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Sample records for acid bacterium lab

  1. 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.

  2. 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

  3. 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.

  4. 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.

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

    PubMed

    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

    2011-12-31

    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.

  6. Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

    PubMed Central

    Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

    2013-01-01

    Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions. PMID:24086270

  7. First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388

    PubMed Central

    Poehlein, Anja; Alghaithi, Hamed S.; Chandran, Lenin; Chibani, Cynthia M.; Davydova, Elena; Dhamotharan, Karthikeyan; Ge, Wanwan; Gutierrez-Gutierrez, David A.; Jagirdar, Advait; Khonsari, Bahar; Nair, Kamal Prakash P. R.

    2014-01-01

    Clostridium litorale is a Gram-positive, rod-shaped, and spore-forming bacterium, which is able to use amino acids such as glycine, sarcosine, proline, and betaine as single carbon and energy sources via Stickland reactions. The genome consists of a circular chromosome (3.41 Mb) and a circular plasmid (27 kb). PMID:25081264

  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. Anaerobic Degradation of Cyanuric Acid, Cysteine, and Atrazine by a Facultative Anaerobic Bacterium

    PubMed Central

    Jessee, J. A.; Benoit, R. E.; Hendricks, A. C.; Allen, G. C.; Neal, J. L.

    1983-01-01

    A facultative anaerobic bacterium that rapidly degrades cyanuric acid (CA) was isolated from the sediment of a stream that received industrial wastewater effluent. CA decomposition was measured throughout the growth cycle by using a high-performance liquid chromatography assay, and the concomitant production of ammonia was also measured. The bacterium used CA or cysteine as a major, if not the sole, carbon and energy source under anaerobic, but not aerobic, conditions in a defined medium. The cell yield was greatly enhanced by the simultaneous presence of cysteine and CA in the medium. Cysteine was preferentially used rather than CA early in the growth cycle, but all of the CA was used without an apparent lag after the cysteine was metabolized. Atrazine was also degraded by this bacterium under anaerobic conditions in a defined medium. PMID:16346187

  10. An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm.

    PubMed

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

    2014-02-01

    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.

  11. 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

  12. 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.

  13. Biosynthesis of the respiratory toxin bongkrekic acid in the pathogenic bacterium Burkholderia gladioli.

    PubMed

    Moebius, Nadine; Ross, Claudia; Scherlach, Kirstin; Rohm, Barbara; Roth, Martin; Hertweck, Christian

    2012-09-21

    Bongkrekic acid (BA), an infamous respiratory toxin of the pathogenic bacterium Burkholderia gladioli, causes lethal intoxications when tempe bongkrek is produced with contaminated Rhizopus oligosporus cultures. Genome sequencing of B. gladioli pathovar cocovenenans unveiled the genetic basis for BA biosynthesis, and pointed to a homologous bon gene cluster in a B. gladioli strain from an infected rice plant. For functional genetics in B. gladioli λ Red recombination was established. Dissection of the modular type I polyketide synthase (a trans-AT PKS) provided insights into complex polyketide assembly. Isoprenoid-like β-branching events and a six-electron oxidation of a methyl group to a carboxylic acid give rise to the unique branched tricarboxylic fatty acid. The role of the cytochrome P450 monooxygenase, BonL, was proven by structural elucidation of deoxybongkrekic acid from a mutant.

  14. Tolerance of the nanocellulose-producing bacterium Gluconacetobacter xylinus to lignocellulose-derived acids and aldehydes.

    PubMed

    Zhang, Shuo; Winestrand, Sandra; Chen, Lin; Li, Dengxin; Jönsson, Leif J; Hong, Feng

    2014-10-08

    Lignocellulosic biomass serves as a potential alternative feedstock for production of bacterial nanocellulose (BNC), a high-value-added product of bacteria such as Gluconacetobacter xylinus. The tolerance of G. xylinus to lignocellulose-derived inhibitors (formic acid, acetic acid, levulinic acid, furfural, and 5-hydroxymethylfurfural) was investigated. Whereas 100 mM formic acid completely suppressed the metabolism of G. xylinus, 250 mM of either acetic acid or levulinic acid still allowed glucose metabolism and BNC production to occur. Complete suppression of glucose utilization and BNC production was observed after inclusion of 20 and 30 mM furfural and 5-hydroxymethylfurfural, respectively. The bacterium oxidized furfural and 5-hydroxymethylfurfural to furoic acid and 5-hydroxymethyl-2-furoic acid, respectively. The highest yields observed were 88% for furoic acid/furfural and 76% for 5-hydroxymethyl-2-furoic acid/5-hydroxymethylfurfural. These results are the first demonstration of the capability of G. xylinus to tolerate lignocellulose-derived inhibitors and to convert furan aldehydes.

  15. 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.

  16. Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation.

    PubMed

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2017-02-01

    Soy sauce is a Japanese traditional seasoning composed of various constituents that are produced by various microbes during a long-term fermentation process. Due to the complexity of the process, the investigation of the constituent profile during fermentation is difficult. Metabolomics, the comprehensive study of low molecular weight compounds in biological samples, is thought to be a promising strategy for deep understanding of the constituent contribution to food flavor characteristics. Therefore, metabolomics is suitable for the analysis of soy sauce fermentation. Unfortunately, only few and unrefined studies of soy sauce fermentation using metabolomics approach have been reported. Therefore, we investigated changes in low molecular weight hydrophilic and volatile compounds of soy sauce using gas chromatography/mass spectrometry (GC/MS)-based non-targeted metabolic profiling. The data were analyzed by statistical analysis to evaluate influences of yeast and lactic acid bacterium on the constituent profile. Consequently, our results suggested a novel finding that lactic acid bacterium affected the production of several constituents such as cyclotene, furfural, furfuryl alcohol and methional in the soy sauce fermentation process.

  17. Efficacy of Lactic Acid Bacteria (LAB) supplement in management of constipation among nursing home residents

    PubMed Central

    2010-01-01

    Background Constipation is a significant problem in the elderly, specifically nursing home and/or extended-care facility residents are reported to suffer from constipation. Lactic acid bacteria (LAB) are beneficial probiotic organisms that contribute to improved nutrition, microbial balance, and immuno-enhancement of the intestinal tract, as well as diarrhea and constipation effect. The objective of this study was to investigate the efficacy of this LAB supplement in the management of nursing home residents. Methods Nineteen subjects (8M, 11F; mean age 77.1 ± 10.1) suffering with chronic constipation were assigned to receive LAB (3.0 × 1011 CFU/g) twice (to be taken 30 minutes after breakfast and dinner) a day for 2 weeks in November 2008. Subjects draw up a questionnaire on defecation habits (frequency of defecation, amount and state of stool), and we collected fecal samples from the subjects both before entering and after ending the trial, to investigate LAB levels and inhibition of harmful enzyme activities. Results were tested with SAS and Student's t-test. Results Analysis of questionnaire showed that there was an increase in the frequency of defecation and amount of stool excreted in defecation habit after LAB treatment, but there were no significant changes. And it also affects the intestinal environment, through significantly increase (p < 0.05) fecal LAB levels. In addition, tryptophanase and urease among harmful enzyme activities of intestinal microflora were significantly decreased (p < 0.05) after LAB treatment. Conclusion LAB, when added to the standard treatment regimen for nursing home residents with chronic constipation, increased defecation habit such as frequency of defecation, amount and state of stool. So, it may be used as functional probiotics to improve human health by helping to prevent constipation. PMID:20137076

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

    PubMed

    Sundset, Monica A; Kohn, Alexandra; Mathiesen, Svein D; Praesteng, 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 x 2.0-3.5 microm) 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.

  20. 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

  1. 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

  2. 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.

  3. 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...

  4. Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

    PubMed Central

    Velly, H.; Abraham, A.-L.; Loux, V.; Delacroix-Buchet, A.; Fonseca, F.; Bouix, M.

    2014-01-01

    Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation. PMID:25377704

  5. 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.

  6. 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)).

  7. A Highly Stable d-Amino Acid Oxidase of the Thermophilic Bacterium Rubrobacter xylanophilus

    PubMed Central

    Furukawara, Makoto; Omae, Keishi; Tadokoro, Namiho; Saito, Yayoi; Abe, Katsumasa; Kera, Yoshio

    2014-01-01

    d-Amino acid oxidase (DAO) is a biotechnologically attractive enzyme that can be used in a variety of applications, but its utility is limited by its relatively poor stability. A search of a bacterial genome database revealed a gene encoding a protein homologous to DAO in the thermophilic bacterium Rubrobacter xylanophilus (RxDAO). The recombinant protein expressed in Escherichia coli was a monomeric protein containing noncovalently bound flavin adenine dinucleotide as a cofactor. This protein exhibited oxidase activity against neutral and basic d-amino acids and was significantly inhibited by a DAO inhibitor, benzoate, but not by any of the tested d-aspartate oxidase (DDO) inhibitors, thus indicating that the protein is DAO. RxDAO exhibited higher activities and affinities toward branched-chain d-amino acids, with the highest specific activity toward d-valine and catalytic efficiency (kcat/Km) toward d-leucine. Substrate inhibition was observed in the case of d-tyrosine. The enzyme had an optimum pH range and temperature of pH 7.5 to 10 and 65°C, respectively, and was stable between pH 5.0 and pH 8.0, with a T50 (the temperature at which 50% of the initial enzymatic activity is lost) of 64°C. No loss of enzyme activity was observed after a 1-week incubation period at 30°C. This enzyme was markedly inactivated by phenylmethylsulfonyl fluoride but not by thiol-modifying reagents and diethyl pyrocarbonate, which are known to inhibit certain DAOs. These results demonstrated that RxDAO is a highly stable DAO and suggested that this enzyme may be valuable for practical applications, such as the determination and quantification of branched-chain d-amino acids, and as a scaffold to generate a novel DAO via protein engineering. PMID:25217016

  8. 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.

  9. 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.

  10. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  11. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    PubMed

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14(T), was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14(T) within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14(T) contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14(T) from the type strains for the related species. The genome size and DNA G+C content of FH14(T) were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14(T) (=HAMBI 3636(T) = LMG 29288(T)) as the type strain.

  12. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM

    PubMed Central

    Altermann, Eric; Russell, W. Michael; Azcarate-Peril, M. Andrea; Barrangou, Rodolphe; Buck, B. Logan; McAuliffe, Olivia; Souther, Nicole; Dobson, Alleson; Duong, Tri; Callanan, Michael; Lick, Sonja; Hamrick, Alice; Cano, Raul; Klaenhammer, Todd R.

    2005-01-01

    Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota. PMID:15671160

  13. Characteristic of phenolic compound and antioxidant activity of fermented broccoli (Brassica oleracea L. ssp.) beverage by lactic acid bacteria (LAB)

    NASA Astrophysics Data System (ADS)

    Maryati, Yati; Susilowati, Agustine; Melanie, Hakiki; Lotulung, Puspa D.

    2017-01-01

    Broccoli (Brassica oleracea L. ssp.) has a relatively high nutrient content, especially as a source of vitamins, minerals and fiber and contain bioactive compounds that act as antioxidants. In order to increase the nutritional value and innovate new products, fermentation process involving rich-antioxidants lactic acid bacteria (LAB) was done. The aim of this study is to determine the content of bioactive components, such as total polyphenols, total acid and antioxidant activity of the mixed culture of LAB (L. bulgaricus, S. thermophulus, L. acidophilus, Bd. bifidum)-fermented broccoli extracts. Ratio of fermented broccoli extract and concentration of starter cultureLAB was varied in the range of 5, 10, 15 and 20% (v/v), and the alterations of characteristics of the fermented broccoli extract, before and after fermentation (0 and 24 hours), were evaluated. The results showed that fermentation functional beverage broccoli with different concentrations of LAB cultures affect the antioxidant activity, total polyphenols, total acid and total cell of LAB generated. The optimum conditions obtained for the highest antioxidant activity of 6.74%, at aculture concentration of 20% during fermentation time of 24 h with a pH value of 4.29, total sugar of 10.89%, total acids of 0.97%, total polyphenols of 0.076%, and total LAB of 13.02 + 0.05 log cfu /ml.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. Lab-on-a-chip nucleic-acid analysis towards point-of-care applications

    NASA Astrophysics Data System (ADS)

    Kopparthy, Varun Lingaiah

    Recent infectious disease outbreaks, such as Ebola in 2013, highlight the need for fast and accurate diagnostic tools to combat the global spread of the disease. Detection and identification of the disease-causing viruses and bacteria at the genetic level is required for accurate diagnosis of the disease. Nucleic acid analysis systems have shown promise in identifying diseases such as HIV, anthrax, and Ebola in the past. Conventional nucleic acid analysis systems are still time consuming, and are not suitable for point-ofcare applications. Miniaturized nucleic acid systems has shown great promise for rapid analysis, but they have not been commercialized due to several factors such as footprint, complexity, portability, and power consumption. This dissertation presents the development of technologies and methods for a labon-a-chip nucleic acid analysis towards point-of-care applications. An oscillatory-flow PCR methodology in a thermal gradient is developed which provides real-time analysis of nucleic-acid samples. Oscillating flow PCR was performed in the microfluidic device under thermal gradient in 40 minutes. Reverse transcription PCR (RT-PCR) was achieved in the system without an additional heating element for incubation to perform reverse transcription step. A novel method is developed for the simultaneous pattering and bonding of all-glass microfluidic devices in a microwave oven. Glass microfluidic devices were fabricated in less than 4 minutes. Towards an integrated system for the detection of amplified products, a thermal sensing method is studied for the optimization of the sensor output. Calorimetric sensing method is characterized to identify design considerations and optimal parameters such as placement of the sensor, steady state response, and flow velocity for improved performance. An understanding of these developed technologies and methods will facilitate the development of lab-on-a-chip systems for point-of-care analysis.

  1. Fractionation of carbon isotopes in biosynthesis of fatty acids by a piezophilic bacterium Moritella japonica strain DSK1

    NASA Astrophysics Data System (ADS)

    Fang, Jiasong; Uhle, Maria; Billmark, Kaycie; Bartlett, Douglas H.; Kato, Chaki

    2006-04-01

    We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica strain DSK1. The bacterium was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using sterile-filtered natural seawater supplied with glucose as the sole carbon source. Strain DSK1 synthesized typical bacterial fatty acids (C 14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6 ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed Δδ FA-glucose (-1.0‰ to -11.9‰) at 0.1 MPa was comparable to or slightly higher than fractionations reported in surface bacteria. However, bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation (Δδ FA-glucose) at high pressures was much higher than that for surface bacteria: -15.7‰, -15.3‰, and -18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions that are affected by hydrostatic pressure and to biosynthetic pathways that are different for short-chain and long-chain fatty acids. A simple quantitative calculation suggests that in situ piezophilic bacterial contribution of polyunsaturated fatty acids to marine sediments is nearly two orders of magnitude higher than that of marine phytoplankton and that the carbon isotope imprint of piezophilic bacteria can override that of surface phytoplankton. Our results have important implications for marine biogeochemistry. Depleted fatty acids reported in marine sediments and the water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i

  2. The amino acid sequence of the cytochrome c-554(547) from the chemolithotrophic bacterium Thiobacillus neapolitanus.

    PubMed Central

    Ambler, R P; Meyer, T E; Trudinger, P A; Kamen, M D

    1985-01-01

    An amino acid sequence is proposed for the cytochrome c-554(547) from the bacterium Thiobacillus neapolitanus N.C.I.B. 8539). It consists of a polypeptide chain of 91 residues, with a pair of haem-attachment cysteine residues at positions 15 and 18. There is similarity in sequence with each of the halves of the sequence of the dihaem cytochromes c4 and with a cytochrome c-554(548) from a halophilic strain of Paracoccus. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50127 (11 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1985) 225, 5. PMID:2988504

  3. Influence of phenolic compounds on the growth and arginine deiminase system in a wine lactic acid bacterium

    PubMed Central

    Alberto, María R.; de Nadra, María C. Manca; Arena, Mario E.

    2012-01-01

    The influence of seven phenolic compounds, normally present in wine, on the growth and arginine deiminase system (ADI) of Lactobacillus hilgardii X1B, a wine lactic acid bacterium, was established. This system provides energy for bacterial growth and produces citrulline that reacts with ethanol forming the carcinogen ethyl carbamate (EC), found in some wines. The influence of phenolic compounds on bacterial growth was compound dependent. Growth and final pH values increased in presence of arginine. Arginine consumption decreased in presence of protocatechuic and gallic acids (31 and 17%, respectively) and increased in presence of quercetin, rutin, catechin and the caffeic and vanillic phenolic acids (between 10 and 13%, respectively). ADI enzyme activities varied in presence of phenolic compounds. Rutin, quercetin and caffeic and vanillic acids stimulated the enzyme arginine deiminase about 37–40%. Amounts of 200 mg/L gallic and protocatechuic acids inhibited the arginine deiminase enzyme between 53 and 100%, respectively. Ornithine transcarbamylase activity was not modified at all concentrations of phenolic compounds. As gallic and protocatechuic acids inhibited the arginine deiminase enzyme that produces citrulline, precursor of EC, these results are important considering the formation of toxic compounds. PMID:24031815

  4. Influence of phenolic compounds on the growth and arginine deiminase system in a wine lactic acid bacterium.

    PubMed

    Alberto, María R; de Nadra, María C Manca; Arena, Mario E

    2012-01-01

    The influence of seven phenolic compounds, normally present in wine, on the growth and arginine deiminase system (ADI) of Lactobacillus hilgardii X1B, a wine lactic acid bacterium, was established. This system provides energy for bacterial growth and produces citrulline that reacts with ethanol forming the carcinogen ethyl carbamate (EC), found in some wines. The influence of phenolic compounds on bacterial growth was compound dependent. Growth and final pH values increased in presence of arginine. Arginine consumption decreased in presence of protocatechuic and gallic acids (31 and 17%, respectively) and increased in presence of quercetin, rutin, catechin and the caffeic and vanillic phenolic acids (between 10 and 13%, respectively). ADI enzyme activities varied in presence of phenolic compounds. Rutin, quercetin and caffeic and vanillic acids stimulated the enzyme arginine deiminase about 37-40%. Amounts of 200 mg/L gallic and protocatechuic acids inhibited the arginine deiminase enzyme between 53 and 100%, respectively. Ornithine transcarbamylase activity was not modified at all concentrations of phenolic compounds. As gallic and protocatechuic acids inhibited the arginine deiminase enzyme that produces citrulline, precursor of EC, these results are important considering the formation of toxic compounds.

  5. Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

    PubMed

    Hongpattarakere, Tipparat; Komeda, Hidenobu; Asano, Yasuhisa

    2005-12-01

    The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

  6. Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritima.

    PubMed Central

    Carballeira, N M; Reyes, M; Sostre, A; Huang, H; Verhagen, M F; Adams, M W

    1997-01-01

    The fatty acid compositions of the hyperthermophilic microorganisms Thermotoga maritima and Pyrococcus furiosus were studied and compared. A total of 37 different fatty acids were identified in T. maritima, including the novel 13,14-dimethyloctacosanedioic acid. In contrast, a total of 18 different fatty acids were characterized, as minor components, in P. furiosus, and these included saturated, monounsaturated, and dicarboxylic acids. This is the first report of fatty acids from an archaeon. PMID:9098079

  7. Fractionation of Carbon Isotopes in Biosynthesis of Fatty Acids by A Piezophilic Bacterium Moritella Japonica DSK1

    NASA Astrophysics Data System (ADS)

    Fang, J.; Uhle, M.; Bartlett, D.; Kato, C.

    2005-12-01

    We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica DSK1. DSK1 was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using natural seawater supplied with glucose with the sole carbon source. DSk1 synthesized typical bacterial fatty acids (C14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed ΔδFA-glucose (-1.0 to -11.9%) at 0.1 MPa was comparable to or slightly higher than fractionations reported on surface bacteria. However, Bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation ΔδFA-glucose) at high pressures was much higher than that for surface bacteria: -15.7, -15.3, and -18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions affected by hydrostatic pressure and to different biosynthetic pathways for short-chain and long-chain fatty acids. Our results have important implications for marine biogeochemistry. The 13C depleted fatty acids in marine sediments and water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i.e., methane). The interpretation of carbon isotope signatures of marine lipids must be based on principles derived from piezophilic bacteria.

  8. 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.

  9. Isolation and characterization of Halomonas sp. strain IMPC, a p-coumaric acid-metabolizing bacterium that decarboxylates other cinnamic acids under hypersaline conditions.

    PubMed

    Abdelkafi, Slim; Labat, Marc; Casalot, Laurence; Chamkha, Mohamed; Sayadi, Sami

    2006-02-01

    A moderately halophilic, mesophilic, Gram-negative, motile, nonsporulating bacterium, designated strain IMPC, was isolated from a table-olive fermentation rich in aromatic compounds, after enrichment on p-coumaric acid under halophilic conditions. Strain IMPC was able to degrade p-coumaric acid. p-hydroxybenzaldehyde and p-hydroxybenzoic acid were detected as breakdown products from p-coumaric acid. Protocatechuic acid was identified as the final aromatic product of p-coumaric acid catabolism before ring fission. Strain IMPC transformed various cinnamic acids with substituent H, OH, CH(3) or OCH(3) in the para- and/or meta-position of the aromatic ring to the corresponding benzoic acids, indicating a specific selection. A beta-oxidation pathway was proposed for these transformations. Phylogenetic analysis of the 16S rRNA gene revealed that this isolate was a member of the genus Halomonas. Strain IMPC was closely related to Halomonas elongata ATCC 33173(T)and Halomonas eurihalina ATCC 49336(T).

  10. A CMP-N-acetylneuraminic acid synthetase purified from a marine bacterium, Photobacterium leiognathi JT-SHIZ-145.

    PubMed

    Kajiwara, Hitomi; Mine, Toshiki; Miyazaki, Tatsuo; Yamamoto, Takeshi

    2011-01-01

    A cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) synthetase was found in a crude extract prepared from Photobacterium leiognathi JT-SHIZ-145, a marine bacterium that also produces a β-galactoside α2,6-sialyltransferase. The CMP-Neu5Ac synthetase was purified from the crude extract of the cells by a combination of anion-exchange and gel filtration column chromatography. The purified enzyme migrated as a single band (60 kDa) on sodium dodecylsulfate-polyacrylamide gel electrophoresis. The activity of the enzyme was maximal at 35 °C at pH 9.0, and the synthetase required Mg(2+) for activity. Although these properties are similar to those of other CMP-Neu5Ac synthetases isolated from bacteria, this synthetase produced not only CMP-Neu5Ac from cytidine triphosphate and Neu5Ac, but also CMP-N-glycolylneuraminic acid from cytidine triphosphate and N-glycolylneuraminic acid, unlike CMP-Neu5Ac synthetase purified from Escherichia coli.

  11. Elongation of exogenous fatty acids by the bioluminescent bacterium Vibrio harveyi

    SciTech Connect

    Byers, D.M.

    1989-01-01

    Bioluminescent bacteria require myristic acid (C14:0) to produce the myristaldehyde substrate of the light-emitting luciferase reaction. Since both endogenous and exogenous C14:0 can be used for this purpose, the metabolism of exogenous fatty acids by luminescent bacteria has been investigated. Both Vibrio harveyi and Vibrio fischeri incorporated label from (1-14C)myristic acid (C14:0) into phospholipid acyl chains as well as into CO2. In contrast, Photobacterium phosphoreum did not exhibit phospholipid acylation or beta-oxidation using exogenous fatty acids. Unlike Escherichia coli, the two Vibrio species can directly elongate fatty acids such as octanoic (C8:0), lauric (C12:0), and myristic acid, as demonstrated by radio-gas liquid chromatography. The induction of bioluminescence in late exponential growth had little effect on the ability of V. harveyi to elongate fatty acids, but it did increase the amount of C14:0 relative to C16:0 labeled from (14C)C8:0. This was not observed in a dark mutant of V. harveyi that is incapable of supplying endogenous C14:0 for luminescence. Cerulenin preferentially decreased the labeling of C16:0 and of unsaturated fatty acids from all 14C-labeled fatty acid precursors as well as from (14C)acetate, suggesting that common mechanisms may be involved in elongation of fatty acids from endogenous and exogenous sources. Fatty acylation of the luminescence-related synthetase and reductase enzymes responsible for aldehyde synthesis exhibited a chain-length preference for C14:0, which also was indicated by reverse-phase thin-layer chromatography of the acyl groups attached to these enzymes. The ability of V. harveyi to activate and elongate exogenous fatty acids may be related to an adaptive requirement to metabolize intracellular C14:0 generated by the luciferase reaction during luminescence development.

  12. Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

    PubMed

    Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

    2007-07-01

    Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

  13. Bile acids are new products of a marine bacterium, Myroides sp. strain SM1.

    PubMed

    Maneerat, Suppasil; Nitoda, Teruhiko; Kanzaki, Hiroshi; Kawai, Fusako

    2005-06-01

    Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, (1)H- and (13)C-NMR spectra and fast atom bombardment mass spectrometry as cholic acid, deoxycholic acid and their glycine conjugates. Type strains of the genus Myroides, M. odoratus JCM7458 and M. odoramitimus JCM7460, also produced these compounds. Myroides sp. strain SM1 possessed a biosynthetic route to cholic acid from cholesterol. Thus, bile acids were found as new products of prokaryotic cells, genus Myroides.

  14. 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.

  15. Characterization and Antibacterial Potential of Lactic Acid Bacterium Pediococcus pentosaceus 4I1 Isolated from Freshwater Fish Zacco koreanus

    PubMed Central

    Bajpai, Vivek K.; Han, Jeong-Ho; Rather, Irfan A.; Park, Chanseo; Lim, Jeongheui; Paek, Woon Kee; Lee, Jong Sung; Yoon, Jung-In; Park, Yong-Ha

    2016-01-01

    This study was undertaken to characterize a lactic acid bacterium 4I1, isolated from the freshwater fish, Zacco koreanus. Morphological, biochemical, and molecular characterization of 4I1 revealed it to be Pediococcus pentosaceus 4I1. The cell free supernatant (CFS) of P. pentosaceus 4I1 exhibited significant (p < 0.05) antibacterial effects (inhibition zone diameters: 16.5–20.4 mm) against tested foodborne pathogenic bacteria with MIC and MBC values of 250–500 and 500–1,000 μg/mL, respectively. Further, antibacterial action of CFS of P. pentosaceus 4I1 against two selected bacteria Staphylococcus aureus KCTC-1621 and Escherichia coli O157:H7 was determined in subsequent assays. The CFS of P. pentosaceus 4I1 revealed its antibacterial action against S. aureus KCTC-1621 and E. coli O157:H7 on membrane integrity as confirmed by a reduction in cell viability, increased potassium ion release (900 and 800 mmol/L), reduced absorption at 260-nm (3.99 and 3.77 OD), and increased relative electrical conductivity (9.9 and 9.7%), respectively. Gas chromatography–mass spectrometry (GC–MS) analysis of the CFS of P. pentosaceus 4I1 resulted in the identification of seven major compounds, which included amino acids, fatty acids and organic acids. Scanning electron microscopic-based morphological analysis further confirmed the antibacterial effect of CFS of P. pentosaceus 4I1 against S. aureus KCTC-1621 and E. coli O157:H7. In addition, the CFS of P. Pentosaceus 4I1 displayed potent inhibitory effects on biofilms formation by S. aureus KCTC-1621 and E. coli O157:H7. The study indicates the CFS of P. pentosaceus 4I1 offers an alternative means of controlling foodborne pathogens. PMID:28066360

  16. Characterization of a nitroreductase with selective nitroreduction properties in the food and intestinal lactic acid bacterium Lactobacillus plantarum WCFS1.

    PubMed

    Guillén, Hugo; Curiel, Jose Antonio; Landete, José María; Muñoz, Rosario; Herraiz, Tomás

    2009-11-11

    Nitroreductases reduce nitroaromatic compounds and other oxidants in living organisms, having interesting implications in environmental and human health. A putative nitrobenzoate reductase encoding gene (lp_0050) was recently annotated in the completed DNA sequence of lactic acid bacterium Lactobacillus plantarum WCFS1 strain. In this research, this L. plantarum gene was cloned and expressed, and the corresponding protein (PnbA) was biochemically characterized. This L. plantarum PnbA reductase is a 216 amino acid residue FMN-flavoprotein, which exhibits 23% identity with Pseudomonas putida and Ralstonia eutropha nitroreductases and <11% identity with those from enterobacteria such as E. cloacae . This reductase also showed 32-43% identity (65-72% similarity) to predicted PnbA proteins from other lactic acid bacteria. It utilized a wide range of electron acceptors including dichlorophenolindophenol (DCPIP), nitroblue tetrazolium (NBT), ferricyanide, and quinones (menadione, benzoquinone), but not pyridinium cations (paraquat and N-methyl-beta-carbolines), and it was inhibited by dicoumarol and diphenyliodonium. HPLC-MS and spectroscopic data showed that it specifically catalyzed the reduction of the 4-nitroaromatic group to the corresponding hydroxylamine in the presence of NAD(P)H. Kinetics parameters (V(max) and K(m)) showed a higher efficiency for the reduction of 2,4-dinitrobenzoate than for the reduction of 4-nitrobenzoate. It was chemoselective for the reduction of 4-nitrobenzoates, being unable to reduce other nitroaromatics. Then, L. plantarum PnbA reductase might be more specific than other microbial nitroreductases that reduce a wider range of nitroaromatic compounds. The physiological and functional role of nitroreductases remain unknown; however, their presence in lactic acid bacteria widely occurring in foods and the human intestinal tract should be of further interest.

  17. Potency of microfiltration membrane process in purifying broccoli (Brassica oleracea L.) fermented by lactic acid bacteria (LAB) as functional food

    NASA Astrophysics Data System (ADS)

    Susilowati, Agustine; Aspiyanto, Maryati, Yati; Melanie, Hakiki; Lotulung, Puspa D.

    2017-01-01

    Purifying broccoli (Brassica oleracea L.) fermented by Lactic Acid Bacteria (LAB) using mixture of L. bulgaricus, S. thermopillus, L. acidophillusand Bifidobacteriumbifidum and fructooligosaccharides (FOS) as carbon source have been performed to recover biomass concentrate for probiotic and antioxidant. Purification of fermented broccoli was conducted through microfiltration (MF) membrane of 0.15 µm at stirrer rotation speed 400 rpm, room temperature and pressure 40 psia for 30 minutes. Fermented broccoli produced via fermentation process with fermentation time 0 (initial) and 48 hours, and LAB concentration 10% and 20% (v/v) represented as biomass of A, B, C and D. The experimental result showed that based on selectivity of total organic acids, separating optimization was achieved at biomass D (fermentation time 48 hours and mixed LAB culture concentration 20%). Concentrate composition produced in this condition were total acids 6.04%, total solids 24.31%, total polyphenol 0.0252%, reducing sugar 68.25 mg/mL, total sugars 30.89 mg/mL, and dissolved protein 28.54 mg/mL with pH 3.94. In this condition, recovery of biomass concentrate of D for total acids 5.64 folds, total solids 1.82 folds, total polyphenol 3.03 folds, reducing sugar 1.16 folds, total sugars 1.19 folds, and dissolved protein 0.67 folds compared with feed (initial process). Identification of monomer of biomass concentrate D as polyphenol derivatives at T2,01 and T3.01 gave monomer with molecular weight (MW) 192.78 Dalton (Da.), and monomer with MW 191.08, 191.49 and 192.07 Da., while lactic acid derivatives showed MW 251.13, 251.6 and 252.14, and monomer with MW 250.63, 252.14 and 254.22 Da.

  18. 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.

  19. 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)).

  20. 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)).

  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.

  2. Oxidation of nitrapyrin to 6-chloropicolinic acid by the ammonia-oxidizing bacterium nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Hooper, A.B.

    1992-07-01

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin (2-chloro-6-(trichloromethyl)-pyridine). Rapid oxidation of nitrapyrin (at a concentration of 10 microM) required the concomitant oxidation of ammonia, hydroxylamine, or hydrazine. The turnover rate was highest in the presence of 10 mM ammonia (0.8 nmol of nitrapyrin per min/mg of protein). The product of the reaction was 6-chloropicolinic acid. By the use of (18)O2, it was shown that one of the oxygens in 6-chloropicolinic acid came from diatomic oxygen and that the other came from water. Approximately 13% of the radioactivity of (2,6-(14)C) nitrapyrin was shown to bind to cells. Most (94%) of the latter was bound indiscriminately to membrane proteins. The nitrapyrin bound to membrane proteins may account for the observed inactivation of ammonia oxidation. (Copyright (c) 1992, American Society for Microbiology.)

  3. Biodegradation of Picolinic Acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ135.

    PubMed

    Qiu, Jiguo; Zhang, Junjie; Zhang, Yanting; Wang, Yuhong; Tong, Lu; Hong, Qing; He, Jian

    2017-04-01

    We isolated a bacterial strain JQ135 from municipal wastewater, which was capable of efficiently degrading picolinic acid (PA). Based on the physico-biochemical characteristics and 16S rDNA analysis, strain JQ135 was identified as Alcaligenes faecalis. In addition, strain JQ135 produced an orange pigment when cultured in the Luria-Bertani medium, which is different from the previously reported strains of A. faecalis. During the degradation of PA by the resting strain JQ135 cells, only one intermediate, 6-hydroxypicolinic acid (6HPA), was detected by ultraviolet spectrophotometry, high-pressure liquid chromatography, and liquid chromatography-mass spectrometry. A random transposon mutagenesis library of strain JQ135 was constructed. One mutant, Mut-G31, could convert PA into 6HPA without further degradation. The disrupted gene (orf2) was amplified from Mut-G31, and its product showed 32% identity to the 3-deoxy-D-manno-octulosonic acid kinase (KdkA) from Haemophilus influenzae. Results from complementation analysis confirmed that GTG was the initiation codon of the kdkA-like orf2, and that it was essential for PA biodegradation by strain JQ135. This study provides the first genetic evidence for the bacterial degradation of PA.

  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. 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.

  6. Distribution and Functions of Phosphotransferase System Genes in the Genome of the Lactic Acid Bacterium Oenococcus oeni

    PubMed Central

    Jamal, Zohra; Miot-Sertier, Cécile; Thibau, François; Dutilh, Lucie; Lonvaud-Funel, Aline; Ballestra, Patricia; Le Marrec, Claire

    2013-01-01

    Oenococcus oeni, the lactic acid bacterium primarily responsible for malolactic fermentation in wine, is able to grow on a large variety of carbohydrates, but the pathways by which substrates are transported and phosphorylated in this species have been poorly studied. We show that the genes encoding the general phosphotransferase proteins, enzyme I (EI) and histidine protein (HPr), as well as 21 permease genes (3 isolated ones and 18 clustered into 6 distinct loci), are highly conserved among the strains studied and may form part of the O. oeni core genome. Additional permease genes differentiate the strains and may have been acquired or lost by horizontal gene transfer events. The core pts genes are expressed, and permease gene expression is modulated by the nature of the bacterial growth substrate. Decryptified O. oeni cells are able to phosphorylate glucose, cellobiose, trehalose, and mannose at the expense of phosphoenolpyruvate. These substrates are present at low concentrations in wine at the end of alcoholic fermentation. The phosphotransferase system (PTS) may contribute to the perfect adaptation of O. oeni to its singular ecological niche. PMID:23524676

  7. The effect of humic acid on uptake/adsorption of copper by a marine bacterium and two marine ciliates.

    PubMed

    Lores, E M; Snyder, R A; Pennock, J R

    1999-01-01

    The effect of humic acid (HA) on Cu uptake by a bacterium and two bacterivorus ciliates was investigated. The presence of HA resulted in a statistically significant (p<0.001) decrease in Cu associated with bacteria that were exposed to 67 microg Cu L(-1). Complexation of Cu appears to lower the availability of Cu with respect to bacterial cell surface binding and uptake. For ciliates, 10 mg HA L(-1) significantly reduced uptake of Cu by Uronema, but did not reduce uptake of Cu by Pleuronema. Uronema exposed to 67 microg Cu L(-1) accumulated 54% less Cu when 10 mg HA L(-1) was present (0.50 pg ciliate(-1) vs 0.23 pg ciliate(-1)). Uronema feeding on V. natriegens, took up less than half as much Cu as unfed Uronema when exposed to Cu without HA (0.41 pg Cu fed ciliate(-1) vs 0.86 pg Cu unfed ciliate(-1), but only 40% less when exposed to Cu and HA (0.31 pg Cu fed ciliate(-1) vs 0.51 pg Cu unfed ciliate(-1)). The lower % reduction attributable to fed ciliates in the presence of HA suggests that some of the Cu associated with HA is available through trophic processes.

  8. 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)).

  9. Application of ethylene diamine tetra acetic acid degrading bacterium Burkholderia cepacia on biotreatment process.

    PubMed

    Chen, Wei-Ting; Shen, Shu-Min; Shu, Chi-Min

    2015-10-01

    Ethylene diamine tetra acetic acid (EDTA), the effluent of secondary biotreatment units, can be properly biodegraded by Burkholderia cepacia. Through batch degradation of EDTA, the raw wastewater of EDTA was controlled at 50 mg/L, and then nutrients was added in diluted wastewater to cultivate activated sludge, which the ratio of composition is depicted as "COD:N:P:Fe = 100:5:1:0.5". After 27 days, the removal efficiency of Fe-EDTA and COD was 100% and 92.0%, correspondingly. At the continuous process, the raw wastewater of EDTA was dictated at 166 mg/L before adding nutrients to cultivate activated sludge, in which the ratio of composition did also follow with batch process. After 22 days, the removal efficiency of Fe-EDTA and COD for experimental group was 71.46% and 62.58%, correspondingly. The results showed that the batch process was more suited for EDTA biodegradation.

  10. Iron sources used by the nonpathogenic lactic acid bacterium Lactobacillus sakei as revealed by electron energy loss spectroscopy and secondary-ion mass spectrometry.

    PubMed

    Duhutrel, Philippe; Bordat, Christian; Wu, Ting-Di; Zagorec, Monique; Guerquin-Kern, Jean-Luc; Champomier-Vergès, Marie-Christine

    2010-01-01

    Lactobacillus sakei is a lactic acid bacterium naturally found on meat. Although it is generally acknowledged that lactic acid bacteria are rare species in the microbial world which do not have iron requirements, the genome sequence of L. sakei 23K has revealed quite complete genetic equipment dedicated to transport and use of this metal. Here, we aimed to investigate which iron sources could be used by this species as well as their role in the bacterium's physiology. Therefore, we developed a microscopy approach based on electron energy loss spectroscopy (EELS) analysis and nano-scale secondary-ion mass spectrometry (SIMS) in order to analyze the iron content of L. sakei cells. This revealed that L. sakei can use iron sources found in its natural ecosystem, myoglobin, hemoglobin, hematin, and transferrin, to ensure long-term survival during stationary phase. This study reveals that analytical image methods (EELS and SIMS) are powerful complementary tools for investigation of metal utilization by bacteria.

  11. 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.

  12. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.

    PubMed

    Honda, Takuya; Fujita, Takashi; Tonouchi, Akio

    2013-10-01

    A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6E(T), were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0-2.5 µm) with two or three lateral flagella. Growth occurred at 20-42 °C (optimum at 37-40 °C), at pH 6.4-8.4 (optimum at pH 7.3) and at 0-1.5 % (w/v) NaCl (optimum at 0-0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, L-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen Methanobacterium formicicum JCM 10132(T), strain 4F6E(T) oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of Fretibacterium fastidiosum, Aminobacterium colombiense and Aminobacterium mobile, members of the family Synergistaceae, were the closest relatives of strain 4F6E(T), with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6E(T) contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of F. fastidiosum, Aminobacterium colombiense and Aminobacterium mobile. On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6E(T) and the type strains of F. fastidiosum and Aminobacterium species, we propose that strain 4F6E(T) represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6E(T) (

  13. 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.

  14. Complete Genome Sequence of the Prototype Lactic Acid Bacterium Lactococcus lactis subsp. cremoris MG1363▿

    PubMed Central

    Wegmann, Udo; O'Connell-Motherway, Mary; Zomer, Aldert; Buist, Girbe; Shearman, Claire; Canchaya, Carlos; Ventura, Marco; Goesmann, Alexander; Gasson, Michael J.; Kuipers, Oscar P.; van Sinderen, Douwe; Kok, Jan

    2007-01-01

    Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category “carbohydrate metabolism and transport,” by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the “lateral gene transfer hot spot” in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research. PMID:17307855

  15. 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.

  16. Isolation and characterisation of lactic acid bacterium for effective fermentation of cellobiose into optically pure homo L-(+)-lactic acid.

    PubMed

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

    2011-02-01

    Effective utilisation of cellulosic biomasses for economical lactic acid production requires a microorganism with potential ability to utilise efficiently its major components, glucose and cellobiose. Amongst 631 strains isolated from different environmental samples, strain QU 25 produced high yields of l-(+)-lactic acid of high optical purity from cellobiose. The QU 25 strain was identified as Enterococcus mundtii based on its sugar fermentation pattern and 16S rDNA sequence. The production of lactate by fermentation was optimised for the E. mundtii QU25 strain. The optimal pH and temperature for batch culturing were found to be 7.0°C and 43°C, respectively. E. mundtii QU 25 was able to metabolise a mixture of glucose and cellobiose simultaneously without apparent carbon catabolite repression. Moreover, under the optimised culture conditions, production of optically pure l-lactic acid (99.9%) increased with increasing cellobiose concentrations. This indicates that E. mundtii QU 25 is a potential candidate for effective lactic acid production from cellulosic hydrolysate materials.

  17. 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.

  18. 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.

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

    PubMed Central

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

    2015-01-01

    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

  20. 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.

  1. 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.

  2. 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

    2010-04-07

    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.

  3. 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

  4. 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.

  5. Factors affecting the rate of hydrolysis of phenylboronic acid in lab-scale precipitate reactor studies

    SciTech Connect

    Bannochie, C.J.; Marek, J.C.; Eibling, R.E.; Baich, M.A.

    1992-01-01

    Removing aromatic carbon from an aqueous slurry of cesium-137 and other alkali tetraphenylborates by acid hydrolysis will be an important step in preparing high-level radioactive waste for vitrification at the Savannah River Site's Defense Waste Processing Facility (DWPF). Kinetic data obtained in bench-scale precipitate hydrolysis reactors suggest changes in operating parameters to improve product quality in the future plant-scale radioactive operation. The rate-determining step is the removal of the fourth phenyl group, i.e. hydrolysis of phenylboronic acid. Efforts to maximize this rate have established the importance of several factors in the system, including the ratio of copper(II) catalyst to formic acid, the presence of nitrite ion, reactions of diphenylmercury, and the purge gas employed in the system.

  6. Factors affecting the rate of hydrolysis of phenylboronic acid in lab-scale precipitate reactor studies

    SciTech Connect

    Bannochie, C.J.; Marek, J.C.; Eibling, R.E.; Baich, M.A.

    1992-10-01

    Removing aromatic carbon from an aqueous slurry of cesium-137 and other alkali tetraphenylborates by acid hydrolysis will be an important step in preparing high-level radioactive waste for vitrification at the Savannah River Site`s Defense Waste Processing Facility (DWPF). Kinetic data obtained in bench-scale precipitate hydrolysis reactors suggest changes in operating parameters to improve product quality in the future plant-scale radioactive operation. The rate-determining step is the removal of the fourth phenyl group, i.e. hydrolysis of phenylboronic acid. Efforts to maximize this rate have established the importance of several factors in the system, including the ratio of copper(II) catalyst to formic acid, the presence of nitrite ion, reactions of diphenylmercury, and the purge gas employed in the system.

  7. 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.

  8. In vitro antagonistic activity evaluation of Lactic Acid Bacteria (LAB) combined with cellulase enzyme against campylobacter jejuni growth in co-culture.

    PubMed

    Dubois-Dauphin, Robin; Sabrina, Vandeplas; Isabelle, Didderen; Christopher, Marcq; Andre, Thewis; Philippe, Thonart

    2011-01-01

    The antibacterial effects of nine lactic acid bacteria (LAB) against Campylobacter jejuni were investigated by using agar gel diffusion and co-culture assays. Some differences were recorded between the inhibition effects measured with these two methods. Only two LAB, Lb. pentosus CWBI B78 and E. faecium THT, exhibited a clear anti- Campylobacter activity in co-culture assay with dehydrated poultry excreta mixed with ground straw (DPE/GS) as the only growth substrate source. It was observed that the supplementation of such medium with a cellulase A complex (Beldem S.A.) enhanced the antimicrobial effect of both LAB strains. The co-culture medium acidification and the C. jejuni were positively correlated with the cellulase A concentration. The antibacterial effect was characterized by the lactic acid production from the homofermentative E. faecium THT and the lactic and acetic acids production from the heterofermentative Lb. pentosus CWBI B78. The antagonistic properties of LAB strains and enzyme combination could be used in strategies aiming at the reduction of Campylobacter prevalence in the poultry production chain and consequently the risk of human infection.

  9. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9.

    PubMed

    Allen, Eric E; Bartlett, Douglas H

    2002-06-01

    Omega-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (20:5n-3; EPA) and docosahexaenoic acid (22:6n-3; DHA) have been shown to be of major importance in the promotion of cardiovascular health, proper human development and the prevention of some cancers. A high proportion of bacterial isolates from low-temperature and high-pressure marine environments produce EPA or DHA. This paper presents the sequence of a 33 kbp locus from the deep-sea bacterium Photobacterium profundum strain SS9 which includes four of the five genes required for EPA biosynthesis. As with other bacterial pfa (polyunsaturated fatty acid) genes, the deduced amino acid sequences encoded by the SS9 genes reveal large multidomain proteins that are likely to catalyse EPA biosynthesis by a novel polyketide synthesis mechanism. RNase protection experiments separated the SS9 pfa genes into two transcriptional units, pfaA-C and pfaD. The pfaA transcriptional start site was identified. Cultivation at elevated hydrostatic pressure or reduced temperature did not increase pfa gene expression despite the resulting increase in percentage composition of EPA under these conditions. However, a regulatory mutant was characterized which showed both increased expression of pfaA-D and elevated EPA percentage composition. This result suggests that a regulatory factor exists which coordinates pfaA-D transcription. Additional consideration regarding the activities required for PUFA synthesis is provided together with comparative analyses of bacterial pfa genes and gene products.

  10. 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.

  11. 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

  12. 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

    2016-12-05

    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.

  13. Analysis of 16S rRNA gene lactic acid bacteria (LAB) isolate from Markisa fruit (Passiflora sp.) as a producer of protease enzyme and probiotics

    NASA Astrophysics Data System (ADS)

    Hidayat, Habibi

    2017-03-01

    16S rRNA gene analysis of bacteria lactic acid (LAB) isolate from Markisa Kuning Fruit (Passiflora edulis var. flavicarpa) as a producer of protease enzyme and probiotics has been done. The aim of the study is to determine the protease enzyme activity and 16S rRNA gene amplification using PCR. The calculation procedure was done to M4 isolate bacteria lactic acid (LAB) Isolate which has been resistant to acids with pH 2.0 in the manner of screening protease enzyme activity test result 6.5 to clear zone is 13 mm againts colony diametre is 2 mm. The results of study enzyme activity used spectrophotometer UV-Vis obtainable the regression equation Y=0.02983+0.001312X, with levels of protein M4 isolate is 0.6594 mg/mL and enzyme activity of obtainable is 0.8626 unit/ml while the spesific enzyme activity produced is 1.308 unit/mg. Then, 16S rRNA gene amplificatiom and DNA sequencing has been done. The results of study showed that the bacteria species contained from M4 bacteria lactic acid (LAB) isolate is Weisella cibiria strain II-I-59. Weisella cibiria strain II-I-59 is one of bacteria could be utilized in the digestive tract.

  14. Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester.

    PubMed

    Ganesan, Akila; Chaussonnerie, Sébastien; Tarrade, Anne; Dauga, Catherine; Bouchez, Théodore; Pelletier, Eric; Le Paslier, Denis; Sghir, Abdelghani

    2008-09-01

    A novel anaerobic, mesophilic, amino-acid-utilizing bacterium, strain 158T, was isolated from an anaerobic digester of a wastewater treatment plant. Cells of strain 158T were non-motile, rod-shaped (2.0-3.0 x 0.8-1.0 microm) and stained Gram-negative. Optimal growth occurred at 37 degrees C and pH 7.0 in an anaerobic basal medium containing 1 % Casamino acids. Strain 158T fermented arginine, histidine, lysine and serine and showed growth on yeast extract, brain-heart infusion (BHI) medium and tryptone, but not on carbohydrates, organic acids or alcohols. The end products of degradation were: acetate, butyrate, H2 and CO2 from arginine; acetate, propionate, butyrate, H2 and CO2 from lysine; and acetate, propionate, butyrate, valerate, H2 and CO2 from histidine, serine, BHI medium, Casamino acids and tryptone. The DNA G+C content was 55.8 mol%. The 16S rRNA gene sequence of strain 158T showed only 92.6 % sequence similarity with that of Synergistes jonesii, the only described species of the 'Synergistes' group. The major cellular fatty acids were iso-C(15:0) (16.63 %), iso-C(15:0) 3-OH (12.41 %) and C(17:1)omega6c (9.46 %) and the polar fatty acids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylamine; these fatty acid profiles did not resemble those of any recognized bacterial species. Due to the considerable differences in genotypic, phenotypic and phylogenetic characteristics between strain 158T and those of its nearest relative, it is proposed that strain 158T represents a novel species in a new genus, Cloacibacillus evryensis gen. nov., sp. nov., in the phylum 'Synergistetes'. The type strain is 158T (=DSM 19522T=JCM 14828T).

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Tech Labs.

    ERIC Educational Resources Information Center

    Lindeman, Cheryl A., Bishop, S. William

    1997-01-01

    Describes a seminar where students explore emerging technologies through a series of labs that help boost their technical skills and their confidence in using and managing technology. Discusses charting the course, laboratory logistics, technology tips, and benefits. (JRH)

  20. 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.

  1. 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)).

  2. 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.

  3. Nucleotide and deduced amino acid sequences of a subtilisin-like serine protease from a deep-sea bacterium, Alkalimonas collagenimarina AC40(T).

    PubMed

    Kurata, Atsushi; Uchimura, Kohsuke; Shimamura, Shigeru; Kobayashi, Tohru; Horikoshi, Koki

    2007-11-01

    The acpI gene encoding an alkaline protease (AcpI) from a deep-sea bacterium, Alkalimonas collagenimarina AC40(T), was shotgun-cloned and sequenced. It had a 1,617-bp open reading frame encoding a protein of 538 amino acids. Based on analysis of the deduced amino acid sequence, AcpI is a subtilisin-like serine protease belonging to subtilase family A. It consists of a prepropeptide, a catalytic domain, and a prepeptidase C-terminal domain like other serine proteases from the genera Pseudomonas, Shewanella, Alteromonas, and Xanthomonas. Heterologous expression of the acpI gene in Escherichia coli cells yielded a 28-kDa recombinant AcpI (rAcpI), suggesting that both the prepropeptide and prepeptidase C-terminal domains were cleaved off to give the mature form. Analysis of N-terminal and C-terminal amino acid sequences of purified rAcpI showed that the mature enzyme would be composed of 273 amino acids. The optimal pH and temperature for the caseinolytic activity of the purified rAcpI were 9.0-9.5 and 45 degrees C in 100 mM glycine-NaOH buffer. Calcium ions slightly enhanced the enzyme activity and stability. The enzyme favorably hydrolyzed gelatin, collagen, and casein. AcpI from A. collagenimarina AC40(T) was also purified from culture broth, and its molecular mass was around 28 kDa, indicating that the cleavage manner of the enzyme is similar to that in E. coli cells.

  4. 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.

  5. Biological degradation of 4-chlorobenzoic acid by a PCB-metabolizing bacterium through a pathway not involving (chloro)catechol.

    PubMed

    Adebusoye, Sunday A

    2017-02-01

    Cupriavidus sp. strain SK-3, previously isolated on polychlorinated biphenyl mixtures, was found to aerobically utilize a wide spectrum of substituted aromatic compounds including 4-fluoro-, 4-chloro- and 4-bromobenzoic acids as a sole carbon and energy source. Other chlorobenzoic acid (CBA) congeners such as 2-, 3-, 2,3-, 2,5-, 3,4- and 3,5-CBA were all rapidly transformed to respective chlorocatechols (CCs). Under aerobic conditions, strain SK-3 grew readily on 4-CBA to a maximum concentration of 5 mM above which growth became impaired and yielded no biomass. Growth lagged significantly at concentrations above 3 mM, however chloride elimination was stoichiometric and generally mirrored growth and substrate consumption in all incubations. Experiments with resting cells, cell-free extracts and analysis of metabolite pools suggest that 4-CBA was metabolized in a reaction exclusively involving an initial hydrolytic dehalogenation yielding 4-hydroxybenzoic acid, which was then hydroxylated to protocatechuic acid (PCA) and subsequently metabolized via the β-ketoadipate pathway. When strain SK-3 was grown on 4-CBA, there was gratuitous induction of the catechol-1,2-dioxygenase and gentisate-1,2-dioxygenase pathways, even if both were not involved in the metabolism of the acid. While activities of the modified ortho- and meta-cleavage pathways were not detectable in all extracts, activity of PCA-3,4-dioxygenase was over ten-times higher than those of catechol-1,2- and gentisate-1,2-dioxygenases. Therefore, the only reason other congeners were not utilized for growth was the accumulation of CCs, suggesting a narrow spectrum of the activity of enzymes downstream of benzoate-1,2-dioxygenase, which exhibited affinity for a number of substituted analogs, and that the metabolic bottlenecks are either CCs or catabolites of the modified ortho-cleavage metabolic route.

  6. 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

  7. 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

  8. The amino acid sequence of the zinc-requiring beta-lactamase II from the bacterium Bacillus cereus 569.

    PubMed

    Ambler, R P; Daniel, M; Fleming, J; Hermoso, J M; Pang, C; Waley, S G

    1985-09-23

    The amino acid sequence of the zinc-requiring beta-lactamase II from Bacillus cereus strain 569 has been determined. It consists of a single polypeptide chain of 227 residues. It is the only example so far fully characterized of a class B beta-lactamase, and is structurally and mechanistically distinct from both the widely distributed class A beta-lactamases (such as the Escherichia coli RTEM enzyme) and from the chromosomally encoded class C enzymes from Gram-negative bacteria.

  9. 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)).

  10. 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)

  11. Identification of a 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase, FlRed, in an alginolytic bacterium Flavobacterium sp. strain UMI-01.

    PubMed

    Inoue, Akira; Nishiyama, Ryuji; Mochizuki, Shogo; Ojima, Takao

    2015-01-16

    In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11). The monosaccharide is non-enzymatically converted to 4-deoxy-L-ery thro-5-hexoseulose uronic acid (DEH), then reduced to 2-keto-3-deoxy-D-gluconate (KDG) by a specific reductase, and metabolized through the Entner-Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR) superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%-88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed) was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

  12. Characterization of lactose utilization and β-galactosidase in Lactobacillus brevis KB290, the hetero-fermentative lactic acid bacterium.

    PubMed

    Honda, Hiroyuki; Yajima, Nobuhiro; Saito, Tadao

    2012-12-01

    Unlike dairy lactic acid bacteria, Lactobacillus brevis cannot ferment milk. We characterized the lactose utilization by L. brevis KB290. In a carbohydrate fermentation assay using API 50 CHL, we showed during 7 days L. brevis did not ferment lactose. L. brevis grew to the stationary phase in 2 weeks in MRS broth containing lactose as the carbon source. L. brevis slowly consumed the lactose in the medium. L. brevis hydrolyzed lactose and a lactose analog, o-nitrophenyl-β-D-galactopyranoside (ONPGal). This β-galactosidase activity for ONPGal was not repressed by glucose, galactose, fructose, xylose, or maltose showing the microorganism may not have carbon catabolite repression. We purified the L. brevis β-galactosidase using ammonium sulfate precipitation and several chromatographies. The enzyme's molecular weight is estimated at 72 and 37 kDa using SDS-PAGE analysis. The N-terminal amino acid sequence of the larger protein was 90 % similar to the sequence of the putative β-galactosidase (YP_796339) and the smaller protein was identical to the sequence of the putative β-galactosidase (YP_796338) in L. brevis ATCC367. This suggests the enzyme is a heterodimeric β-galactosidase. The specific activity of the purified enzyme for lactose is 55 U/mg. We speculate inhibition of lactose transport delays the lactose utilization in L. brevis KB290.

  13. 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)).

  14. In Silico and Wet Lab Studies Reveal the Cholesterol Lowering Efficacy of Lauric Acid, a Medium Chain Fat of Coconut Oil.

    PubMed

    Lekshmi Sheela, Devi; Nazeem, Puthiyaveetil Abdulla; Narayanankutty, Arunaksharan; Manalil, Jeksy Jos; Raghavamenon, Achuthan C

    2016-12-01

    The coconut oil (CO) contains 91 % of saturated fatty acids in which 72 % are medium chain fatty acids (MCFAs) like lauric, capric and caprylic acids. In contrast to animal fat, coconut oil has no cholesterol. Despite this fact, CO is sidelined among other vegetable oils due to the health hazards attributed to the saturated fatty acids. Though various medicinal effects of CO have been reported including the hypolipidemic activity, people are still confused in the consumption of this natural oil. In silico analyses and wet lab experiments have been carried out to identify the hypolipidemic properties of MCFAs and phenolic acids in CO by using different protein targets involved in cholesterol synthesis. The molecular docking studies were carried out using CDOCKER protocol in Accelery's Discovery Studio, by taking different proteins like HMG- CoA reductase and cholesterol esterase as targets and the different phytocompounds in coconut as ligands. Molecular docking highlighted the potential of lauric acid in inhibiting the protein targets involved in hyperlipidemics. Further, validation of in silico results was carried out through in vivo studies. The activity of key enzymes HMG- CoA reductase and lipoprotein lipase were found reduced in animals fed with lauric acid and CO.

  15. Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.

    PubMed

    Hernandez, J M; Baker, S H; Lorbach, S C; Shively, J M; Tabita, F R

    1996-01-01

    The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme.

  16. 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.

  17. Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough.

    PubMed

    Toffin, Laurent; Zink, Klaus; Kato, Chiaki; Pignet, Patricia; Bidault, Adeline; Bienvenu, Nadège; Birrien, Jean-Louis; Prieur, Daniel

    2005-01-01

    A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at pH 7.0 was 4-50 degrees C, with the optimum at 37-40 degrees C. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2(T) (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).

  18. Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.

    PubMed Central

    Hernandez, J M; Baker, S H; Lorbach, S C; Shively, J M; Tabita, F R

    1996-01-01

    The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme. PMID:8550452

  19. 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)).

  20. Effects of phenazine-1-carboxylic acid on the biology of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae.

    PubMed

    Xu, Shu; Pan, Xiayan; Luo, Jianying; Wu, Jian; Zhou, Zehua; Liang, Xiaoyu; He, Yawen; Zhou, Mingguo

    2015-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) is the casual agent of bacterial blight, which is one of the most serious diseases of rice. The antibiotic phenazine-1-carboxylic acid (PCA), which is primarily produced by Pseudomonas spp., was found and previously reported very effective against Xoo. However, the biological effects of PCA on Xoo remain unclear. In this study, we found that PCA increased the accumulation of reactive oxygen species (ROS) and reduced the activities of catalase (CAT) and superoxide dismutase (SOD) in Xoo. Xoo was more sensitive to H2O2 than Xanthomonas oryzae pv. oryzicola (Xoc), and had a much lower expression of CAT genes. In addition, proteomic analysis indicated that PCA inhibited carbohydrate metabolism and nutrient uptake in Xoo, and analysis of carbon source utilization further confirmed that carbohydrate metabolism in Xoo was repressed by PCA. In conclusion, PCA acted as a redox-cycling agent that disturbed the redox balance in Xoo and reduced CAT and SOD activities, resulting in higher accumulation of ROS, altered carbohydrate metabolism, and lower energy production and nutrient uptake. Moreover, a deficient antioxidant system in Xoo made it very sensitive to PCA.

  1. Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6.

    PubMed

    Dong, Yiran; Sanford, Robert A; Chang, Yun-Juan; McInerney, Michael J; Fouke, Bruce W

    2017-01-03

    Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe2O3), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.

  2. Automation of Silica Bead-based Nucleic Acid Extraction on a Centrifugal Lab-on-a-Disc Platform

    NASA Astrophysics Data System (ADS)

    Kinahan, David J.; Mangwanya, Faith; Garvey, Robert; Chung, Danielle WY; Lipinski, Artur; Julius, Lourdes AN; King, Damien; Mohammadi, Mehdi; Mishra, Rohit; Al-Ofi, May; Miyazaki, Celina; Ducrée, Jens

    2016-10-01

    We describe a centrifugal microfluidic ‘Lab-on-a-Disc’ (LoaD) technology for DNA purification towards eventual integration into a Sample-to-Answer platform for detection of the pathogen Escherichia coli O157:H7 from food samples. For this application, we use a novel microfluidic architecture which combines ‘event-triggered’ dissolvable film (DF) valves with a reaction chamber gated by a centrifugo-pneumatic siphon valve (CPSV). This architecture permits comprehensive flow control by simple changes in the speed of the platform innate spindle motor. Even before method optimisation, characterisation by DNA fluorescence reveals an extraction efficiency of 58%, which is close to commercial spin columns.

  3. Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring.

    PubMed

    Yoneda, Yasuko; Yoshida, Takashi; Kawaichi, Satoshi; Daifuku, Takashi; Takabe, Keiji; Sako, Yoshihiko

    2012-07-01

    A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1(T), was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0-3.0 µm long) and motile due to peritrichous flagella. Strain Ug1(T) grew chemolithoautotrophically on CO (100% in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H(2) and CO(2) were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N(2) atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50-70 °C, with an optimum at 65 °C. The pH(25 °C) range for growth was 4.6-8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus, with sequence similarities of 94.1-96.6% to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1(T) (=DSM 23698(T)=NBRC 107576(T)).

  4. 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.

  5. 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.

  6. Antifungal and sprout regulatory bioactivities of phenylacetic acid, indole-3-acetic acid, and tyrosol isolated from the potato dry rot suppressive bacterium Enterobacter cloacae S11:T:07.

    PubMed

    Slininger, P J; Burkhead, K D; Schisler, D A

    2004-12-01

    Enterobacter cloacae S11: T:07 (NRRL B-21050) is a promising biological control agent that has significantly reduced both fungal dry rot disease and sprouting in laboratory and pilot potato storages. The metabolites phenylacetic acid (PAA), indole-3-acetic acid (IAA), and tyrosol (TSL) were isolated from S11:T:07 liquid cultures provided with three different growth media. The bioactivities of these metabolites were investigated via thin-layer chromatography bioautography of antifungal activity, wounded potato assays of dry rot suppressiveness, and cored potato eye assays of sprout inhibition. Relative accumulations of PAA, IAA, and TSL in cultures were nutrient dependent. For the first time, IAA, TSL, and PAA were shown to have antifungal activity against the dry rot causative pathogen Gibberella pulicaris, and to suppress dry rot infection of wounded potatoes. Disease suppression was optimal when all three metabolites were applied in combination. Dosages of IAA that resulted in disease suppression also resulted in sprout inhibition. These results suggest the potential for designing culture production and formulation conditions to achieve a dual purpose biological control agent able to suppress both dry rot and sprouting of stored potatoes.

  7. Evaluation of lactic acid bacterium fermentation products and food-grade chemicals to control Listeria monocytogenes in blue crab (Callinectes sapidus) meat.

    PubMed Central

    Degnan, A J; Kaspar, C W; Otwell, W S; Tamplin, M L; Luchansky, J B

    1994-01-01

    Fresh blue crab (Callinectes sapidus) meat was obtained from retail markets in Florida and sampled for viable Listeria monocytogenes. The pathogen was found in crabmeat in three of four different lots tested by enrichment and at levels of 75 CFU/g in one of the same four lots by direct plating. Next, crabmeat was steam sterilized, inoculated with a three-strain mixture of L. monocytogenes (ca. 5.5 log10 CFU/g), washed with various lactic acid bacterium fermentation products (2,000 to 20,000 arbitrary units [AU]/ml of wash) or food-grade chemicals (0.25 to 4 M), and stored at 4 degrees C. Counts of the pathogen remained relatively constant in control samples during storage for 6 days, whereas in crabmeat washed with Perlac 1911 or MicroGard (10,000 to 20,000 AU), numbers initially decreased (0.5 to 1.0 log10 unit/g) but recovered to original levels within 6 days. Numbers of L. monocytogenes cells decreased 1.5 to 2.7 log10 units/g of crabmeat within 0.04 day when washed with 10,000 to 20,000 AU of Alta 2341, enterocin 1083, or Nisin per ml. Thereafter, counts increased 0.5 to 1.6 log10 units within 6 days. After washing with food-grade chemicals, modest reductions (0.4 to 0.8 log10 unit/g) were observed with sodium acetate (4 M), sodium diacetate (0.5 or 1 M), sodium lactate (1 M), or sodium nitrite (1.5 M). However, Listeria counts in crabmeat washed with 2 M sodium diacetate decreased 2.6 log10 units/g within 6 days. In addition, trisodium phosphate reduced L. monocytogenes counts from 1.7 (0.25 M) to > 4.6 (1 M) log10 units/g within 6 days.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7944362

  8. 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.

  9. 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.

  10. 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)

  11. 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

  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. Recovery of fermented inulin fiber by lactic acid bacteria (LAB) from inulin hydrolysate using fungi inulinase enzymes of Scopulariopsis sp.-CBS1 and class of Deuteromycetes-CBS4 as cholesterol binder

    NASA Astrophysics Data System (ADS)

    Susilowati, Agustine; Melanie, Hakiki; Maryati, Yati; Aspiyanto

    2017-01-01

    Fermentation of Lactobacillus Acid Bacteria (LAB) which are mixtures of Lactobacillus acidophilus, Bifidobacteriumbifidum, Lactobacillus bulgaricus and Streptococcus thermophillus on hydrolysate as a result of inulin hydrolysis using inulinase enzymes obtained from endophytic fungi ofScopulariopsis sp.-CBS1 (inulin hydrolysate of S) and Class of Deuteromycetes-CBS4 (inulin hydrolysate of D) generate potential fermented inulin fiber as cholesterol binder. Fermentation process was conducted under concentrations of inulin hydrolysate 50% (w/v), LAB 15% (v/v) and skim milk 12.5% (w/v) at room temperature and 40°C for 0, 12, 24, 36 and 48 hours, respectively. Result of experimental work showed that longer time of LAB fermentation increased total acids, TPC and CBC at pH 2, but decreased total sugar, reducing, IDF, SDF, CBC pH 2 and CBC pH 7. Based on Cholesterol Binding Capacity (CBC), optimization of fermentation process on inulin hydrolysate of S was achieved by combining treatment at 40°C for 24 hours resulted in CBC pH 2 of 19.11 mg/g TDF and inulin hydrolysate of D was achieved by fermentation at 40 °C for 48 hours resulted in CBC pH 2 of 24.28 mg/g TDF. Inulin hydrolysate of class of Deutrymecetes CBS4 fermented by LAB had better functional property as cholesterol binder than that inulin hydrolysate of S fermented by LAB. This is due to cholesterol binder and cholesterol derivatives as a result of degradation of LAB on digestive system (stomach) when compared to higher colon under optimal process condition.

  14. 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.

  15. 3-mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus.

    PubMed

    Bruland, Nadine; Wübbeler, Jan Hendrik; Steinbüchel, Alexander

    2009-01-02

    The thioether 3,3-thiodipropionic acid can be used as precursor substrate for biotechnological synthesis of 3-mercaptopropionic acid-containing polythioesters. Therefore, the hitherto unknown catabolism of this compound was elucidated to engineer novel and improved polythioester biosynthesis pathways in the future. Bacteria capable of using 3,3-thiodipropionic acid as the sole source of carbon and energy for growth were enriched from the environment. From eleven isolates, TBEA3, TBEA6, and SFWT were morphologically and physiologically characterized. Their 16 S rDNAs and other features affiliated these isolates to the beta-subgroup of the proteobacteria. Tn5::mob mutagenesis of isolate Variovorax paradoxus TBEA6 yielded ten mutants fully or partially impaired in growth on 3,3-thiodipropionic acid. Genotypic characterization of two 3,3-thiodipropionic acid-negative mutants demonstrated the involvement of a bacterial cysteine dioxygenase (EC 1.13.11.22) homologue in the further catabolism of the 3,3-thiodipropionic acid cleavage product 3-mercaptopropionic acid. Detection of 3-sulfinopropionate in the supernatant of one of these mutants during cultivation on 3,3-thiodipropionic acid as well as in vivo and in vitro enzyme assays using purified protein demonstrated oxygenation of 3-mercaptopropionic acid to 3-sulfinopropionate by this enzyme; cysteine and cysteamine were not used as substrate. Beside cysteine dioxygenase and cysteamine dioxygenase, this 3-mercaptopropionic acid dioxygenase is the third example for a thiol dioxygenase and the first report about the microbial catabolism of 3-mercaptopropionic acid. Insertion of Tn5::mob in a gene putatively coding for a family III acyl-CoA-transferase resulted in the accumulation of 3-sulfinopropionate during cultivation on 3,3-thiodipropionic acid, indicating that this compound is further metabolized to 3-sulfinopropionyl-CoA and subsequently to propionyl-CoA.

  16. Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius

    PubMed Central

    Li, Leilei; Illeghems, Koen; Van Kerrebroeck, Simon; Borremans, Wim; Cleenwerck, Ilse; Smagghe, Guy; De Vuyst, Luc

    2016-01-01

    The whole-genome sequence of Bombella intestini LMG 28161T, an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161T was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161T genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host. PMID:27851750

  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. Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase.

    PubMed

    Story, Sandra; Brigmon, Robin L

    2017-03-01

    Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soil resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. These results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.

  19. 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)

  20. Deciphering Your Lab Report

    MedlinePlus

    ... be limited. Home Visit Global Sites Search Help? Advertisement Proceeds from website advertising help sustain Lab Tests ... for trustworthy health information. Verify Compliance . Produced by Advertisement

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Falcatimonas natans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor of cattle waste.

    PubMed

    Watanabe, Misa; Kaku, Nobuo; Ueki, Katsuji; Ueki, Atsuko

    2016-11-01

    A strictly anaerobic bacterial strain (WN011T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells of the strain were Gram-stain-negative curved rods with a polar flagellum. Spores were not produced. The optimum temperature for growth was 35-37 °C and the optimum pH was 6.7. The strain did not utilize carbohydrates as growth substrates. The strain grew in PY medium and produced acetate, butyrate, isovalerate and H2 as well as propionate and isobutyrate as minor products. Amino acids (l-isoleucine, l-leucine, l-lysine, l-serine, l-threonine and l-valine) added to PY medium enhanced growth of the strain and increased the amounts of fermentation products. Oxidase, catalase and nitrate-reducing activities were negative. Hydrogen sulfide was produced. The genomic DNA G+C content was 38.8 mol%. Compounds related to iso-C15 : 0 (fatty acid, dimethylacetal and aldehyde) were detected as predominant components by the cellular fatty acids analysis. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequences, three clones from wastewater were very closely related to strain WN011T (up to 99.9 % sequence similarity). The most closely related described species were those in cluster XIVa of the class Clostridia such as Ruminococcus gauvreauii (93.8 % 16S rRNA gene sequence similarity), Clostridium fimetarium (93.5 %) and Clostridium bolteae(93.5 %). Based on the distinct differences in phylogenetic and phenotypic characteristics of strain WN011T from those of related species, it is concluded that strain WN011T represents a novel species of a new genus in the family Lachnospiraceae, for which the name Falcatimonas natans gen. nov., sp. nov. is proposed. The type strain of the type species is WN011T (=JCM 16476T=DSM 22923T).

  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. 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…

  8. 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.

  9. 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…

  10. 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…

  11. 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…

  12. Lab Report Blues

    ERIC Educational Resources Information Center

    Diaz, Andrew

    2004-01-01

    For middle school students, writing a formal lab report can be challenging. For middle level teachers, reading students lab reports can be overwhelming. After grading report after report with incomplete procedures, incorrect graphs, and missing conclusions, the author's frustration level was at an all-time high. Ready to try anything, he thought,…

  13. 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.

  14. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant.

    PubMed

    Kim, Byung-Chun; Seung Jeon, Byoung; Kim, Seil; Kim, Hyunook; Um, Youngsoon; Sang, Byoung-In

    2015-12-01

    A strictly anaerobic, Gram-stain-positive, non-spore-forming, rod-shaped bacterial strain, designated BS-1T, was isolated from an anaerobic digestion reactor during a study of bacteria utilizing galactitol as the carbon source. Its cells were 0.3-0.5 μm × 2-4 μm, and they grew at 35-45 °C and at pH 6.0-8.0. Strain BS-1T produced H2, CO2, ethanol, acetic acid, butyric acid and caproic acid as metabolic end products of anaerobic fermentation. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain BS-1T represented a novel bacterial genus within the family Ruminococcaceae, Clostridium Cluster IV. The type strains that were most closely related to strain BS-1T were Clostridium sporosphaeroides KCTC 5598T (94.5 %), Clostridium leptum KCTC 5155T (94.3 %), Ruminococcus bromii ATCC 27255T (92.1 %) and Ethanoligenens harbinense YUAN-3T (91.9 %). Strain BS-1T had 17.6 % and 20.9 % DNA-DNA relatedness values with C. sporosphaeroides DSM 1294T and C. leptum DSM 753T, respectively. The major components of the cellular fatty acids were C16 : 0 dimethyl aldehyde (DMA) (22.1 %), C16 : 0 aldehyde (14.1 %) and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA; 10.0 %). The genomic DNA G+C content was 50.0 mol%. Phenotypic and phylogenetic characteristics allowed strain BS-1T to be clearly distinguished from other taxa of the genus Clostridium Cluster IV. On the basis of these data, the isolate is considered to represent a novel genus and novel species within Clostridium Cluster IV, for which the name Caproiciproducens galactitolivorans gen. nov., sp. nov. is proposed. The type species is BS-1T ( = JCM 30532T and KCCM 43048T).

  15. Total mesophilic counts underestimate in many cases the contamination levels of psychrotrophic lactic acid bacteria (LAB) in chilled-stored food products at the end of their shelf-life.

    PubMed

    Pothakos, Vasileios; Samapundo, Simbarashe; Devlieghere, Frank

    2012-12-01

    The major objective of this study was to determine the role of psychrotrophic lactic acid bacteria (LAB) in spoilage-associated phenomena at the end of the shelf-life of 86 various packaged (air, vacuum, modified-atmosphere) chilled-stored retail food products. The current microbiological standards, which are largely based on the total viable mesophilic counts lack discriminatory capacity to detect psychrotrophic LAB. A comparison between the total viable counts on plates incubated at 30 °C (representing the mesophiles) and at 22 °C (indicating the psychrotrophs) for 86 food samples covering a wide range - ready-to-eat vegetable salads, fresh raw meat, cooked meat products and composite food - showed that a consistent underestimation of the microbial load occurs when the total aerobic mesophilic counts are used as a shelf-life parameter. In 38% of the samples, the psychrotrophic counts had significantly higher values (+0.5-3 log CFU/g) than the corresponding total aerobic mesophilic counts. A total of 154 lactic acid bacteria, which were unable to proliferate at 30 °C were isolated. In addition, a further 43 with a poor recovery at this temperature were also isolated. This study highlights the potential fallacy of the total aerobic mesophilic count as a reference shelf-life parameter for chilled food products as it can often underestimate the contamination levels at the end of the shelf-life.

  16. 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.

  17. 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

  18. Characterization of the multiple molecular mechanisms underlying RsaL control of phenazine-1-carboxylic acid biosynthesis in the rhizosphere bacterium Pseudomonas aeruginosa PA1201.

    PubMed

    Sun, Shuang; Chen, Bo; Jin, Zi-Jing; Zhou, Lian; Fang, Yun-Ling; Thawai, Chitti; Rampioni, Giordano; He, Ya-Wen

    2017-03-18

    Phenazines are important secondary metabolites that have been found to affect a broad spectrum of organisms. Two almost identical gene clusters phz1 and phz2 are responsible for phenazines biosynthesis in the rhizobacterium Pseudomonas aeruginosa PA1201. Here, we show that the transcriptional regulator RsaL is a potent repressor of phenazine-1-carboxylic acid (PCA) biosynthesis. RsaL negatively regulates phz1 expression and positively regulates phz2 expression via multiple mechanisms. First, RsaL binds to a 25-bp DNA region within the phz1 promoter to directly repress phz1 expression. Second, RsaL indirectly regulates the expression of both phz clusters by decreasing the activity of the las and pqs quorum sensing (QS) systems, and by promoting the rhl QS system. Finally, RsaL represses phz1 expression through the downstream transcriptional regulator CdpR. RsaL directly binds to the promoter region of cdpR to positively regulate its expression, and subsequently CdpR regulates phz1 expression in a negative manner. We also show that RsaL represents a new mechanism for the turnover of the QS signal molecule N-3-oxododecanoyl-homoserine lactone (3-oxo-C12-HSL). Overall, this study elucidates RsaL control of phenazines biosynthesis and indicates that a PA1201 strain harboring deletions in both the rsaL and cdpR genes could be used to improve the industrial production of PCA.

  19. Growth of Leuconostoc mesenteroides NRRL-B523 in an alkaline medium: suboptimal pH growth inhibition of a lactic acid bacterium.

    PubMed

    Wolf, Barry F; Fogler, H Scott

    2005-01-05

    Bacterial profile modification (BPM), a form of tertiary oil recovery, diverts water from the water-flooded high-permeability zone into the oil-bearing low-permeability zone. During field use, exopolymer-producing bacteria plug the high-permeability zone only in the immediate vicinity of the injection point (the near-well bore region). For effective BPM the plug must penetrate far into the formation. Slowing the specific growth rate, lengthening the lag phase, and slowing the polymerization rate are techniques that can prolong the onset of biopolymer gelation and extend the depth of the biological plug. In batch experiments, the growth of Leuconostoc mesenteroides NRRL-B523 was inhibited by the synergistic effects of high substrate loading and an alkaline pH. Exponential growth was delayed up to 190 h. It was observed that cell division was significantly retarded until the medium pH, reduced by the acid byproducts of fermentation, reached a critical value of 6.79 +/- 0.06. A mathematical model was developed to describe the relationship between specific growth rate, lag time, and medium pH.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Canadian ADL Partnership Lab

    DTIC Science & Technology

    2009-08-19

    WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Canadian Defense Academy,PO Box 17000 Station Forces ,Kingston ON CANADA K7K 7B4...CMP Canadian ADL Partnership Lab Presentation by CDA Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the... Canadian ADL Partnership Lab 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f

  6. SmallSat Lab

    DTIC Science & Technology

    2014-03-05

    CubeSat. Mr. Alvarez worked with four students on the PCB layout for the solar panels and the construction of the 6U CubeSat mockup . Support for Mr...Hull and Mr. Alvarez was $49k including fringe benefits. !! Purchases: During this time period a license for MatLab software and the Princeton...Satellite ToolBox was purchased using funds from this award. This software adds tremendous capability to the SmallSat Lab by enabling students to analyze

  7. 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.

  8. 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…

  9. Computer Labs: New Perceptions.

    ERIC Educational Resources Information Center

    Prochaska, Nancy

    1989-01-01

    Describes the use of computer labs in a Texas high school. Highlights include word processing; a study skills course; software programs currently in use by English and English-as-a-Second-Language classes; physical layout, including security considerations and furniture; hardware, including printers; and guidelines for the selection of software.…

  10. Modifying Cookbook Labs.

    ERIC Educational Resources Information Center

    Clark, Robert, L.; Clough, Michael P.; Berg, Craig A.

    2000-01-01

    Modifies an extended lab activity from a cookbook approach for determining the percent mass of water in copper sulfate pentahydrate crystals to one which incorporates students' prior knowledge, engenders active mental struggling with prior knowledge and new experiences, and encourages metacognition. (Contains 12 references.) (ASK)

  11. Materials Lab Equipment

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The photo shows one of the waveguide setups in the Electromaganetic Properties Measurements Lab (EPML). This setup is for measuring permittivity and permeability of the materials at the L-band frequencies (1.12-1.7 ghz). The EMPL is in the Elecromagnetics Research Branch at NASA Langley.

  12. 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…

  13. The Haunted Physics Lab

    NASA Astrophysics Data System (ADS)

    Zepf, Thomas H.

    2004-10-01

    During the Halloween season at Creighton University, our students and the public are treated to a haunted physics laboratory. Visitors to the lab learn physics while having fun as they are confronted with a maze of exhibits that demonstrate optical, electrical, and mechanical phenomena in the context of Halloween.

  14. 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.

  15. 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)

  16. 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.…

  17. 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)

  18. ERLN Lab Compendium Fact Sheet

    EPA Pesticide Factsheets

    The Compendium is an online database of environmental testing laboratories nationwide. It enables labs to create profiles of their capabilities, so emergency responders can quickly identify a lab that will meet their support needs.

  19. 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

    2016-05-03

    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.

  20. 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

  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. 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.

  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. ERLN Technical Support for Labs

    EPA Pesticide Factsheets

    The Environmental Response Laboratory Network provides policies and guidance on lab and data requirements, Standardized Analytical Methods, and technical support for water and radiological sampling and analysis

  6. 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...

  7. Alternatives to Traditional Labs: a Discovery Lab Based on Analogy

    NASA Astrophysics Data System (ADS)

    Liff, Mark I.

    2006-12-01

    In search for alternatives to traditional labs, it is worthwhile to turn to the creativity research. Analogy is believed by many to be at the heart of creativity. A discovery lab that requires use of analogy had been developed. A basis of the lab is a re-discovery of Gough-Joule effect of contraction of stretched rubber upon heating. The difficulties of designing an analogybased lab are discussed. The students' reaction to the unusual lab is analyzed. The data suggest that the students need to be provided with the base for analogy use. They also need to be given directions for the search of solution by changing and modification of analogies, and weeding out the misleading ones and selectively retaining productive analogies. This study shows that thought processes of divergent nature--commonly accessible only to experts--can be employed under the discussed conditions by novices as well.

  8. 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.

  9. 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…

  10. Plasma Levels of Uric Acid, Urea and Creatinine in Diabetics Who Visit the Clinical Analysis Laboratory (CAn-Lab) at Kwame Nkrumah University of Science and Technology, Kumasi, Ghana

    PubMed Central

    Amartey, N.A.A.; Mensah, F.O.

    2015-01-01

    Introduction: Diabetes mellitus is one of the most common metabolic diseases worldwide. This metabolic disorder contributes greatly to the significant proportion of the burden of renal damage and dysfunction. The aim of the study was to investigate the renal function of the diabetic patients who visit the Clinical Analysis Laboratory (CAn-Lab) at the Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana. Materials and Methods: Demographic data as well as medical history were obtained through the administration of a questionnaire. Anthro-pometric measurements were taken and blood samples were analysed for glucose, uric acid, urea and creatinine. Data collected were analysed using SPSS version 16.0. Results: A total of 34 diabetic patients, aged from 40-77 y were recruited, 22 (64.7%) of them were males with mean age of 57.40 ± 11.8 y (±SD), while 12 (35.3%) were females with mean age of 58.17 ± 7.47 y. There was a statistically significant difference between the mean duration of the disease, as the females had longer duration, 12.50 ± 6.95 y, as compared to 7.32 ± 4.48 y in males (p=0.033). The mean plasma creatinine level in the females was 84.17 ± 54.73 μmol/l. In the diabetic population, there was a positive correlation between age and plasma creatinine level, (r=0.375, p=0.029). In the female diabetics, there was a positive correlation between fasting blood sugar (FBS) and the measured metabolic end products (r>0.5, p<0.05), a positive correlation between body mass index (BMI) and uric acid (r=0.576, p=0.005) and a positive correlation between BMI and FBS (r= 0.625, p= 0.030). Conclusion: Our results on the parameters measured; show that the diabetic population was experiencing mild kidney dysfunction, compared to non-diabetic controls. PMID:25859443

  11. A "MICROTUBULE" IN A BACTERIUM

    PubMed Central

    van Iterson, Woutera; Hoeniger, Judith F. M.; van Zanten, Eva Nijman

    1967-01-01

    A study of the anchorage of the flagella in swarmers of Proteus mirabilis led to the incidental observation of microtubules. These microtubules were found in thin sections and in whole mount preparations of cells from which most of the content had been released by osmotic shock before staining negatively with potassium phosphotungstate (PTA). The microtubules are in negatively stained preparations about 200 A wide, i.e. somewhat thicker than the flagella (approximately 130 A). They are thus somewhat thinner than most microtubules recorded for other cells. They are referred to as microtubules because of their smooth cylindrical wall, or cortex, surrounding a hollow core which is readily filled with PTA when stained negatively. Since this is probably the first time that such a structure is described inside a bacterium, we do not know for certain whether it represents a normal cell constituent or an abnormality, for instance of the type of "polysheaths" (16). PMID:10976198

  12. Thinking Outside the Lab

    NASA Astrophysics Data System (ADS)

    Colter, Tabitha

    2017-01-01

    As an undergraduate physics major who spent 2015 deep in a quantum optics lab at Oak Ridge National Laboratory, I knew my 2016 experience with the House of Representatives Energy and Commerce Committee would be a completely new challenge. I have long had a passion for the bridge of communication between the technical and non-technical worlds but it was only through my AIP Mather internship this summer that I was able to see that passion come to life in the realm of science policy. Suddenly, I went from squeezing political philosophy classes into my packed schedule to witnessing the political process first-hand. I was thrilled to find that the skills of critical thinking and communicating complex issues I have developed throughout my training as a physicist were directly applicable to my work in Congress. Overall, my experience this summer has given me insight into the inner workings of the federal policy process, deepened my appreciation for the work of government employees to keep Congressional members informed on the pressing current issues, and exposed me to a whole range of alternative careers within science. AIP and SPS

  13. Methamphetamine Lab Incidents, 2004-2014

    MedlinePlus

    ... Liderazgo de la DEA Resource Center » Statistics & Facts » Methamphetamine Lab Incidents Methamphetamine Lab Incidents, 2004-2014 NOTE: These maps include all meth incidents, including labs, "dumpsites" or "chemical and glassware" ...

  14. The lipopolysaccharide of a chloridazon-degrading bacterium.

    PubMed

    Weisshaar, R; Lingens, F

    1983-12-01

    Lipopolysaccharide of a chloridazon-degrading bacterium was obtained by a two-stage extraction procedure with phenol/EDTA in a yield of 0.3% of dried bacteria. The carbohydrate moiety consisted of heptose, 3-deoxyoctulosonic acid and D-glucose in a molar ratio of 1:2:2 X 3. Lipid A was composed of 1 mol 2,3-diamino-2,3-dideoxy-D-glucose, 2 mol amide-bound and 2.6 mol ester-bound fatty acids/mol. Amide-bound fatty acids were 3-hydroxydodecanoic acid and 3-hydroxyhexadecanoic acid; dodecanoic acid and R-(-)-3-hydroxydodec-5-cis-enoic acid were found to be present in ester linkage. Under conditions of acidic hydrolysis, the latter was converted into the cis and trans isomers of 5-hexyltetrahydrofuran-2-acetic acid. Dodecanoic acid was demonstrated to be linked with the hydroxy groups of the amide-bound fatty acids. The taxonomic significance of these results, especially the demonstration of 2,3-diamino-2, 3-dideoxy-D-glucose, is discussed.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. The PRIME Lab biomedical program

    NASA Astrophysics Data System (ADS)

    Jackson, George S.; Elmore, David; Rickey, Frank A.; Musameh, Sharif M.; Sharma, Pankaj; Hillegonds, Darren; Coury, Louis; Kissinger, Peter

    2000-10-01

    The biomedical accelerator mass spectrometry (AMS) initiative at PRIME Lab including the status of equipment and sample preparation is described. Several biomedical projects are underway involving one or more of the nuclides: 14C, 26Al and 41Ca. Routine production of CaF 2 and graphite is taking place. Finally, the future direction and plans for improvement of the biomedical program at PRIME Lab are discussed.

  20. 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

  1. 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.

  2. Jigsaw Cooperative Learning Improves Biology Lab Courses.

    ERIC Educational Resources Information Center

    Colosi, Joseph C.; Zales, Charlotte Rappe

    1998-01-01

    Describes how a jigsaw cooperative learning structure divides lab work in a constructive, efficient way and provides a mechanism for sharing information. Pre-lab lectures are replaced with focused student discussions about the lab exercises. Students become more involved with the lab exercises, take responsibility for their own learning, and are…

  3. 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

  4. 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...

  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. 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.

  7. 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.

  8. Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.

    PubMed

    Kant, Ravi; Rasinkangas, Pia; Satokari, Reetta; Pietilä, Taija E; Palva, Airi

    2015-04-02

    Anaerostipes hadrus PEL 85, which was isolated from human feces, is a Gram-positive rod-shaped bacterium. The species may play an important role in gut health, as it was previously reported to produce butyric acid. Here, we present the genome assembly of PEL 85, a novel strain of A. hadrus.

  9. Academic Pipeline and Futures Lab

    DTIC Science & Technology

    2016-02-01

    level for summer time programs. The Academic Pipeline will also work with other programs at AFRL and with other universities and organizations to...AFRL-RY-WP-TR-2015-0186 ACADEMIC PIPELINE AND FUTURES LAB Brian D. Rigling Wright State University FEBRUARY 2016...PUBLICATION IN ACCORDANCE WITH ASSIGNED DISTRIBUTION STATEMENT. // Signature// // Signature// KELLY MILLER, Program Manager CHRISTINA

  10. 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 ...

  11. 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)

  12. 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…

  13. 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…

  14. Safety Equipment in the Lab.

    ERIC Educational Resources Information Center

    Denham, Willard A.S.

    1964-01-01

    Findings of two recent surveys on safety equipment in laboratory facilities are presented. The first survey was a pilot study of emergency shower and eye wash equipment. This study was followed by a more comprehensive random survey of safety equipment in 2,820 labs. Among other findings, the surveys indicate that many plants are underequipped, or…

  15. 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.

  16. Research Perspectives at Jefferson Lab

    SciTech Connect

    Kees de Jager

    2005-06-05

    The plans for upgrading the CEBAF accelerator at Jefferson Lab to 12 GeV are presented. The research program supporting that upgrade is illustrated with a few selected examples. The instrumentation under design to carry out that research program is discussed.

  17. 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.

  18. 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.

  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. The domestication of the probiotic bacterium Lactobacillus acidophilus.

    PubMed

    Bull, Matthew J; Jolley, Keith A; Bray, James E; Aerts, Maarten; Vandamme, Peter; Maiden, Martin C J; Marchesi, Julian R; Mahenthiralingam, Eshwar

    2014-11-26

    Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

  1. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26205853

  3. Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

    PubMed

    Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

    2010-09-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

  4. 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)

  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. Reactivity of the Monoterpenoid Nerol with p-Toluenesulfonic and Chlorosulfonic Acids: Selective Syntheses of alpha-Terpineol and alpha-Cyclogeraniol. An Activity for the Undergraduate Organic Lab

    ERIC Educational Resources Information Center

    Linares-Palomino, Pablo J.; Salido, Sofia; Altarejos, Joaquin; Nogueras, Manuel; Sanchez, Adolfo

    2006-01-01

    The selective syntheses of the cyclic monoterpenoids alpha-terpineol or alpha-cyclogeraniol from the acyclic monoterpenoid nerol using p-toluenesulfonic acid or chlorosulfonic acid as cyclizing agents, respectively, are described. The different behavior of nerol under diverse experimental conditions such as nature of the acid agents, solvents, and…

  7. 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

  8. 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.

  9. 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

  10. 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

  11. Effects of rheological change by addition of carboxymethylcellulose in culture media of an air-lift fermentor on poly-D-3-hydroxybutyric acid productivity in autotrophic culture of hydrogen-oxidizing bacterium, Alcaligenes eutrophus.

    PubMed

    Taga, N; Tanaka, K; Ishizaki, A

    1997-03-05

    The effects of rheological change by addition of sodium carboxymethylcellulose (CMC) to culture medium in an air-lift-type fermentor on autotrophic production of poly-(D-3-hydroxybutyric acid) [P(3HB)] by two-stage culture of Alcaligenes eutrophus is investigated. Addition of 0.05% CMC increased P(3HB) production rate during the P(3HB) accumulation phase to twice that of the control culture. It was thought that addition of a small amount of CMC was beneficial for production of P(3HB) employing the air-lift fermentor under safe autotrophic culture conditions in wich oxygen concentration was maintained below 6.9% (v/v). the volumetric mass transfer coefficient (K(L)a) observed in the presence of CMC is shown to correlated with the P(3HB) production rate obtained. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 529-533, 1997.

  12. 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

  13. Antagonistic Activity and Mode of Action of Phenazine-1-Carboxylic Acid, Produced by Marine Bacterium Pseudomonas aeruginosa PA31x, Against Vibrio anguillarum In vitro and in a Zebrafish In vivo Model.

    PubMed

    Zhang, Linlin; Tian, Xueying; Kuang, Shan; Liu, Ge; Zhang, Chengsheng; Sun, Chaomin

    2017-01-01

    Phenazine and its derivatives are very important secondary metabolites produced from Pseudomonas spp. and have exhibited broad-spectrum antifungal and antibacterial activities. However, till date, there are few reports about marine derived Pseudomonas and its production of phenazine metabolites. In this study, we isolated a marine Pseudomonas aeruginosa strain PA31x which produced natural product inhibiting the growth of Vibrio anguillarum C312, one of the most serious bacterial pathogens in marine aquaculture. Combining high-resolution electro-spray-ionization mass spectroscopy and nuclear magnetic resonance spectroscopy analyses, the functional compound against V. anguillarum was demonstrated to be phenazine-1-carboxylic acid (PCA), an important phenazine derivative. Molecular studies indicated that the production of PCA by P. aeruginosa PA31x was determined by gene clusters phz1 and phz2 in its genome. Electron microscopic results showed that treatment of V. anguillarum with PCA developed complete lysis of bacterial cells with fragmented cytoplasm being released to the surrounding environment. Additional evidence indicated that reactive oxygen species generation preceded PCA-induced microbe and cancer cell death. Notably, treatment with PCA gave highly significant protective activities against the development of V. anguillarum C312 on zebrafish. Additionally, the marine derived PCA was further found to effectively inhibit the growth of agricultural pathogens, Acidovorax citrulli NP1 and Phytophthora nicotianae JM1. Taken together, this study reveals that marine Pseudomonas derived PCA carries antagonistic activities against both aquacultural and agricultural pathogens, which broadens the application fields of PCA.

  14. Antagonistic Activity and Mode of Action of Phenazine-1-Carboxylic Acid, Produced by Marine Bacterium Pseudomonas aeruginosa PA31x, Against Vibrio anguillarum In vitro and in a Zebrafish In vivo Model

    PubMed Central

    Zhang, Linlin; Tian, Xueying; Kuang, Shan; Liu, Ge; Zhang, Chengsheng; Sun, Chaomin

    2017-01-01

    Phenazine and its derivatives are very important secondary metabolites produced from Pseudomonas spp. and have exhibited broad-spectrum antifungal and antibacterial activities. However, till date, there are few reports about marine derived Pseudomonas and its production of phenazine metabolites. In this study, we isolated a marine Pseudomonas aeruginosa strain PA31x which produced natural product inhibiting the growth of Vibrio anguillarum C312, one of the most serious bacterial pathogens in marine aquaculture. Combining high-resolution electro-spray-ionization mass spectroscopy and nuclear magnetic resonance spectroscopy analyses, the functional compound against V. anguillarum was demonstrated to be phenazine-1-carboxylic acid (PCA), an important phenazine derivative. Molecular studies indicated that the production of PCA by P. aeruginosa PA31x was determined by gene clusters phz1 and phz2 in its genome. Electron microscopic results showed that treatment of V. anguillarum with PCA developed complete lysis of bacterial cells with fragmented cytoplasm being released to the surrounding environment. Additional evidence indicated that reactive oxygen species generation preceded PCA-induced microbe and cancer cell death. Notably, treatment with PCA gave highly significant protective activities against the development of V. anguillarum C312 on zebrafish. Additionally, the marine derived PCA was further found to effectively inhibit the growth of agricultural pathogens, Acidovorax citrulli NP1 and Phytophthora nicotianae JM1. Taken together, this study reveals that marine Pseudomonas derived PCA carries antagonistic activities against both aquacultural and agricultural pathogens, which broadens the application fields of PCA. PMID:28289406

  15. Ethanol production from wet-exploded wheat straw hydrolysate by thermophilic anaerobic bacterium Thermoanaerobacter BG1L1 in a continuous immobilized reactor.

    PubMed

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

    2008-03-01

    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 degrees 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/l. The organism, thermophilic anaerobic bacterium Thermoanaerobacter BG1L1, exhibited significant resistance to high levels of acetic acid (up to 10 g/l) 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.

  16. 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.

  17. Paradigms: examples from the bacterium Xylella fastidiosa.

    PubMed

    Purcell, Alexander

    2013-01-01

    The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species.

  18. Pneumonia caused by a previously undescribed bacterium.

    PubMed Central

    Hopfer, R L; Mills, K; Fainstein, V; Fischer, H E; Luna, M P

    1982-01-01

    A new and as yet unidentified bacterium was isolated from the lung tissue of a cancer patient with bilateral pneumonia. Clinically, the pneumonia was consistent with legionellosis; the organism cultured from the lung grew only on the charcoal-yeast extract agar routinely used for Legionella isolation. Subsequent testing, however, showed the organism to be quite distinct from the known Legionella species in its biochemical, antigenic, and growth characteristics. Images PMID:7130363

  19. 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.

  20. Coprisamides A and B, new branched cyclic peptides from a gut bacterium of the dung beetle Copris tripartitus.

    PubMed

    Um, Soohyun; Park, So Hyun; Kim, Jihye; Park, Hyen Joo; Ko, Keebeom; Bang, Hea-Son; Lee, Sang Kook; Shin, Jongheon; Oh, Dong-Chan

    2015-03-06

    Coprisamides A and B (1 and 2) were isolated from a bacterium in the gut of the dung beetle Copris tripartitus. Spectroscopic analysis revealed that the planar structures of 1 and 2 are novel cyclic heptapeptides bearing unusual units, such as β-methylaspartic acid and 2,3-diaminopropanoic acid branched to valine and 2-heptatrienyl cinnamic acid. Absolute configurations were established by chemical derivatization and chiroptical spectroscopy. The coprisamides displayed significant activity for induction of quinone reductase.

  1. Injecting Inquiry into Undergraduate Astronomy Labs

    NASA Astrophysics Data System (ADS)

    Gezari, S.; Noel-Storr, J.; Spiegel, D.

    2002-12-01

    We present examples and results of instructors using inquiry-based teaching strategies in the undergraduate astronomy lab at Columbia University. Each instructor integrated varying degrees of inquiry depending on the topic of the lab and their own preferences for this style of instruction. We use student surveys to quantify how well the spectrum of inquiry-based labs, from guided activities to independent investigations, reached our educational goals of building scientific knowledge, skills and attitudes.

  2. 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.

  3. Curricular Adaptations in Introductory Physics Labs

    NASA Astrophysics Data System (ADS)

    Dreyfus, Benjamin W.; Ewell, Mary; Moore, Kimberly

    2017-01-01

    When curricular materials are disseminated to new sites, there can be a tension between fidelity to the original intent of the developers and adaptation to local needs. In this case study we look at a lab activity that was initially developed for an introductory physics for the life sciences (IPLS) course at the University of Maryland, then implemented at George Mason University with significant adaptations. The goals of the two implementations were overlapping, but also differed in ways that are reflected in the two versions of the lab. We compare student lab report data from the two sites to examine the impacts of the adaptation on how students engaged with the lab.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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).

  12. 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.

  13. Fred Keller and the Flex Lab.

    ERIC Educational Resources Information Center

    Richards, Beverly

    The Flex Lab at Santa Fe Community College, in New Mexico, is a self-paced, computer-assisted training center that allows students to accommodate college credit courses into their schedules. The Lab offers courses in introductory computers, keyboarding, and various computer programs and emphasizes several features of the Personalized System of…

  14. 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…

  15. 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…

  16. 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…

  17. 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.

  18. 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.

  19. 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…

  20. 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…

  1. Science Action Labs Part 1: Sciencing.

    ERIC Educational Resources Information Center

    Shevick, Ed; Adams, Linda, Ed.

    This book contains innovative hands-on science laboratory activities that teach basic scientific method skills and are designed to be used directly with 4th- through 9th-grade students. The background materials and instructions included in each activity are written for students to work together in teams. Lab titles are: observation lab,…

  2. 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.

  3. 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...

  4. 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…

  5. SPARC_LAB present and future

    NASA Astrophysics Data System (ADS)

    Ferrario, M.; Alesini, D.; Anania, M.; Bacci, A.; Bellaveglia, M.; Bogdanov, O.; Boni, R.; Castellano, M.; Chiadroni, E.; Cianchi, A.; Dabagov, S. B.; De Martinis, C.; Di Giovenale, D.; Di Pirro, G.; Dosselli, U.; Drago, A.; Esposito, A.; Faccini, R.; Gallo, A.; Gambaccini, M.; Gatti, C.; Gatti, G.; Ghigo, A.; Giulietti, D.; Ligidov, A.; Londrillo, P.; Lupi, S.; Mostacci, A.; Pace, E.; Palumbo, L.; Petrillo, V.; Pompili, R.; Rossi, A. R.; Serafini, L.; Spataro, B.; Tomassini, P.; Turchetti, G.; Vaccarezza, C.; Villa, F.; Dattoli, G.; Di Palma, E.; Giannessi, L.; Petralia, A.; Ronsivalle, C.; Spassovsky, I.; Surrenti, V.; Gizzi, L.; Labate, L.; Levato, T.; Rau, J. V.

    2013-08-01

    A new facility named SPARC_LAB has been recently launched at the INFN National Laboratories in Frascati, merging the potentialities of the former projects SPARC and PLASMONX. We describe in this paper the status and the future perspectives at the SPARC_LAB facility.

  6. Uses of Labs and Learning Spaces

    ERIC Educational Resources Information Center

    van den Blink, Clare

    2009-01-01

    How can an IT department transform traditional computer labs given the resource limits of a university setting? Before engaging a redesign team, conduct some groundwork and initial research to help guide design and resource decisions. When the author and her colleagues considered modifying the lab spaces at Cornell, they initially engaged in…

  7. 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…

  8. Isolation of a hop-sensitive variant of Lactobacillus lindneri and identification of genetic markers for beer spoilage ability of lactic acid bacteria.

    PubMed

    Suzuki, Koji; Iijima, Kazumaru; Ozaki, Kazutaka; Yamashita, Hiroshi

    2005-09-01

    We have isolated a hop-sensitive variant of the beer spoilage bacterium Lactobacillus lindneri DSM 20692. The variant lost a plasmid carrying two contiguous open reading frames (ORF s) designated horB(L) and horC(L) that encode a putative regulator and multidrug transporter presumably belonging to the resistance-nodulation-cell division superfamily. The loss of hop resistance ability occurred with the loss of resistance to other drugs, including ethidium bromide, novobiocin, and cetyltrimethylammonium bromide. PCR and Southern blot analysis using 51 beer spoilage strains of various species of lactic acid bacteria (LAB) revealed that 49 strains possessed homologs of horB and horC. No false-positive results have been observed for nonspoilage LAB or frequently encountered brewery isolates. These features are superior to those of horA and ORF 5, previously reported genetic markers for determining the beer spoilage ability of LAB. It was further shown that the combined use of horB/horC and horA is able to detect all 51 beer spoilage strains examined in this study. Furthermore sequence comparison of horB and horC homologs identified in four different beer spoilage species indicates these homologs are 96.6 to 99.5% identical, which is not typical of distinct species. The wide and exclusive distribution of horB and horC homologs among beer spoilage LAB and their sequence identities suggest that the hop resistance ability of beer spoilage LAB has been acquired through horizontal gene transfer. These insights provide a foundation for applying trans-species genetic markers to differentiating beer spoilage LAB including previously unencountered species.

  9. Isolation of a Hop-Sensitive Variant of Lactobacillus lindneri and Identification of Genetic Markers for Beer Spoilage Ability of Lactic Acid Bacteria

    PubMed Central

    Suzuki, Koji; Iijima, Kazumaru; Ozaki, Kazutaka; Yamashita, Hiroshi

    2005-01-01

    We have isolated a hop-sensitive variant of the beer spoilage bacterium Lactobacillus lindneri DSM 20692. The variant lost a plasmid carrying two contiguous open reading frames (ORF s) designated horBL and horCL that encode a putative regulator and multidrug transporter presumably belonging to the resistance-nodulation-cell division superfamily. The loss of hop resistance ability occurred with the loss of resistance to other drugs, including ethidium bromide, novobiocin, and cetyltrimethylammonium bromide. PCR and Southern blot analysis using 51 beer spoilage strains of various species of lactic acid bacteria (LAB) revealed that 49 strains possessed homologs of horB and horC. No false-positive results have been observed for nonspoilage LAB or frequently encountered brewery isolates. These features are superior to those of horA and ORF 5, previously reported genetic markers for determining the beer spoilage ability of LAB. It was further shown that the combined use of horB/horC and horA is able to detect all 51 beer spoilage strains examined in this study. Furthermore sequence comparison of horB and horC homologs identified in four different beer spoilage species indicates these homologs are 96.6 to 99.5% identical, which is not typical of distinct species. The wide and exclusive distribution of horB and horC homologs among beer spoilage LAB and their sequence identities suggest that the hop resistance ability of beer spoilage LAB has been acquired through horizontal gene transfer. These insights provide a foundation for applying trans-species genetic markers to differentiating beer spoilage LAB including previously unencountered species. PMID:16151091

  10. Carbohydrates act as receptors for the periodontitis-associated bacterium Porphyromonas gingivalis: a study of bacterial binding to glycolipids.

    PubMed

    Hellström, Ulrika; Hallberg, Eva C; Sandros, Jens; Rydberg, Lennart; Bäcker, Annika E

    2004-06-01

    In this study we show for the first time the use of carbohydrate chains on glycolipids as receptors for the periodontitis-associated bacterium Porphyromonas gingivalis. Previous studies have shown that this bacterium has the ability to adhere to and invade the epithelial lining of the dental pocket. Which receptor(s) the adhesin of P. gingivalis exploit in the adhesion to epithelial cells has not been shown. Therefore, the binding preferences of this specific bacterium to structures of carbohydrate origin from more than 120 different acid and nonacid glycolipid fractions were studied. The bacteria were labeled externally with (35)S and used in a chromatogram binding assay. To enable detection of carbohydrate receptor structures for P. gingivalis, the bacterium was exposed to a large number of purified total glycolipid fractions from a variety of organs from different species and different histo-blood groups. P. gingivalis showed a preference for fractions of human and pig origin for adhesion. Both nonacid and acid glycolipids were used by the bacterium, and a preference for shorter sugar chains was noticed. Bacterial binding to human acid glycolipid fractions was mainly obtained in the region of the chromatograms where sulfated carbohydrate chains usually are found. However, the binding pattern to nonacid glycolipid fractions suggests a core chain of lactose bound to the ceramide part as a tentative receptor structure. The carbohydrate binding of the bacterium might act as a first step in the bacterial invasion process of the dental pocket epithelium, subsequently leading to damage to periodontal tissue and tooth loss.

  11. 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.

  12. An electrochemical Lab-on-a-CD system for parallel whole blood analysis.

    PubMed

    Li, Tingjie; Fan, Yaxi; Cheng, Yang; Yang, Jun

    2013-07-07

    Lab-on-a-CD, as a main branch of Lab-on-a-chip technology, has led to several very successful commercial products. Most of these existing Lab-on-a-CD systems present complex system designs and thus are relatively expensive. In this work, we have developed a simple but robust Lab-on-a-CD system for parallel whole blood analyses. This Lab-on-a-CD system incorporates electrochemical bioanalysis and a simple blood sample separation mechanism into the centrifugal platform, and thus reduces the system's complexity. To demonstrate the applicability, the system was applied to perform basic metabolic panel tests, for example, the concentrations of glucose, lactate and uric acids of whole blood samples. Using only 16 μL of whole blood, within a few minutes, the Lab-on-a-CD system could produce results that agreed in general with the data by a conventional system. Therefore, this proof-of-concept Lab-on-a-CD system has demonstrated the potential to become a robust and simple-to-use device for parallel blood analyses.

  13. 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)

  14. 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.

  15. 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.

  16. 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

    2011-06-03

    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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    PubMed

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism.

  2. Developing a Focused Reading Lab for L2 Students.

    ERIC Educational Resources Information Center

    Stoller, Fredericka L.

    1994-01-01

    Presents a model reading lab design for advanced English for Academic Purposes students and describes the four major instructional components of the lab as well as the logistics of running a lab. (44 references) (Author/CK)

  3. Utilization of Phenylpropanoids by Newly Isolated Bacterium Pseudomonas sp. TRMK1.

    PubMed

    T R, Monisha; I, Mukram; B, Kirankumar; Reddy, Pooja V; Nayak, Anand S; Karegoudar, T B

    2017-01-25

    A bacterium Pseudomonas sp. TRMK1 capable of utilizing various phenylpropanoids was isolated from agro-industrial waste by enrichment culture technique. It is gram-negative, motile, aerobic, and able to utilize three different phenolic acids such as p-coumaric, ferulic, and caffeic acids at concentrations of 5, 10, and 15 mM in 18 h of incubation. The residual concentration of phenolic acids was analyzed by HPLC. The catabolic pathway of p-coumaric, ferulic, and caffeic acids is suggested based on the characterization of metabolic intermediates by GC, GC-HRMS, and different enzymatic assays. Further, Pseudomonas sp. TRMK1 utilizes a wide range of mixture of phenolic acids present in the synthetic effluent.

  4. 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.

  5. Extracellular protease derived from lactic acid bacteria stimulates the fermentative lactic acid production from the by-products of rice as a biomass refinery function.

    PubMed

    Watanabe, Masanori; Techapun, Charin; Kuntiya, Ampin; Leksawasdi, Noppol; Seesuriyachan, Phisit; Chaiyaso, Thanongsak; Takenaka, Shinji; Maeda, Isamu; Koyama, Masahiro; Nakamura, Kozo

    2017-02-01

    A lactic acid producing bacterium, Lactobacillus rhamnosus M-23, newly isolated from a rice washing drainage storage tank was found to produce l-(+)-lactic acid from a non-sterilized mixture of rice washing drainage and rice bran without any additions of nutrients under the simultaneous saccharification and fermentation (SSF) process. This strain has the ability to utilize the non-sterilized rice washing drainage and rice bran as a source of carbohydrate, saccharifying enzymes and nutrients for lactic acid production. Observation of extracellular protease activity in SSF culture broth showed that a higher protease activity was present in strain M-23 than in other isolated lactic acid producing bacteria (LABs). To investigate the structural changes of solid particles of rice washing drainage throughout LAB cultivation, scanning electron microscopic (SEM) observation and Fourier transform infrared-spectroscopy (FT-IR) analysis were performed. The results of the SEM observation showed that the surface material could be removed from solid particles of rice washing drainage treated by culture broth (supernatant) of strain M-23, thus exposing the crystal structure of the starch particle surface. The results of the FT-IR analysis revealed that the specific transmittance decrease of the CC and CO stretching and OH group of the solid particles of the rice washing drainage were highly correlated with the produced lactic acid concentration and extracellular protease activity, respectively. These results demonstrate the high lactic acid producing ability of strain M-23 from a non-sterilized mixture of rice washing drainage and rice bran under the SSF condition due to the removal of proteinaceous material and exposure of the starch particle surface by extracellular protease.

  6. Copper-binding characteristics of exopolymers from a freshwater-sediment bacterium

    SciTech Connect

    Mittelman, M.W.; Geesey, G.G.

    1985-04-01

    Copper-binding activity by exopolymers from adherent cells of freshwater-sediment bacterium was demonstrated by a combination of equilibrium dialysis and flameless atomic absorption spectrometry. Crude, cell-free exopolymer preparations containing protein and polysaccharide components bound up to 37 nmol of Cu per mg (dry weight). A highly purified exopolysaccharide preparation bound up to 253 nmol of Cu per mg of carbohydrate. The conditional stability constant for the crude exopolymer-Cu complex was 7.3 x 10/sup 8/. This value was similar to those obtained for Cu complexes formed with humic acids and xanthan, an exopolysaccharide produced by Xanthomonas campestris. Studies conducted at copper concentrations, pHs, and temperatures found in sediments from which the bacterium was isolated indicated that the exopolymers were capable of binding copper under natural conditions.

  7. 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.

  8. Draft Genome Sequence of the Suttonella ornithocola Bacterium

    PubMed Central

    Waldman Ben-Asher, Hiba; Yerushalmi, Rebecca; Wachtel, Chaim; Barbiro-Michaely, Efrat

    2017-01-01

    ABSTRACT   We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge, this is the first publication of the Suttonella ornithocola genome sequence. The genetic profile provides a basis for further analysis of its infection pathways. PMID:28209820

  9. 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.

  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. 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)

  12. The Language Lab: Renaissance or Extinction?

    ERIC Educational Resources Information Center

    Froehlich, Jurgen

    1982-01-01

    Discusses ways to combine technological innovations in the areas of visual aids and computers with existing language lab equipment in order to motivate students in the area of second language learning. (EKN)

  13. Microspectroscopy At Beamline 73 MAX-lab

    SciTech Connect

    Engdahl, Anders

    2010-02-03

    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.

  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. Laboratory Professionals: Who's Who in the Lab

    MedlinePlus

    ... in one particular area, such as in clinical chemistry, immunology, molecular pathology, microbiology, or blood bank /transfusion ... certain areas of the lab, such as clinical chemistry, and may be certified by the BOC or ...

  16. Developing an Advanced Lab course from scratch

    NASA Astrophysics Data System (ADS)

    Michalak, Rudi

    2012-10-01

    A few years ago the Alpha group in APS organized faculty with interests in advanced lab courses in physics. At the University of Wyoming, we re-launched an advanced lab course after doing more than 15 years without one. Our majors had to take an electronic course in the Electrical Engineering department to get familiar with any kind of electronic equipment. Now we are in the fourth teaching session of the advanced Modern Physics lab and we will expand the course into a two-term course beginning spring 2013. Forty-five majors have gone through our labs, We developed an oral exam tradition, which is now beginning to lend our department upper level outcome assessment credibility for campus wide assessment.

  17. Merging lab, drug data boosts disease management.

    PubMed

    2000-02-01

    Merging lab and pharmacy data can benefit disease management. Integrating lab data with other data sets gave Blue Cross Blue Shield of Southeast Michigan a way to focus its diabetes disease management program, assess the effectiveness of therapy, and profile physicians. Learn how the plan's experience in data integration can apply to hospital systems and why pursuing a partner in such a project might be a wise move.

  18. 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.

  19. 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

  20. Progress in engineering acid stress resistance of lactic acid bacteria.

    PubMed

    Wu, Chongde; Huang, Jun; Zhou, Rongqing

    2014-02-01

    Lactic acid bacteria (LAB) are widely used for the production of a variety of fermented foods, and are considered as probiotic due to their health-promoting effect. However, LAB encounter various environmental stresses both in industrial fermentation and application, among which acid stress is one of the most important survival challenges. Improving the acid stress resistance may contribute to the application and function of probiotic action to the host. Recently, the advent of genomics, functional genomics and high-throughput technologies have allowed for the understanding of acid tolerance mechanisms at a systems level, and many method to improve acid tolerance have been developed. This review describes the current progress in engineering acid stress resistance of LAB. Special emphasis is placed on engineering cellular microenvironment (engineering amino acid metabolism, introduction of exogenous biosynthetic capacity, and overproduction of stress response proteins) and maintaining cell membrane functionality. Moreover, strategies to improve acid tolerance and the related physiological mechanisms are also discussed.

  1. Evolution of a biomass-fermenting bacterium to resist lignin phenolics.

    PubMed

    Cerisy, Tristan; Souterre, Tiffany; Torres-Romero, Ismael; Boutard, Magali; Dubois, Ivan; Patrouix, Julien; Labadie, Karine; Berrabah, Wahiba; Salanoubat, Marcel; Doring, Volker; Tolonen, Andrew

    2017-03-31

    Increasing the resistance of plant-fermenting bacteria to lignocellulosic inhibitors is useful to understand microbial adaptation and to develop candidate strains for consolidated bioprocessing. Here we study and improve inhibitor resistance in Clostridium phytofermentans (also called Lachnoclostridium phytofermentans), a model anaerobe that ferments lignocellulosic biomass. We survey the resistance of this bacterium to a panel of biomass inhibitors, and then evolve strains that grow in increasing concentrations of the lignin phenolic, ferulic acid, by automated, long-term growth selection in an anaerobic GM3 automat. Ultimately, strains resist multiple inhibitors and grow robustly at the solubility limit of ferulate while retaining the ability to ferment cellulose. We analyze genome-wide transcription patterns during ferulate stress and genomic variants that arose along the ferulate growth selection, revealing how cells adapt to inhibitors by changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for evolution of anaerobes and gives insight into the genetic mechanisms by which bacteria survive exposure to chemical inhibitors.Importance Fermentation of plant biomass is a key part of carbon cycling in diverse ecosystems. Further, industrial biomass fermentation could provide a renewable alternative to fossil fuels. Plants are primarily composed of lignocellulose, a matrix of polysaccharides and polyphenolic lignin. Thus, when microorganisms degrade lignocellulose to access sugars, they also release phenolic and acidic inhibitors. Here, we study how the plant-fermenting bacterium Clostridium phytofermentans resists plant inhibitors using the lignin phenolic, ferulic acid. We examine how the cell responds to abrupt ferulate stress by measuring changes in gene expression. We evolve increasingly resistant strains by automated, long-term cultivation at progressively higher

  2. 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.

  3. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum.

    PubMed

    Hensen, Daniela; Sperling, Detlef; Trüper, Hans G; Brune, Daniel C; Dahl, Christiane

    2006-11-01

    Two different pathways for thiosulphate oxidation are present in the purple sulphur bacterium Allochromatium vinosum: oxidation to tetrathionate and complete oxidation to sulphate with obligatory formation of sulphur globules as intermediates. The tetrathionate:sulphate ratio is strongly pH-dependent with tetrathionate formation being preferred under acidic conditions. Thiosulphate dehydrogenase, a constitutively expressed monomeric 30 kDa c-type cytochrome with a pH optimum at pH 4.2 catalyses tetrathionate formation. A periplasmic thiosulphate-oxidizing multienzyme complex (Sox) has been described to be responsible for formation of sulphate from thiosulphate in chemotrophic and phototrophic sulphur oxidizers that do not form sulphur deposits. In the sulphur-storing A. vinosum we identified five sox genes in two independent loci (soxBXA and soxYZ). For SoxA a thiosulphate-dependent induction of expression, above a low constitutive level, was observed. Three sox-encoded proteins were purified: the heterodimeric c-type cytochrome SoxXA, the monomeric SoxB and the heterodimeric SoxYZ. Gene inactivation and complementation experiments proved these proteins to be indispensable for thiosulphate oxidation to sulphate. The intermediary formation of sulphur globules in A. vinosum appears to be related to the lack of soxCD genes, the products of which are proposed to oxidize SoxY-bound sulphane sulphur. In their absence the latter is instead transferred to growing sulphur globules.

  4. Lab-on-a-Foil: microfluidics on thin and flexible films.

    PubMed

    Focke, Maximilian; Kosse, Dominique; Müller, Claas; Reinecke, Holger; Zengerle, Roland; von Stetten, Felix

    2010-06-07

    This critical review is motivated by an increasing interest of the microfluidics community in developing complete Lab-on-a-Chip solutions based on thin and flexible films (Lab-on-a-Foil). Those implementations benefit from a broad range of fabrication methods that are partly adopted from well-established macroscale processes or are completely new and promising. In addition, thin and flexible foils enable various features like low thermal resistance for efficient thermocycling or integration of easily deformable chambers paving the way for new means of on-chip reagent storage or fluid transport. From an economical perspective, Lab-on-a-Foil systems are characterised by low material consumption and often low-cost materials which are attractive for cost-effective high-volume fabrication of self-contained disposable chips. The first part of this review focuses on available materials, fabrication processes and approaches for integration of microfluidic functions including liquid control and transport as well as storage and release of reagents. In the second part, an analysis of the state of Lab-on-a-Foil applications is provided with a special focus on nucleic acid analysis, immunoassays, cell-based assays and home care testing. We conclude that the Lab-on-a-Foil approach is very versatile and significantly expands the toolbox for the development of Lab-on-a-Chip solutions.

  5. 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.

  6. 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…

  7. 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

  8. 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

  9. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    PubMed

    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.

  10. 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…

  11. Lab safety, Part 2. Safety in the lab: practices and predictions.

    PubMed

    Maher, L

    1996-09-01

    Precautions related to bloodborne pathogens, and the handling of specimens and waste are among the chief concerns of laboratorians today. Find out how your lab stacks up and how safety will impact tomorrow's lab workers in the conclusion to MLO's latest survey.

  12. 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.

  13. 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…

  14. 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.

  15. 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.

  16. 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

  17. eComLab: remote laboratory platform

    NASA Astrophysics Data System (ADS)

    Pontual, Murillo; Melkonyan, Arsen; Gampe, Andreas; Huang, Grant; Akopian, David

    2011-06-01

    Hands-on experiments with electronic devices have been recognized as an important element in the field of engineering to help students get familiar with theoretical concepts and practical tasks. The continuing increase the student number, costly laboratory equipment, and laboratory maintenance slow down the physical lab efficiency. As information technology continues to evolve, the Internet has become a common media in modern education. Internetbased remote laboratory can solve a lot of restrictions, providing hands-on training as they can be flexible in time and the same equipment can be shared between different students. This article describes an on-going remote hands-on experimental radio modulation, network and mobile applications lab project "eComLab". Its main component is a remote laboratory infrastructure and server management system featuring various online media familiar with modern students, such as chat rooms and video streaming.

  18. Environment monitoring using LabVIEW

    SciTech Connect

    Hawtree, J.

    1995-01-01

    A system has been developed for electronically recording and monitoring temperature, humidity, and other environmental variables at the Silicon Detector Facility located in Lab D. The data is collected by LabVIEW software, which runs in the background on an Apple Macintosh. The software is completely portable between Macintosh, MS Windows, and Sun platforms. The hardware includes a Macintosh with 8 MB of RAM; an external ADC-1 analog-to-digital converter that uses a serial port; LabVIEW software; temperature sensors; humidity sensors; and other voltage/current sensing devices. ADC values are converted to ASCII strings and entered into files which are read over Ethernet. Advantages include automatic logging, automatic recovery after power interruptions, and the availability of stand-alone applications for other locations with inexpensive software and hardware.

  19. Vista and Pemex in LAB deal

    SciTech Connect

    Morris, G.D.L.

    1993-01-20

    Vista Chemical (Houston) and Petroleos Mexicanos (Pemex; Mexico City) have firmed up their long-negotiated plans for Pemex to supply feedstock for a linear alkylbenzene (LAB) plant that Vista will build in Mexico (CW, Sept. 16, 1992 p. 8). Specifically, the two companies have signed an agreement of understanding to pursue negotiations and finalize agreements. The plant would cost $250 million, produce 260 million-330 million lbs/year of LAB, and create about 200 permanent jobs. Final agreements, including a site selection, are expected to be completed by midyear. Vista expects startup in 1996, and is considering forming aj oint venture with a Mexican partner.

  20. Laboratory Accreditation Bureau (L-A-B)

    DTIC Science & Technology

    2011-03-28

    2011 EMDQ Workshop • Arlington, VA Laboratory Accreditation Bureau (L-A-B) Recognized by: Report Documentation Page Form ApprovedOMB No. 0704...2011 to 00-00-2011 4. TITLE AND SUBTITLE Laboratory Accreditation Bureau (L-A-B) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Laboratory Accreditation Bureau

  1. 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.

  2. Structure of the O-specific polysaccharide of the bacterium Proteus vulgaris O23.

    PubMed

    Perepelov, A V; Shashkov, A S; Babichka, D; Senchenkova, S N; Bartodziejska, B; Rozalski, A; Knirel, Y A

    2000-09-01

    An acidic O-specific polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of the bacterium Proteus vulgaris O23 (strain PrK 44/57) and found to contain 2-acetamido-2-deoxy-D-galactose, 2-acetamido-2-deoxy-D-glucose, and D-galacturonic acid. Based on 1H- and 13C-NMR spectroscopic studies, including two-dimensional correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY), nuclear Overhauser effect spectroscopy (NOESY), and 1H,13C heteronuclear multiple-quantum coherence (HMQC) experiments, the following structure of the branched tetrasaccharide repeating unit of the polysaccharide was established: [figure], where the degree of O-acetylation of the terminal GalA residue at position 4 is about 80%. A structural similarity of the O-specific polysaccharides of P. vulgaris O23 and P. mirabilis O23 is discussed.

  3. 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

  4. Overproduction of Hydrogen From an Anaerobic Bacterium

    DTIC Science & Technology

    2008-12-01

    ADM002187. Proceedings of the Army Science Conference (26th) Held in Orlando, Florida on 1-4 December 2008, The original document contains color images...0.02 mg/L folic acid, 0.1 mg/L pyridoxine-HCl, 0.05 mg/L thiamine-HCl, 0.05 mg/L riboflavin , 0.05 mg/L nicotinic acid, 0.05 mg/L calcium

  5. Biochemical characterization of cellulose-binding proteins (CBPA and CBPB) from the rumen cellulolytic bacterium Eubacterium cellulosolvens 5.

    PubMed

    Yoshimatsu, Miho; Toyoda, Atsushi; Onizawa, Naoki; Nakamura, Yutaka; Minato, Hajime

    2007-10-01

    The cellulose-binding proteins, CBPA and CBPB, of rumen cellulolytic bacterium Eubacterium cellulosolvens 5 were biochemically characterized, and their properties were compared. Recombinant CBPA and CBPB were a typical 1,4-beta-endoglucanase. Both proteins bound to insoluble polysaccharides such as Avicel cellulose, acid swollen cellulose, lichenan, chitin, and oat spelt xylan. On the other hand, only recombinant CBPB bound to agarose and starch.

  6. 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...

  7. Computational Labs Using VPython Complement Conventional Labs in Online and Regular Physics Classes

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.

    2009-03-01

    Fairmont State University has developed online physics classes for the high-school teaching certificate based on the text book Matter and Interaction by Chabay and Sherwood. This lead to using computational VPython labs also in the traditional class room setting to complement conventional labs. The computational modeling process has proven to provide an excellent basis for the subsequent conventional lab and allows for a concrete experience of the difference between behavior according to a model and realistic behavior. Observations in the regular class room setting feed back into the development of the online classes.

  8. 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…

  9. 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…

  10. 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.

  11. 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…

  12. Berkeley Lab's Cool Your School Program

    SciTech Connect

    Ivan Berry

    2012-07-30

    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.

  13. 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…

  14. 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.

  15. 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…

  16. 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…

  17. Pilot Plants Enhance Brazosport Lab Courses.

    ERIC Educational Resources Information Center

    Krieger, James

    1986-01-01

    Describes an experiential lab program for a two-year college's chemical technology program. Discusses student experiences in six miniature pilot plants that represent the essential instrumentation and chemical processes found in the chemical industry. Recognizes the industries that helped implement the program. (TW)

  18. 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)

  19. 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…

  20. 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…

  1. 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.

  2. A Successful Individualized Writing Lab Module.

    ERIC Educational Resources Information Center

    Douglas, Michael A.

    1993-01-01

    Describes and evaluates the effectiveness of an individualized Writing Lab module, developed to prepare students enrolled in Savannah State College's Developmental Studies English Fundamentals classes for the post-Collegiate Placement Examination. The module uses instructor-authored, computer-assisted instruction to provide immediate feedback on…

  3. 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…

  4. Unconventional lab ideas for Introductory Astronomy

    NASA Astrophysics Data System (ADS)

    Ingram, Doug

    2001-10-01

    A collection of ideas recently developed for a group of advanced undergraduates in introductory Astronomy courses will be discussed. These ideas represent a departure from more traditional lab topics and include use of the Internet, leading discussions with political overtones, applications to current NASA missions and SETI research.

  5. 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…

  6. Integrating Language Lab Materials into Advanced Russian.

    ERIC Educational Resources Information Center

    Allar, Gregory

    1986-01-01

    Describes the use of language lab materials supplied by the pedagogical journal "Russkij Jazyk Za Rubezom" in an advanced Russian-language class. Each week students were given a relevant picture and vocabulary list prior to listening to a taped story. The story was used as the basis for conversation. (LMO)

  7. 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.

  8. Apples and Arias in the Language Lab.

    ERIC Educational Resources Information Center

    Leamon, Patricia

    1999-01-01

    Describes a French teacher's efforts to substitute interactive video/computer technologies for textbook materials. She designed special language-lab events to introduce eighth graders to the vocabulary of animals, colors, simple adjectives, fruits, flowers, and natural landscapes and to cultural artifacts, such as paintings, arias, poems, and…

  9. Encouraging Creativity in the Science Lab

    ERIC Educational Resources Information Center

    Eyster, Linda

    2010-01-01

    Although science is a creative endeavor (NRC 1996, p. 46), many students think they are not encouraged--or even allowed--to be creative in the laboratory. When students think there is only one correct way to do a lab, their creativity is inhibited. Park and Seung (2008) argue for the importance of creativity in science classrooms and for the…

  10. EPA Mobile Lab Screens Austin Residents Soil

    EPA Pesticide Factsheets

    DALLAS - (April 15, 2015) Scientists from the U.S. Environmental Protection Agency (EPA) used a mobile lab facility to screen soil samples from Austin residences recently. Participants were able to bring soil from their garden or yard and have it as

  11. 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…

  12. 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…

  13. 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,…

  14. 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…

  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. Electronics Lab Instructors' Approaches to Troubleshooting Instruction

    ERIC Educational Resources Information Center

    Dounas-Frazer, Dimitri R.; Lewandowski, H. J.

    2017-01-01

    In this exploratory qualitative study, we describe instructors' self-reported practices for teaching and assessing students' ability to troubleshoot in electronics lab courses. We collected audio data from interviews with 20 electronics instructors from 18 institutions that varied by size, selectivity, and other factors. In addition to describing…

  17. 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…

  18. 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

  19. Evidence for distinct L-methionine catabolic pathways in the yeast Geotrichum candidum and the bacterium Brevibacterium linens.

    PubMed

    Arfi, Kenza; Landaud, Sophie; Bonnarme, Pascal

    2006-03-01

    Tracing experiments were carried out to identify volatile and nonvolatile L-methionine degradation intermediates and end products in the yeast Geotrichum candidum and in the bacterium Brevibacterium linens, both of which are present in the surface flora of certain soft cheeses and contribute to the ripening reactions. Since the acid-sensitive bacterium B. linens is known to produce larger amounts and a greater variety of volatile sulfur compounds (VSCs) than the yeast G. candidum produces, we examined whether the L-methionine degradation routes of these microorganisms differ. In both microorganisms, methanethiol and alpha-ketobutyrate are generated; the former compound is the precursor of other VSCs, and the latter is subsequently degraded to 2,3-pentanedione, which has not been described previously as an end product of L-methionine catabolism. However, the L-methionine degradation pathways differ in the first steps of L-methionine degradation. L-Methionine degradation is initiated by a one-step degradation process in the bacterium B. linens, whereas a two-step degradation pathway with 4-methylthio-2-oxobutyric acid (MOBA) and 4-methylthio-2-hydroxybutyric acid (MHBA) as intermediates is used in the yeast G. candidum. Since G. candidum develops earlier than B. linens during the ripening process, MOBA and MHBA generated by G.candidum could also be used as precursors for VSC production by B. linens.

  20. 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.

  1. 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

  2. Manganese Ion Increases LAB-yeast Mixed-species Biofilm Formation.

    PubMed

    Nozaka, Soma; Furukawa, Soichi; Sasaki, Miwa; Hirayama, Satoru; Ogihara, Hirokazu; Morinaga, Yasushi

    2014-01-01

    Remarkable LAB-yeast mixed-species biofilm was formed by lactic acid bacteria (LAB) Lactobacillus plantarum ML11-11 isolated from Fukuyama pot vinegar and Saccharomyces cerevisiae. This mixed-species biofilm formation increased in proportion to the YPD medium concentration but decreased in proportion to the MRS medium concentration. The effect of MRS components on mixed-species biofilm formation was investigated in a YPD medium environment, and it was clarified that beef extract (one of the MRS medium components) decreased mixed-species biofilm formation. On the other hand, manganese sulfate (another component in MRS) remarkably increased both LAB single- and LAB-yeast mixed-species biofilm formation. LAB single- and mixed-species biofilm formation were increased in proportion to the manganese sulfate concentration up to 1 mM and 100 μM, respectively. The growth of L. plantarum ML11-11 was increased significantly by the addition of 10 μM manganese sulfate and was resistant to higher concentration of up to 100 mM, but growth of S. cerevisiae was sensitive to manganese ion above 100 μM. These results suggested that mixed-species biofilm formation could be controlled artificially by controlling the manganese ion level.

  3. 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...

  4. 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.

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

    DOE PAGES

    Aston, John E.; Apel, William A.; Lee, Brady D.; ...

    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

  6. 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.

  7. Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA.

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T).

  8. 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…

  9. 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…

  10. Effectiveness of a Lab Manual Delivered on CD-ROM

    ERIC Educational Resources Information Center

    Brickman, Peggy; Ketter, Catherine A. Teare; Pereira, Monica

    2005-01-01

    Although electronic instructional media are becoming increasingly prevalent in science classrooms, their worth remains unproven. Here, student perceptions and performance using CD-ROM delivery of lab materials are assessed. Numerous learning barriers that produced lower lab grades for students using a CD-ROM lab manual in comparison to a print…

  11. 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.

  12. 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…

  13. 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.

  14. 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.

  15. Lab-on-a-Chip Multiplex Assays.

    PubMed

    Peter, Harald; Wienke, Julia; Bier, Frank F

    2017-01-01

    Lab-on-a-chip multiplex assays allow a rapid identification of multiple parameters in an automated manner. Here we describe a lab-based preparation followed by a rapid and fully automated DNA microarray hybridization and readout in less than 10 min using the Fraunhofer in vitro diagnostics (ivD) platform to enable rapid identification of bacterial species and detection of antibiotic resistance. The use of DNA microarrays allows a fast adaptation of new biomarkers enabling the identification of different genes as well as single-nucleotide-polymorphisms (SNPs) within these genes. In this protocol we describe a DNA microarray developed for identification of Staphylococcus aureus and the mecA resistance gene.

  16. Expert system for scheduling simulation lab sessions

    NASA Technical Reports Server (NTRS)

    Lund, Chet

    1990-01-01

    Implementation and results of an expert system used for scheduling session requests for the Systems Engineering Simulator (SES) laboratory at the NASA Johnson Space Center (JSC) are discussed. Weekly session requests are received from astronaut crew trainers, procedures developers, engineering assessment personnel, software developers, and various others who wish to access the computers, scene generators, and other simulation equipment available to them in the SES lab. The expert system under discussion is comprised of a data acquisition portion - two Pascal programs run on a personal computer - and a CLIPS program installed on a minicomputer. A brief introduction to the SES lab and its scheduling background is given. A general overview of the system is provided, followed by a detailed description of the constraint-reduction process and of the scheduler itself. Results from a ten-week trial period using this approach are discussed. Finally, a summary of the expert system's strengths and shortcomings are provided.

  17. Jefferson Lab Data Acquisition Run Control System

    SciTech Connect

    Vardan Gyurjyan; Carl Timmer; David Abbott; William Heyes; Edward Jastrzembski; David Lawrence; Elliott Wolin

    2004-10-01

    A general overview of the Jefferson Lab data acquisition run control system is presented. This run control system is designed to operate the configuration, control, and monitoring of all Jefferson Lab experiments. It controls data-taking activities by coordinating the operation of DAQ sub-systems, online software components and third-party software such as external slow control systems. The main, unique feature which sets this system apart from conventional systems is its incorporation of intelligent agent concepts. Intelligent agents are autonomous programs which interact with each other through certain protocols on a peer-to-peer level. In this case, the protocols and standards used come from the domain-independent Foundation for Intelligent Physical Agents (FIPA), and the implementation used is the Java Agent Development Framework (JADE). A lightweight, XML/RDF-based language was developed to standardize the description of the run control system for configuration purposes.

  18. The U.S. Lab is rotated

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In the Space Station Processing Facility, the U.S. Laboratory Destiny is about to undergo rotation in its workstand. A component of the International Space Station, Destiny is scheduled to fly on mission STS-98 in early 2001. During the mission, the crew will install the Lab during a series of three space walks. The STS-98 mission will provide the station with science research facilities and expand its power, life support and control capabilities. The U.S. Lab module continues a long tradition of microgravity materials research, first conducted by Skylab and later Shuttle and Spacelab missions. Destiny is expected to be a major feature in future research, providing facilities for biotechnology, fluid physics, combustion, and life sciences research.

  19. The U.S. Lab is rotated

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In the Space Station Processing Facility, a worker checks the U.S. Laboratory Destiny as it rotates. A component of the International Space Station, Destiny is scheduled to fly on mission STS-98 in early 2001. During the mission, the crew will install the Lab during a series of three space walks. The STS-98 mission will provide the station with science research facilities and expand its power, life support and control capabilities. The U.S. Lab module continues a long tradition of microgravity materials research, first conducted by Skylab and later Shuttle and Spacelab missions. Destiny is expected to be a major feature in future research, providing facilities for biotechnology, fluid physics, combustion, and life sciences research.

  20. The U.S. Lab is rotated

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In the Space Station Processing Facility, a worker controls the rotation of the U.S. Laboratory Destiny. A component of the International Space Station, Destiny is scheduled to fly on mission STS-98 in early 2001. During the mission, the crew will install the Lab during a series of three space walks. The STS-98 mission will provide the station with science research facilities and expand its power, life support and control capabilities. The U.S. Lab module continues a long tradition of microgravity materials research, first conducted by Skylab and later Shuttle and Spacelab missions. Destiny is expected to be a major feature in future research, providing facilities for biotechnology, fluid physics, combustion, and life sciences research.

  1. 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

  2. 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.

  3. Commerce Lab: Mission analysis. Payload integration study

    NASA Technical Reports Server (NTRS)

    Marvin, G. D.

    1984-01-01

    The objectives of the commerce lab mission analysis and payload integration study are discussed. A mission model which accommodates commercial users and provides a basic data base for future mission planning is described. The data bases developed under this study include: (1) user requirements; (2) apparatus capabilities and availabilities; and (3) carrier capabilities. These data bases are synthesized in a trades and analysis phase along with the STS flight opportunities. Optimum missions are identified.

  4. Jefferson Lab Science: Present and Future

    SciTech Connect

    McKeown, Robert D.

    2015-02-12

    The Continuous Electron Beam Accelerator Facility (CEBAF) and associated experimental equipment at Jefferson Lab comprise a unique facility for experimental nuclear physics. Furthermore, this facility is presently being upgraded, which will enable a new experimental program with substantial discovery potential to address important topics in nuclear, hadronic, and electroweak physics. Further in the future, it is envisioned that the Laboratory will evolve into an electron-ion colliding beam facility.

  5. Overview of Nuclear Physics at Jefferson Lab

    SciTech Connect

    McKeown, Robert D.

    2013-08-01

    The Continuous Electron Beam Accelerator Facility (CEBAF) and associated experimental equipment at Jefferson Lab comprise a unique facility for experimental nuclear physics. This facility is presently being upgraded, which will enable a new experimental program with substantial discovery potential to address important topics in nuclear, hadronic, and electroweak physics. Further in the future, it is envisioned that the Laboratory will evolve into an electron-ion colliding beam facility.

  6. Setting new sights for standards lab

    NASA Astrophysics Data System (ADS)

    Banks, Michael

    2008-03-01

    It may be best known as the home of the world's first atomic clock, which led to a new definition of the second. But the National Physical Laboratory (NPL), which develops and maintains the country's measurement standards, was in fact founded in 1900 to promote links between science and commerce. That tradition, which saw staff at the lab also inventing radar, early computers and modern network packet switching, is something that John Pethica - NPL's new chief scientist - is keen to build on.

  7. Berkeley's Advanced Labs for Undergraduate Astronomy Majors

    NASA Astrophysics Data System (ADS)

    Heiles, C.

    1998-12-01

    We currently offer three advanced laboratory courses for undergraduate majors: optical, IR, and radio. These courses contain both intellectual and practical content; in this talk we focus on the radio lab as a representative example. The first half of the semester concentrates on fundamentals of microwave electronics and radio astronomy techniques in four formal laboratory exercises which emphasize hands-on use of microwave devices, laboratory instruments, and computer-controlled data taking. The second half of the course emphasizes astronomy, using a horn with ~ 1 m(2) aperture to map the HI in the Galaxy and a two-element interferometer composed of ~ 1 m diameter dishes on a ~ 10 m baseline to measure accurate positions of radio sources and accurate diameters for the Sun and Moon. These experiments and observations offer ideal opportunities for teaching coordinates, time, rotation matrices, data reduction techniques, least squares, signal processing, image processing, Fourier transforms, and laboratory and astronomical instrumentation. The students can't get along without using computers as actually used by astronomers. We stay away from packaged software such as IRAF, which are ``black boxes''; rather, students learn far more by writing their own software, usually for the first time. They use the IDL language to take and reduce data and prepare them for the lab reports. We insist on quality reports---including tables, postscript graphs and images, correct grammar, spelling, and all the rest---and we strongly urge (successfully!) the students to use LATEX. The other two lab courses have the same emphasis: the guiding spirit is to place the students in a real-life research-like situation. There is too much to do, so students perform the work in small groups of 3 or 4 and groups are encouraged to share their knowledge. Lab reports are written individually. These courses are very demanding, requiring an average of 20 hours per week from the students (and probably

  8. Berkeley Lab Computing Sciences: Accelerating Scientific Discovery

    SciTech Connect

    Hules, John A

    2008-12-12

    Scientists today rely on advances in computer science, mathematics, and computational science, as well as large-scale computing and networking facilities, to increase our understanding of ourselves, our planet, and our universe. Berkeley Lab's Computing Sciences organization researches, develops, and deploys new tools and technologies to meet these needs and to advance research in such areas as global climate change, combustion, fusion energy, nanotechnology, biology, and astrophysics.

  9. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    PubMed

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  10. The NASA Langley Isolator Dynamics Research Lab

    NASA Technical Reports Server (NTRS)

    Middleton, Troy F.; Balla, Robert J.; Baurle, Robert A.; Humphreys, William M.; Wilson, Lloyd G.

    2010-01-01

    The Isolator Dynamics Research Lab (IDRL) is under construction at the NASA Langley Research Center in Hampton, Virginia. A unique test apparatus is being fabricated to support both wall and in-stream measurements for investigating the internal flow of a dual-mode scramjet isolator model. The test section is 24 inches long with a 1-inch by 2-inch cross sectional area and is supplied with unheated, dry air through a Mach 2.5 converging-diverging nozzle. The test section is being fabricated with two sets (glass and metallic) of interchangeable sidewalls to support flow visualization and laser-based measurement techniques as well as static pressure, wall temperature, and high frequency pressure measurements. During 2010, a CFD code validation experiment will be conducted in the lab in support of NASA s Fundamental Aerodynamics Program. This paper describes the mechanical design of the Isolator Dynamics Research Lab test apparatus and presents a summary of the measurement techniques planned for investigating the internal flow field of a scramjet isolator model.

  11. A pseudokinase couples signaling pathways to enable asymmetric cell division in a bacterium

    PubMed Central

    Childers, W. S.; Shapiro, Lucy

    2014-01-01

    Bacteria face complex decisions when initiating developmental events such as sporulation, nodulation, virulence, and asymmetric cell division. These developmental decisions require global changes in genomic readout, and bacteria typically employ intricate (yet poorly understood) signaling networks that enable changes in cell function. The bacterium Caulobacter crescentus divides asymmetrically to yield two functionally distinct cells: a motile, chemotactic swarmer cell, and a sessile stalked cell with replication and division capabilities. Work from several Caulobacter labs has revealed that differentiation requires concerted regulation by several two-component system (TCS) signaling pathways that are differentially positioned at the poles of the predivisional cell (Figure 1). The strict unidirectional flow from histidine kinase (HK) to the response regulator (RR), observed in most studied TCS, is difficult to reconcile with the notion that information can be transmitted between two or more TCS signaling pathways. In this study, we uncovered a mechanism by which daughter cell fate, which is specified by the DivJ-DivK-PleC system and effectively encoded in the phosphorylation state of the single-domain RR DivK, is communicated to the CckA-ChpT-CtrA signaling pathway that regulates more than 100 genes for polar differentiation, replication initiation and cell division. Using structural biology and biochemical findings we proposed a mechanistic basis for TCS pathway coupling in which the DivL pseudokinase is repurposed as a sensor rather than participant in phosphotransduction.

  12. Why engineering lactic acid bacteria for biobutanol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Gram-positive Lactic acid bacteria (LAB) are considered attractive biocatalysts for biomass to biofuels for several reasons. They have GRAS (Generally Recognized As Safe) status that are acceptable in food, feed, and medical applications. LAB are fermentative: selected strains are capable of f...

  13. 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

  14. 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.

  15. Chitin Utilization by the Insect-Transmitted Bacterium Xylella fastidiosa▿ †

    PubMed Central

    Killiny, Nabil; Prado, Simone S.; Almeida, Rodrigo P. P.

    2010-01-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa. PMID:20656858

  16. Are Virtual Labs as Effective as Hands-on Labs for Undergraduate Physics? A Comparative Study at Two Major Universities

    NASA Astrophysics Data System (ADS)

    Darrah, Marjorie; Humbert, Roxann; Finstein, Jeanne; Simon, Marllin; Hopkins, John

    2014-12-01

    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 alternative or supplement to these traditional hands-on labs. However, physics professors may be very hesitant to give up the hands-on labs, which have been such a central part of their courses, for a more cost and time-saving virtual alternative. Thus, it is important to investigate how the learning from these virtual experiences compares to that acquired through a hands-on experience. This study evaluated a comprehensive set of virtual labs for introductory level college physics courses and compared them to a hands-on physics lab experience. Each of the virtual labs contains everything a student needs to conduct a physics laboratory experiment, including: objectives, background theory, 3D simulation, brief video, data collection tools, pre- and postlab questions, and postlab quiz. This research was conducted with 224 students from two large universities and investigated the learning that occurred with students using the virtual labs either in a lab setting or as a supplement to hands-on labs versus a control group of students using the traditional hands-on labs only. Findings from both university settings showed the virtual labs to be as effective as the traditional hands-on physics labs.

  17. 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.

  18. 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

  19. Cellobiohydrolase B, a second exo-cellobiohydrolase from the cellulolytic bacterium Cellulomonas fimi.

    PubMed Central

    Shen, H; Gilkes, N R; Kilburn, D G; Miller, R C; Warren, R A

    1995-01-01

    The gene cbhB from the cellulolytic bacterium Cellulomonas fimi encodes a polypeptide of 1090 amino acids. Cellobiohydrolase B (CbhB) is 1037 amino acids long, with a calculated molecular mass of 109765 Da. The enzyme comprises five domains: an N-terminal catalytic domain of 643 amino acids, three fibronectin type III repeats of 97 amino acids each, and a C-terminal cellulose-binding domain of 104 amino acids. The catalytic domain belongs to family 48 of glycosyl hydrolases. CbhB has a very low activity on CM-cellulose. Viscometric analysis of CM-cellulose hydrolysis indicates that the enzyme is an exoglucanase. Cellobiose is the major product of hydrolysis of cellulose. In common with two other exoglycanases from C. fimi, CbhB has low but detectable endoglucanase activity. CbhB is the second exo-cellobiohydrolase found in C. fimi. Therefore, the cellulase system of C. fimi resembles those of fungi in comprising multiple endoglucanases and cellobiohydrolases. Images Figure 5 PMID:7575482

  20. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

    PubMed

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

    2016-01-04

    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.

  1. 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.

  2. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ruminococcus albus 7 is a highly cellulolytic rumen bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome for this microbe. This genome will be useful for rumen microbiology, cellulosome biology, and in biofuel production, as one of its major fermentation product...

  3. 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.

  4. (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

  5. Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

    PubMed

    Vasilyeva, Lina V; Omelchenko, Marina V; Berestovskaya, Yulia Y; Lysenko, Anatolii M; Abraham, Wolf-Rainer; Dedysh, Svetlana N; Zavarzin, George A

    2006-09-01

    A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).

  6. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    PubMed

    Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Stams, Alfons J M

    2010-09-01

    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 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). 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.

  7. 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.

  8. 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.

  9. Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester.

    PubMed

    Hori, Tomoyuki; Akuzawa, Masateru; Haruta, Shin; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2014-12-01

    Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which (13)C-labeled glucose was supplemented repeatedly. (13)CH4 and (13)CO2 were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester.

  10. 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)

  11. E-Labs - Learning with Authentic Data

    SciTech Connect

    Bardeen, Marjorie G.; Wayne, Mitchell

    2016-01-01

    the success teachers have had providing an opportunity for students to: • Organize and conduct authentic research. • Experience the environment of scientific collaborations. • Possibly make real contributions to a burgeoning scientific field. We've created projects that are problem-based, student driven and technology dependent. Students reach beyond classroom walls to explore data with other students and experts and share results, publishing original work to a worldwide audience. Students can discover and extend the research of other students, modeling the processes of modern, large-scale research projects. From start to finish e-Labs are student-led, teacher-guided projects. Students need only a Web browser to access computing techniques employed by professional researchers. A Project Map with milestones allows students to set the research plan rather than follow a step-by-step process common in other online projects. Most importantly, e-Labs build the learning experience around the students' own questions and let them use the very tools that scientists use. Students contribute to and access shared data, most derived from professional research databases. They use common analysis tools, store their work and use metadata to discover, replicate and confirm the research of others. This is where real scientific collaboration begins. Using online tools, students correspond with other research groups, post comments and questions, prepare summary reports, and in general participate in the part of scientific research that is often left out of classroom experiments. Teaching tools such as student and teacher logbooks, pre- and post-tests and an assessment rubric aligned with learner outcomes help teachers guide student work. Constraints on interface designs and administrative tools such as registration databases give teachers the "one-stop-shopping" they seek for multiple e-Labs. Teaching and administrative tools also allow us to track usage and assess the impact on

  12. Molecular screening of wine lactic acid bacteria degrading hydroxycinnamic acids.

    PubMed

    de las Rivas, Blanca; Rodríguez, Héctor; Curiel, José Antonio; Landete, José María; Muñoz, Rosario

    2009-01-28

    The potential to produce volatile phenols from hydroxycinnamic acids was investigated for lactic acid bacteria (LAB) isolated from Spanish grape must and wine. A PCR assay was developed for the detection of LAB that potentially produce volatile phenols. Synthetic degenerate oligonucleotides for the specific detection of the pdc gene encoding a phenolic acid decarboxylase were designed. The pdc PCR assay amplifies a 321 bp DNA fragment from phenolic acid decarboxylase. The pdc PCR method was applied to 85 strains belonging to the 6 main wine LAB species. Lactobacillus plantarum, Lactobacillus brevis, and Pediococcus pentosaceus strains produce a positive response in the pdc PCR assay, whereas Oenococcus oeni, Lactobacillus hilgardii, and Leuconostoc mesenteroides strains did not produce the expected PCR product. The production of vinyl and ethyl derivatives from hydroxycinnamic acids in culture media was determined by high-performance liquid chromatography. A relationship was found between pdc PCR amplification and volatile phenol production, so that the LAB strains that gave a positive pdc PCR response produce volatile phenols, whereas strains that did not produce a PCR amplicon did not produce volatile phenols. The proposed method could be useful for a preliminary identification of LAB strains able to produce volatile phenols in wine.

  13. Microbes to Biomes at Berkeley Lab

    SciTech Connect

    2015-10-28

    Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

  14. Quark Hadron Duality - Recent Jefferson Lab Results

    SciTech Connect

    Niculescu, Maria Ioana

    2016-08-01

    The duality between the partonic and hadronic descriptions of electron--nucleon scattering is a remarkable feature of nuclear interactions. When averaged over appropriate energy intervals the cross section at low energy which is dominated by nucleon resonances resembles the smooth behavior expected from perturbative QCD. Recent Jefferson Lab results indicate that quark-hadron duality is present in a variety of observables, not just the proton F2 structure function. An overview of recent results, especially local quark-hadron duality on the neutron, are presented here.

  15. DOSAR/CalLab Operations Manual

    SciTech Connect

    Bogard, J.S.

    2000-03-01

    The Life Sciences Division (LSD) of Oak Ridge National Laboratory (ORNL) has a long record of radiation dosimetry research, primarily using the Health Physics Research Reactor (HPRR) and the Dosimetry Applications Research (DOSAR) Program Calibration Laboratory (CalLab), referred to formerly as the Radiation Calibration Laboratory. These facilities have been used by a broad segment of the research community to perform a variety of experiments in areas including, but not limited to, radiobiology, radiation dosimeter and instrumentation development and calibration, and the testing of materials in a variety of radiation environments.

  16. Painless dental laser - Keith Murry in lab

    NASA Technical Reports Server (NTRS)

    2000-01-01

    NASA inventor Keith Murray checks out laser technology that promises to make painless dental lasers affordable for dentists and their patients. Developed at NASA Langley Research Center, Hampton, Va., the dual-wavelength laser can be electronically switched between the two laser frequencies important to dentists. Co-inventors of the technology are Murray, Norman Barnes, also of Langley, and Ralph Hutcheson of Scientific Materials Corp., Bozeman, Montana. The technology was originally developed for studies of atmospheric wind change. Photographed in building 1202, laser lab.

  17. Phoenix Carries Soil to Wet Chemistry Lab

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This image taken by the Surface Stereo Imager on NASA's Phoenix Mars Lander shows the lander's Robotic Arm scoop positioned over the Wet Chemistry Lab delivery funnel on Sol 29, the 29th Martian day after landing, or June 24, 2008. The soil will be delivered to the instrument on Sol 30.

    This image has been enhanced to brighten the scene.

    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.

  18. Microbes to Biomes at Berkeley Lab

    ScienceCinema

    None

    2016-07-12

    Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

  19. The bacterial transformation of abietic acid

    PubMed Central

    Cross, B. E.; Myers, P. L.

    1968-01-01

    An Alcaligenes species, which was isolated from soil, can utilize abietic acid as its sole carbon source. During growth, the bacterium transforms abietic acid into 5α-hydroxyabietic acid (I, R=OH), a product considered to be 7β-hydroxy-13-isopropyl-8ξ-podocarp-13-en-15-oic acid (II, R=H) and a compound, C20H28O3, which is believed to be an epoxy-γ-lactone. PMID:5665894

  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.

  1. The Mysterious Death: An HPLC Lab Experiment. An Undergraduate Forensic Lab

    ERIC Educational Resources Information Center

    Beussman, Douglas J.

    2007-01-01

    A high-performance liquid chromatography (HPLC) laboratory experiment based on the separation of four prescription drugs (disopyramide, lidocaine, procainamide, and quinidine) is presented. The experiment is set within the forensic science context of the discovery of a patient's mysterious death where a drug overdose is suspected. Each lab group…

  2. WetLab-2: Wet Lab RNA SmartCycler Providing PCR Capability on ISS

    NASA Technical Reports Server (NTRS)

    Parra, Macarena; Schonfeld, Julie

    2015-01-01

    The WetLab-2 system will provide sample preparation and qRT-PCR analysis on-board the ISS, a capability to enable using the ISS as a real laboratory. The system will be validated on SpX-7, and is planned for its first PI use on SpX-9.

  3. The Design of NetSecLab: A Small Competition-Based Network Security Lab

    ERIC Educational Resources Information Center

    Lee, C. P.; Uluagac, A. S.; Fairbanks, K. D.; Copeland, J. A.

    2011-01-01

    This paper describes a competition-style of exercise to teach system and network security and to reinforce themes taught in class. The exercise, called NetSecLab, is conducted on a closed network with student-formed teams, each with their own Linux system to defend and from which to launch attacks. Students are expected to learn how to: 1) install…

  4. OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework.

    PubMed

    List, Markus; Franz, Michael; Tan, Qihua; Mollenhauer, Jan; Baumbach, Jan

    2015-10-06

    Electronic laboratory notebooks (ELNs) are more accessible and reliable than their paper based alternatives and thus find widespread adoption. While a large number of commercial products is available, small- to mid-sized laboratories can often not afford the costs or are concerned about the longevity of the providers. Turning towards free alternatives, however, raises questions about data protection, which are not sufficiently addressed by available solutions. To serve as legal documents, ELNs must prevent scientific fraud through technical means such as digital signatures. It would also be advantageous if an ELN was integrated with a laboratory information management system to allow for a comprehensive documentation of experimental work including the location of samples that were used in a particular experiment. Here, we present OpenLabNotes, which adds state-of-the-art ELN capabilities to OpenLabFramework, a powerful and flexible laboratory information management system. In contrast to comparable solutions, it allows to protect the intellectual property of its users by offering data protection with digital signatures. OpenLabNotes effectively closes the gap between research documentation and sample management, thus making Open-LabFramework more attractive for laboratories that seek to increase productivity through electronic data management.

  5. MarsLab: A HEDS Lander Concept

    NASA Technical Reports Server (NTRS)

    Hecht, M. H.; McKay, C.; Connolly, J.

    2000-01-01

    Recognizing that the human exploration of Mars will be a science-focused enterprise, the Human Exploration and Development of Space (HEDS) program set out three years ago to develop a mix of science and technology Lander payloads as a first step toward a human mission. With three experiments ready for flight and four more in development, the HEDS Mars program has the capability to stage missions with considerable impact. This presentation describes one such mission design by no means unique. Ambitious in scope, it encompasses elements of all seven HEDS payloads in a configuration with a uniquely HEDS character. Pragmatically, a subset of these elements could be selected for existing small Lander platforms. Bristling with scientific experiments, technology demonstrations, and outreach elements, MarsLab represents a prototype of a manned science station or scientific outpost. A cartoon overview of MarsLab defines its major elements, explained more fully in the sections that follow. The concept is endorsed by PI's of the various HEDS payloads, details of which are presented elsewhere at this workshop.

  6. A Bernoulli's Law Lab in a Bottle:

    NASA Astrophysics Data System (ADS)

    David, Guerra; Plaisted, Aaron; Smith, Michael

    2004-03-01

    Bernoulli's law is a fundamental relationship in fluid dynamics, which is covered in most introductory physics classes. The concept is used to explain many important phenomena from fluid flow in pipes to aircraft flight. In an effort to help demonstrate the way in which Bernoulli's law is often applied in fluid dynamics, we have developed a laboratory exercise that employs a common physics lab motion sensor to measure the time it takes water to drain out of an inverted plastic seltzer bottle. Using a series of bottle caps with different sized holes drilled in them, students can easily measure the drain time for systems with different parameters. With the simple data analysis capabilities provided with the sensor students can attain good agreement between experiment and theory. This simple lab gives students an example of how Bernoulli's equation, the continuity equation (conservation of mass), and a few fundamental equations of kinematics can be combined to predict the behavior of a fluid dynamic system. In addition, a closer look at the data also provides an opportunity to discuss some of the subtleties of the system.

  7. PC/104 Embedded IOCs at Jefferson Lab

    SciTech Connect

    Jianxun Yan, Trent Allison, Sue Witherspoon, Anthony Cuffe

    2009-10-01

    Jefferson Lab has developed embedded IOCs based on PC/104 single board computers (SBC) for low level control systems. The PC/104 IOCs run EPICS on top of the RTEMS operating system. Two types of control system configurations are used in different applications, PC/104 SBC with commercial PC/104 I/O cards and PC/104 SBC with custom designed FPGA-based boards. RTEMS was built with CEXP shell to run on the PC/104 SBC. CEXP shell provides the function of dynamic object loading, which is similar to the widely used VxWorks operating system. Standard software configurations were setup for PC/104 IOC application development to provide a familiar format for new projects as well as ease the conversion of applications from VME based IOCs to PC/104 IOCs. Many new projects at Jefferson Lab are going to employ PC/104 SBCs as IOCs and some applications have already been running them for accelerator operations. The PC/104 - RTEMS IOC provides a free open source Real-Time Operating System (RTOS), low cost/maintenance, easily installed/ configured, flexible, and reliable solution for accelerator control and 12GeV Upgrade projects.

  8. On my association with Bell Labs

    NASA Astrophysics Data System (ADS)

    Sondhi, M. Mohan

    2001-05-01

    I joined the Acoustics Research department at Bell Labs in 1962, just eight days before AT&T launched the first communications satellite, Telstar. During the 39 years between 1962 and my retirement in 2001, I worked on several problems related in one way or another to the processing of speech signals. Schroeder and Flanagan are presenting talks from a broad perspective in this session, so I will confine this talk to just my own contributions and collaborations for some of the topics on which I worked, e.g., echo cancellation, inverse problems in acoustics, speech analysis, synthesis, and recognition. I will tell you about one of these contributions that fortunately turned out to yield considerable profits to AT&T. To give you a flavor of the spirit of free inquiry at Bell Labs during that period, I will tell you about the contribution that I am most proud of (which was supported for several years even though it had no monetary value). And I will also mention the contribution that is most often cited of all my papers (which was in collaboration with two mathematicians, and had nothing at all to do with acoustics).

  9. 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.

  10. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity

    PubMed Central

    Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A.

    2013-01-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645T was isolated from human subgingival dental plaque. Bacterial cells were 4–40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30–42 °C and 4.9–7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645T formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645T represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645T ( = HM-480T; deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

  11. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.

    PubMed

    Sizova, Maria V; Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A; Epstein, Slava S

    2013-04-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30-42 °C and 4.9-7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645(T) formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645(T) represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645(T) ( = HM-480(T); deposited in BEI Resources, an NIH collection managed by the ATCC).

  12. Phenolic Biotransformations during Conversion of Ferulic Acid to Vanillin by Lactic Acid Bacteria

    PubMed Central

    Kaur, Baljinder; Kumar, Balvir

    2013-01-01

    Vanillin is widely used as food additive and as a masking agent in various pharmaceutical formulations. Ferulic acid is an important precursor of vanillin that is available in abundance in cell walls of cereals like wheat, corn, and rice. Phenolic biotransformations can occur during growth of lactic acid bacteria (LAB), and their production can be made feasible using specialized LAB strains that have been reported to produce ferulic acid esterases. The present study aimed at screening a panel of LAB isolates for their ability to release phenolics from agrowaste materials like rice bran and their biotransformation to industrially important compounds such as ferulic acid, 4-ethyl phenol, vanillic acid, vanillin, and vanillyl alcohol. Bacterial isolates were evaluated using ferulic acid esterase, ferulic acid decarboxylase, and vanillin dehydrogenase assays. This work highlights the importance of lactic acid bacteria in phenolic biotransformations for the development of food grade flavours and additives. PMID:24066293

  13. 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.

  14. A Mutant Strain of a Surfactant-Producing Bacterium with Increased Emulsification Activity

    NASA Astrophysics Data System (ADS)

    Liu, Qingmei; Yao, Jianming; Pan, Renrui; Yu, Zengliang

    2005-06-01

    As reported in this paper, a strain of oil-degrading bacterium Sp-5-3 was determined to belong to Enterobacteriaceae, which would be useful for microbial enhanced oil recovery (MEOR). The aim of our study was to generate a mutant using low energy N+ beam implantation. With 10 keV of energy and 5.2 × 1014 N+/cm2 of dose - the optimum condition, a mutant, S-34, was obtained, which had nearly a 5-fold higher surface and a 13-fold higher of emulsification activity than the wild type. The surface activity was measured by two methods, namely, a surface tension measuring instrument and a recording of the repulsive circle of the oil film; the emulsification activity was scaled through measuring the separating time of the oil-fermentation mixture. The metabolic acid was determined as methane by means of gas chromatography.

  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. Continuous synthesis and excretion of the compatible solute ectoine by a transgenic, nonhalophilic bacterium.

    PubMed

    Schubert, Torsten; Maskow, Thomas; Benndorf, Dirk; Harms, Hauke; Breuer, Uta

    2007-05-01

    The compatible solute 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) acts in microorganisms as an osmotic counterweight against halostress and has attracted commercial attention as a protecting agent. Its production and application are restricted by the drawbacks of the discontinuous harvesting procedure involving salt shocks, which reduces volumetric yield, increases reactor corrosion, and complicates downstream processing. In order to synthesize ectoine continuously in less-aggressive media, we introduced the ectoine genes ectABC of the halophilic bacterium Chromohalobacter salexigens into an Escherichia coli strain using the expression vector pASK-IBA7. Under the control of a tet promoter, the transgenic E. coli synthesized 6 g liter-1 ectoine with a space-time yield of 40 mg liter-1 h-1, with the vast majority of the ectoine being excreted.

  17. Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961.

    PubMed

    González-García, Yolanda; Nungaray, Jesús; Córdova, Jesús; González-Reynoso, Orfil; Koller, Martin; Atlic, Aid; Braunegg, Gerhart

    2008-06-01

    The marine bacterium Saccharophagus degradans was investigated for the synthesis of polyhydroxyalkanoates (PHAs), using glucose as the sole source of carbon in a two-step batch culture. In the first step the microorganism grew under nutrient balanced conditions; in the second step the cells were cultivated under limitation of nitrogen source. The biopolymer accumulated in S. degradans cells was detected by Nile red staining and FT-IR analysis. From GC-MS analysis, it was found that this strain produced a homopolymer of 3-hydroxybutyric acid. The cellular polymer concentration, its molecular mass, glass transition temperature, melting point and heat of fusion were 17.2+/-2.7% of dry cell weight, 54.2+/-0.6 kDa, 37.4+/-6.0 degrees C, 165.6+/-5.5 degrees C and 59.6+/-2.2 J g(-1), respectively. This work is the first report determining the capacity of S. degradans to synthesize PHAs.

  18. Expression of multiple complex polysaccharide-degrading enzyme systems by marine bacterium strain 2-40.

    PubMed

    Ensor; Stosz; Weiner

    1999-08-01

    Saprophytic marine bacterium strain 2-40 (2-40) can degrade numerous complex polysaccharides (CP) including agar, alginic acid, carrageenan, carboxymethylcellulose, chitin, beta-glucan, laminarin, pectin, pullulan, starch, and xylan. The growth of 2-40 was assessed in minimal media containing one of 16 CP or simple carbohydrates, with the result that all supported growth. Each of the carbohydrase systems was elicited at highest levels by the homologous substrate. Each, excluding amylase, was repressed when 2-40 was cultured in glucose minimal synthetic media. Cyclic adenosine monophosphate alleviated the repression. Agarose as sole carbon source supported the synthesis of the most heterologous complex carbohydrase systems, although, generally, at a lower level of activity than the homologous CP.

  19. 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.

  20. 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.

  1. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.

    PubMed

    Bolotin, Alexander; Quinquis, Benoît; Renault, Pierre; Sorokin, Alexei; Ehrlich, S Dusko; Kulakauskas, Saulius; Lapidus, Alla; Goltsman, Eugene; Mazur, Michael; Pusch, Gordon D; Fonstein, Michael; Overbeek, Ross; Kyprides, Nikos; Purnelle, Bénédicte; Prozzi, Deborah; Ngui, Katrina; Masuy, David; Hancy, Frédéric; Burteau, Sophie; Boutry, Marc; Delcour, Jean; Goffeau, André; Hols, Pascal

    2004-12-01

    The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.

  2. Legionnaires' disease: isolation of a bacterium and demonstration of its role in other respiratory disease.

    PubMed

    McDade, J E; Shepard, C C; Fraser, D W; Tsai, T R; Redus, M A; Dowdle, W R

    1977-12-01

    To identify the etiologic agent of Legionnaire's disease, we examined patients' serum and tissue specimens in a search for toxins, bacteria, fungi, chlamydiae, rickettsiae and viruses. From the lungs of four of six patients we isolated a gram-negative, non-acid-fast bacillus in guinea pigs. The bacillus could be transferred to yolk sacs of embryonated eggs. Classification of this organism is incomplete. We used yolk-sac cultures of the bacillus as antigen to survey suspected serum specimens, employing antihuman-globulin fluorescent antibody. When compared to controls, specimens from 101 to 111 patients meeting clinical criteria of Legionnaires' disease showed diagnostic increases in antibody titers. Diagnostic increases were also found in 54 recent sporadic cases of severe pneumonia and, retrospectively, in stored serum from most patients in two other previously unsolved outbreaks of respiratory disease. We conclude that Legionnaires' disease is caused by a gram-negative bacterium that may be responsible for widespread infection.

  3. 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.

  4. Photocopy of photograph (original negative located in LBNL Photo Lab ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of photograph (original negative located in LBNL Photo Lab Collection). March 2005. BEVATRON SHIELDING - University of California Radiation Laboratory, Bevatron, 1 Cyclotron Road, Berkeley, Alameda County, CA

  5. The interventional cardiologist as cath lab team leader.

    PubMed

    Blankenship, James C; Feldman, Barry; Ranaweera, Priyantha; Dent, John; Huang, Xiaoyan; Singer, Sara

    2015-06-01

    Interventional cardiologists act as leaders every time they step into a catheterization laboratory (cath lab), but leadership training is rarely included in cardiology training programs. Cath lab physicians should cultivate and practice effective leadership skills. Specifically, (1) before each procedure assess whether the cath lab team is prepared; (2) delegate authority to trainees and team members when appropriate; (3) use every procedure to improve the performance of team members through teaching, coaching, and mentorship; (4) debrief the team after adverse events; (5) develop the traits, styles, and skills associated with successful leadership; and (6) provide team training for the cath lab team.

  6. Stream piracy in the Black Hills: A geomorphology lab exercise

    USGS Publications Warehouse

    Zaprowski, B.J.; Evenson, E.B.; Epstein, J.B.

    2002-01-01

    The Black Hills of South Dakota exhibits many fine examples of stream piracy that are very suitable for teaching geomorphology lab exercises. This lab goes beyond standard topographic map interpretation by using geologic maps, well logs, gravel provenance and other types of data to teach students about stream piracy. Using a step-by-step method in which the lab exercises ramp up in difficulty, students hone their skills in deductive reasoning and data assimilation. The first exercises deal with the identification of stream piracy at a variety of spatial scales and the lab culminates with an exercise on landscape evolution and drainage rearrangement.

  7. The History of Science and Technology at Bell Labs

    NASA Astrophysics Data System (ADS)

    Bishop, David

    2008-03-01

    Over the last 80 years, Bell Labs has been one of the most scientifically and technologically productive research labs in the world. Inventions such as the transistor, laser, cell phone, solar cell, negative feedback amplifier, communications satellite and many others were made there. Scientific breakthroughs such as discovery of the Big Bang, the wave nature of the electron, electron localization and the fractional quantum hall effect were also made there making Bell Labs almost unique in terms of large impacts in both science and technology. In my talk, I will discuss the history of the lab, talk about the present and give some suggestions for how I see it evolving into the future.

  8. Collaborative Environments to Support Professional Communities: A Living Lab Approach

    NASA Astrophysics Data System (ADS)

    Schaffers, Hans; Budweg, Steffen; Ruland, Rudolf; Kristensen, Kjetil

    The living labs approach within ECOSPACE focuses on early user community building and active user involvement in the process of developing, testing and evaluating new collaboration concepts and tools. This paper reports about implementing and evaluating the living labs approach to facilitate innovation in collaborative work environments to enhance professional communities. The living lab approach is considered as a strategy for innovation, change and adoption. The perspective of socio-technical systems is used to understand and explain the change-catalyzing role of the living lab approach.

  9. EPICS Channel Access Server for LabVIEW

    SciTech Connect

    Zhukov, Alexander P.

    2016-10-01

    It can be challenging to interface National Instruments LabVIEW (http://www.ni.com/labview/) with EPICS (http://www.aps.anl.gov/epics/). Such interface is required when an instrument control program was developed in LabVIEW but it also has to be part of global control system. This is frequently useful in big accelerator facilities. The Channel Access Server is written in LabVIEW, so it works on any hardware/software platform where LabVIEW is available. It provides full server functionality, so any EPICS client can communicate with it.

  10. Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.

    PubMed

    Feio, Maria J; Zinkevich, Vitaly; Beech, Iwona B; Llobet-Brossa, Enric; Eaton, Peter; Schmitt, Jürgen; Guezennec, Jean

    2004-09-01

    A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

  11. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga.

    PubMed

    Verma, Ashish; Ojha, Anup Kumar; Kumari, Parveen; Sundharam, Shiva S; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

    2016-12-01

    A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas. Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth (L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA-DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas, for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).

  12. Molecular Characterization and In Vitro Analyses of a Sporogenous Bacterium with Potential Probiotic Properties.

    PubMed

    Sen, Ramkrishna; Pal, Dibyarupa; Kodali, Vidya Prabhakar; Das, Subhasish; Ghosh, Sudip Kumar

    2010-10-01

    The Gram-positive thin rods of a Bacillus species were identified and designated as Bacillus coagulans RK - 02 through the standard microbiological and biochemical characterization procedures, followed by data analysis and comparison with the characteristics given in Bergey's manual of systematic bacteriology. The culture was further characterized and confirmed as Bacillus coagulans by 16S rDNA sequence analysis wherein about 755 nucleotides of 16S rDNA was amplified and cloned in pGEM-T vector and subsequently sequenced. Sequence was blasted against the nr database of NCBI. Multiple alignments were done with some selected and related sequences using Clustal W. Phylogenetic trees were drawn with the same software after the distances were determined by neighbor-joining algorithm. The in vitro studies on the probiotic properties demonstrated that our isolate could prove to be a potential probiotic with spore-forming and lactic acid-producing abilities coupled with acid and bile tolerance properties and antimicrobial action. In addition to these characteristics, the bacterium also produced enzymes such as amylase, cellulase, lipase, protease, lactase and catalase, which can help in improving digestion and overall health, alleviate lactose intolerance and remove oxidative stresses, required for the well-being of the consumers. In our previously reported studies, an exopolysaccharide (EPS), a probioactive molecule produced by the same bacterium, showed very significant antioxidant, antihyperglycemic and emulsification activities. Thus, Bacillus coagulans RK - 02 is a well-characterized promising probiotic for its potential commercial applications to pharmaceutical, nutraceutical and functional food formulations with care-free storage.

  13. EarthLabs Meet Sister Corita Kent

    NASA Astrophysics Data System (ADS)

    Quartini, E.; Ellins, K. K.; Cavitte, M. G.; Thirumalai, K.; Ledley, T. S.; Haddad, N.; Lynds, S. E.

    2013-12-01

    The EarthLabs project provides a framework to enhance high school students' climate literacy and awareness of climate change. The project provides climate science curriculum and teacher professional development, followed by research on students' learning as teachers implement EarthLabs climate modules in the classroom. The professional development targets high school teachers whose professional growth is structured around exposure to current climate science research, data observation collection and analysis. During summer workshops in Texas and Mississippi, teachers work through the laboratories, experiments, and hand-on activities developed for their students. In summer 2013, three graduate students from the University of Texas at Austin Institute for Geophysics with expertise in climate science participated in two weeklong workshops. The graduate students partnered with exemplary teacher leaders to provide scientific content and lead the EarthLabs learning activities. As an experiment, we integrated a visit to the Blanton Museum and an associated activity in order to motivate participants to think creatively, as well as analytically, about science. This exercise was inspired by the work and educational philosophy of Sister Corita Kent. During the visit to the Blanton Museum, we steered participants towards specific works of art pre-selected to emphasize aspects of the climate of Texas and to draw participants' attention to ways in which artists convey different concepts. For example, artists use of color, lines, and symbols conjure emotional responses to imagery in the viewer. The second part of the exercise asked participants to choose a climate message and to convey this through a collage. We encouraged participants to combine their experience at the museum with examples of Sister Corita Kent's artwork. We gave them simple guidelines for the project based on techniques and teaching of Sister Corita Kent. Evaluation results reveal that participants enjoyed the

  14. 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).

  15. 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.

  16. 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.

  17. Isolation and Characterization of a Chlorinated-Pyridinol-Degrading Bacterium

    PubMed Central

    Feng, Y.; Racke, K. D.; Bollag, J.

    1997-01-01

    The isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (TCP) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. The bacterium was identified as a Pseudomonas sp. and designated ATCC 700113. [2,6-(sup14)C]TCP degradation yielded (sup14)CO(inf2), chloride, and unidentified polar metabolites. PMID:16535719

  18. Initiation of Chromosomal Replication in Predatory Bacterium Bdellovibrio bacteriovorus

    PubMed Central

    Makowski, Łukasz; Donczew, Rafał; Weigel, Christoph; Zawilak-Pawlik, Anna; Zakrzewska-Czerwińska, Jolanta

    2016-01-01

    Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase) and replicating cells (the intracellular-growth phase). The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although, we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC) is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box [5′-NN(A/T)TCCACA-3′]. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus). We compared the architecture of the DnaA–oriC complexes (orisomes) in homologous (oriC and DnaA from B. bacteriovorus) and heterologous (BdoriC and DnaA from prey, Escherichia coli or Pseudomonas aeruginosa) systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium. PMID:27965633

  19. [Fractionation of sulfur isotopes by phototrophic sulfur bacterium Ectothiorhodospira shaposhnikovii].

    PubMed

    Ivanov, M V; Gogotova, G I; Matrosov, A G; Ziakun, A M

    1976-01-01

    Two processes of sulphur isotope fractionation have been found in experiments with the sulphur purple bacterium Ectothiorhodospira shaposhnikovii. As a result, a light isotope, 32S, is concentrated in residual hydrogen sulphide, and a heavy isotope, 34S, in elementary suphur which is deposited outside the cell. The sulphate produced is lighter than elementary sulphur. Fractionation of sulphur isotopes is observed in natural conditions and is confined to places of mass growth of photosynthetic sulphur bacteria.

  20. Nucleon Form Factors - A Jefferson Lab Perspective

    SciTech Connect

    John Arrington, Kees de Jager, Charles F. Perdrisat

    2011-06-01

    The charge and magnetization distributions of the proton and neutron are encoded in their elastic electromagnetic form factors, which can be measured in elastic electron--nucleon scattering. By measuring the form factors, we probe the spatial distribution of the proton charge and magnetization, providing the most direct connection to the spatial distribution of quarks inside the proton. For decades, the form factors were probed through measurements of unpolarized elastic electron scattering, but by the 1980s, progress slowed dramatically due to the intrinsic limitations of the unpolarized measurements. Early measurements at several laboratories demonstrated the feasibility and power of measurements using polarization degrees of freedom to probe the spatial structure of the nucleon. A program of polarization measurements at Jefferson Lab led to a renaissance in the field of study, and significant new insight into the structure of matter.

  1. Characterization of Tri-lab Tantalum Plate.

    SciTech Connect

    Buchheit, Thomas E.; Cerreta, Ellen K.; Deibler, Lisa Anne; Chen, Shu-Rong; Michael, Joseph R.

    2014-09-01

    This report provides a detailed characterization Tri-lab Tantalum (Ta) plate jointly purchased from HCStark Inc. by Sandia, Los Alamos and Lawrence Livermore National Laboratories. Data in this report was compiled from series of material and properties characterization experiments carried out at Sandia (SNL) and Los Alamos (LANL) Laboratories through a leveraged effort funded by the C2 campaign. Results include microstructure characterization detailing the crystallographic texture of the material and an increase in grain size near the end of the rolled plate. Mechanical properties evaluations include, compression cylinder, sub-scale tension specimen, micohardness and instrumented indentation testing. The plate was found to have vastly superior uniformity when compare with previously characterized wrought Ta material. Small but measurable variations in microstructure and properties were noted at the end, and at the top and bottom edges of the plate.

  2. Wuenscher Examines Sky lab Experiment Facility

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Hans F. Wuenscher, assistant director for Advanced Space Projects Engineering Laboratory at Marshall Space Flight Center (MSFC), examined the facility to be used by Skylab astronauts in performing a number of experiments in material science and manufacturing in space. The equipment shown here is a duplicate of the M512 Experiment hardware flown in the Multiple Docking Adapter section of the Sky lab. This equipment, itself an experiment, was be used for conducting 5 other experiments in the round vacuum chamber. Inside was a cavity which held the M518 Multipurpose Electric Furnace, a facility which was used for conducting other experiments. In all, a total of 17 experiments were conducted using this facility and furnace.

  3. Smartphones as portable oscilloscopes for physics labs

    NASA Astrophysics Data System (ADS)

    Forinash, Kyle; Wisman, Raymond F.

    2012-04-01

    Given that today's smartphones are mobile and have more computing power and means to measure the external world than early PCs, they may also revolutionize data collection, both in structured physics laboratory settings and in less predictable situations, outside the classroom. Several examples using the internal sensors available in a smartphone were presented in earlier papers in this column.1, 2 But data collection is not limited only to the phone's internal sensors since most also have a headphone port for connecting an external microphone and speakers. This port can be used to connect to external equipment in much the same way as the game port on the early Apple II was used in school labs. Below is an illustration using the headphone port to receive data from an external circuit: smartphones as a portable oscilloscope using commercially available hardware and applications.

  4. Making the Case for Jefferson Lab

    NASA Astrophysics Data System (ADS)

    Gross, Franz

    2011-05-01

    This chapter is a personal account of the initial planning and competition for a new laboratory, which eventually became known as the Thomas Jefferson National Accelerator Facility, with the official nickname "Jefferson Lab." The period covered starts as far back as 1964, with the introduction of quarks, and extends up to the late 1980s after the initial team was assembled, the superconducting design was in place, and construction was well underway. I describe some of the major experiments that were proposed to justify the laboratory, reflect on the present status of those initially proposed experiments, and very briefly outline some of the new ideas that emerged after the laboratory was constructed. The science is presented in a simple manner intended for a lay audience, with some of the ideas illustrated by cartoons that were often used in popular lectures given during this period.

  5. Toward Better Physics Labs for Future Biologists

    NASA Astrophysics Data System (ADS)

    Giannini, John; Moore, Kim; Losert, Wolfgang

    2014-03-01

    We have developed a set of laboratories and hands on activities to accompany a new two-semester interdisciplinary physics course that has been successfully developed and tested in two small test classes of students at the University of Maryland, College Park (UMD) in 2012-2013, and is currently being used on a wider scale. We have designed the laboratories to be taken accompanying a reformed course in the student's second year, with calculus, biology, and chemistry as prerequisites. This permits the laboratories to include significant content on physics relevant to cellular scales, from chemical interactions to random motion and charge screening in fluids. One major focus of the laboratories is to introduce the students to research-grade equipment and modern physics analysis tools in contexts relevant to biology, while maintaining the pedagogically valuable open-ended laboratory structure of reformed laboratories. Lab development procedures along with some preliminary student results from these two small test classes are discussed.

  6. Nucleon spin structure at Jefferson Lab

    SciTech Connect

    Angela Biselli

    2011-10-01

    In the past decade an extensive experimental program to measure the spin structure of the nucleon has been carried out in the three halls at Jefferson Lab. Using a longitudinally polarized beam scattering off longitudinally or transversely polarized 3He, NH3 and ND3 targets, the double spin asymmetries A|| and A[perpendicular] were measured, providing data of impressively high precision that gives a better understanding of the structure of the nucleon in the deep inelastic scattering and the valence quarks regions. The virtual photon asymmetries A1,2 and polarized structure functions g1,2 were also extracted for the proton, neutron and deuteron over large kinematic ranges, allowing the extraction of first moments and the testing of sum rules and duality.

  7. Making the Case for Jefferson Lab

    SciTech Connect

    Gross, Franz

    2011-06-01

    This chapter is a personal account of the initial planning and competition for a new laboratory, which eventually became known as the Thomas Jefferson National Accelerator Facility, with the official nickname "Jefferson Lab." The period covered starts as far back as 1964, with the introduction of quarks, and extends up to the late 1980s after the initial team was assembled, the superconducting design was in place, and construction was well underway. I describe some of the major experiments that were proposed to justify the laboratory, reflect on the present status of those initially proposed experiments, and very briefly outline some of the new ideas that emerged after the laboratory was constructed. The science is presented in a simple manner intended for a lay audience, with some of the ideas illustrated by cartoons that were often used in popular lectures given during this period.

  8. Transversity and SIDIS at Jefferson Lab

    SciTech Connect

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

    2005-02-01

    Remarkable progress in the study of spin-dependent structure functions has been made since the discovery of the ''proton spin puzzle'' in the late 1980's. Very active spin-physics programs have been pursued at many facilities including SLAC, CERN, HERA, JLab, and RHIC. In recent years, new experimental tools such as semi-inclusive polarized DIS, polarized proton-proton collision, and deeply exclusive reactions have been employed to address various aspects of the proton spin. In this paper, we present the plans at the Jefferson Lab to use the semi-inclusive DIS (SIDIS) reactions to measure various unpolarized and polarized nucleon parton distribution and fragmentation functions. In addition, the prospect of probing the flavor structure of the kaon fragmentation function is discussed.

  9. The Jefferson Lab frozen spin target

    NASA Astrophysics Data System (ADS)

    Keith, C. D.; Brock, J.; Carlin, C.; Comer, S. A.; Kashy, D.; McAndrew, J.; Meekins, D. G.; Pasyuk, E.; Pierce, J. J.; Seely, M. L.

    2012-08-01

    A frozen spin polarized target, constructed at Jefferson Lab for use inside a large acceptance spectrometer, is described. The target has been utilized for photoproduction measurements with polarized tagged photons of both longitudinal and circular polarization. Protons in TEMPO-doped butanol were dynamically polarized to approximately 90% outside the spectrometer at 5 T and 200-300 mK. Photoproduction data were acquired with the target inside the spectrometer at a frozen-spin temperature of approximately 30 mK with the polarization maintained by a thin, superconducting coil installed inside the target cryostat. A 0.56 T solenoid was used for longitudinal target polarization and a 0.50 T dipole for transverse polarization. Spin-lattice relaxation times as high as 4000 h were observed. We also report polarization results for deuterated propanediol doped with the trityl radical OX063.

  10. The SPARC_LAB Thomson source

    NASA Astrophysics Data System (ADS)

    Vaccarezza, C.; Alesini, D.; Anania, M. P.; Bacci, A.; Biagioni, A.; Bisesto, F.; Bellaveglia, M.; Cardarelli, P.; Cardelli, F.; Cianchi, A.; Chiadroni, E.; Croia, M.; Curcio, A.; Delogu, P.; Giovenale, D. Di; Domenico, G. Di; Pirro, G. Di; Drebot, I.; Ferrario, M.; Filippi, F.; Gallo, A.; Galletti, M.; Gambaccini, M.; Giribono, A.; Golosio, B.; Li, W.; Mostacci, A.; Oliva, P.; Palmer, D.; Petrillo, V.; Petrarca, M.; Pioli, S.; Piersanti, L.; Pompili, R.; Romeo, S.; Rossi, A. R.; Scifo, J.; Serafini, L.; Suliman, G.; Villa, F.

    2016-09-01

    The SPARC_LAB Thomson source is a compact X-ray source based on the Thomson backscattering process presently under its second phase of commissioning at the LNF. The electron beam energy ranges between 30 and 150 MeV, the electrons collide head-on with the Ti:Sapphire FLAME laser pulse the energy of which ranges between 1 and 5 J with pulse lengths in the 25 fs-10 ps range, this provides an X-ray energy tunability in the range of 20-500 keV, with the further capability to generate strongly non-linear phenomena and to drive diffusion processes due to multiple and plural scattering effects. The experimental results of the obtained X-ray radiation are presented.

  11. The Jefferson Lab Frozen Spin Target

    SciTech Connect

    Christopher Keith, James Brock, Christopher Carlin, Sara Comer, David Kashy, Josephine McAndrew, David Meekins, Eugene Pasyuk, Joshua Pierce, Mikell Seely

    2012-08-01

    A frozen spin polarized target, constructed at Jefferson Lab for use inside a large acceptance spectrometer, is described. The target has been utilized for photoproduction measurements with polarized tagged photons of both longitudinal and circular polarization. Protons in TEMPO-doped butanol were dynamically polarized to approximately 90% outside the spectrometer at 5 T and 200-300 mK. Photoproduction data were acquired with the target inside the spectrometer at a frozen-spin temperature of approximately 30 mK with the polarization maintained by a thin, superconducting coil installed inside the target cryostat. A 0.56 T solenoid was used for longitudinal target polarization and a 0.50 T dipole for transverse polarization. Spin relaxation times as high as 4000 hours were observed. We also report polarization results for deuterated propanediol doped with the trityl radical OX063.

  12. The Jefferson Lab High Power Light Source

    SciTech Connect

    James R. Boyce

    2006-01-01

    Jefferson Lab has designed, built and operated two high average power free-electron lasers (FEL) using superconducting RF (SRF) technology and energy recovery techniques. Between 1999-2001 Jefferson Lab operated the IR Demo FEL. This device produced over 2 kW in the mid-infrared, in addition to producing world record average powers in the visible (50 W), ultraviolet (10 W) and terahertz range (50 W) for tunable, short-pulse (< ps) light. This FEL was the first high power demonstration of an accelerator configuration that is being exploited for a number of new accelerator-driven light source facilities that are currently under design or construction. The driver accelerator for the IR Demo FEL uses an Energy Recovered Linac (ERL) configuration that improves the energy efficiency and lowers both the capital and operating cost of such devices by recovering most of the power in the spent electron beam after optical power is extracted from the beam. The IR Demo FEL was de-commissioned in late 2001 for an upgraded FEL for extending the IR power to over 10 kW and the ultraviolet power to over 1 kW. The FEL Upgrade achieved 10 kW of average power in the mid-IR (6 microns) in July of 2004, and its IR operation currently is being extended down to 1 micron. In addition, we have demonstrated the capability of on/off cycling and recovering over a megawatt of electron beam power without diminishing machine performance. A complementary UV FEL will come on-line within the next year. This paper presents a summary of the FEL characteristics, user community accomplishments with the IR Demo, and planned user experiments.

  13. Lab-on a-Chip

    NASA Technical Reports Server (NTRS)

    1999-01-01

    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 (ISS). 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. The portable, handheld Lab-on-a Chip Application Development Portable Test System (LOCAD-PTS) made its debut flight aboard Discovery during the STS-116 mission launched December 9, 2006. The system allowed crew members to monitor their environment for problematic contaminants such as yeast, mold, and even E.coli, and salmonella. Once LOCAD-PTS reached the ISS, the Marshall team continued to manage the experiment, monitoring the study from a console in the Payload Operations Center at MSFC. The results of these studies will help NASA researchers refine the technology for future Moon and Mars missions. (NASA/MSFC/D.Stoffer)

  14. Selection and use of phytate-degrading LAB to improve cereal-based products by mineral solubilization during dough fermentation.

    PubMed

    Anastasio, Marilena; Pepe, Olimpia; Cirillo, Teresa; Palomba, Simona; Blaiotta, Giuseppe; Villani, Francesco

    2010-01-01

    New producers of phytate-degrading enzymes, especially lactic acid bacteria (LAB), were used to improve mineral solubilization during dough fermentation. In all, among strains from different sources by microorganisms (150 lactic acid bacteria, 36 yeasts), 38 (24%) exhibited a clear zone around the colonies by hydrolyzing hexacalcium phytate contained in solid medium. When phytase-positive strains from plate assay were tested for phytase activity in liquid medium, 6 of the strains (37%) exhibited phytate-degrading activity in at least one of the 3 different media used. Of the LAB, the highest phytase values were found for Enterococcus faecium A86 (0.74 U/mL) and Lactobacillus plantarum H5 (0.71 U/mL). Two different starter cultures obtained by combinations of phytase-positive (phy+: L. plantarum H5 and L3, Leuconostoc gelidum A16, and E. faecium A86) or phytase-negative (phy-: L. gelidum LM249, L. plantarum H19, and L. plantarum L8) selected LAB strains, were used to measure mineral concentrations of iron, zinc, and manganese during dough fermentation. Although the 2 kinds of starter showed similar acidic values, the presence of phytate-degrading LAB strains increased mineral solubilization in comparison to the starter phy-.

  15. Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea.

    PubMed

    Chi, Won-Jae; Youn, Young Sang; Park, Jae-Seon; Hong, Soon-Kwang

    2015-07-01

    A xylan-degrading bacterium, designated as MS5(T) strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5(T) was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035(T) (98.7%) and Bacillus korlensis ZLC-26(T) (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5(T) was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5(T) and two closely related species, B. beringensis BR035(T) and B. korlensis ZLC-26(T), were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5(T) constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5(T) (=DSM25506(T) =KCTC13895(T)).

  16. Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

    PubMed Central

    Crusoe, Michael R.; Brown, C. Titus

    2016-01-01

    The khmer software project provides both research and production functionality for largescale nucleic-acid sequence analysis. The software implements several novel data structures and algorithms that perform data pre-fltering for common bioinformatics tasks, including sequence mapping and de novo assembly. Development is driven by a small lab with one full-time developer (MRC), as well as several graduate students and a professor (CTB) who contribute regularly to research features. Here we describe our efforts to bring better design, testing, and more open development to the khmer software project as of version 1.1. The khmer software is developed openly at http://github.com/dib-lab/khmer/. PMID:27942385

  17. Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii.

    PubMed

    Basen, Mirko; Rhaesa, Amanda M; Kataeva, Irina; Prybol, Cameron J; Scott, Israel M; Poole, Farris L; Adams, Michael W W

    2014-01-01

    The thermophilic bacterium Caldicellulosiruptor bescii grows at 78 °C on high concentrations (200 g L(-1)) of both crystalline cellulose and unpretreated switchgrass, while low concentrations (<20 g L(-1)) of acid-pretreated switchgrass inhibit growth. Degradation of crystalline cellulose, but not that of unpretreated switchgrass, was limited by nitrogen and vitamin (folate) availability. Under optimal conditions, C. bescii solubilized approximately 60% of the crystalline cellulose and 30% of the unpretreated switchgrass using initial substrate concentrations of 50 g L(-1). Further fermentation of crystalline cellulose and of switchgrass was inhibited by organic acid end-products and by a specific inhibitor of C. bescii growth that did not affect other thermophilic bacteria, respectively. Soluble mono- and oligosaccharides, organic acids, carbon dioxide, and microbial biomass, quantitatively accounted for the crystalline cellulose and plant biomass carbon utilized. C. bescii therefore degrades industrially-relevant concentrations of lignocellulosic biomass that have not undergone pretreatment thereby demonstrating its potential utility in biomass conversion.

  18. 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.

  19. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Rhee, Moon-Soo; Kwon, O-Yu; Shin, Kee-Sun

    2009-10-01

    A novel cellulolytic bacterium, strain S23(T), was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, alpha-galactosidase, and beta-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C(15:0) (51.9%), iso-C(16:0) (14.7%), and iso-C(15:0) (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23(T) and other Paenibacillus species were between 89.9% and 95.9%, and S23(T) was most closely related to Paenibacillus tarimensis SA-7-6(T). On the basis of phylogenetic and phenotypic properties of strain S23(T), the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23(T) (=KCTC 13695(T) =KACC 14199(T) =JCM 16419(T)).

  20. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

    PubMed

    Wang, Dan-Dan; Kim, Yeon-Ju; Hoang, Van-An; Nguyen, Ngoc-Lan; Singh, Priyanka; Wang, Chao; Chun-Yang, Deok

    2016-04-01

    A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).

  1. 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

  2. Connecting phenome to genome in Pseudomonas stutzeri 5190: an artwork biocleaning bacterium.

    PubMed

    Bosch-Roig, Pilar; Decorosi, Francesca; Giovannetti, Luciana; Ranalli, Giancarlo; Viti, Carlo

    Research on biotechnology applications for cultural heritage restoration has shown how microorganisms can be efficient at cleaning particularly complex or ingrained substances through the process called "biocleaning". Bacteria are able to synthesize groups of specific enzymes for the degradation of complex materials present on artwork. Biocleaning has been shown to be less hazardous than some traditional mechanical or chemical techniques for the artwork, to be environmentally-friendly and safe for restorers to use. In order to improve our knowledge of the metabolic mechanisms involved in biocleaning, we analyzed the relationship between the genome and phenome of Pseudomonas stutzeri 5190 in order to identify and confirm the benefits and drawbacks of this bacterium used on on-site artwork as a biocleaning agent. Main phenotype microarray (PM) assays showed that P. stutzeri 5190 was able to use: i) 51 of the 190 carbon sources tested, where 32 were used efficiently, among which there were six amino acids (l-proline, l-alanine, d-alanine, l-glutamic acid, l-asparagine and l-glutamine); ii) 74 of the 95 nitrogen sources tested, where 50 compounds were used efficiently, among which were 28 amino acids and the inorganic nitrate and nitrite compounds, supporting the hypothesis of the strain's ability to remove nitrate salt efflorescence from frescoes. Furthermore, high tolerance to osmotic stress, to basic pH and to toxic compounds was revealed by PM. Putative genes compatible with these phenotypes are described.

  3. 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.

  4. Cloning, expression, and characterization of a new phytase from the phytopathogenic bacterium Pectobacterium wasabiae DSMZ 18074.

    PubMed

    Shao, Na; Huang, Huoqing; Meng, Kun; Luo, Huiying; Wang, Yaru; Yang, Peilong; Yao, Bin

    2008-07-01

    The soft rot bacterium Pectobacterium wasabiae is an economically important pathogen of many crops. A new phytase gene, appA, was cloned from P. wasabiae by degenerate PCR and TAIL-PCR. The open reading frame of appA consisted of 1,302 bp encoding 433 amino acid residues, including 27 residues of a putative signal peptide. The mature protein had a molecular mass of 45 kDa and a theoretical pI of 5.5. The amino acid sequence contained the conserved active site residues RHGXRXP and HDTN of typical histidine acid phosphatases, and showed the highest identity of 48.5% to PhyM from Pseudomonas syringae. The gene fragment encoding the mature phytase was expressed in Escherichia coli BL21 (DE3), and the purified recombinant phytase had a specific activity of 1,072+/-47 U/mg for phytate substrate. The optimum pH and temperature for the purified phytase were pH 5.0 and 50 degrees C, respectively. The Km value was 0.17 mM, with a Vmax of 1,714 micromol/min/mg. This is the first report of the identification and isolation of phytase from Pectobacterium.

  5. Being a Clinical Psychologist at the Lab School of Baltimore

    ERIC Educational Resources Information Center

    Oliver, Edwin

    2010-01-01

    Each day, seeking to address the never ending challenge of helping students with learning disabilities, the author's Baltimore Lab School and Lab School of Washington (LSW) colleagues remember a similar situation in the past and they try to recall what Sally Smith taught them. Smith taught the author a lot in his seven years of working with…

  6. Incorporating a Career Planning Lab into a Managerial Communications Course

    ERIC Educational Resources Information Center

    May, Gary L.

    2005-01-01

    This article describes how a small business school, as part of a strategic planning initiative to improve career services, added a self-directed career planning lab to an existing managerial communication course. The lab concept and the learning design are innovative because they met a student need without creating additional time demands on the…

  7. Development and Implementation of a Lab Course for Introductory Astronomy

    ERIC Educational Resources Information Center

    McCrady, Nate; Rice, Emily

    2008-01-01

    The typical "Astro 101" lecture-based course is passive, and adding well-designed learner-centered labs allows students to experience science as a pattern of thought. In this article, we present an approach to developing an introductory lab course. Identification of goals and student outcomes, particularly skills, and process and attitudinal…

  8. Engineering Students' Experiences from Physics Group Work in Learning Labs

    ERIC Educational Resources Information Center

    Mellingsaeter, Magnus Strøm

    2014-01-01

    Background: This paper presents a case study from a physics course at a Norwegian university college, investigating key aspects of a group-work project, so-called learning labs, from the participating students' perspective. Purpose: In order to develop these learning labs further, the students' perspective is important. Which aspects are essential…

  9. Implementation of Siemens USS protocol into LabVIEW.

    PubMed

    Hosek, P; Diblik, M

    2011-10-01

    This article gives basic overview of the USS protocol as a communication interface to drive Siemens frequency inverters. It presents our implementation of this protocol into LabVIEW, as there was permanent demand from the community of the users to have native LabVIEW implementation of the USS protocol. It also states encountered problems and their solutions.

  10. Time Trials--An AP Physics Challenge Lab

    ERIC Educational Resources Information Center

    Jones, David

    2009-01-01

    I have come to the conclusion that for high school physics classroom and laboratory experiences, simpler is better! In this paper I describe a very simple and effective lab experience that my AP students have thoroughly enjoyed year after year. I call this lab exercise "Time Trials." The experiment is simple in design and it is a lot of fun for…

  11. A Computer Lab that Students Use but Never See

    ERIC Educational Resources Information Center

    Young, Jeffrey R.

    2008-01-01

    North Carolina State University may never build another computer lab. Instead the university has installed racks of equipment in windowless rooms where students and professors never go. This article describes a project called the Virtual Computing Lab. Users enter it remotely from their own computers in dormitory rooms or libraries. They get all…

  12. LIVING LAB: User-Driven Innovation for Sustainability

    ERIC Educational Resources Information Center

    Liedtke, Christa; Welfens, Maria Jolanta; Rohn, Holger; Nordmann, Julia

    2012-01-01

    Purpose: The purpose of this paper is to summarize and discuss the results from the LIVING LAB design study, a project within the 7th Framework Programme of the European Union. The aim of this project was to develop the conceptual design of the LIVING LAB Research Infrastructure that will be used to research human interaction with, and stimulate…

  13. The Technology Teaching Lab: Meeting the ISTE Challenge.

    ERIC Educational Resources Information Center

    Bucci, Terri Teal

    2003-01-01

    Assessed whether preservice teachers could reach the expectations of the ISTE Profile Standards for Professional Performance through participation in technology teaching labs (2-hour labs running concurrently with preservice methods blocks), noting types of technology infusion used to meet the standards and students' perceived ability following…

  14. What is the purpose of undergraduate physics labs?

    NASA Astrophysics Data System (ADS)

    Sams, William; Paesler, Michael; Chafin, Cliff

    2011-10-01

    In recent years, enrollment in undergraduate physics courses at NC State has grown significantly, especially in introductory physics. Since most of these courses involve a laboratory component, the increased enrollment is leading to a shortage of laboratory space. Starting this spring NC State will implement kit labs in calculus-based mechanics labs. These kits will make it possible for students to have laboratory experiences outside of the standard lab rooms, decreasing space demands. During the implementation the kit labs will be evaluated with an instrument developed for this purpose. This paper discusses the first step of designing this instrument, determining what the specific goals and purposes of the labs are. Literature reviews have led to focus on three primary areas where students should make gains during lab: content knowledge, scientific process, and affect. Physics faculty members were surveyed to identify specific areas considered important for our labs. Using results from our survey and published literature we have developed a specific set of goals for our labs, and we are using this to guide the development of our assessment instrument.

  15. The Multisensory Sound Lab: Sounds You Can See and Feel.

    ERIC Educational Resources Information Center

    Lederman, Norman; Hendricks, Paula

    1994-01-01

    A multisensory sound lab has been developed at the Model Secondary School for the Deaf (District of Columbia). A special floor allows vibrations to be felt, and a spectrum analyzer displays frequencies and harmonics visually. The lab is used for science education, auditory training, speech therapy, music and dance instruction, and relaxation…

  16. Online Writing Labs as Sites for Community Engagement

    ERIC Educational Resources Information Center

    Wells, Jaclyn Michelle

    2010-01-01

    This dissertation investigates the Community Writing and Education Station (CWEST), a community engagement project that partners a community adult basic literacy program with a university writing lab. The author argues that the community and university partners, the Lafayette Adult Resource Academy (LARA) and the Purdue Writing Lab, offer positive…

  17. Letters Home as an Alternative to Lab Reports

    ERIC Educational Resources Information Center

    Lane, W. Brian

    2014-01-01

    The traditional lab report is known to create several pedagogical shortcomings in the introductory physics course, particularly with regard to promoting student engagement and encouraging quality writing. This paper discusses the use of a "letter home" written to a non-physicist as an alternative to lab reports that creates a more…

  18. Networking Labs in the Online Environment: Indicators for Success

    ERIC Educational Resources Information Center

    Lahoud, Hilmi A.; Krichen, Jack P.

    2010-01-01

    Several techniques have been used to provide hands-on educational experiences to online learners, including remote labs, simulation software, and virtual labs, which offer a more structured environment, including simulations and scheduled asynchronous access to physical resources. This exploratory study investigated how these methods can be used…

  19. Macromolecules Inquiry: Transformation of a Standard Biochemistry Lab

    ERIC Educational Resources Information Center

    Unsworth, Elizabeth

    2014-01-01

    Identification of macromolecules in food is a standard introductory high school biology lab. The intent of this article is to describe the conversion of this standard cookbook lab into an inquiry investigation. Instead of verifying the macromolecules found in food, students use their knowledge of the macromolecules in food to determine the…

  20. Genomics Education in Practice: Evaluation of a Mobile Lab Design

    ERIC Educational Resources Information Center

    Van Mil, Marc H. W.; Boerwinkel, Dirk Jan; Buizer-Voskamp, Jacobine E.; Speksnijder, Annelies; Waarlo, Arend Jan

    2010-01-01

    Dutch genomics research centers have developed the "DNA labs on the road" to bridge the gap between modern genomics research practice and secondary-school curriculum in the Netherlands. These mobile DNA labs offer upper-secondary students the opportunity to experience genomics research through experiments with laboratory equipment that…