butyrate and hexanoate also supported growth of strain SBT in coculture with Desulfovibrio strain G11. Strain SBT grew in pure culture with crotonate, producing acetate, butyrate, caproate, and hydrogen. The molar growth yield was 17 +/- 1 g cell dry mass per mol of crotonate. Strain SBT did not grow with fumarate, iron(III), polysulfide, or oxyanions of sulfur or nitrogen as electron acceptors with benzoate as the electron donor. The DNA base composition of strain SBT was 43.1 mol% G+C. Analysis of the 16 S rRNA gene sequence placed strain SBT in the delta-subdivision of the Proteobacteria, with sulfate-reducing bacteria. Strain SBT was most closely related to members of the genus Syntrophus. The clear phenotypic and genotypic differences between strain SBT and the two described species in the genus Syntrophus justify the formation of a new species, Syntrophus aciditrophicus.

  2. Acetobacter senegalensis sp. nov., a thermotolerant acetic acid bacterium isolated in Senegal (sub-Saharan Africa) from mango fruit (Mangifera indica L.).

    PubMed

    Ndoye, Bassirou; Cleenwerck, Ilse; Engelbeen, Katrien; Dubois-Dauphin, Robin; Guiro, Amadou Tidiane; Van Trappen, Stefanie; Willems, Anne; Thonart, Phillipe

    2007-07-01

    A thermotolerant acetic acid bacterium, designated strain CWBI-B418(T), isolated in Senegal from mango fruit (Mangifera indica), was characterized in detail by means of genotypic and phenotypic methods. The novel strain was strictly aerobic and exhibited optimal growth on YGM medium at 35 degrees C. Cells were Gram-negative, motile and coccoid. The strain was assigned to the genus Acetobacter on the basis of 16S rRNA gene sequence analysis. DNA-DNA hybridization experiments with its phylogenetically closest relatives showed that strain CWBI-B418(T) represented a novel Acetobacter genospecies. The DNA G+C content of strain CWBI-B418(T) was 56.0 mol%. Phenotypic characteristics enabling the differentiation of strain CWBI-B418(T) from phylogenetically related Acetobacter species were: production of 2-keto-D-gluconic acid from D-glucose, but not 5-keto-D-gluconic acid, production of catalase but not oxidase, growth on yeast extract with 30 % d-glucose, growth with ammonium as sole nitrogen source with ethanol as carbon source, utilization of glycerol and ethanol but not maltose or methanol as carbon sources, and growth in the presence of 10 % ethanol. Based on the genotypic and phenotypic data presented, strain CWBI-B418(T) clearly represents a novel Acetobacter species, for which the name Acetobacter senegalensis sp. nov. is proposed. The type strain is CWBI-B418(T) (=LMG 23690(T)=DSM 18889(T)).

  3. Fructose metabolism of the purple non-sulfur bacterium Rhodospirillum rubrum: effect of carbon dioxide on growth, and production of bacteriochlorophyll and organic acids.

    PubMed

    Rudolf, Christiane; Grammel, Hartmut

    2012-04-01

    During fermentative metabolism, carbon dioxide fixation plays a key role in many bacteria regarding growth and production of organic acids. The present contribution, dealing with the facultative photosynthetic bacterium Rhodospirillum rubrum, reveals not only the strong influence of ambient carbon dioxide on the fermentative break-down of fructose but also a high impact on aerobic growth with fructose as sole carbon source. Both growth rates and biomass yield increased with increasing carbon dioxide supply in chemoheterotrophic aerobic cultures. Furthermore, intracellular metabolite concentration measurements showed almost negligible concentrations of the tricarboxylic acid cycle intermediates succinate, fumarate and malate under aerobic growth, in contrast to several metabolites of the glycolysis. In addition, we present a dual phase fed-batch process, where an aerobic growth phase is followed by an anaerobic production phase. The biosynthesis of bacteriochlorophyll and the secretion of organic acids were both affected by the carbon dioxide supply, the pH value and by the cell density at the time of switching from aerobic to anaerobic conditions. The formation of pigmented photosynthetic membranes and the amount of bacteriochlorophyll were inversely correlated to the secretion of succinate. Accounting the high biotechnological potential of R. rubrum, optimization of carbon dioxide supply is important because of the favored application of fructose-containing fermentable feedstock solutions in bio-industrial processes.

  4. Effects of hydrostatic pressure and temperature on the uptake and respiration of amino acids by a facultatively psychrophilic marine bacterium.

    NASA Technical Reports Server (NTRS)

    Paul, K. L.; Morita, R. Y.

    1971-01-01

    Studies of pressure and temperature effects on glutamic acid transport and utilization indicated that hydrostatic pressure and low temperature inhibit glutamate transport more than glutamate respiration. The effects of pressure on transport were reduced at temperatures near the optimum. Similar results were obtained for glycine, phenylalanine, and proline. Pressure effects on the transport systems of all four amino acids were reversible to some degree. Both proline and glutamic acid were able to protect their transport proteins against pressure damage. The data presented indicate that the uptake of amino acids by cells under pressure is inhibited, which is the cause of their inability to grow under pressure.

  5. Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells

    PubMed Central

    Wang, Ling; Wang, Zhouli; Yuan, Yahong; Cai, Rui; Niu, Chen; Yue, Tianli

    2015-01-01

    The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2–4.0, and enhanced significantly at pH 4.0–6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0–6.0). PMID:26581099

  6. Growth and gas formation by Lactobacillus wasatchensis, a novel obligatory heterofermentative nonstarter lactic acid bacterium, in Cheddar-style cheese made using a Streptococcus thermophilus starter.

    PubMed

    Ortakci, Fatih; Broadbent, Jeffery R; Oberg, Craig J; McMahon, Donald J

    2015-11-01

    A novel slow-growing, obligatory heterofermentative, nonstarter lactic acid bacterium (NSLAB), Lactobacillus wasatchensis WDC04, was studied for growth and gas production in Cheddar-style cheese made using Streptococcus thermophilus as the starter culture. Cheesemaking trials were conducted using S. thermophilus alone or in combination with Lb. wasatchensis deliberately added to cheese milk at a level of ~10(4) cfu/mL. Resulting cheeses were ripened at 6 or 12°C. At d 1, starter streptococcal numbers were similar in both cheeses (~10(9) cfu/g) and fast-growing NSLAB lactobacilli counts were below detectable levels (<10(2) cfu/g). As expected, Lactobacillus wasatchensis counts were 3×10(5) cfu/g in cheeses inoculated with this bacterium and below enumeration limits in the control cheese. Starter streptococci decreased over time at both storage temperatures but declined more rapidly at 12°C, especially in cheese also containing Lb. wasatchensis. Populations of fast-growing NSLAB and the slow-growing Lb. wasatchensis reached 5×10(7) and 2×10(8) cfu/g, respectively, after 16 wk of storage at 12°C. Growth of NSLAB coincided with a reduction in galactose concentration in the cheese from 0.6 to 0.1%. Levels of galactose at 6°C had similar decrease. Gas formation and textural defects were only observed in cheese with added Lb. wasatchensis ripened at 12°C. Use of S. thermophilus as starter culture resulted in galactose accumulation that Lb. wasatchensis can use to produce CO2, which contributes to late gas blowing in Cheddar-style cheeses, especially when the cheese is ripened at elevated temperature.

  7. Growth and gas formation by Lactobacillus wasatchensis, a novel obligatory heterofermentative nonstarter lactic acid bacterium, in Cheddar-style cheese made using a Streptococcus thermophilus starter.

    PubMed

    Ortakci, Fatih; Broadbent, Jeffery R; Oberg, Craig J; McMahon, Donald J

    2015-11-01

    A novel slow-growing, obligatory heterofermentative, nonstarter lactic acid bacterium (NSLAB), Lactobacillus wasatchensis WDC04, was studied for growth and gas production in Cheddar-style cheese made using Streptococcus thermophilus as the starter culture. Cheesemaking trials were conducted using S. thermophilus alone or in combination with Lb. wasatchensis deliberately added to cheese milk at a level of ~10(4) cfu/mL. Resulting cheeses were ripened at 6 or 12°C. At d 1, starter streptococcal numbers were similar in both cheeses (~10(9) cfu/g) and fast-growing NSLAB lactobacilli counts were below detectable levels (<10(2) cfu/g). As expected, Lactobacillus wasatchensis counts were 3×10(5) cfu/g in cheeses inoculated with this bacterium and below enumeration limits in the control cheese. Starter streptococci decreased over time at both storage temperatures but declined more rapidly at 12°C, especially in cheese also containing Lb. wasatchensis. Populations of fast-growing NSLAB and the slow-growing Lb. wasatchensis reached 5×10(7) and 2×10(8) cfu/g, respectively, after 16 wk of storage at 12°C. Growth of NSLAB coincided with a reduction in galactose concentration in the cheese from 0.6 to 0.1%. Levels of galactose at 6°C had similar decrease. Gas formation and textural defects were only observed in cheese with added Lb. wasatchensis ripened at 12°C. Use of S. thermophilus as starter culture resulted in galactose accumulation that Lb. wasatchensis can use to produce CO2, which contributes to late gas blowing in Cheddar-style cheeses, especially when the cheese is ripened at elevated temperature. PMID:26364109

  8. Desulfotomaculum geothermicum sp. nov., a thermophilic, fatty acid-degrading, sulfate-reducing bacterium isolated with H2 from geothermal ground water.

    PubMed

    Daumas, S; Cord-Ruwisch, R; Garcia, J L

    1988-01-01

    A strictly anaerobic, thermophilic, fatty acids-degrading, sporulating sulfate-reducing bacterium was isolated from geothermal ground water. The organism stained Gram-negative and formed gas vacuoles during sporulation. Lactate, ethanol, fructose and saturated fatty acids up to C18 served as electron donors and carbon sources with sulfate as external electron acceptor. Benzoate was not used. Stoichiometric measurements revealed a complete oxidation of part of butyrate although growth with acetate as only electron donor was not observed. The rest of butyrate was oxidized to acetate. The strain grew chemolithoautotrophically with hydrogen plus sulfate as energy source and carbon dioxide as carbon source without requirement of additional organic carbon like acetate. The strain contained a c-type cytochrome and presumably a sulfite reductase P582. Optimum temperature, pH and NaCl concentration for growth were 54 degrees C, pH 7.3-7.5 and 25 to 35 g NaCl/l. The G + C content of DNA was 50.4 mol %. Strain BSD is proposed as a new species of the spore-forming sulfate-reducing genus Desulfotomaculum, D. geothermicum.

  9. Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5).

    PubMed

    Yu, Jiang; Guan, Xuejiao; Liu, Chongxi; Xiang, Wensheng; Yu, Zhenhua; Liu, Xiaobing; Wang, Guanghua

    2016-10-01

    A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

  10. Favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, Shewanella violacea DSS12, at high-hydrostatic pressures.

    PubMed

    Kawamoto, Jun; Sato, Takako; Nakasone, Kaoru; Kato, Chiaki; Mihara, Hisaaki; Esaki, Nobuyoshi; Kurihara, Tatsuo

    2011-08-01

    Shewanella violacea DSS12, a deep-sea bacterium, produces eicosapentaenoic acid (EPA) as a component of membrane phospholipids. Although various isolates from the deep sea, such as Photobacterium profundum SS9, Colwellia psychrerythraea 34H and various Shewanella strains, produce EPA- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. In this article, we illustrate the physiological importance of EPA for high-pressure adaptation in strain DSS12 with the help of an EPA-deficient mutant (DSS12(pfaA)). DSS12(pfaA) showed significant growth retardation at 30 MPa, but not at 0.1 MPa. We also found that DSS12(pfaA) grown at 30 MPa forms filamentous cells. When an EPA-containing phospholipid (sn-1-oleoly-sn-2-eicosapentaenoyl phosphatidylethanolamine) was supplemented, the growth retardation and the morphological defect of DSS12(pfaA) were suppressed, indicating that the externally added EPA-containing phospholipid compensated for the loss of endogenous EPA. In contrast, the addition of an oleic acid-containing phospholipid (sn-1,2-dioleoyl phosphatidylethanolamine) did not affect the growth and the morphology of the cells. Immunofluorescent microscopic analysis with anti-FtsZ antibody revealed a number of Z-rings and separated nucleoids in DSS12(pfaA) grown at 30 MPa. These results demonstrate the physiological importance of EPA for the later step of Z-ring formation of S. violacea DSS12 under high-pressure conditions. PMID:21518217

  11. Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS.

    PubMed

    Hvidsten, Ina; Mjøs, Svein Are; Bødtker, Gunhild; Barth, Tanja

    2015-09-01

    The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.

  12. Utilization of CO2 fixating bacterium Actinobacillus succinogenes 130Z for simultaneous biogas upgrading and biosuccinic acid production.

    PubMed

    Gunnarsson, Ingólfur B; Alvarado-Morales, Merlin; Angelidaki, Irini

    2014-10-21

    Biogas is an attractive renewable energy carrier. However, it contains CO2 which limits its use for certain applications. Here we report a novel approach for removing CO2 from biogas and capturing it as a biochemical through a biological process. This approach entails converting CO2 into biosuccinic acid using the bacterial strain Actinobacillus succinogenes 130 Z, and simultaneously producing high-purity CH4 (> 95%). Results showed that when pressure during fermentation was increased from 101.325 to 140 kPa, higher CO2 solubility was achieved, thereby positively affecting final succinic acid yield and titer, CO2 consumption rate, and CH4 purity. When using biogas as the only CO2 source at 140 kPa, the CO2 consumption rate corresponded to 2.59 L CO2 L(-1) d(-1) with a final succinic acid titer of 14.4 g L(-1). Under this pressure condition, the highest succinic acid yield and biogas quality reached corresponded to 0.635 g g(-1) and 95.4% (v v(-1)) CH4 content, respectively, after 24 h fermentation. This work represents the first successful attempt to develop a system capable of upgrading biogas to vehicle fuel/gas grid quality and simultaneously produce biosuccinic acid, a valuable building block with large market potential in the near term.

  13. Diversity of the Lactic Acid Bacterium and Yeast Microbiota in the Switch from Firm- to Liquid-Sourdough Fermentation

    PubMed Central

    Di Cagno, Raffaella; Pontonio, Erica; Buchin, Solange; De Angelis, Maria; Lattanzi, Anna; Valerio, Francesca; Calasso, Maria

    2014-01-01

    Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent. Lactobacillus plantarum dominated firm sourdoughs over time. Leuconostoc lactis and Lactobacillus brevis dominated only some firm sourdoughs, and Lactobacillus sanfranciscensis persisted for some time only in some firm sourdoughs. Leuconostoc citreum persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by Leuconostoc mesenteroides in some sourdoughs. Saccharomyces cerevisiae, Candida humilis, Saccharomyces servazzii, Saccharomyces bayanus-Kazachstania sp., and Torulaspora delbrueckii were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap–/solid-phase microextraction–gas chromatography-mass spectrometry (PT–/SPME–GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time. PMID:24632249

  14. Eicosapentaenoic acid plays a beneficial role in membrane organization and cell division of a cold-adapted bacterium, Shewanella livingstonensis Ac10.

    PubMed

    Kawamoto, Jun; Kurihara, Tatsuo; Yamamoto, Kentaro; Nagayasu, Makiko; Tani, Yasushi; Mihara, Hisaaki; Hosokawa, Masashi; Baba, Takeshi; Sato, Satoshi B; Esaki, Nobuyoshi

    2009-01-01

    Shewanella livingstonensis Ac10, a psychrotrophic gram-negative bacterium isolated from Antarctic seawater, produces eicosapentaenoic acid (EPA) as a component of phospholipids at low temperatures. EPA constitutes about 5% of the total fatty acids of cells grown at 4 degrees C. We found that five genes, termed orf2, orf5, orf6, orf7, and orf8, are specifically required for the synthesis of EPA by targeted disruption of the respective genes. The mutants lacking EPA showed significant growth retardation at 4 degrees C but not at 18 degrees C. Supplementation of a synthetic phosphatidylethanolamine that contained EPA at the sn-2 position complemented the growth defect. The EPA-less mutant became filamentous, and multiple nucleoids were observed in a single cell at 4 degrees C, indicating that the mutant has a defect in cell division. Electron microscopy of the cells by high-pressure freezing and freeze-substitution revealed abnormal intracellular membranes in the EPA-less mutant at 4 degrees C. We also found that the amounts of several membrane proteins were affected by the depletion of EPA. While polyunsaturated fatty acids are often considered to increase the fluidity of the hydrophobic membrane core, diffusion of a small hydrophobic molecule, pyrene, in the cell membranes and large unilamellar vesicles prepared from the lipid extracts was very similar between the EPA-less mutant and the parental strain. These results suggest that EPA in S. livingstonensis Ac10 is not required for bulk bilayer fluidity but plays a beneficial role in membrane organization and cell division at low temperatures, possibly through specific interaction between EPA and proteins involved in these cellular processes. PMID:19011019

  15. The Antisense RNA Approach: a New Application for In Vivo Investigation of the Stress Response of Oenococcus oeni, a Wine-Associated Lactic Acid Bacterium

    PubMed Central

    Darsonval, Maud; Msadek, Tarek; Alexandre, Hervé

    2015-01-01

    Oenococcus oeni is a wine-associated lactic acid bacterium mostly responsible for malolactic fermentation in wine. In wine, O. oeni grows in an environment hostile to bacterial growth (low pH, low temperature, and ethanol) that induces stress response mechanisms. To survive, O. oeni is known to set up transitional stress response mechanisms through the synthesis of heat stress proteins (HSPs) encoded by the hsp genes, notably a unique small HSP named Lo18. Despite the availability of the genome sequence, characterization of O. oeni genes is limited, and little is known about the in vivo role of Lo18. Due to the lack of genetic tools for O. oeni, an efficient expression vector in O. oeni is still lacking, and deletion or inactivation of the hsp18 gene is not presently practicable. As an alternative approach, with the goal of understanding the biological function of the O. oeni hsp18 gene in vivo, we have developed an expression vector to produce antisense RNA targeting of hsp18 mRNA. Recombinant strains were exposed to multiple stresses inducing hsp18 gene expression: heat shock and acid shock. We showed that antisense attenuation of hsp18 affects O. oeni survival under stress conditions. These results confirm the involvement of Lo18 in heat and acid tolerance of O. oeni. Results of anisotropy experiments also confirm a membrane-protective role for Lo18, as previous observations had already suggested. This study describes a new, efficient tool to demonstrate the use of antisense technology for modulating gene expression in O. oeni. PMID:26452552

  16. The Antisense RNA Approach: a New Application for In Vivo Investigation of the Stress Response of Oenococcus oeni, a Wine-Associated Lactic Acid Bacterium.

    PubMed

    Darsonval, Maud; Msadek, Tarek; Alexandre, Hervé; Grandvalet, Cosette

    2015-10-09

    Oenococcus oeni is a wine-associated lactic acid bacterium mostly responsible for malolactic fermentation in wine. In wine, O. oeni grows in an environment hostile to bacterial growth (low pH, low temperature, and ethanol) that induces stress response mechanisms. To survive, O. oeni is known to set up transitional stress response mechanisms through the synthesis of heat stress proteins (HSPs) encoded by the hsp genes, notably a unique small HSP named Lo18. Despite the availability of the genome sequence, characterization of O. oeni genes is limited, and little is known about the in vivo role of Lo18. Due to the lack of genetic tools for O. oeni, an efficient expression vector in O. oeni is still lacking, and deletion or inactivation of the hsp18 gene is not presently practicable. As an alternative approach, with the goal of understanding the biological function of the O. oeni hsp18 gene in vivo, we have developed an expression vector to produce antisense RNA targeting of hsp18 mRNA. Recombinant strains were exposed to multiple stresses inducing hsp18 gene expression: heat shock and acid shock. We showed that antisense attenuation of hsp18 affects O. oeni survival under stress conditions. These results confirm the involvement of Lo18 in heat and acid tolerance of O. oeni. Results of anisotropy experiments also confirm a membrane-protective role for Lo18, as previous observations had already suggested. This study describes a new, efficient tool to demonstrate the use of antisense technology for modulating gene expression in O. oeni.

  17. Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor.

    PubMed

    Díaz, C; Baena, S; Fardeau, M-L; Patel, B K C

    2007-08-01

    Strain ILE-2(T) was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2-4 x 0.1 microm) stained Gram-negative and grew optimally at 42 degrees C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2(T) was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2(T) was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2(T) represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2(T) (=DSM 16581(T) =JCM 14039(T)). PMID:17684281

  18. Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor.

    PubMed

    Díaz, C; Baena, S; Fardeau, M-L; Patel, B K C

    2007-08-01

    Strain ILE-2(T) was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2-4 x 0.1 microm) stained Gram-negative and grew optimally at 42 degrees C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2(T) was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2(T) was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2(T) represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2(T) (=DSM 16581(T) =JCM 14039(T)).

  19. Fluorescence detection in Lab-on-a-chip systems using ultrafast nucleic acid amplification methods

    NASA Astrophysics Data System (ADS)

    Gransee, Rainer; Schneider, Tristan; Elyorgun, Deniz; Strobach, Xenia; Schunck, Tobias; Gatscha, Theresia; Höth, Julian

    2014-05-01

    Today, nucleic amplification plays a key role in modern molecular biology allowing fast and specific laboratory diagnostics testing. An ultrafast microfluidic module (allowing 30 polymeric chain reaction (PCR) cycles in 6 minutes) based on an oscillating fluid plug concept was previously developed[1]. This system allows the amplification of native genomic deoxyribonucleic acid molecules (DNA) even from whole blood samples but still lacks some functionality compared to commercial bench top systems. This work presents the actual status of the renewed and advanced system, permitting the automated optical detection of not only the fluid plug position but also fluorescence detection. The system uses light emitting diodes (LED) for illumination and a low cost CMOS web-camera for optical detection. Image data processing allows the automated process control of the overall system components. Therefore, the system enables the performance of rapid and robust nucleic acid amplifications together with the integration of real time measurement technology. This allows the amplification and simultaneous quantification of the DNA molecules. The possibility to integrate swift nucleic amplification and optical detection into complex sample-to-answer analysis platforms opens up new pathways towards fast and transportable low-cost point of care devices.

  20. WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis.

    PubMed

    Mamat, Uwe; Schmidt, Helgo; Munoz, Eva; Lindner, Buko; Fukase, Koichi; Hanuszkiewicz, Anna; Wu, Jing; Meredith, Timothy C; Woodard, Ronald W; Hilgenfeld, Rolf; Mesters, Jeroen R; Holst, Otto

    2009-08-14

    The hyperthermophile Aquifex aeolicus belongs to the deepest branch in the bacterial genealogy. Although it has long been recognized that this unique Gram-negative bacterium carries genes for different steps of lipopolysaccharide (LPS) formation, data on the LPS itself or detailed knowledge of the LPS pathway beyond the first committed steps of lipid A and 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) synthesis are still lacking. We now report the functional characterization of the thermostable Kdo transferase WaaA from A. aeolicus and provide evidence that the enzyme is monofunctional. Compositional analysis and mass spectrometry of purified A. aeolicus LPS, showing the incorporation of a single Kdo residue as an integral component of the LPS, implicated a monofunctional Kdo transferase in LPS biosynthesis of A. aeolicus. Further, heterologous expression of the A. aeolicus waaA gene in a newly constructed Escherichia coli DeltawaaA suppressor strain resulted in synthesis of lipid IVA precursors substituted with one Kdo sugar. When highly purified WaaA of A. aeolicus was subjected to in vitro assays using mass spectrometry for detection of the reaction products, the enzyme was found to catalyze the transfer of only a single Kdo residue from CMP-Kdo to differently modified lipid A acceptors. The Kdo transferase was capable of utilizing a broad spectrum of acceptor substrates, whereas surface plasmon resonance studies indicated a high selectivity for the donor substrate. PMID:19546212

  1. Construction and application of chromosomally integrated lac-lux gene markers to monitor the fate of a 2,4-dichlorophenoxyacetic acid-degrading bacterium in contaminated soils.

    PubMed

    Masson, L; Comeau, Y; Brousseau, R; Samson, R; Greer, C

    1993-03-01

    A reporter gene system, containing luxAB and lacZY, was constructed and integrated, using Tn7 transposition, into the chromosome of a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading soil bacterium, Pseudomonas cepacia (BRI6001), to monitor its fate when introduced into soil microcosms. The genes were stably maintained in the modified strain of BRI6001, BRI6001L, for more than 300 generations in the absence of selection pressure, and had no apparent effects on biochemical or physiological properties. BRI6001L was easily and rapidly identified as light-emitting blue colonies on 2,4-D medium containing XGal (5-bromo-4-chloro-indolyl-beta-D-galacto-pyranoside) in the presence of n-decanal. Survival rates of BRI6001L introduced into non-sterile soil microcosms were substrate- and contaminant-dependent. The decrease in population density was lowest in a 2,4-D-amended agricultural soil, and highest in a wood-treatment facility soil contaminated with pentachlorophenol, creosote and heavy metals. A viable cell density as low as 10 cfu g-1 was detected in soil microcosms. The biochemical and growth properties of BRI6001 and BRI6001L, and their behaviour when introduced into soil microcosms indicates that BRI6001L can be used as a reliable model to predict the fate of BRI6001 when used to bioaugment contaminated soil. PMID:7506623

  2. WaaA of the Hyperthermophilic Bacterium Aquifex aeolicus Is a Monofunctional 3-Deoxy-d-manno-oct-2-ulosonic Acid Transferase Involved in Lipopolysaccharide Biosynthesis*

    PubMed Central

    Mamat, Uwe; Schmidt, Helgo; Munoz, Eva; Lindner, Buko; Fukase, Koichi; Hanuszkiewicz, Anna; Wu, Jing; Meredith, Timothy C.; Woodard, Ronald W.; Hilgenfeld, Rolf; Mesters, Jeroen R.; Holst, Otto

    2009-01-01

    The hyperthermophile Aquifex aeolicus belongs to the deepest branch in the bacterial genealogy. Although it has long been recognized that this unique Gram-negative bacterium carries genes for different steps of lipopolysaccharide (LPS) formation, data on the LPS itself or detailed knowledge of the LPS pathway beyond the first committed steps of lipid A and 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) synthesis are still lacking. We now report the functional characterization of the thermostable Kdo transferase WaaA from A. aeolicus and provide evidence that the enzyme is monofunctional. Compositional analysis and mass spectrometry of purified A. aeolicus LPS, showing the incorporation of a single Kdo residue as an integral component of the LPS, implicated a monofunctional Kdo transferase in LPS biosynthesis of A. aeolicus. Further, heterologous expression of the A. aeolicus waaA gene in a newly constructed Escherichia coli ΔwaaA suppressor strain resulted in synthesis of lipid IVA precursors substituted with one Kdo sugar. When highly purified WaaA of A. aeolicus was subjected to in vitro assays using mass spectrometry for detection of the reaction products, the enzyme was found to catalyze the transfer of only a single Kdo residue from CMP-Kdo to differently modified lipid A acceptors. The Kdo transferase was capable of utilizing a broad spectrum of acceptor substrates, whereas surface plasmon resonance studies indicated a high selectivity for the donor substrate. PMID:19546212

  3. Aureispira marina gen. nov., sp. nov., a gliding, arachidonic acid-containing bacterium isolated from the southern coastline of Thailand.

    PubMed

    Hosoya, Shoichi; Arunpairojana, Vullapa; Suwannachart, Chatrudee; Kanjana-Opas, Akkharawit; Yokota, Akira

    2006-12-01

    Three strains of gliding bacteria, 24(T), 62 and 71, isolated from a marine sponge and algae from the southern coastline of Thailand, were studied using a polyphasic approach to clarify their taxonomic positions. A phylogenetic analysis based on 16S rRNA gene sequences showed that the three isolates formed a distinct lineage within the family 'Saprospiraceae' of the phylum Bacteroidetes and were related to members of the genus Saprospira. The G+C contents of the isolates were in the range 38-39 mol%. The major respiratory quinone was MK-7. The predominant cellular fatty acids were 20 : 4omega6c (arachidonic acid), 16 : 0 and iso-17 : 0. On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA hybridization data and 16S rRNA gene sequences, the isolates represent a novel species of a novel genus, for which the name Aureispira marina gen. nov., sp. nov. is proposed. The type strain of Aureispira marina is 24(T) (=IAM 15389(T)=TISTR 1719(T)).

  4. Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5).

    PubMed

    Yu, Jiang; Guan, Xuejiao; Liu, Chongxi; Xiang, Wensheng; Yu, Zhenhua; Liu, Xiaobing; Wang, Guanghua

    2016-10-01

    A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)). PMID:27401830

  5. Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations.

    PubMed

    Ohta, Hiroyuki; Hattori, Reiko; Ushiba, Yuuji; Mitsui, Hisayuki; Ito, Masao; Watanabe, Hiroshi; Tonosaki, Akira; Hattori, Tsutomu

    2004-11-01

    The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213(T), was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0.1-0.4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl(2) was added, the cells grew quite normally and aberrant cells were no longer found at 0.1-0.5 % (w/v) NaCl. Chemotaxonomically, strain S213(T) contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C(18 : 1) and C(16 : 0) as major fatty acids, C(14 : 0) 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213(T) belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500(T) (98.3 %), Sphingomonas pruni IFO 15498(T) (98.0 %), Sphingomonas asaccharolytica IFO 15499(T) (97.9 %) and Sphingomonas echinoides DSM 1805(T) (97.8 %). The results of DNA-DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213(T) represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213(T) (=JCM 12082(T)=CIP 107926(T)).

  6. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes.

    PubMed

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bouallagui, Hassib; Hamdi, Moktar; Bonin, Patricia; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-02-01

    A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102(T), was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6-2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102(T) grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102(T) required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102(T) oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102(T) was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102(T) was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes. On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102(T) is proposed to represent a novel species of the genus Aminobacterium, Aminobacterium thunnarium sp. nov. The type strain is OTA 102(T) ( = DSM 27500(T) = JCM 19320(T)).

  7. Influence of nitrogen substrates and substrate C:N ratios on the nitrogen isotopic composition of amino acids from the marine bacterium Vibrio harveyi

    NASA Astrophysics Data System (ADS)

    Maki, K.; Ohkouchi, N.; Chikaraishi, Y.; Fukuda, H.; Miyajima, T.; Nagata, T.

    2014-09-01

    Nitrogen (N) isotopic compositions of individual hydrolysable amino acids (δ15NAAs) in N pools have been increasingly used for trophic position assessment and evaluation of sources and transformation processes of organic matter in marine environments. However, there are limited data about variability in δ15NAAs patterns and how this variability influences marine bacteria, an important mediator of trophic transfer and organic matter transformation. We explored whether marine bacterial δ15NAAs profiles change depending on the type and C:N ratio of the substrate. The δ15NAAs profile of a marine bacterium, Vibrio harveyi, was examined using medium containing either glutamate, alanine or ammonium as the N source [substrate C:N ratios (range, 3 to 20) were adjusted with glucose]. The data were interpreted as a reflection of isotope fractionations associated with de novo synthesis of amino acids by bacteria. Principal component analysis (PCA) using the δ15N offset values normalized to glutamate + glutamine δ15N revealed that δ15NAAs profiles differed depending on the N source and C:N ratio of the substrate. High variability in the δ15N offset of alanine and valine largely explained this bacterial δ15NAAs profile variability. PCA was also conducted using bacterial and phytoplankton (cyanobacteria and eukaryotic algae) δ15NAAs profile data reported previously. The results revealed that bacterial δ15NAAs patterns were distinct from those of phytoplankton. Therefore, the δ15NAAs profile is a useful indicator of biochemical responses of bacteria to changes in substrate conditions, serving as a potentially useful method for identifying organic matter sources in marine environments.

  8. Genome Sequence of a Food Spoilage Lactic Acid Bacterium, Leuconostoc gasicomitatum LMG 18811T, in Association with Specific Spoilage Reactions ▿ †

    PubMed Central

    Johansson, Per; Paulin, Lars; Säde, Elina; Salovuori, Noora; Alatalo, Edward R.; Björkroth, K. Johanna; Auvinen, Petri

    2011-01-01

    Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium causing spoilage of cold-stored, modified-atmosphere-packaged (MAP), nutrient-rich foods. Its role has been verified by challenge tests in gas and slime formation, development of pungent acidic and buttery off odors, and greening of beef. MAP meats have especially been prone to L. gasicomitatum spoilage. In addition, spoilage of vacuum-packaged vegetable sausages and marinated herring has been reported. The genomic sequencing project of L. gasicomitatum LMG 18811T was prompted by a need to understand the growth and spoilage potentials of L. gasicomitatum, to study its phylogeny, and to be able to knock out and overexpress the genes. Comparative genomic analysis was done within L. gasicomitatum LMG 18811T and the three fully assembled Leuconostoc genomes (those of Leuconostoc mesenteroides, Leuconostoc citreum, and Leuconostoc kimchii) available. The genome of L. gasicomitatum LMG 18811T is plasmid-free and contains a 1,954,080-bp circular chromosome with an average GC content of 36.7%. It includes genes for the phosphoketolase pathway and alternative pathways for pyruvate utilization. As interesting features associated with the growth and spoilage potential, LMG 18811T possesses utilization strategies for ribose, external nucleotides, nucleosides, and nucleobases and it has a functional electron transport chain requiring only externally supplied heme for respiration. In respect of the documented specific spoilage reactions, the pathways/genes associated with a buttery off odor, meat greening, and slime formation were recognized. Unexpectedly, genes associated with platelet binding and collagen adhesion were detected, but their functionality and role in food spoilage and processing environment contamination need further study. PMID:21571876

  9. Mineralization of the textile dye acid yellow 42 by solar photoelectro-Fenton in a lab-pilot plant.

    PubMed

    Espinoza, Carolina; Romero, Julio; Villegas, Loreto; Cornejo-Ponce, Lorena; Salazar, Ricardo

    2016-12-01

    A complete mineralization of a textile dye widely used in the Chilean textile industry, acid yellow 42 (AY42), was studied. Degradation was carried out in an aqueous solution containing 100mgL(-1) of total organic carbon (TOC) of dye using the advanced solar photoelectro-Fenton (SPEF) process in a lab-scale pilot plant consisting of a filter press cell, which contains a boron doped diamond electrode and an air diffusion cathode (BDD/air-diffusion cell), coupled with a solar photoreactor for treat 8L of wastewater during 270min of electrolysis. The main results obtained during the degradation of the textile dye were that a complete transformation to CO2 depends directly on the applied current density, the concentration of Fe(2+) used as catalyst, and the solar radiation intensity. The elimination of AY42 and its organic intermediates was due to hydroxyl radicals formed at the anode surface from water oxidation and in the bulk from Fenton's reaction between electrogenerated H2O2 and added Fe(2+). The application of solar radiation in the process (SPEF) yield higher current efficiencies and lower energy consumptions than electro-Fenton (EF) and electro-oxidation with electrogenerated H2O2 (E OH2O2) by the additional production of hydroxyl radicals from the photolysis of Fe(III) hydrated species and the photodecomposition of Fe(III) complexes with organic intermediates. Moreover, some products and intermediates formed during mineralization of dye, such as inorganic ions, carboxylic acids and aromatic compounds were determined by photometric and chromatographic methods. An oxidation pathway is proposed for the complete conversion to CO2.

  10. Mineralization of the textile dye acid yellow 42 by solar photoelectro-Fenton in a lab-pilot plant.

    PubMed

    Espinoza, Carolina; Romero, Julio; Villegas, Loreto; Cornejo-Ponce, Lorena; Salazar, Ricardo

    2016-12-01

    A complete mineralization of a textile dye widely used in the Chilean textile industry, acid yellow 42 (AY42), was studied. Degradation was carried out in an aqueous solution containing 100mgL(-1) of total organic carbon (TOC) of dye using the advanced solar photoelectro-Fenton (SPEF) process in a lab-scale pilot plant consisting of a filter press cell, which contains a boron doped diamond electrode and an air diffusion cathode (BDD/air-diffusion cell), coupled with a solar photoreactor for treat 8L of wastewater during 270min of electrolysis. The main results obtained during the degradation of the textile dye were that a complete transformation to CO2 depends directly on the applied current density, the concentration of Fe(2+) used as catalyst, and the solar radiation intensity. The elimination of AY42 and its organic intermediates was due to hydroxyl radicals formed at the anode surface from water oxidation and in the bulk from Fenton's reaction between electrogenerated H2O2 and added Fe(2+). The application of solar radiation in the process (SPEF) yield higher current efficiencies and lower energy consumptions than electro-Fenton (EF) and electro-oxidation with electrogenerated H2O2 (E OH2O2) by the additional production of hydroxyl radicals from the photolysis of Fe(III) hydrated species and the photodecomposition of Fe(III) complexes with organic intermediates. Moreover, some products and intermediates formed during mineralization of dye, such as inorganic ions, carboxylic acids and aromatic compounds were determined by photometric and chromatographic methods. An oxidation pathway is proposed for the complete conversion to CO2. PMID:26971051

  11. Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes.

    PubMed

    Qiu, Yan-Ling; Hanada, Satoshi; Kamagata, Yoichi; Guo, Rong-Bo; Sekiguchi, Yuji

    2014-06-01

    A mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7(T), was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7(T) were motile, curved rods (0.7-1.0×5.0-8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25-40 °C) and pH 7.0 (pH 6.0-7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864(T), strain 7WAY-8-7(T) could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, L-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called 'PD-UASB-13' in the Greengenes database) in the bacterial phylum Synergistetes, showing less than 90% sequence similarity with closely related described species such as Aminivibrio pyruvatiphilus and Aminobacterium colombiense (89.7% and 88.7%, respectively). The major cellular fatty acids were iso-C(13 : 0), iso-C(15 : 0), anteiso-C(15 : 0), C(18 : 1), C(19 : 1), C(20 : 1) and C(21 : 1). A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7(T) ( = JCM 17151(T

  12. LabDisk with complete reagent prestorage for sample-to-answer nucleic acid based detection of respiratory pathogens verified with influenza A H3N2 virus.

    PubMed

    Stumpf, F; Schwemmer, F; Hutzenlaub, T; Baumann, D; Strohmeier, O; Dingemanns, G; Simons, G; Sager, C; Plobner, L; von Stetten, F; Zengerle, R; Mark, D

    2016-01-01

    Portable point-of-care devices for pathogen detection require easy, minimal and user-friendly handling steps and need to have the same diagnostic performance compared to centralized laboratories. In this work we present a fully automated sample-to-answer detection of influenza A H3N2 virus in a centrifugal LabDisk with complete prestorage of reagents. Thus, the initial supply of the sample remains the only manual handling step. The self-contained LabDisk automates by centrifugal microfluidics all necessary process chains for PCR-based pathogen detection: pathogen lysis, magnetic bead based nucleic acid extraction, aliquoting of the eluate into 8 reaction cavities, and real-time reverse transcription polymerase chain reaction (RT-PCR). Prestored reagents comprise air dried specific primers and fluorescence probes, lyophilized RT-PCR mastermix and stick-packaged liquid reagents for nucleic acid extraction. Employing two different release frequencies for the stick-packaged liquid reagents enables on-demand release of highly wetting extraction buffers, such as sequential release of lysis and binding buffer. Microfluidic process-flow was successful in 54 out of 55 tested LabDisks. We demonstrate successful detection of the respiratory pathogen influenza A H3N2 virus in a total of 18 LabDisks with sample concentrations down to 2.39 × 10(4) viral RNA copies per ml, which is in the range of clinical relevance. Furthermore, we detected RNA bacteriophage MS2 acting as internal control in 3 LabDisks with a sample concentration down to 75 plaque forming units (pfu) per ml. All experiments were applied in a 2 kg portable, laptop controlled point-of-care device. The turnaround time of the complete analysis from sample-to-answer was less than 3.5 hours. PMID:26610171

  13. Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9

    PubMed Central

    2011-01-01

    overexpressed genes involved in amino acid transport and metabolism as well as DNA replication. Conclusions The genome of S. thermophilus LMD-9 is shaped by its domestication in the dairy environment, with gene features that conferred rapid growth in milk, stress response mechanisms and host defense systems that are relevant to its industrial applications. The presence of a unique exopolysaccharide gene cluster and cell surface protein orthologs commonly associated with probiotic functionality revealed potential probiotic applications of LMD-9. PMID:21995282

  14. Genomic features of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid.

    PubMed

    Shimizu-Kadota, Mariko; Kato, Hiroaki; Shiwa, Yuh; Oshima, Kenshiro; Machii, Miki; Araya-Kojima, Tomoko; Zendo, Takeshi; Hattori, Masahira; Sonomoto, Kenji; Yoshikawa, Hirofumi

    2013-01-01

    Lactococcus lactis IO-1 (JCM7638) produces L-lactic acid predominantly when grown at high xylose concentrations, and its utilization is highly desired in the green plastics industry. Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and several restriction-modification systems), and (ii) genes for the synthetic pathways of amino acids and vitamins in the IO-1 genome. In view of the results of this analysis, we consider their meanings in strain IO-1.

  15. Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa.

    PubMed

    Kraatz, Mareike; Wallace, R John; Svensson, Liselott

    2011-04-01

    Strain A2 is an anaerobic, variably Gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of 'Olsenella (basonym Atopobium) oviles'. Three phenotypically similar bacterial strains (lac15, lac16 and lac31(T)) were isolated in concert with Veillonella magna lac18(T) from the mucosal jejunum of a pig. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strains A2, lac15, lac16 and lac31(T) formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella-Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31(T) were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA-DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31(T) represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31(T) ( = CCUG 58604(T)  = DSM 22620(T)  = JCM 16156(T)) as the type strain and A2 ( = CCUG 58212

  16. Effects of acid pH and urea on the spectral properties of the LHII antenna complex from the photosynthetic bacterium Ectothiorhodospira sp.

    PubMed

    Buche, A; Ramirez, J M; Picorel, R

    2000-06-01

    The aim of this study was to investigate the spectral modifications of the LHII antenna complex from the purple bacterium Ectothiorhodospira sp. upon acid pH titration both in the presence and absence of urea. A blue shift specifically and reversibly affected the B850 band around pH 5.5-6.0 suggesting that a histidine residue most probably participated in the in vivo absorption red shifting mechanism. This transition was observed in the presence and absence of urea. Under strong chaotropic conditions, a second transition occurred around pH 2.0, affecting the B800 band irreversibly and the B850 reversibly. Under these conditions a blue shift from 856 to 842 nm occurred and a new and strong circular dichroism signal from the new 842 nm band was observed. Reverting to the original experimental conditions induced a red shift of the B850 band up to 856 nm but the circular dichroism signal remained mostly unaffected. Under the same experimental conditions, i.e. pH 2.1 in the presence of urea, part of the B800 band was irreversibly destroyed with concomitant appearance of a band around 770 nm due to monomeric bacteriochlorophyll from the disrupted B800. Furthermore, Gaussian deconvolution and second derivative of the reverted spectra at pH 8.0 after strong-acid treatment indicated that the new B850 band was actually composed of two bands centered at 843 and 858 nm. We ascribed the 858 nm band to bacteriochlorophylls that underwent reversible spectral shift and the 843 nm band to oligomeric bacteriopheophytin formed from a part of the B850 bacteriochlorophyll. This new oligomer would be responsible for the observed strong and mostly conservative circular dichroism signal. The presence of bacteriopheophytin in the reverted samples was definitively demonstrated by HPLC pigment analysis. The pheophytinization process progressed as the pH decreased below 2.1, and at a certain point (i.e. pH 1.5) all bacteriochlorophylls, including those from the B800 band, became converted to

  17. Effects of the organic acids produced by a lactic acid bacterium in Apis mellifera colony development, Nosema ceranae control and fumagillin efficiency.

    PubMed

    Maggi, Matías; Negri, Pedro; Plischuk, Santiago; Szawarski, Nicolás; De Piano, Fiorella; De Feudis, Leonardo; Eguaras, Martín; Audisio, Carina

    2013-12-27

    The European honey bee Apis mellifera is known to be affected by many parasites and pathogens that have great impact over the insect development. Among parasites affecting bee health, Nosema ceranae is one of the main biotic factors affecting colony populations. As honey bee populations decline, interest in pathogenic and mutualistic relationships between bees and microorganisms has increased. The main goal of the current study was to assess the effect of the oral administration of the metabolites produced by Lactobacillus johnsonii CRL1647 (mainly organic acids) supplemented in syrup, on: (I) N. ceranae sporulation dynamics before and after fumagillin application, and (II) performance of A. mellifera colonies. Different experiments were conducted to evaluate the effects of these bacterial metabolites on bees: in vitro administration revealed no toxic effects against bees. Colonies fed with the lactic acids incremented their beehive population and also the amount of fat bodies per bee. Finally, the organic acids reduced the intensity of the pathogen after the second application of treatment as well as enhanced the fumagillin efficiency. This study provides important information for the development of new control substances against nosemosis.

  18. Effects of the organic acids produced by a lactic acid bacterium in Apis mellifera colony development, Nosema ceranae control and fumagillin efficiency.

    PubMed

    Maggi, Matías; Negri, Pedro; Plischuk, Santiago; Szawarski, Nicolás; De Piano, Fiorella; De Feudis, Leonardo; Eguaras, Martín; Audisio, Carina

    2013-12-27

    The European honey bee Apis mellifera is known to be affected by many parasites and pathogens that have great impact over the insect development. Among parasites affecting bee health, Nosema ceranae is one of the main biotic factors affecting colony populations. As honey bee populations decline, interest in pathogenic and mutualistic relationships between bees and microorganisms has increased. The main goal of the current study was to assess the effect of the oral administration of the metabolites produced by Lactobacillus johnsonii CRL1647 (mainly organic acids) supplemented in syrup, on: (I) N. ceranae sporulation dynamics before and after fumagillin application, and (II) performance of A. mellifera colonies. Different experiments were conducted to evaluate the effects of these bacterial metabolites on bees: in vitro administration revealed no toxic effects against bees. Colonies fed with the lactic acids incremented their beehive population and also the amount of fat bodies per bee. Finally, the organic acids reduced the intensity of the pathogen after the second application of treatment as well as enhanced the fumagillin efficiency. This study provides important information for the development of new control substances against nosemosis. PMID:23978352

  19. 2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94.

    PubMed

    Hayashi, Shohei; Sano, Tomoki; Suyama, Kousuke; Itoh, Kazuhito

    2016-01-01

    Herbicides 2,4-dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading Bradyrhizobium strains possess tfdAα and/or cadABC as degrading genes. It has been reported that root-nodulating bacteria belonging to Bradyrhizobium elkanii also have tfdAα and cadA like genes but lack the ability to degrade these herbicides and that the cadA genes in 2,4-D-degrading and non-degrading Bradyrhizobium are phylogenetically different. In this study, we identified cadRABCK in the genome of a type strain of soybean root-nodulating B. elkanii USDA94 and demonstrated that the strain could degrade the herbicides when cadABCK was forcibly expressed. cadABCK-cloned Escherichia coli also showed the degrading ability. Because co-spiked phenoxyacetic acid (PAA) could induce the degradation of 2,4-D in B. elkanii USDA94, the lack of degrading ability in this strain was supposed to be due to the low inducing potential of the herbicides for the degrading gene cluster. On the other hand, tfdAα from B. elkanii USDA94 showed little potential to degrade the herbicides, but it did for 4-chlorophenoxyacetic acid and PAA. The 2,4-D-degrading ability of the cad cluster and the inducing ability of PAA were confirmed by preparing cadA deletion mutant. This is the first study to demonstrate that the cad cluster in the typical root-nodulating bacterium indeed have the potential to degrade the herbicides, suggesting that degrading genes for anthropogenic compounds could be found in ordinary non-degrading bacteria. PMID:27296963

  20. 2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94.

    PubMed

    Hayashi, Shohei; Sano, Tomoki; Suyama, Kousuke; Itoh, Kazuhito

    2016-01-01

    Herbicides 2,4-dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading Bradyrhizobium strains possess tfdAα and/or cadABC as degrading genes. It has been reported that root-nodulating bacteria belonging to Bradyrhizobium elkanii also have tfdAα and cadA like genes but lack the ability to degrade these herbicides and that the cadA genes in 2,4-D-degrading and non-degrading Bradyrhizobium are phylogenetically different. In this study, we identified cadRABCK in the genome of a type strain of soybean root-nodulating B. elkanii USDA94 and demonstrated that the strain could degrade the herbicides when cadABCK was forcibly expressed. cadABCK-cloned Escherichia coli also showed the degrading ability. Because co-spiked phenoxyacetic acid (PAA) could induce the degradation of 2,4-D in B. elkanii USDA94, the lack of degrading ability in this strain was supposed to be due to the low inducing potential of the herbicides for the degrading gene cluster. On the other hand, tfdAα from B. elkanii USDA94 showed little potential to degrade the herbicides, but it did for 4-chlorophenoxyacetic acid and PAA. The 2,4-D-degrading ability of the cad cluster and the inducing ability of PAA were confirmed by preparing cadA deletion mutant. This is the first study to demonstrate that the cad cluster in the typical root-nodulating bacterium indeed have the potential to degrade the herbicides, suggesting that degrading genes for anthropogenic compounds could be found in ordinary non-degrading bacteria.

  1. Virtual Labs.

    ERIC Educational Resources Information Center

    Russo, Ruth

    1997-01-01

    Discusses the potential of computers in teaching laboratories to spare the lives of animals; however, it is felt that in areas of physiology education, virtual labs are not as desirable a learning experience for advanced students as live animal labs. (Author/AIM)

  2. Isolation and characterization of potential lactic acid bacteria (LAB) from freshwater fish processing wastes for application in fermentative utilisation of fish processing waste.

    PubMed

    R, Jini; Hc, Swapna; Rai, Amit Kumar; R, Vrinda; Pm, Halami; Nm, Sachindra; N, Bhaskar

    2011-10-01

    Proteolytic and/or lipolytic lactic acid bacteria (LAB) were isolated from visceral wastes of different fresh water fishes. LAB count was found to be highest in case of visceral wastes of Mrigal (5.88 log cfu/g) and lowest in that of tilapia (4.22 log cfu/g). Morphological, biochemical and molecular characterization of the selected LAB isolates were carried out. Two isolates FJ1 (E. faecalis NCIM5367) and LP3 (P. acidilactici NCIM5368) showed both proteolytic and lipolytic properties. All the six native isolates selected for characterization showed antagonistic properties against several human pathogens. All the native isolates were sensitive to antibiotics cephalothin and clindamycin; and, resistant to cotrimoxazole and vancomycin. Considering individually, P. acidilactici FM37, P. acidilactici MW2 and E. faecalis FD3 were sensitive to erythromycin. The two strains FJ1 (E. faecalis NCIM 5367) and LP3 (P. acidilactici NCIM 5368) that had both proteolytic and lipolytic properties have the potential for application in fermentative recovery of lipids and proteins from fish processing wastes.

  3. Isolation and characterization of potential lactic acid bacteria (LAB) from freshwater fish processing wastes for application in fermentative utilisation of fish processing waste.

    PubMed

    R, Jini; Hc, Swapna; Rai, Amit Kumar; R, Vrinda; Pm, Halami; Nm, Sachindra; N, Bhaskar

    2011-10-01

    Proteolytic and/or lipolytic lactic acid bacteria (LAB) were isolated from visceral wastes of different fresh water fishes. LAB count was found to be highest in case of visceral wastes of Mrigal (5.88 log cfu/g) and lowest in that of tilapia (4.22 log cfu/g). Morphological, biochemical and molecular characterization of the selected LAB isolates were carried out. Two isolates FJ1 (E. faecalis NCIM5367) and LP3 (P. acidilactici NCIM5368) showed both proteolytic and lipolytic properties. All the six native isolates selected for characterization showed antagonistic properties against several human pathogens. All the native isolates were sensitive to antibiotics cephalothin and clindamycin; and, resistant to cotrimoxazole and vancomycin. Considering individually, P. acidilactici FM37, P. acidilactici MW2 and E. faecalis FD3 were sensitive to erythromycin. The two strains FJ1 (E. faecalis NCIM 5367) and LP3 (P. acidilactici NCIM 5368) that had both proteolytic and lipolytic properties have the potential for application in fermentative recovery of lipids and proteins from fish processing wastes. PMID:24031786

  4. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    SciTech Connect

    Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Loanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C.; Fields, Matthew W.

    2015-03-12

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

  5. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    PubMed Central

    Ramsay, Bradley D.; Hwang, Chiachi; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Ioanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy

    2015-01-01

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction. PMID:25767232

  6. Advanced LabVIEW Labs

    SciTech Connect

    Jones, Eric D.

    1999-06-17

    In the world of computer-based data acquisition and control, the graphical interface program LabVIEW from National Instruments is so ubiquitous that in many ways it has almost become the laboratory standard. To date, there have been approximately fifteen books concerning LabVIEW, but Professor Essick's treatise takes on a completely different tack than all of the previous discussions. In the more standard treatments of the ways and wherefores of LabVIEW such as LabVIEW Graphical Programming: Practical Applications in Instrumentation and Control by Gary W. Johnson (McGraw Hill, NY 1997), the emphasis has been instructing the reader how to program LabVIEW to create a Virtual Instrument (VI) on the computer for interfacing to a particular instruments. LabVIEW is written in "G" a graphical programming language developed by National Instruments. In the past the emphasis has been on training the experimenter to learn "G". Without going into details here, "G" incorporates the usual loops, arithmetic expressions, etc., found in many programming languages, but in an icon (graphical) environment. The net result being that LabVIEW contains all of the standard methods needed for interfacing to instruments, data acquisition, data analysis, graphics, and also methodology to incorporate programs written in other languages into LabVIEW. Historically, according to Professor Essick, he developed a series of experiments for an upper division laboratory course for computer-based instrumentation. His observation was that while many students had the necessary background in computer programming languages, there were students who had virtually no concept about writing a computer program let alone a computer- based interfacing program. Thus the beginnings of a concept for not only teaching computer- based instrumentation techniques, but aiso a method for the beginner to experience writing a com- puter program. Professor Essick saw LabVIEW as the "perfect environment in which to teach

  7. Advanced LabVIEW Labs

    SciTech Connect

    Jones, Eric D.

    1999-06-17

    In the world of computer-based data acquisition and control, the graphical interface program LabVIEW from National Instruments is so ubiquitous that in many ways it has almost become the laboratory standard. To date, there have been approximately fifteen books concerning LabVIEW, but Professor Essick's treatise takes on a completely different tack than all of the previous discussions. In the more standard treatments of the ways and wherefores of LabVIEW such as LabVIEW Graphical Programming: Practical Applications in Instrumentation and Control by Gary W. Johnson (McGraw Hill, NY 1997), the emphasis has been instructing the reader how to program LabVIEW to create a Virtual Instrument (VI) on the computer for interfacing to a particular instruments. LabVIEW is written in G a graphical programming language developed by National Instruments. In the past the emphasis has been on training the experimenter to learn G . Without going into details here, G incorporates the usual loops, arithmetic expressions, etc., found in many programming languages, but in an icon (graphical) environment. The net result being that LabVIEW contains all of the standard methods needed for interfacing to instruments, data acquisition, data analysis, graphics, and also methodology to incorporate programs written in other languages into LabVIEW. Historically, according to Professor Essick, he developed a series of experiments for an upper division laboratory course for computer-based instrumentation. His observation was that while many students had the necessary background in computer programming languages, there were students who had virtually no concept about writing a computer program let alone a computer- based interfacing program. Thus the beginnings of a concept for not only teaching computer- based instrumentation techniques, but aiso a method for the beginner to experience writing a com- puter program. Professor Essick saw LabVIEW as the perfect environment in which to teach computer

  8. Labs: 1987.

    ERIC Educational Resources Information Center

    Igelsrud, Don, Ed.

    1988-01-01

    This article presents a variety of topics discussed in this column and at a biology teachers' workshop concerning the quality and value of lab techniques used for teaching high school biology. Topics included are Drosophila salivary glands, sea urchins, innovations, dyes and networking. (CW)

  9. Reading Lab.

    ERIC Educational Resources Information Center

    Burt, Lorna

    This guide is intended for use in conducting a reading lab for a broad group of workers ranging from nonreaders to persons reading at a fifth-grade level. Presented first is a course overview that includes the following: information on the course's targeted population, student selection process, and demographics; strategies for adult remediation;…

  10. Lab architecture

    NASA Astrophysics Data System (ADS)

    Crease, Robert P.

    2008-04-01

    There are few more dramatic illustrations of the vicissitudes of laboratory architecturethan the contrast between Building 20 at the Massachusetts Institute of Technology (MIT) and its replacement, the Ray and Maria Stata Center. Building 20 was built hurriedly in 1943 as temporary housing for MIT's famous Rad Lab, the site of wartime radar research, and it remained a productive laboratory space for over half a century. A decade ago it was demolished to make way for the Stata Center, an architecturally striking building designed by Frank Gehry to house MIT's computer science and artificial intelligence labs (above). But in 2004 - just two years after the Stata Center officially opened - the building was criticized for being unsuitable for research and became the subject of still ongoing lawsuits alleging design and construction failures.

  11. Production of Indole-3-Acetic Acid via the Indole-3-Acetamide Pathway in the Plant-Beneficial Bacterium Pseudomonas chlororaphis O6 Is Inhibited by ZnO Nanoparticles but Enhanced by CuO Nanoparticles

    PubMed Central

    Zeng, Jia; McLean, Joan E.; Britt, David W.; Zhan, Jixun; Anderson, Anne J.

    2012-01-01

    The beneficial bacterium Pseudomonas chlororaphis O6 produces indole-3-acetic acid (IAA), a plant growth regulator. However, the pathway involved in IAA production in this bacterium has not been reported. In this paper we describe the involvement of the indole-3-acetamide (IAM) pathway in IAA production in P. chlororaphis O6 and the effects of CuO and ZnO nanoparticles (NPs). Sublethal levels of CuO and ZnO NPs differentially affected the levels of IAA secreted in medium containing tryptophan as the precursor. After 15 h of growth, CuO NP-exposed cells had metabolized more tryptophan than the control and ZnO NP-challenged cells. The CuO NP-treated cells produced higher IAA levels than control cultures lacking NPs. In contrast, ZnO NPs inhibited IAA production. Mixing of CuO and ZnO NPs resulted in an intermediate level of IAA production relative to the levels in the separate CuO and ZnO NP treatments. The effect of CuO NPs on IAA levels could be duplicated by ions at the concentrations released from the NPs. However, ion release did not account for the inhibition caused by the ZnO NPs. The mechanism underlying changes in IAA levels cannot be accounted for by effects on transcript accumulation from genes encoding a tryptophan permease or the IAM hydrolase in 15-h cultures. These findings raise the issue of whether sublethal doses of NPs would modify the beneficial effects of association between plants and bacteria. PMID:22210218

  12. Use of Potential Probiotic Lactic Acid Bacteria (LAB) Biofilms for the Control of Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7 Biofilms Formation

    PubMed Central

    Gómez, Natacha C.; Ramiro, Juan M. P.; Quecan, Beatriz X. V.; de Melo Franco, Bernadette D. G.

    2016-01-01

    Use of probiotic biofilms can be an alternative approach for reducing the formation of pathogenic biofilms in food industries. The aims of this study were (i) to evaluate the probiotic properties of bacteriocinogenic (Lactococcus lactis VB69, L. lactis VB94, Lactobacillus sakei MBSa1, and Lactobacillus curvatus MBSa3) and non-bacteriocinogenic (L. lactis 368, Lactobacillus helveticus 354, Lactobacillus casei 40, and Weissela viridescens 113) lactic acid bacteria (LAB) isolated from Brazilian’s foods and (ii) to develop protective biofilms with these strains and test them for exclusion of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella Typhimurium. LAB were tested for survival in acid and bile salt conditions, surface properties, biosurfactant production, β-galactosidase and gelatinase activity, antibiotic resistance and presence of virulence genes. Most strains survived exposure to pH 2 and 4% bile salts. The highest percentages of auto-aggregation were obtained after 24 h of incubation. Sixty-seven percentage auto-aggregation value was observed in W. viridescens 113 and Lactobacillus curvatus MBSa3 exhibited the highest co-aggregation (69% with Listeria monocytogenes and 74.6% with E. coli O157:H7), while the lowest co-aggregation was exhibited by W. viridescens 113 (53.4% with Listeria monocytogenes and 38% with E. coli O157:H7). Tests for hemolytic activity, bacterial cell adherence with xylene, and drop collapse confirmed the biosurfactant-producing ability of most strains. Only one strain (L. lactis 368) produced β-galactosidase. All strains were negative for virulence genes cob, ccf, cylLL, cylLs, cyllM, cylB, cylA and efaAfs and gelatinase production. The antibiotic susceptibility tests indicated that the MIC for ciprofloxacin, clindamycin, gentamicin, kanamycin, and streptomycin did not exceed the epidemiological cut-off suggested by the European Food Safety Authority. Some strains were resistant to one or more antibiotics and

  13. Use of Potential Probiotic Lactic Acid Bacteria (LAB) Biofilms for the Control of Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7 Biofilms Formation.

    PubMed

    Gómez, Natacha C; Ramiro, Juan M P; Quecan, Beatriz X V; de Melo Franco, Bernadette D G

    2016-01-01

    Use of probiotic biofilms can be an alternative approach for reducing the formation of pathogenic biofilms in food industries. The aims of this study were (i) to evaluate the probiotic properties of bacteriocinogenic (Lactococcus lactis VB69, L. lactis VB94, Lactobacillus sakei MBSa1, and Lactobacillus curvatus MBSa3) and non-bacteriocinogenic (L. lactis 368, Lactobacillus helveticus 354, Lactobacillus casei 40, and Weissela viridescens 113) lactic acid bacteria (LAB) isolated from Brazilian's foods and (ii) to develop protective biofilms with these strains and test them for exclusion of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella Typhimurium. LAB were tested for survival in acid and bile salt conditions, surface properties, biosurfactant production, β-galactosidase and gelatinase activity, antibiotic resistance and presence of virulence genes. Most strains survived exposure to pH 2 and 4% bile salts. The highest percentages of auto-aggregation were obtained after 24 h of incubation. Sixty-seven percentage auto-aggregation value was observed in W. viridescens 113 and Lactobacillus curvatus MBSa3 exhibited the highest co-aggregation (69% with Listeria monocytogenes and 74.6% with E. coli O157:H7), while the lowest co-aggregation was exhibited by W. viridescens 113 (53.4% with Listeria monocytogenes and 38% with E. coli O157:H7). Tests for hemolytic activity, bacterial cell adherence with xylene, and drop collapse confirmed the biosurfactant-producing ability of most strains. Only one strain (L. lactis 368) produced β-galactosidase. All strains were negative for virulence genes cob, ccf, cylLL, cylLs, cyllM, cylB, cylA and efaAfs and gelatinase production. The antibiotic susceptibility tests indicated that the MIC for ciprofloxacin, clindamycin, gentamicin, kanamycin, and streptomycin did not exceed the epidemiological cut-off suggested by the European Food Safety Authority. Some strains were resistant to one or more antibiotics and resistance

  14. Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.

    PubMed

    Fu, Yingnan; Wang, Rui; Zhang, Zilian; Jiao, Nianzhi

    2016-01-01

    Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. PMID:27587825

  15. Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea

    PubMed Central

    Fu, Yingnan; Wang, Rui

    2016-01-01

    Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. PMID:27587825

  16. Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.

    PubMed

    Fu, Yingnan; Wang, Rui; Zhang, Zilian; Jiao, Nianzhi

    2016-01-01

    Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained.

  17. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

    PubMed Central

    2013-01-01

    Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of

  18. Draft genome sequence of Sporolactobacillus inulinus strain CASD, an efficient D-lactic acid-producing bacterium with high-concentration lactate tolerance capability.

    PubMed

    Yu, Bo; Su, Fei; Wang, Limin; Xu, Ke; Zhao, Bo; Xu, Ping

    2011-10-01

    Sporolactobacillus inulinus CASD is an efficient D-lactic acid producer with high optical purity. Here we report for the first time the draft genome sequence of S. inulinus (2,930,096 bp). The large number of annotated two-component system genes makes it possible to explore the mechanism of extraordinary lactate tolerance of S. inulinus CASD.

  19. Decisions Shape a Lab (Lab Notes).

    ERIC Educational Resources Information Center

    Porter, Bernajean

    1992-01-01

    Offers questions to guide both initial and ongoing development of a computer writing lab. Discusses ways mobile workstations (consisting of a computer, printer, overhead, and a LCD projection unit) will extend the writing lab. (SR)

  20. Role of two amino acid residues' insertion on thermal stability of thermophilic α-amylase AMY121 from a deep sea bacterium Bacillus sp. SCSIO 15121.

    PubMed

    Li, Lizhen; Yang, Jian; Li, Jie; Long, Lijuan; Xiao, Yunzhu; Tian, Xinpeng; Wang, Fazuo; Zhang, Si

    2015-05-01

    α-Amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) are both important industrial enzymes with high similarity in structure but significant differences in thermostability. The mechanisms underlying this discrepancy are still poorly understood. Here, we investigated the role of two amino acids' insertion on the thermostability of these two group amylases. A newly obtained thermophilic amylase AMY121 was found much closer to BLA in both primary structure and enzymological properties. Two amino acids' insertion widespread among BAA group α-amylases was identified as one of the key factors leading to the thermostability differences, since thermostability of insertion mutants (AMY121-EG and AMY121-AA) from AMY121 significantly decreased, while that of deletion mutant from BAA increased. Moreover, we proposed that conformational disturbance caused by insertion mutation might weaken the calcium-binding affinity and consequently decrease the enzyme thermostability.

  1. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  2. Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production.

    PubMed

    Hu, Xiao-long; Du, Hai; Xu, Yan

    2015-12-01

    Chinese strong-aroma type liquor (CSAL) is a popular distilled alcoholic beverage in China. It is produced by a complex fermentation process that is conducted in pits in the ground. Ethyl caproate is a key flavor compound in CSAL and is thought to originate from caproic acid produced by Clostridia inhabiting the fermentation pit mud. However, the particular species of Clostridium associated with this production are poorly understood and problematic to quantify by culturing. In this study, a total of 28 closest relatives including 15 Clostridia and 8 Bacilli species in pit muds from three CSAL distilleries, were detected by culture-dependent and -independent methods. Among them, Clostridium kluyveri was identified as the main producer of caproic acid. One representative strain C. kluyveri N6 could produce caproic, butyric and octanoic acids and their corresponding ethyl esters, contributing significantly to CSAL flavor. A real time quantitative PCR assay of C. kluyveri in pit muds developed showed that a concentration of 1.79×10(7) 16S rRNA gene copies/g pit mud in LZ-old pit was approximately six times higher than that in HLM and YH pits and sixty times higher than that in LZ-new pit respectively. This method can be used to improve the management of pit mud microbiology and its impact on CSAL quality. PMID:26267890

  3. Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids.

    PubMed

    Takii, Susumu; Hanada, Satoshi; Tamaki, Hideyuki; Ueno, Yutaka; Sekiguchi, Yuji; Ibe, Akihiro; Matsuura, Katsumi

    2007-10-01

    A sulfate-reducing enrichment culture originating from coastal marine sediment of the eutrophic Tokyo Bay, Japan, was successfully established with Casamino acids as a substrate. A thiosulfate reducer, strain C/G2(T), was isolated from the enrichment culture after further enrichment with glutamate. Cells of strain C/G2(T) were non-motile rods (0.6-0.8 microm x 2.2-4.8 microm) and were found singly or in pairs and sometimes in short chains. Spores were not formed. Cells of strain C/G2(T) stained Gram-negatively, despite possessing Gram-positive cell walls. The optimum temperature for growth was 28-30 degrees C, the optimum pH was around 7.8 and the optimum salt concentration was 20-30 g l(-1). Lactate, pyruvate, serine, cysteine, threonine, glutamate, histidine, lysine, arginine, Casamino acids, peptone and yeast extract were fermented as single substrates and no sugar was used as a fermentative substrate. A Stickland reaction was observed with some pairs of amino acids. Fumarate, alanine, proline, phenylalanine, tryptophan, glutamine and aspartate were utilized only in the presence of thiosulfate. Strain C/G2(T) fermented glutamate to H2, CO2, acetate and propionate. Thiosulfate and elemental sulfur were reduced to sulfide. Sulfate, sulfite and nitrate were not utilized as electron acceptors. The growth of strain C/G2(T) on Casamino acids or glutamate was enhanced by co-culturing with Desulfovibrio sp. isolated from the original mixed culture enriched with Casamino acids. The DNA G+C content of strain C/G2(T) was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C/G2(T) formed a distinct cluster with species of the genus Sedimentibacter. The closest relative was Sedimentibacter hydroxybenzoicus (with a gene sequence similarity of 91 %). On the basis of its phylogenetic and phenotypic properties, strain C/G2(T) (=JCM 13356(T)=NBRC 101112(T)=DSM 17477(T)) is proposed as representing a new genus and novel species, Dethiosulfatibacter

  4. Underwater lab

    NASA Astrophysics Data System (ADS)

    Bell, Peter M.

    The University of Southern California's Catalina Marine Science Center (CMSC) has announced plans to build an underwater marine research laboratory near Santa Catalina Island off the California coast. The project, which will take 2 years to build, will be sponsored by the National Oceanic and Atmospheric Administration (NOAA). The laboratory will be similar in concept to the U.S. Navy Sea Lab III, which was canceled some time ago.The project's purpose is to give divers access to a laboratory without having to surface. The project leader, Andrew Pilmanis, of the University of Southern California, stated recently (Industrial Research and Development, July 1983): “By the nature of the work, scientists require a lot of bottom time, and to do it by scuba isn't practical…. The only way to do that is with saturation diving. Once the diver is saturated with inert gas, whether the individual stays a few days or for months, only one decompression is required.” Divers will typically stay in the laboratory for 7-10 days. The laboratory will initially be placed at a depth of 20 m, later to be refloated and located at depths to 37 m.

  5. Modeling the acid-base properties of bacterial surfaces: A combined spectroscopic and potentiometric study of the gram-positive bacterium Bacillus subtilis.

    PubMed

    Leone, Laura; Ferri, Diego; Manfredi, Carla; Persson, Per; Shchukarev, Andrei; Sjöberg, Staffan; Loring, John

    2007-09-15

    In this study, macroscopic and spectroscopic data were combined to develop a surface complexation model that describes the acid-base properties of Bacillus subtilis. The bacteria were freeze-dried and then resuspended in 0.1 M NaCl ionic medium. Macroscopic measurements included potentiometric acid-base titrations and electrophoretic mobility measurements. In addition, ATR-FTIR spectra of wet pastes from suspensions of Bacillus subtilis at different pH values were collected. The least-squares program MAGPIE was used to generate a surface complexation model that takes into account the presence of three acid-base sites on the surface: tripple bond COOH, tripple bond NH+, and tripple bond PO-, which were identified previously by XPS measurements. Both potentiometric titration data and ATR-FTIR spectra were used quantitatively, and electrostatic effects at the charged bacterial surface were accounted for using the constant capacitance model. The model was calculated using two different approaches: in the first one XPS data were used to constrain the ratio of the total concentrations of all three surface sites. The capacitance of the double layer, the total buffer capacity, and the deprotonation constants of the tripple bond NH+, tripple bond POH, and tripple bond COOH species were determined in the fit. A second approach is presented in which the ratio determined by XPS of the total concentrations of tripple bond NH+ to tripple bond PO- sites is relaxed. The total concentration of tripple bond PO- sites was determined in the fit, while the deprotonation constant for tripple bond POH was manually varied until the minimization led to a model which predicted an isoelectric point that resulted in consistency with electrophoretic mobility data. The model explains well the buffering capacity of Bacillus subtilis suspensions in a wide pH range (between pH=3 and pH=9) which is of considerable environmental interest. In particular, a similar quantitative use of the IR data

  6. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993.

    PubMed

    Belova, Svetlana E; Kulichevskaya, Irina S; Bodelier, Paul L E; Dedysh, Svetlana N

    2013-03-01

    A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T)  = VKM B-2545(T)) is the type strain. PMID:22707532

  7. Acid-base titrations of functional groups on the surface of the thermophilic bacterium Anoxybacillus flavithermus: comparing a chemical equilibrium model with ATR-IR spectroscopic data.

    PubMed

    Heinrich, Hannah T M; Bremer, Phil J; Daughney, Christopher J; McQuillan, A James

    2007-02-27

    Acid-base functional groups at the surface of Anoxybacillus flavithermus (AF) were assigned from the modeling of batch titration data of bacterial suspensions and compared with those determined from in situ infrared spectroscopic titration analysis. The computer program FITMOD was used to generate a two-site Donnan model (site 1: pKa = 3.26, wet concn = 2.46 x 10(-4) mol g(-1); site 2: pKa = 6.12, wet concn = 6.55 x 10(-5) mol g(-1)), which was able to describe data for whole exponential phase cells from both batch acid-base titrations at 0.01 M ionic strength and electrophoretic mobility measurements over a range of different pH values and ionic strengths. In agreement with information on the composition of bacterial cell walls and a considerable body of modeling literature, site 1 of the model was assigned to carboxyl groups, and site 2 was assigned to amino groups. pH difference IR spectra acquired by in situ attenuated total reflection infrared (ATR-IR) spectroscopy confirmed the presence of carboxyl groups. The spectra appear to show a carboxyl pKa in the 3.3-4.0 range. Further peaks were assigned to phosphodiester groups, which deprotonated at slightly lower pH. The presence of amino groups could not be confirmed or discounted by IR spectroscopy, but a positively charged group corresponding to site 2 was implicated by electrophoretic mobility data. Carboxyl group speciation over a pH range of 2.3-10.3 at two different ionic strengths was further compared to modeling predictions. While model predictions were strongly influenced by the ionic strength change, pH difference IR data showed no significant change. This meant that modeling predictions agreed reasonably well with the IR data for 0.5 M ionic strength but not for 0.01 M ionic strength.

  8. Fe(III)-enhanced anaerobic transformation of 2,4-dichlorophenoxyacetic acid by an iron-reducing bacterium Comamonas koreensis CY01.

    PubMed

    Wu, Chun-Yuan; Zhuang, Li; Zhou, Shun-Gui; Li, Fang-Bai; Li, Xiao-Min

    2010-01-01

    This work studied the ability of Comamonas koreensis CY01 to reduce Fe(III) (hydr)oxides by coupling the oxidation of electron donors and the enhanced biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the presence of Fe(III) (hydr)oxides. The experimental results suggested that strain CY01 can utilize ferrihydrite, goethite, lepidocrocite or hematite as the terminal electron acceptor and citrate, glycerol, glucose or sucrose as the electron donor. Strain CY01 could transform 2,4-D to 4-chlorophenol through reductive side-chain removal and dechlorination. Under the anaerobic conditions, Fe(III) reduction and 2,4-D biodegradation by strain CY01 occurred simultaneously. The presence of Fe(III) (hydr)oxides would significantly enhance 2,4-D biodegradation, probably due to the fact that the reactive mineral-bound Fe(II) species generated from Fe(III) reduction can abiotically reduce 2,4-D. This is the first report of a strain of C. koreensis capable of reducing Fe(III) (hydr)oxides and 2,4-D, which extends the diversity of iron-reducing bacteria associated with dechlorination.

  9. A tightly bound quinone functions in the ubiquinone reaction sites of quinoprotein alcohol dehydrogenase of an acetic acid bacterium, Gluconobacter suboxydans.

    PubMed

    Matsushita, Kazunobu; Kobayashi, Yoshiki; Mizuguchi, Mitsuhiro; Toyama, Hirohide; Adachi, Osao; Sakamoto, Kimitoshi; Miyoshi, Hideto

    2008-10-01

    Quinoprotein alcohol dehydrogenase (ADH) of acetic acid bacteria is a membrane-bound enzyme that functions as the primary dehydrogenase in the ethanol oxidase respiratory chain. It consists of three subunits and has a pyrroloquinoline quinone (PQQ) in the active site and four heme c moieties as electron transfer mediators. Of these, three heme c sites and a further site have been found to be involved in ubiquinone (Q) reduction and ubiquinol (QH2) oxidation respectively (Matsushita et al., Biochim. Biophys. Acta, 1409, 154-164 (1999)). In this study, it was found that ADH solubilized and purified with dodecyl maltoside, but not with Triton X-100, had a tightly bound Q, and thus two different ADHs, one having the tightly bound Q (Q-bound ADH) and Q-free ADH, could be obtained. The Q-binding sites of both the ADHs were characterized using specific inhibitors, a substituted phenol PC16 (a Q analog inhibitor) and antimycin A. Based on the inhibition kinetics of Q2 reductase and ubiquinol-2 (Q2H2) oxidase activities, it was suggested that there are one and two PC16-binding sites in Q-bound ADH and Q-free ADH respectively. On the other hand, with antimycin A, only one binding site was found for Q2 reductase and Q2H2 oxidase activities, irrespective of the presence of bound Q. These results suggest that ADH has a high-affinity Q binding site (QH) besides low-affinity Q reduction and QH2 oxidation sites, and that the bound Q in the QH site is involved in the electron transfer between heme c moieties and bulk Q or QH2 in the low-affinity sites.

  10. Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli.

    PubMed

    Mayer, C; Romero, M; Muras, A; Otero, A

    2015-11-01

    Acyl homoserine lactones (AHLs) are produced by many Gram-negative bacteria to coordinate gene expression in cellular density dependent mechanisms known as quorum sensing (QS). Since the disruption of the communication systems significantly reduces virulence, the inhibition of quorumsensing processes or quorum quenching (QQ) represents an interesting anti-pathogenic strategy to control bacterial infections. Escherichia coli does not produce AHLs but possesses an orphan AHL receptor, SdiA, which is thought to be able to sense the QS signals produced by other bacteria and controls important traits as the expression of glutamate-dependent acid resistance mechanism, therefore constituting a putative target for QQ. A novel AHL-lactonase, named Aii20J, has been identified, cloned and over expressed from the marine bacterium Tenacibaculum sp. strain 20 J presenting a wide-spectrum QQ activity. The enzyme, belonging to the metallo-β-lactamase family, shares less than 31 % identity with the lactonase AiiA from Bacillus spp. Aii20J presents a much higher specific activity than the Bacillus enzyme, maintains its activity after incubation at 100 ºC for 10 minutes, is resistant to protease K and α-chymotrypsin, and is unaffected by wide ranges of pH. The addition of Aii20J (20 μg/mL) to cultures of E. coli K-12 to which OC6-HSL was added resulted in a significant reduction in cell viability in comparison with the acidresistant cultures derived from the presence of the signal. Results confirm the interaction between AHLs and SdiA in E. coli for the expression of virulence-related genes and reveal the potential use of Aii20J as anti-virulence strategy against important bacterial pathogens and in other biotechnological applications.

  11. Isolation, Characterization, and U(VI)-Reducing Potential of a Facultatively Anaerobic, Acid-Resistant Bacterium from Low-pH, Nitrate- and U(VI)-Contaminated Subsurface Sediment and Description of Salmonella subterranea sp. nov.

    PubMed Central

    Shelobolina, Evgenya S.; Sullivan, Sara A.; O'Neill, Kathleen R.; Nevin, Kelly P.; Lovley, Derek R.

    2004-01-01

    A facultatively anaerobic, acid-resistant bacterium, designated strain FRCl, was isolated from a low-pH, nitrate- and U(VI)-contaminated subsurface sediment at site FW-024 at the Natural and Accelerated Bioremediation Research Field Research Center in Oak Ridge, Tenn. Strain FRCl was enriched at pH 4.5 in minimal medium with nitrate as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Clones with 16S ribosomal DNA (rDNA) sequences identical to the sequence of strain FRCl were also detected in a U(VI)-reducing enrichment culture derived from the same sediment. Cells of strain FRCl were gram-negative motile regular rods 2.0 to 3.4 μm long and 0.7 to 0.9 μm in diameter. Strain FRCl was positive for indole production, by the methyl red test, and for ornithine decarboxylase; it was negative by the Voges-Proskauer test (for acetylmethylcarbinol production), for urea hydrolysis, for arginine dihydrolase, for lysine decarboxylase, for phenylalanine deaminase, for H2S production, and for gelatin hydrolysis. Strain FRCl was capable of using O2, NO3−, S2O32−, fumarate, and malate as terminal electron acceptors and of reducing U(VI) in the cell suspension. Analysis of the 16S rDNA sequence of the isolate indicated that this strain was 96.4% similar to Salmonella bongori and 96.3% similar to Enterobacter cloacae. Physiological and phylogenetic analyses suggested that strain FRCl belongs to the genus Salmonella and represents a new species, Salmonella subterranea sp. nov. PMID:15128557

  12. Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli.

    PubMed

    Mayer, C; Romero, M; Muras, A; Otero, A

    2015-11-01

    Acyl homoserine lactones (AHLs) are produced by many Gram-negative bacteria to coordinate gene expression in cellular density dependent mechanisms known as quorum sensing (QS). Since the disruption of the communication systems significantly reduces virulence, the inhibition of quorumsensing processes or quorum quenching (QQ) represents an interesting anti-pathogenic strategy to control bacterial infections. Escherichia coli does not produce AHLs but possesses an orphan AHL receptor, SdiA, which is thought to be able to sense the QS signals produced by other bacteria and controls important traits as the expression of glutamate-dependent acid resistance mechanism, therefore constituting a putative target for QQ. A novel AHL-lactonase, named Aii20J, has been identified, cloned and over expressed from the marine bacterium Tenacibaculum sp. strain 20 J presenting a wide-spectrum QQ activity. The enzyme, belonging to the metallo-β-lactamase family, shares less than 31 % identity with the lactonase AiiA from Bacillus spp. Aii20J presents a much higher specific activity than the Bacillus enzyme, maintains its activity after incubation at 100 ºC for 10 minutes, is resistant to protease K and α-chymotrypsin, and is unaffected by wide ranges of pH. The addition of Aii20J (20 μg/mL) to cultures of E. coli K-12 to which OC6-HSL was added resulted in a significant reduction in cell viability in comparison with the acidresistant cultures derived from the presence of the signal. Results confirm the interaction between AHLs and SdiA in E. coli for the expression of virulence-related genes and reveal the potential use of Aii20J as anti-virulence strategy against important bacterial pathogens and in other biotechnological applications. PMID:26092757

  13. The intestinal LABs.

    PubMed

    Vaughan, Elaine E; de Vries, Maaike C; Zoetendal, Erwin G; Ben-Amor, Kaouther; Akkermans, Antoon D L; de Vos, Willem M

    2002-08-01

    The complete gastrointestinal (GI) tract of humans is colonised soon after birth by a myriad of microbial species with a characteristic distribution depending on the location. GI-tract ecology has been experiencing a revival due to the development of molecular techniques, especially those based on 16S RNA (zRNA) genes. A richer ecosystem than previously imagined of novel species is being discovered that is significantly influenced by our host genotype. Special attention has been focused on the bifidobacteria and the lactic acid bacterial (LAB) populations, both those that are naturally present within this complex ecosystem and those that are ingested as probiotics in functional foods. Overall this interest stems from a increasing awareness of interplay between microflora, diet and the health of the host, and is further stimulated by an increasing incidence of gastrointestinal illnesses, and atopy. Substantial documentation of benefits to host health has especially distinguished the LAB for multidisciplinary research aimed to determine the molecular mechanisms involved. Recent advances in molecular technologies, including high-throughput genomics-based approaches, can significantly advance our understanding of the microbe--diet--host interactions and offer valuable information for design and application of health-targeted microbes. PMID:12369201

  14. Deciphering Your Lab Report

    MedlinePlus

    ... what a lab report may look like. (Note: Pathology reports, such as for a biopsy , will look ... lab report. For some examples of what a pathology report may look like, see The Doctor’s Doctor: ...

  15. Virtual Reality Lab Assistant

    NASA Technical Reports Server (NTRS)

    Saha, Hrishikesh; Palmer, Timothy A.

    1996-01-01

    Virtual Reality Lab Assistant (VRLA) demonstration model is aligned for engineering and material science experiments to be performed by undergraduate and graduate students in the course as a pre-lab simulation experience. This will help students to get a preview of how to use the lab equipment and run experiments without using the lab hardware/software equipment. The quality of the time available for laboratory experiments can be significantly improved through the use of virtual reality technology.

  16. Single Bacterium Detection Using Sers

    NASA Astrophysics Data System (ADS)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  17. Reflections on Three Corporate Research Labs: Bell Labs, HP Labs, Agilent Labs

    NASA Astrophysics Data System (ADS)

    Hollenhorst, James

    2008-03-01

    This will be a personal reflection on corporate life and physics-based research in three industrial research labs over three decades, Bell Labs during the 1980's, HP Labs during the 1990's, and Agilent Labs during the 2000's. These were times of great change in all three companies. I'll point out some of the similarities and differences in corporate cultures and how this impacted the research and development activities. Along the way I'll mention some of the great products that resulted from physics-based R&D.

  18. Computer Lab Configuration.

    ERIC Educational Resources Information Center

    Wodarz, Nan

    2003-01-01

    Describes the layout and elements of an effective school computer lab. Includes configuration, storage spaces, cabling and electrical requirements, lighting, furniture, and computer hardware and peripherals. (PKP)

  19. School Science Labs

    ERIC Educational Resources Information Center

    Schachter, Ron

    2008-01-01

    This article talks about the declining state of many school science laboratories. The author describes how school districts are renovating their science labs to improve student learning. The author also offers tips from those who have already renovated their school science labs.

  20. PRIME Lab Radiocarbon Measurements

    NASA Astrophysics Data System (ADS)

    Hillegonds, D. J.; Mueller, K. A.; Ma, X.; Lipschutz, M. E.

    1996-03-01

    The Purdue Rare Isotope Measurement Laboratory (PRIME Lab) is one of three NSF national facilities for accelerator mass spectrometry (AMS), and is the only one capable of determining six cosmogenic radionuclides: 10Be, 14C, 26Al, 36Cl, 41Ca, and 129I. This abstract describes the current status of the radiocarbon analysis program at PRIME Lab.

  1. Making Real Virtual Labs

    ERIC Educational Resources Information Center

    Keller, Harry E.; Keller, Edward E.

    2005-01-01

    Francis Bacon began defining scientific methodology in the early 17th century, and secondary school science classes began to implement science labs in the mid-19th century. By the early 20th century, leading educators were suggesting that science labs be used to develop scientific thinking habits in young students, and at the beginning of the 21st…

  2. Physics Labs with Flavor

    ERIC Educational Resources Information Center

    Agrest, Mikhail M.

    2009-01-01

    This paper describes my attempts to look deeper into the so-called "shoot for your grade" labs, started in the '90s, when I began applying my teaching experience in Russia to introductory physics labs at the College of Charleston and other higher education institutions in South Carolina. The term "shoot for your grade" became popular among…

  3. LabSkills

    ERIC Educational Resources Information Center

    O'Brien, Nick

    2010-01-01

    This article describes LabSkills, a revolutionary teaching tool to improve practical science in schools. LabSkills offers the chance to help improve the exposure that the average Key Stage 5 (age 16-19) student has to practical work. This is a huge area for development being highlighted by universities who are seeing a worryingly growing trend in…

  4. The Lab School.

    ERIC Educational Resources Information Center

    Cardellichio, Thomas

    1997-01-01

    To circumvent typical public schooling restrictions, an upstate New York middle school established a Lab School that functions outside the regular program. Lab School aims to provide practice in intellectual inquiry, delve into complex, demanding topics, create an interdisciplinary, problem-oriented curriculum, and experiment with assessment…

  5. NOT Another Lab Report

    ERIC Educational Resources Information Center

    Ende, Fred

    2012-01-01

    Ask students to name the aspects of science class they enjoy most, and working on labs will undoubtedly be mentioned. What often won't be included, however, is writing lab reports. For many students, the process of exploration and data collection is paramount, while the explanation and analysis of findings often takes a backseat. After all, if…

  6. A Museum Learning Lab

    ERIC Educational Resources Information Center

    Vandiver, Kathleen M.; Bijur, Jon Markowitz; Epstein, Ari W.; Rosenthal, Beryl; Stidsen, Don

    2008-01-01

    The "Learning Lab: The Cell" exhibit was developed by the Massachusetts Institute of Technology (MIT) Museum and the MIT Center for Environmental Health Sciences (CEHS). Specially designed for middle and high school students, the Learning Lab provides museum visitors of all ages with fascinating insights into how our living cells work. The…

  7. Lactobionic and cellobionic acid production profiles of the resting cells of acetic acid bacteria.

    PubMed

    Kiryu, Takaaki; Kiso, Taro; Nakano, Hirofumi; Murakami, Hiromi

    2015-01-01

    Lactobionic acid was produced by acetic acid bacteria to oxidize lactose. Gluconobacter spp. and Gluconacetobacter spp. showed higher lactose-oxidizing activities than Acetobacter spp. Gluconobacter frateurii NBRC3285 produced the highest amount of lactobionic acid per cell, among the strains tested. This bacterium assimilated neither lactose nor lactobionic acid. At high lactose concentration (30%), resting cells of the bacterium showed sufficient oxidizing activity for efficient production of lactobionic acid. These properties may contribute to industrial production of lactobionic acid by the bacterium. The bacterium showed higher oxidizing activity on cellobiose than that on lactose and produced cellobionic acid. PMID:25965080

  8. Jefferson Lab Virtual Tour

    SciTech Connect

    2013-07-13

    Take a virtual tour of the campus of Thomas Jefferson National Accelerator Facility. You can see inside our two accelerators, three experimental areas, accelerator component fabrication and testing areas, high-performance computing areas and laser labs.

  9. GeneLab

    NASA Technical Reports Server (NTRS)

    Berrios, Daniel C.; Thompson, Terri G.

    2015-01-01

    NASA GeneLab is expected to capture and distribute omics data and experimental and process conditions most relevant to research community in their statistical and theoretical analysis of NASAs omics data.

  10. Jefferson Lab Virtual Tour

    ScienceCinema

    None

    2016-07-12

    Take a virtual tour of the campus of Thomas Jefferson National Accelerator Facility. You can see inside our two accelerators, three experimental areas, accelerator component fabrication and testing areas, high-performance computing areas and laser labs.

  11. Virtual labs: a substitute for traditional labs?

    PubMed

    Scheckler, Rebecca K

    2003-01-01

    Current technologies give us the ability to enhance and replace developmental biology classes with computer-based resources, often called virtual labs. In the process of using these resources, teachers may be tempted to neglect the simpler technologies and lab bench activities, which can be labor intensive. In this paper, I take a critical look at the role of computer-based materials for the teaching of developmental biology in order to aid teachers in assessing their value. I conclude that while digital tools have value, they should not replace all of the traditional laboratory activities. Clearly, both computer-enhanced activities and traditional labs must be included in laboratory exercises. Reliance on only one or the other is inappropriate. In order to determine when it is appropriate to use a particular educational tool, the goals of the course and the needs of biology students for an education that gives them a realistic and engaged view of biology must be understood. In this paper, I dispel some of the myths of computer tools and give specific guidelines for assessing their usage, taking into account the special needs of a developmental biology class and the difficulties of observing all the developmental stages of subject organisms in the timescale of class meetings. PMID:12705675

  12. Lab 6 winding facility

    SciTech Connect

    Guerra, J.; Hansen, S.; Mangene, C.

    1983-02-02

    This note describes the winding machine installed by the facility support group at lab 6 in the Fermilab village. It is available for use by outside users and groups within the lab. The machine can wind wire planes whose longest dimension is less than 10 feet. The Wire spacing range has an upper practical limit of about 5mm. Spacing beyond this requires a very long index time and therefore slows down the winding speed prohibitively.

  13. Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium

    PubMed Central

    Little, C. Deane; Palumbo, Anthony V.; Herbes, Stephen E.; Lidstrom, Mary E.; Tyndall, Richard L.; Gilmer, Penny J.

    1988-01-01

    Trichloroethylene (TCE), a common groundwater contaminant, is a suspected carcinogen that is highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a type I methanotrophic bacterium, degraded TCE if grown on methane or methanol, producing CO2 and water-soluble products. Gas chromatography and 14C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a cometabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. It is proposed that TCE biodegradation by methanotrophs occurs by formation of TCE epoxide, which breaks down spontaneously in water to form dichloroacetic and glyoxylic acids and one-carbon products. Images PMID:16347616

  14. LCOGT Imaging Lab

    NASA Astrophysics Data System (ADS)

    Tufts, Joseph R.; Lobdill, Rich; Haldeman, Benjamin J.; Haynes, Rachel; Hawkins, Eric; Burleson, Ben; Jahng, David

    2008-07-01

    The Las Cumbres Observatory Global Telescope Network (LCOGT) is an ambitious project to build and operate, within 5 years, a worldwide robotic network of 50 0.4, 1, and 2 m telescopes sharing identical instrumentation and optimized for precision photometry of time-varying sources. The telescopes, instrumentation, and software are all developed in house with two 2 m telescopes already installed. The LCOGT Imaging Lab is responsible for assembly and characterization of the network's cameras and instrumentation. In addition to a fully equipped CNC machine shop, two electronics labs, and a future optics lab, the Imaging Lab is designed from the ground up to be a superb environment for bare detectors, precision filters, and assembled instruments. At the heart of the lab is an ISO class 5 cleanroom with full ionization. Surrounding this, the class 7 main lab houses equipment for detector characterization including QE and CTE, and equipment for measuring transmission and reflection of optics. Although the first science cameras installed, two TEC cooled e2v 42-40 deep depletion based units and two CryoTiger cooled Fairchild Imaging CCD486-BI based units, are from outside manufacturers, their 18 position filter wheels and the remainder of the network's science cameras, controllers, and instrumentation will be built in house. Currently being designed, the first generation LCOGT cameras for the network's 1 m telescopes use existing CCD486-BI devices and an in-house controller. Additionally, the controller uses digital signal processing to optimize readout noise vs. speed, and all instrumentation uses embedded microprocessors for communication over ethernet.

  15. SenseLab

    PubMed Central

    Crasto, Chiquito J.; Marenco, Luis N.; Liu, Nian; Morse, Thomas M.; Cheung, Kei-Hoi; Lai, Peter C.; Bahl, Gautam; Masiar, Peter; Lam, Hugo Y.K.; Lim, Ernest; Chen, Huajin; Nadkarni, Prakash; Migliore, Michele; Miller, Perry L.; Shepherd, Gordon M.

    2009-01-01

    This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab’s unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources. PMID:17510162

  16. The NOAO Data Lab

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, M.; Olsen, K.; Stobie, E. B.; Mighell, K. J.; Norris, P.

    2015-09-01

    We describe the NOAO Data Lab to help community users take advantage of current large surveys and prepare them even larger surveys in the era of LSST. The Data Lab will allow users to efficiently utilize catalogs of billions of objects, combine traditional telescope image and spectral data with external archives, share custom results with collaborators, publish data products to other users, and experiment with analysis toolkits. Specific science cases will be used to develop a prototype framework and tools, allowing us to work directly with scientists from survey teams to ensure development remains focused on scientifically productive tasks.

  17. Classification of the Legionnaires' disease bacterium: Legionella pneumophila, genus novum, species nova, of the family Legionellaceae, familia nova.

    PubMed

    Brenner, D J; Steigerwalt, A G; McDade, J E

    1979-04-01

    Deoxyribonucleic acid (DNA) relatedness was used to classify strains of the Legionnaires' disease (LD) bacterium. These DNA comparisons showed that all strains of the LD bacterium were members of the same species. Included were strains isolated from the environment and strains with three different O-antigens. The DNA from the LD bacterium was not significantly related to DNA from any other group of bacteria that was tested. Biochemical data, growth characteristics, and guanine-plus-cytosine ratios were used to rule out the possibility that the LD bacterium was significantly related to members of genera whose DNA was not tested. In view of these data we propose that the LD bacterium be named Legionella pneumophila species nova, the type species of Legionella, genus novum. The type strain of L. pneumophila is Philadelphia 1.

  18. Ultrasound-assisted hydrolysis and chemical derivatization combined to lab-on-valve solid-phase extraction for the determination of sialic acids in human biofluids by μ-liquid chromatography-laser induced fluorescence.

    PubMed

    Orozco-Solano, M I; Priego-Capote, F; Luque de Castro, M D

    2013-03-01

    The determination of sialic acids (SIAs) has recently gained interest because of their potential role as markers of inflammatory disorders or chronic diseases. Hydrolysis of conjugated derivatives, solid-phase extraction (SPE) and derivatization steps constitute sample preparation prior to insertion of the analytical sample into a μ-liquid chromatograph-laser induced fluorescence (μ-LC-LIF) detector in the present method for the determination of two representative SIAs of human metabolism. Ultrasound-accelerated hydrolysis released free SIAs, which were efficiently concentrated in a dynamic manner using a lab-on-valve (LOV) module that allows automation of SPE for preconcentration and cleanup. This step was on-line connected with DMB-labeling of SIAs (derivatization), which was shortened from 180 min required with the conventional heating method to 20min with ultrasound assistance. Individual separation of the target analytes was achieved within 20 min by μ-LC, while LIF detection endowed the overall method with high sensitivity. The LODs and LOQs provided by the method ranged 0.1-0.8 ng mL(-1) and 0.4-1.0 ng mL(-1) (between 0.1-0.8 pg and 0.4-1.0 pg expressed as on-column amount), respectively. High efficiency for interferents removal by SPE enabled the application of the method to four different biofluids-serum, urine, saliva and breast milk-for the determination of the target metabolites.

  19. Ultrasound-assisted hydrolysis and chemical derivatization combined to lab-on-valve solid-phase extraction for the determination of sialic acids in human biofluids by μ-liquid chromatography-laser induced fluorescence.

    PubMed

    Orozco-Solano, M I; Priego-Capote, F; Luque de Castro, M D

    2013-03-01

    The determination of sialic acids (SIAs) has recently gained interest because of their potential role as markers of inflammatory disorders or chronic diseases. Hydrolysis of conjugated derivatives, solid-phase extraction (SPE) and derivatization steps constitute sample preparation prior to insertion of the analytical sample into a μ-liquid chromatograph-laser induced fluorescence (μ-LC-LIF) detector in the present method for the determination of two representative SIAs of human metabolism. Ultrasound-accelerated hydrolysis released free SIAs, which were efficiently concentrated in a dynamic manner using a lab-on-valve (LOV) module that allows automation of SPE for preconcentration and cleanup. This step was on-line connected with DMB-labeling of SIAs (derivatization), which was shortened from 180 min required with the conventional heating method to 20min with ultrasound assistance. Individual separation of the target analytes was achieved within 20 min by μ-LC, while LIF detection endowed the overall method with high sensitivity. The LODs and LOQs provided by the method ranged 0.1-0.8 ng mL(-1) and 0.4-1.0 ng mL(-1) (between 0.1-0.8 pg and 0.4-1.0 pg expressed as on-column amount), respectively. High efficiency for interferents removal by SPE enabled the application of the method to four different biofluids-serum, urine, saliva and breast milk-for the determination of the target metabolites. PMID:23427802

  20. Lab with Dad

    ERIC Educational Resources Information Center

    Havers, Brenda; Delmotte, Karen

    2012-01-01

    Family science nights are fantastic, but planning one can be overwhelming, especially when one considers the already overloaded schedule of a classroom teacher. To overcome this challenge, the authors--colleagues with a mutual love of science--developed a much simpler annual event called "Lab With Dad." The purpose was for one target age group of…

  1. Writing Better Lab Reports

    ERIC Educational Resources Information Center

    Porter, Rhiannon; Guarienti, Kristy; Brydon, Barbara; Robb, Jeanine; Royston, Ann; Painter, Heidi; Sutherland, Alex; Passmore, Cynthia; Smith, Martin H.

    2010-01-01

    As science teachers at a suburban California high school, the authors were concerned about the lab report conclusions written by their upper-level chemistry, biology, and ecology students--which were consistently of poor quality. Their work lacked inferences derived from data and support for their concluding statements. Working as part of a…

  2. A Big Bang Lab

    ERIC Educational Resources Information Center

    Scheider, Walter

    2005-01-01

    The February 2005 issue of The Science Teacher (TST) reminded everyone that by learning how scientists study stars, students gain an understanding of how science measures things that can not be set up in lab, either because they are too big, too far away, or happened in a very distant past. The authors of "How Far are the Stars?" show how the…

  3. Inside Linden Lab

    ERIC Educational Resources Information Center

    Atkinson, Tom

    2008-01-01

    In this article, the author provides an overview of Second Life[trademark], or simply SL, which was developed at Linden Lab, a San Francisco-based corporation. SL is an online society within a threee-dimensional virtual world entirely built and owned by its residents, where they can explore, build, socialize and participate in their own economy.…

  4. Serial Dilution Simulation Lab

    ERIC Educational Resources Information Center

    Keler, Cynthia; Balutis, Tabitha; Bergen, Kim; Laudenslager, Bryanna; Rubino, Deanna

    2010-01-01

    Serial dilution is often a difficult concept for students to understand. In this short dry lab exercise, students perform serial dilutions using seed beads. This exercise helps students gain skill at performing dilutions without using reagents, bacterial cultures, or viral cultures, while being able to visualize the process.

  5. The Crime Lab Project.

    ERIC Educational Resources Information Center

    Hein, Annamae J.

    2003-01-01

    Describes the Crime Lab Project, which takes an economical, hands-on, interdisciplinary approach to studying the career of forensics in the middle or high school classroom. Includes step-by-step student requirements for the investigative procedure, a sample evidence request form, and an assessment rubric. (KHR)

  6. Elemental Chem Lab

    ERIC Educational Resources Information Center

    Franco Mariscal, Antonio Joaquin

    2008-01-01

    This educative material uses the symbols of 45 elements to spell the names of 32 types of laboratory equipment usually found in chemical labs. This teaching material has been divided into three puzzles according to the type of the laboratory equipment: (i) glassware as reaction vessels or containers; (ii) glassware for measuring, addition or…

  7. Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care

    PubMed Central

    2016-01-01

    We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone’s motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging. PMID:26898247

  8. Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care.

    PubMed

    Priye, Aashish; Wong, Season; Bi, Yuanpeng; Carpio, Miguel; Chang, Jamison; Coen, Mauricio; Cope, Danielle; Harris, Jacob; Johnson, James; Keller, Alexandra; Lim, Richard; Lu, Stanley; Millard, Alex; Pangelinan, Adriano; Patel, Neal; Smith, Luke; Chan, Kamfai; Ugaz, Victor M

    2016-05-01

    We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

  9. Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care.

    PubMed

    Priye, Aashish; Wong, Season; Bi, Yuanpeng; Carpio, Miguel; Chang, Jamison; Coen, Mauricio; Cope, Danielle; Harris, Jacob; Johnson, James; Keller, Alexandra; Lim, Richard; Lu, Stanley; Millard, Alex; Pangelinan, Adriano; Patel, Neal; Smith, Luke; Chan, Kamfai; Ugaz, Victor M

    2016-05-01

    We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging. PMID:26898247

  10. Labs That Are a Blast.

    ERIC Educational Resources Information Center

    Hendrix, Laura

    1996-01-01

    Presents activities that use a simple homemade apparatus called "the cannon" to demonstrate Newton's Third Law. Reviews the chemistry concepts behind the ignition of the cannon and presents the Momentum Lab and the Projectile Motion Lab. (JRH)

  11. The Protective Roles of the Antioxidant Enzymes Superoxide Dismutase and Catalase in the Green Photosynthetic Bacterium Chloroflexus Aurantiacus

    NASA Technical Reports Server (NTRS)

    Blankenship, Robert E.; Rothschild, Lynn (Technical Monitor)

    2004-01-01

    The purpose of this study was to examine the biochemical response of the green thermophilic photosynthetic bacterium Chloroflexus aurantiacus to oxidative stress. Lab experiments focused primarily on characterizing the antioxidant enzyme superoxide dismutase and the response of this organism to oxidative stress. Experiments in the field at the hotsprings in Yellowstone National Park focused on the changes in the level of these enzymes during the day in response to oxidants and to the different types of ultraviolet radiation.

  12. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel anaerobic, mesophilic, amino-acid-fermenting bacterium, designated strain CL-84T, was isolated from the swine intestinal tract on mucin-based media. The bacterium had curved-rod cells (0.8-1.2 µm x 3.5-5.0 µm), stained Gram negative, and was non-motile with no evidence of spores. CL-84T pro...

  13. Cell wall structure and function in lactic acid bacteria

    PubMed Central

    2014-01-01

    The cell wall of Gram-positive bacteria is a complex assemblage of glycopolymers and proteins. It consists of a thick peptidoglycan sacculus that surrounds the cytoplasmic membrane and that is decorated with teichoic acids, polysaccharides, and proteins. It plays a major role in bacterial physiology since it maintains cell shape and integrity during growth and division; in addition, it acts as the interface between the bacterium and its environment. Lactic acid bacteria (LAB) are traditionally and widely used to ferment food, and they are also the subject of more and more research because of their potential health-related benefits. It is now recognized that understanding the composition, structure, and properties of LAB cell walls is a crucial part of developing technological and health applications using these bacteria. In this review, we examine the different components of the Gram-positive cell wall: peptidoglycan, teichoic acids, polysaccharides, and proteins. We present recent findings regarding the structure and function of these complex compounds, results that have emerged thanks to the tandem development of structural analysis and whole genome sequencing. Although general structures and biosynthesis pathways are conserved among Gram-positive bacteria, studies have revealed that LAB cell walls demonstrate unique properties; these studies have yielded some notable, fundamental, and novel findings. Given the potential of this research to contribute to future applied strategies, in our discussion of the role played by cell wall components in LAB physiology, we pay special attention to the mechanisms controlling bacterial autolysis, bacterial sensitivity to bacteriophages and the mechanisms underlying interactions between probiotic bacteria and their hosts. PMID:25186919

  14. The Effect of LAB Silage Inoculants on the Rumen Environment--Current Research Status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inoculants containing mainly lactic acid bacteria (LAB) are the most common additives used in making silage. Their function is to promote intensive production of lactic acid and rapid decrease in pH and so minimize fermentation losses. Some LAB inoculants reduce aerobic spoilage. In addition, feedin...

  15. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. PMID:26853478

  16. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments.

  17. e-Learning - Physics Labs

    NASA Astrophysics Data System (ADS)

    Mohottala, Hashini

    2014-03-01

    The general student population enrolled in any college level class is highly diverse. An increasing number of ``nontraditional'' students return to college and most of these students follow distance learning degree programs while engaging in their other commitments, work and family. However, those students tend to avoid taking science courses with labs, mostly because of the incapability of remotely completing the lab components in such courses. In order to address this issue, we have come across a method where introductory level physics labs can be taught remotely. In this process a lab kit with the critical lab components that can be easily accessible are conveniently packed into a box and distributed among students at the beginning of the semester. Once the students are given the apparatus they perform the experiments at home and gather data All communications with reference to the lab was done through an interactive user-friendly webpage - Wikispaces (WikiS). Students who create pages on WikiS can submit their lab write-ups, embed videos of the experiments they perform, post pictures and direct questions to the lab instructor. The students who are enrolled in the same lab can interact with each other through WikiS to discuss labs and even get assistance.

  18. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    PubMed

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. PMID:26965627

  19. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    PubMed

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol.

  20. Introducing ADS Labs

    NASA Astrophysics Data System (ADS)

    Accomazzi, Alberto; Henneken, E.; Grant, C. S.; Kurtz, M. J.; Di Milia, G.; Luker, J.; Thompson, D. M.; Bohlen, E.; Murray, S. S.

    2011-05-01

    ADS Labs is a platform that ADS is introducing in order to test and receive feedback from the community on new technologies and prototype services. Currently, ADS Labs features a new interface for abstract searches, faceted filtering of results, visualization of co-authorship networks, article-level recommendations, and a full-text search service. The streamlined abstract search interface provides a simple, one-box search with options for ranking results based on a paper relevancy, freshness, number of citations, and downloads. In addition, it provides advanced rankings based on collaborative filtering techniques. The faceted filtering interface allows users to narrow search results based on a particular property or set of properties ("facets"), allowing users to manage large lists and explore the relationship between them. For any set or sub-set of records, the co-authorship network can be visualized in an interactive way, offering a view of the distribution of contributors and their inter-relationships. This provides an immediate way to detect groups and collaborations involved in a particular research field. For a majority of papers in Astronomy, our new interface will provide a list of related articles of potential interest. The recommendations are based on a number of factors, including text similarity, citations, and co-readership information. The new full-text search interface allows users to find all instances of particular words or phrases in the body of the articles in our full-text archive. This includes all of the scanned literature in ADS as well as a select portion of the current astronomical literature, including ApJ, ApJS, AJ, MNRAS, PASP, A&A, and soon additional content from Springer journals. Fulltext search results include a list of the matching papers as well as a list of "snippets" of text highlighting the context in which the search terms were found. ADS Labs is available at http://adslabs.org

  1. Phoenix's Wet Chemistry Lab

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is an illustration of soil analysis on NASA's Phoenix Mars Lander's Wet Chemistry Lab (WCL) on board the Microscopy, Electrochemistry, and Conductivity Analyzer (MECA) instrument. By dissolving small amounts of soil in water, WCL will attempt to determine the pH, the abundance of minerals such as magnesium and sodium cations or chloride, bromide and sulfate anions, as well as the conductivity and redox potential.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  2. Phoenix's Wet Chemistry Lab

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is an illustration of the analytical procedure of NASA's Phoenix Mars Lander's Wet Chemistry Lab (WCL) on board the Microscopy, Electrochemistry, and Conductivity Analyzer (MECA) instrument. By dissolving small amounts of soil in water, WCL can determine the pH, the abundance of minerals such as magnesium and sodium cations or chloride, bromide and sulfate anions, as well as the conductivity and redox potential.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  3. Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products.

    PubMed

    Yu, Hai; Yin, Yongqi; Xu, Lin; Yan, Ming; Fang, Weiming; Ge, Qingfeng

    2015-07-23

    Klebsiella pneumoniae strain YZUSK-4, isolated from Chinese RuGao ham, is an efficient branched-chain aminotransferase-producing bacterium that can be used widely in fermented meat products to enhance flavor. The draft genome sequence of strain YZUSK-4 may provide useful genetic information on branched-chain amino acid aminotransferase production and branched-chain amino acid metabolism.

  4. Inexpensive DAQ based physics labs

    NASA Astrophysics Data System (ADS)

    Lewis, Benjamin; Clark, Shane

    2015-11-01

    Quality Data Acquisition (DAQ) based physics labs can be designed using microcontrollers and very low cost sensors with minimal lab equipment. A prototype device with several sensors and documentation for a number of DAQ-based labs is showcased. The device connects to a computer through Bluetooth and uses a simple interface to control the DAQ and display real time graphs, storing the data in .txt and .xls formats. A full device including a larger number of sensors combined with software interface and detailed documentation would provide a high quality physics lab education for minimal cost, for instance in high schools lacking lab equipment or students taking online classes. An entire semester’s lab course could be conducted using a single device with a manufacturing cost of under $20.

  5. A plant growth-promoting bacterium that decreases nickel toxicity in seedlings

    SciTech Connect

    Burd, G.I.; Dixon, D.G.; Glick, B.R.

    1998-10-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

  6. Lab at Home: Hardware Kits for a Digital Design Lab

    ERIC Educational Resources Information Center

    Oliver, J. P.; Haim, F.

    2009-01-01

    An innovative laboratory methodology for an introductory digital design course is presented. Instead of having traditional lab experiences, where students have to come to school classrooms, a "lab at home" concept is proposed. Students perform real experiments in their own homes, using hardware kits specially developed for this purpose. They…

  7. Learning LabVIEW in Introductory Physics Labs

    NASA Astrophysics Data System (ADS)

    Ethridge, Eric

    2007-11-01

    LabVIEW is a graphical programming language, commonly used in physics and engineering research. ELVIS stands for Electronics Laboratory Virtual Instrumentation Suite. It is designed to replace all of the instruments commonly found on an electronics lab bench. Vernier Instruments sells adaptors which allow the Vernier sensors to be hooked into a breadboard, and controlled via a LabVIEW Virtual Instrument (VI.) While basic VI's exist for running the sensors through LabVIEW, more sophisticated VI's are necessary for plotting one quantity versus another. Introducing LabVIEW and ELVIS in the introductory physics laboratory course is useful for physics and engineering majors who will be ready to use the equipment more extensively in upper-level courses.

  8. Physics Labs with Flavor II

    ERIC Educational Resources Information Center

    Agrest, Mikhail M.

    2011-01-01

    This paper was inspired by the numerous requests from "TPT" readers to expand the number of examples of "recurrent study" lab exercises described in my previous paper "Physics Labs with Flavor." I recommend that readers examine it first in order to better understand this one as my attempt here is to be brief. In that paper, one can find details…

  9. Report from the banding lab

    USGS Publications Warehouse

    Tautin, J.

    1995-01-01

    Mr. Tautin reported on the seemingly everchanging structure of biological science units within the Interior Department. Current Congressional proposals would either change the name of the Bird Banding Lab's parent agency or make it part of the Geological Survey. The current Congress has not looked favorably on science budgets within the Interior Department, and the Banding Lab's budget is being squeezed ever tighter.

  10. Polyaromatic hydrocarbon (PAH) degradation potential of a new acid tolerant, diazotrophic P-solubilizing and heavy metal resistant bacterium Cupriavidus sp. MTS-7 isolated from long-term mixed contaminated soil.

    PubMed

    Kuppusamy, Saranya; Thavamani, Palanisami; Megharaj, Mallavarapu; Lee, Yong Bok; Naidu, Ravi

    2016-11-01

    An isolate of Cupriavidus (strain MTS-7) was identified from a long-term PAHs and heavy metals mixed contaminated soil with the potential to biodegrade both LMW and HMW PAHs with added unique traits of acid and alkali tolerance, heavy metal tolerance, self-nutrient assimilation by N fixation and P solubilization. This strain completely degraded the model 3 (150 mg L(-1) Phe), 4 (150 mg L(-1) Pyr) and 5 (50 mg L(-1) BaP) ring PAHs in 4, 20 and 30 days, respectively. It could mineralize 90-100% of PAHs (200 mg L(-1) of Phe and Pyr) within 15 days across pH ranging from 5 to 8 and even in the presence of toxic metal contaminations. During biodegradation, the minimum inhibitory concentrations were 5 (Cu(2+)) and 3 (Cd(2+), Pb(2+), Zn(2+)) mg L(-1) of the potentially bioavailable metal ions and over 17 mg L(-1) metal levels was lethal for the microbe. Further, it could fix 217-274 μg mL(-1) of N and solubilize 79-135 μg mL(-1) of P while PAHs degradation. MTS-7 as a superior candidate could be thus used in the enhanced bioaugmentation and/or phytoremediation of long-term mixed contaminated sites. PMID:27475295

  11. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico

    PubMed Central

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A.

    2015-01-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  12. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico.

    PubMed

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A; Setién, Alvaro Aguilar

    2015-12-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc.

  13. Ethanol Production from Wet-Exploded Wheat Straw Hydrolysate by Thermophilic Anaerobic Bacterium Thermoanaerobacter BG1L1 in a Continuous Immobilized Reactor

    NASA Astrophysics Data System (ADS)

    Georgieva, Tania I.; Mikkelsen, Marie J.; Ahring, Birgitte K.

    Thermophilic ethanol fermentation of wet-exploded wheat straw hydrolysate was investigated in a continuous immobilized reactor system. The experiments were carried out in a lab-scale fluidized bed reactor (FBR) at 70°C. Undetoxified wheat straw hydrolysate was used (3-12% dry matter), corresponding to sugar mixtures of glucose and xylose ranging from 12 to 41 g/1. The organism, thermophilic anaerobic bacterium Thermoanaerobacter BG1L1, exhibited significant resistance to high levels of acetic acid (up to 10 g/1) and other metabolic inhibitors present in the hydrolysate. Although the hydrolysate was not detoxified, ethanol yield in a range of 0.39-0.42 g/g was obtained. Overall, sugar efficiency to ethanol was 68-76%. The reactor was operated continuously for approximately 143 days, and no contamination was seen without the use of any agent for preventing bacterial infections. The tested microorganism has considerable potential to be a novel candidate for lignocellulose bioconversion into ethanol. The work reported here also demonstrates that the use of FBR configuration might be a viable approach for thermophilic anaerobic ethanol fermentation.

  14. Neutron Transversity at Jefferson Lab

    SciTech Connect

    Jian-Ping Chen; Xiaodong Jiang; Jen-chieh Peng; Lingyan Zhu

    2005-09-07

    Nucleon transversity and single transverse spin asymmetries have been the recent focus of large efforts by both theorists and experimentalists. On-going and planned experiments from HERMES, COMPASS and RHIC are mostly on the proton or the deuteron. Presented here is a planned measurement of the neutron transversity and single target spin asymmetries at Jefferson Lab in Hall A using a transversely polarized {sup 3}He target. Also presented are the results and plans of other neutron transverse spin experiments at Jefferson Lab. Finally, the factorization for semi-inclusive DIS studies at Jefferson Lab is discussed.

  15. What's your lab's strategy?

    PubMed

    Francis, Peter

    2016-07-01

    Important strategic choices cascade throughout a laboratory. Senior management should create a document that answers each of the five key questions explained on page 60. Once this has been detailed in writing, it remains important to disseminate the basics to all employees so they are singing the same tune. A useful way to accomplish this is through a coherent strategy statement that specifies three components: 1) objectives; 2) scope; and 3) advantages. Commercial and hospital outreach labs should be in business to win. It all starts with a definition of what winning looks like. To "participate" in your market contributes to mediocrity-and it's self-defeating. With no clear strategic direction of where-to-play and how-to-win choices that associate with the aspiration, a mission or vision statement can be frustrating rather than inspiring for employees. Articulate it plainly and concisely for everybody. With a care-fully prepared and designed strategy, you will be on your way to winning in the zero-sum game! PMID:27548928

  16. What's your lab's strategy?

    PubMed

    Francis, Peter

    2016-07-01

    Important strategic choices cascade throughout a laboratory. Senior management should create a document that answers each of the five key questions explained on page 60. Once this has been detailed in writing, it remains important to disseminate the basics to all employees so they are singing the same tune. A useful way to accomplish this is through a coherent strategy statement that specifies three components: 1) objectives; 2) scope; and 3) advantages. Commercial and hospital outreach labs should be in business to win. It all starts with a definition of what winning looks like. To "participate" in your market contributes to mediocrity-and it's self-defeating. With no clear strategic direction of where-to-play and how-to-win choices that associate with the aspiration, a mission or vision statement can be frustrating rather than inspiring for employees. Articulate it plainly and concisely for everybody. With a care-fully prepared and designed strategy, you will be on your way to winning in the zero-sum game!

  17. Phylogenetic Diversity of Lactic Acid Bacteria Associated with Paddy Rice Silage as Determined by 16S Ribosomal DNA Analysis

    PubMed Central

    Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

    2003-01-01

    A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the predominant groups indicated by phenotypic analysis and to determine the phylogenetic affiliation of representative strains. The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank reference strains (between 98.7 and 99.8%). Phylogenetic trees based on the 16S rDNA sequence displayed high consistency, with nodes supported by high bootstrap values. With the exception of one species, the genetic data was in agreement with the phenotypic identification. The prevalent LAB, predominantly homofermentative (66%), consisted of Lactobacillus plantarum (24%), Lactococcus lactis (22%), Leuconostoc pseudomesenteroides (20%), Pediococcus acidilactici (11%), Lactobacillus brevis (11%), Enterococcus faecalis (7%), Weissella kimchii (3%), and Pediococcus pentosaceus (2%). The present study, the first to fully document rice-associated LAB, showed a very diverse community of LAB with a relatively high number of species involved in the fermentation process of paddy rice silage. The comprehensive 16S rDNA-based approach to describing LAB community structure was valuable in revealing the large diversity of bacteria inhabiting paddy rice silage and enabling the future design of appropriate inoculants aimed at improving its fermentation quality. PMID:12514026

  18. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Deal, P. H.

    1977-01-01

    A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

  19. State of the Lab 2012

    ScienceCinema

    King, Alex

    2016-07-12

    Ames Laboratory Director Alex King delivers the annual State of the Lab address on Thursday, May 17, 2012, the 65th Anniversary of the founding of The Ames Laboratory. This video contains highlights from the address.

  20. State of the Lab 2012

    SciTech Connect

    King, Alex

    2012-01-01

    Ames Laboratory Director Alex King delivers the annual State of the Lab address on Thursday, May 17, 2012, the 65th Anniversary of the founding of The Ames Laboratory. This video contains highlights from the address.

  1. Generalized Nanosatellite Avionics Testbed Lab

    NASA Technical Reports Server (NTRS)

    Frost, Chad R.; Sorgenfrei, Matthew C.; Nehrenz, Matt

    2015-01-01

    The Generalized Nanosatellite Avionics Testbed (G-NAT) lab at NASA Ames Research Center provides a flexible, easily accessible platform for developing hardware and software for advanced small spacecraft. A collaboration between the Mission Design Division and the Intelligent Systems Division, the objective of the lab is to provide testing data and general test protocols for advanced sensors, actuators, and processors for CubeSat-class spacecraft. By developing test schemes for advanced components outside of the standard mission lifecycle, the lab is able to help reduce the risk carried by advanced nanosatellite or CubeSat missions. Such missions are often allocated very little time for testing, and too often the test facilities must be custom-built for the needs of the mission at hand. The G-NAT lab helps to eliminate these problems by providing an existing suite of testbeds that combines easily accessible, commercial-offthe- shelf (COTS) processors with a collection of existing sensors and actuators.

  2. GridLAB-D/SG

    SciTech Connect

    2011-08-30

    GridLAB-D is a new power system simulation tool that provides valuable information to users who design and operate electric power transmission and distribution systems, and to utilities that wish to take advantage of the latest smart grid technology. This special release of GridLAB-D was developed to study the proposed Smart Grid technology that is used by Battelle Memorial Institute in the AEP gridSMART demonstration project in Northeast Columbus, Ohio.

  3. Halobacterium saccharovorum sp. nov., a carbohydrate-metabolizing, extremely halophilic bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1976-01-01

    The previously described extremely halophilic bacterium, strain M6, metabolizes a variety of carbohydrates with the production of acid. In addition, the organism produces nitrite (but no gas) from nitrate, is motile, and grows most rapidly at about 50 C. These characteristics distinguish it from all previously described halophilic bacteria in the genus Halobacterium. It is suggested that it be designated as a new species, Halobacterium saccharovorum.

  4. Virtual Labs and Virtual Worlds

    NASA Astrophysics Data System (ADS)

    Boehler, Ted

    2006-12-01

    Virtual Labs and Virtual Worlds Coastline Community College has under development several virtual lab simulations and activities that range from biology, to language labs, to virtual discussion environments. Imagine a virtual world that students enter online, by logging onto their computer from home or anywhere they have web access. Upon entering this world they select a personalized identity represented by a digitized character (avatar) that can freely move about, interact with the environment, and communicate with other characters. In these virtual worlds, buildings, gathering places, conference rooms, labs, science rooms, and a variety of other “real world” elements are evident. When characters move about and encounter other people (players) they may freely communicate. They can examine things, manipulate objects, read signs, watch video clips, hear sounds, and jump to other locations. Goals of critical thinking, social interaction, peer collaboration, group support, and enhanced learning can be achieved in surprising new ways with this innovative approach to peer-to-peer communication in a virtual discussion world. In this presentation, short demos will be given of several online learning environments including a virtual biology lab, a marine science module, a Spanish lab, and a virtual discussion world. Coastline College has been a leader in the development of distance learning and media-based education for nearly 30 years and currently offers courses through PDA, Internet, DVD, CD-ROM, TV, and Videoconferencing technologies. Its distance learning program serves over 20,000 students every year. sponsor Jerry Meisner

  5. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

    PubMed

    Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

    2011-05-01

    The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

  6. Detection of Salmonella bacterium in drinking water using microring resonator.

    PubMed

    Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

    2016-01-01

    A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

  7. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).

  8. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)). PMID:27572507

  9. Advanced Physics Lab at TCU

    NASA Astrophysics Data System (ADS)

    Quarles, C. A.

    2009-04-01

    The one semester, one credit hour Modern Physics Lab is viewed as a transition between the structured Physics 1 and 2 labs and junior/senior research. The labs focus on a variety of experiments built around a multichannel analyzer, various alpha, beta and gamma ray detectors and weak radioactive sources. Experiments include radiation safety and detection with a Geiger counter and NaI detector, gamma ray spectroscopy with a germanium detector, beta spectrum, alpha energy loss, gamma ray absorption, Compton effect, nuclear and positron annihilation lifetime, speed of gamma rays. Other experiments include using the analog oscilloscope, x-ray diffraction of diamond and using an SEM/EDX. Error analysis is emphasized throughout. The semester ends with an individual project, often an extension of one of the earlier experiments, and students present their results as a paper and an APS style presentation to the department.

  10. A bacterium that can grow by using arsenic instead of phosphorus.

    PubMed

    Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

    2011-06-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  11. A bacterium that can grow by using arsenic instead of phosphorus

    USGS Publications Warehouse

    Wolfe-Simon, Felisa; Blum, J.S.; Kulp, T.R.; Gordon, G.W.; Hoeft, S.E.; Pett-Ridge, J.; Stolz, J.F.; Webb, S.M.; Weber, P.K.; Davies, P.C.W.; Anbar, A.D.; Oremland, R.S.

    2011-01-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  12. A bacterium that can grow by using arsenic instead of phosphorus

    SciTech Connect

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2010-11-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

  13. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium.

    PubMed Central

    Heitkamp, M A; Franklin, W; Cerniglia, C E

    1988-01-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G + C content of the DNA, and high-molecular-weight mycolic acids (C58 to C64). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30 degrees C and minimally at 35 degrees C. No growth was observed at 5 or 42 degrees C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings. Images PMID:3202633

  14. Wavelength Shifters and Interactions of EDTA with Acrylic & LAB

    NASA Astrophysics Data System (ADS)

    Mohan, Yuvraj; SNO+ Collaboration

    2014-09-01

    The SNO + experiment, an upgrade to the Sudbury Neutrino Observatory, will use linear alkyl-benzene (LAB) liquid scintillator to probe new physics, including 0 νββ decay. Event detection efficiency is heavily affected by radioactive backgrounds, two sources being Rn-222 and Po-210 daughters, some of which has become embedded in the SNO + acrylic vessel after years underground. The leading candidate for polonium leaching is Ethylenediaminetetraacetic acid (EDTA). Before deployment on-site, EDTA's effects on the mechanical integrity of acrylic must be determined. It also must not be soluble in LAB or must be removed before scintillator fill of the vessel, as its presence would result in reduced light yield due to scattering. It was found that EDTA had negligible effects on the Young's Modulus of acrylic. EDTA is also slightly soluble in LAB, but can be completely removed by rinsing with water. Additionally, the study of the light yield and alpha/beta timing profiles of two wavelength shifters - bisMSB and perylene - is critical to determining which should be added to the 0 νββ isotope (tellurium) LAB cocktail. Small-scale results hint that perylene might be better, but this is being confirmed with larger-scale tests. The SNO + experiment, an upgrade to the Sudbury Neutrino Observatory, will use linear alkyl-benzene (LAB) liquid scintillator to probe new physics, including 0 νββ decay. Event detection efficiency is heavily affected by radioactive backgrounds, two sources being Rn-222 and Po-210 daughters, some of which has become embedded in the SNO + acrylic vessel after years underground. The leading candidate for polonium leaching is Ethylenediaminetetraacetic acid (EDTA). Before deployment on-site, EDTA's effects on the mechanical integrity of acrylic must be determined. It also must not be soluble in LAB or must be removed before scintillator fill of the vessel, as its presence would result in reduced light yield due to scattering. It was found that EDTA

  15. Biodiversity Lab: Using Local Resources.

    ERIC Educational Resources Information Center

    Gillie, Lynn L.

    1997-01-01

    Examining living organisms in one's own backyard is a key first step toward appreciating the scope and importance of biological diversity throughout the world. The goals of this lab are to involve students in exploring the biodiversity around them, appreciating its scope, and asking questions of new organisms that they may never have noticed…

  16. The Mobile Math Lab Project.

    ERIC Educational Resources Information Center

    Gray, Elaine

    1991-01-01

    Describes a mobile computer lab set up in a converted bus that is used by fourth graders as part of the math curriculum. The program, which emphasizes problem solving and spatial visualization, also addresses gender differences and in-service teacher training. The physical arrangements, including provisions for computer security, are described.…

  17. A Simple, Successful Capacitor Lab

    ERIC Educational Resources Information Center

    Ennis, William

    2011-01-01

    Capacitors are a fundamental component of modern electronics. They appear in myriad devices and in an enormous range of sizes. Although our students are taught the function and analysis of capacitors, few have the opportunity to use them in our labs.

  18. State of the Lab Address

    SciTech Connect

    King, Alex

    2010-01-01

    In his third-annual State of the Lab address, Ames Laboratory Director Alex King called the past year one of "quiet but strong progress" and called for Ames Laboratory to continue to build on its strengths while responding to changing expectations for energy research.

  19. Fraud strikes top genome lab

    SciTech Connect

    Marshall, E.

    1996-11-08

    Francis Collins, head of NIH`s Human Genome Project has informed colleagues that a junior researcher in his lab facke data in five papers co-authored by Collins. This article describes the whole scenario, how it was discovered, and what the reprocussions are.

  20. Evaluating E-Labs' Experimentation

    ERIC Educational Resources Information Center

    Plaisent, Michel; Maguiraga, Lassana; Bernard, Prosper; Larhrib, Samir

    2004-01-01

    This communication discusses preliminary results on an experimentation of e-Learning with MIS students, mainly in order to cope with the logistics of lab organization. A learning management software was installed which changed completely the learning process, from content to logistics. Students have expressed their satisfaction with the e-Learning…

  1. Physical Therapist Assistant Fitness Lab.

    ERIC Educational Resources Information Center

    Backstrom, Kurt; And Others

    Colby Community College's (CCC) Fitness Lab was established to provide the Physical Therapist Assistant (PTA) Program with a learning laboratory in which students can practice classroom-acquired skills, while at the same time promoting the physical, emotional, social, and intellectual well-being of CCC students and staff, and community members. A…

  2. A Lab for All Reasons.

    ERIC Educational Resources Information Center

    Cronin-Jones, Linda L.

    1990-01-01

    Described is a demonstration science laboratory at the University of Florida. Discussed is laboratory design, including instructional space, lab stations, sink areas, safety areas, and a storage and distribution area. The impact of this type of design is cited. Diagrams and photographs are included. (CW)

  3. State of the Lab Address

    ScienceCinema

    King, Alex

    2016-07-12

    In his third-annual State of the Lab address, Ames Laboratory Director Alex King called the past year one of "quiet but strong progress" and called for Ames Laboratory to continue to build on its strengths while responding to changing expectations for energy research.

  4. Where Lab Tests Are Performed

    MedlinePlus

    ... labs also vary in complexity, the volume of tests performed, the technology utilized, and the number and type of professionals who conduct the testing . There are important differences among the various testing settings. This information will be useful in ... Proudly sponsored by ... Learn ...

  5. Logistics in the Computer Lab.

    ERIC Educational Resources Information Center

    Cowles, Jim

    1989-01-01

    Discusses ways to provide good computer laboratory facilities for elementary and secondary schools. Topics discussed include establishing the computer lab and selecting hardware; types of software; physical layout of the room; printers; networking possibilities; considerations relating to the physical environment; and scheduling methods. (LRW)

  6. Δ6-fatty acid desaturase and fatty acid elongase mRNA expression, phagocytic activity and weight-to-length relationships in channel catfish (Ictalurus punctatus) fed alternative diets with soy oil and a probiotic.

    PubMed

    Santerre, A; Téllez-Bañuelos, M C; Casas-Solís, J; Castro-Félix, P; Huízar-López, M R; Zaitseva, G P; Horta-Fernández, J L; Trujillo-García, E A; de la Mora-Sherer, D; Palafox-Luna, J A; Juárez-Carrillo, E

    2015-09-22

    A time-course feeding trial was conducted for 120 days on juvenile channel catfish (Ictalurus punctatus) to study the effects of diets differing in oil source (fish oil or soy oil) and supplementation with a commercial probiotic. Relative levels of Δ6-fatty acid desaturase (Δ6-FAD) and fatty acid elongase (FAE) expression were assessed in brain and liver tissues. Both genes showed similar expression levels in all groups studied. Fish weight-to-length relationships were evaluated using polynomial regression analyses, which identified a burst in weight and length in the channel catfish on day 105 of treatment; this increase was related to an increase in gene expression. Mid-intestinal lactic acid bacterium (LAB) count was determined according to morphological and biochemical criteria using API strips. There was no indication that intestinal LAB count was affected by the modified diets. The Cunningham glass adherence method was applied to evaluate phagocytic cell activity in peripheral blood. Reactive oxygen species (ROS) generation was assessed through the respiratory burst activity of spleen macrophages by the NBT reduction test. Probiotic-supplemented diets provided a good substrate for innate immune system function; the phagocytic index was significantly enhanced in fish fed soy oil and the probiotic, and at the end of the experimental period, ROS production increased in fish fed soy oil. The substitution of fish oil by soy oil is recommended for food formulation and will contribute to promoting sustainable aquaculture. Probiotics are also recommended for channel catfish farming as they may act as immunonutrients.

  7. Flexible HVAC System for Lab or Classroom.

    ERIC Educational Resources Information Center

    Friedan, Jonathan

    2001-01-01

    Discusses an effort to design a heating, ventilation, and air conditioning system flexible enough to accommodate an easy conversion of classrooms to laboratories and dry labs to wet labs. The design's energy efficiency and operations and maintenance are examined. (GR)

  8. Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria.

    PubMed

    Vesterlund, Satu; Karp, Matti; Salminen, Seppo; Ouwehand, Arthur C

    2006-06-01

    There is increasing evidence that Staphylococcus aureus may colonize the intestinal tract, especially among hospitalized patients. As Staph. aureus has been found to be associated with certain gastrointestinal diseases, it has become important to study whether this bacterium can colonize the intestinal tract and if so, whether it is possible to prevent colonization. Adhesion is the first step in colonization; this study shows that Staph. aureus adheres to mucus from resected human intestinal tissue. Certain lactic acid bacteria (LAB), mainly commercial probiotics, were able to reduce adhesion and viability of adherent Staph. aureus. In displacement assays the amount of adherent Staph. aureus in human intestinal mucus was reduced 39-44% by Lactobacillus rhamnosus GG, Lactococcus lactis subsp. lactis and Propionibacterium freudenreichii subsp. shermanii. Moreover, adherent Lactobacillus reuteri, Lc. lactis and P. freudenreichii reduced viability of adherent Staph. aureus by 27-36%, depending on the strain, after 2 h incubation. This was probably due to the production of organic acids and hydrogen peroxide and possibly in the case of L. reuteri to the production of reuterin. This study shows for the first time that Staph. aureus can adhere to human intestinal mucus and adherent bacteria can be displaced and killed by certain LAB strains via in situ production of antimicrobial substances.

  9. Agrobacterium tumefaciens Is a Diazotrophic Bacterium

    PubMed Central

    Kanvinde, Lalita; Sastry, G. R. K.

    1990-01-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grow on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15N supplied as 15N2. As with most other well-characterized diazotrophic bacteria, the presence of NH4+ in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship. Images PMID:16348237

  10. Agrobacterium tumefaciens is a diazotrophic bacterium

    SciTech Connect

    Kanvinde, L.; Sastry, G.R.K. )

    1990-07-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

  11. Immobilization of the Methanogenic bacterium methanosarcina barkeri

    SciTech Connect

    Scherer, P.; Kluge, M.; Klein, J.; Sahm, H.

    1981-05-01

    Whole cells of the methanogen Methanosarcina barkeri were immobilized in an alginate network which was crosslinked with Ca/sup 2+/ calcium ions. The rates of methanol conversion to methane of entrapped cells were found to be in the same range as the corresponding rates of free cells. Furthermore, immobilized cells were active for a longer period than free cells. The particle size of the spherical alginate beads and thus diffusion has no obvious influence on the turnover of methanol. The half-value period for methanol conversion activity determined in a buffer medium was approximately 4 days at 37/degree/C for entrapped cells. The high rates of methanol degradation indicated that the immobilization technique preserved the cellular functions of this methanogenic bacterium. 24 refs.

  12. The chemical formula of a magnetotactic bacterium.

    PubMed

    Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

    2012-05-01

    Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life.

  13. The Development of MSFC Usability Lab

    NASA Technical Reports Server (NTRS)

    Cheng, Yiwei; Richardson, Sally

    2010-01-01

    This conference poster reviews the development of the usability lab at Marshall Space Flight Center. The purpose of the lab was to integrate a fully functioning usability laboratory to provide a resource for future human factor assessments. and to implement preliminary usability testing on a MSFC website to validate the functionality of the lab.

  14. Experiences with Lab-Centric Instruction

    ERIC Educational Resources Information Center

    Titterton, Nathaniel; Lewis, Colleen M.; Clancy, Michael J.

    2010-01-01

    Lab-centric instruction emphasizes supervised, hands-on activities by substituting lab for lecture time. It combines a multitude of pedagogical techniques into the format of an extended, structured closed lab. We discuss the range of benefits for students, including increased staff interaction, frequent and varied self-assessments, integrated…

  15. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    USGS Publications Warehouse

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  16. A serine sensor for multicellularity in a bacterium

    PubMed Central

    Subramaniam, Arvind R; DeLoughery, Aaron; Bradshaw, Niels; Chen, Yun; O’Shea, Erin; Losick, Richard; Chai, Yunrong

    2013-01-01

    We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.001 PMID:24347549

  17. Design labs: Students' expectations and reality

    NASA Astrophysics Data System (ADS)

    Etkina, Eugenia; Murthy, Sahana

    2006-02-01

    In a study reported in PERC 2004 the authors described how introductory physics labs in which students design their own experiments help them develop scientific abilities. These include the ability to design an experiment to solve a problem, to collect and analyze data and to communicate the details of the experimental procedure. The goal of the present study is to investigate the social aspect of student learning in these labs: whether students' expectations are consistent with the goals of the labs, whether student assessment of their learning in the labs matches the goals, and whether students perceive the labs as helpful in learning useful skills.

  18. New Features in ADS Labs

    NASA Astrophysics Data System (ADS)

    Accomazzi, Alberto; Kurtz, M. J.; Henneken, E. A.; Grant, C. S.; Thompson, D.; Di Milia, G.; Luker, J.; Murray, S. S.

    2013-01-01

    The NASA Astrophysics Data System (ADS) has been working hard on updating its services and interfaces to better support our community's research needs. ADS Labs is a new interface built on the old tried-and-true ADS Abstract Databases, so all of ADS's content is available through it. In this presentation we highlight the new features that have been developed in ADS Labs over the last year: new recommendations, metrics, a citation tool and enhanced fulltext search. ADS Labs has long been providing article-level recommendations based on keyword similarity, co-readership and co-citation analysis of its corpus. We have now introduced personal recommendations, which provide a list of articles to be considered based on a individual user's readership history. A new metrics interface provides a summary of the basic impact indicators for a list of records. These include the total and normalized number of papers, citations, reads, and downloads. Also included are some of the popular indices such as the h, g and i10 index. The citation helper tool allows one to submit a set of records and obtain a list of top 10 papers which cite and/or are cited by papers in the original list (but which are not in it). The process closely resembles the network approach of establishing "friends of friends" via an analysis of the citation network. The full-text search service now covers more than 2.5 million documents, including all the major astronomy journals, as well as physics journals published by Springer, Elsevier, the American Physical Society, the American Geophysical Union, and all of the arXiv eprints. The full-text search interface interface allows users and librarians to dig deep and find words or phrases in the body of the indexed articles. ADS Labs is available at http://adslabs.org

  19. Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium

    PubMed Central

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  20. Idiomarina maris sp. nov., a marine bacterium isolated from sediment.

    PubMed

    Zhang, Yan-Jiao; Zhang, Xi-Ying; Zhao, Hui-Lin; Zhou, Ming-Yang; Li, Hui-Juan; Gao, Zhao-Ming; Chen, Xiu-Lan; Dang, Hong-Yue; Zhang, Yu-Zhong

    2012-02-01

    A protease-producing marine bacterium, designated CF12-14(T), was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14(T) formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52(T) (94.7 %), Idiomarina seosinensis CL-SP19(T) (94.6 %) and other members of the genus Idiomarina (91.9-94.6 %). Cells were gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14(T) grew at 4-42 °C (optimum 30-35 °C) and with 0.1-15 % (w/v) NaCl (optimum 2-3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C(15 : 0) (27.4 %), iso-C(17 : 0) (16.0 %) and iso-C(17 : 1)ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14(T) ( = CCTCC AB 208166(T) = KACC 13974(T)).

  1. Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125 ▿ †

    PubMed Central

    Wilmes, Boris; Kock, Holger; Glagla, Susanne; Albrecht, Dirk; Voigt, Birgit; Markert, Stephanie; Gardebrecht, Antje; Bode, Rüdiger; Danchin, Antoine; Feller, Georges; Hecker, Michael; Schweder, Thomas

    2011-01-01

    The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments. PMID:21183643

  2. Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila.

    PubMed

    Tsuihiji, Hisayoshi; Yamazaki, Yoichi; Kamikubo, Hironari; Imamoto, Yasushi; Kataoka, Mikio

    2006-03-01

    Halorhodospira halophila is a halophilic photosynthetic bacterium classified as a purple sulfur bacterium. We found that H. halophila generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction. In order to consider the applied possibilities of this photobiological hydrogen generation, we cloned and characterized the structural and regulatory genes encoding the nitrogenase, nifH, nifD and nifA, from H. halophila. This is the first description of the nif genes for a purple sulfur bacterium. The amino-acid sequences of NifH and NifD indicated that these proteins are an Fe protein and a part of a MoFe protein, respectively. The important residues are conserved completely. The sequence upstream from the nifH region and sequence similarities of nifH and nifD with those of the other organisms suggest that the regulatory system might be a NifL-NifA system; however, H. halophila lacks nifL. The amino-acid sequence of H. halophila NifA is closer to that of the NifA of the NifL-NifA system than to that of NifA without NifL. H. halophila NifA does not conserve either the residue that interacts with NifL or the important residues involved in NifL-independent regulation. These results suggest the existence of yet another regulatory system, and that the development of functional systems and their molecular counterparts are not necessarily correlated throughout evolution. All of these Nif proteins of H. halophila possess an excess of acidic residues, which acts as a salt-resistant mechanism.

  3. Chitoporin from the Marine Bacterium Vibrio harveyi

    PubMed Central

    Chumjan, Watcharin; Winterhalter, Mathias; Schulte, Albert; Benz, Roland; Suginta, Wipa

    2015-01-01

    VhChiP is a sugar-specific porin present in the outer membrane of the marine bacterium Vibrio harveyi. VhChiP is responsible for the uptake of chitin oligosaccharides, with particular selectivity for chitohexaose. In this study, we employed electrophysiological and biochemical approaches to demonstrate that Trp136, located at the mouth of the VhChiP pore, plays an essential role in controlling the channel's ion conductivity, chitin affinity, and permeability. Kinetic analysis of sugar translocation obtained from single channel recordings indicated that the Trp136 mutations W136A, W136D, W136R, and W136F considerably reduce the binding affinity of the protein channel for its best substrate, chitohexaose. Liposome swelling assays confirmed that the Trp136 mutations decreased the rate of bulk chitohexaose permeation through the VhChiP channel. Notably, all of the mutants show increases in the off-rate for chitohexaose of up to 20-fold compared with that of the native channel. Furthermore, the cation/anion permeability ratio Pc/Pa is decreased in the W136R mutant and increased in the W136D mutant. This demonstrates that the negatively charged surface at the interior of the protein lumen preferentially attracts cationic species, leading to the cation selectivity of this trimeric channel. PMID:26082491

  4. Characterizations of intracellular arsenic in a bacterium

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Yannone, S. M.; Tainer, J. A.

    2011-12-01

    Life requires a key set of chemical elements to sustain growth. Yet, a growing body of literature suggests that microbes can alter their nutritional requirements based on the availability of these chemical elements. Under limiting conditions for one element microbes have been shown to utilize a variety of other elements to serve similar functions often (but not always) in similar molecular structures. Well-characterized elemental exchanges include manganese for iron, tungsten for molybdenum and sulfur for phosphorus or oxygen. These exchanges can be found in a wide variety of biomolecules ranging from protein to lipids and DNA. Recent evidence suggested that arsenic, as arsenate or As(V), was taken up and incorporated into the cellular material of the bacterium GFAJ-1. The evidence was interpreted to support As(V) acting in an analogous role to phosphate. We will therefore discuss our ongoing efforts to characterize intracellular arsenate and how it may partition among the cellular fractions of the microbial isolate GFAJ-1 when exposed to As(V) in the presence of various levels of phosphate. Under high As(V) conditions, cells express a dramatically different proteome than when grown given only phosphate. Ongoing studies on the diversity and potential role of proteins and metabolites produced in the presence of As(V) will be reported. These investigations promise to inform the role and additional metabolic potential for As in biology. Arsenic assimilation into biomolecules contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

  5. Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics.

    PubMed

    Ting, Lily; Williams, Timothy J; Cowley, Mark J; Lauro, Federico M; Guilhaus, Michael; Raftery, Mark J; Cavicchioli, Ricardo

    2010-10-01

    The cold marine environment constitutes a large proportion of the Earth's biosphere. Sphingopyxis alaskensis was isolated as a numerically abundant bacterium from several cold marine locations, and has been extensively studied as a model marine bacterium. Recently, a metabolic labelling platform was developed to comprehensively identify and quantify proteins from S. alaskensis. The approach incorporated data normalization and statistical validation for the purpose of generating highly confident quantitative proteomics data. Using this approach, we determined quantitative differences between cells grown at 10°C (low temperature) and 30°C (high temperature). Cold adaptation was linked to specific aspects of gene expression: a dedicated protein-folding system using GroESL, DnaK, DnaJ, GrpE, SecB, ClpB and PPIase; polyhydroxyalkanoate-associated storage materials; a link between enzymes in fatty acid metabolism and energy generation; de novo synthesis of polyunsaturated fatty acids in the membrane and cell wall; inorganic phosphate ion transport by a phosphate import PstB homologue; TonB-dependent receptor and bacterioferritin in iron homeostasis; histidine, tryptophan and proline amino acid metabolism; and a large number of proteins without annotated functions. This study provides a new level of understanding on how important marine bacteria can adapt to compete effectively in cold marine environments. This study is also a benchmark for comparative proteomic analyses with other important marine bacteria and other cold-adapted organisms. PMID:20482592

  6. Pangenome Evolution in the Marine Bacterium Alteromonas

    PubMed Central

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  7. Pangenome Evolution in the Marine Bacterium Alteromonas.

    PubMed

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  8. Updated version of an interim connection space LabPQR for spectral color reproduction: LabLab.

    PubMed

    Cao, Qian; Wan, Xiaoxia; Li, Junfeng; Liang, Jingxing

    2016-09-01

    In this paper, we propose a new interim connection space (ICS) called LabLab, which is an updated version of LabPQR, to overcome the drawback that the last three dimensions of LabPQR have no definite colorimetric meanings. We extended and improved the method by which the first three dimensions of LabPQR are deduced to obtain an ICS consisting of two sets of CIELAB values under different illuminants, and the reconstructed spectra from LabLab were obtained by minimizing colorimetric errors by means of the computational formula of the CIE-XYZ tristimulus values combined with least-squares best fit. The improvement obtained from the proposed method was tested to compress and reconstruct the reflectance spectra of the 1950 Natural Color System color chips and more than 50,000 ISO SOCS color patches as well as six multispectral images acquired by multispectral image acquisition systems using 1600 glossy Munsell color chips as training samples. The performance was evaluated by the mean values of color differences between the original and reconstructed spectra under the CIE 1931 standard colorimetric observer and the CIE standard illuminants D50, D55, D65, D75, F2, F7, F11, and A as well as five multichip white LED light sources. The mean and maximum values of the root mean square errors between the original and reconstructed spectra were also calculated. The experimental results show that the proposed three LabLab interim connection spaces significantly outperform principal component analysis, LabPQR, XYZLMS, Fairman-Brill, and LabRGB in colorimetric reconstruction accuracy at the cost of slight reduction of spectral reconstruction accuracy and illuminant independence of color differences of the suggested LabLab interim connection spaces outperform other interim connection spaces. In addition, the presented LabLab interim connection spaces could be quite compatible with the extensively used colorimetric management system since each dimension has definite colorimetric

  9. NCL Objective #5 - Nanotechnology Characterization Lab (NCL)

    Cancer.gov

    Nanotechnology Characterization Lab (NCL) Objective #5: Engage and Facilitate Academic and Industrial-based Knowledge Sharing of Nanomaterial Performance Data and Behavior Resulting from Pre-Clinical Testing.

  10. MatLab Script and Functional Programming

    NASA Technical Reports Server (NTRS)

    Shaykhian, Gholam Ali

    2007-01-01

    MatLab Script and Functional Programming: MatLab is one of the most widely used very high level programming languages for scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. The MatLab seminar covers the functional and script programming aspect of MatLab language. Specific expectations are: a) Recognize MatLab commands, script and function. b) Create, and run a MatLab function. c) Read, recognize, and describe MatLab syntax. d) Recognize decisions, loops and matrix operators. e) Evaluate scope among multiple files, and multiple functions within a file. f) Declare, define and use scalar variables, vectors and matrices.

  11. Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine

    SciTech Connect

    Bhupathiraju, V.K.; Sharma, P.K.; Tanner, R.S.; McInerney, M.J.; Oren, A.; Woese, C.R.

    1994-07-01

    A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 {micro}m. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO{sub 2}, and H{sub 2}. The major components of the cellular fatty acids were C{sub 14:0}, C{sub 16:0}, C{sub 16:1}, and C{sub 17:0 cyc} acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752{sup T} was most closely related to Haloanaerobium praevalens GSL{sup T} (ATCC 33744), the sole member of the genus Haloanaerobium. The authors propose that strain VS-752 (ATCC 51327) by established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium. 40 refs., 3 figs, 5 tabs.

  12. FlareLab: early results

    NASA Astrophysics Data System (ADS)

    Soltwisch, H.; Kempkes, P.; Mackel, F.; Stein, H.; Tenfelde, J.; Arnold, L.; Dreher, J.; Grauer, R.

    2010-12-01

    The FlareLab experiment at Bochum University has been constructed to generate and investigate plasma-filled magnetic flux tubes similar to arch-shaped solar prominences, which often result in coronal mass ejections (CMEs). In its first version, the device has been used to reproduce and extend previous studies of Bellan et al (1998 Phys. Plasmas 5 1991). Here the plasma source consists of two electrodes, which can be connected to a 1.0 kJ capacitor bank, and of a horseshoe magnet, which provides an arch-shaped guiding field. The discharge is ignited in a cloud of hydrogen gas that has been puffed into the space above the electrodes. In the first few microseconds the plasma current rises at a rate of several kA µs-1, causing the plasma column to pinch along the guiding B-field and to form an expanding loop structure. The observed dynamics of the magnetic flux tubes is analysed by means of three-dimensional MHD simulations in order to determine the influence of parameters like the initial magnetic field geometry on magnetic stability. At present, FlareLab is redesigned to mimic a model that was proposed by Titov and Démoulin (1999 Astron. Astrophys. 351 707) to investigate twisted magnetic configurations in solar flares.

  13. Aerosciences at Sandia National Labs.

    SciTech Connect

    Payne, Jeffrey L.

    2010-10-01

    A brief overview of Sandia National Laboratories will be presented highlighting the mission of Engineering Science Center. The Engineering Science Center provides a wide range of capabilities to support the lab's missions. As part of the Engineering Science Center the Aeroscience department provides research, development and application expertise in both experimental and computation compressible fluid mechanics. The role of Aeroscience at Sandia National Labs will be discussed with a focus on current research and development activities within the Aeroscience Department. These activities will be presented within the framework of a current program to highlight the synergy between computational and experimental work. The research effort includes computational and experimental activities covering fluid and structural dynamics disciplines. The presentation will touch on: probable excitation sources that yield the level of random vibration observed during flight; the methods that have been developed to model the random pressure fields in the turbulent boundary layer using a combination of CFD codes and a model of turbulent boundary layer pressure fluctuations; experimental measurement of boundary layer fluctuations; the methods of translating the random pressure fields to time-domain spatially correlated pressure fields.

  14. Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli

    PubMed Central

    Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul

    2013-01-01

    Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic

  15. Expression of a Clostridium perfringens genome-encoded putative N-acetylmuramoyl-L-alanine amidase as a potential antimicrobial to control the bacterium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium that plays a substantial role in non-foodborne human, animal and avian diseases as well as human foodborne disease. Previously discovered C. perfringens bacteriophage lytic enzyme amino acid sequences were utilized to iden...

  16. Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius

    SciTech Connect

    Aston, John E.; Apel, William A.; Lee, Brady D.; Thompson, David N.; Lacey, Jeffrey A.; Newby, Deborah T.; Reed, David. W.; Thompson, Vicki S.

    2015-11-05

    Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium, has a repertoire of thermo- and acid-stable enzymes that deconstruct lignocellulosic compounds. The work presented here describes the ability of A. acidocaldarius to reduce the concentration of the phenolic compounds: phenol, ferulic acid, ρ-coumaric acid and sinapinic acid during growth conditions. The extent and rate of the removal of these compounds were significantly increased by the presence of micro-molar copper concentrations, suggesting activity by copper oxidases that have been identified in the genome of A. acidocaldarius. Substrate removal kinetics was first order for phenol, ferulic acid, ρ-coumaric acid and sinapinic acid in the presence of 50 μM copper sulfate. In addition, laccase enzyme assays of cellular protein fractions suggested significant activity on a lignin analog between the temperatures of 45 and 90 °C. As a result, this work shows the potential for A. acidocaldarius to degrade phenolic compounds, demonstrating potential relevance to biofuel production and other industrial processes.

  17. Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius

    DOE PAGES

    Aston, John E.; Apel, William A.; Lee, Brady D.; Thompson, David N.; Lacey, Jeffrey A.; Newby, Deborah T.; Reed, David. W.; Thompson, Vicki S.

    2015-11-05

    Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium, has a repertoire of thermo- and acid-stable enzymes that deconstruct lignocellulosic compounds. The work presented here describes the ability of A. acidocaldarius to reduce the concentration of the phenolic compounds: phenol, ferulic acid, ρ-coumaric acid and sinapinic acid during growth conditions. The extent and rate of the removal of these compounds were significantly increased by the presence of micro-molar copper concentrations, suggesting activity by copper oxidases that have been identified in the genome of A. acidocaldarius. Substrate removal kinetics was first order for phenol, ferulic acid, ρ-coumaric acid and sinapinic acid in the presence ofmore » 50 μM copper sulfate. In addition, laccase enzyme assays of cellular protein fractions suggested significant activity on a lignin analog between the temperatures of 45 and 90 °C. As a result, this work shows the potential for A. acidocaldarius to degrade phenolic compounds, demonstrating potential relevance to biofuel production and other industrial processes.« less

  18. LabWrite: Transforming Lab Reports from Busy Work to Meaningful Learning Opportunities

    ERIC Educational Resources Information Center

    Ferzli, Miriam; Carter, Michael; Wiebe, Eric

    2005-01-01

    Lab reports are the dreaded assignments of the laboratory course. Students dislike them, because they can be tedious and time-consuming. Instructors dislike them, because they significantly increase the grading load. For this reason, lab reports are often omitted or replaced by alternatives such as responses to lab questions, fill-in-the-blank lab…

  19. Bacillus spp. produce antibacterial activities against lactic acid bacteria that contaminate fuel ethanol plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lactic acid bacteria (LAB) frequently contaminate commercial fuel ethanol fermentations, reducing yields and decreasing profitability of biofuel production. Microorganisms from environmental sources in different geographic regions of Thailand were tested for antibacterial activity against LAB. Fou...

  20. Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice.

    PubMed

    Auman, Ann J; Breezee, Jennifer L; Gosink, John J; Kämpfer, Peter; Staley, James T

    2006-05-01

    A gas vacuolate bacterium, designated strain 37T, was isolated from a sea ice core collected from Point Barrow, Alaska, USA. Cells of strain 37T were large (6-14 microm in length), rod-shaped, contained gas vacuoles of two distinct morphologies, and grew well at NaCl concentrations of 1-10 % and at temperatures of -12 to 10 degrees C. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c comprised 67 % of the total fatty acid content. Phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium was closely related to members of the genus Psychromonas, with highest sequence similarity (96.8 %) to Psychromonas antarctica. Phenotypic analysis differentiated strain 37T from P. antarctica on the basis of several characteristics, including cell morphology, growth temperature range and the ability to hydrolyse polymers. DNA-DNA hybridization experiments revealed a level of relatedness of 37 % between strain 37T and P. antarctica, providing further support that it represents a distinct species. The name Psychromonas ingrahamii sp. nov. is proposed for this novel species. The type strain is 37T (=CCUG 51855T=CIP 108865T).

  1. Structural characterization of the lipid A from the LPS of the haloalkaliphilic bacterium Halomonas pantelleriensis.

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Casillo, Angela; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Parrilli, Michelangelo; Giuliano, Mariateresa; Cammarota, Marcella; Lanzetta, Rosa; Corsaro, Maria Michela

    2016-09-01

    Halomonas pantelleriensis DSM9661(Τ) is a Gram-negative haloalkaliphilic bacterium isolated from the sand of the volcanic Venus mirror lake, closed to seashore in the Pantelleria Island in the south of Italy. It is able to optimally grow in media containing 3-15 % (w/v) total salt and at pH between 9 and 10. To survive in these harsh conditions, the bacterium has developed several strategies that probably concern the bacteria outer membrane, a barrier regulating the exchange with the environment. In such a context, the lipopolysaccharides (LPSs), which are among the major constituent of the Gram-negative outer membrane, are thought to contribute to the restrictive membrane permeability properties. The structure of the lipid A family derived from the LPS of Halomonas pantelleriensis DSM 9661(T) is reported herein. The lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different numbers of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of ESI FT-ICR mass spectrometry and chemical analysis. Preliminary immunological assays were performed, and a comparison with the lipid A structure of the phylogenetic proximal Halomonas magadiensis is also reported.

  2. Structural characterization of the lipid A from the LPS of the haloalkaliphilic bacterium Halomonas pantelleriensis.

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Casillo, Angela; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Parrilli, Michelangelo; Giuliano, Mariateresa; Cammarota, Marcella; Lanzetta, Rosa; Corsaro, Maria Michela

    2016-09-01

    Halomonas pantelleriensis DSM9661(Τ) is a Gram-negative haloalkaliphilic bacterium isolated from the sand of the volcanic Venus mirror lake, closed to seashore in the Pantelleria Island in the south of Italy. It is able to optimally grow in media containing 3-15 % (w/v) total salt and at pH between 9 and 10. To survive in these harsh conditions, the bacterium has developed several strategies that probably concern the bacteria outer membrane, a barrier regulating the exchange with the environment. In such a context, the lipopolysaccharides (LPSs), which are among the major constituent of the Gram-negative outer membrane, are thought to contribute to the restrictive membrane permeability properties. The structure of the lipid A family derived from the LPS of Halomonas pantelleriensis DSM 9661(T) is reported herein. The lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different numbers of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of ESI FT-ICR mass spectrometry and chemical analysis. Preliminary immunological assays were performed, and a comparison with the lipid A structure of the phylogenetic proximal Halomonas magadiensis is also reported. PMID:27329160

  3. BOREAS TE-1 SSA Soil Lab Data

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Knapp, David E. (Editor); Nerbas, Tim; Anderson, Darwin

    2000-01-01

    This data set was collected by TE-1 to provide a set of soil properties for BOREAS investigators in the SSA. The soil samples were collected at sets of soil pits in 1993 and 1994. Each set of soil pits was in the vicinity of one of the five flux towers in the BOREAS SSA. The collected soil samples were sent to a lab, where the major soil properties were determined. These properties include, but are not limited to, soil horizon; dry soil color; pH; bulk density; total, organic, and inorganic carbon; electric conductivity; cation exchange capacity; exchangeable sodium, potassium, calcium, magnesium, and hydrogen; water content at 0.01, 0.033, and 1.5 MPascals; nitrogen; phosphorus; particle size distribution; texture; pH of the mineral soil and of the organic soil; extractable acid; and sulfur. The data are stored in tabular ASCII text files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  4. The DVCS program at Jefferson Lab

    SciTech Connect

    Niccolai, Silvia

    2014-06-01

    Recent promising results, obtained at Jefferson Lab, on cross sections and asymmetries for DVCS and their link to the Generalized Parton Distributions are the focus of this paper. The extensive experimental program to measure DVCS with the 12-GeV-upgraded CEBAF in three experimental Halls (A, B, C) of Jefferson Lab, will also be presented.

  5. Innovation - A view from the Lab

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA Ag Lab in Peoria helps bridge the gap between agricultural producers and commercial manufacturers. In 2015, the Ag Lab, officially known as the Agricultural Research Service (ARS) National Center for Agricultural Utilization Research (NCAUR), is celebrating 75 years of research in Peoria. T...

  6. LANGUAGE LABS--AN UPDATED REPORT.

    ERIC Educational Resources Information Center

    1963

    REPORTS FROM SEVERAL SCHOOL DISTRICTS ON THE USE OF AND PLANNING OF LANGUAGE LABORATORIES ARE PRESENTED. LABORATORIES SHOULD BE ARRANGED FOR FLEXIBLE USE. THE AVERAGE HIGH SCHOOL STUDENT CAN USE A LAB PROFITABLY FOR 20 TO 25 MINUTES. THERE ARE THREE DIFFERENT TYPES OF LANGUAGE LABORATORIES THAT ARE DESCRIBED. THE SATELLITE LAB IS DIVIDED BY A…

  7. Magnetic Viscous Drag for Friction Labs

    ERIC Educational Resources Information Center

    Gaffney, Chris; Catching, Adam

    2016-01-01

    The typical friction lab performed in introductory mechanics courses is usually not the favorite of either the student or the instructor. The measurements are not all that easy to make, and reproducibility is usually a troublesome issue. This paper describes the augmentation of such a friction lab with a study of the viscous drag on a magnet…

  8. Supercharging Lessons with a Virtual Lab

    ERIC Educational Resources Information Center

    Stewart, Jefferson; Vincent, Daniel

    2013-01-01

    The authors describes their experiences incorporating the virtual lab into a simple circuit lesson during an energy unit in a sixth-grade class. The lesson included a hands-on group experiment using wire, batteries, and light bulbs to make a circuit and an online simulation, using a virtual lab. Class discussions, student inquiries, and the study…

  9. Berkeley Lab 2nd Grader Outreach

    SciTech Connect

    Scoggins, Jackie; Louie, Virginia

    2012-01-01

    The Berkeley Lab IT Department sponsored a community outreach program aimed at teaching young children about computers and networks. Second graders from LeConte Elementary School joined Lab IT Staff for a day of in-depth exercises and fun.

  10. A Virtual Lab in Research Methods

    ERIC Educational Resources Information Center

    Sommer, Barbara A.; Sommer, Robert

    2003-01-01

    A hands-on lab for a lower division research methods course used an online format with Web page, Web forms, an e-mail listproc, and chat room. The virtual section received a higher rating for overall value than did the in-person labs. Students liked its convenience and flexibility. There were no significant differences in examination performance…

  11. Practical Physics Labs: A Resource Manual.

    ERIC Educational Resources Information Center

    Goodwin, Peter

    This resource manual focuses on physics labs that relate to the world around us and utilize simple equipment and situations. Forty-five laboratories are included that relate to thermodynamics, electricity, magnetism, dynamics, optics, wave transmission, centripetal force, and atomic physics. Each lab has three sections. The first section…

  12. Extracurricular Science Labs for STEM Talent Support

    ERIC Educational Resources Information Center

    Hausamann, Dieter

    2012-01-01

    In the past decade, a growing lack of engineers, natural scientists, information technology experts, and mathematicians has been noted, especially in Europe. Corresponding to the need to attract young people to science and technology, numerous extracurricular science labs ("out-of-school labs") have been established, especially in Germany. One of…

  13. California State University, Northridge: Hybrid Lab Courses

    ERIC Educational Resources Information Center

    EDUCAUSE, 2014

    2014-01-01

    California State University, Northridge's Hybrid Lab course model targets high failure rate, multisection, gateway courses in which prerequisite knowledge is a key to success. The Hybrid Lab course model components incorporate interventions and practices that have proven successful at CSUN and other campuses in supporting students, particularly…

  14. Conducting First Quarter Labs with Few Chemicals.

    ERIC Educational Resources Information Center

    Kelly, Michael J.

    2002-01-01

    Outlines chemistry labs used during the first quarter of study and advises about framing the course for students. Topics of the labs include observation; blind observation; measurement, determination of conversion factors, and percent error; taking and reporting data over time; and density. (DDR)

  15. Berkeley Lab 2nd Grader Outreach

    ScienceCinema

    Scoggins, Jackie; Louie, Virginia

    2016-07-12

    The Berkeley Lab IT Department sponsored a community outreach program aimed at teaching young children about computers and networks. Second graders from LeConte Elementary School joined Lab IT Staff for a day of in-depth exercises and fun.

  16. Multigenre Lab Reports: Connecting Literacy and Science

    ERIC Educational Resources Information Center

    Rochwerger, Leonora; Peterson, Shelley Stagg; Calovini, Theresa

    2006-01-01

    The development of communication skills is a key component in any science program. However, students do not see the connections between writing and science. In particular, students lack the enthusiasm when the time comes to write lab reports. Students say that they do not see why they should have to write dry, boring lab reports following an…

  17. Hydrogel Beads: The New Slime Lab?

    ERIC Educational Resources Information Center

    Brockway, Debra; Libera, Matthew; Welner, Heidi

    2011-01-01

    Creating slime fascinates students. Unfortunately, though intrigue is at its peak, the educational aspect of this activity is often minimal. This article describes a chemistry lab that closely relates to the slime lab and allows high school students to explore the concepts of chemical bonding, properties, and replacement reactions. It involves the…

  18. Latest results from FROST at Jefferson Lab

    SciTech Connect

    Ritchie, Barry G.

    2014-06-01

    The spectrum of broad and overlapping nucleon excitations can be greatly clarified by use of a polarized photon beam incident on a polarized target in meson photoproduction experiments. At Jefferson Lab, a program of such measurements has made use of the Jefferson Lab FROzen Spin Target (FROST). An overview of preliminary results are presented.

  19. Traditional Labs + New Questions = Improved Student Performance.

    ERIC Educational Resources Information Center

    Rezba, Richard J.; And Others

    1992-01-01

    Presents three typical lab activities involving the breathing rate of fish, the behavior of electromagnets, and tests for water hardness to demonstrate how labs can be modified to teach process skills. Discusses how basic concepts about experimentation are developed and ways of generating and improving science experiments. Includes a laboratory…

  20. Z Machine at Sandia Labs

    SciTech Connect

    2007-10-17

    Sandia Labs' Z machine is the largest laboratory source of x-rays in the world. For the few nanoseconds of a Z Machine test, its electrical output equals the output of 50x the electrical generating stations of all the power plants on earth. The Z Machine complex encompasses an area roughly the size of a major college basketball arena. Originally created to validate nuclear weapons models, the Z Machine is also considered a "dark horse" in the race for viable fusion energy production. After the famous "arcs and sparks" photo of Z (a photo no longer possible after its refurbishment), this is a fast-motion video of workers completing Z's recent refurbishment.

  1. Jefferson Lab: Present and Future

    NASA Astrophysics Data System (ADS)

    Rossi, Patrizia

    2016-08-01

    The continuous electron beam accelerator facility and associated experimental equipment at Jefferson Lab comprise a unique facility for nuclear physics research whose upgrade is presently underway, with completion expected in 2017. The upgraded facility will accelerate electron beams to 11 GeV for experiments in the existing Halls A, B and C. In addition, a 12 GeV beam can be provided to a new experimental hall, Hall D, to generate a 9 GeV tagged photon beam. This upgrade will enable a new experimental program with substantial discovery potential to address important topics in hadronic, nuclear, and electroweak physics. Further in the future, it is envisioned that the Laboratory will evolve into an electron-ion colliding beam facility.

  2. SLAC All Access: Laser Labs

    ScienceCinema

    Minitti, Mike; Woods Mike

    2016-07-12

    From supermarket checkouts to video game consoles, lasers are ubiquitous in our lives. Here at SLAC, high-power lasers are critical to the cutting-edge research conducted at the laboratory. But, despite what you might imagine, SLAC's research lasers bear little resemblance to the blasters and phasers of science fiction. In this edition of All Access we put on our safety goggles for a peek at what goes on inside some of SLAC's many laser labs. LCLS staff scientist Mike Minitti and SLAC laser safety officer Mike Woods detail how these lasers are used to study the behavior of subatomic particles, broaden our understanding of cosmic rays and even unlock the mysteries of photosynthesis.

  3. Jefferson Lab's Trim Card II

    SciTech Connect

    Trent Allison; Sarin Philip; C. Higgins; Edward Martin; William Merz

    2005-05-01

    Jefferson Lab's Continuous Electron Beam Accelerator Facility (CEBAF) uses Trim Card I power supplies to drive approximately 1900 correction magnets. These trim cards have had a long and illustrious service record. However, some of the employed technology is now obsolete, making it difficult to maintain the system and retain adequate spares. The Trim Card II is being developed to act as a transparent replacement for its aging predecessor. A modular approach has been taken in its development to facilitate the substitution of sections for future improvements and maintenance. The resulting design has been divided into a motherboard and 7 daughter cards which has also allowed for parallel development. The Trim Card II utilizes modern technologies such as a Field Programmable Gate Array (FPGA) and a microprocessor to embed trim card controls and diagnostics. These reprogrammable devices also provide the versatility to incorporate future requirements.

  4. SLAC All Access: Laser Labs

    SciTech Connect

    Minitti, Mike; Woods Mike

    2013-03-01

    From supermarket checkouts to video game consoles, lasers are ubiquitous in our lives. Here at SLAC, high-power lasers are critical to the cutting-edge research conducted at the laboratory. But, despite what you might imagine, SLAC's research lasers bear little resemblance to the blasters and phasers of science fiction. In this edition of All Access we put on our safety goggles for a peek at what goes on inside some of SLAC's many laser labs. LCLS staff scientist Mike Minitti and SLAC laser safety officer Mike Woods detail how these lasers are used to study the behavior of subatomic particles, broaden our understanding of cosmic rays and even unlock the mysteries of photosynthesis.

  5. A Comparative Study on Real Lab and Simulation Lab in Communication Engineering from Students' Perspectives

    ERIC Educational Resources Information Center

    Balakrishnan, B.; Woods, P. C.

    2013-01-01

    Over the years, rapid development in computer technology has engendered simulation-based laboratory (lab) in addition to the traditional hands-on (physical) lab. Many higher education institutions adopt simulation lab, replacing some existing physical lab experiments. The creation of new systems for conducting engineering lab activities has raised…

  6. Space Science Lab at PARI

    NASA Astrophysics Data System (ADS)

    Castelaz, Michael W.; Blake, M.; Clavier, D.; Whitworth, C.; Cline, J. D.

    2006-12-01

    Native American, Hispanic, African American, and other underrepresented high school students in rural Western North Carolina have unprecedented opportunity as researchers in the Space Science Lab to conduct visible and radio observations of the Sun. The program involves 90 students over a three year period. The students conduct their own research and also interact with scientists around the world. The primary goal is to reach students who otherwise would not have this opportunity and motivate them to develop the critical thinking skills necessary for objective scientific inquiry. Students develop skills in electronics, computer sciences, astronomy, physics and earth sciences. Equally important is the hope that the students will become interested in pursuing careers in research or other science-related areas. The program objectives are aligned with the North Carolina Standard Course of Study for grades 9-12 in the areas of Earth/Environmental Science, Physical Science and Physics. The first group of 27 students spent a week in the Space Science Lab located on the campus of the Pisgah Astronomical Research Institute (PARI) during the Summer 2006. Students constructed their own JOVE radio telescopes that they took home to continue their observations. They share their results during four follow-up sessions throughout the school year. The students also have Internet access to radio telescopes and solar monitoring equipment at PARI. We expect their enthusiasm for science will increase by experiencing research investigations that are fun and relevant to their understanding of the world around them. We gratefully acknowledge support from the Burroughs Wellcome Fund Student Science Enrichment Program.

  7. H CANYON PROCESSING IN CORRELATION WITH FH ANALYTICAL LABS

    SciTech Connect

    Weinheimer, E.

    2012-08-06

    number of samples being sent to F/H Labs. All analyses of these samples are imperative to safe and efficient processing. The important campaigns to occur would be impossible without feedback from analyses such as chemical makeup of solutions, concentrations of dissolution acids and nuclear material, as well as nuclear isotopic data. The necessity of analysis for radiochemical processing is evident. Processing devoid of F/H Lab's feedback would go against the ideals of a safety-conscious and highly accomplished processing facility such as H Canyon.

  8. Nonproliferation through international lab-to-lab technology cooperation

    SciTech Connect

    Dunlop, W H

    1998-09-10

    Lab-to- Lab activities are currently with the FSU, that experience is leading to important and productive interactions with other countries and regions, most significantly, China and the Middle East. In contrast to the Cold War years, when most technologies developed at LLNL were solely for the US national defense efforts and therefore classified, many of NAI's new technologies and tools are unclassified and designed for use in a multilateral security environment. PPAC is the proliferation "Prevention" element of NAI's four-element "Prevention-Reversal-Response-Avoid Surprise" program. We direct some twenty different projects. which have realized about a factor of ten growth in the last four years.

  9. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium.

    PubMed Central

    Beller, H R; Spormann, A M; Sharma, P K; Cole, J R; Reinhard, M

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of toluene consumed was consistent with the theoretical ratio for mineralization of toluene coupled with the reduction of sulfate to hydrogen sulfide. Strain PRTOL1 also transforms o- and p-xylene to metabolic products when grown with toluene. However, xylene transformation by PRTOL1 is slow relative to toluene degradation and cannot be sustained over time. Stable isotope-labeled substrates were used in conjunction with gas chromatography-mass spectrometry to investigate the by-products of toluene and xylene metabolism. The predominant by-products from toluene, o-xylene, and p-xylene were benzylsuccinic acid, (2-methylbenzyl)succinic acid, and 4-methylbenzoic acid (or p-toluic acid), respectively. Metabolic by-products accounted for nearly all of the o-xylene consumed. Enzyme assays indicated that acetyl coenzyme A oxidation proceeded via the carbon monoxide dehydrogenase pathway. Compared with the only other reported toluene-degrading, sulfate-reducing bacterium, strain PRTOL1 is distinct in that it has a novel 16S rRNA gene sequence and was derived from a freshwater rather than marine environment. PMID:8919780

  10. Coiled to diffuse: Brownian motion of a helical bacterium.

    PubMed

    Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

    2012-09-11

    We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

  11. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    PubMed Central

    Pradhan, Nirakar; Dipasquale, Laura; d’Ippolito, Giuliana; Panico, Antonio; Lens, Piet N. L.; Esposito, Giovanni; Fontana, Angelo

    2015-01-01

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production. PMID:26053393

  12. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.

    PubMed

    Pradhan, Nirakar; Dipasquale, Laura; d'Ippolito, Giuliana; Panico, Antonio; Lens, Piet N L; Esposito, Giovanni; Fontana, Angelo

    2015-06-04

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.

  13. Understanding the detailed motion of a model bacterium

    NASA Astrophysics Data System (ADS)

    Thawani, Akanksha; Tirumkudulu, Mahesh

    2014-11-01

    Inspired by the motion of flagellated bacteria such as Escherichia coli and Bacillus subtilis, we have built a macroscopic model bacterium, in order to investigate the intricate aspects of their motion which cannot be visualized under a microscope. The flagellated rod shaped cells were approximated with a spherical head attached to a rigid metal helix, via a plastic hook. The motion of model bacterium was observed in a high viscosity silicone oil to replicate the low Reynolds number flow conditions. A significant wobble was observed even in the absence of an off-axis flagellum. We suspect that the flexibility in the hook connecting the head and flagellum is the cause for wobble, since wobble was observed to increase significantly with hook-flexibility. The motion of the model bacterium was predicted using the Slender Body theory of Lighthill, and was compared with the measured trajectories.

  14. Cloning, production, and functional expression of the bacteriocin sakacin A (SakA) and two SakA-derived chimeras in lactic acid bacteria (LAB) and the yeasts Pichia pastoris and Kluyveromyces lactis.

    PubMed

    Jiménez, Juan J; Borrero, Juan; Diep, Dzung B; Gútiez, Loreto; Nes, Ingolf F; Herranz, Carmen; Cintas, Luis M; Hernández, Pablo E

    2013-09-01

    Mature sakacin A (SakA, encoded by sapA) and its cognate immunity protein (SakI, encoded by sapiA), and two SakA-derived chimeras mimicking the N-terminal end of mature enterocin P (EntP/SakA) and mature enterocin A (EntA/SakA) together with SakI, were fused to different signal peptides (SP) and cloned into the protein expression vectors pNZ8048 and pMG36c for evaluation of their production and functional expression by different lactic acid bacteria. The amount, antimicrobial activity, and specific antimicrobial activity of SakA and its chimeras produced by Lactococcus lactis subsp. cremoris NZ9000 depended on the SP and the expression vector. Only L. lactis NZ9000 (pNUPS), producing EntP/SakA, showed higher bacteriocin production and antimicrobial activity than the natural SakA-producer Lactobacillus sakei Lb706. The lower antimicrobial activity of the SakA-producer L. lactis NZ9000 (pNUS) and that of the EntA/SakA-producer L. lactis NZ9000 (pNUAS) could be ascribed to secretion of truncated bacteriocins. On the other hand, of the Lb. sakei Lb706 cultures transformed with the pMG36c-derived vectors only Lb. sakei Lb706 (pGUS) overproducing SakA showed a higher antimicrobial activity than Lb. sakei Lb706. Finally, cloning of SakA and EntP/SakA into pPICZαA and pKLAC2 permitted the production of SakA and EntP/SakA by recombinant Pichia pastoris X-33 and Kluyveromyces lactis GG799 derivatives although their antimicrobial activity was lower than expected from their production.

  15. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2012-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  16. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  17. Metabolite Profiles of Lactic Acid Bacteria in Grass Silage▿

    PubMed Central

    Broberg, Anders; Jacobsson, Karin; Ström, Katrin; Schnürer, Johan

    2007-01-01

    The metabolite production of lactic acid bacteria (LAB) on silage was investigated. The aim was to compare the production of antifungal metabolites in silage with the production in liquid cultures previously studied in our laboratory. The following metabolites were found to be present at elevated concentrations in silos inoculated with LAB strains: 3-hydroxydecanoic acid, 2-hydroxy-4-methylpentanoic acid, benzoic acid, catechol, hydrocinnamic acid, salicylic acid, 3-phenyllactic acid, 4-hydroxybenzoic acid, (trans, trans)-3,4-dihydroxycyclohexane-1-carboxylic acid, p-hydrocoumaric acid, vanillic acid, azelaic acid, hydroferulic acid, p-coumaric acid, hydrocaffeic acid, ferulic acid, and caffeic acid. Among these metabolites, the antifungal compounds 3-phenyllactic acid and 3-hydroxydecanoic acid were previously isolated in our laboratory from liquid cultures of the same LAB strains by bioassay-guided fractionation. It was concluded that other metabolites, e.g., p-hydrocoumaric acid, hydroferulic acid, and p-coumaric acid, were released from the grass by the added LAB strains. The antifungal activities of the identified metabolites in 100 mM lactic acid were investigated. The MICs against Pichia anomala, Penicillium roqueforti, and Aspergillus fumigatus were determined, and 3-hydroxydecanoic acid showed the lowest MIC (0.1 mg ml−1 for two of the three test organisms). PMID:17616609

  18. Isolation and Characterization of a Phosphate-Solubilizing Halophilic Bacterium Kushneria sp. YCWA18 from Daqiao Saltern on the Coast of Yellow Sea of China

    PubMed Central

    Zhu, Fengling; Qu, Lingyun; Hong, Xuguang; Sun, Xiuqin

    2011-01-01

    Phosphate-solubilizing bacteria (PSB) function in soil phosphorus cycle, increasing the bioavailability of soil phosphorus for plants. Isolation and application of salt-tolerant or halophilic PSB will facilitate the development of saline-alkali soil-based agriculture. A moderately halophilic bacterium was isolated from the sediment of Daqiao saltern on the eastern coast of China, which also performs phosphate-solubilizing ability. The bacterium was assigned to genus Kushneria according to its 16S rRNA gene sequence, and accordingly named as Kushneria sp. YCWA18. The fastest growth was observed when the culturing temperature was 28°C and the concentration of NaCl was 6% (w/v). It was founds that the bacterium can survive at a concentration of NaCl up to 20%. At the optimum condition, the bacterium solubilized 283.16 μg/mL phosphorus in 11 days after being inoculated in 200 mL Ca3(PO4)2 containing liquid medium, and 47.52 μg/mL phosphorus in 8 days after being inoculated in 200 mL lecithin-containing liquid medium. The growth of the bacterium was concomitant with a significant decrease of acidity of the medium. PMID:21716683

  19. Isolation and characterization of endophytic bacterium LRE07 from cadmium hyperaccumulator Solanum nigrum L. and its potential for remediation.

    PubMed

    Luo, Shenglian; Wan, Yong; Xiao, Xiao; Guo, Hanjun; Chen, Liang; Xi, Qiang; Zeng, Guangming; Liu, Chengbin; Chen, Jueliang

    2011-03-01

    Valuable endophytic strains facilitating plants growth and detoxification of heavy metals are required because the application of plant-endophyte symbiotic system is a promising potential technique to improve efficiency of phytoremediation. In this study, endophytic bacterium LRE07 was isolated from cadmium hyperaccumulator Solanum nigrum L. It was identified as Serratia sp. by 16S rRNA sequence analysis. The endophytic bacterium LRE07 was resistant to the toxic effects of heavy metals, solubilized mineral phosphate, and produced indoleacetic acid and siderophore. The heavy metal detoxification was studied in growing LRE07 cells. The strain bound over 65% of cadmium and 35% of zinc in its growing cells from single metal solutions 72 h after inoculation. Besides the high removal efficiencies in single-ion system, an analogous removal phenomenon was also observed in multi-ions system, indicating that the endophyte possesses specific and remarkable heavy metal remediation abilities. PMID:20953602

  20. Alteromonas infernus sp. nov., a new polysaccharide-producing bacterium isolated from a deep-sea hydrothermal vent.

    PubMed

    Raguénès, G H; Peres, A; Ruimy, R; Pignet, P; Christen, R; Loaec, M; Rougeaux, H; Barbier, G; Guezennec, J G

    1997-04-01

    A deep-sea, aerobic, mesophilic and heterotrophic new bacterium was isolated from a sample of fluid collected among a dense population of Riftia pachyptila, in the vicinity of an active hydrothermal vent of the Southern depression of the Guaymas basin (Gulf of California). On the basis of phenotypic and phylogenetic analyses and DNA/DNA relatedness, the strain GY785 was recognized as a new species of the genus Alteromonas and the name of Alteromonas infernus is proposed. During the stationary phase in batch cultures in the presence of glucose, this bacterium secreted two unusual polysaccharides. The water-soluble exopolysaccharide-1 produced contained glucose, galactose, galacturonic and glucuronic acids as monosaccharides. The gel-forming exopolysaccharide-2 was separated from the bacterial cells by dialysis against distilled water and partially characterized. PMID:9134716

  1. Labs21 Environmental Performance Criteria: Toward 'LEED (trademark) for Labs'

    SciTech Connect

    Mathew, Paul; Sartor, Dale; Lintner, William; Wirdzek, Phil

    2002-10-14

    Laboratory facilities present a unique challenge for energy efficient and sustainable design, with their inherent complexity of systems, health and safety requirements, long-term flexibility and adaptability needs, energy use intensity, and environmental impacts. The typical laboratory is about three to five times as energy intensive as a typical office building and costs about three times as much per unit area. In order to help laboratory stakeholders assess the environmental performance of their laboratories, the Labs21 program, sponsored by the US Environmental Protection Agency and the US Department of Energy, is developing the Environmental Performance Criteria (EPC), a point-based rating system that builds on the LEED(TM) rating system. Currently, LEED(TM) is the primary tool used to rate the sustainability of commercial buildings. However, it lacks some attributes essential to encouraging the application of sustainable design principles to laboratory buildings. Accordingly, the EPC has additions and modifications to the prerequisites and credits in each of the six sections of LEED(TM). It is being developed in a consensus-based approach by a diverse group of architects, engineers, consulting experts, health & safety personnel and facilities personnel. This report describes the EPC version 2.0, highlighting the underlying technical issues, and describes implications for the development of a LEED version for Laboratories.

  2. Microcalorimetric Measurements of Glucose Metabolism by Marine Bacterium Vibrio alginolyticus

    PubMed Central

    Gordon, Andrew S.; Millero, Frank J.; Gerchakov, Sol M.

    1982-01-01

    Microcalorimetric measurements of heat production from glucose by Vibrio alginolyticus were made to assess the viability of calorimetry as a technique for studying the metabolism of marine bacteria at organic nutrient concentrations found in marine waters. The results show that the metabolism of glucose by this bacterium can be measured by calorimetry at submicromolar concentrations. A linear correlation between glucose concentration and total heat production was observed over a concentration range of 8 mM to 0.35 μM. It is suggested that these data indicate a constant efficiency of metabolism for this bacterium over the wide range of glucose concentrations studied. PMID:16346131

  3. Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae

    PubMed Central

    Xu, Linghua; Zeng, Xian-Chun; Nie, Yao; Luo, Xuesong; Zhou, Enmin; Zhou, Lingli; Pan, Yunfan; Li, Wenjun

    2014-01-01

    Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T). PMID:24647674

  4. Studies of the Extracellular Glycocalyx of the Anaerobic Cellulolytic Bacterium Ruminococcus albus 7▿

    PubMed Central

    Weimer, Paul J.; Price, Neil P. J.; Kroukamp, Otini; Joubert, Lydia-Marie; Wolfaardt, Gideon M.; Van Zyl, Willem H.

    2006-01-01

    Anaerobic cellulolytic bacteria are thought to adhere to cellulose via several mechanisms, including production of a glycocalyx containing extracellular polymeric substances (EPS). As the compositions and structures of these glycocalyces have not been elucidated, variable-pressure scanning electron microscopy (VP-SEM) and chemical analysis were used to characterize the glycocalyx of the ruminal bacterium Ruminococcus albus strain 7. VP-SEM revealed that growth of this strain was accompanied by the formation of thin cellular extensions that allowed the bacterium to adhere to cellulose, followed by formation of a ramifying network that interconnected individual cells to one another and to the unraveling cellulose microfibrils. Extraction of 48-h-old whole-culture pellets (bacterial cells plus glycocalyx [G] plus residual cellulose [C]) with 0.1 N NaOH released carbohydrate and protein in a ratio of 1:5. Boiling of the cellulose fermentation residue in a neutral detergent solution removed almost all of the adherent cells and protein while retaining a residual network of adhering noncellular material. Trifluoroacetic acid hydrolysis of this residue (G plus C) released primarily glucose, along with substantial amounts of xylose and mannose, but only traces of galactose, the most abundant sugar in most characterized bacterial exopolysaccharides. Linkage analysis and characterization by nuclear magnetic resonance suggested that most of the glucosyl units were not present as partially degraded cellulose. Calculations suggested that the energy demand for synthesis of the nonprotein fraction of EPS by this organism represents only a small fraction (<4%) of the anabolic ATP expenditure of the bacterium. PMID:17028224

  5. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    SciTech Connect

    Imam, S.H.; Greene, R.V.; Griffin, H.L. )

    1990-05-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. {sup 35}S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA (ethylene hlycol-bis({beta}-aminoethyl ether)-N,N,N{prime}N{prime}-tetraacetic acid) had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction.

  6. Integrating Robotic Observatories into Astronomy Labs

    NASA Astrophysics Data System (ADS)

    Ruch, Gerald T.

    2015-01-01

    The University of St. Thomas (UST) and a consortium of five local schools is using the UST Robotic Observatory, housing a 17' telescope, to develop labs and image processing tools that allow easy integration of observational labs into existing introductory astronomy curriculum. Our lab design removes the burden of equipment ownership by sharing access to a common resource and removes the burden of data processing by automating processing tasks that are not relevant to the learning objectives.Each laboratory exercise takes place over two lab periods. During period one, students design and submit observation requests via the lab website. Between periods, the telescope automatically acquires the data and our image processing pipeline produces data ready for student analysis. During period two, the students retrieve their data from the website and perform the analysis. The first lab, 'Weighing Jupiter,' was successfully implemented at UST and several of our partner schools. We are currently developing a second lab to measure the age of and distance to a globular cluster.

  7. Experiences with lab-centric instruction

    NASA Astrophysics Data System (ADS)

    Titterton, Nathaniel; Lewis, Colleen M.; Clancy, Michael J.

    2010-06-01

    Lab-centric instruction emphasizes supervised, hands-on activities by substituting lab for lecture time. It combines a multitude of pedagogical techniques into the format of an extended, structured closed lab. We discuss the range of benefits for students, including increased staff interaction, frequent and varied self-assessments, integrated collaborative activities, and a systematic sequence of activities that gradually increases in difficulty. Instructors also benefit from a deeper window into student progress and understanding. We follow with discussion of our experiences in courses at U.C. Berkeley, and using data from some of these investigate the effects of lab-centric instruction on student learning, procrastination, and course pacing. We observe that the lab-centric format helped students on exams but hurt them on extended programming assignments, counter to our hypothesis. Additionally, we see no difference in self-ratings of procrastination and limited differences in ratings of course pace. We do find evidence that the students who choose to attend lab-centric courses are different in several important ways from students who choose to attend the same course in a non-lab-centric format.

  8. Effect of fermented broth from lactic acid bacteria on pathogenic bacteria proliferation.

    PubMed

    Gutiérrez, S; Martínez-Blanco, H; Rodríguez-Aparicio, L B; Ferrero, M A

    2016-04-01

    In this study, the effect that 5 fermented broths of lactic acid bacteria (LAB) strains have on the viability or proliferation and adhesion of 7 potentially pathogenic microorganisms was tested. The fermented broth from Lactococcus lactis C660 had a growth inhibitory effect on Escherichia coli K92 that reached of 31%, 19% to Pseudomonas fluorescens, and 76% to Staphylococcus epidermidis. The growth of Staph. epidermidis was negatively affected to 90% by Lc. lactis 11454 broth, whereas the growth of P. fluorescens (25%) and both species of Staphylococcus (35% to Staphylococcus aureus and 76% to Staph. epidermidis) were inhibited when they were incubated in the presence of Lactobacillus casei 393 broth. Finally, the fermented broth of Lactobacillus rhamnosus showed an inhibitory effect on growth of E. coli K92, Listeria innocua, and Staph. epidermidis reached values of 12, 28, and 76%, respectively. Staphylococcus epidermidis was the most affected strain because the effect was detected from the early stages of growth and it was completely abolished. The results of bacterial adhesion revealed that broths from Lc. lactis strains, Lactobacillus paracasei, and Lb. rhamnosus caused a loss of E. coli K92 adhesion. Bacillus cereus showed a decreased of adhesion in the presence of the broths of Lc. lactis strains and Lb. paracasei. Listeria innocua adhesion inhibition was observed in the presence of Lb. paracasei broth, and the greatest inhibitory effect was registered when this pathogenic bacterium was incubated in presence of Lc. lactis 11454 broth. With respect to the 2 Pseudomonas, we observed a slight adhesion inhibition showed by Lactobacillus rhamnosus broth against Pseudomonas putida. These results confirm that the effect caused by the different LAB assayed is also broth- and species-specific and reveal that the broth from LAB tested can be used as functional bioactive compounds to regulate the adhesion and biofilm synthesis and ultimately lead to preventing food and

  9. Effect of fermented broth from lactic acid bacteria on pathogenic bacteria proliferation.

    PubMed

    Gutiérrez, S; Martínez-Blanco, H; Rodríguez-Aparicio, L B; Ferrero, M A

    2016-04-01

    In this study, the effect that 5 fermented broths of lactic acid bacteria (LAB) strains have on the viability or proliferation and adhesion of 7 potentially pathogenic microorganisms was tested. The fermented broth from Lactococcus lactis C660 had a growth inhibitory effect on Escherichia coli K92 that reached of 31%, 19% to Pseudomonas fluorescens, and 76% to Staphylococcus epidermidis. The growth of Staph. epidermidis was negatively affected to 90% by Lc. lactis 11454 broth, whereas the growth of P. fluorescens (25%) and both species of Staphylococcus (35% to Staphylococcus aureus and 76% to Staph. epidermidis) were inhibited when they were incubated in the presence of Lactobacillus casei 393 broth. Finally, the fermented broth of Lactobacillus rhamnosus showed an inhibitory effect on growth of E. coli K92, Listeria innocua, and Staph. epidermidis reached values of 12, 28, and 76%, respectively. Staphylococcus epidermidis was the most affected strain because the effect was detected from the early stages of growth and it was completely abolished. The results of bacterial adhesion revealed that broths from Lc. lactis strains, Lactobacillus paracasei, and Lb. rhamnosus caused a loss of E. coli K92 adhesion. Bacillus cereus showed a decreased of adhesion in the presence of the broths of Lc. lactis strains and Lb. paracasei. Listeria innocua adhesion inhibition was observed in the presence of Lb. paracasei broth, and the greatest inhibitory effect was registered when this pathogenic bacterium was incubated in presence of Lc. lactis 11454 broth. With respect to the 2 Pseudomonas, we observed a slight adhesion inhibition showed by Lactobacillus rhamnosus broth against Pseudomonas putida. These results confirm that the effect caused by the different LAB assayed is also broth- and species-specific and reveal that the broth from LAB tested can be used as functional bioactive compounds to regulate the adhesion and biofilm synthesis and ultimately lead to preventing food and

  10. Teachers' Perspectives on Online Virtual Labs vs. Hands-On Labs in High School Science

    NASA Astrophysics Data System (ADS)

    Bohr, Teresa M.

    This study of online science teachers' opinions addressed the use of virtual labs in online courses. A growing number of schools use virtual labs that must meet mandated laboratory standards to ensure they provide learning experiences comparable to hands-on labs, which are an integral part of science curricula. The purpose of this qualitative case study was to examine teachers' perceptions of the quality and effectiveness of high school virtual labs. The theoretical foundation was constructivism, as labs provide student-centered activities for problem solving, inquiry, and exploration of phenomena. The research questions focused on experienced teachers' perceptions of the quality of virtual vs. hands-on labs. Data were collected through survey questions derived from the lab objectives of The Next Generation Science Standards . Eighteen teachers rated the degree of importance of each objective and also rated how they felt virtual labs met these objectives; these ratings were reported using descriptive statistics. Responses to open-ended questions were few and served to illustrate the numerical results. Many teachers stated that virtual labs are valuable supplements but could not completely replace hands-on experiences. Studies on the quality and effectiveness of high school virtual labs are limited despite widespread use. Comprehensive studies will ensure that online students have equal access to quality labs. School districts need to define lab requirements, and colleges need to specify the lab experience they require. This study has potential to inspire positive social change by assisting science educators, including those in the local school district, in evaluating and selecting courseware designed to promote higher order thinking skills, real-world problem solving, and development of strong inquiry skills, thereby improving science instruction for all high school students.

  11. Teaching Chemistry Lab Safety through Comics

    NASA Astrophysics Data System (ADS)

    di Raddo, Pasquale

    2006-04-01

    As a means for raising students' interest in aspects pertaining to chemistry lab safety, this article presents a novel approach to teaching this important subject. Comic book lab scenes that involve fictional characters familiar to many students are presented and discussed as to the safety concerns represented in those images. These are discussed in a safety prelab session. For the sake of comparison, students are then shown images taken from current chemistry journals of safety-conscious contemporary chemists at work in their labs. Finally the need to adhere to copyright regulations for the use of the images is discussed so as to increase students' awareness of academic honesty and copyright issues.

  12. Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives.

    PubMed

    Rokop, Z P; Horton, M A; Newton, I L G

    2015-10-01

    In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific "core" members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of "noncore" and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited. PMID:26253685

  13. Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

    PubMed Central

    Rokop, Z. P.; Horton, M. A.

    2015-01-01

    In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific “core” members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of “noncore” and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited. PMID:26253685

  14. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions

    PubMed Central

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Hosseini Salekdeh, Ghasem; Karimi, Keikhosro

    2016-01-01

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated. PMID:26725518

  15. Lawrence Berkeley Lab Indexing Toolbox

    SciTech Connect

    Sauter, Nicholas K.

    2003-09-08

    The Lawrence Berkeley Lab Indexing Toolbox is intended to be used in the context of X-ray crystallography experiments involving biological macromolecules. Macromolecules such as proteins form 3-dimensional periodic arrays (crystal) which in turn lead to lattice-like diffraction patterns when the crystal sample is irradiated with collimated X-rays from a synchrotron or other X-ray source. Once the diffraction pattern is captured on an imaging device the next step is to deduce the periodic nature of the crystal sample, along with its internal symmetry. this analysis, known as "indexing" is a well-studied problem. However, there are no other implementations designed to operate in an automated setting, in which the human experimentalist is not prosent to manually verify the results of indexing. In particular LABELIT uses three novel algorithms to facilitate automation: a more robust way to verify the position of the incident X-ray beam on the image, a better way to verify that the deduced lattice is consistent with the observed crystal lattice, and new method to deduce the internal symmetry from measurements of the lattice. Moreover, the algorithms are implemented in a Python framework that permits indexing to fail (in rare cases) without crashing the program, thus allowing the software to be incorporated in robotic systems where unattended operation is expected. It will be especially useful for high throughput operations at snychrotron beamlines.

  16. Lab-on-a-Chip

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Labs on chips are manufactured in many shapes and sizes and can be used for numerous applications, from medical tests to water quality monitoring to detecting the signatures of life on other planets. The eight holes on this chip are actually ports that can be filled with fluids or chemicals. Tiny valves control the chemical processes by mixing fluids that move in the tiny channels that look like lines, connecting the ports. Scientists at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama designed this chip to grow biological crystals on the International Space Station. Through this research, they discovered that this technology is ideally suited for solving the challenges of the Vision for Space Exploration. For example, thousands of chips the size of dimes could be loaded on a Martian rover looking for biosignatures of past or present life. Other types of chips could be placed in handheld devices used to monitor microbes in water or to quickly conduct medical tests on astronauts. (NASA/MSFC/D.Stoffer)

  17. Jefferson Lab's Distributed Data Acquisition

    SciTech Connect

    Trent Allison; Thomas Powers

    2006-05-01

    Jefferson Lab's Continuous Electron Beam Accelerator Facility (CEBAF) occasionally experiences fast intermittent beam instabilities that are difficult to isolate and result in downtime. The Distributed Data Acquisition (Dist DAQ) system is being developed to detect and quickly locate such instabilities. It will consist of multiple Ethernet based data acquisition chassis distributed throughout the seven-eights of a mile CEBAF site. Each chassis will monitor various control system signals that are only available locally and/or monitored by systems with small bandwidths that cannot identify fast transients. The chassis will collect data at rates up to 40 Msps in circular buffers that can be frozen and unrolled after an event trigger. These triggers will be derived from signals such as periodic timers or accelerator faults and be distributed via a custom fiber optic event trigger network. This triggering scheme will allow all the data acquisition chassis to be triggered simultaneously and provide a snapshot of relevant CEBAF control signals. The data will then be automatically analyzed for frequency content and transients to determine if and where instabilities exist.

  18. Lawrence Berkeley Lab Indexing Toolbox

    2003-09-08

    The Lawrence Berkeley Lab Indexing Toolbox is intended to be used in the context of X-ray crystallography experiments involving biological macromolecules. Macromolecules such as proteins form 3-dimensional periodic arrays (crystal) which in turn lead to lattice-like diffraction patterns when the crystal sample is irradiated with collimated X-rays from a synchrotron or other X-ray source. Once the diffraction pattern is captured on an imaging device the next step is to deduce the periodic nature of themore » crystal sample, along with its internal symmetry. this analysis, known as "indexing" is a well-studied problem. However, there are no other implementations designed to operate in an automated setting, in which the human experimentalist is not prosent to manually verify the results of indexing. In particular LABELIT uses three novel algorithms to facilitate automation: a more robust way to verify the position of the incident X-ray beam on the image, a better way to verify that the deduced lattice is consistent with the observed crystal lattice, and new method to deduce the internal symmetry from measurements of the lattice. Moreover, the algorithms are implemented in a Python framework that permits indexing to fail (in rare cases) without crashing the program, thus allowing the software to be incorporated in robotic systems where unattended operation is expected. It will be especially useful for high throughput operations at snychrotron beamlines.« less

  19. Labs not in a lab: A case study of instructor and student perceptions of an online biology lab class

    NASA Astrophysics Data System (ADS)

    Doiron, Jessica Boyce

    Distance learning is not a new phenomenon but with the advancement in technology, the different ways of delivering an education have increased. Today, many universities and colleges offer their students the option of taking courses online instead of sitting in a classroom on campus. In general students like online classes because they allow for flexibility, the comfort of sitting at home, and the potential to save money. Even though there are advantages to taking online classes, many students and instructors still debate the effectiveness and quality of education in a distant learning environment. Many universities and colleges are receiving pressure from students to offer more and more classes online. Research argues for both the advantages and disadvantages of online classes and stresses the importance of colleges and universities weighing both sides before deciding to adopt an online class. Certain classes may not be suitable for online instruction and not all instructors are suitable to teach online classes. The literature also reveals that there is a need for more research on online biology lab classes. With the lack of information on online biology labs needed by science educators who face the increasing demand for online biology labs, this case study hopes to provide insight into the use of online biology lab classes and the how students and an instructor at a community college in Virginia perceive their online biology lab experience as well as the effectiveness of the online labs.

  20. Acid Rain Classroom Projects.

    ERIC Educational Resources Information Center

    Demchik, Michael J.

    2000-01-01

    Describes a curriculum plan in which students learn about acid rain through instructional media, research and class presentations, lab activities, simulations, design, and design implementation. Describes the simulation activity in detail and includes materials, procedures, instructions, examples, results, and discussion sections. (SAH)

  1. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae.

    PubMed

    Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi

    2012-11-01

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae.

  2. Polaribacter butkevichii sp. nov., a novel marine mesophilic bacterium of the family Flavobacteriaceae.

    PubMed

    Nedashkovskaya, Olga I; Kim, Seung Bum; Lysenko, Anatoly M; Kalinovskaya, Nataliya I; Mikhailov, Valery V; Kim, In Seop; Bae, Kyung Sook

    2005-12-01

    A novel heterotrophic, yellow pigmented, aerobic, Gram-negative, nonmotile, oxidase- and catalase-positive bacterium KMM 3,938(T) was isolated from sea water collected in the Sea of Japan, Russia. The strain grew at mesophilic temperature range, and required the presence of NaCl for growth. 16S rRNA gene sequence analysis revealed that strain KMM 3,938(T) is a member of the family Flavobacteriaceae. The predominant fatty acids were C13:0 iso, C14:0 iso, C15:0 iso, C15:0, C15:1Delta6, 3OH-C15:0:3 iso, and 3OH-C15:0. The G + C content of the DNA of KMM 3938(T) was 32.4 mol%. On the basis of phenotypic, chemotaxonomic, genotypic, and phylogenetic characteristics, the novel bacterium was assigned to the genus Polaribacter as Polaribacter butkevichii sp. nov. The type strain is KMM 3938(T )(= KCTC 12100(T) = CCUG 48005(T)).

  3. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage

    PubMed Central

    Mehboob, Farrakh; van Gelder, Antonie H.; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Stams, Alfons J. M.

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5–0.8 μm in diameter, and 2–8 μm in length, growing as single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H2/CO2 to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO2. The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts. PMID:20680263

  4. Non-specific immune response of bullfrog Rana catesbeiana to intraperitoneal injection of bacterium Aeromonas hydrophila

    NASA Astrophysics Data System (ADS)

    Zhang, Junjie; Zou, Wenzheng; Yan, Qingpi

    2008-08-01

    Non-specific immune response of bullfrog Rana catesbeiana to pathogenic Aeromonas hydrophila was studied to 60 individuals in two groups. Each bullfrog in bacterium-injected group was injected intraperitoneally (i.p.) with 0.2 ml bacterial suspension at a density of 5.2 × 106 CFU/ml, while each one in control group injected i.p. with 0.2 ml sterile saline solution (0.85%, w/v). Three bullfrogs in both groups were sampled at 0, 1, 3, 7, 11, 15 and 20 days post-injection (dpi) for the evaluation of non-specific immune parameters. It was observed that intraperitoneal injection of A. hydrophila significantly increased the number of leucocytes and that of NBT-positive cells in peripheral blood. Significant increases in serum bactericidal activity and serum acid phosphatase activity were also observed in the bacterium-injected frogs when compared with those in the control group. However, a significant reduction was detected in vitro in phagocytosis activity of peripheral blood phagocytes. No significant difference in changes in the number of peripheral erythrocytes, serum superoxide dismutase (SOD) activity, and lysozyme activity was detected between the two groups. It is suggested that bullfrogs may produce a series of non-specific immune reactions in response to the A. hydrophila infection.

  5. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    USGS Publications Warehouse

    Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  6. Biomass yield efficiency of the marine anammox bacterium, "Candidatus Scalindua sp.," is affected by salinity.

    PubMed

    Awata, Takanori; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2015-01-01

    The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium "Candidatus Scalindua sp." is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of "Ca. Scalindua sp." enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0-10 mM) were observed under varying salinities (0.5%-4%). Anammox activity was high at 0.5%-3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%-3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium "Ca. Scalindua sp." was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency.

  7. A symbiotic bacterium differentially influences arsenate absorption and transformation in Dunaliella salina under different phosphate regimes.

    PubMed

    Wang, Ya; Zhang, Chun Hua; Lin, Man Man; Ge, Ying

    2016-11-15

    In this study, we investigated the effects of a symbiotic bacterium and phosphate (PO4(3-)) nutrition on the toxicity and metabolism of arsenate (As(V)) in Dunaliella salina. The bacterium was identified as Alteromonas macleodii based on analysis of its 16S rRNA gene sequence. When no As(V) was added, A. macleodii significantly enhanced the growth of D. salina, irrespective of PO4(3-) nutrition levels, but this effect was reversed after As(V)+PO4(3-) treatment (1.12mgL(-1)) for 3 days. Arsenic (As) absorption by the non-axenic D. salina was significantly higher than that by its axenic counterpart during incubation with 1.12mgL(-1) PO4(3-). However, when the culture was treated with 0.112mgL(-1) PO4(3-), As(V) reduction and its subsequent arsenite (As(III)) excretion by non-axenic D. salina were remarkably enhanced, which, in turn, contributed to lower As absorption in non-axenic algal cells from days 7 to 9. Moreover, dimethylarsinic acid was synthesized by D. salina alone, and the rates of its production and excretion were accelerated when the PO4(3-) concentration was 0.112mgL(-1). Our data demonstrate that A. macleodii strongly affected As toxicity, uptake, and speciation in D. salina, and these impacts were mediated by PO4(3-) in the cultures.

  8. Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers

    PubMed Central

    Bottomley, Peter J.

    2015-01-01

    Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS. PMID:26092466

  9. Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers.

    PubMed

    Mellbye, Brett L; Bottomley, Peter J; Sayavedra-Soto, Luis A

    2015-09-01

    Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS.

  10. Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

    PubMed

    Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

    2010-09-01

    The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa.

  11. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

    SciTech Connect

    Suen, Garret; Stevenson, David M; Bruce, David; Chertkov, Olga; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Ivanova, N; Kyrpides, Nikos C; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Ovchinnikova, Galina; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Boyum, Julie; Mead, David; Weimer, Paul J

    2011-01-01

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  12. Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis

    PubMed Central

    Faulkner, Matthew; Liu, Xuan; Huang, Fang; Darby, Alistair C.; Hall, Neil

    2016-01-01

    Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces bacteriochlorophyll b. Here we report an improved genome sequence of Blastochloris viridis DSM133, which is instrumental to the studies of photosynthesis, metabolic versatility, and genetic engineering of this microorganism. PMID:26798090

  13. NCL Objective #3 - Nanotechnology Characterization Lab (NCL)

    Cancer.gov

    The Nanotechnology Characterization Lab (NCL) Objective #3: Identify and Characterize Critical Parameters Related to Nanomaterials' Absorption, Distribution, Metabolism, Excretion, and Acute Toxicity (ADME/Tox) Profile in Animal Models.

  14. Administrator Helps Students Discover Lab Day

    NASA Video Gallery

    NASA Administrator Charles Bolden visited the Langdon Elementary School in Washington to support National Lab Day. Bolden, a veteran of four space shuttle flights, spoke with the fifth graders abou...

  15. NCL Objective #4 - Nanotechnology Characterization Lab (NCL)

    Cancer.gov

    The Nanotechnology Characterization Lab (NCL) Objective #4: Examine the Biological and Functional Characteristics of MultiComponent/Combinatorial Aspects of Nanoscaled Therapeutic, Molecular and Clinical Diagnostics, and Detection Platforms.

  16. Microspectroscopy At Beamline 73 MAX-lab

    NASA Astrophysics Data System (ADS)

    Engdahl, Anders

    2010-02-01

    Presentation of some projects at the infrared microspectroscopy experimental station at beamline 73 MAX-lab. Among the subjects are found identification of organic residues in fossil material and examination of the chemistry in an old oak wood wreck.

  17. Thanatology for Everyone: Developmental Labs and Workshops

    ERIC Educational Resources Information Center

    O'Connell, Walter E.; And Others

    1977-01-01

    In an effort to "treat" the growing death concerns of many medical staffs, an experiential death and dying lab was created. Its evolution to meet changing needs is discussed, as well as future potential for work in this area. (Author)

  18. Isolation and Characterization of a Facultatively Aerobic Bacterium That Reductively Dehalogenates Tetrachloroethene to cis-1,2-Dichloroethene

    PubMed Central

    Sharma, P. K.; McCarty, P. L.

    1996-01-01

    A rapidly-growing facultatively aerobic bacterium that transforms tetrachloroethene (PCE) via trichloroethene (TCE) to cis-1,2-dichloroethene (cis-1,2-DCE) at high rates in a defined medium was isolated from a contaminated site. Metabolic characterization, cellular fatty acid analysis, and partial sequence analysis of 16S rRNA showed that the new isolate, strain MS-1, has characteristics matching those of the members of the family Enterobacteriaceae. Strain MS-1 can oxidize about 58 substrates including many carbohydrates, short-chain fatty acids, amino acids, purines, and pyrimidines. It can transform up to 1 mM PCE (aqueous) at a rate of about 0.5 (mu)mol of PCE(middot) h(sup-1)(middot)mg (dry weight) of cell(sup-1). PCE transformation occurs following growth on or with the addition of single carbon sources such as glucose, pyruvate, formate, lactate, or acetate or with complex nutrient sources such as yeast extract or a mixture of amino acids. PCE dehalogenation requires the absence of oxygen, nitrate, and high concentrations of fermentable compounds such as glucose. Enterobacter agglomerans biogroup 5 (ATCC 27993), a known facultative bacterium that is closely related to strain MS-1, also reductively dehalogenated PCE to cis-1,2-DCE. To our knowledge, this is the first report on isolation of a facultative bacterium that can reductively transform PCE to cis-1,2-DCE under defined physiological conditions. Also, this is the first report of the ability of E. agglomerans to dehalogenate PCE. PMID:16535267

  19. PLC Support Software at Jefferson Lab

    SciTech Connect

    P. Chevtsov; S. Higgins; S. Schaffner; D. Seidman

    2002-10-01

    Several Automation Direct (DirectNet) Programmable Logic Controllers (PLCs) have been integrated into the accelerator control system at Jefferson Lab. The integration is based on new software that consists of three main parts: a PLC driver with a state machine control block, a device support module, and a common serial driver. The components of new software and experience gained with the use of this software for beam dump systems at Jefferson Lab are presented.

  20. Addition of microbially-treated sugar beet residue and a native bacterium increases structural stability in heavy metal-contaminated Mediterranean soils.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Kohler, J; Roldán, A

    2009-10-15

    A mesocosm experiment was conducted to investigate the effect of the addition of Aspergillus niger-treated sugar beet waste, in the presence of rock phosphate, and inoculation with a native, metal-tolerant bacterium, Bacillus thuringiensis, on the stabilisation of soil aggregates of two mine tailings, with differing pH values, from a semiarid Mediterranean area and on the stimulation of growth of Piptatherum miliaceum. Bacterium combined with organic amendment enhanced structural stability (38% in acidic soil and 106% in neutral soil compared with their corresponding controls). Only the organic amendment increased pH, electrical conductivity, water-soluble C, water-soluble carbohydrates and plant growth, in both soils. While in neutral soil both organic amendment and bacterium increased dehydrogenase activity, only organic amendment had a significant effect in acidic soil. This study demonstrates that the use of P. miliaceum in combination with organic amendment and bacterium is a suitable tool for the stabilisation of the soil structure of degraded mine tailings, although its effectiveness is dependent on soil pH. PMID:19660785

  1. A comparative study on real lab and simulation lab in communication engineering from students' perspectives

    NASA Astrophysics Data System (ADS)

    Balakrishnan, B.; Woods, P. C.

    2013-05-01

    Over the years, rapid development in computer technology has engendered simulation-based laboratory (lab) in addition to the traditional hands-on (physical) lab. Many higher education institutions adopt simulation lab, replacing some existing physical lab experiments. The creation of new systems for conducting engineering lab activities has raised concerns among educators on the merits and shortcomings of both physical and simulation labs; at the same time, many arguments have been raised on the differences of both labs. Investigating the effectiveness of both labs is complicated, as there are multiple factors that should be considered. In view of this challenge, a study on students' perspectives on their experience related to key aspects on engineering laboratory exercise was conducted. In this study, the Visual Auditory Read and Kinetic model was utilised to measure the students' cognitive styles. The investigation was done through a survey among participants from Multimedia University, Malaysia. The findings revealed that there are significant differences for most of the aspects in physical and simulation labs.

  2. The Cardiac Electrophysiology Web Lab.

    PubMed

    Cooper, Jonathan; Scharm, Martin; Mirams, Gary R

    2016-01-19

    Computational modeling of cardiac cellular electrophysiology has a long history, and many models are now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviors so that we can choose a model as a suitable basis for a new study or to characterize how a particular model behaves in different scenarios? We have created an online resource for the characterization and comparison of electrophysiological cell models in a wide range of experimental scenarios. The details of the mathematical model (quantitative assumptions and hypotheses formulated as ordinary differential equations) are separated from the experimental protocol being simulated. Each model and protocol is then encoded in computer-readable formats. A simulation tool runs virtual experiments on models encoded in CellML, and a website (https://chaste.cs.ox.ac.uk/WebLab) provides a friendly interface, allowing users to store and compare results. The system currently contains a sample of 36 models and 23 protocols, including current-voltage curve generation, action potential properties under steady pacing at different rates, restitution properties, block of particular channels, and hypo-/hyperkalemia. This resource is publicly available, open source, and free, and we invite the community to use it and become involved in future developments. Investigators interested in comparing competing hypotheses using models can make a more informed decision, and those developing new models can upload them for easy evaluation under the existing protocols, and even add their own protocols.

  3. The Cardiac Electrophysiology Web Lab.

    PubMed

    Cooper, Jonathan; Scharm, Martin; Mirams, Gary R

    2016-01-19

    Computational modeling of cardiac cellular electrophysiology has a long history, and many models are now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviors so that we can choose a model as a suitable basis for a new study or to characterize how a particular model behaves in different scenarios? We have created an online resource for the characterization and comparison of electrophysiological cell models in a wide range of experimental scenarios. The details of the mathematical model (quantitative assumptions and hypotheses formulated as ordinary differential equations) are separated from the experimental protocol being simulated. Each model and protocol is then encoded in computer-readable formats. A simulation tool runs virtual experiments on models encoded in CellML, and a website (https://chaste.cs.ox.ac.uk/WebLab) provides a friendly interface, allowing users to store and compare results. The system currently contains a sample of 36 models and 23 protocols, including current-voltage curve generation, action potential properties under steady pacing at different rates, restitution properties, block of particular channels, and hypo-/hyperkalemia. This resource is publicly available, open source, and free, and we invite the community to use it and become involved in future developments. Investigators interested in comparing competing hypotheses using models can make a more informed decision, and those developing new models can upload them for easy evaluation under the existing protocols, and even add their own protocols. PMID:26789753

  4. Supplemental Guidelines, JCE Lab-Experiment Manuscripts

    NASA Astrophysics Data System (ADS)

    2000-05-01

    These guidelines supplement the Guide to Submissions (published in J. Chem. Educ. 2000, 77, 29-30 and at http://jchemed.chem.wisc.edu/Journal/Authors/ Guidelines.html or available on request from the JCE editorial office). Manuscripts that describe laboratory experiments should first follow the Guide to Submissions and then apply these Supplemental Guidelines. Rationale JCE receives many submissions that describe laboratory experiments. The broad range of experiments readers can find each month is one of our most important features. These supplemental guidelines have been designed to make published laboratory experiments as useful as possible to readers. They are based on four fundamental ideas:

    • peer review of a lab-experiment manuscript should be based to a large degree on the written and technology-based materials used by students in the laboratory, not just on a description of those materials;
    • JCE should print the information a reader needs to decide whether to try to use the experiment; this includes information about possible safety hazards;
    • readers who decide to use a lab should be able to adapt it to their circumstances quickly and easily;
    • detailed information, including student materials, should be available to adopters of an experiment in a format that is modifiable and easily adapted for use by faculty, students, and support staff.
    To support these goals we require that a manuscript that describes a laboratory experiment must consist of a Lab Summary and Lab Documentation. (Each of these is described in detail below.) If, after peer review, a lab-experiment manuscript is published, only the Lab Summary will be printed in JCE. The Abstract, the Lab Summary, and all Lab Documentation will be published via JCE Online. Lab Documentation is placed on the Web as PDF files that can be displayed and printed by Acrobat Reader, and as Word or Word Perfect files that can be edited by those who adopt a lab. Those without Web

  5. Assessing Usage and Maximizing Finance Lab Impact: A Case Exploration

    ERIC Educational Resources Information Center

    Noguera, Magdy; Budden, Michael Craig; Silva, Alberto

    2011-01-01

    This paper reports the results of a survey conducted to assess students' usage and perceptions of a finance lab. Finance labs differ from simple computer labs as they typically contain data boards, streaming market quotes, terminals and software that allow for real-time financial analyses. Despite the fact that such labs represent significant and…

  6. The genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia.

    PubMed

    Kube, Michael; Migdoll, Alexander Michael; Müller, Ines; Kuhl, Heiner; Beck, Alfred; Reinhardt, Richard; Geider, Klaus

    2008-09-01

    The complete genome of the bacterium Erwinia tasmaniensis strain Et1/99 consisting of a 3.9 Mb circular chromosome and five plasmids was sequenced. Strain Et1/99 represents an epiphytic plant bacterium related to Erwinia amylovora and E. pyrifoliae, which are responsible for the important plant diseases fire blight and Asian pear shoot blight, respectively. Strain Et1/99 is a non-pathogenic bacterium and is thought to compete with these and other bacteria when occupying the same habitat during initial colonization. Genome analysis revealed tools for colonization, cellular communication and defence modulation, as well as genes coding for the synthesis of levan and a not detected capsular exopolysaccharide. Strain Et1/99 may secrete indole-3-acetic acid to increase availability of nutrients provided on plant surfaces. These nutrients are subsequently accessed and metabolized. Secretion systems include the hypersensitive response type III pathway present in many pathogens. Differences or missing parts within the virulence-related factors distinguish strain Et1/99 from pathogens such as Pectobacterium atrosepticum and the related Erwinia spp. Strain Et1/99 completely lacks the sorbitol operon, which may also affect its inability to invade fire blight host plants. Erwinia amylovora in contrast depends for virulence on utilization of sorbitol, the dominant carbohydrate in rosaceous plants. The presence of other virulence-associated factors in strain Et1/99 indicates the ancestral genomic background of many plant-associated bacteria.

  7. Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.

    PubMed

    Zhang, Wen-wu; Fang, Ming-xu; Tan, Hai-qin; Zhang, Xin-qi; Wu, Min; Zhu, Xu-fen

    2012-09-01

    A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TY(T), was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l(-1). Strain TY(T) produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C(14 : 0) DMA (18.7 %), C(15 : 0) (15.4 %), anteiso-C(18 : 1) (15.2 %), C(11 : 0) (13.3 %) and summed feature 5 (C(17 : 1)ω7c and/or C(17 : 2)) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TY(T) represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TY(T) is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TY(T) = JCM 17499(T) = DSM 24661(T)).

  8. Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.

    PubMed

    Zhang, Wen-wu; Fang, Ming-xu; Tan, Hai-qin; Zhang, Xin-qi; Wu, Min; Zhu, Xu-fen

    2012-09-01

    A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TY(T), was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l(-1). Strain TY(T) produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C(14 : 0) DMA (18.7 %), C(15 : 0) (15.4 %), anteiso-C(18 : 1) (15.2 %), C(11 : 0) (13.3 %) and summed feature 5 (C(17 : 1)ω7c and/or C(17 : 2)) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TY(T) represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TY(T) is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TY(T) = JCM 17499(T) = DSM 24661(T)). PMID:22058316

  9. Nanomechanical properties of the sea-water bacterium Paracoccus seriniphilus--a scanning force microscopy approach.

    PubMed

    Davoudi, Neda; Müller-Renno, Christine; Ziegler, Christiane; Raid, Indek; Seewig, Jörg; Schlegel, Christin; Muffler, Kai; Ulber, Roland

    2015-03-02

    The measurement of force-distance curves on a single bacterium provides a unique opportunity to detect properties such as the turgor pressure under various environmental conditions. Marine bacteria are very interesting candidates for the production of pharmaceuticals, but are only little studied so far. Therefore, the elastic behavior of Paracoccus seriniphilus, an enzyme producing marine organism, is presented in this study. After a careful evaluation of the optimal measurement conditions, the spring constant and the turgor pressure are determined as a function of ionic strength and pH. Whereas the ionic strength changes the turgor pressure passively, the results give a hint that the change to acidic pH increases the turgor pressure by an active mechanism. Furthermore, it could be shown, that P. seriniphilus has adhesive protrusions outside its cell wall.

  10. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.

    PubMed

    Rivas, Raúl; Trujillo, Martha E; Mateos, P F; Martínez-Molina, E; Velázquez, Encarna

    2004-03-01

    A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99.0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11(T) in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA-DNA hybridization with C. humilata ATCC 25174(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11(T) should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11(T) (=LMG 21723(T)=CECT 5729(T)) as the type strain.

  11. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    PubMed

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. PMID:23186687

  12. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru

    PubMed Central

    O’Neal, Lindsey; Obregón-Tito, Alexandra J.; Tito, Raul Y.; Ozga, Andrew T.; Polo, Susan I.; Lewis, Cecil M.; Lawson, Paul A.

    2015-01-01

    A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08VT, was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth on glucose were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08VT (DSM 23598T = CCUG 59712T). PMID:26123611

  13. Cytochrome P450 enzymes from the metabolically diverse bacterium Rhodopseudomonas palustris

    SciTech Connect

    Bell, Stephen G. . E-mail: stephen.bell@chem.ox.ac.uk; Hoskins, Nicola; Xu Feng; Caprotti, Domenico; Rao Zihe; Wong, L.-L. . E-mail: luet.wong@chem.ox.ac.uk

    2006-03-31

    Four (CYP195A2, CYP199A2, CYP203A1, and CYP153A5) of the seven P450 enzymes, and palustrisredoxin A, a ferredoxin associated with CYP199A2, from the metabolically diverse bacterium Rhodopseudomonas palustris have been expressed and purified. A range of substituted benzenes, phenols, benzaldehydes, and benzoic acids was shown to bind to the four P450 enzymes. Monooxygenase activity of CYP199A2 was reconstituted with palustrisredoxin A and putidaredoxin reductase of the P450cam system from Pseudomonas putida. We found that 4-ethylbenzoate and 4-methoxybenzoate were oxidized to single products, and 4-methoxybenzoate was demethylated to form 4-hydroxybenzoate. Crystals of substrate-free CYP199A2 which diffracted to {approx}2.0 A have been obtained.

  14. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. PMID:27471578

  15. Biodegradation of nitrobenzene in a lysogeny broth medium by a novel halophilic bacterium Bacillus licheniformis.

    PubMed

    Li, Tian; Deng, Xinping; Wang, Jinjun; Chen, Yucheng; He, Lin; Sun, Yuchuan; Song, Caixia; Zhou, Zhifeng

    2014-12-15

    The Bacillus licheniformis strain YX2, a novel nitrobenzene-degrading halophilic bacterium, was isolated from active sludge obtained from a pesticide factory. Strain YX2 can withstand highly acidic and alkaline conditions and high temperatures. Degradation of nitrobenzene (200mgL(-1)) by YX2 exceeded 70% after 72h in lysogeny broth medium (pH 4-9). Under optimal degradation conditions (33°C, pH 7 in LB medium) YX2 degraded 50, 100, 200, and 600mgL(-1) nitrobenzene within 36, 36, 72, and 156h, respectively. Even in the presence of benzene, phenol or aniline, strain YX2 efficiently degraded nitrobenzene. Furthermore, strain YX2 completely degraded 600mgL(-1) nitrobenzene in 7% NaCl (w/w). Thus, our data show that strain YX2 may have promise for removing nitrobenzene from complex wastewaters with high salinity and variable pH.

  16. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    PubMed

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation.

  17. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

    PubMed

    Saw, Jimmy H W; Yuryev, Anton; Kanbe, Masaomi; Hou, Shaobin; Young, Aaron G; Aizawa, Shin-Ichi; Alam, Maqsudul

    2012-03-19

    Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

  18. Are Virtual Labs as Effective as Hands-on Labs for Undergraduate Physics? A Comparative Study at Two Major Universities

    ERIC Educational Resources Information Center

    Darrah, Marjorie; Humbert, Roxann; Finstein, Jeanne; Simon, Marllin; Hopkins, John

    2014-01-01

    Most physics professors would agree that the lab experiences students have in introductory physics are central to the learning of the concepts in the course. It is also true that these physics labs require time and money for upkeep, not to mention the hours spent setting up and taking down labs. Virtual physics lab experiences can provide an…

  19. Rhodococcus percolatus sp. nov., a bacterium degrading 2,4,6-trichlorophenol.

    PubMed

    Briglia, M; Rainey, F A; Stackebrandt, E; Schraa, G; Salkinoja-Salonen, M S

    1996-01-01

    A bacterial strain that was able to mineralize 2,4,6-trichlorophenol was isolated from a chlorophenol-fed percolator and was identified as a member of the genus Rhodococcus on the basis of chemotaxonomic characteristics and 16S RNA phylogenetic inference data. This organism (strain MBS1T [T = type strain]) exhibited a typical irregular rod-coccus cycle, and the cells had fimbria-like structures on their surfaces. The diagnostic cell wall amino acid was meso-diaminopimelic acid, and the sugars were arabinose and galactose; the mycolic acids contained 46 to 54 carbon atoms. The main menaquinone was MK-8(H2), and MK-9(H2) was a minor component. The cellular phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol, and diphosphatidylglycerol. Tuberculostearic acid was present. The whole-cell fatty acids were straight-chain acids with 14 to 18 C atoms. The G+C content of the DNA was 67.4 mol%. This organism grew on sucrose, pyruvate, and 2,4,6-trichlorophenol, and it oxidized a large number of carbon compounds, including catechol, 3-hydroxyphenylacetic acid, and phenol. It also exhibited beta-galactosidase, urease, and 2-acetyl-lactate decarboxylase activities. On a phylogenetic tree that was based on 16S ribosomal DNA gene sequences strain MBS1T was found among the rhodococci on an independent branch. On the basis of the chemotaxonomic and phenotypic characteristics of strain MBS1T and its phylogenetic position we suggest that this bacterium should be placed in a new species, Rhodococcus percolatus; the specific epithet was chosen because the organism was isolated by using an enriched percolator. The type strain is strain MBS1. PMID:8573500

  20. Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut.

    PubMed

    Selma, María V; Tomás-Barberán, Francisco A; Beltrán, David; García-Villalba, Rocio; Espín, Juan C

    2014-07-01

    Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15P(T), capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-b(T), the type and only reported strain of the only species of the genus Gordonibacter, with about 97% 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. L-Fucose, D-fructose, turanose, D-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15P(T), while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70%); strain CEBAS 1/15P(T) differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae. The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1-6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15P(T) ( = DSM 27213(T) = CCUG 64261(T)) as the type strain.

  1. Communication acoustics in Bell Labs

    NASA Astrophysics Data System (ADS)

    Flanagan, J. L.

    2001-05-01

    Communication aoustics has been a central theme in Bell Labs research since its inception. Telecommunication serves human information exchange. And, humans favor spoken language as a principal mode. The atmospheric medium typically provides the link between articulation and hearing. Creation, control and detection of sound, and the human's facility for generation and perception are basic ingredients of telecommunication. Electronics technology of the 1920s ushered in great advances in communication at a distance, a strong economical impetus being to overcome bandwidth limitations of wireline and cable. Early research established criteria for speech transmission with high quality and intelligibility. These insights supported exploration of means for efficient transmission-obtaining the greatest amount of speech information over a given bandwidth. Transoceanic communication was initiated by undersea cables for telegraphy. But these long cables exhibited very limited bandwidth (order of few hundred Hz). The challenge of sending voice across the oceans spawned perhaps the best known speech compression technique of history-the Vocoder, which parametrized the signal for transmission in about 300 Hz bandwidth, one-tenth that required for the typical waveform channel. Quality and intelligibility were grave issues (and they still are). At the same time parametric representation offered possibilities for encryption and privacy inside a traditional voice bandwidth. Confidential conversations between Roosevelt and Churchill during World War II were carried over high-frequency radio by an encrypted vocoder system known as Sigsaly. Major engineering advances in the late 1940s and early 1950s moved telecommunications into a new regime-digital technology. These key advances were at least three: (i) new understanding of time-discrete (sampled) representation of signals, (ii) digital computation (especially binary based), and (iii) evolving capabilities in microelectronics that

  2. RoboLab and virtual environments

    NASA Technical Reports Server (NTRS)

    Giarratano, Joseph C.

    1994-01-01

    A useful adjunct to the manned space station would be a self-contained free-flying laboratory (RoboLab). This laboratory would have a robot operated under telepresence from the space station or ground. Long duration experiments aboard RoboLab could be performed by astronauts or scientists using telepresence to operate equipment and perform experiments. Operating the lab by telepresence would eliminate the need for life support such as food, water and air. The robot would be capable of motion in three dimensions, have binocular vision TV cameras, and two arms with manipulators to simulate hands. The robot would move along a two-dimensional grid and have a rotating, telescoping periscope section for extension in the third dimension. The remote operator would wear a virtual reality type headset to allow the superposition of computer displays over the real-time video of the lab. The operators would wear exoskeleton type arms to facilitate the movement of objects and equipment operation. The combination of video displays, motion, and the exoskeleton arms would provide a high degree of telepresence, especially for novice users such as scientists doing short-term experiments. The RoboLab could be resupplied and samples removed on other space shuttle flights. A self-contained RoboLab module would be designed to fit within the cargo bay of the space shuttle. Different modules could be designed for specific applications, i.e., crystal-growing, medicine, life sciences, chemistry, etc. This paper describes a RoboLab simulation using virtual reality (VR). VR provides an ideal simulation of telepresence before the actual robot and laboratory modules are constructed. The easy simulation of different telepresence designs will produce a highly optimum design before construction rather than the more expensive and time consuming hardware changes afterwards.

  3. Stress Physiology of Lactic Acid Bacteria.

    PubMed

    Papadimitriou, Konstantinos; Alegría, Ángel; Bron, Peter A; de Angelis, Maria; Gobbetti, Marco; Kleerebezem, Michiel; Lemos, José A; Linares, Daniel M; Ross, Paul; Stanton, Catherine; Turroni, Francesca; van Sinderen, Douwe; Varmanen, Pekka; Ventura, Marco; Zúñiga, Manuel; Tsakalidou, Effie; Kok, Jan

    2016-09-01

    Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance. PMID:27466284

  4. Stress Physiology of Lactic Acid Bacteria.

    PubMed

    Papadimitriou, Konstantinos; Alegría, Ángel; Bron, Peter A; de Angelis, Maria; Gobbetti, Marco; Kleerebezem, Michiel; Lemos, José A; Linares, Daniel M; Ross, Paul; Stanton, Catherine; Turroni, Francesca; van Sinderen, Douwe; Varmanen, Pekka; Ventura, Marco; Zúñiga, Manuel; Tsakalidou, Effie; Kok, Jan

    2016-09-01

    Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

  5. Localization of propionibacterium acnes in granulomas supports a possible etiologic link between sarcoidosis and the bacterium.

    PubMed

    Negi, Mariko; Takemura, Tamiko; Guzman, Josune; Uchida, Keisuke; Furukawa, Asuka; Suzuki, Yoshimi; Iida, Tadatsune; Ishige, Ikuo; Minami, Junko; Yamada, Tetsuo; Kawachi, Hiroshi; Costabel, Ulrich; Eishi, Yoshinobu

    2012-09-01

    Sarcoidosis likely results from the exposure of a genetically susceptible subject to an environmental agent, possibly an infectious one. Mycobacterial and propionibacterial organisms are the most commonly implicated potential etiologic agents. Propionibacterium acnes is the only microorganism, however, found in sarcoid lesions by bacterial culture. To evaluate the pathogenic role of this indigenous bacterium, we screened for the bacterium in sarcoid and non-sarcoid tissues using immunohistochemical methods with novel P. acnes-specific monoclonal antibodies that react with cell-membrane-bound lipoteichoic acid (PAB antibody) and ribosome-bound trigger-factor protein (TIG antibody). We examined formalin-fixed and paraffin-embedded samples of lungs and lymph nodes from 196 patients with sarcoidosis, and corresponding control samples from 275 patients with non-sarcoidosis diseases. The samples were mostly from Japanese patients, with 64 lymph node samples from German patients. Immunohistochemistry with PAB antibody revealed small round bodies within sarcoid granulomas in 20/27 (74%) video-assisted thoracic surgery lung samples, 24/50 (48%) transbronchial lung biopsy samples, 71/81 (88%) Japanese lymph node samples, and 34/38 (89%) German lymph node samples. PAB antibody did not react with non-sarcoid granulomas in any of the 45 tuberculosis samples or the 34 samples with sarcoid reaction. In nongranulomatous areas, small round bodies detected by PAB antibody were found in alveolar macrophages of lungs and paracortical macrophages of lymph nodes from many sarcoid and some non-sarcoid patients. Large-spheroidal acid-fast bodies, Hamazaki-Wesenberg bodies, which were found in 50% of sarcoid and 15% of non-sarcoid lymph node samples, reacted with both PAB and TIG antibodies. Electron microscopy revealed that these Hamazaki-Wesenberg bodies had a single bacterial structure and lacked a cell wall with occasional protrusions from the body. The high frequency and specificity

  6. Do Online Labs Work? An Assessment of an Online Lab on Cell Division

    ERIC Educational Resources Information Center

    Gilman, Sharon L.

    2006-01-01

    Some studies show students successfully learning science through online courses. This study compared students doing an online and in-class lab exercise on cell division. Online students performed slightly but significantly better on a follow-up content quiz, however, about half those expressed a strong preference for in-class lab work.

  7. Improving the Quality of Lab Reports by Using Them as Lab Instructions

    ERIC Educational Resources Information Center

    Haagen-Schuetzenhoefer, Claudia

    2012-01-01

    Lab exercises are quite popular in teaching science. Teachers have numerous goals in mind when teaching science laboratories. Nevertheless, empirical research draws a heterogeneous picture of the benefits of lab work. Research has shown that it does not necessarily contribute to the enhancement of practical abilities or content knowledge. Lab…

  8. Δ6-fatty acid desaturase and fatty acid elongase mRNA expression, phagocytic activity and weight-to-length relationships in channel catfish (Ictalurus punctatus) fed alternative diets with soy oil and a probiotic.

    PubMed

    Santerre, A; Téllez-Bañuelos, M C; Casas-Solís, J; Castro-Félix, P; Huízar-López, M R; Zaitseva, G P; Horta-Fernández, J L; Trujillo-García, E A; de la Mora-Sherer, D; Palafox-Luna, J A; Juárez-Carrillo, E

    2015-01-01

    A time-course feeding trial was conducted for 120 days on juvenile channel catfish (Ictalurus punctatus) to study the effects of diets differing in oil source (fish oil or soy oil) and supplementation with a commercial probiotic. Relative levels of Δ6-fatty acid desaturase (Δ6-FAD) and fatty acid elongase (FAE) expression were assessed in brain and liver tissues. Both genes showed similar expression levels in all groups studied. Fish weight-to-length relationships were evaluated using polynomial regression analyses, which identified a burst in weight and length in the channel catfish on day 105 of treatment; this increase was related to an increase in gene expression. Mid-intestinal lactic acid bacterium (LAB) count was determined according to morphological and biochemical criteria using API strips. There was no indication that intestinal LAB count was affected by the modified diets. The Cunningham glass adherence method was applied to evaluate phagocytic cell activity in peripheral blood. Reactive oxygen species (ROS) generation was assessed through the respiratory burst activity of spleen macrophages by the NBT reduction test. Probiotic-supplemented diets provided a good substrate for innate immune system function; the phagocytic index was significantly enhanced in fish fed soy oil and the probiotic, and at the end of the experimental period, ROS production increased in fish fed soy oil. The substitution of fish oil by soy oil is recommended for food formulation and will contribute to promoting sustainable aquaculture. Probiotics are also recommended for channel catfish farming as they may act as immunonutrients. PMID:26400353

  9. Isolation of a Bacterium Capable of Degrading Peanut Hull Lignin

    PubMed Central

    Kerr, Thomas J.; Kerr, Robert D.; Benner, Ronald

    1983-01-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter sp., was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled [14C]lignin-labeled lignocellulose and [14C]cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade [14C]Kraft lignin from slash pine. After 10 days of incubation with [14C]cellulose-labeled lignocellulose or [14C]lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. Images PMID:16346424

  10. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    SciTech Connect

    Elias, Dwayne A; Wall, Judy D.; Mormile, Dr. Melanie R.; Begemann, Matthew B

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  11. Isolation of the Legionnaires' disease bacterium from environmental samples.

    PubMed

    Morris, G K; Patton, C M; Feeley, J C; Johnson, S E; Gorman, G; Martin, W T; Skaliy, P; Mallison, G F; Politi, B D; Mackel, D C

    1979-04-01

    We analyzed 24 environmental samples collected in or near the Indiana Memorial Union, where an epidemic of Legionnaires' disease occurred in early 1978. We conducted fluorescent antibody analyses and culture on F-G and charcoal yeast extract agars of each sample directly; splenic tissue of guinea pigs inoculated with the sample; and yolk sacs from embryonated eggs inoculated with splenic tissue of guinea pigs injected with the sample. Legionnaires' disease (LD) bacterium was isolated from seven of the 24 samples: one water sample from the air-conditioner cooling tower of the Union; three water samples from a stream near the Union; and three mud samples from the same stream. The LD bacterium strains were of three different serotypes. These findings indicate that LD bacteria may be widespread in nature. PMID:373549

  12. Isolation of a bacterium capable of degrading peanut hull lignin

    SciTech Connect

    Kerr, T.A.; Kerr, R.D.; Benner, R.

    1983-11-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter species, was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled (/sup 14/C) lignin-labeled lignocellulose and (/sup 14/C)cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade (/sup 14/C) Kraft lignin from slash pine. After 10 days of incubation with (/sup 14/C) cellulose-labeled lignocellulose or (/sup 14/C) lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. (Refs. 24).

  13. Thermostable purified endoglucanase from thermophilic bacterium acidothermus cellulolyticus

    DOEpatents

    Tucker, Melvin P.; Grohmann, Karel; Himmel, Michael E.; Mohagheghi, Ali

    1992-01-01

    A substantially purified high molecular weight cellulase enzyme having a molecular weight of between about 156,000 to about 203,400 daltons isolated from the bacterium Acidothermus cellulolyticus (ATCC 43068) and a method of producing it are disclosed. The enzyme is water soluble, possesses both C.sub.1 and C.sub.x types of enzymatic activity, has a high degree of stability toward heat and exhibits both a high optimum temperature activity and high inactivation characteristics.

  14. ESA SnowLab project

    NASA Astrophysics Data System (ADS)

    Wiesmann, Andreas; Caduff, Rafael; Frey, Othmar; Werner, Charles

    2016-04-01

    Retrieval of the snow water equivalaent (SWE) from passive microwave observations dates back over three decades to initial studies made using the first operational radiometers in space. However, coarse spatial resolution (25 km) is an acknowledged limitation for the application of passive microwave measurements. The natural variability of snow cover itself is also notable; properties such as stratigraphy and snow microstructure change both spatially and over time, affecting the microwave signature. To overcome this deficit, the satellite mission COld REgions Hydrology High-resolution Observatory (CoReH2O) was proposed to the European Space Agency (ESA) in 2005 in response to the call for Earth Explorer 7 candidate missions. CoReH2O was a dual frequency (X- and Ku-band) SAR mission aimed to provide maps of SWE over land and snow accumulation on glaciers at a spatial resolution of 200 to 500 meters with an unprecedented accuracy. Within the frame of preparatory studies for CoReH2O Phase A, ESA undertook several research initiatives from 2009 to 2013 to study the mission concept and capabilities of the proposed sensor. These studies provided a wealth of information on emission and backscattering signatures of natural snow cover, which can be exploited to study new potential mission concepts for retrieval of snow cover properties and other elements of the cryosphere. Currently data related to multi-frequency, multi-polarisation, multitemporal of active and passive microwave measurements are still not available. In addition, new methods related to e.g. tomography are currently under development and need to be tested with real data. Also, the potential of interferometric and polarimetric measurements of the snow cover and its possible impact for novel mission/retrieval concepts must be assessed. . The objective of the SnowLab activity is to fill this gap and complement these datasets from earlier campaigns by acquiring a comprehensive multi-frequency, multi

  15. An on-bacterium flow cytometric immunoassay for protein quantification.

    PubMed

    Lan, Wen-Jun; Lan, Wei; Wang, Hai-Yan; Yan, Lei; Wang, Zhe-Li

    2013-09-01

    The polystyrene bead-based flow cytometric immunoassay has been widely reported. However, the preparation of functional polystyrene bead is still inconvenient. This study describes a simple and easy on-bacterium flow cytometric immunoassay for protein quantification, in which Staphylococcus aureus (SAC) is used as an antibody-antigen carrier to replace the polystyrene bead. The SAC beads were prepared by carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling, paraformaldehyde fixation and antibody binding. Carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA 21-1) proteins were used as models in the test system. Using prepared SAC beads, biotinylated proteins, and streptavidin-phycoerythrin (SA-PE), the on-bacterium flow cytometric immunoassay was validated by quantifying CEA and CYFRA 21-1 in sample. Obtained data demonstrated a concordant result between the logarithm of the protein concentration and the logarithm of the PE mean fluorescence intensity (MFI). The limit of detection (LOD) in this immunoassay was at least 0.25 ng/ml. Precision and accuracy assessments appeared that either the relative standard deviation (R.S.D.) or the relative error (R.E.) was <10%. The comparison between this immunoassay and a polystyrene bead-based flow cytometric immunoassay showed a correlation coefficient of 0.998 for serum CEA or 0.996 for serum CYFRA 21-1. In conclusion, the on-bacterium flow cytometric immunoassay may be of use in the quantification of serum protein. PMID:23739299

  16. In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella

    PubMed Central

    Sheik, Abdul R; Muller, Emilie EL; Audinot, Jean-Nicolas; Lebrun, Laura A; Grysan, Patrick; Guignard, Cedric; Wilmes, Paul

    2016-01-01

    Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium Candidatus Microthrix parvicella (Ca. M. parvicella) has been found to fine-tune its gene expression for optimized substrate assimilation. Here we investigated in situ substrate assimilation by single cells of Ca. M. parvicella using nano-scale secondary-ion mass spectrometry (nanoSIMS). NanoSIMS imaging highlighted phenotypic heterogeneity among Ca. M. parvicella cells of the same filament, whereby 13C-oleic acid and 13C-glycerol-3-phosphate assimilation occurred in ≈21–55% of cells, despite non-assimilating cells being intact and alive. In response to alternating aerobic–anoxic regimes, 13C-oleic acid assimilation occurred among subpopulations of Ca. M. parvicella cells (≈3–28% of cells). Furthermore, Ca. M. parvicella cells exhibited two temperature optima for 13C-oleic acid assimilation and associated growth rates. These results suggest that phenotypic heterogeneity among Ca. M. parvicella cells allows the population to adapt rapidly to fluctuating environmental conditions facilitating its widespread occurrence in biological wastewater treatment plants. PMID:26505828

  17. Coexistence of and interaction relationships between an aflatoxin-producing fungus and a bacterium.

    PubMed

    Yan, Quan-Hong; Zhou, Jian-Xiang; Li, Hong-Zhou; Zhi, Qing-Qing; Zhou, Xiao-Ping; He, Zhu-Mei

    2015-07-01

    The interactions between aflatoxin-producing fungi and bacteria have opened up a new avenue for identifying biological agents suitable for controlling aflatoxin contamination. In this study, we analysed the interactions between A. flavus and the bacterium Burkholderia gladioli M3 that coexist in rice that is naturally contaminated with A. flavus. Our results showed that a cell-free culture filtrate (CCF) and the metabolite bongkrekic acid of the M3 strain potently suppressed the mycelial growth and spore production, and then affected the production of aflatoxin of A. flavus. Bongkrekic acid secreted by the M3 strain exhibited higher antifungal activity than did analogues. The CCF of the M3 strain and its metabolite bongkrekic acid can inhibit the growth of A. flavus, but the metabolites of A. flavus, aflatoxins, exerted no inhibitory effect on the growth of the M3 strain. Furthermore, we determined that the M3 cells could use the dead mycelia of A. flavus as energy sources for reproduction, while A. flavus could not grow in a solution containing dead M3 cells. In summary, these results indicated that B. gladioli has a competitive advantage in survival when it coexists with its fungal partner A. flavus.

  18. Deinococcus puniceus sp. nov., a bacterium isolated from soil-irradiated gamma radiation.

    PubMed

    Lee, Jae-Jin; Srinivasan, Sathiyaraj; Lim, Sangyong; Joe, Minho; Im, Seonghun; Kim, Myung Kyum

    2015-04-01

    A Gram-positive, coccus-shaped, crimson-color-pigmented bacterium was isolated from soil irradiated with 5 kGy gamma radiation and was designated strain DY1(T). Cells showed growth at 10-30 °C and pH 7-11 and were oxidase-negative and catalase-positive. Phylogenetic analyses of the 16S rRNA gene showed that the strain DY1(T) belonged to the genus Deinococcus with sequence similarities to Deinococcus aquatilis CCUG 53370(T) (96.2 %) and Deinococcus navajonensis KR-114(T) (94.1 %). Strain DY1(T) showed low level of DNA relatedness with D. aquatilis CCUG 53370(T) (41.3 ± 3.9 %). The DNA G + C content of DY1(T) was 58.7 mol%. Predominant fatty acids were summed feature 3 (C16:1 ω7c/ω6c), C16:0, and C17:0. The major amino acids were D-alanine, L-glutamic acid, glycine, and L-ornithine in the peptidoglycan. The major polar lipids were unknown phosphoglycolipids (PGL). Strain DY1(T) has resistance to gamma radiation and was found to be a novel species. Therefore, the strain was designated as DY1(T) (=KCTC 33027(T) = JCM 18576(T)), and the name Deinococcus puniceus sp. nov. is herein proposed.

  19. Biodegradation of bisphenol A and other bisphenols by a gram-negative aerobic bacterium

    SciTech Connect

    Lobos, J.H.; Leib, T.K. ); Tahmun Su )

    1992-06-01

    A novel bacterium designated strain MV1 was isolated from a sludge enrichmet takes from the wastewater treatment plant at a plastics manufacturing facility and shown to degrade 2,2-bis(4-hydroxyphenyl)propane (4,4[prime]-isopropylidenediphenol or bisphenol A). Strain MV1 is a gram-negative, aerobic bacillus that grows on bisphenol A as a sole source of carbon and energy. Total carbon analysis for bisphenol A degradation demonstrated that 60% of the carbon was mineralized to CO[sub 2], 20% was associated with the bacterial cells, and 20% was converted to soluble organic compounds. Metabolic intermediates detected in the culture medium during growth on bisphenol A were identified as 4-hydroxybenzoic acid, 4-hydroxyacetophenone, 2,2-bis(4-hydroxyphenyl)-1-propanol, and 2,3-bis(4-hydroxyphenyl)-1,2-propanediol. Most of the bisphenol A degraded by strain MV1 is cleaved in some way to form 4-hydroxybenzoic acid and 4-hydroxyacetophenone, which are subsequently mineralized or assimilated into cell carbon. In addition, about 20% of the bisphenol A is hydroxylated to form 2,2-bis(4-hydroxyphenyl)-1-propanol, which is slowly biotransformed to 2,3-bis(4-hydroxyphenyl)-1,2-propanediol. Cells that were grown on bisphenol A degraded a variety of bisphenol alkanes, hydroxylated benzoic acids, and hydroxylated acetophenones during resting-cell assays. Transmission electron microscopy of cells grown on bisphenol A revealed lipid storage granules and intracytoplasmic membranes.

  20. Oceanobacillus bengalensis sp. nov., a bacterium isolated from seawater of the Bay of Bengal.

    PubMed

    Yongchang, Ouyang; Xiang, Wenzhou; Wang, Guanghua

    2015-11-01

    A Gram-stain positive, motile, and subterminal endospore-forming rod-shaped bacterium, designated strain Ma-21(T), was isolated from seawater of the Bay of Bengal. Strain Ma-21(T) was found to grow optimally at 37 °C and pH 8.0 with 3% (w/v) NaCl. Phylogenetic analyses showed that strain Ma-21(T) forms a distinct phylogenetic lineage close to Oceanobacillus chungangensis CAU 1051(T), Oceanobacillus caeni S-11(T), Oceanobacillus arenosus CAU 1183(T), Oceanobacillus halophilum GD01(T) and Ornithinibacillus heyuanensis GIESS003(T) in the family Bacillaceae. The cell wall of strain Ma-21(T) was found to contain meso-diaminopimelic acid as the diagnostic diamino acid, which is in line with those of members of the genus Oceanobacillus. The genomic DNA G+C content was determined to be 35.9 mol%. The only respiratory quinone detected was MK-7. The major cellular fatty acids were identified as anteiso-C(15:0) and anteiso-C(17:0). The major polar lipids were found to be diphosphatidylglycerol and phosphatidylglycerol. On the basis of phylogenetic, chemotaxonomic and phenotypic properties, strain Ma-21(T) is suggested to represent a novel species in the genus Oceanobacillus, for which the name Oceanobacillus bengalensis sp. nov. is proposed. The type strain is Ma-21(T) (=CGMCC 1.12799(T) = KCTC 33416(T) = MCCC 1K00260(T)).

  1. BEAMS Lab at MIT: Status report

    PubMed Central

    Liberman, Rosa G.; Skipper, Paul L.; Tannenbaum, Steven R.

    2009-01-01

    The Biological Engineering Accelerator Mass Spectrometry (BEAMS) Lab at the Massachusetts Institute of Technology is a facility dedicated to incorporating AMS into life sciences research. As such, it is focused exclusively on radiocarbon and tritium AMS and makes use of a particularly compact instrument of a size compatible with most laboratory space. Recent developments at the BEAMS Lab were aimed to improve different stages of the measurement process, such as the carbon sample injection interface, the simultaneous detection of tritium and hydrogen and finally, the overall operation of the system. Upgrades and results of those efforts are presented here. PMID:20383276

  2. Magnetic Viscous Drag for Friction Labs

    NASA Astrophysics Data System (ADS)

    Gaffney, Chris; Catching, Adam

    2016-09-01

    The typical friction lab performed in introductory mechanics courses is usually not the favorite of either the student or the instructor. The measurements are not all that easy to make, and reproducibility is usually a troublesome issue. This paper describes the augmentation of such a friction lab with a study of the viscous drag on a magnet sliding down a conducting ramp, e.g., an aluminum ramp (Fig. 1). The measurements are simple and quite reproducible, and it appears to readily catch the interest of students.

  3. An Online Lab Manual for Neurophysiology

    PubMed Central

    Olivo, Richard F.

    2003-01-01

    A combination of student interest, a grant for computers, and a suggestion from a colleague led me to convert the printed lab manual for my neurophysiology course into an online version. The web-based version incorporates videos of procedures, color photos, diagrams, links to articles, and other supplementary materials. This paper discusses designing for the web, retaining compatibility with print, layering information, making videos in digital format, and sharing self-published resources. The labs themselves (appendix) are traditional “wet” experiments with crayfish that have been used in many neurobiology courses. PMID:23494073

  4. [Semiotic Studies Lab for Patient Care Interactions].

    PubMed

    Nunes, Dulce Maria; Portella, Jean Cristtus; Bianchi e Silva, Laura

    2011-12-01

    The aim of this experience report is to present the Semiotic Studies Lab for Patient Care Interactions (Laboratório de Estudos Semióticos nas Interações de Cuidado - LESIC). The lab was set up at the Nursing School of the Federal University of Rio Grande do Sul (UFRGS), Brazil in 2010. It has the purpose of providing didactic and pedagogical updates, based on the Theory developed by the Paris School of Semiotics, that enable the increase of knowledge and interactive/observational skills regarding the nature and mastery of human care.

  5. Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost.

    PubMed

    Sakai, Masao; Deguchi, Daigo; Hosoda, Akifumi; Kawauchi, Tomohiro; Ikenaga, Makoto

    2015-02-01

    A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0-8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) ( = NBRC 109510(T) = KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

  6. Improving the Quality of Lab Reports by Using Them as Lab Instructions

    NASA Astrophysics Data System (ADS)

    Haagen-Schuetzenhoefer, Claudia

    2012-10-01

    Lab exercises are quite popular in teaching science. Teachers have numerous goals in mind when teaching science laboratories. Nevertheless, empirical research draws a heterogeneous picture of the benefits of lab work. Research has shown that it does not necessarily contribute to the enhancement of practical abilities or content knowledge. Lab activities are frequently based on recipe-like, step-by-step instructions ("cookbook style"), which do not motivate students to engage cognitively. Consequently, students put the emphasis on "task completion" or "manipulating equipment."2

  7. Awakening interest in the natural sciences - BASF's Kids' Labs.

    PubMed

    Lang, Cinthia

    2012-01-01

    At BASF's Ludwigshafen headquarters, kids and young adults in grades 1-13 can learn about chemistry in the Kids' Labs. Different programs exist for different levels of knowledge. In the two 'Hands-on Lab H(2)O & Co.' Kids' Labs, students from grades 1-6 explore the secrets of chemistry. BASF Kids' Labs have now been set up in over 30 countries. In Switzerland alone, almost 2,000 students have taken part in the 'Water Loves Chemistry' Kids' Lab since it was started in 2011. In Alsace, 600 students have participated to date. In the Teens' Lab 'Xplore Middle School', middle school students explore five different programs with the themes 'substance labyrinth', 'nutrition', 'coffee, caffeine & co.', 'cosmetics' and 'energy'. Biotechnological methods are the focus of the Teens' Lab 'Xplore Biotech' for students taking basic and advanced biology courses. In the 'Xplore High School' Teens' Lab, chemistry teachers present their own experimental lab instruction for students in basic and advanced chemistry courses. The Virtual Lab has been expanding the offerings of the BASF Kids' Labs since 2011. The online lab was developed by the company for the International Year Of Chemistry and gives kids and young adults the opportunity to do interactive experiments outside of the lab.

  8. Awakening interest in the natural sciences - BASF's Kids' Labs.

    PubMed

    Lang, Cinthia

    2012-01-01

    At BASF's Ludwigshafen headquarters, kids and young adults in grades 1-13 can learn about chemistry in the Kids' Labs. Different programs exist for different levels of knowledge. In the two 'Hands-on Lab H(2)O & Co.' Kids' Labs, students from grades 1-6 explore the secrets of chemistry. BASF Kids' Labs have now been set up in over 30 countries. In Switzerland alone, almost 2,000 students have taken part in the 'Water Loves Chemistry' Kids' Lab since it was started in 2011. In Alsace, 600 students have participated to date. In the Teens' Lab 'Xplore Middle School', middle school students explore five different programs with the themes 'substance labyrinth', 'nutrition', 'coffee, caffeine & co.', 'cosmetics' and 'energy'. Biotechnological methods are the focus of the Teens' Lab 'Xplore Biotech' for students taking basic and advanced biology courses. In the 'Xplore High School' Teens' Lab, chemistry teachers present their own experimental lab instruction for students in basic and advanced chemistry courses. The Virtual Lab has been expanding the offerings of the BASF Kids' Labs since 2011. The online lab was developed by the company for the International Year Of Chemistry and gives kids and young adults the opportunity to do interactive experiments outside of the lab. PMID:23394237

  9. Pseudomonas sp. strain CA5 (a selenite-reducing bacterium) 16S rRNA gene complete sequence. National Institute of Health, National Center for Biotechnology Information, GenBank sequence. Accession FJ422810.1.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used 1321 base pair 16S rRNA gene sequence methods to confirm the phylogenetic position of a soil isolate as a bacterium belonging to the genus Pesudomonas sp. Morphological, biochemical characteristics, and fatty acid profiles are consistent with the 16S rRNA gene sequence identification...

  10. Life Lab Computer Support System's Manual.

    ERIC Educational Resources Information Center

    Lippman, Beatrice D.; Walfish, Stephen

    Step-by-step procedures for utilizing the computer support system of Miami-Dade Community College's Life Lab program are described for the following categories: (1) Registration--Student's Lists and Labels, including three separate computer programs for current listings, next semester listings, and grade listings; (2) Competence and Resource…

  11. A New Take on Student Lab Reports

    ERIC Educational Resources Information Center

    Hazzard, Edmund

    2014-01-01

    The written lab report--a concise and accurate accounting of an experiment, including a summary of the procedure, presentation of the results, reasoned analysis, and thoughtful explanation--is essential to the scientific endeavor and a key expression and product of inquiry. Generally, however, students and teachers dislike these reports, the…

  12. Surfactant Adsorption: A Revised Physical Chemistry Lab

    ERIC Educational Resources Information Center

    Bresler, Marc R.; Hagen, John P.

    2008-01-01

    Many physical chemistry lab courses include an experiment in which students measure surface tension as a function of surfactant concentration. In the traditional experiment, the data are fit to the Gibbs isotherm to determine the molar area for the surfactant, and the critical micelle concentration is used to calculate the Gibbs energy of micelle…

  13. Computer Labs Report to the Holodeck

    ERIC Educational Resources Information Center

    Raths, David

    2011-01-01

    In many ways, specialized computer labs are the black holes of IT organizations. Budgets, equipment, employees--even space itself--are sucked in. Given a choice, many IT shops would engage warp drive and escape their gravitational pull forever. While Captain Kirk might have looked to Scotty for a fix to the problem, colleges and universities are…

  14. From Computer Lab to Technology Class.

    ERIC Educational Resources Information Center

    Sherwood, Sandra

    1999-01-01

    Discussion of integrating technology into elementary school classrooms focuses on teacher training that is based on a three-year plan developed at an elementary school in Marathon, New York. Describes the role of a technology teacher who facilitates technology integration by running the computer lab, offering workshops, and developing inservice…

  15. Every Day Is National Lab Day

    ERIC Educational Resources Information Center

    Bull, Glen

    2010-01-01

    President Barack Obama recently issued a call for increased hands-on learning in U.S. schools in an address at the National Academy of Sciences. Obama concluded that the future of the United States depends on one's ability to encourage young people to "create, and build, and invent." In this article, the author discusses National Lab Day (NLD)…

  16. World's Tallest Barometer, an Educational Lab Apparatus

    NASA Astrophysics Data System (ADS)

    Bennett, T. E.

    2012-12-01

    The barometer has been around since the early 1640's when Italian scientists Berte inadvertently made a water barometer and Torricelli purposely made a mercury barometer. A water barometer has the problem of high vapor pressure, so that it does not maintain a good vacuum above the water column unless continually vacuum pumped. The high density of mercury and its low vapor pressure allows a mercury barometer to be a compact and accurate lab apparatus. The newly being built barometer at Portland State University's Maseeh College of Engineering atrium makes use of doubly distilled synthetic vacuum pump oil as the working fluid. The fluid has a specific gravity of 0.83 and very low vapor pressure. The nominal height of this barometer is expected to be 12.4m. This barometer will be used in the Civil Engineering Fluids Lab as a lab apparatus and the reservoir has the capability of being pressurized or depressurized artificially, so that the fluid column can be manipulated and measured by the lab students. With the placement of the tall barometer in the atrium of the Engineering Building, the barometer will be visible to the public and to touring student groups.

  17. Chemistry Lab Adapted for Blind Students.

    ERIC Educational Resources Information Center

    Seltzer, Richard J.

    1986-01-01

    Discusses a project at the University of Louisville in which chemistry laboratories are being adapted for use by blind students. Describes the operational analysis of tasks normally performed in labs. Provides specific recommendations on how to utilize new technologies to enable blind students to conduct hands-on learning experiments. (TW)

  18. Pierre in the lab's everyday life

    NASA Astrophysics Data System (ADS)

    Kahane, Claudine

    2012-10-01

    I shall evoke, through some memories of the pioneers years of the Grenoble Astrophysics Group, how Pierre played a decisive role in the lab's everyday life, as a computer wizard, as an insatiable inquiring mind and as an always careful and warm colleague.

  19. A New Twist on Torque Labs

    ERIC Educational Resources Information Center

    Lane, W. Brian

    2014-01-01

    The traditional introductory-level meterstick-balancing lab assumes that students already know what torque is and that they readily identify it as a physical quantity of interest. We propose a modified version of this activity in which students qualitatively and quantitatively measure the amount of force required to keep the meterstick level. The…

  20. Designing Inquiry-Oriented Science Lab Activities

    ERIC Educational Resources Information Center

    Longo, Christopher M.

    2011-01-01

    Mr. Smith and Ms. D'Amico are two veteran science teachers in a well-performing school district. Both teachers use weekly lab exercises and experiments as formative assessments. In their middle school classrooms, children are engaged and eager to learn. As students walk into Mr. Smith's classroom, a prescribed, step-by-step procedure of the day's…

  1. Developing and Maintaining a Multimedia Language Lab

    ERIC Educational Resources Information Center

    Bingham, Scott; Humphries, Marshall

    1998-01-01

    Recent trends in education have pushed for multimedia to be made a part of every effective language program. As a result, language programs around the world are incorporating computer labs into their curricula. However, as many instructors and administrators are unfamiliar with this newer technology, integrating computer assisted language learning…

  2. Special Report: Hazardous Wastes in Academic Labs.

    ERIC Educational Resources Information Center

    Sanders, Howard J.

    1986-01-01

    Topics and issues related to toxic wastes in academic laboratories are addressed, pointing out that colleges/universities are making efforts to dispose of hazardous wastes safely to comply with tougher federal regulations. University sites on the Environmental Protection Agency Superfund National Priorities List, costs, and use of lab packs are…

  3. Tap Teens' Curiosity with Lab Band.

    ERIC Educational Resources Information Center

    Saunders, Jane

    2002-01-01

    Describes the Lab Band project used with 12th grade students at the Westgate Collegiate and Vocational Institute in Thunder Bay, Ontario (Canada). Explains that each band student taught a peer how to play their instrument which created versatility in the band. States that all students kept a reflective journal. (CMK)

  4. How Do New Teachers Choose New Labs?

    ERIC Educational Resources Information Center

    DeMeo, Stephen

    2007-01-01

    Forty-eight new secondary science teachers participated in a study that required a listing, discussion, and application of criteria to rank three chemistry laboratory procedures. The three similar lab procedures involved synthesis of a compound from its elements. The top criteria noted by teachers focused on procedural issues (i.e., timeliness,…

  5. Ames Lab 101: Single Crystal Growth

    ScienceCinema

    Schlagel, Deborah

    2016-07-12

    Ames Laboratory scientist Deborah Schlagel talks about the Lab's research in growing single crystals of various metals and alloys. The single crystal samples are vital to researchers' understanding of the characteristics of a materials and what gives these materials their particular properties.

  6. Ames Lab 101: Single Crystal Growth

    SciTech Connect

    Schlagel, Deborah

    2013-09-27

    Ames Laboratory scientist Deborah Schlagel talks about the Lab's research in growing single crystals of various metals and alloys. The single crystal samples are vital to researchers' understanding of the characteristics of a materials and what gives these materials their particular properties.

  7. A Natural Selection Lab for Environmental Biology.

    ERIC Educational Resources Information Center

    Fiero, Brad; Mackie, Steve

    1997-01-01

    Presents a lab that investigates the evolution of genetic resistance, the importance of genetic variability in the process of adaptation, and the ecological and economic consequences of pesticide use. Allows students to investigate the relationship between population size, genetic variability, and adaptability. Appendices contain the genetic card…

  8. Design Lab. USMES "How To" Series.

    ERIC Educational Resources Information Center

    Donahoe, Charles; And Others

    The major emphasis in all Unified Sciences and Mathematics for Elementary Schools (USMES) units is on open-ended, long-range investigations of real problems. Since children often design and build things in USMES, 26 "Design Lab" cards provide information on the safe use and simple maintenance of tools. Each card has a large photograph of the tool…

  9. A "Language Lab" for Architectural Design.

    ERIC Educational Resources Information Center

    Mackenzie, Arch; And Others

    This paper discusses a "language lab" strategy in which traditional studio learning may be supplemented by language lessons using computer graphics techniques to teach architectural grammar, a body of elements and principles that govern the design of buildings belonging to a particular architectural theory or style. Two methods of teaching Frank…

  10. "Probeware" on Increase in Schools' Science Labs

    ERIC Educational Resources Information Center

    Trotter, Andrew

    2008-01-01

    Though the term, "probeware" may not be a household word, it has grown more familiar to science educators over the past decade, as a new generation of high-tech instruments for collecting and analyzing data from the physical world have been introduced into school science labs. Today, those tools include digital scientific probes or sensors that…

  11. Nonverbal Communication and Writing Lab Tutorials.

    ERIC Educational Resources Information Center

    Claywell, Gina

    Writing labs should utilize the knowledge gained from a variety of fields to enhance further their programs, particularly with regard to the study of nonverbal communication. Regardless of the sincerity and importance of the tutor's suggestions, nonverbal messages often are sent to the student which undermine the session. Various channels of…

  12. The Hidden Costs of Wireless Computer Labs

    ERIC Educational Resources Information Center

    Daly, Una

    2005-01-01

    Various elementary schools and middle schools across the U.S. have purchased one or more mobile laboratories. Although the wireless labs have provided more classroom computing, teachers and technology aides still have mixed views about their cost-benefit ratio. This is because the proliferation of viruses and spyware has dramatically increased…

  13. Folding Inquiry into Cookbook Lab Activities

    ERIC Educational Resources Information Center

    Gooding, Julia; Metz, Bill

    2012-01-01

    Cookbook labs have been a part of science programs for years, even though they serve little purpose other than to verify phenomena that have been previously presented by means other than through investigations. Cookbook science activities follow a linear path to a known outcome, telling students what procedures to follow, which materials to use,…

  14. Berkeley Lab's Cool Your School Program

    ScienceCinema

    Ivan Berry

    2016-07-12

    Cool Your School is a series of 6th-grade, classroom-based, science activities rooted in Berkeley Lab's cool-surface and cool materials research and aligned with California science content standards. The activities are designed to build knowledge, stimulate curiosity, and carry the conversation about human-induced climate change, and what can be done about it, into the community.

  15. Lab-on a-Chip

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Helen Cole, the project manager for the Lab-on-a-Chip Applications Development program, and Lisa Monaco, the project scientist for the program, insert a lab on a chip into the Caliper 42 which is specialized equipment that controls processes on commercial chips to support development of lab-on-a-chip applications. The system has special microscopes and imaging systems, so scientists can process and study different types of fluid, chemical, and medical tests conducted on chips. For example, researchers have examined fluorescent bacteria as it flows through the chips' fluid channels or microfluidic capillaries. Researchers at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama, have been studying how the lab-on-a-chip technology can be used for microbial detection, water quality monitoring, and detecting biosignatures of past or present life on Mars. The Marshall Center team is also collaborating with scientists at other NASA centers and at universities to develop custom chip designs for not only space applications, but for many Earth applications, such as for detecting deadly microbes in heating and air systems. (NASA/MSFC/D.Stoffer)

  16. Technology Rich Biology Labs: Effects of Misconceptions.

    ERIC Educational Resources Information Center

    Kuech, Robert; Zogg, Gregory; Zeeman, Stephan; Johnson, Mark

    This paper describes a study conducted on the lab sections of the general biology course for non-science majors at the University of New England, and reports findings of student misconceptions about photosynthesis and the mass/carbon uptake during plant growth. The current study placed high technology analytic tools in the hands of introductory…

  17. Medical Lab Technician. Post Secondary Curriculum Guide.

    ERIC Educational Resources Information Center

    Simpson, Bruce; And Others

    Intended to provide a model for organizing vocational instructional content, this curriculum guide consists of information pertinent to conducting a postsecondary level course for training medical lab technicians. While the guide is primarily oriented towards the classroom, whether as a primary resource or as a supplement to other teaching…

  18. Gapminder: An AP Human Geography Lab Assignment

    ERIC Educational Resources Information Center

    Keller, Kenneth H.

    2012-01-01

    This lesson is designed as a lab assignment for Advanced Placement (AP) Human Geography students wherein they use the popular Gapminder web site to compare levels of development in countries from different world regions. For this lesson, it is important for the teacher to practice with Gapminder before giving the assignment to students. (Contains…

  19. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    PubMed Central

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  20. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

    PubMed

    Bao, Zhihua; Sato, Yoshinori; Fujimura, Reiko; Ohta, Hiroyuki

    2014-03-01

    A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18 : 1ω7c, C18 : 0, C16 : 1ω7c and C16 : 0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) ( = NBRC 107718(T) = CGMCC 1.12214(T)).

  1. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress

    PubMed Central

    Chen, Yanmei; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong

    2016-01-01

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd2+ MIC, >250 mg liter−1) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. PMID:26729719

  2. Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

    PubMed Central

    Vance, Tyler D. R.; Olijve, Luuk L. C.; Campbell, Robert L.; Voets, Ilja K.; Davies, Peter L.; Guo, Shuaiqi

    2014-01-01

    The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches. PMID:24892750

  3. Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake.

    PubMed

    Hua, Ngoc-Phuc; Hamza-Chaffai, Amel; Vreeland, Russell H; Isoda, Hiroko; Naganuma, Takeshi

    2008-10-01

    A Gram-positive, endospore-forming, rod-shaped and moderately halophilic bacterium was isolated from a salt-crust sample collected from Gharsa salt lake (Chott el Gharsa), Tunisia. The newly isolated bacterium, designated SA-Vb1(T), was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Strain SA-Vb1(T) was closely related to the type strains of Virgibacillus marismortui and Virgibacillus olivae, with 16S rRNA gene sequence similarities of 99.7 and 99.4 %, respectively. However, strain SA-Vb1(T) was distinguished from these two type strains on the basis of phenotypic characteristics and DNA-DNA relatedness (29.4 and 5.1 %, respectively). The genetic relationship between strain SA-Vb1(T) and Virgibacillus pantothenticus IAM 11061(T) (the type strain of the type species) and other type strains of the genus was 96-98 % based on 16S rRNA gene sequence similarity and 18.3-22.3 % based on DNA-DNA hybridization. Biochemical analysis resulted in determination of major fatty acids iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0) (33.3, 29.2 and 9.8 %, respectively); phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the main polar lipids and MK-7 was the predominant menaquinone ( approximately 100 %). The distinct characteristics demonstrated by strain SA-Vb1(T) represent properties of a novel species of the genus Virgibacillus, for which the name Virgibacillus salarius sp. nov. is proposed. The type strain is SA-Vb1(T) (=JCM 12946(T) =DSM 18441(T)). PMID:18842865

  4. Gene identification and molecular characterization of solvent stable protease from a moderately haloalkaliphilic bacterium, Geomicrobium sp. EMB2.

    PubMed

    Karan, Ram; Singh, Raj Kumar Mohan; Kapoor, Sanjay; Khare, S K

    2011-02-01

    Cloning and characterization of the gene encoding a solvent-tolerant protease from the haloalkaliphilic bacterium Geomicrobium sp. EMB2 are described. Primers designed based on the N-terminal amino acid sequence of the purified EMB2 protease helped in the amplification of a 1,505-bp open reading frame that had a coding potential of a 42.7-kDa polypeptide. The deduced EMB2 protein contained a 35.4-kDa mature protein of 311 residues, with a high proportion of acidic amino acid residues. Phylogenetic analysis placed the EMB2 gene close to a known serine protease from Bacillus clausii KSM-K16. Primary sequence analysis indicated a hydrophobic inclination of the protein; and the 3D structure modeling elucidated a relatively higher percentage of small (glycine, alanine, and valine) and borderline (serine and threonine) hydrophobic residues on its surface. The structure analysis also highlighted enrichment of acidic residues at the cost of basic residues. The study indicated that solvent and salt stabilities in Geomicrobium sp. protease may be accorded to different structural features; that is, the presence of a number of small hydrophobic amino acid residues on the surface and a higher content of acidic amino acid residues, respectively. PMID:21364294

  5. Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product.

    PubMed

    Nakano, Chisa; Takahashi, Naoto; Tanaka, Naoto; Okada, Sanae

    2015-02-01

    A novel, moderately thermophilic, acidophilic, Gram-variable, rod-shaped, endospore-forming bacterium was isolated from a spoiled mixed vegetable and fruit juice product that had the off-flavour of guaiacol. The bacterium, strain 4F(T), grew aerobically at 20-50 °C (optimum 40 °C) and pH 3.0-6.0 (optimum pH 4.0) and produced acid from glycerol, d-galactose and d-glucose. It contained menaquinone-7 (MK-7) as the major isoprenoid quinone and the DNA G+C content was 49.6 mol%. The predominant cellular fatty acids of strain 4F(T) were ω-alicyclic (ω-cyclohexane fatty acids), which are characteristic of the genus Alicyclobacillus. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the Alicyclobacillus cluster, and is related most closely to the type strains of Alicyclobacillus acidoterrestris (97.4 % similarity) and Alicyclobacillus fastidiosus (97.3 %). Strain 4F(T) produced guaiacol from vanillic acid. It can be distinguished from related species by its acid production type and guaiacol production. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, it can be concluded that the strain represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus dauci sp. nov. is proposed; the type strain is 4F(T) ( = DSM 28700(T) = NBRC 108949(T) = NRIC 0938(T)).

  6. NASA GeneLab Concept of Operations

    NASA Technical Reports Server (NTRS)

    Thompson, Terri; Gibbs, Kristina; Rask, Jon; Coughlan, Joseph; Smith, Jeffrey

    2014-01-01

    NASA's GeneLab aims to greatly increase the number of scientists that are using data from space biology investigations on board ISS, emphasizing a systems biology approach to the science. When completed, GeneLab will provide the integrated software and hardware infrastructure, analytical tools and reference datasets for an assortment of model organisms. GeneLab will also provide an environment for scientists to collaborate thereby increasing the possibility for data to be reused for future experimentation. To maximize the value of data from life science experiments performed in space and to make the most advantageous use of the remaining ISS research window, GeneLab will apply an open access approach to conducting spaceflight experiments by generating, and sharing the datasets derived from these biological studies in space.Onboard the ISS, a wide variety of model organisms will be studied and returned to Earth for analysis. Laboratories on the ground will analyze these samples and provide genomic, transcriptomic, metabolomic and proteomic data. Upon receipt, NASA will conduct data quality control tasks and format raw data returned from the omics centers into standardized, annotated information sets that can be readily searched and linked to spaceflight metadata. Once prepared, the biological datasets, as well as any analysis completed, will be made public through the GeneLab Space Bioinformatics System webb as edportal. These efforts will support a collaborative research environment for spaceflight studies that will closely resemble environments created by the Department of Energy (DOE), National Center for Biotechnology Information (NCBI), and other institutions in additional areas of study, such as cancer and environmental biology. The results will allow for comparative analyses that will help scientists around the world take a major leap forward in understanding the effect of microgravity, radiation, and other aspects of the space environment on model organisms

  7. To pre-challenge lactic acid bacteria with simulated gastrointestinal conditions is a suitable approach to studying potential probiotic properties.

    PubMed

    Huang, Hui-Ying; Hsieh, Hsin-Yi; King, V An-Erl; Chi, Li-Ling; Tsen, Jen-Horng

    2014-12-01

    The potential probiotic properties of lactic acid bacteria (LAB) after treatment with gastrointestinal (GI) conditions were investigated. Some LAB strains that survived simulated GI treatment retained their adhesiveness and antagonism against the pathogen. Therefore pre-challenging LAB with simulated GI conditions is a suitable way for potential probiotic studies. PMID:25281473

  8. Fast Neutron Irradiation of the Highly Radioresistant Bacterium Deinococcus Radiodurans

    NASA Astrophysics Data System (ADS)

    Case, Diane Louise

    Fast neutron dose survival curves were generated for the bacterium Deinococcus radiodurans, which is renowned for its unusually high resistance to gamma, x-ray, and ultraviolet radiation, but for which fast neutron response was unknown. The fast neutrons were produced by the University of Massachusetts Lowell 5.5-MV, type CN Van de Graaff accelerator through the ^7Li(p,n)^7 Be reaction by bombarding a thick metallic lithium target with a 4-MeV proton beam. The bacteria were uniformly distributed on 150-mm agar plates and were exposed to the fast neutron beam under conditions of charged particle equilibrium. The plates were subdivided into concentric rings of increasing diameter from the center to the periphery of the plate, within which the average neutron dose was calculated as the product of the precisely known neutron fluence at the average radius of the ring and the neutron energy dependent kerma factor. The neutron fluence and dose ranged from approximately 3 times 1013 n cm^ {-2} to 1 times 1012 n cm^ {-2}, and 200 kilorad to 5 kilorad, respectively, from the center to the periphery of the plate. Percent survival for Deinococcus radiodurans as a function of fast neutron dose was derived from the ability of the irradiated cells to produce visible colonies within each ring compared to that of a nonirradiated control population. The bacterium Escherichia coli B/r (CSH) was irradiated under identical conditions for comparative purposes. The survival response of Deinococcus radiodurans as a result of cumulative fast neutron exposures was also investigated. The quantification of the ability of Deinococcus radiodurans to survive cellular insult from secondary charged particles, which are produced by fast neutron interactions in biological materials, will provide valuable information about damage and repair mechanisms under extreme cellular stress, and may provide new insight into the origin of this bacterium's unprecedented radiation resistance.

  9. Towards a Manifesto for Living Lab Co-creation

    NASA Astrophysics Data System (ADS)

    Følstad, Asbjørn; Brandtzæg, Petter Bae; Gulliksen, Jan; Börjeson, Mikael; Näkki, Pirjo

    There is a growing interest in Living Labs for innovation and development in the field of information and communication technology. In particular there seem to be a tendency that current Living Labs aim to involve users for co-creative purposes. However, the current literature on Living Lab co-creation is severely limited. Therefore an Interact workshop is arranged as a first step towards a manifesto for Living Lab co-creation.

  10. Production of amino acids using auxotrophic mutants of methylotrophic bacillus

    DOEpatents

    Hanson, Richard S.; Flickinger, Michael C.; Schendel, Frederick J.; Guettler, Michael V.

    2001-07-17

    A method of producing amino acids by culturing an amino acid auxotroph of a biologically pure strain of a type I methylotrophic bacterium of the genus Bacillus which exhibits sustained growth at 50.degree. C. using methanol as a carbon and energy source and requiring vitamin B.sub.12 and biotin is provided.

  11. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    SciTech Connect

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  12. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    SciTech Connect

    Brown, A.E.; Gilbert, C.W.; Guy, R.; Arntzen, C.J.

    1984-10-01

    The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa Q/sub B/ protein of chloroplast membranes. 42 references, 6 figures, 1 table.

  13. CORNEAL REACTIONS TO BACTERIUM GRANULOSIS AND OTHER MICROORGANISMS

    PubMed Central

    Olitsky, Peter K.; Knutti, Ralph E.; Tyler, Joseph R.

    1932-01-01

    The conclusions which may be drawn from the results of the experiments here presented are: 1. The cornea of the rabbit is highly sensitive to the action of various injected bacteria. The lesions vary from insignificant, transient changes to severe, destructive panophthalmitis, with fine gradations from the mildest to the violent form of inflammation. Moreover, animals that receive the same organisms show like changes. 2. The varying degree of inflammatory reaction is related to the pathogenicity of the special culture employed; as, for example, is shown by the reactions to Type I pneumococci and to Bacterium granulosis. It is evident that when a microorganism having a certain degree of virulence is used, a lesion of localized vasculonebulous keratitis resembling pannus tenuis or vasculosus of human trachoma can be induced. Thus Bacterium granulosis, Bacillus xerosis, Hemophilus influenzae, Pneumococcus Type II, Streptococcus viridans, and gonococcus can cause the pannus-like corneal changes in the rabbit. Of these organisms, however, only Bacterium granulosis induces early, uncomplicated and enduring keratitic lesions; the others cause first, diffuse keratitis with suppurative lesions; then, as a residual effect, transient, localized, vasculonebulous changes in the cornea. These changes, in contradistinction to the granulosis lesions, are, therefore delayed, complicated, and transient. When, on the other hand, the invasiveness and infecting power of the organisms are low, as is the case with the filtrable, Gram-negative bacillus and the small, Gram-negative bacilli ultimately derived from cases of folliculosis, no marked effect is produced by their intracorneal inoculation. If the pathogenicity of bacteria is high (as shown by Pneumococcus Type I, hemolytic streptococcus, and the remaining bacteria), intracorneal inoculation of the microorganisms leads to serious suppurative or destructive changes. 3. The results of experiments with monkeys indicate that while

  14. Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

    PubMed

    Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

    2016-04-21

    Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain. PMID:26972517

  15. USMES Design Lab Manual. Fifth Edition. Trial Edition.

    ERIC Educational Resources Information Center

    Manfre, Edward; Donahoe, Charles

    This manual serves as a resource for Design Labs in the Unified Sciences and Mathematics for Elementary Schools (USMES) program. A Design Lab is not a customary "shop" where students receive training in woodworking, metalworking, and other crafts. Instead, when a construction need arises during USMES units, a Design Lab becomes the central…

  16. Constructing the Components of a Lab Report Using Peer Review

    ERIC Educational Resources Information Center

    Berry, David E.; Fawkes, Kelli L.

    2010-01-01

    A protocol that emphasizes lab report writing using a piecemeal approach coupled with peer review is described. As the lab course progresses, the focus of the report writing changes sequentially through the abstract and introduction, the discussion, and the procedure. Two styles of lab programs are presented. One style rotates the students through…

  17. Student Plagiarism and Faculty Responsibility in Undergraduate Engineering Labs

    ERIC Educational Resources Information Center

    Parameswaran, Ashvin; Devi, Poornima

    2006-01-01

    In undergraduate engineering labs, lab reports are routinely copied. By ignoring this form of plagiarism, teaching assistants and lab technicians neglect their role responsibility. By designing courses that facilitate it, however inadvertently, professors neglect their causal responsibility. Using the case of one university, we show via interviews…

  18. Revising Geology Labs To Explicitly Use the Scientific Method.

    ERIC Educational Resources Information Center

    Hannula, Kimberly A.

    2003-01-01

    Proposes that content- or skill-based labs can be revised to explicitly involve the scientific method by asking students to propose hypotheses before making observations. Students' self-assessment showed they felt that they learned a great deal from this style of labs and found the labs to be fun; however, students felt that they learned little…

  19. The Portable Usability Testing Lab: A Flexible Research Tool.

    ERIC Educational Resources Information Center

    Hale, Michael E.; And Others

    A group of faculty at the University of Georgia obtained funding for a research and development facility called the Learning and Performance Support Laboratory (LPSL). One of the LPSL's primary needs was obtaining a portable usability lab for software testing, so the facility obtained the "Luggage Lab 2000." The lab is transportable to any site…

  20. LabNet: Toward a Community of Practice.

    ERIC Educational Resources Information Center

    Wood, M. G., Ed.

    1992-01-01

    A brief overview of LabNet, a project aimed at enhancing physics education, is provided. The article focuses on a description of LabNetwork which is one of several mechanisms designed to offer LabNet participants opportunities to give and receive peer support. (ZWH)

  1. Introduction to Computing: Lab Manual. Faculty Guide [and] Student Guide.

    ERIC Educational Resources Information Center

    Frasca, Joseph W.

    This lab manual is designed to accompany a college course introducing students to computing. The exercises are designed to be completed by the average student in a supervised 2-hour block of time at a computer lab over 15 weeks. The intent of each lab session is to introduce a topic and have the student feel comfortable with the use of the machine…

  2. Behind the Scenes at Berkeley Lab - The Mechanical Fabrication Facility

    SciTech Connect

    Wells, Russell; Chavez, Pete; Davis, Curtis; Bentley, Brian

    2013-05-17

    Part of the Behind the Scenes series at Berkeley Lab, this video highlights the lab's mechanical fabrication facility and its exceptional ability to produce unique tools essential to the lab's scientific mission. Through a combination of skilled craftsmanship and precision equipment, machinists and engineers work with scientists to create exactly what's needed - whether it's measured in microns or meters.

  3. Behind the Scenes at Berkeley Lab - The Mechanical Fabrication Facility

    ScienceCinema

    Wells, Russell; Chavez, Pete; Davis, Curtis; Bentley, Brian

    2016-07-12

    Part of the Behind the Scenes series at Berkeley Lab, this video highlights the lab's mechanical fabrication facility and its exceptional ability to produce unique tools essential to the lab's scientific mission. Through a combination of skilled craftsmanship and precision equipment, machinists and engineers work with scientists to create exactly what's needed - whether it's measured in microns or meters.

  4. Validation study for using lab-on-chip technology for Coxiella burnetii multi-locus-VNTR-analysis (MLVA) typing: application for studying genotypic diversity of strains from domestic ruminants in France.

    PubMed

    Prigent, Myriam; Rousset, Elodie; Yang, Elise; Thiéry, Richard; Sidi-Boumedine, Karim

    2015-01-01

    Coxiella burnetii, the etiologic bacterium of Q fever zoonosis, is still difficult to control. Ruminants are often carriers and involved in human epidemics. MLVA is a promising genotyping method for molecular epidemiology. Different techniques are used to resolve the MLVA band profiles such as electrophoresis on agarose gels, capillary electrophoresis or using the microfluidic Lab-on-Chip system. In this study, system based on microfluidics electrophoresis with Lab-on-Chip technology was assessed and applied on DNA field samples to investigate the genotypic diversity of C. burnetii strains circulating in France. The Lab-on-Chip technology was first compared to agarose gel electrophoresis. Subsequently, the set-up Lab-on-Chip technology was applied on 97 samples collected from ruminants in France using the 17 markers previously described. A discordance rate of 27% was observed between Lab-on-Chip and agarose gel electrophoresis. These discrepancies were checked and resolved by sequencing. The cluster analysis revealed classification based on host species and/or geographic origin criteria. Moreover, the circulation of different genotypic strains within the same farm was also observed. In this study, MLVA with Lab-on-Chip technology was shown to be more accurate, reproducible, user friendly and safer than gel electrophoresis. It also provides an extended data set from French ruminant C. burnetii circulating strains useful for epidemiological investigations. Finally, it raises some questions regarding the standardization and harmonization of C. burnetii MLVA genotyping.

  5. Identification and characterization of Clostridium paraputrificum M-21, a chitinolytic, mesophilic and hydrogen-producing bacterium.

    PubMed

    Evvyernie, D; Yamazaki, S; Morimoto, K; Karita, S; Kimura, T; Sakka, K; Ohmiya, K

    2000-01-01

    A strictly anaerobic, mesophilic and chitinolytic bacterial strain, M-21, was isolated from a soil sample collected from Mie University campus and identified as Clostridium paraputrificum based on morphological and physiological characteristics, and 16S rRNA sequence analysis. C. paraputrificum M-21 utilized chitin and N-acetyl-D-glucosamine (GlcNAc), a constituent monosaccharide of chitin, to produce a large amount of gas along with acetic acid and propionic acid as major fermentation products. Hydrogen and carbon dioxide accounted for 65% and 35% of the gas evolved, respectively. The conditions for 1 l batch culture of C. paraputrificum, including pH of the medium, incubation temperature and agitation speed, were optimized for hydrogen production with GlcNAc as the carbon source. The bacterium grew rapidly on GlcNAc with a doubling time of around 30 min, and produced hydrogen gas with a yield of 1.9 mol H2/mol GlcNAc under the following cultivation conditions: initial medium pH of 6.5, incubation temperature of 45 degrees C, agitation speed of 250 rpm, and working volume of 50% of the fermentor. The dry cell weight harvested from this culture was 2.0 g/l.

  6. Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti.

    PubMed

    Starks, Courtney M; Francois, Julie A; MacArthur, Kelly M; Heard, Brittney Z; Kappock, T Joseph

    2007-01-01

    The crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 A resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol-disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol-disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid-mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side-chain ionization.

  7. Purification and characterization of catalase from marine bacterium Acinetobacter sp. YS0810.

    PubMed

    Fu, Xinhua; Wang, Wei; Hao, Jianhua; Zhu, Xianglin; Sun, Mi

    2014-01-01

    The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT) was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability.

  8. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.

    PubMed

    Khudyakov, Jane I; D'haeseleer, Patrik; Borglin, Sharon E; Deangelis, Kristen M; Woo, Hannah; Lindquist, Erika A; Hazen, Terry C; Simmons, Blake A; Thelen, Michael P

    2012-08-01

    To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.

  9. The Lipid A from the haloalkaliphilic bacterium Salinivibrio sharmensis strain BAG(T).

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, Maria Michela

    2013-01-21

    Lipid A is a major constituent of the lipopolysaccharides (or endotoxins), which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS) of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR) mass spectrometry and chemical analysis.

  10. The Lipid A from the Haloalkaliphilic Bacterium Salinivibrio sharmensis Strain BAGT

    PubMed Central

    Carillo, Sara; Pieretti, Giuseppina; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, Maria Michela

    2013-01-01

    Lipid A is a major constituent of the lipopolysaccharides (or endotoxins), which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS) of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR) mass spectrometry and chemical analysis. PMID:23337252

  11. A new κ-carrageenase CgkS from marine bacterium Shewanella sp. Kz7

    NASA Astrophysics Data System (ADS)

    Wang, Linna; Li, Shangyong; Zhang, Shilong; Li, Jiejing; Yu, Wengong; Gong, Qianhong

    2015-08-01

    A new κ-carrageenase gene cgkS was cloned from marine bacterium Shewanella sp. Kz7 by using degenerate and site-finding PCR. The gene was comprised of an open reading frame of 1224 bp, encoding 407 amino acid residues, with a signal peptide of 24 residues. Based on the deduced amino acid sequence, the κ-carrageenase CgkS was classified into the Glycoside Hydrolase family 16. The cgkS gene was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity with a specific activity of 716.8 U mg-1 and a yield of 69%. Recombinant CgkS was most active at 45°C and pH 8.0. It was stable at pH 6.0-9.0 and below 30°C. The enzyme did not require NaCl for activity, although its activity was enhanced by NaCl. CgkS degraded κ-carrageenan in an endo-fashion releasing tetrasaccharides and disaccharides as main hydrolysis products.

  12. Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

    PubMed

    Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

    2012-03-01

    A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

  13. Effects of Inorganic Particles on Metabolism by a Periphytic Marine Bacterium

    PubMed Central

    Gordon, Andrew S.; Gerchakov, Sol M.; Millero, Frank J.

    1983-01-01

    Measurements were made of adsorption of a periphytic marine bacterium, glucose, and glutamic acid to inorganic particles in seawater and defined bacterial growth medium. Measurements of the metabolism of bacteria were made in the presence and absence of particles by microcalorimetry and radiorespirometry. It was found that hydroxyapatite adsorbs glutamic acid, but not glucose, from the experimental medium. It was also found that hydroxyapatite adsorbs essentially all of the bacteria from the medium when the bacterial concentration is approximately 6 × 105 bacteria per ml. If the bacterial concentration is approximately 6 × 107, then only a small fraction of cells become attached. It was therefore possible to select bacterial concentrations and organic nutrients so that bacterial attachment, organic nutrient adsorption, or both would occur in different experiments. In this experimental system the metabolism by attached and nonattached bacteria of adsorbing and nonadsorbing organic nutrients was measured. The results show that bacterial activity in this model system was not enhanced by the particles, regardless of whether the bacteria, the organic nutrient, or both were associated with the surface. In fact, the respiratory activity of the attached bacteria was diminished in comparison with that of free bacteria. PMID:16346191

  14. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.

    PubMed

    Khudyakov, Jane I; D'haeseleer, Patrik; Borglin, Sharon E; Deangelis, Kristen M; Woo, Hannah; Lindquist, Erika A; Hazen, Terry C; Simmons, Blake A; Thelen, Michael P

    2012-08-01

    To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance. PMID:22586090

  15. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    PubMed

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed. PMID:27030972

  16. Identification of salt-inducible peptide with putative kinase activity in halophilic bacterium Virgibacillus halodenitrificans.

    PubMed

    Rafiee, Mahmoud-Reza; Sokhansanj, Ashrafaddin; Yoosefi, Mitra; Naghizadeh, Mohammad-Ali

    2007-09-01

    Strain XII, a moderately halophilic bacterium, expressed a peptide in response to saline media. This peptide was designated as salt-inducible factor (Sif-A). The purpose of this study is to describe Sif-A, which might be involved in the osmoresistance mechanism of strain XII. The complete sequence of sif-A was determined using PCR. sif-A codes for a polypeptide of 20.518 kDa. The polypeptide has a putative signal peptide of 27 amino acids (2.667 kDa) preceding the mature protein (17.869 kDa). Motif analysis of the deduced amino acid sequence indicated that there is a p-loop NTPase domain on the C-terminal of the peptide, which might correlate with its function. The sequence of the 16S rRNA gene was analyzed phylogenetically to classify strain XII. This organism was found to have the closest association with Virgibacillus halodenitrificans, which was proven by its phenotypic characteristics. PMID:17964480

  17. Production of Value-added Products by Lactic Acid Bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lactic acid bacteria (LAB) are a group of facultative anaerobic, catalase negative, nonmotile and nonsporeforming–Gram positive bacteria. Most LAB utilize high energy C sources including monomer sugars to produce energy to maintain cellular structure and function. This anaerobic fermentation proce...

  18. Effects of lactic acid bacteria contamination on lignocellulosic ethanol fermentation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Slower fermentation rates, mixed sugar compositions, and lower sugar concentrations may make lignocellulosic fermentations more susceptible to contamination by lactic acid bacteria (LAB), which is a common and costly problem to the corn-based fuel ethanol industry. To examine the effects of LAB con...

  19. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway

    PubMed Central

    Yu, Fang-Bo; Li, Xiao-Dan; Ali, Shinawar Waseem; Shan, Sheng-Dao; Luo, Lin-Ping; Guan, Li-Bo

    2014-01-01

    A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation. PMID:25763034

  20. Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis).

    PubMed

    Kittiwongwattana, Chokchai; Thawai, Chitti

    2015-01-01

    A Gram-stain-variable, rod-shaped and endospore-forming bacterium, designated strain L7-75, was isolated from duckweed (Lemna aequinoctialis). Cells were motile with a monopolar flagellum. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L7-75(T) belonged to the genus Paenibacillus, and the closest phylogenetically related species were Paenibacillus uliginis N3/975(T) (98.5% 16S rRNA gene sequence similarity), Paenibacillus purispatii ES_M17(T) (98.5%), Paenibacillus lactis MB 1871(T) (98.2%), Paenibacillus campinasensis 324(T) (97.7%), Paenibacillus glucanolyticus S93(T) (97.7%) and Paenibacillus lautus ATCC 43898(T) (97.4%). Growth of strain L7-75(T) was observed at pH 7-10 and at 20-40 °C, and NaCl concentrations up to 5% (w/v) were tolerated. Major cellular fatty acids included anteiso-C15 : 0, C16 : 0 and anteiso-C17:0 that were present at 36.0%, 14.2 % and 10.0% of the total cellular fatty acid profile, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. MK-7 was the predominant menaquinone. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 49.1 mol% (Tm). DNA-DNA relatedness values between strain L7-75(T) and its closest relatives ranged from 4.4 to 47.8%. These results indicate that strain L7-75(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lemnae sp. nov. is proposed. The type strain is L7-75(T) ( = BCC 67838(T) = NBRC 109972(T)).