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Sample records for psychrophilic enrichment cultures

  1. Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core

    NASA Technical Reports Server (NTRS)

    Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

    2003-01-01

    The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.

  2. Phylogenetic Analysis of Anaerobic Psychrophilic Enrichment Cultures Obtained from a Greenland Glacier Ice Core

    PubMed Central

    Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

    2003-01-01

    The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at −9°C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 × 107 cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at −2°C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years. PMID:12676695

  3. Psychrophiles

    NASA Astrophysics Data System (ADS)

    Siddiqui, Khawar S.; Williams, Timothy J.; Wilkins, David; Yau, Sheree; Allen, Michelle A.; Brown, Mark V.; Lauro, Federico M.; Cavicchioli, Ricardo

    2013-05-01

    Psychrophilic (cold-adapted) microorganisms make a major contribution to Earth's biomass and perform critical roles in global biogeochemical cycles. The vast extent and environmental diversity of Earth's cold biosphere has selected for equally diverse microbial assemblages that can include archaea, bacteria, eucarya, and viruses. Underpinning the important ecological roles of psychrophiles are exquisite mechanisms of physiological adaptation. Evolution has also selected for cold-active traits at the level of molecular adaptation, and enzymes from psychrophiles are characterized by specific structural, functional, and stability properties. These characteristics of enzymes from psychrophiles not only manifest in efficient low-temperature activity, but also result in a flexible protein structure that enables biocatalysis in nonaqueous solvents. In this review, we examine the ecology of Antarctic psychrophiles, physiological adaptation of psychrophiles, and properties of cold-adapted proteins, and we provide a view of how these characteristics inform studies of astrobiology.

  4. Culture-independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments.

    PubMed

    Abreu, Fernanda; Carolina, Ana; Araujo, V; Leão, Pedro; Silva, Karen Tavares; Carvalho, Fabíola Marques de; Cunha, Oberdan de Lima; Almeida, Luiz Gonzaga; Geurink, Corey; Farina, Marcos; Rodelli, Daniel; Jovane, Luigi; Pellizari, Vivian H; Vasconcelos, Ana Tereza de; Bazylinski, Dennis A; Lins, Ulysses

    2016-12-01

    Magnetotactic bacteria (MTB) are a heterogeneous group of ubiquitous aquatic microorganisms capable of biomineralizing nano-sized, membrane-bound, magnetic iron-rich mineral particles called magnetosomes. MTB are found in chemically-stratified aquatic sediments and/or water columns with a wide range of salinities, moderate to high temperatures, and pH varying from neutral to strongly alkaline. MTB from very cold environments have not been investigated to any great degree and here we characterize MTB from the low temperature Antarctic maritime region. Sediment samples were collected at nine sampling sites within Admiralty Bay, King George Island (62°23'S 58°27'W) from 2009 to 2013. Samples from five sites contained MTB and those from two of these sites contained large number of magnetotactic cocci that were studied using electron microscopy and molecular techniques. The magnetotactic cocci contained magnetosomes either arranged as two or four chains or as a disorganized cluster. The crystalline habit and composition of all magnetosomes analyzed with high-resolution transmission electron microscopy and energy dispersive X-ray microanalysis were consistent with elongated prismatic crystals of magnetite (Fe3 O4 ). The retrieved 16S rRNA gene sequences from magnetically-enriched magnetotactic cocci clustered into three distinct groups affiliated with the Alphaproteobacteria class of the Proteobacteria. Novel sequences of each phylogenetic cluster were confirmed using fluorescent in situ hybridization. Metagenomic data analysis of magnetically-enriched magnetotactic cocci revealed the presence of mam genes and MTB-specific hypothetical protein coding genes. Sequence homology and phylogenetic analysis indicated that predicted proteins are related to those of cultivated alphaproteobacterial MTB. The consistent and continuous low temperature of the sediment where the magnetotactic cocci are present (always below 1°C) suggests that these MTB from maritime Antarctica are

  5. Cultural Enrichment through Community Action.

    ERIC Educational Resources Information Center

    Wilson, O. J.

    This project was conceived as a technique for helping to eliminate a cultural void in the areas of art, music, and theatre in the service area of Western Kentucky University. To implement this concept, demonstrations were conducted in art, music, theatre, and in library and lecture resources in 16 counties over a four-year period. The attendance…

  6. CUE (CULTURE, UNDERSTANDING, ENRICHMENT)--SCIENCE.

    ERIC Educational Resources Information Center

    BROWN, ROBERT M.; AND OTHERS

    THIS PUBLICATION IS A TEACHING GUIDE TO PROVIDE GUIDANCE FOR INTEGRATING CAREFULLY SELECTED AUDIOVISUAL ITEMS INTO EXISTING NINTH-GRADE CURRICULUMS IN SCIENCE. IT IS ONE OF FIVE GUIDES PREPARED FOR USE IN PROJECT CUE, AN EXPERIMENTAL PROGRAM DESIGNED TO INCREASE CULTURAL UNDERSTANDING AND ENRICHMENT IN THE EDUCATIONAL PROGRAMS OF HIGH SCHOOLS. THE…

  7. CUE (CULTURE, UNDERSTANDING, ENRICHMENT)--INDUSTRIAL ARTS.

    ERIC Educational Resources Information Center

    BROWN, ROBERT M.; AND OTHERS

    THIS PUBLICATION IS A TEACHING GUIDE TO PROVIDE GUIDANCE FOR INTEGRATING CAREFULLY SELECTED AUDIOVISUAL ITEMS INTO EXISTING NINTH-GRADE CURRICULUMS IN INDUSTRIAL ARTS. IT IS ONE OF FIVE GUIDES PREPARED FOR USE IN PROJECT CUE, AN EXPERIMENTAL PROGRAM DESIGNED TO INCREASE CULTURAL UNDERSTANDING AND ENRICHMENT IN THE EDUCATIONAL PROGRAMS OF HIGH…

  8. CUE (CULTURE, UNDERSTANDING, ENRICHMENT)--SOCIAL STUDIES.

    ERIC Educational Resources Information Center

    BROWN, ROBERT M.; AND OTHERS

    THIS PUBLICATION IS A TEACHING GUIDE TO PROVIDE GUIDANCE FOR INTEGRATING CAREFULLY SELECTED AUDIOVISUAL ITEMS INTO EXISTING NINTH-GRADE CURRICULUMS IN SOCIAL STUDIES. IT IS ONE OF FIVE GUIDES PREPARED FOR USE IN PROJECT CUE. AN EXPERIMENTAL PROGRAM DESIGNED TO INCREASE CULTURAL UNDERSTANDING AND ENRICHMENT IN THE EDUCATIONAL PROGRAMS OF HIGH…

  9. 21 CFR 866.2330 - Enriched culture medium.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Enriched culture medium. 866.2330 Section 866.2330...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2330 Enriched culture medium. (a) Identification. An enriched culture medium is a device that consists primarily of liquid...

  10. 21 CFR 866.2330 - Enriched culture medium.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Enriched culture medium. 866.2330 Section 866.2330...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2330 Enriched culture medium. (a) Identification. An enriched culture medium is a device that consists primarily of liquid...

  11. 21 CFR 866.2330 - Enriched culture medium.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Enriched culture medium. 866.2330 Section 866.2330...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2330 Enriched culture medium. (a) Identification. An enriched culture medium is a device that consists primarily of liquid...

  12. 21 CFR 866.2330 - Enriched culture medium.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Enriched culture medium. 866.2330 Section 866.2330...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2330 Enriched culture medium. (a) Identification. An enriched culture medium is a device that consists primarily of liquid...

  13. 21 CFR 866.2330 - Enriched culture medium.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Enriched culture medium. 866.2330 Section 866.2330...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2330 Enriched culture medium. (a) Identification. An enriched culture medium is a device that consists primarily of liquid...

  14. [Phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, Artic].

    PubMed

    Yu, Yong; Li, Hui-Rong; Chen, Bo; Zeng, Yin-Xin; He, Jian-Feng

    2006-04-01

    The phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'N - 81 degrees 12'N), Canadian Basin and Greenland sea Arctic, was investigated. A total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microL of each dilution ice-melt sample was spreaded onto the surface of Marine 2216 agar (DIFCO laboratories, Detroit, MI) and incubated for 2 to 6 weeks at 4 degrees C; ( ii ) bath culture and spread plate method: 1 mL of sample was added to 9mL of NSW (unamended natural seawater, 0.2 microm prefiltered and autoclaved) and incubated for 1 months at - 1 degrees C, then spread plate method was used to isolate bacterial strains from the pre-cultured samples; ( iii ) cold shock, bath culture and spread plate method: samples were exposed to - 20 degrees C for 24h, then bacterial strains isolated by bath culture and spread plate method under aerobic conditions. Nearly half of psychrophilic strains are isolated by using method iii . 16S rDNA nearly full-length sequence analysis reveal that psychrophilic strains fall in two phylogenetic divisions, gamma-proteobacteria (in the genera Colwellia, Marinobacter, Shewanella, Thalassomonas, Glaciecola, Marinomonas and Pseudoalteromonas) and Cytophaga-Flexibacter-Bacteroides (in the genera Flavobacterium and Psychroflexus). Nine of bacterial isolates (BSi20007, BSi20497, BSi20517, BSi20537, BSi20170, BSi20001, BSi20002, BSi20675 and BSi20101) quite likely represent novel species (16S rDNA sequence similarity below 97%). One of strains (BSi20002) from Canadian Basin shows 100% sequence similarity to the Antarctic Weddell sea ice isolate Marinobacter sp. ANT8277, suggesting bacteria may have a bipolar distribution at the species level. AF283859 sequences were submitted to the BLAST search program of the National Center for Biotechnology Information website (NCBI, http://www. ncbi. nlm.nih. gov). Twenty sequences

  15. Bacteriophages may bias outcome of bacterial enrichment cultures.

    PubMed

    Muniesa, Maite; Blanch, Anicet R; Lucena, Francisco; Jofre, Juan

    2005-08-01

    Enrichment cultures are widely used for the isolation of bacteria in clinical, biotechnological, and environmental studies. However, competition, relative growth rates, or inhibitory effects may alter the outcome of enrichment cultures, causing the phenomenon known as enrichment bias. Bacteriophages are a major component in many microbial systems, and it abounds in natural settings. This abundance means that bacteriophages are likely to be present in many laboratory enrichment cultures. Our hypothesis was that bacteriophages present in the sample might bias the enriched subpopulation, since it can infect and lyse the target bacteria during the enrichment step once the bacteria reach a given density. Here we show that the presence of bacteriophages in Salmonella and Shigella enrichment cultures produced a significant reduction (more than 1 log unit) in the number of these bacteria compared with samples in which bacteriophages had been reduced by filtration through 0.45-microm non-protein-binding membranes. Furthermore, our data indicate that the Salmonella biotypes isolated after the enrichment culture change if bacteriophages are present, thus distorting the results of the analysis.

  16. Mineralization of trichloroethylene by heterotrophic enrichment cultures

    SciTech Connect

    Phelps, T.J.; Ringelberg, D.; Mikell, A.T.; White, D.C. |; Fliermans, C.B.

    1988-12-31

    Microbial consortia capable of aerobically degrading greater than 99% of 50 mg/l exogenous trichloroethylene (TCE) have been enriched from TCE contaminated subsurface sediments. Concentrations of TCE greater than 300 mg/l were not degraded nor was TCE used as a sole energy source. Successful electron donors for growth included tryptone-yeast extract, methanol, methane or propane. The optimum temperature for growth was 22--37 C and the ph optimum was 7.0--8.1. Utilization of TCE occurred only after apparent microbial growth had ceased. The major end products recovered were hydrochloric acid and carbon dioxide. Minor products included dichloroethylene, vinylidine chloride and possibly chloroform.

  17. Protein Chips for Detection of Salmonella spp. from Enrichment Culture

    PubMed Central

    Poltronieri, Palmiro; Cimaglia, Fabio; De Lorenzis, Enrico; Chiesa, Maurizio; Mezzolla, Valeria; Reca, Ida Barbara

    2016-01-01

    Food pathogens are the cause of foodborne epidemics, therefore there is a need to detect the pathogens in food productions rapidly. A pre-enrichment culture followed by selective agar plating are standard detection methods. Molecular methods such as qPCR have provided a first rapid protocol for detection of pathogens within 24 h of enrichment culture. Biosensors also may provide a rapid tool to individuate a source of Salmonella contamination at early times of pre-enrichment culture. Forty mL of Salmonella spp. enrichment culture were processed by immunoseparation using the Pathatrix, as in AFNOR validated qPCR protocols. The Salmonella biosensor combined with immunoseparation showed a limit of detection of 100 bacteria/40 mL, with a 400 fold increase to previous results. qPCR analysis requires processing of bead-bound bacteria with lysis buffer and DNA clean up, with a limit of detection of 2 cfu/50 μL. Finally, a protein chip was developed and tested in screening and identification of 5 common pathogen species, Salmonella spp., E. coli, S. aureus, Campylobacter spp. and Listeria spp. The protein chip, with high specificity in species identification, is proposed to be integrated into a Lab-on-Chip system, for rapid and reproducible screening of Salmonella spp. and other pathogen species contaminating food productions. PMID:27110786

  18. Biodegradation of mixed pesticides by mixed pesticide enriched cultures.

    PubMed

    Krishna, K Rama; Philip, Ligy

    2009-01-01

    This paper discusses the degradation kinetics of mixed (lindane, methyl parathion and carbofuran) pesticides by mixed pesticide enriched cultures (MEC) under various environmental conditions. The bacterial strains isolated from the mixed microbial consortium were identified as Pseudomonas aeruginosa (MTCC 9236), Bacillus sp. (MTCC 9235) and Chryseobacterium joostei (MTCC 9237). Batch studies were conducted to estimate the biokinetic parameters like the maximum specific growth rate (mu(max)), Yield Coefficient (Y(T)), half saturation concentration (K(s)) and inhibition concentration (Ki) for individual and mixed pesticide enriched cultures. The cultures enriched in a particular pollutant always showed high growth rate and low inhibition in that particular pollutant compared to MEC. After seven weeks of incubation, mixed pesticide enriched cultures were able to degrade 72% lindane, 95% carbofuran and 100% of methyl parathion in facultative co-metabolic conditions. In aerobic systems, degradation efficiencies of lindane methyl parathion and carbofuran were increased by the addition of 2g L(- 1) of dextrose. Though many metabolic compounds of mixed pesticides were observed at different time intervals, none of the metabolites were persistent. Based on the observed metabolites, a degradation pathway was postulated for different pesticides under various environmental conditions.

  19. Substrate versatility of polyhydroxyalkanoate producing glycerol grown bacterial enrichment culture.

    PubMed

    Moralejo-Gárate, Helena; Kleerebezem, Robbert; Mosquera-Corral, Anuska; Campos, José Luis; Palmeiro-Sánchez, Tania; van Loosdrecht, Mark C M

    2014-12-01

    Waste-based polyhydroxyalkanoate (PHA) production by bacterial enrichments generally follows a three step strategy in which first the wastewater is converted into a volatile fatty acid rich stream that is subsequently used as substrate in a selector and biopolymer production units. In this work, a bacterial community with high biopolymer production capacity was enriched using glycerol, a non-fermented substrate. The substrate versatility and PHA production capacity of this community was studied using glucose, lactate, acetate and xylitol as substrate. Except for xylitol, very high PHA producing capacities were obtained. The PHA accumulation was comparable or even higher than with glycerol as substrate. This is the first study that established a high PHA content (≈70 wt%) with glucose as substrate in a microbial enrichment culture. The results presented in this study support the development of replacing pure culture based PHA production by bacterial enrichment cultures. A process where mixtures of substrates can be easily handled and the acidification step can potentially be avoided is described.

  20. Optimizing enrichment culture conditions for detecting Helicobacter pylori in foods.

    PubMed

    Jiang, Xiuping; Doyle, Michael P

    2002-12-01

    The survival and growth of Helicobacter pylori under enrichment conditions in fresh, autoclaved and irradiated ground beef were determined. H. pylori grew in autoclaved ground beef at 37 degrees C under microaerobic conditions in brain heart infusion broth with 7% horse serum at pH 7.3 after 3 to 7 days of lag time but did not grow within 7 days in irradiated (10 kGy) ground beef under the same enrichment conditions. Adjustment of the enrichment broth to pH 5.5 enabled the growth (ca. 2 log10 CFU/ml) of H. pylori within 7 days in the presence of irradiated ground beef and the prolific growth (ca. 3 to 4 log10 CFU/ml) of H. pylori within 3 days in the presence of autoclaved beef. H. pylori in fresh ground beef could not be isolated from enrichment media with antibiotics; however. H. pylori ureA could be detected by polymerase chain reaction (PCR) in such enrichment media after 1 to 3 days of incubation at 37 degrees C. The addition of supplements, i.e., 0.3% mucin, 0.05% ferrous sulfate, and 0.05% sodium pyruvate or 0.008 M urea, or the adjustment of the enrichment broth pH to 5.5 or 4.5 enabled the detection of H. pylori ureA in enrichment media incubated for 1, 2, 3, and/or 7 days at 37 degrees C. H. pylori in sterile milk refrigerated at 4 degrees C at an initial level of 10(6) CFU/ml was inactivated to an undetectable level within 6 days; however, H. pylori was not detected either by a PCR assay or by the plating of enrichment cultures of 120 raw bovine milk samples.

  1. [Reductive Dechlorination of Trichloroethylene by Benzoate-Enriched Anaerobic Cultures].

    PubMed

    Li, Jiang-wei; Yang, Xiao-yong; Hu, An-yi; Yu, Chang-ping

    2015-10-01

    Gas chromatography was used to monitor the reductive dechlorination of trichloroethylene (TCE) by anaerobic enrichment cultures with benzoate as the sole carbon source. The 454 pyrosequencing technique was used to investigate the microbial community and the real-time quantitative PCR was used to quantify the gene copies of Dehalococcoides spp. (DHC). The results showed that TCE was dechlorinated to vinyl chloride along with the formation of methane in 94 days. The anaerobic enrichment cultures exhibited a high diversity, which were classified into 16 phyla, 33 classes, 52 orders, 88 families and 129 genera, while 51.2% of them belonged to unclassified group, which inferred that there were a large portion of bacteria with unknown functional in this system. Degradation of TCE was accomplished by reductive dechlorinating and other functional populations, and the DHC which carried tceA gene could be the dominant reductive dechlorinating populations in the system.

  2. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture.

    PubMed Central

    González, J M; Whitman, W B; Hodson, R E; Moran, M A

    1996-01-01

    Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the alpha-subclass of Proteobacteria, and the other two were in the gamma-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented. PMID:8953714

  3. Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

    PubMed Central

    Sibley, Christopher D.; Grinwis, Margot E.; Field, Tyler R.; Eshaghurshan, Christina S.; Faria, Monica M.; Dowd, Scot E.; Parkins, Michael D.; Rabin, Harvey R.; Surette, Michael G.

    2011-01-01

    The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured. PMID:21829484

  4. Absence of microbial mineralization of lignin in anaerobic enrichment cultures.

    PubMed Central

    Odier, E; Monties, B

    1983-01-01

    The existence of anaerobic biodegradation of lignin was examined in mixed microflora. Egyptian soil samples, in which rapid mineralization of organic matter takes place in the presence of an important anaerobic microflora, were used to obtain the anaerobic enrichment cultures for this study. Specifically, 14CO2 or [14C]lignin wood was used to investigate the release of labeled gaseous or soluble degradation products of lignin in microbial cultures. No conversion of 14C-labeled lignin to 14CO2 or 14CH4 was observed after 6 months of incubation at 30 degrees C in anaerobic conditions with or without NO3-. A small increase in soluble radioactivity was observed in certain cultures, but it could not be related to the release of catabolic products during the anaerobic biodegradation of lignin. PMID:6639020

  5. Anaerobic oxidation of acetylene by estuarine sediments and enrichment cultures

    USGS Publications Warehouse

    Culbertson, Charles W.; Zehnder, Alexander J. B.; Oremland, Ronald S.

    1981-01-01

    Acetylene disappeared from the gas phase of anaerobically incubated estuarine sediment slurries, and loss was accompanied by increased levels of carbon dioxide. Acetylene loss was inhibited by chloramphenicol, air, and autoclaving. Addition of 14C2H2 to slurries resulted in the formation of 14CO2 and the transient appearance of 14C-soluble intermediates, of which acetate was a major component. Acetylene oxidation stimulated sulfate reduction; however, sulfate reduction was not required for the loss of C2H2 to occur. Enrichment cultures were obtained which grew anaerobically at the expense of C2H2.

  6. Anaerobic Oxidation of Acetylene by Estuarine Sediments and Enrichment Cultures

    PubMed Central

    Culbertson, Charles W.; Zehnder, Alexander J. B.; Oremland, Ronald S.

    1981-01-01

    Acetylene disappeared from the gas phase of anaerobically incubated estuarine sediment slurries, and loss was accompanied by increased levels of carbon dioxide. Acetylene loss was inhibited by chloramphenicol, air, and autoclaving. Addition of 14C2H2 to slurries resulted in the formation of 14CO2 and the transient appearance of 14C-soluble intermediates, of which acetate was a major component. Acetylene oxidation stimulated sulfate reduction; however, sulfate reduction was not required for the loss of C2H2 to occur. Enrichment cultures were obtained which grew anaerobically at the expense of C2H2. PMID:16345714

  7. Effect of Enrichment Medium on Real-time Detection of Salmonella enterica from Lettuce and Tomato Enrichment Cultures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    vThree commonly used enrichment broths for detection of Salmonella (Buffered Peptone Water – BPW, Tryptic Soy Broth – TSB, and Universal Preenrichment Broth – UPB) were compared for use in real time SYBR Green PCR detection of Salmonella introduced into enrichment cultures made from store bought let...

  8. Enrichment of spinal cord cell cultures with motoneurons

    PubMed Central

    1978-01-01

    Spinal cord cell cultures contain several types of neurons. Two methods are described for enriching such cultures with motoneurons (defined here simply as cholinergic cells that are capable of innervating muscle). In the first method, 7-day embryonic chick spinal cord neurons were separated according to size by 1 g velocity sedimentation. It is assumed that cholinergic motoneurons are among the largest cells present at this stage. The spinal cords were dissociated vigorously so that 95-98% of the cells in the initial suspension were isolated from one another. Cells in leading fractions (large cell fractions: LCFs) contain about seven times as much choline acetyltransferase (CAT) activity per unit cytoplasm as do cells in trailing fractions (small cell fractions: SCFs). Muscle cultures seeded with LCFs develop 10-70 times as much CAT as cultures seeded with SCFs and six times as much CAT as cultures seeded with control (unfractionated) spinal cord cells. More than 20% of the large neurons in LCF-muscle cultures innervate nearby myotubes. In the second method, neurons were gently dissociated from 4-day embryonic spinal cords and maintained in vitro. This approach is based on earlier observations that cholinergic neurons are among the first cells to withdraw form the mitotic cycle in the developing chick embryo (Hamburger, V. 1948. J. Comp. Neurol. 88:221- 283; and Levi-Montalcini, R. 1950. J. Morphol. 86:253-283). 4-Day spinal cord-muscle cultures develop three times as much CAT as do 7-day spinal cord-muscle plates, prepared in the same (gentle) manner. More than 50% of the relatively large 4-day neurons innervate nearby myotubes. Thus, both methods are useful first steps toward the complete isolation of motoneurons. Both methods should facilitate study of the development of cholinergic neurons and of nerve-muscle synapse formation. PMID:566275

  9. Dimethylamine biodegradation by mixed culture enriched from drinking water biofilter.

    PubMed

    Liao, Xiaobin; Chen, Chao; Zhang, Jingxu; Dai, Yu; Zhang, Xiaojian; Xie, Shuguang

    2015-01-01

    Dimethylamine (DMA) is one of the important precursors of drinking water disinfection by-product N-nitrosodimethylamine (NDMA). Reduction of DMA to minimize the formation of carcinogenic NDMA in drinking water is of practical importance. Biodegradation plays a major role in elimination of DMA pollution in the environment, yet information on DMA removal by drinking water biofilter is still lacking. In this study, microcosms with different treatments were constructed to investigate the potential of DMA removal by a mixed culture enriched from a drinking water biofilter and the effects of carbon and nitrogen sources. DMA could be quickly mineralized by the enrichment culture. Amendment of a carbon source, instead of a nitrogen source, had a profound impact on DMA removal. A shift in bacterial community structure was observed with DMA biodegradation, affected by carbon and nitrogen sources. Proteobacteria was the predominant phylum group in DMA-degrading microcosms. Microorganisms from a variety of bacterial genera might be responsible for the rapid DMA mineralization.

  10. Biotransformation of acyclovir by an enriched nitrifying culture.

    PubMed

    Xu, Yifeng; Yuan, Zhiguo; Ni, Bing-Jie

    2017-03-01

    This work evaluates the biodegradation of the antiviral drug acyclovir by an enriched nitrifying culture during ammonia oxidation and without the addition of ammonium. The study on kinetics was accompanied with the structural elucidation of biotransformation products through batch biodegradation experiments at two different initial levels of acyclovir (15 mg L(-1) and 15 μg L(-1)). The pseudo first order kinetic studies of acyclovir in the presence of ammonium indicated the higher degradation rates under higher ammonia oxidation rates than those constant degradation rates in the absence of ammonium. The positive correlation was found between acyclovir degradation rate and ammonia oxidation rate, confirming the cometabolism of acyclovir by the enriched nitrifying culture in the presence of ammonium. Formation of the product carboxy-acyclovir (P239) indicated the main biotransformation pathway was aerobic oxidation of the terminal hydroxyl group, which was independent on the metabolic type (i.e. cometabolism or metabolism). This enzyme-linked reaction might be catalyzed by monooxygenase from ammonia oxidizing bacteria or heterotrophs. The formation of carboxy-acyclovir was demonstrated to be irrelevant to the acyclovir concentrations applied, indicating the revealed biotransformation pathway might be the dominant removal pathway of acyclovir in wastewater treatment.

  11. Rare bacterium of new genus isolated with prolonged enrichment culture.

    PubMed

    Hashizume, Akiko; Fudou, Ryosuke; Jojima, Yasuko; Nakai, Ryohsuke; Hiraishi, Akira; Tabuchi, Akira; Sen, Kikuo; Shibai, Hiroshiro

    2004-01-01

    Dynamic change in microbial flora was monitored with an oxygen electrode. The 1st phase microorganisms, which first grew well in LB medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. In a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. Based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existence of rare microorganisms. From these culture liquids, four slow-growing bacteria (provisionally named Shinshu-ah1, -ah2, -ah3, and -ah4), which formed scarcely visible small colonies, were isolated. Sequence analysis of their 16S rDNA showed that Shinshu-ah1 had 97% homology with Bradyrhizobium japonicum and uncultured alpha proteobacterium clone blaii 16, Shinshu-ah2 91% with Rasbo bacterium, Alpha proteobacterium 34619, Bradyrhizobium genosp. P, Afipia felis and an unidentified bacterium, Shinshu-ah3 99% with Methylobacterium mesophilicum, and Shinshu-ah4 95% with Agromyces ramosus DSM 43045. Phylogenetic study indicated that Shinshu-ah2 had a possibility to form a new family, Shinshu-ah1 a new genus, and Shinshu-ah4 a new species.

  12. Cellulases from psychrophilic microorganisms: a review.

    PubMed

    Kasana, Ramesh C; Gulati, Arvind

    2011-12-01

    Cellulases are hydrolytic enzymes that catalyze total hydrolysis of cellulose into sugars. Cellulases are produced by various groups of microorganisms and animals; however, psychrophiles are the ideal candidates for the production of enzymes active at low temperature and stable under alkaline conditions, in the presence of oxidants and detergents, which are in large demand as laundry additives. The cellulases from psychrophiles also find application in environmental bioremediation, food industry and molecular biology. Research work on cellulase has been done over the last six decades, but there is no exclusive review available on the cellulases from psychrophiles. This review is an attempt to fill this gap by providing all the relevant information exclusively for cellulases from psychrophiles, with a focus on the present status of knowledge on their activity, molecular characteristics, gene cloning, statistical experimental designs, crystal structure, and strategies for the improvement of psychrophilic cellulases.

  13. Selective enrichment media bias the types of Salmonella enterica strains isolated from mixed strain cultures and complex enrichment broths.

    PubMed

    Gorski, Lisa

    2012-01-01

    For foodborne outbreak investigations it can be difficult to isolate the relevant strain from food and/or environmental sources. If the sample is contaminated by more than one strain of the pathogen the relevant strain might be missed. In this study mixed cultures of Salmonella enterica were grown in one set of standard enrichment media to see if culture bias patterns emerged. Nineteen strains representing four serogroups and ten serotypes were compared in four-strain mixtures in Salmonella-only and in cattle fecal culture enrichment backgrounds using Salmonella enrichment media. One or more strain(s) emerged as dominant in each mixture. No serotype was most fit, but strains of serogroups C2 and E were more likely to dominate enrichment culture mixtures than strains of serogroups B or C1. Different versions of Rappaport-Vassiliadis (RV) medium gave different patterns of strain dominance in both Salmonella-only and fecal enrichment culture backgrounds. The fittest strains belonged to serogroups C1, C2, and E, and included strains of S. Infantis, S. Thompson S. Newport, S. 6,8:d:-, and S. Give. Strains of serogroup B, which included serotypes often seen in outbreaks such as S. Typhimurium, S. Saintpaul, and S. Schwarzengrund were less likely to emerge as dominant strains in the mixtures when using standard RV as part of the enrichment. Using a more nutrient-rich version of RV as part of the protocol led to a different pattern of strains emerging, however some were still present in very low numbers in the resulting population. These results indicate that outbreak investigations of food and/or other environmental samples should include multiple enrichment protocols to ensure isolation of target strains of Salmonella.

  14. Biotechnological uses of enzymes from psychrophiles

    PubMed Central

    Cavicchioli, R.; Charlton, T.; Ertan, H.; Omar, S. Mohd; Siddiqui, K. S.; Williams, T. J.

    2011-01-01

    Summary The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold‐adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning. PMID:21733127

  15. Isolation and physiological characterization of psychrophilic denitrifying bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway).

    PubMed

    Canion, Andy; Prakash, Om; Green, Stefan J; Jahnke, Linda; Kuypers, Marcel M M; Kostka, Joel E

    2013-05-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(3) -10(6) cells of psychrophilic nitrate-respiring bacteria g(-1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40°C demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15°C, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  16. Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

    NASA Technical Reports Server (NTRS)

    Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

    2013-01-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  17. Psychrophilic Lipase from Arctic Bacterium

    PubMed Central

    Ramle, Zakiah; Rahim, Rashidah Abdul

    2016-01-01

    A lipase producer psychrophilic microorganism isolated from Arctic sample was studied. The genomic DNA of the isolate was extracted using modified CTAB method. Identification of the isolate by morphological and 16S rRNA sequence analysis revealed that the isolate is closely related to Arthrobacter gangotriensis (97% similarity). A. gangotriensis was determined as positive lipase producer based on the plate screening using specific and sensitive plate assay of Rhodamine B. The PCR result using Arthrobacter sp.’s full lipase gene sequence as the template primers emphasised a possible lipase gene at 900 bp band size. The gene is further cloned in a suitable vector system for expression of lipase. PMID:27965754

  18. The New Stories/New Cultures after-school enrichment program: a direct cultural intervention.

    PubMed

    Frank, G; Fishman, M; Crowley, C; Blair, B; Murphy, S T; Montoya, J A; Hickey, M P; Brancaccio, M V; Bensimon, E M

    2001-01-01

    This article describes the organization, curriculum, and outcomes for New Stories/New Cultures, an activity-based program for after-school enrichment in five schools in the low-income neighborhood near a major American university. The program encourages students (70% Hispanic-American, 30% African-American) to experience themselves as producers of culture, not just as consumers. Its methods include (a) creative team use of video equipment and other expressive media and (b) lessons about media literacy (i.e., making critical choices about images and activities depicted in popular culture and commercials). Outcome measures with the cohort of fifth and sixth graders support the programs occupation-based philosophy. They show that students are more likely to experience themselves as building skills when engaged in activities that are both challenging and enjoyable. The students reported greatest engagement and enjoyment in activities that were creative, team-based, and involving media production. These same activities were correlated with increased self-esteem. The term direct cultural intervention is used to describe the application of occupational principles and critical perspectives to provide a population with conceptual tools and skills for interpreting and successfully navigating the social world.

  19. Atrazine and its metabolites degradation in mineral salts medium and soil using an enrichment culture.

    PubMed

    Kumar, Anup; Singh, Neera

    2016-03-01

    An atrazine-degrading enrichment culture was used to study degradation of atrazine metabolites viz. hydroxyatrazine, deethylatrazine, and deisopropylatrazine in mineral salts medium. Results suggested that the enrichment culture was able to degrade only hydroxyatrazine, and it was used as the sole source of carbon and nitrogen. Hydroxyatrazine degradation slowed down when sucrose and/or ammonium hydrogen phosphate were supplemented as the additional sources of carbon and nitrogen, respectively. The enrichment culture could degrade high concentrations of atrazine (up to 110 μg/mL) in mineral salts medium, and neutral pH was optimum for atrazine degradation. Further, except in an acidic soil, enrichment culture was able to degrade atrazine in three soil types having different physico-chemical properties. Raising the pH of acidic soil to neutral or alkaline enabled the enrichment culture to degrade atrazine suggesting that acidic pH inhibited atrazine-degrading ability. The study suggested that the enrichment culture can be successfully utilized to achieve complete degradation of atrazine and its persistent metabolite hydroxyatrazine in the contaminated soil and water.

  20. Indian Culture Master Plan. A Master Plan for Enriching the Background of Public School Personnel in Native American Cultures.

    ERIC Educational Resources Information Center

    Montana State Board of Education, Helena.

    Recognizing that the cultural and historical contributions of Native Americans should be part of the basic education of all citizens in the state, the 1974 Montana legislature directed that an Indian Culture Master Plan be devised to enrich the background of all public school teachers. The plan was to provide means by which all public school…

  1. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture

    PubMed Central

    Zheng, Shiling; Zhang, Hongxia; Li, Ying; Zhang, Hua; Wang, Oumei; Zhang, Jun; Liu, Fanghua

    2015-01-01

    Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates. PMID:26441876

  2. Characteristics of enriched cultures for bio-huff-`n`-puff tests at Jilin oil field

    SciTech Connect

    Xiu-Yuan Wang; Gang Dai; Yan-Fen Xue; Shu-Hua Xie

    1995-12-31

    Three enriched cultures (48, 15a, and 26a), selected from more than 80 soil and water samples, could grow anaerobically in the presence of crude oil at 30{degrees}C and could ferment molasses to gases and organic acids. Oil recovery by culture 48 in the laboratory model experiment was enhanced by 25.2% over the original reserves and by 53.7% over the residual reserves. Enriched culture 48 was composed of at least 4 species belonging to the genera Eubacterium, Fusobacterium, and Bacteroides. This enriched culture was used as inoculum for MEOR field trials at Jilin oil field with satisfactory results. The importance of the role of these isolates in EOR was confirmed by their presence and behavior in the fluids produced from the microbiologically treated reservoir.

  3. Inupiaq Cultural Enrichment Program. Junior High-High School.

    ERIC Educational Resources Information Center

    Ahngasuk, Margaret; And Others

    Part of a project to teach Inupiaq culture and language, the teacher's guide contains 18 lessons about survival. The lessons focus on survival on ice, water, and land; hunting gear; fall and early winter weather; emergency shelters; landmarks; traditional clothing; land and water transportation; first aid; search and rescue; sewing; traditional…

  4. Enrich Your Kindergarten Program with a Cross-Cultural Connection.

    ERIC Educational Resources Information Center

    Salmon, Michaele; Akaran, Susan Evans

    2001-01-01

    Describes a pen pal connection between a New Jersey kindergarten class and an Alaskan Eskimo first-grade class. Details how they used monthly e-mail and regular mail, and exchanged class projects to heighten respect and understanding about others' cultures. Provides examples of monthly contact during one school year and websites for finding a…

  5. Two-stage mineralization of phenanthrene by estuarine enrichment cultures

    SciTech Connect

    Guerin, W.F.; Jones, G.E.

    1988-04-01

    The polycyclic aromatic hydrocarbon phenanthrene was mineralized in two stages by soil, estuarine water, and sediment microbial populations. At high concentrations, phenanthrene was degraded, with the concomitant production of biomass and accumulation of Folin-Ciocalteau-reactive aromatic intermediates. Subsequent consumption of these intermediates resulted in a secondary increase in biomass. Analysis of intermediates by high-performance liquid chromatography, thin-layer chromatography, and UV absorption spectrometry showed 1-hydroxy-2-naphthoic acid (1H2NA) to be the predominant product. A less pronounced two-stage mineralization pattern was also observed by monitoring /sup 14/CO/sub 2/ production from low concentrations (0.5 mg liter/sup -1/) of radiolabeled phenanthrene. Here, mineralization of /sup 14/C-labeled 1H2NA could explain the incremental /sup 14/CO/sub 2/ produced during the later part of the incubations. Accumulation of 1H2NA by isolates obtained from enrichments was dependent on the initial phenanthrene concentration. The production of metabolites during polycyclic aromatic hydrocarbon biodegradation is discussed with regard to its possible adaptive significance and its methodological implications.

  6. Differential Gene Expression Profiling of Enriched Human Spermatogonia after Short- and Long-Term Culture

    PubMed Central

    Conrad, Sabine; Azizi, Hossein; Hatami, Maryam; Kubista, Mikael; Bonin, Michael; Hennenlotter, Jörg; Renninger, Markus; Skutella, Thomas

    2014-01-01

    This study aimed to provide a molecular signature for enriched adult human stem/progenitor spermatogonia during short-term (<2 weeks) and long-term culture (up to more than 14 months) in comparison to human testicular fibroblasts and human embryonic stem cells. Human spermatogonia were isolated by CD49f magnetic activated cell sorting and collagen−/laminin+ matrix binding from primary testis cultures obtained from ten adult men. For transcriptomic analysis, single spermatogonia-like cells were collected based on their morphology and dimensions using a micromanipulation system from the enriched germ cell cultures. Immunocytochemical, RT-PCR and microarray analyses revealed that the analyzed populations of cells were distinct at the molecular level. The germ- and pluripotency-associated genes and genes of differentiation/spermatogenesis pathway were highly expressed in enriched short-term cultured spermatogonia. After long-term culture, a proportion of cells retained and aggravated the “spermatogonial” gene expression profile with the expression of germ and pluripotency-associated genes, while in the majority of long-term cultured cells this molecular profile, typical for the differentiation pathway, was reduced and more genes related to the extracellular matrix production and attachment were expressed. The approach we provide here to study the molecular status of in vitro cultured spermatogonia may be important to optimize the culture conditions and to evaluate the germ cell plasticity in the future. PMID:24738045

  7. Synergistic degradation of deca-BDE by an enrichment culture and zero-valent iron.

    PubMed

    Chen, Xingjuan; Chen, Guilan; Qiu, Mengde; Sun, Guoping; Guo, Jun; Xu, Meiying

    2014-01-01

    Debromination of decabromodiphenyl ether (deca-BDE) by microbe and by zero-valent iron (ZVI) has been reported previously. However, no study has indicated the presence of microorganisms and their effect on ZVI-mediated reduction of deca-BDE. Synergistic degradation of deca-BDE by an enrichment culture and ZVI was studied. It was found that synergistic effects enhanced the debromination of deca-BDE as well as promoting the reduction of lower brominated products. ZVI stimulated microbial debromination by serving as an electron donor. Correlation analysis also confirmed that ZVI was capable of enhancing microbial population in the debromination of deca-BDE. Conversely, the enrichment culture produced acid which maintained pH stability and stimulated the oxidation of ZVI. The enrichment culture supplied its energy requirements by the oxidation of ZVI and concomitant reduction of deca-BDE, but incapable of growth and reduction of BDE-209 without ZVI and vice versa. Compared to the initial culture, the microbial community of the enrichment culture became dominated by several bacterial genera based on the results of 16S rRNA-gene pyrosequencing.

  8. Newly cultured bacteria with broad diversity isolated from 8 week continuous culture enrichments of cow feces on complex polysaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the fascinating functions of the mammalian intestinal microbiota is the fermentation of plant cell wall components. Eight week continuous culture enrichments of cow feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were ...

  9. Cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil.

    PubMed

    Smith, Daniel; Alvey, Sam; Crowley, David E

    2005-07-01

    Atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. Here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. The species composition of the culture was determined by PCR-DGGE. The bacterial species included Agrobacterium tumefaciens, Caulobacter crescentus, Pseudomonas putida, Sphingomonas yaniokuyae, Nocardia sp., Rhizobium sp., Flavobacterium oryzihabitans, and Variovorax paradoxus. All of the isolates were screened for the presence of known genes that function for atrazine degradation including atzA,-B,-C,-D,-E,-F and trzD,-N. Dechlorination of atrazine, which was obligatory for complete mineralization, was carried out exclusively by Nocardia sp., which contained the trzN gene. Following dechlorination, the resulting product, hydroxyatrazine was further degraded via two separate pathways. In one pathway Nocardia converted hydroxyatrazine to N-ethylammelide via an unidentified gene product. In the second pathway, hydroxyatrazine generated by Nocardia sp. was hydrolyzed to N-isopropylammelide by Rhizobium sp., which contained the atzB gene. Each member of the enrichment culture contained atzC, which is responsible for ring cleavage, but none of the isolates carried the atzD,-E, or -F genes. Each member further contained either trzD or exhibited urease activity. The enrichment culture was destabilized by loss of Nocardia sp. when grown on ethylamine, ethylammelide, and cyanuric acid, after which the consortium was no longer able to degrade atrazine. The analysis of this enrichment culture highlights the broad level bacterial community interactions that may be involved in atrazine degradation in nature.

  10. A study of psychrophilic organisms isolated from the manufacture and assembly areas of spacecraft to be used in the Viking mission

    NASA Technical Reports Server (NTRS)

    Foster, T. L.; Winans, L., Jr.

    1974-01-01

    The ability of psychrophilic microorganisms to grow in some of the environmental conditions suggested for Mars is studied with particular attention given to the effects of moisture and nutrients on growth. Results of growth with the slide culture technique are presented and indicate that this technique can be a rapid and sensitive technique for demonstration of microbial growth under various environmental conditions. Additional soil samples have been obtained from Cape Kennedy, and results of these assays at various low temperatures for psychrophilic populations are presented. The heat resistance of some of the psychrophilic sporeformers have been determined. Psychrophilic organisms were isolated from the teflon ribbons at Cape Kennedy and characterization of these was begun. In addition, heat survivors from the teflon ribbons are being investigated, and partial characterizations of these are presented.

  11. Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the fascinating functions of the mammalian intestinal microbiota is the fermentation of plant cell wall components. We used 8 week continuous culture enrichments of pig feces with cellulose and xylan/pectin to isolated bacteria from this community. A total of 575 bacterial isolates were class...

  12. Using Enrichment Clusters to Address the Needs of Culturally and Linguistically Diverse Learners

    ERIC Educational Resources Information Center

    Allen, Jennifer K.; Robbins, Margaret A.; Payne, Yolanda Denise; Brown, Katherine Backes

    2016-01-01

    Using data from teacher interviews, classroom observations, and a professional development workshop, this article explains how one component of the schoolwide enrichment model (SEM) has been implemented at a culturally diverse elementary school serving primarily Latina/o and African American students. Based on a broadened conception of giftedness,…

  13. Biodegradation of Endocrine Disruptors in Solid-Liquid Two-Phase Partitioning Systems by Enrichment Cultures

    PubMed Central

    dos Santos, Silvia Cristina Cunha; Ouellette, Julianne; Juteau, Pierre; Lépine, François; Déziel, Eric

    2013-01-01

    Naturally occurring and synthetic estrogens and other molecules from industrial sources strongly contribute to the endocrine disruption of urban wastewater. Because of the presence of these molecules in low but effective concentrations in wastewaters, these endocrine disruptors (EDs) are only partially removed after most wastewater treatments, reflecting the presence of these molecules in rivers in urban areas. The development of a two-phase partitioning bioreactor (TPPB) might be an effective strategy for the removal of EDs from wastewater plant effluents. Here, we describe the establishment of three ED-degrading microbial enrichment cultures adapted to a solid-liquid two-phase partitioning system using Hytrel as the immiscible water phase and loaded with estrone, estradiol, estriol, ethynylestradiol, nonylphenol, and bisphenol A. All molecules except ethynylestradiol were degraded in the enrichment cultures. The bacterial composition of the three enrichment cultures was determined using 16S rRNA gene sequencing and showed sequences affiliated with bacteria associated with the degradation of these compounds, such as Sphingomonadales. One Rhodococcus isolate capable of degrading estrone, estradiol, and estriol was isolated from one enrichment culture. These results highlight the great potential for the development of TPPB for the degradation of highly diluted EDs in water effluents. PMID:23728808

  14. Enrichment of cancer stem cell-like cells by culture in alginate gel beads.

    PubMed

    Xu, Xiao-xi; Liu, Chang; Liu, Yang; Yang, Li; Li, Nan; Guo, Xin; Sun, Guang-wei; Ma, Xiao-jun

    2014-05-10

    Cancer stem cells (CSCs) are most likely the reason of cancer reoccurrence and metastasis. For further elucidation of the mechanism underlying the characteristics of CSCs, it is necessary to develop efficient culture systems to culture and expand CSCs. In this study, a three-dimensional (3D) culture system based on alginate gel (ALG) beads was reported to enrich CSCs. Two cell lines derived from different histologic origins were encapsulated in ALG beads respectively and the expansion of CSCs was investigated. Compared with two-dimensional (2D) culture, the proportion of cells with CSC-like phenotypes was significantly increased in ALG beads. Expression levels of CSC-related genes were greater in ALG beads than in 2D culture. The increase of CSC proportion after being cultured within ALG beads was further confirmed by enhanced tumorigenicity in vivo. Moreover, increased metastasis ability and higher anti-cancer drug resistance were also observed in 3D-cultured cells. Furthermore, we found that it was hypoxia, through the upregulation of hypoxia-inducible factors (HIFs) that occurred in ALG beads to induce the increasing of CSC proportion. Therefore, ALG bead was an efficient culture system for CSC enrichment, which might provide a useful platform for CSC research and promote the development of new anti-cancer therapies targeting CSCs.

  15. Identification of triclosan-degrading bacteria in a triclosan enrichment culture using stable isotope probing.

    PubMed

    Lee, Do Gyun; Cho, Kun-Ching; Chu, Kung-Hui

    2014-02-01

    Triclosan, a widely used antimicrobial agent, is an emerging contaminant in the environment. Despite its antimicrobial character, biodegradation of triclosan has been observed in pure cultures, soils and activated sludge. However, little is known about the microorganisms responsible for the degradation in mixed cultures. In this study, active triclosan degraders in a triclosan-degrading enrichment culture were identified using stable isotope probing (SIP) with universally (13)C-labeled triclosan. Eleven clones contributed from active microorganisms capable of uptake the (13)C in triclosan were identified. None of these clones were similar to known triclosan-degraders/utilizers. These clones distributed among α-, β-, or γ-Proteobacteria: one belonging to Defluvibacter (α-Proteobacteria), seven belonging to Alicycliphilus (β-Proteobacteria), and three belonging to Stenotrophomonas (γ-Proteobacteria). Successive additions of triclosan caused a significant shift in the microbial community structure of the enrichment culture, with dominant ribotypes belonging to the genera Alicycliphilus and Defluvibacter. Application of SIP has successfully identified diverse uncultivable triclosan-degrading microorganisms in an activated sludge enrichment culture. The results of this study not only contributed to our understanding of the microbial ecology of triclosan biodegradation in wastewater, but also suggested that triclosan degraders are more phylogenetically diverse than previously reported.

  16. Prospecting for ice association: characterization of freeze-thaw selected enrichment cultures from latitudinally distant soils.

    PubMed

    Wilson, Sandra L; Grogan, Paul; Walker, Virginia K

    2012-04-01

    Freeze-thaw stress has previously been shown to alter soil community structure and function. We sought to further investigate this stress on enriched microbial consortia with the aim of identifying microbes with ice-associating adaptations that facilitate survival. Enrichments were established to obtain culturable psychrotolerant microbes from soil samples from the latitudinal extremes of the Canadian Shield plateau. The resulting consortia were subjected to consecutive freeze-thaw cycles, and survivors were putatively identified by their 16S rRNA gene sequences. Even though the northerly site was exposed to longer, colder winters and large spring-time temperature fluctuations, the selective regime similarly affected both enriched consortia. Quantitative PCR and metagenomic sequencing were used to determine the frequency of a subset of the resistant microbes in the original enrichments. The metagenomes showed 22 initial genera, only 6 survived and these were not dominant prior to selection. When survivors were assayed for ice recrystallization inhibition and ice nucleation activities, over 60% had at least one of these properties. These phenotypes were not more prevalent in the northern enrichment, indicating that regarding these adaptations, the enrichment strategy yielded seemingly functionally similar consortia from each site.

  17. Cholera Rapid Test with Enrichment Step Has Diagnostic Performance Equivalent to Culture

    PubMed Central

    Ontweka, Lameck N.; Deng, Lul O.; Rauzier, Jean; Debes, Amanda K.; Tadesse, Fisseha; Parker, Lucy A.; Wamala, Joseph F.; Bior, Bior K.; Lasuba, Michael; But, Abiem Bona; Grandesso, Francesco; Jamet, Christine; Cohuet, Sandra; Ciglenecki, Iza; Serafini, Micaela; Sack, David A.; Quilici, Marie-Laure; Azman, Andrew S.; Luquero, Francisco J.

    2016-01-01

    Cholera rapid diagnostic tests (RDT) could play a central role in outbreak detection and surveillance in low-resource settings, but their modest performance has hindered their broad adoption. The addition of an enrichment step may improve test specificity. We describe the results of a prospective diagnostic evaluation of the Crystal VC RDT (Span Diagnostics, India) with enrichment step and of culture, each compared to polymerase chain reaction (PCR), during a cholera outbreak in South Sudan. RDTs were performed on alkaline peptone water inoculated with stool and incubated for 4–6 hours at ambient temperature. Cholera culture was performed from wet filter paper inoculated with stool. Molecular detection of Vibrio cholerae O1 by PCR was done from dry Whatman 903 filter papers inoculated with stool, and from wet filter paper supernatant. In August and September 2015, 101 consecutive suspected cholera cases were enrolled, of which 36 were confirmed by PCR. The enriched RDT had 86.1% (95% CI: 70.5–95.3) sensitivity and 100% (95% CI: 94.4–100) specificity compared to PCR as the reference standard. The sensitivity of culture versus PCR was 83.3% (95% CI: 67.2–93.6) for culture performed on site and 72.2% (95% CI: 54.8–85.8) at the international reference laboratory, where samples were tested after an average delay of two months after sample collection, and specificity was 98.5% (95% CI: 91.7–100) and 100% (95% CI: 94.5–100), respectively. The RDT with enrichment showed performance comparable to that of culture and could be a sustainable alternative to culture confirmation where laboratory capacity is limited. PMID:27992488

  18. Cholera Rapid Test with Enrichment Step Has Diagnostic Performance Equivalent to Culture.

    PubMed

    Ontweka, Lameck N; Deng, Lul O; Rauzier, Jean; Debes, Amanda K; Tadesse, Fisseha; Parker, Lucy A; Wamala, Joseph F; Bior, Bior K; Lasuba, Michael; But, Abiem Bona; Grandesso, Francesco; Jamet, Christine; Cohuet, Sandra; Ciglenecki, Iza; Serafini, Micaela; Sack, David A; Quilici, Marie-Laure; Azman, Andrew S; Luquero, Francisco J; Page, Anne-Laure

    2016-01-01

    Cholera rapid diagnostic tests (RDT) could play a central role in outbreak detection and surveillance in low-resource settings, but their modest performance has hindered their broad adoption. The addition of an enrichment step may improve test specificity. We describe the results of a prospective diagnostic evaluation of the Crystal VC RDT (Span Diagnostics, India) with enrichment step and of culture, each compared to polymerase chain reaction (PCR), during a cholera outbreak in South Sudan. RDTs were performed on alkaline peptone water inoculated with stool and incubated for 4-6 hours at ambient temperature. Cholera culture was performed from wet filter paper inoculated with stool. Molecular detection of Vibrio cholerae O1 by PCR was done from dry Whatman 903 filter papers inoculated with stool, and from wet filter paper supernatant. In August and September 2015, 101 consecutive suspected cholera cases were enrolled, of which 36 were confirmed by PCR. The enriched RDT had 86.1% (95% CI: 70.5-95.3) sensitivity and 100% (95% CI: 94.4-100) specificity compared to PCR as the reference standard. The sensitivity of culture versus PCR was 83.3% (95% CI: 67.2-93.6) for culture performed on site and 72.2% (95% CI: 54.8-85.8) at the international reference laboratory, where samples were tested after an average delay of two months after sample collection, and specificity was 98.5% (95% CI: 91.7-100) and 100% (95% CI: 94.5-100), respectively. The RDT with enrichment showed performance comparable to that of culture and could be a sustainable alternative to culture confirmation where laboratory capacity is limited.

  19. Erythrocyte Enrichment in Hematopoietic Progenitor Cell Cultures Based on Magnetic Susceptibility of the Hemoglobin

    PubMed Central

    Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V.; Moore, Lee R.; Chalmers, Jeffrey J.; Zborowski, Maciej

    2012-01-01

    Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes. PMID:22952572

  20. Erythrocyte enrichment in hematopoietic progenitor cell cultures based on magnetic susceptibility of the hemoglobin.

    PubMed

    Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V; Moore, Lee R; Chalmers, Jeffrey J; Zborowski, Maciej

    2012-01-01

    Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes.

  1. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph

    SciTech Connect

    Dunfield, P.F. |; Liesack, W.; Henckel, T.; Conrad, R.; Knowles, R.

    1999-03-01

    Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH{sub 4}). After 4 years of growth and periodic dilution, a mixed culture was obtained which displayed an apparent half-saturation constant [K{sub m(app)}] for CH{sub 4} of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the K{sub m(app)} increased when the culture was transferred to higher mixing ratios of CH{sub 4}. Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH{sub 4} revealed a single gene product of pmoA, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH{sub 4} and phylogenetically positioned based on its 16S rRNA, pmoA, and mxaF gene sequences as a type II strain of the Methlocystis/Methylosinus group. A coculture of this strain with a Variovorax sp., when grown on <275 ppmv of CH{sub 4}, had a K{sub m(app)} similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH{sub 4} varies with growth conditions and that the oxidation of atmospheric CH{sub 4} observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species.

  2. Microbial characterization of anode-respiring bacteria within biofilms developed from cultures previously enriched in dissimilatory metal-reducing bacteria.

    PubMed

    Pierra, Mélanie; Carmona-Martínez, Alessandro A; Trably, Eric; Godon, Jean-Jacques; Bernet, Nicolas

    2015-11-01

    This work evaluated the use of a culture enriched in DMRB as a strategy to enrich ARB on anodes. DMRB were enriched with Fe(III) as final electron acceptor and then transferred to a potentiostatically-controlled system with an anode as sole final electron acceptor. Three successive iron-enrichment cultures were carried out. The first step of enrichment revealed a successful selection of the high current-producing ARB Geoalkalibacter subterraneus. After few successive enrichment steps, the microbial community analysis in electroactive biofilms showed a significant divergence with an impact on the biofilm electroactivity. Enrichment of ARB in electroactive biofilms through the pre-selection of DMRB should therefore be carefully considered.

  3. Developments in techniques for the isolation, enrichment, main culture conditions and identification of spermatogonial stem cells.

    PubMed

    He, Yanan; Chen, Xiaoli; Zhu, Huabin; Wang, Dong

    2015-12-01

    The in vitro culture system of spermatogonial stem cells (SSCs) provides a basis for studies on spermatogenesis, and also contributes to the development of new methods for the preservation of livestock and animal genetic modification. In vitro culture systems have mainly been established for mouse SSCs, but are lacking for farm animals. We reviewed and analyzed the current progress in SSC techniques such as isolation, purification, cultivation and identification. Based on the published studies, we concluded that two-step enzyme digestion and magnetic-activated cell sorting are fast becoming the main methods for isolation and enrichment of SSCs. With regard to the culture systems, serum and feeders were earlier thought to play an important role in the self-renewal and proliferation of SSCs, but serum- and feeder-free culture systems as a means of overcoming the limitations of SSC differentiation in long-term SSC culture are being explored. However, there is still a need to establish more efficient and ideal culture systems that can also be used for SSC culture in larger mammals. Although the lack of SSC-specific surface markers has seriously affected the efficiency of purification and identification, the transgenic study is helpful for our identification of SSCs. Therefore, future studies on SSC techniques should focus on improving serum- and feeder-free culture techniques, and discovering and identifying specific surface markers of SSCs, which will provide new ideas for the optimization of SSC culture systems for mice and promote related studies in farm animals.

  4. Innovative Approaches Using Lichen Enriched Media to Improve Isolation and Culturability of Lichen Associated Bacteria

    PubMed Central

    Biosca, Elena G.; Flores, Raquel; Santander, Ricardo D.; Díez-Gil, José Luis; Barreno, Eva

    2016-01-01

    Lichens, self-supporting mutualistic associations between a fungal partner and one or more photosynthetic partners, also harbor non-photosynthetic bacteria. The diversity and contribution of these bacteria to the functioning of lichen symbiosis have recently begun to be studied, often by culture-independent techniques due to difficulties in their isolation and culture. However, culturing as yet unculturable lichenic bacteria is critical to unravel their potential functional roles in lichen symbiogenesis, to explore and exploit their biotechnological potential and for the description of new taxa. Our objective was to improve the recovery of lichen associated bacteria by developing novel isolation and culture approaches, initially using the lichen Pseudevernia furfuracea. We evaluated the effect of newly developed media enriched with novel lichen extracts, as well as the influence of thalli washing time and different disinfection and processing protocols of thalli. The developed methodology included: i) the use of lichen enriched media to mimic lichen nutrients, supplemented with the fungicide natamycin; ii) an extended washing of thalli to increase the recovery of ectolichenic bacteria, thus allowing the disinfection of thalli to be discarded, hence enhancing endolichenic bacteria recovery; and iii) the use of an antioxidant buffer to prevent or reduce oxidative stress during thalli disruption. The optimized methodology allowed significant increases in the number and diversity of culturable bacteria associated with P. furfuracea, and it was also successfully applied to the lichens Ramalina farinacea and Parmotrema pseudotinctorum. Furthermore, we provide, for the first time, data on the abundance of culturable ecto- and endolichenic bacteria that naturally colonize P. furfuracea, R. farinacea and P. pseudotinctorum, some of which were only able to grow on lichen enriched media. This innovative methodology is also applicable to other microorganisms inhabiting these

  5. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

    PubMed Central

    Tan, Boonfei; Jane Fowler, S; Laban, Nidal Abu; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

    2015-01-01

    Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities. PMID:25734684

  6. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples.

    PubMed

    Tan, Boonfei; Fowler, S Jane; Abu Laban, Nidal; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

    2015-09-01

    Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.

  7. Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots.

    PubMed

    Simon, Holly M; Jahn, Courtney E; Bergerud, Luke T; Sliwinski, Marek K; Weimer, Paul J; Willis, David K; Goodman, Robert M

    2005-08-01

    Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.

  8. Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots

    PubMed Central

    Simon, Holly M.; Jahn, Courtney E.; Bergerud, Luke T.; Sliwinski, Marek K.; Weimer, Paul J.; Willis, David K.; Goodman, Robert M.

    2005-01-01

    Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture. PMID:16085872

  9. Biodegradation of munitions compounds by a sulfate reducing bacterial enrichment culture

    SciTech Connect

    Boopathy, R.; Manning, J.

    1997-08-01

    The degradation of several munitions compounds was studied. The compounds included 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine, 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrotoluene. All of the compounds studied were degraded by the sulfate reducing bacterial (SRB) enrichment culture. The SRB culture did not use the munitions compounds as their sole source of carbon. However, all the munitions compounds tested served as the sole source of nitrogen for the SRB culture. Degradation of munitions compounds was achieved by a co-metabolic process. The SRB culture used a variety of carbon sources including pyruvate, ethanol, formate, lactate, and H{sub 2}-CO{sub 2}. The SRB culture was an incomplete oxidizer, unable to carry out the terminal oxidation of organic substrates to CO{sub 2} as the sole product, and it did not use acetate or methanol as a carbon source. In addition to serving as nitrogen sources, the munitions compounds also served as electron acceptors in the absence of sulfate. A soil slurry experiment with 5% and 10% munitions compounds-contaminated soil showed that the contaminant TNT was metabolized by the SRB culture in the presence of pyruvate as electron donor. This culture may be useful in decontaminating munitions compounds-contaminated soil and water under anaerobic conditions.

  10. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    PubMed

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  11. High-efficiency hydrogen production by an anaerobic, thermophilic enrichment culture from an Icelandic hot spring.

    PubMed

    Koskinen, Perttu E P; Lay, Chyi-How; Puhakka, Jaakko A; Lin, Ping-Jei; Wu, Shu-Yii; Orlygsson, Jóhann; Lin, Chiu-Yue

    2008-11-01

    Dark fermentative hydrogen production from glucose by a thermophilic culture (33HL), enriched from an Icelandic hot spring sediment sample, was studied in two continuous-flow, completely stirred tank reactors (CSTR1, CSTR2) and in one semi-continuous, anaerobic sequencing batch reactor (ASBR) at 58 degrees C. The 33HL produced H2 yield (HY) of up to 3.2 mol-H2/mol-glucose along with acetate in batch assay. In the CSTR1 with 33HL inoculum, H2 production was unstable. In the ASBR, maintained with 33HL, the H2 production enhanced after the addition of 6 mg/L of FeSO4 x H2O resulting in HY up to 2.51 mol-H2/mol-glucose (H2 production rate (HPR) of 7.85 mmol/h/L). The H2 production increase was associated with an increase in butyrate production. In the CSTR2, with ASBR inoculum and FeSO4 supplementation, stable, high-rate H2 production was obtained with HPR up to 45.8 mmol/h/L (1.1 L/h/L) and HY of 1.54 mol-H2/mol-glucose. The 33HL batch enrichment was dominated by bacterial strains closely affiliated with Thermobrachium celere (99.8-100%). T. celere affiliated strains, however, did not thrive in the three open system bioreactors. Instead, Thermoanaerobacterium aotearoense (98.5-99.6%) affiliated strains, producing H2 along with butyrate and acetate, dominated the reactor cultures. This culture had higher H2 production efficiency (HY and specific HPR) than reported for mesophilic mixed cultures. Further, the thermophilic culture readily formed granules in CSTR and ASBR systems. In summary, the thermophilic culture as characterized by high H2 production efficiency and ready granulation is considered very promising for H2 fermentation from carbohydrates.

  12. Integrated biogas upgrading and hydrogen utilization in an anaerobic reactor containing enriched hydrogenotrophic methanogenic culture.

    PubMed

    Luo, Gang; Angelidaki, Irini

    2012-11-01

    Biogas produced by anaerobic digestion, is mainly used in a gas motor for heat and electricity production. However, after removal of CO(2) , biogas can be upgraded to natural gas quality, giving more utilization possibilities, such as utilization as autogas, or distant utilization by using the existing natural gas grid. The current study presents a new biological method for biogas upgrading in a separate biogas reactor, containing enriched hydrogenotrophic methanogens and fed with biogas and hydrogen. Both mesophilic- and thermophilic anaerobic cultures were enriched to convert CO(2) to CH(4) by addition of H(2) . Enrichment at thermophilic temperature (55°C) resulted in CO(2) and H(2) bioconversion rate of 320 mL CH(4) /(gVSS h), which was more than 60% higher than that under mesophilic temperature (37°C). Different dominant species were found at mesophilic- and thermophilic-enriched cultures, as revealed by PCR-DGGE. Nonetheless, they all belonged to the order Methanobacteriales, which can mediate hydrogenotrophic methanogenesis. Biogas upgrading was then tested in a thermophilic anaerobic reactor under various operation conditions. By continuous addition of hydrogen in the biogas reactor, high degree of biogas upgrading was achieved. The produced biogas had a CH(4) content, around 95% at steady-state, at gas (mixture of biogas and hydrogen) injection rate of 6 L/(L day). The increase of gas injection rate to 12 L/(L day) resulted in the decrease of CH(4) content to around 90%. Further study showed that by decreasing the gas-liquid mass transfer by increasing the stirring speed of the mixture the CH(4) content was increased to around 95%. Finally, the CH(4) content around 90% was achieved in this study with the gas injection rate as high as 24 L/(L day).

  13. Molecular Detection of Culture-Confirmed Bacterial Bloodstream Infections with Limited Enrichment Time

    PubMed Central

    Moore, Miranda S.; McCann, Chase D.

    2013-01-01

    Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and pyrosequencing protocols, the molecular approach yielded results in 11.8 ± 2.9 h compared to means of 27.9 ± 13.6 h to obtain the Gram stain results and 81.6 ± 24.0 h to generate the final culture-based identification. The molecular approach enabled accurate detection of most bacteria present in incubating blood culture bottles on average about 16 h sooner than Gram stain results became available and approximately 3 days sooner than the phenotypic identification was entered in the Laboratory Information System. If implemented, this more rapid molecular approach could minimize the number of doses of unnecessary or ineffective antibiotics administered to patients. PMID:23985915

  14. Thermolabile triose phosphate isomerase in a psychrophilic Clostridium.

    NASA Technical Reports Server (NTRS)

    Shing, Y. W.; Akagi, J. M.; Himes, R. H.

    1972-01-01

    It was found that a psychrophilic Clostridium contains a triose phosphate isomerase which is very labile at moderate temperatures. An investigation showed that the optimal growth temperature of the psychrophile was between 15 and 20 deg C. No growth occurred at 25 deg C. The thermostability of the glycolytic enzymes in the cell-free extracts of Clostridium sp. strain 69 was studied. The data obtained show that the triose phosphate isomerase is quite labile at moderate temperatures. The instability of the enzyme is sufficient to explain the low maximum growth temperature of the psychrophile.

  15. Anaerobic Degradation of Pristane in Nitrate-Reducing Microcosms and Enrichment Cultures

    PubMed Central

    Bregnard, T. P.; Haner, A.; Hohener, P.; Zeyer, J.

    1997-01-01

    Microcosm studies were conducted under nitrate-reducing conditions with diesel fuel-contaminated aquifer material from a site treated by in situ bioremediation. In the microcosms, the consumption of nitrate and the production of inorganic carbon were strongly stimulated by the addition of the isoprenoid alkane pristane (2,6,10,14-tetramethylpentadecane). Within 102 days enrichment cultures degraded more than 90% of the pristane supplied as coatings on reticulated sinter glass rings. The study demonstrates that pristane can no longer be regarded as recalcitrant under anaerobic conditions. PMID:16535616

  16. Neonicotinoid Insecticides Alter the Gene Expression Profile of Neuron-Enriched Cultures from Neonatal Rat Cerebellum

    PubMed Central

    Kimura-Kuroda, Junko; Nishito, Yasumasa; Yanagisawa, Hiroko; Kuroda, Yoichiro; Komuta, Yukari; Kawano, Hitoshi; Hayashi, Masaharu

    2016-01-01

    Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children’s health. Here we examined the effects of long-term (14 days) and low dose (1 μM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, ≥1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain. PMID:27782041

  17. Neonicotinoid Insecticides Alter the Gene Expression Profile of Neuron-Enriched Cultures from Neonatal Rat Cerebellum.

    PubMed

    Kimura-Kuroda, Junko; Nishito, Yasumasa; Yanagisawa, Hiroko; Kuroda, Yoichiro; Komuta, Yukari; Kawano, Hitoshi; Hayashi, Masaharu

    2016-10-04

    Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children's health. Here we examined the effects of longterm (14 days) and low dose (1 μM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, ≥1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain.

  18. Effect of oxygen enrichment on morphology, growth, and heterologous protein production in chemostat cultures of Aspergillus niger B1-D.

    PubMed

    Wongwicharn, A; McNeil, B; Harvey, L M

    1999-11-20

    The response of steady state chemostat cultures of a recombinant Aspergillus niger (B1-D), secreting both a heterologous enzyme (Hen Egg White Lysozyme [HEWL]) and a native enzyme (Glucoamylase), to varying levels of O2 enrichment of the process gas was evaluated. Formation of both the native and the foreign enzyme increased with increasing O2 supply. Conversely, biomass levels and total extracellular protein levels were generally not increased under O2 enriched conditions. Two distinct micromorphologies were apparent in these cultures, one, typically seen under O2 limiting conditions (i. e. at 0 and 10% enrichment levels), tended to be represented by long, sparsely branched hyphal elements, with low percentages of "active" length (i. e. how much of the hypha is cytoplasm filled); whilst, a second micromorphology, typical of O2 enriched cultures at 30 and 50% O2 enrichment, was represented by shorter hyphal elements, with more branching and a higher % "active" length. At these higher O2 levels, formation of a yellow pigment occurred, and signs of culture autolysis were noted. At 50% enrichment, a "stranded" aggregate morphology was apparent, possibly as a response to a hyperoxidant state. Production of both the native enzyme and HEWL correlated well with a simple morphological measure (tip number) or, with % "active" length. It is proposed the morphological changes noted in the cultures were associated with the increased production of both HEWL and glucoamylase.

  19. [ATP pool and bioluminescence in psychrophilic bacteria Photobacterium phosphoreum].

    PubMed

    Alekserova, L É; Alenina, K A; Efremenko, E N; Mazhul', M M; Piskunova, N F; Ismailov, A D

    2014-01-01

    Bioluminescence activity and ATP pool were investigated in the culture of psychrophilic bacteria Photobacterium phosphoreum collected-from the exponential and stationary growth phases, as well as immobilized in polyvinyl alcohol (PVA) cryogel. In liquid culture, ATP pool remained at an almost a constant level throughout the luminescence cycle (over 100 h). The ATP pool in the stationary-phase and PVA-immobilizedl cells remained constant throughout their incubation in the medium (over 200 h) and in 3% NaCl solution (over 100 h): Quantitative assessment of integral photon yield and ATP pool indicated that bioluminescence decay in growing or stationary cells was not caused by limitation by the energy substrates of the luciferase reaction. Kinetic and quantitative parameters of emission activity and ATP pool excluded the possibility of formation of the aldehyde substrate for luciferase via reduction of the relevant fatty acids in NADPH and ATP-dependent reductase reaction and its oxidation in the monooxygenase reaction. Our results indicate that the aliphatic aldehyde is not utilized in the process of light emission.

  20. DEPENDENCE OF A HIGH-RATE, PCE-DECHLORINATING ENRICHMENT CULTURE ON METHANOGENIC ACTIVITY. (R825549C053)

    EPA Science Inventory

    The role served by the presence of methanogenic activity within a tetrachloroethene (PCE)-dechlorinating culture was investigated through a series of supplementation experiments. An acclimated lactate-enrichment culture (LEC 1) capable of rapidly converting PCE to ethene was s...

  1. Dry-heat resistance of selected psychrophiles.

    PubMed

    Winans, L; Pflug, I J; Foster, T L

    1977-08-01

    The dry-heat resistance characteristics of spores of psychrophilic organisms isolated from soil samples from the Viking spacecraft assembly areas at Cape Kennedy Space Flight Center, Cape Canaveral, Fla., were studied. Spore suspensions were produced, and dry-heat D values were determined for the microorganisms that demonstrated growth or survival under a simulated Martian environment. The dry-heat tests were carried out by using the planchet-boat-hot plate system at 110 and 125 degrees C with an ambient relative humidity of 50% at 22 degrees C. The spores evaluated had a relatively low resistance to dry heat. D(110 degrees C) values ranged from 7.5 to 122 min, whereas the D(123 degrees C) values ranged from less than 1.0 to 9.8 min.

  2. Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph

    2002-01-01

    Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryopreserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 C. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep-sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica

  3. Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph; Six, N. Frank (Technical Monitor)

    2001-01-01

    Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryo-preserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 T. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica

  4. Impact of arachidonic acid enrichment of live rotifer prey on bacterial communities in rotifer and larval fish cultures.

    PubMed

    Seychelles, Laurent H; Doiron, Kim; Audet, Céline; Tremblay, Réjean; Pernet, Fabrice; Lemarchand, Karine

    2013-03-01

    Rotifers (Brachionus plicatilis), commonly used at first feeding in commercial fish hatcheries, carry a large bacteria load. Because they are relatively poor in essential fatty acids, it is common practice to enrich them with fatty acids, including arachidonic acid (AA). This study aims to determine whether prey enrichment with AA may act as a prebiotic and modify the microbial community composition either in AA-enriched rotifer cultures or in larval-rearing water using winter flounder (Pseudopleuronectes americanus) as a larval fish model. AA enrichment modified the bacterial community composition in both the rotifer culture tanks and the larval-rearing tanks. We observed an increase in the number of cultivable bacteria on TCBS (thiosulfate-citrate-bile salts-sucrose) agar, used as a proxy for the abundance of Vibrio sp. The results suggest that AA may also play an indirect role in larval health.

  5. Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures

    USGS Publications Warehouse

    Goodwin, K.D.; Schaefer, J.K.; Oremland, R.S.

    1998-01-01

    Bacterial oxidation of 14CH2Br2 and 14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of 14CH2Br2 and comparatively less 14CH3Br. Bacterial oxidation of 14CH3Br was rapid in freshwater samples compared to bacterial oxidation of 14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2 was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2 as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.

  6. Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture.

    PubMed

    Callac, Nolwenn; Rouxel, Olivier; Lesongeur, Françoise; Liorzou, Céline; Bollinger, Claire; Pignet, Patricia; Chéron, Sandrine; Fouquet, Yves; Rommevaux-Jestin, Céline; Godfroy, Anne

    2015-05-01

    Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

  7. Persistence of pentolite (PETN and TNT) in soil microcosms and microbial enrichment cultures.

    PubMed

    Arbeli, Ziv; Garcia-Bonilla, Erika; Pardo, Cindy; Hidalgo, Kelly; Velásquez, Trigal; Peña, Luis; C, Eliana Ramos; Avila-Arias, Helena; Molano-Gonzalez, Nicolás; Brandão, Pedro F B; Roldan, Fabio

    2016-05-01

    Pentolite is a mixture (1:1) of 2,4,6-trinitrotoluene (TNT) and pentaerythritol tetranitrate (PETN), and little is known about its fate in the environment. This study was aimed to determine the dissipation of pentolite in soils under laboratory conditions. Microcosm experiments conducted with two soils demonstrated that dissipation rate of PETN was significantly slower than that of TNT. Interestingly, the dissipation of PETN was enhanced by the presence of TNT, while PETN did not enhanced the dissipation of TNT. Pentolite dissipation rate was significantly faster under biostimulation treatment (addition of carbon source) in soil from the artificial wetland, while no such stimulation was observed in soil from detonation field. In addition, the dissipation rate of TNT and PETN in soil from artificial wetland under biostimulation was significantly faster than the equivalent abiotic control, although it seems that non-biological processes might also be important for the dissipation of TNT and PETN. Transformation of PETN was also slower during establishment of enrichment culture using pentolite as the sole nitrogen source. In addition, transformation of these explosives was gradually reduced and practically stopped after the forth cultures transfer (80 days). DGGE analysis of bacterial communities from these cultures indicates that all consortia were dominated by bacteria from the order Burkholderiales and Rhodanobacter. In conclusion, our results suggest that PETN might be more persistent than TNT.

  8. Reductive dechlorination of tetrachloroethene to cis-1, 2-dichloroethene by a thermophilic anaerobic enrichment culture.

    PubMed

    Kengen, S W; Breidenbach, C G; Felske, A; Stams, A J; Schraa, G; de Vos, W M

    1999-06-01

    Thermophilic anaerobic biodegradation of tetrachloroethene (PCE) was investigated with various inocula from geothermal and nongeothermal areas. Only polluted harbor sediment resulted in a stable enrichment culture that converted PCE via trichloroethene to cis-1, 2-dichloroethene at the optimum temperature of 60 to 65 degrees C. After several transfers, methanogens were eliminated from the culture. Dechlorination was supported by lactate, pyruvate, fructose, fumarate, and malate as electron donor but not by H2, formate, or acetate. Fumarate and L-malate led to the highest dechlorination rate. In the absence of PCE, fumarate was fermented to acetate, H2, CO2, and succinate. With PCE, less H2 was formed, suggesting that PCE competed for the reducing equivalents leading to H2. PCE dechlorination, apparently, was not outcompeted by fumarate as electron acceptor. At the optimum dissolved PCE concentration of approximately 60 microM, a high dechlorination rate of 1.1 micromol h-1 mg-1 (dry weight) was found, which indicates that the dechlorination is not a cometabolic activity. Microscopic analysis of the fumarate-grown culture showed the dominance of a long thin rod. Molecular analysis, however, indicated the presence of two dominant species, both belonging to the low-G+C gram positives. The highest similarity was found with the genus Dehalobacter (90%), represented by the halorespiring organism Dehalobacter restrictus, and with the genus Desulfotomaculum (86%).

  9. Reductive Dechlorination of Tetrachloroethene to cis-1,2-Dichloroethene by a Thermophilic Anaerobic Enrichment Culture

    PubMed Central

    Kengen, Servé W. M.; Breidenbach, Caroline G.; Felske, Andreas; Stams, Alfons J. M.; Schraa, Gosse; de Vos, Willem M.

    1999-01-01

    Thermophilic anaerobic biodegradation of tetrachloroethene (PCE) was investigated with various inocula from geothermal and nongeothermal areas. Only polluted harbor sediment resulted in a stable enrichment culture that converted PCE via trichloroethene to cis-1,2-dichloroethene at the optimum temperature of 60 to 65°C. After several transfers, methanogens were eliminated from the culture. Dechlorination was supported by lactate, pyruvate, fructose, fumarate, and malate as electron donor but not by H2, formate, or acetate. Fumarate and l-malate led to the highest dechlorination rate. In the absence of PCE, fumarate was fermented to acetate, H2, CO2, and succinate. With PCE, less H2 was formed, suggesting that PCE competed for the reducing equivalents leading to H2. PCE dechlorination, apparently, was not outcompeted by fumarate as electron acceptor. At the optimum dissolved PCE concentration of ∼60 μM, a high dechlorination rate of 1.1 μmol h−1 mg−1 (dry weight) was found, which indicates that the dechlorination is not a cometabolic activity. Microscopic analysis of the fumarate-grown culture showed the dominance of a long thin rod. Molecular analysis, however, indicated the presence of two dominant species, both belonging to the low-G+C gram positives. The highest similarity was found with the genus Dehalobacter (90%), represented by the halorespiring organism Dehalobacter restrictus, and with the genus Desulfotomaculum (86%). PMID:10347007

  10. Detection of Yersinia spp. in meat products by enrichment culture, immunomagnetic separation and nested PCR.

    PubMed

    Estrada, Cecilia S M Lucero; Velázquez, Lidia Del Carmen; Favier, Gabriela Isabel; Genaro, María Silvia Di; Escudero, María Esther

    2012-05-01

    The prevalence of Yersinia enterocolitica in meat products was assessed by four methods: cold enrichment in trypticase soy broth (A), enrichment in modified Rappaport broth at 25 °C (B), concentration by immunomagnetic separation (C) and yadA nested PCR (D). Furthermore, the pathogenic potentials of the isolates were established by phenotypic and genotypic tests, and their genomic relationships were determined by pulsed-field gel electrophoresis (PFGE). A total of 238 samples were collected at retail level in the city of San Luis, Argentina, during the period 2007-2008. The highest Yersinia prevalence in meat products was observed by method D (92 positive samples), followed by methods A (13 positive samples) and C (5 positive samples); however, no isolation was obtained by method B. Fourteen Y. enterocolitica and 4 Yersinia intermedia strains were recovered by culture. All Y. enterocolitica 2/O:9 strains gave results related to virulence by phenotypic tests and exhibited the genotype virF(+)myfA(+)ail(+)ystA(+). Two biotype 1A strains showed a genotype virF(-)myfA(-)ail(+)ystA(+)ystB(+). The 14 Y. enterocolitica strains isolated during this work plus one reference strain were separated into 11 genomic types by PFGE. This genomic heterogeneity of the isolates shows the diversity of Y. enterocolitica strains in our region. It is the first time that IMS was used to search Y. enterocolitica strains from naturally contaminated meat products.

  11. Selective enrichment and production of highly urease active bacteria by non-sterile (open) chemostat culture.

    PubMed

    Cheng, Liang; Cord-Ruwisch, Ralf

    2013-10-01

    In general, bioprocesses can be subdivided into naturally occurring processes, not requiring sterility (e.g., beer brewing, wine making, lactic acid fermentation, or biogas digestion) and other processes (e.g., the production of enzymes and antibiotics) that typically require a high level of sterility to avoid contaminant microbes overgrowing the production strain. The current paper describes the sustainable, non-sterile production of an industrial enzyme using activated sludge as inoculum. By using selective conditions (high pH, high ammonia concentration, and presence of urea) for the target bacterium, highly active ureolytic bacteria, physiologically resembling Sporosarcina pasteurii were reproducibly enriched and then continuously produced via chemostat operation of the bioreactor. When using a pH of 10 and about 0.2 M urea in a yeast extract-based medium, ureolytic bacteria developed under aerobic chemostat operation at hydraulic retention times of about 10 h with urease levels of about 60 μmol min⁻¹ ml⁻¹ culture. For cost minimization at an industrial scale the costly protein-rich yeast extract medium could be replaced by commercial milk powder or by lysed activated sludge. Glutamate, molasses, or glucose-based media did not result in the enrichment of ureolytic bacteria by the chemostat. The concentration of intracellular urease was sufficiently high such that the produced raw effluent from the reactor could be used directly for biocementation in the field.

  12. Development of bioconcrete material using an enrichment culture of novel thermophilic anaerobic bacteria.

    PubMed

    Ghosh, P; Mandal, S; Pal, S; Bandyopadhyaya, G; Chattopadhyay, B D

    2006-04-01

    In the biosphere, bacteria can function as geo-chemical agents, promoting the dispersion, fractionation and/or concentration of materials. Microbial mineral precipitation is resulted from metabolic activities of microorganisms. Based on this biomineralogy concept, an attempt has been made to develop bioconcrete material incorporating of an enrichment culture of thermophilic and anaerobic bacteria within cement-sand mortar/concrete. The results showed a significant increase in compressive strength of both cement-sand mortar and concrete due to the development of filler material within the pores of cement sand matrix. Maximum strength was observed at concentration 10(5)cell/ml of water used in mortar/concrete. Addition of Escherichia coil or media composition on mortar showed no such improvement in strength.

  13. Study of selenocompounds from selenium-enriched culture of edible sprouts.

    PubMed

    Funes-Collado, Virginia; Morell-Garcia, Albert; Rubio, Roser; López-Sánchez, José Fermín

    2013-12-15

    Selenium is recognised as an essential micronutrient for humans and animals. One of the main sources of selenocompounds in the human diet is vegetables. Therefore, this study deals with the Se species present in different edible sprouts grown in Se-enriched media. We grew alfalfa, lentil and soy in a hydroponic system amended with soluble salts, containing the same proportion of Se, in the form of Se(VI) and Se(IV). Total Se in the sprouts was determined by acidic digestion in a microwave system and by ICP/MS. Se speciation was carried out by enzymatic extraction (Protease XIV) and measured by LC-ICP/MS. The study shows that the Se content of plants depends on the content in the growth culture, and that part of the inorganic Se was biotransformed mainly into SeMet. These results contribute to our understanding of the uptake of inorganic Se and its biotransformation by edible plants.

  14. Inhibitory effect of 5- and 6-ring PAHs on pyrene mineralization by a mixed enrichment culture

    SciTech Connect

    Molina, M.; Agraujo, R.

    1995-12-31

    This research investigates the mineralization of pyrene in mixtures of PAHs to identify potential synergistic or antagonistic interactions that affect the degradation of individual compounds. Mineralization of {sup 14}C pyrene (25 RM) by a mixed enrichment culture was studied in systems containing mixtures of 5- and 6-ring PAHs in minimal salts medium (MSM). In the absence of the High Molecular Weight (HMW)-PAHs, the culture mineralized 62% of the added pyrene. Addition of an equal mixture of benzo(a)pyrene, dibenzanthracene, and benzo(g,h,i)peryiene (25 {micro}M total concentration) reduced pyrene mineralization to 25% after a 9-day lag phase. An increase on the molar concentration of the HMW-PAH mixture to 75 and 125 {micro}M decreased pyrene mineralization to 9.2 and 1%, respectively. Results from treatments containing individual (25 {micro}M each), or pairs of the HMW-compounds demonstrated that none of the three individual compounds caused a significant reduction in the extent of pyrene mineralization. However, the combination of benzo(a)pyrene and benzanthracene significantly inhibited pyrene activity. In addition, the presence of both benzo(a)pyrene and benzo(g,h,i)peryiene reduced mineralization by almost 23%. Determination of bacterial density by epifluorescence microscopy showed that mineralization of pyrene coincides with growth of the bacterial culture; presence of the 5- and 6-ring PAHs delayed growth with a concurrent inhibition of mineralization. When growth resumes, the inhibitory effect is reduced. A decrease of pyrene inhibition was also noted when MSM was replaced with sediment extract, or when sediment (1 {micro}g/ml) was added to the medium. These results suggest a synergistic inhibitory effect by combinations of specific HMW-PAHs rather than inhibition by individual compounds of the mixture on both the growth of the bacterial culture and the extent of pyrene mineralization.

  15. Genomics of an extreme psychrophile, Psychromonas ingrahamii

    SciTech Connect

    Riley, Monica; Staley, James T.; Danchin, Antoine; Wang, T.; Brettin, Tom; Hauser, Loren John; Land, Miriam L; Thompson, Linda S

    2008-05-01

    Background: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Results: Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. Conclusion: The results of this genomic analysis provide a

  16. Genomics of an extreme psychrophile, Psychromonas ingrahamii

    PubMed Central

    Riley, Monica; Staley, James T; Danchin, Antoine; Wang, Ting Zhang; Brettin, Thomas S; Hauser, Loren J; Land, Miriam L; Thompson, Linda S

    2008-01-01

    Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Results Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. Conclusion The results of this genomic analysis provide a

  17. Selective enrichment media bias the types of salmonella enterica strains isolated from mixed strain cultures and complex enrichment broths

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For foodborne outbreak investigations it can be difficult to isolate the relevant strain from food and/or environmental sources. If the sample is contaminated by more than one strain of the organism the relevant strain might be missed. In this study mixed cultures of Salmonella enterica were grown...

  18. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures.

    PubMed

    Sosa, Oscar A; Gifford, Scott M; Repeta, Daniel J; DeLong, Edward F

    2015-12-01

    The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4-6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.

  19. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures

    PubMed Central

    Sosa, Oscar A; Gifford, Scott M; Repeta, Daniel J; DeLong, Edward F

    2015-01-01

    The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them. PMID:25978545

  20. MICROBIAL REDUCTIVE DECHLORINATION OF HEXACHLORO-1,3-BUTADIENE IN A METHANOGENIC ENRICHMENT CULTURE. (R825513C007)

    EPA Science Inventory

    Sequential reductive dechlorination of hexachloro-1,3-butadiene (HCBD) was achieved by a mixed, methanogenic culture enriched from a contaminated estuarine sediment. Both methanol and lactate served as carbon and electron sources. Methanol was stoichiometrically converted to m...

  1. Structural investigation and biological activity of the lipooligosaccharide from the psychrophilic bacterium Pseudoalteromonas haloplanktis TAB 23.

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Parrilli, Ermenegilda; Tutino, Maria L; Gemma, Sabrina; Molteni, Monica; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, Maria M

    2011-06-14

    Pseudoalteromonas haloplanktis TAB 23 is a Gram-negative psychrophilic bacterium isolated from the Antarctic coastal sea. To survive in these conditions psychrophilic bacteria have evolved typical membrane lipids and "antifreeze" proteins to protect the inner side of the microorganism. As for Gram-negative bacteria, the outer membrane is mainly constituted by lipopoly- or lipooligosaccharides (LPS or LOS, respectively), which lean towards the external environment. Despite this, very little is known about the peculiarity of LPS from Gram-negative psychrophilic bacteria and what their role is in adaptation to cold temperature. Here we report the complete structure of the LOS from P. haloplanktis TAB 23. The lipid A was characterized by MALDI-TOF MS analysis and was tested in vitro showing a significant inhibitory effect on the LPS-induced pro-inflammatory cytokine production when added in culture with LPS from Escherichia coli. The product obtained after de-O-acylation of the LPS was analyzed by MALDI-TOF MS revealing the presence of several molecular species, differing in phosphorylation degree and oligosaccharide length. The oligosaccharide portion released after strong alkaline hydrolysis was purified by anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) to give three main fractions, characterized by means of 2D NMR spectroscopy, which showed a very short highly phosphorylated saccharidic chain with the following general structure. α-Hepp3R,6R,4R'-(1→5)-α-Kdop4P-(2→6)-β-GlcpN4R-(1→6)-α-GlcpN1P (R=-H(2)PO(3) or -H; R'=α-Galp-(1→4)-β-Galp-(1→ or H-).

  2. The Learning Effects of an Ecology Enrichment Summer Program on Gifted Students from Mainstream and Diverse Cultural Backgrounds: A Preliminary Study

    ERIC Educational Resources Information Center

    Wang, Wen-Ling; Wu, Jiun-Wei; Lin, Yu-Chin

    2006-01-01

    Enrichment is one of the important educational models for gifted students. However, the research on gifted enrichment programs rarely leads to instructional interventions for culturally diverse students. The purposes of this study were: (a) to propose an ecology enrichment summer program for gifted students from mainstream and diverse cultural…

  3. Sphere Culture of Murine Lung Cancer Cell Lines Are Enriched with Cancer Initiating Cells

    PubMed Central

    Morrison, Brian J.

    2012-01-01

    Cancer initiating cells (CICs) represent a unique cell population essential for the maintenance and growth of tumors. Most in vivo studies of CICs utilize human tumor xenografts in immunodeficient mice. These models provide limited information on the interaction of CICs with the host immune system and are of limited value in assessing therapies targeting CICs, especially immune-based therapies. To assess this, a syngeneic cancer model is needed. We examined the sphere-forming capacity of thirteen murine lung cancer cell lines and identified TC-1 and a metastatic subclone of Lewis lung carcinoma (HM-LLC) as cell lines that readily formed and maintained spheres over multiple passages. TC-1 tumorspheres were not enriched for expression of CD133 or CD44, putative CIC markers, nor did they demonstrate Hoechst 33342 side population staining or Aldefluor activity compared to adherent TC-1 cells. However, in tumorsphere culture, these cells exhibited self-renewal and long-term symmetric division capacity and expressed more Oct-4 compared to adherent cells. HM-LLC sphere-derived cells exhibited increased Oct-4, CD133, and CD44 expression, demonstrated a Hoechst 33342 side population and Aldefluor activity compared to adherent cells or a low metastatic subclone of LLC (LM-LLC). In syngeneic mice, HM-LLC sphere-derived cells required fewer cells to initiate tumorigenesis compared to adherent or LM-LLC cells. Similarly TC-1 sphere-derived cells were more tumorigenic than adherent cells in syngeneic mice. In contrast, in immunocompromised mice, less than 500 sphere or adherent TC-1 cells and less than 1,000 sphere or adherent LLC cells were required to initiate a tumor. We suggest that no single phenotypic marker can identify CICs in murine lung cancer cell lines. Tumorsphere culture may provide an alternative approach to identify and enrich for murine lung CICs. Furthermore, we propose that assessing tumorigenicity of murine lung CICs in syngeneic mice better models the

  4. Some like it cold: understanding the survival strategies of psychrophiles

    PubMed Central

    De Maayer, Pieter; Anderson, Dominique; Cary, Craig; Cowan, Don A

    2014-01-01

    Much of the Earth’s surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern “omic” technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field. PMID:24671034

  5. The Culture of Cancer Cell Lines as Tumorspheres Does Not Systematically Result in Cancer Stem Cell Enrichment

    PubMed Central

    Calvet, Christophe Y.; André, Franck M.; Mir, Lluis M.

    2014-01-01

    Cancer stem cells (CSC) have raised great excitement during the last decade and are promising targets for an efficient treatment of tumors without relapses and metastases. Among the various methods that enable to enrich cancer cell lines in CSC, tumorspheres culture has been predominantly used. In this report, we attempted to generate tumorspheres from several murine and human cancer cell lines: B16-F10, HT-29, MCF-7 and MDA-MB-231 cells. Tumorspheres were obtained with variable efficiencies from all cell lines except from MDA-MB-231 cells. Then, we studied several CSC characteristics in both tumorspheres and adherent cultures of the B16-F10, HT-29 and MCF-7 cells. Unexpectedly, tumorspheres-forming cells were less clonogenic and, in the case of B16-F10, less proliferative than attached cells. In addition, we did not observe any enrichment in the population expressing CSC surface markers in tumorspheres from B16-F10 (CD133, CD44 and CD24 markers) or MCF-7 (CD44 and CD24 markers) cells. On the contrary, tumorspheres culture of HT-29 cells appeared to enrich in cells expressing colon CSC markers, i.e. CD133 and CD44 proteins. For the B16-F10 cell line, when 1 000 cells were injected in syngenic C57BL/6 mice, tumorspheres-forming cells displayed a significantly lower tumorigenic potential than adherent cells. Finally, tumorspheres culture of B16-F10 cells induced a down-regulation of vimentin which could explain, at least partially, the lower tumorigenicity of tumorspheres-forming cells. All these results, along with the literature, indicate that tumorspheres culture of cancer cell lines can induce an enrichment in CSC but in a cell line-dependent manner. In conclusion, extensive characterization of CSC properties in tumorspheres derived from any cancer cell line or cancer tissue must be performed in order to ensure that the generated tumorspheres are actually enriched in CSC. PMID:24586931

  6. Unique Kinetic Properties of Phenol-Degrading Variovorax Strains Responsible for Efficient Trichloroethylene Degradation in a Chemostat Enrichment Culture

    PubMed Central

    Futamata, Hiroyuki; Nagano, Yayoi; Watanabe, Kazuya; Hiraishi, Akira

    2005-01-01

    A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities (H. Futamata, S. Harayama, and K. Watanabe, Appl. Environ. Microbiol. 67:4671-4677, 2001). To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter−1 day−1) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter−1 day−1 (enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a Variovorax ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus Variovorax and were shown to have high-affinity-type LmPHs. The LmPH of the Variovorax strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the Variovorax strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information

  7. Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment.

    PubMed

    Könneke, Martin; Kuever, Jan; Galushko, Alexander; Jørgensen, Bo Barker

    2013-03-01

    A sulfate-reducing bacterium, designated JHA1(T), was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 °C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1(T) was a psychrophile, growing fastest between 14 and 16 °C and not growing above 20 °C. Fastest growth was found at neutral pH (pH 7.2-7.4) and at marine concentrations of NaCl (20-30 g l(-1)). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1(T) was a member of the family Desulfobacteraceae in the Deltaproteobacteria. The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384(T) and Desulfobacula toluolica DSM 7467(T) (both <95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1(T) grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1(T) could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl. Phylogenetic differentiation from other genera was further supported by DsrAB and AprBA sequence analysis. Based on the described phylogenetic and phenotypic differences between strain JHA1(T) and its closest relatives, the establishment of a novel genus and a novel species, Desulfoconvexum algidum gen. nov., sp. nov. is proposed. The type strain is JHA1(T) ( = DSM 21856(T)  = JCM 16085(T)).

  8. Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

    PubMed

    Oberoi, Akashdeep Singh; Philip, Ligy; Bhallamudi, S Murty

    2015-08-01

    Present study focused on the screening of bacterial consortium for biodegradation of monocyclic aromatic hydrocarbon (MAH) and polycyclic aromatic hydrocarbons (PAHs). Target compounds in the present study were naphthalene, acenaphthene, phenanthrene (PAHs), and benzene (MAH). Microbial consortia enriched with the above target compounds were used in screening experiments. Naphthalene-enriched consortium was found to be the most efficient consortium, based on its substrate degradation rate and its ability to degrade other aromatic pollutants with significantly high efficiency. Substrate degradation rate with naphthalene-enriched culture followed the order benzene > naphthalene > acenaphthene > phenanthrene. Chryseobacterium and Rhodobacter were discerned as the predominant species in naphthalene-enriched culture. They are closely associated to the type strain Chryseobacterium arthrosphaerae and Rhodobacter maris, respectively. Single substrate biodegradation studies with naphthalene (PAH) and benzene (MAH) were carried out using naphthalene-enriched microbial consortium (NAPH). Phenol and 2-hydroxybenzaldehyde were identified as the predominant intermediates during benzene and naphthalene degradation, respectively. Biodegradation of toluene, ethyl benzene, xylene, phenol, and indole by NAPH was also investigated. Monod inhibition model was able to simulate biodegradation kinetics for benzene, whereas multiple substrate biodegradation model was able to simulate biodegradation kinetics for naphthalene.

  9. Anaerobic alkane biodegradation by cultures enriched from oil sands tailings ponds involves multiple species capable of fumarate addition.

    PubMed

    Tan, BoonFei; Semple, Kathleen; Foght, Julia

    2015-05-01

    A methanogenic short-chain alkane-degrading culture (SCADC) was enriched from oil sands tailings and transferred several times with a mixture of C6, C7, C8 and C10 n-alkanes as the predominant organic carbon source, plus 2-methylpentane, 3-methylpentane and methylcyclopentane as minor components. Cultures produced ∼40% of the maximum theoretical methane during 18 months incubation while depleting the n-alkanes, 2-methylpentane and methylcyclopentane. Substrate depletion correlated with detection of metabolites characteristic of fumarate activation of 2-methylpentane and methylcyclopentane, but not n-alkane metabolites. During active methanogenesis with the mixed alkanes, reverse-transcription PCR confirmed the expression of functional genes (assA and bssA) associated with hydrocarbon addition to fumarate. Pyrosequencing of 16S rRNA genes amplified during active alkane degradation revealed enrichment of Clostridia (particularly Peptococcaceae) and methanogenic Archaea (Methanosaetaceae and Methanomicrobiaceae). Methanogenic cultures transferred into medium containing sulphate produced sulphide, depleted n-alkanes and produced the corresponding succinylated alkane metabolites, but were slow to degrade 2-methylpentane and methylcyclopentane; these cultures were enriched in Deltaproteobacteria rather than Clostridia. 3-Methylpentane was not degraded by any cultures. Thus, nominally methanogenic oil sands tailings harbour dynamic and versatile hydrocarbon-degrading fermentative syntrophs and sulphate reducers capable of degrading n-, iso- and cyclo-alkanes by addition to fumarate.

  10. Survey of Naegleria from Taiwan recreational waters using culture enrichment combined with PCR.

    PubMed

    Huang, Shih-Wei; Hsu, Bing-Mu

    2011-08-01

    Naegleria is a free-living amoeba. Pathogenic Naegleria may pose a health risk to people who come in contact with recreational waters. Here, we used Naegleria culture enrichment with PCR to identify the Naegleria species and investigated the distribution of Naegleria spp. in recreational waters including spring water, stream water and raw domestic water in central and southern Taiwan. In this study, Naegleria spp. were detected in 19 (17.8%) of the water samples. The occurrence of Naegleria in raw domestic water was 28.6%, higher than in stream water (14.7%) and in spring water (6.5%). The most frequently identified species exhibiting the closest phylogenetic relationships to the isolates were N. australiensis (n=4) and N. canariensis (n=4), followed by N. clarki (n=3) and N. philippinensis (n=3); N. americana (n=2). N. lovaniensis, N. dobsoni, and N. gruberi were each detected once. The pathogenic species N. fowleri was not detected, probably due to the low incubation temperature; however, the isolates exhibiting the closest phylogenetic relationships to the pathogenic species in mice of PAM, N. australiensis and N. philippinensis, were found. Results of this survey suggest the distribution of Naegleria spp. excluding N. fowleri in recreational waters. It should be considered a potential threat for health associated with human activities in recreational waters.

  11. Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture

    PubMed Central

    Gambelli, Lavinia; Cremers, Geert; Mesman, Rob; Guerrero, Simon; Dutilh, Bas E.; Jetten, Mike S. M.; Op den Camp, Huub J. M.; van Niftrik, Laura

    2016-01-01

    With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study. PMID:27877158

  12. Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes

    PubMed Central

    Liang, Xiaoming; Molenda, Olivia; Tang, Shuiquan

    2015-01-01

    Many reductive dehalogenases (RDases) have been identified in organohalide-respiring microorganisms, and yet their substrates, specific activities, and conditions for expression are not well understood. We tested whether RDase expression varied depending on the substrate-exposure history of reductive dechlorinating communities. For this purpose, we used the enrichment culture KB-1 maintained on trichloroethene (TCE), as well as subcultures maintained on the intermediates cis-dichloroethene (cDCE) and vinyl chloride (VC). KB-1 contains a TCE-to-cDCE dechlorinating Geobacter and several Dehalococcoides strains that together harbor many of the known chloroethene reductases. Expressed RDases were identified using blue native polyacrylamide gel electrophoresis, enzyme assays in gel slices, and peptide sequencing. As anticipated but never previously quantified, the RDase from Geobacter was only detected transiently at the beginning of TCE dechlorination. The Dehalococcoides RDase VcrA and smaller amounts of TceA were expressed in the parent KB-1 culture during complete dechlorination of TCE to ethene regardless of time point or amended substrate. The Dehalococcoides RDase BvcA was only detected in enrichments maintained on cDCE as growth substrates, in roughly equal abundance to VcrA. Only VcrA was detected in subcultures enriched on VC. Enzyme assays revealed that 1,1-DCE, a substrate not used for culture enrichment, afforded the highest specific activity. trans-DCE was substantially dechlorinated only by extracts from cDCE enrichments expressing BvcA. RDase gene distribution indicated enrichment of different strains of Dehalococcoides as a function of electron acceptor TCE, cDCE, or VC. Each chloroethene reductase has distinct substrate preferences leading to strain selection in mixed communities. PMID:25934625

  13. Psychrophilic Biomass Producers in the Trophic Chain of the Microbial Community of Lake Untersee, Antarctica

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-01-01

    The study of photosynthetic microorganisms from the Lake Untersee samples showed dispersed distribution of phototrophs within 80 m water column. Lake Untersee represents a unique ecosystem that experienced complete isolation: sealed by the Anuchin Glacier for many millennia. Consequently, its biocenosis has evolved over a significant period of time without exchange or external interaction with species from other environments. The major producers of organic matter in Lake Untersee are represented by phototrophic and chemolithotrophic microorganisms. This is the traditional trophic scheme for lacustrine ecosystems on Earth. Among the phototrophs, diatoms were not found, which differentiates this lake from other known ecosystems. The dominant species among phototrophs was Chlamydomonas sp. with typical morphostructure: green chloroplasts, bright red round spot, and two polar flagella near the opening. As expected, the physiology of studied phototrophs was limited by low temperature, which defined them as obligate psychrophilic microorganisms. By the quantity estimation of methanogenesis in this lake, the litho-autotrophic production of organic matter is competitive with phototrophic production. However, pure cultures of methanogens have not yet been obtained. We discuss the primary producers of organic matter and the participation of our novel psychrophilic homoacetogen into the litho-autotrophic link of biomass production in Lake Untersee.

  14. Bacterial community analysis in chlorpyrifos enrichment cultures via DGGE and use of bacterial consortium for CP biodegradation.

    PubMed

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2014-10-01

    The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6-7.4 mg L(-1) day(-1) of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L(-1) day(-1) of CP (100 mg L(-1)). Addition of glucose as an additional C source increased the degradation capacity by 8-14 %. After inoculation of contaminated soil with CP (200 mg kg(-1)) disappearance rates were 3.83-4.30 mg kg(-1) day(-1) for individual strains and 4.76 mg kg(-1) day(-1) for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  15. Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process.

    PubMed

    Fu, Liang; Ding, Jing; Lu, Yong-Ze; Ding, Zhao-Wei; Zeng, Raymond J

    2017-02-06

    The co-culture system of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) has a potential application in wastewater treatment plant. This study explored the effects of permutation and combination of nitrate, nitrite, and ammonium on the culture enrichment from freshwater sediments. The co-existence of NO3(-), NO2(-), and NH4(+) shortened the enrichment time from 75 to 30 days and achieved a total nitrogen removal rate of 106.5 mg/L/day on day 132. Even though ammonium addition led to Anammox bacteria increase and a higher nitrogen removal rate, DAMO bacteria still dominated in different reactors with the highest proportion of 64.7% and the maximum abundance was 3.07 ± 0.25 × 10(8) copies/L (increased by five orders of magnitude) in the nitrite reactor. DAMO bacteria showed greater diversity in the nitrate reactor, and one was similar to M. oxyfera; DAMO bacteria in the nitrite reactor were relatively unified and similar to M. sinica. Interestingly, no DAMO archaea were found in the nitrate reactor. This study will improve the understanding of the impact of nitrogen source on DAMO and Anammox co-culture enrichment.

  16. Enrichment of a mixed microbial culture for polyhydroxyalkanoates production: Effect of pH and N and P concentrations.

    PubMed

    Montiel-Jarillo, Gabriela; Carrera, Julián; Suárez-Ojeda, María Eugenia

    2017-04-01

    Polyhydroxyalkanoates (PHA) are biopolymers that can be an alternative against conventional plastics. The study reported herein evaluated the enrichment of a mixed microbial culture (MMC) operated under feast/famine regime and different pHs in a sequencing batch reactor (SBR) using acetate as sole carbon source to produce polyhydroxyalkanoates (PHAs). The enrichment step was evaluated at controlled pH of 7.5 and also without pH control (averaged value of 9.0). The acetate uptake rate (-qS) of both enrichments at the end of the experimental period exhibited similar behaviour being about 0.18CmolAcCmolX(-1)h(-1) and 0.19CmolAcCmolX(-1)h(-1) for SBR-A and SBR-B, respectively. However, the PHA-storing capacity of the biomass enriched without pH control was better, exhibiting a maximum PHA content of 36% (gPHAg(-1) VSS) with a PHA production rate (qPHA) of 0.16CmolPHACmolX(-1)h(-1). Batch experiments were performed to evaluate PHA-storing capacity of the enriched culture at different pHs and nutrients concentrations. In the pH experiments (without nutrient limitation), it was found that in the absence of controlled pH, the enriched biomass exhibited a PHA content of 44% gPHAg(-1) VSS with -qS and PHA to substrate yield (YPHA/Ac) of 0.57CmolAcCmolX(-1)h(-1) and 0.33CmolPHACmolAc(-1), respectively. Regarding the experiments at variable nutrients concentration (pH ranging 8.8 to 9.2), the results indicate that the PHA content in the enriched biomass is significantly higher being around 51% gPHAg(-1) VSS under nitrogen limitation. This work demonstrated the feasibility of the enrichment of a MMC with PHA storage ability without pH control. Results also suggest that better PHAs contents and substrate uptake rates are obtained without controlling the pH in the accumulation step. Finally, this work also highlights the importance of understanding the role of nutrients concentration during the accumulation step.

  17. Building Learning Communities for Research Collaboration and Cross-Cultural Enrichment in Science Education

    NASA Astrophysics Data System (ADS)

    Sparrow, E. B.

    2003-12-01

    The GLOBE program has provided opportunities for environmental science research and education collaborations among scientists, teachers and K-12 students, and for cross-cultural enrichment nationally and abroad. In Alaska, GLOBE has also provided funding leverage in some cases, and a base for several other science education programs that share a common goal of increasing student interest, understanding, process skills and achievement in science, through involvement in ongoing research investigations. These programs that use GLOBE methodologies (standardized scientific measurements and learning activities developed by scientists and educators) are: Global Change Education Using Western Science and Native Knowledge also known as "Observing Locally, Connecting Globally" (OLCG); Alaska Earth System Science Education Alliance: Improving Understanding of Climate Variability and Its Relevance to Rural Alaska; Schoolyard Long Term Ecological Research; Alaska Rural Research Partnership; Alaska Partnership for Teacher Enhancement; Alaska Lake Ice and Snow Observatory Network; Alaska Boreal Forest Council Education Outreach; Calypso Farm and Ecology Center; Environmental Education Outreach; and also GLOBE Arctic POPs (persistent organic pollutants) a program that involves countries in the circumpolar North. The University of Alaska GLOBE Partnership has collaborated with the BLM Campbell Creek Science Center Globe Partnership in facilitating GLOBE Training Workshops and providing teacher support. GLOBE's extensive website including data entry, archive, analysis and visualization capabilities; GLOBE Teacher Guide, videos and other materials provided; excellent GLOBE science research and education staff, training support office, GLOBE help desk, alignment of GLOBE curriculum with national science education standards and GLOBE certification of teachers trained on even just one GLOBE investigation, have made it easier to implement GLOBE in the classroom. Using GLOBE, whole

  18. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil

    SciTech Connect

    Rabus, R.; Widdel, F.; Fukui, Manabu

    1996-10-01

    Production of sulfide in oil field waters, a process which is referred to as souring, has been of concern. Hydrogen sulfide may lead to poisoning, contamination of oil and gas, corrosion of pipelines, conversion of iron mineral to ferrous sulfide. This study used a previously established sulfate-reducing enrichment culture on crude oil as a model system of bacterial habitats in which crude oil is the only potential source of organic substrates, and the enrichment culture was studied in detail including substrate preferences and major nutritional types of sulfate-reducing bacteria in the enrichment culture. 74 refs., 2 figs., 2 tabs.

  19. Effect of free ammonia and free nitrous acid concentration on the anabolic and catabolic processes of an enriched Nitrosomonas culture.

    PubMed

    Vadivelu, Vel M; Keller, Jurg; Yuan, Zhiguo

    2006-12-05

    The effects of free ammonia (FA; NH(3)) and free nitrous acid (FNA; HNO(2)) concentrations on the metabolisms of an enriched ammonia oxidizing bacteria (AOB) culture were investigated using a method allowing the decoupling of growth and energy generation processes. A lab-scale sequencing batch reactor (SBR) was operated for the enrichment of an AOB culture. Fluorescent in-situ hybridization (FISH) analysis showed that 82% of the bacterial population in the SBR bound to the NEU probe specifically designed for Nitrosomonas europaea. Batch tests were carried out to measure the oxygen and ammonium consumption rates by the culture at various FA and FNA levels, in the presence or absence of inorganic carbon (CO(2), HCO(3) (-), and CO(3) (2-)). It was revealed that FA of up to 16.0 mgNH(3)-N . L(-1), which was the highest concentration used in this study, did not have any inhibitory effect on either the catabolic or anabolic processes of the Nitrosomonas culture. In contrast, FNA inhibited both the growth and energy production capabilities of the Nitrosomonas culture. The inhibition on growth initiated at approximately 0.10 mgHNO(2)-N . L(-1), and the data suggested that the biosynthesis was completely stopped at an FNA concentration of 0.40 mgHNO(2)-N . L(-1). The inhibition on energy generation initiated at a slightly lower level but the Nitrosomonas culture was still oxidizing ammonia at half of the maximum rate at an FNA concentration of 0.50-0.63 mgHNO(2)-N . L(-1). The affinity constant of the Nitrosomonas culture with respect to ammonia was determined to be 0.36 mgNH(3)-N . L(-1), independent of the presence or absence of inorganic carbon.

  20. Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation.

    PubMed

    Trueba-Santiso, Alba; Parladé, Eloi; Rosell, Mònica; Lliros, Marc; Mortan, Siti Hatijah; Martínez-Alonso, Maira; Gaju, Nuria; Martín-González, Lucía; Vicent, Teresa; Marco-Urrea, Ernest

    2017-03-01

    Biodegradation of dichloromethane (DCM) under reducing conditions is of major concern due to its widespread detection in contaminated groundwaters. Here, we report an anaerobic enrichment culture derived from a membrane bioreactor operating in an industrial wastewater treatment plant, capable of fermenting DCM and the brominated analogue dibromomethane (DBM). Comparative analysis of bacterial 16S rDNA-DGGE profiles from fresh liquid medium inoculated with single colonies picked from serial dilution-to-extinction agar vials showed that cultures degrading DCM contained a predominant band belonging to Dehalobacterium, however this band was absent in cultures unable to degrade DCM. Analysis of the microbial composition of the enrichment by bacterial 16S rRNA gene amplicon paired-end sequencing confirmed the presence of Dehalobacterium together with three additional phylotypes belonging to Acetobacterium, Desulfovibrio, and Wolinella, representing all four operational taxonomic units >99.9% of the retrieved sequences. The carbon isotopic fractionation (ε) determined for DCM degradation in this culture was -27±2‰. This value differs from the ε previously reported for the DCM-fermentative bacteria Dehalobacter (-15.5±1.5‰) but they are both significantly different from those reported for facultative methylotrophic organisms (ranging from -45 to -61‰). This significant difference in the ε allows differentiating between hydrolytic transformation of DCM via glutathione-dependent dehalogenases and fermentation pathway.

  1. Study of interferon-β antiviral activity against Herpes simplex virus type 1 in neuron-enriched trigeminal ganglia cultures.

    PubMed

    Low-Calle, Ana Maria; Prada-Arismendy, Jeanette; Castellanos, Jaime E

    2014-02-13

    Herpes simplex virus type 1 (HSV-1) causes a lytic infection in epithelial cells before being captured and moved via retrograde axonal transport to the nuclei of the sensory neurons of the trigeminal ganglion or dorsal root, where it establishes a latent infection. HSV-1 infection induces an antiviral response through the production of Beta Interferon (IFN-β) in infected trigeminal ganglia. The aim of this work was to characterize the response induced by IFN-β in neuron-enriched trigeminal ganglia primary cultures infected with HSV-1. An antiviral effect of IFN-β in these cultures was observed, including reduced viral production and increased cell survival. In contrast, viral infection significantly decreased both double stranded RNA dependent protein kinase (Pkr) transcription and Jak-1 and Stat-1 phosphorylation, suggesting a possible HSV-1 immune evasion mechanism in trigeminal cells. Additionally, HSV-1 infection upregulated Suppressor of Cytokine Signaling-3 (Socs3) mRNA; upregulation of socs3 was inhibited in IFN-β treated cultures. HSV-1 infection increased the number of Socs3 positive cells and modified the intracellular distribution of Socs3 protein, in infected cells. This neuron-enriched trigeminal ganglia culture model could be used to elucidate the HSV-1 viral cycle in sensory neurons and to study cellular antiviral responses and possible viral evasion mechanisms that underlie the choice between viral replication and latency.

  2. Improved enrichment culture technique for methane-oxidizing bacteria from marine ecosystems: the effect of adhesion material and gas composition.

    PubMed

    Vekeman, Bram; Dumolin, Charles; De Vos, Paul; Heylen, Kim

    2017-02-01

    Cultivation of microbial representatives of specific functional guilds from environmental samples depends largely on the suitability of the applied growth conditions. Especially the cultivation of marine methanotrophs has received little attention, resulting in only a limited number of ex situ cultures available. In this study we investigated the effect of adhesion material and headspace composition on the methane oxidation activity in methanotrophic enrichments obtained from marine sediment. Addition of sterilized natural sediment or alternatively the addition of acid-washed silicon dioxide significantly increased methane oxidation. This positive effect was attributed to bacterial adhesion on the particles via extracellular compounds, with a minimum amount of particles required for effect. As a result, the particles were immobilized, thus creating a stratified environment in which a limited diffusive gas gradients could build up and various microniches were formed. Such diffusive gas gradient might necessitate high headspace concentrations of CH4 and CO2 for sufficient concentrations to reach the methane-oxidizing bacteria in the enrichment culture technique. Therefore, high concentrations of methane and carbon dioxide, in addition to the addition of adhesion material, were tested and indeed further stimulated methane oxidation. Use of adhesion material in combination with high concentrations of methane and carbon dioxide might thus facilitate the cultivation and subsequent enrichment of environmentally important members of this functional guild. The exact mechanism of the observed positive effects on methane oxidation and the differential effect on methanotrophic diversity still needs to be explored.

  3. Development and evaluation of a rapid, simple, and sensitive immunochromatographic assay to detect thermostable direct hemolysin produced by Vibrio parahaemolyticus in enrichment cultures of stool specimens.

    PubMed

    Kawatsu, Kentaro; Ishibashi, Masanori; Tsukamoto, Teizo

    2006-05-01

    Thermostable direct hemolysin (TDH) is considered to be a major virulence factor in Vibrio parahaemolyticus, and most cases of V. parahaemolyticus diarrhea in humans are caused by tdh gene-positive strains. In the present study, we developed an immunochromatographic assay to detect TDH (TDH-ICA) and evaluated the utility of TDH-ICA for the diagnosis of V. parahaemolyticus diarrhea. TDH-ICA allowed the detection of 0.2 ng/ml of TDH within 10 min. Fecal homogenates were spiked with various numbers of tdh-positive V. parahaemolyticus organisms, and their enrichment cultures were tested with TDH-ICA. The results of detection of TDH in the enrichment cultures by TDH-ICA were in accord with the results of recovery of the spiked V. parahaemolyticus organisms from the enrichment cultures by plating onto thiosulfate-citrate-bile salts-sucrose agar. When enrichment cultures of 217 stool specimens from patients with diarrhea were tested with TDH-ICA, the TDH-ICA results showed 100% sensitivity and specificity compared to the results of isolation of V. parahaemolyticus from the stool specimens by a conventional bacterial culture test. Since TDH-ICA was able to detect TDH in a fecal enrichment culture within 10 min, TDH-ICA testing of a fecal enrichment culture could be completed rapidly and easily within approximately 16 h, including incubation time for the fecal enrichment culture. These results indicate that TDH-ICA is a rapid, simple, and sensitive TDH detection method and that TDH-ICA testing of a fecal enrichment culture is useful as an adjunct to facilitate the early diagnosis of V. parahaemolyticus diarrhea.

  4. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

    NASA Technical Reports Server (NTRS)

    Ward, D. M.; Santegoeds, C. M.; Nold, S. C.; Ramsing, N. B.; Ferris, M. J.; Bateson, M. M.

    1997-01-01

    We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

  5. Evidence for the existence of psychrophilic methanogenic communities in anoxic sediments of deep lakes.

    PubMed

    Nozhevnikova, Alla N; Zepp, Kornelia; Vazquez, Francisco; Zehnder, Alexander J B; Holliger, Christof

    2003-03-01

    In order to obtain evidence for the existence of psychrophilic methanogenic communities in sediments of deep lakes that are low-temperature environments (4 to 5 degrees C), slurries were first incubated at temperatures between 4 and 60 degrees C for several weeks, at which time they were amended, or not, with an additional substrate, such as cellulose, butyrate, propionate, acetate, or hydrogen, and further incubated at 6 degrees C. Initial methane production rates were highest in slurries preincubated at temperatures between 4 and 15 degrees C, with maximal rates in slurries kept at 6 degrees C. Hydrogen-amended cultures were the only exceptions, with the highest methane production rates at 6 degrees C after preincubation at 30 degrees C.

  6. Embedded Voices: Building a Non-Learning Culture within a Learning Enrichment Programme

    ERIC Educational Resources Information Center

    Hymer, Barry; Watkins, Chris; Dawson, Elizabeth; Buxton, Ruth

    2015-01-01

    The researchers examined transcripts of comments made and dialogues engaged in by children, teachers and student teaching assistants during a 10-week enrichment programme for gifted and talented children aged 7-9 years. Attempts were made to match these utterances with the programme's aims and aspirations as expressed in a promotional document.…

  7. Anaerobic Biotransformation of High Concentrations of Chloroform by an Enrichment Culture and Two Bacterial Isolates ▿ †

    PubMed Central

    Shan, Huifeng; Kurtz, Harry D.; Mykytczuk, Nadia; Trevors, Jack T.; Freedman, David L.

    2010-01-01

    A fermentative enrichment culture (designated DHM-1) was developed that is capable of cometabolically biotransforming high concentrations of chloroform (CF) to nontoxic end products. Two Pantoea spp. were isolated from DHM-1 that also possess this dechlorination capability. Following acclimation to increasing levels of CF, corn syrup-grown DHM-1 was able to transform over 500 mg/liter CF in the presence of vitamin B12 (approximately 3% of CF on a molar basis) at a rate as high as 22 mg/liter/day in a mineral salts medium. CO, CO2, and organic acids were the predominant biodegradation products, suggesting that hydrolytic reactions predominate during CF transformation. DHM-1 was capable of growing on corn syrup in the presence of high concentrations of CF (as may be present near contaminant source zones in groundwater), which makes it a promising culture for bioaugmentation. Strains DHM-1B and DHM-1T transform CF at rates similar to that of the DHM-1 enrichment culture. The ability of these strains to grow in the presence of high concentrations of CF appears to be related to alteration of membrane fluidity or homeoviscous and homeophasic adaptation. PMID:20693443

  8. Enrichment and Molecular Characterization of a Bacterial Culture That Degrades Methoxy-Methyl Urea Herbicides and Their Aniline Derivatives

    PubMed Central

    El-Fantroussi, Said

    2000-01-01

    Soil treated with linuron for more than 10 years showed high biodegradation activity towards methoxy-methyl urea herbicides. Untreated control soil samples taken from the same location did not express any linuron degradation activity, even after 40 days of incubation. Hence, the occurrence in the field of a microbiota having the capacity to degrade a specific herbicide was related to the long-term treatment of the soil. The enrichment culture isolated from treated soil showed specific degradation activity towards methoxy-methyl urea herbicides, such as linuron and metobromuron, while dimethyl urea herbicides, such as diuron, chlorotoluron, and isoproturon, were not transformed. The putative metabolic intermediates of linuron and metobromuron, the aniline derivatives 3,4-dichloroaniline and 4-bromoaniline, were also degraded. The temperature of incubation drastically affected degradation of the aniline derivatives. Whereas linuron was transformed at 28 and 37°C, 3,4-dichloroaniline was transformed only at 28°C. Monitoring the enrichment process by reverse transcription-PCR and denaturing gradient gel electrophoresis (DGGE) showed that a mixture of bacterial species under adequate physiological conditions was required to completely transform linuron. This research indicates that for biodegradation of linuron, several years of adaptation have led to selection of a bacterial consortium capable of completely transforming linuron. Moreover, several of the putative species appear to be difficult to culture since they were detectable by DGGE but were not culturable on agar plates. PMID:11097876

  9. An agarose gel-based neurosphere culture system leads to enrichment of neuronal lineage cells in vitro.

    PubMed

    Park, Kyuhee; Nam, Yeonju; Choi, Yongmun

    2015-05-01

    Stem cell-based therapy holds great potential especially for neurological disorders. However, clinical applications await further understanding of many aspects of stem cell differentiation and development of technology enabling manipulation of stem cells into desired cell types in the central nervous system. Here, we developed a new method that leads to enrichment of neuronal lineage cells in neural stem cell cultures. The protocol involves cultivation of primary cells derived from the forebrains of rat E18 embryos above a layer of nonadhesive hard agarose gel in the form of neurospheres. In contrast to the neurospheres that were cultured above an anti-adhesive hydrogel layer, the primary cells that were cultured above a layer of agarose gel preferentially differentiated into β-III tubulin-positive neurons when allowed to undergo differentiation in vitro.In an effort to investigate the mechanism behind this observation, we found that the gene expression of a vertebrate neuronal determination gene (neurogenin1) was enhanced in the neurospheres that proliferated above a layer of agarose gel as compared with the control, and the gene expression level of neurogenin1 was quite well correlated with the rigidity of agarose gel. These results indicate that agarose gel can contribute, at least in part, to enrich neuronal progenitors and immature postmitotic neurons during neurosphere formation and may provide additional information to establish efficient protocols for the neural stem cell-based study.

  10. Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

    PubMed Central

    Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

    2016-01-01

    Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types. PMID:27485896

  11. Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

    NASA Astrophysics Data System (ADS)

    Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

    2016-08-01

    Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

  12. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability.

    PubMed

    Wei, Xiao-Meng; He, Ruo; Chen, Min; Su, Yao; Ma, Ruo-Chan

    2016-04-01

    Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments.

  13. Diversity of bacteria and Archaea in sulphate-reducing enrichment cultures inoculated from serial dilution of Zostera noltii rhizosphere samples.

    PubMed

    Cifuentes, Ana; Antón, Josefa; De Wit, Rutger; Rodríguez-Valera, Francisco

    2003-09-01

    We have analysed the diversity of culturable sulphate-reducing bacteria (SRB) in Zostera noltii colonized sediments from Bassin d'Arcachon (France). Four organic substrates have been tested as well as the combination of H2 and CO2 to select for lithotrophic SRB. All energy sources were supplied in parallel cultures that were amended with yeast extract plus NH4+ and prepared without a source of combined nitrogen, the latter to select for diazotrophic SRB. The 10 different enrichment media were inoculated from serial dilution of rhizosphere samples. The highest dilution cultures yielding positive growth (i.e. 10-7) were studied by molecular techniques (16S rDNA clone libraries, RISA and ARDRA). Lactate as a single organic substrate in combination with a source of combined nitrogen resulted in selection of members of the Desulfovibrionaceae. Surprisingly, when lactate was added without a source of combined nitrogen, Desulfobacteriaceae were selected. A strong influence of the presence or absence of combined nitrogen was also observed for the substrates sucrose and fructose. Whereas the liquid culture growing on sucrose and NH4+ systematically yielded 16S rDNA clones related to an environmental unidentified green sulphur bacterium (OPS185), on plates we were able to isolate a SRB related to Desulfovibrio dechloracetivorans, which likely represents a non-described species. Under diazotrophic conditions, sucrose selected for SRB clones related to the cluster formed by Desulfovibrio zosterae, Desulfovibrio salexigens and Desulfovibrio bastinii. The corresponding isolate obtained on plates showed only low sequence similarity with this closest neighbour (93.8%), and we suggest that it also represents a non-described species. Surprisingly, a 16S rDNA sequence corresponding to an archaeon, i.e. a non-extremophile Crenoarchaeota, was retrieved from several of the SRB enrichment cultures even after subsequent transfers.

  14. Enrichment and identification of Δ(9)-Tetrahydrocannabinolic acid synthase from Pichia pastoris culture supernatants.

    PubMed

    Lange, Kerstin; Poetsch, Ansgar; Schmid, Andreas; Julsing, Mattijs K

    2015-09-01

    This data article refers to the report Δ(9)-Tetrahydrocannabinolic acid synthase (THCAS) production in Pichia pastoris enables chemical synthesis of cannabinoids (Lange et. al. 2015) [2]. THCAS was produced on a 2 L lab scale using recombinant P. pastoris KM71 KE1. Enrichment of THCAS as a technically pure enzyme was realized using dialysis and cationic exchange chromatography. nLC-ESI-MS/MS analysis identified THCAS in different fractions obtained by cationic exchange chromatography.

  15. Extracellular matrix-enriched polymeric scaffolds as a substrate for hepatocyte cultures: in vitro and in vivo studies.

    PubMed

    Zavan, B; Brun, P; Vindigni, V; Amadori, A; Habeler, W; Pontisso, P; Montemurro, D; Abatangelo, G; Cortivo, R

    2005-12-01

    Tissue engineering is a promising approach to developing hepatic tissue suitable for the functional replacement of a failing liver. The aim of the present study was to investigate whether an extracellular cell matrix obtained from fibroblasts-cultured within scaffolds of hyaluronic acid (HYAFF) could influence the proliferation rate and survival of rat hepatocytes both during long-term culture and after in vivo transplantation. Cultures were evaluated by histological and morphological analysis, a proliferation assay and metabolic activity (albumin secretion). Hepatocytes cultured in extracellular matrix-enriched scaffolds exhibited a round cellular morphology and re-established cell-cell contacts, growing into aggregates of several cells along and/or among fibers in the fabric. Hepatocytes were able to secrete albumin up to 14 days in culture. In vivo results demonstrated the biocompatibility of HYAFF-11 implanted in nude mice, in which hepatocytes maintained small well-organised aggregates until the 35th day. In conclusion, the presence of a fibroblast-secreted extracellular matrix improved the biological properties of the hyaluronan scaffold, favoring the survival and morphological integrity of hepatocytes in vitro and in vivo.

  16. Microbial succession in response to pollutants in batch-enrichment culture.

    PubMed

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-02-24

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.

  17. Microbial succession in response to pollutants in batch-enrichment culture

    PubMed Central

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  18. Passport to Cultural Enrichment: The Peace Corps World Wise Schools Experience

    ERIC Educational Resources Information Center

    Carano, Kenneth T.

    2009-01-01

    In recent studies, youths in the United States have demonstrated a remarkable lack of cultural literacy. As the world is becoming increasingly interconnected, it is imperative that students enhance their understanding of other cultures. A classroom correspondence match with a Peace Corps volunteer through the Coverdell Peace Corps World Wise…

  19. Characterization of an isoproturon mineralizing bacterial culture enriched from a French agricultural soil.

    PubMed

    Hussain, Sabir; Sørensen, Sebastian R; Devers-Lamrani, Marion; El-Sebai, Talaat; Martin-Laurent, Fabrice

    2009-11-01

    The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to IPU. Molecular analysis of the bacterial culture by DNA fingerprinting, cloning and sequencing of the 16S rRNA genes revealed that it consisted of six different members among whom the dominant was related to Sphingomonas sp. Six bacterial strains belonging to genera Ancylobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Variovorax and Agrobacterium were isolated from the IPU-degrading culture. None of these were able to degrade IPU in pure culture and only the intact culture sustained the ability to mineralize IPU. The composition of the culture appeared stable suggesting that yet unknown interactions are involved in the IPU mineralization. IPU degradation involved the transitory accumulation of three known IPU metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, and 4-isopropylaniline and their further degradation. Thus, it indicates a metabolic pathway initiated by two successive N-demethylations, followed by cleavage of the urea side chain. This culture did not degrade other structurally related phenylurea herbicides. The degrading activity of the bacterial culture was deeply influenced by the pH, being completely inhibited at pH 5.5 and optimal at pH 7.5.

  20. Psychrophilic dry anaerobic digestion of dairy cow feces: Long-term operation

    SciTech Connect

    Massé, Daniel I. Cata Saady, Noori M.

    2015-02-15

    Highlights: • Psychrophilic dry anaerobic digestion (PDAD) of cow feces (CF) is feasible. • PDAD of CF is as efficient as mesophilic and thermophilic AD at TCL 21 days. • CF (13–16% TS at OLR 5.0 g TCOD{sub fed} kg{sup −1} inoculum d{sup −1}) yielded 222 ± 27 {sub N}L CH{sub 4} kg{sup −1} VS fed. - Abstract: This paper reports experimental results which demonstrate psychrophilic dry anaerobic digestion of cow feces during long-term operation in sequence batch reactor. Cow feces (13–16% total solids) has been anaerobically digested in 12 successive cycles (252 days) at 21 days treatment cycle length (TCL) and temperature of 20 °C using psychrotrophic anaerobic mixed culture. An average specific methane yield (SMY) of 184.9 ± 24.0, 189.9 ± 27.3, and 222 ± 27.7 {sub N}L CH{sub 4} kg{sup −1} of VS fed has been achieved at an organic loading rate of 3.0, 4.0, and 5.0 g TCOD kg{sup −1} inoculum d{sup −1} and TCL of 21 days, respectively. The corresponding substrate to inoculum ratio (SIR) was 0.39 ± 0.06, 0.48 ± .02, 0.53 ± 0.05, respectively. Average methane production rate of 10 ± 1.4 {sub N}L CH{sub 4} kg{sup −1} VS fed d{sup −1} has been obtained. The low concentration of volatile fatty acids indicated that hydrolysis was the reaction limiting step.

  1. N2O production rate of an enriched ammonia-oxidising bacteria culture exponentially correlates to its ammonia oxidation rate.

    PubMed

    Law, Yingyu; Ni, Bing-Jie; Lant, Paul; Yuan, Zhiguo

    2012-06-15

    The relationship between the ammonia oxidation rate (AOR) and nitrous oxide production rate (N(2)OR) of an enriched ammonia-oxidising bacteria (AOB) culture was investigated. The AOB culture was enriched in a nitritation system fed with synthetic anaerobic digester liquor. The AOR was controlled by adjusting the dissolved oxygen (DO) and pH levels and also by varying the initial ammonium (NH(4)(+)) concentration in batch experiments. Tests were also performed directly on the parent reactor where a stepwise decrease/increase in DO was implemented to alter AOR. The experimental data indicated a clear exponential relationship between the biomass specific N(2)OR and AOR. Four metabolic models were used to analyse the experimental data. The metabolic model formulated based on aerobic N(2)O production from the decomposition of nitrosyl radical (NOH) predicted the exponential correlation observed experimentally. The experimental data could not be reproduced by models developed on the basis of N(2)O production through nitrite (NO(2)(-)) and nitric oxide (NO) reduction by AOB.

  2. mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species.

    PubMed

    Brzostowicz, Patricia C; Walters, Dana M; Thomas, Stuart M; Nagarajan, Vasantha; Rouvière, Pierre E

    2003-01-01

    mRNA differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. Thirteen DNA fragments randomly amplified from the total RNA of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. Nine of these DNA fragments are part of genes encoding three distinct Baeyer-Villiger cyclohexanone monooxygenases from three different bacterial species present in the enrichment culture. In Arthrobacter sp. strain BP2 and Rhodococcus sp. strain Phi2, the monooxygenase is part of a gene cluster that includes all the genes required for the degradation of cyclohexanone, while in Rhodococcus sp. strain Phi1 the genes surrounding the monooxygenase are not predicted to be involved in this degradation pathway but rather seem to belong to a biosynthetic pathway. Furthermore, in the case of Arthrobacter strain BP2, three other genes flanking the monooxygenase were identified by differential display, demonstrating that the repeated sampling of bacterial operons shown earlier for a pure culture (D. M. Walters, R. Russ, H. Knackmuss, and P. E. Rouvière, Gene 273:305-315, 2001) is also possible for microbial communities. The activity of the three cyclohexanone monooxygenases was confirmed and characterized following their expression in Escherichia coli.

  3. Evaluation of liquid and solid culture media for the recovery and enrichment of Burkholderia cenocepacia from distilled water.

    PubMed

    Ahn, Youngbeom; Kim, Jeong Myeong; Ahn, Hyeri; Lee, Yong-Jin; LiPuma, John J; Hussong, David; Cerniglia, Carl E

    2014-07-01

    Burkholderia cepacia complex (BCC) presence has been the cause of recalls of both sterile and non-sterile pharmaceutical products since these opportunistic pathogens have been implicated to cause infections to susceptible individuals. BCC are ubiquitous in nature, but in pharmaceutical settings the most common source is contaminated water systems. Some strains of BCC, previously described as Pseudomonas cepacia, were not readily detected by standard culture methods. We have explored different strategies to recover and enrich Burkholderia cenocepacia previously cultured in distilled water for 40 days. Enrichment media of varied nutrient concentrations and composition were used, including modified Tryptic Soy Agar or Broth (TSA or TSB), Reasoner's 2nd Agar or Broth (R2A or R2AB), Brain-Heart Infusion Broth (BHIB), Mueller-Hinton Broth (MHB), and Ashdown's (ASH) medium. Of the various broth media tested, cell growth was significantly greater in TSB and R2AB than in BHIB, MHB, or ASH broth. TSB and R2AB were also compared for their recovery efficiency. Generally, there was no significant difference between the numbers of B. cenocepacia grown on 15 differently modified TSA and five modified R2A solid media. Overall, however, diluted TSA and TSB media, and R2A and R2AB showed better recovery efficiency than TSA and TSB for inocula containing small numbers of cells. All strains persisted in distilled water for 40 days. Broth media were more effective than solid media for recovery of B. cenocepacia from distilled water. These results may assist in improving detection assays with recovery and enrichment strategies to maximize recovery of these fastidious organisms.

  4. Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

    PubMed Central

    Sutton, Nora B.; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H. M.

    2015-01-01

    While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

  5. Culturing bias in marine heterotrophic flagellates analyzed through seawater enrichment incubations.

    PubMed

    del Campo, Javier; Balagué, Vanessa; Forn, Irene; Lekunberri, Itziar; Massana, Ramon

    2013-10-01

    The diversity of heterotrophic flagellates is generally based on cultivated strains, on which ultrastructural, physiological, and molecular studies have been performed. However, the relevance of these cultured strains as models of the dominant heterotrophic flagellates in the marine planktonic environment is unclear. In fact, molecular surveys typically recover novel eukaryotic lineages that have refused cultivation so far. This study was designed to directly address the culturing bias in planktonic marine heterotrophic flagellates. Several microcosms were established adding increasing amounts and sources of organic matter to a confined natural microbial community pre-filtered by 3 μm. Growth dynamics were followed by epifluorescence microscopy and showed the expected higher yield of bacteria and heterotrophic flagellates at increased organic matter additions. Moreover, protist diversity analyzed by molecular tools showed a clear substitution in the community, which differed more and more from the initial sample as the organic matter increased. Within this gradient, there was also an increase of sequences related to cultured organisms as well as a decrease in diversity. Culturing bias is partly explained by the use of organic matter in the isolation process, which drives a shift in the community to conditions closer to laboratory cultures. An intensive culturing effort using alternative isolation methods is necessary to allow the access to the missing heterotrophic flagellates that constitute the abundant and active taxa in marine systems.

  6. Preparation of Membrane Vesicles Enriched in ATP-Dependent Proton Transport from Suspension Cultures of Tomato Cells

    PubMed Central

    Dupont, Frances M.; Zabala, Maria De Gracia

    1985-01-01

    Membranes enriched in ATP-dependent proton transport were prepared from suspension cultures of tomato cells (Lycopersicon esculentum Mill cv VF36). Suspension cultures were a source of large quantities of membranes from rapidly growing, undifferentiated cells. Proton transport activity was assayed as quench of acridine orange fluorescence. The activity of the proton translocating ATPase and of several other membrane enzymes was measured as a function of the cell culture cycle. The relative distribution of the enzymes between the 3,000, 10,000, and 100,000g pellets remained the same throughout the cell culture cycle, but yield of total activity and activity per gram fresh weight with time had a unique profile for each enzyme tested. Maximal yield of the proton translocating ATPase activity was obtained from cells in the middle logarithmic phase of growth, and from 50 to 90% of the activity was found in the 10,000g pellet. The proton translocating ATPase activity was separable from NADPH cytochrome c reductase and cytochrome c oxidase on a sucrose gradient. Proton transport activity had a broad pH optimum (7.0-8.0), was stimulated by KCl with a Km of 5 to 10 millimolar, stimulation being due to the anion, Cl−, and not the cation, K+, and was not inhibited by vanadate, but was inhibited by NO3−. The activity is tentatively identified as the tonoplast ATPase. PMID:16664030

  7. Applicability of a Lactobacillus amylovorus strain as co-culture for natural folate bio-enrichment of fermented milk.

    PubMed

    Laiño, Jonathan Emiliano; Juarez del Valle, Marianela; Savoy de Giori, Graciela; LeBlanc, Jean Guy Joseph

    2014-11-17

    The ability of 55 strains from different Lactobacillus species to produce folate was investigated. In order to evaluate folic acid productivity, lactobacilli were cultivated in the folate-free culture medium (FACM). Most of the tested strains needed folate for growth. The production and the extent of vitamin accumulation were distinctive features of individual strains. Lactobacillus amylovorus CRL887 was selected for further studies because of its ability to produce significantly higher concentrations of vitamin (81.2 ± 5.4 μg/L). The safety of this newly identified folate producing strain was evaluated through healthy experimental mice. No bacterial translocation was detected in liver and spleen after consumption of CRL887 during 7 days and no undesirable side effects were observed in the animals that received this strain. This strain in co-culture with previously selected folate producing starter cultures (Lactobacillus bulgaricus CRL871, and Streptococcus thermophilus CRL803 and CRL415) yielded a yogurt containing high folate concentrations (263.1 ± 2.4 μg/L); a single portion of which would provide 15% of the recommended dietary allowance. This is the first report where a Lactobacillus amylovorus strain was successfully used as co-culture for natural folate bio-enrichment of fermented milk.

  8. A new protocol to detect multiple foodborne pathogens with PCR dipstick DNA chromatography after a six-hour enrichment culture in a broad-range food pathogen enrichment broth.

    PubMed

    Hayashi, Masahiro; Natori, Tatsuya; Kubota-Hayashi, Sayoko; Miyata, Machiko; Ohkusu, Kiyofumi; Kawamoto, Keiko; Kurazono, Hisao; Makino, Souichi; Ezaki, Takayuki

    2013-01-01

    A quick foodborne pathogen screening method after six-hour enrichment culture with a broad-range food pathogen enrichment broth is described. Pathogenic factors of Salmonella enterica, Shigella spp., enteroinvasive Escherichia coli, and enterohemorrhagic E. coli are amplified with a cocktail primer and rapid polymerase chain reaction (PCR), which finishes amplification in 30 min. The PCR amplicon was differentiated with a dipstick DNA chromatography assay in 5-10 min. Starting from a four- to six-hour enrichment culture, this assay was finished within 45 min. Detection sensitivity of this protocol was less than 2.5 CFU/25 g for S. enterica and 3.3 CFU/25 g for enterohemorrhagic E. coli in spiked ground meat experiments.

  9. Culture enrichment assists the diagnosis of cattle botulism by a monoclonal antibody based sandwich ELISA.

    PubMed

    Brooks, C E; Clarke, H J; Finlay, D A; McConnell, W; Graham, D A; Ball, H J

    2010-07-29

    Monoclonal antibodies (MAbs) obtained from a mouse immunised with Clostridium botulinum type D toxoid were developed into a sandwich ELISA (sELISA) format that was able to detect type D toxin and types C and D toxin complexes. The sELISA was examined for its potential to replace the mouse bioassay as an alternative in vitro assay for the diagnosis of cattle botulism. Its application directly to intestinal samples collected from suspect cattle botulism cases and prepared for testing for the standard mouse bioassay showed poor correlation and sensitivity with the mouse bioassay results. However, anaerobic pre-enrichment of the samples after heat treatment at 80 degrees C for 10 min to activate any residual C. botulinum spores greatly improved the sELISA detection rate of the toxin by increasing the sample toxin levels. All of the mouse bioassay positive cattle cases tested were detected by the sELISA from the heated and pre-enriched samples tested after 24h incubation. Toxin was detected by sELISA and subsequently confirmed by mouse bioassay in samples from an additional 3 cases that had been originally mouse bioassay negative. The results indicate that the application of this procedure for screening intestinal samples for C. botulinum strains that produce types C and D toxins from suspect cattle botulism cases would improve the diagnostic rate as well as significantly reduce the number of mice involved in diagnosis.

  10. Autologous fibrin scaffolds cultured dermal fibroblasts and enriched with encapsulated bFGF for tissue engineering.

    PubMed

    de la Puente, Pilar; Ludeña, Dolores; Fernández, Ana; Aranda, Jose L; Varela, Gonzalo; Iglesias, Javier

    2011-12-15

    Autologous fibrin scaffolds (AFSs) enriched with cells and specific growth factors represent a promising biocompatible scaffold for tissue engineering. Here, we analyzed the in vitro behavior of dermal fibroblasts (DFs) (cellular attachment, distribution, viability and proliferation, histological and immunohistochemical changes), comparing AFS with and without alginate microcapsules loaded with basic fibroblast growth factor (bFGF), to validate our scaffold in a future animal model in vivo. In all cases, DFs showed good adhesion and normal distribution, while in scaffolds with bFGF at 14 days, the cell counts detected in proliferation and viability assays were greatly improved, as was the proliferative state, and there was a decrease in muscle specific actin expression and collagen synthesis in comparison with the scaffolds without bFGF. In addition, the use of plasma without fibrinogen concentration methods, together with the maximum controlled release of bFGF at 14 days, favored cell proliferation. To conclude, we have been able to create an AFS enriched with fully functional DFs and release-controlled bFGF that could be used in multiple applications for tissue engineering.

  11. Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil.

    PubMed

    Solomon, Robinson David Jebakumar; Kumar, Amit; Satheeja Santhi, Velayudhan

    2013-12-01

    Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process.

  12. Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil

    PubMed Central

    Solomon, Robinson David Jebakumar; Kumar, Amit; Satheeja Santhi, Velayudhan

    2013-01-01

    Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process. PMID:24302716

  13. Lactate induces tumour necrosis factor-alpha, interleukin-6 and interleukin-1beta release in microglial- and astroglial-enriched primary cultures.

    PubMed

    Andersson, Anna K; Rönnbäck, Lars; Hansson, Elisabeth

    2005-06-01

    Hyperammonaemia has deleterious effects on the CNS in patients with liver dysfunction. Cellular mechanisms underlying the effects of hyperammonaemia are largely unknown, although astrocytes have been the main target of interest. This study investigated how treatment with NH4Cl and lactate, which increase in the brain as a consequence of hyperammonaemia, affects cells in primary rat cultures enriched in either astrocytes or microglia. Morphological changes were studied over time using light microscopy. Release of the proinflammatory cytokines tumour necrosis factor-alpha (TNF-alpha), interleukin (IL)-6 and IL-1beta was measured using ELISA. NH4Cl was found to induce vacuole formation in both culture systems. Lactate treatment altered astrocytic appearance, resulting in increased space between individual cells. Microglia adopted a round morphology with either NH4Cl or lactate treatment. Lactate, but not NH4Cl, induced release of TNF-alpha and IL-6 in both astroglial- and microglial-enriched cultures, while IL-1beta was released only in microglial cultures. Cytokine release was higher in the microglial- than in the astroglial-enriched cultures. Additionally, the astroglial-enriched cultures containing approximately 10% microglial cells released more cytokines than cultures containing about 5% microglial cells. Taken together, our data suggest that most TNF-alpha, IL-6 and IL-1beta release comes from microglia. Thus, microglia could play an important role in the pathological process of hyperammonaemia.

  14. One health from a social-ecological systems perspective: enriching social and cultural dimensions.

    PubMed

    Ross, Helen

    2013-01-01

    This chapter offers insights from the environmental management paradigm of 'social-ecological systems' and related bodies of theory on people-environment relationships to assist the evolution of the One Health interdisciplinary endeavour of health promotion across human-animal ecosystem relationships. It also seeks to expand thinking about the social and cultural dimensions that are likely to prove important in the development of thinking and practice in the One Health field. It advocates consideration of cultural and economic relationships affecting people's interactions with domesticated and wild animal species and ecosystems, and exploration of the cognitive and behavioural aspects of these interactions.

  15. Anaerobic psychrophiles from Lake Zub and Lake Untersee, Antarctica

    NASA Astrophysics Data System (ADS)

    Townsend, Alisa; Pikuta, Elena V.; Guisler, Melissa; Stahl, Sarah; Hoover, Richard B.

    2009-08-01

    The study of samples from Antarctica 2008 and 2009 expeditions organized and successfully conducted by Richard Hoover led to the isolation of diverse anaerobic strains with psychrotolerant and psychrophilic physiology. Due to the fact that Lake Untersee has never been subject to microbiological study, this work with the samples has significant and pioneering impact to the knowledge about the biology of this unique ecosystem. Also, the astrobiological significance for the study of these ecosystems is based on new findings of ice covered water systems on other bodies of our solar system. Anaerobic psychrotolerant strain LZ-22 was isolated from a frozen sample of green moss with soils around the rhizosphere collected near Lake Zub in Antarctica. Morphology of strain LZ-22 was observed to be motile, rod shaped and spore-forming cells with sizes 1 x 5-10 μm. This new isolate is a mesophile with the maximum temperature of growth at 40°C. Strain LZ-22 is able to live on media without NaCl and in media with up to 7 % (w/v) NaCl. It is catalase negative and grows only on sugars with the best growth rate being on lactose. The strain is a neutrophile and grows between pH 5 and 9.0 with the optimum at 7.8. Another two strains UL7-96mG and LU-96m7P were isolated from deep water samples of Lake Untersee. Proteolytic strain LU-96m7P had a truly psychrophilic nature and refused to grow at room temperature. Sugarlytic strain UL7-96mG was found to be psychrotolerant, but its rate of growth at 3°C was very high compared with other mesophiles. Two homoacetogenic psychrophilic strains A7AC-96m and AC-DS7 were isolated and purified from samples of Lake Untersee; both of them are able to grow chemolithotrophically on H2+CO2. In the presence of lactate, these strains are able to grow only at 0-18 °C, and growth at 22 °C was observed only with yeast extract stimulation. In this paper, physiological and morphological characteristics of novel psychrophilic and psychrotolerant isolates

  16. Anaerobic Psychrophiles from Lake Zub and Lake Untersee, Antarctica

    NASA Technical Reports Server (NTRS)

    Townsend, Alisa; Pikuta, Elena V.; Guisler, Melissa; Stahl, Sarah; Hoover, Richard B.

    2009-01-01

    The study of samples from Antarctica 2008 and 2009 expeditions organized and successfully conducted by Richard Hoover led to the isolation of diverse anaerobic strains with psychrotolerant and psychrophilic physiology. Due to the fact that Lake Untersee has never been subject to microbiological study, this work with the samples has significant and pioneering impact to the knowledge about the biology of this unique ecosystem. Also, the astrobiological significance for the study of these ecosystems is based on new findings of ice covered water systems on other bodies of our solar system. Anaerobic psychrotolerant strain LZ-22 was isolated from a frozen sample of green moss with soils around the rhizosphere collected near Lake Zub in Antarctica. Morphology of strain LZ-22 was observed to be motile, rod shaped and spore-forming cells with sizes 1 x 5-10 micron. This new isolate is a mesophile with the maximum temperature of growth at 40C. Strain LZ-22 is able to live on media without NaCl and in media with up to 7% (w/v) NaCl. It is catalase negative and grows only on sugars with the best growth rate being on lactose. The strain is a neutrophile and grows between pH 5 and 9.0 with the optimum at 7.8. Another two strains UL7-96mG and LU-96m7P were isolated from deep water samples of Lake Untersee. Proteolytic strain LU-96m7P had a truly psychrophilic nature and refused to grow at room temperature. Sugarlytic strain UL7-96mG was found to be psychrotolerant, but its rate of growth at 3C was very high compared with other mesophiles. Two homoacetogenic psychrophilic strains A7AC-96m and AC-DS7 were isolated and purified from samples of Lake Untersee; both of them are able to grow chemolithotrophically on H2+CO2. In the presence of lactate, these strains are able to grow only at 0-18C, and growth at 22C was observed only with yeast extract stimulation. In this paper, physiological and morphological characteristics of novel psychrophilic and psychrotolerant isolates from

  17. Afro-Hispanic Literature: Cultural and Literary Enrichment for the Foreign Language Classroom.

    ERIC Educational Resources Information Center

    Cyrus, Stanley A.; Legge, June M.

    Millions of people of African descent in Spanish-speaking countries are commonly omitted from the cultural, literary, and linguistic content of Spanish classes. Afro-Spanish literature can be integrated into the Spanish curriculum from the first year. This literature is not easily defined, but does reflect and aid in understanding the black…

  18. Culturally Diverse Literature: Enriching Variety in an Era of Common Core State Standards

    ERIC Educational Resources Information Center

    Boyd, Fenice B.; Causey, Lauren L.; Galda, Lee

    2015-01-01

    The authors argue for the overwhelming importance of finding and including culturally diverse literature into the curricula teachers are authorized to teach. They discuss the implications of use and offer ideas on how to identify quality literature to include in classroom and school libraries.

  19. Growth enhancement of fowls by dietary administration of recombinant yeast cultures containing enriched growth hormone.

    PubMed

    Chen, C M; Cheng, W T; Chang, Y C; Chang, T J; Chen, H L

    2000-09-15

    In present study the methylotrophic yeast, Pichia pastoris, was used to express a recombinant growth hormone (rGH) gene of swine. A synthetic secretion cassette was constructed using the promoter of the alcohol oxidase1 gene (AOX1), and a alpha-factor signal peptide. After electroporatic transformation and zeocin selection, several clones exhibited high levels of rGH protein expression constituting more than 20% of total yeast protein. Over 95% of rGH was shown to be export into the culture supernatant. Yeast transformant containing the highest recombinant growth hormone level (rGH yeast) and native GS115 Pichia pastoris (non-rGH yeast, as a control) were separately cultured, harvested and adsorbed by wheat bran. Yeast cultures of four dosages (0.05, 0.1, 0.2, and 0.4%) were mixed respectively with chick basal diet and fed to simulated country chickens for 9 weeks. The results showed that, when compared to control chicks, the percentage of body weight gain was improved significantly (P<0.05) in chicks fed with diets containing 0.1 or 0.2% rGH-rich yeast culture at brooding stage, and in chicks fed with 0.4% rGH-rich yeast culture at growing stage. The average weight gain in rGH yeast treated groups for the full-term (0 to 63d) and short term (43 to 63d) of growth were 10.6 and 9.4%, respectively, better than the non-rGH yeast control group. These experimental data suggest that the use of rGH-containing yeast as a supplement in fed provided an alternative approach for growth improvement in simulated country chickens.

  20. Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

    NASA Astrophysics Data System (ADS)

    Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C. M.; Zeng, Raymond J.

    2014-06-01

    The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 +/- 0.06, 1.0 +/- 0.13 and 0.4 +/- 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.

  1. Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens.

    PubMed

    Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C M; Zeng, Raymond J

    2014-06-12

    The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 ± 0.06, 1.0 ± 0.13 and 0.4 ± 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.

  2. Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

    PubMed Central

    Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C. M.; Zeng, Raymond J.

    2014-01-01

    The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 ± 0.06, 1.0 ± 0.13 and 0.4 ± 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation. PMID:24920064

  3. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions.

    PubMed

    Lu, Yue; Ramiro-Garcia, Javier; Vandermeeren, Pieter; Herrmann, Steffi; Cichocka, Danuta; Springael, Dirk; Atashgahi, Siavash; Smidt, Hauke

    2017-03-01

    Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.

  4. Psychrophilic enzymes: from folding to function and biotechnology.

    PubMed

    Feller, Georges

    2013-01-01

    Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.

  5. Real-time PCR detection of Campylobacter spp.: A comparison to classic culturing and enrichment.

    PubMed

    de Boer, P; Rahaoui, H; Leer, R J; Montijn, R C; van der Vossen, J M B M

    2015-10-01

    The major disadvantage of the current gold standard for detection of the food pathogen Campylobacter, i.e. culturing, is the lengthy procedure. In this study we assessed the use of real-time PCR for detection of Campylobacter. To this end, 926 poultry samples, taken from transport containers and broiler caeca in The Netherlands in 2007, were subjected to three different real-time PCR detection methods: one targeting the Campylobacter jejuni hipO gene, one targeting the Campylobacter coli glyA gene, and one generically targeting Campylobacter spp. 16S rDNA sequence. The PCR results from the three different PCR protocols were compared to the work of Nauta et al. (2009) who analyzed the same set of samples collected from 62 broiler flocks by means of enrichment culturing. The results indicate that the generic 16S campylobacter PCR detection is equally reliable but much faster (4 h instead of ≥2 days) than detection by means of culturing. Moreover, PCR detection targeting the hipO and the glyA gene provide the possibility of C. jejuni and C. coli species discrimination. The generic Campylobacter spp. PCR analysis also confirmed the high incidence of Campylobacter spp. in poultry samples (∼90%) and the species specific PCR showed the simultaneous presence of C. jejuni and C. coli in ∼24% of the samples. Furthermore, the results from the three PCR analyses suggested the occurrence of alternative Campylobacter species in almost 10% of the samples. The campylobacter PCR detection methods reported here can replace traditional culturing because of being quicker and more reliable.

  6. Enrichment, Isolation, and Cultural Characteristics of Marine Strains of Clostridium botulinum Type C

    PubMed Central

    Segner, W. P.; Schmidt, C. F.; Boltz, J. K.

    1971-01-01

    Terrestrial strains of Clostridium botulinum type C, designated 468 and 571, were used to screen various media for growth and sporulation at 30 C. Of the various formulations tested, only egg meat medium fortified with 1% additions of yeast extract, ammonium sulfate, and glucose (FEM medium) gave good growth and satisfactory sporulation. FEM medium was used to recover four marine type C isolates from inshore sediments collected along the Atlantic, the Gulf of Mexico, and the Pacific coasts of the United States. The isolation techniques involved repeated transfer of cultures showing type C toxin in FEM medium and purification by a deep tube method. The medium used for purification was beef infusion-agar supplemented with 0.14% sodium bicarbonate and 0.1% l-cysteine hydrochloride. l-Cysteine was adopted in preference to sodium thioglycolate, because some lots of the latter were definitely inhibitory for growth. The addition of bicarbonate markedly increased viable spore counts of both the marine and terrestrial strains. Various cultural and biochemical characteristics of the marine and the terrestrial strains were compared. With the exception of some variations in their fermentation patterns, both groups showed similar characteristics. Of 23 fermentable compounds tested, the terrestrial strains attacked only glucose and mannose. The marine strains fermented glucose, mannose, galactose, and ribose actively; dextrin, inositol, maltose, and melibiose were weakly fermented. PMID:4944800

  7. Enriching the Content Provided by Cultural Catalogues with Data from Institutional Repositories

    NASA Astrophysics Data System (ADS)

    Rodríguez Miranda, Á.; Valle Melón, J. M.; Porcal-Gonzalo, M. C.

    2013-07-01

    Institutional repositories play a key role in universities and research centers for the preservation and dissemination of the knowledge generated or collected by these agents. Part of the information contained is related with Cultural Heritage and, therefore, it could be taken into account by thematic catalogues such as Europeana. In this paper, the opportunities and limitations of this connection are considered and presented by means of an ongoing case at the University of the Basque Country's institutional repository. In particular, we will deal with the information gathered about San Prudencio's Monastery (Clavijo, Spain), which includes a wide range of data from original datasets (photographs, pointclouds, coordinates, sketches and so on) up to finals results (reports, plans, 3D models, papers and so on).

  8. Pilot-scale chitin extraction from shrimp shell waste by deproteination and decalcification with bacterial enrichment cultures.

    PubMed

    Bajaj, Mini; Freiberg, Andrea; Winter, Josef; Xu, Youmei; Gallert, Claudia

    2015-11-01

    Extraction of chitin from mechanically pre-purified shrimp shells can be achieved by successive NaOH/HCl treatment, protease/HCl treatment or by environmentally friendly fermentation with proteolytic/lactic acid bacteria (LAB). For the last mentioned alternative, scale-up of shrimp shell chitin purification was investigated in 0.25 L (F1), 10 L (F2), and 300 L (F3) fermenters using an anaerobic, chitinase-deficient, proteolytic enrichment culture from ground meat for deproteination and a mixed culture of LAB from bio-yoghurt for decalcification. Protein removal in F1, F2, and F3 proceeded in parallel within 40 h at an efficiency of 89-91 %. Between 85 and 90 % of the calcit was removed from the shells by LAB in another 40 h in F1, F2, and F3. After deproteination of shrimp shells in F3, spent fermentation liquor was re-used for a next batch of 30-kg shrimp shells in F4 (300 L) which eliminated 85.5 % protein. The purity of the resulting chitin was comparable in F1, F2, F3, and F4. Viscosities of chitosan, obtained after chitin deacetylation and of chitin, prepared biologically or chemically in the laboratory, were much higher than those of commercially available chitin and chitosan.

  9. Impact of estuarine gradients on reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin in river sediment enrichment cultures.

    PubMed

    Dam, Hang T; Häggblom, Max M

    2017-02-01

    Polychlorinated dibenzo-p-dioxins (PCDDs) are among the most persistent organic pollutants. Although the total input of PCDDs into the environment has decreased substantially over the past four decades, their input via non-point sources is still increasing, especially in estuarine metropolitan areas. Here we report on the microbially mediated reductive dechlorination of PCDDs in anaerobic enrichment cultures established from sediments collected from five locations along the Hackensack River, NJ and investigate the impacts of sediment physicochemical characteristics on dechlorination activity. Dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) and abundance of Dehalococcoides spp. negatively correlated with salinity and sulfate concentration in sediments used to establish the cultures. 1,2,3,4-TeCDD was dechlorinated to a lesser extent in cultures established from sediments from the tidally influenced estuarine mouth of the river. In cultures established from low salinity sediments, 1,2,3,4-TeCDD was reductively dechlorinated with the accumulation of 2-monochlorodibenzo-p-dioxin as the major product. Sulfate concentrations above 2 mM inhibited 1,2,3,4-TecDD dechlorination activity. Consecutive lateral- and peri- dechlorination took place in enrichment cultures with a minimal accumulation of 2,3-dichlorodibenzo-p-dioxin in active cultures. A Dehalococcoides spp. community was enriched and accounted for up to 64% of Chloroflexi detected in these sediment cultures.

  10. An extracellular ice-binding glycoprotein from an Arctic psychrophilic yeast.

    PubMed

    Lee, Jong Kyu; Park, Kyoung Sun; Park, Seungil; Park, Hyun; Song, Young Hwan; Kang, Sung-Ho; Kim, Hak Jun

    2010-04-01

    A psychrophilic yeast was isolated from an Arctic pond and its culture supernatant showed ice-binding activity. This isolate, identified as Leucosporidium sp. based on an analysis of the D1/D2 and ITS regions of its ribosomal DNA, produced a secretory ice-binding protein (IBP). Yeast IBP was purified from the culture medium to near homogeneity by the ice affinity method and appeared to be glycosylated with a molecular mass of approximately 26 kDa. In addition, the yeast IBP was shown to have thermal hysteresis (TH) and recrystallization inhibition (RI) activities. The full-length cDNA for yeast IBP was determined and was found to encode a 261 amino acid protein with molecular weight of 26.8 kDa that includes an N-terminal signal peptide and one potential N-glycosylation site. The deduced protein showed high sequence identity with other IBPs and hypothetical IBPs from fungi, diatoms, and bacteria, clustering with a class of ice-active proteins.

  11. Psychrophilic yeasts from worldwide glacial habitats: diversity, adaptation strategies and biotechnological potential.

    PubMed

    Buzzini, Pietro; Branda, Eva; Goretti, Marta; Turchetti, Benedetta

    2012-11-01

    Glacial habitats (cryosphere) include some of the largest unexplored and extreme biospheres on Earth. These habitats harbor a wide diversity of psychrophilic prokaryotic and eukaryotic microorganisms. These highly specialized microorganisms have developed adaptation strategies to overcome the direct and indirect life-endangering influence of low temperatures. For many years Antarctica has been the geographic area preferred by microbiologists for studying the diversity of psychrophilic microorganisms (including yeasts). However, there have been an increasing number of studies on psychrophilic yeasts sharing the non-Antarctic cryosphere. The present paper provides an overview of the distribution and adaptation strategies of psychrophilic yeasts worldwide. Attention is also focused on their biotechnological potential, especially on their exploitation as a source of cold-active enzymes and for bioremediation purposes.

  12. Halophilic-Psychrophilic Bacteria from Tirich Mir Glacier, Pakistan, as Potential Candidate for Astrobiological Studies

    NASA Astrophysics Data System (ADS)

    Rafiq, M. R.; Anesio, A. M. A.; Hayat, M. H.; Zada, S. Z.; Sajjad, W. S.; Shah, A. A. S.; Hasan, F. H.

    2016-09-01

    Hindu Kush, Karakoram, and Himalaya region is referred to as 'third pole' and could be suitable as a terrestrial analog of Mars and increased possibility of finding polyextremophiles. Study is focused on halophilic psychrophiles.

  13. Enrichment of hepatocytes in a HepaRG culture using spatially selective photodynamic treatment

    NASA Astrophysics Data System (ADS)

    Bednarkiewicz, Artur; Rodrigues, Robim M.; Whelan, Maurice P.

    2010-03-01

    The human hepatoma HepaRG cell line is an in vitro cell model that is becoming an important tool in drug metabolism, hepatotoxicity, genotoxicity, and enzyme induction studies. The cells are highly proliferative during their undifferentiated state but once committed, they differentiate into two distinctly different cell types, namely, hepatocyte-like and biliary epithelial-like cells. The presence of the latter in the cell culture is considered to be a drawback of the cell model. Since the proliferating undifferentiated HepaRG cells have a bipotent character, the only way to improve the content ratio of hepatic versus biliary cells of differentiated HepaRG cells is to eradicate biliary cells in situ, in a way that free surface space does not become available and thus no transdifferentiation can occur. Spatially selective photodynamic therapy has proven to be effective for that purpose. First, all the cells were administered aminolevulinic acid (δ-ALA) to stimulate the synthesis of protoporphyrin IX (PpIX), a naturally occurring photosensitizer. Then, the biliary cells were automatically identified and outlined by bright-field image processing. Last, UV light patterns were projected onto the epithelial cells alone by a spatial light modulation device connected to an optical microscope; therefore, only these cells were destroyed by photodynamic therapy.

  14. Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants.

    PubMed

    Stępniewska, Zofia; Goraj, Weronika; Kuźniar, Agnieszka; Łopacka, Natalia; Małysza, Magdalena

    2017-03-09

    Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1-20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density-OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.

  15. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture.

    PubMed

    Pernthaler, J; Posch, T; Simek, K; Vrba, J; Pernthaler, A; Glöckner, F O; Nübel, U; Psenner, R; Amann, R

    2001-05-01

    We investigated whether individual populations of freshwater bacteria in mixed experimental communities may exhibit specific responses to the presence of different bacterivorous protists. In two successive experiments, a two-stage continuous cultivation system was inoculated with nonaxenic batch cultures of the cryptophyte Cryptomonas sp. Algal exudates provided the sole source of organic carbon for growth of the accompanying microflora. The dynamics of several 16S rRNA-defined bacterial populations were followed in the experimental communities. Although the composition and stability of the two microbial communities differed, numerous members of the first assemblage could again be detected during the second experiment. The introduction of a size-selectively feeding mixotrophic nanoflagellate (Ochromonas sp.) always resulted in an immediate bloom of a single phylotype population of members of the class Actinobacteria (Ac1). These bacteria were phylogenetically affiliated with an uncultured lineage of gram-positive bacteria that have been found in freshwater habitats only. The Ac1 cells were close to the average size of freshwater bacterioplankton and significantly smaller than any of the other experimental community members. In contrast, no increase of the Ac1 population was observed in vessels exposed to the bacterivorous ciliate Cyclidium glaucoma. However, when the Ochromonas sp. was added after the establishment of C. glaucoma, the proportion of population Ac1 within the microbial community rapidly increased. Populations of a beta proteobacterial phylotype related to an Aquabacterium sp. decreased relative to the total bacterial communities following the addition of either predator, albeit to different extents. The community structure of pelagic microbial assemblages can therefore be influenced by the taxonomic composition of the predator community.

  16. Characterization of cultures enriched from acidic polycyclic aromatic hydrocarbon-contaminated soil for growth on pyrene at low pH.

    PubMed

    Uyttebroek, Maarten; Vermeir, Steven; Wattiau, Pierre; Ryngaert, Annemie; Springael, Dirk

    2007-05-01

    Two polycyclic aromatic hydrocarbon (PAH)-contaminated soils of pH 2 were successfully used as inoculum to enrich cultures growing on phenanthrene and pyrene at different pHs, including pH 3. Selected pyrene-utilizing cultures obtained at pH 3, pH 5, and pH 7 were further characterized. All showed rapid [14C]pyrene mineralization at pH 3 and pH 5 and grew on pyrene at pH values ranging from 2 to 6. Eubacterial and mycobacterial 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and sequencing indicated that the cultures were dominated by a single bacterium closely related to Mycobacterium montefiorense, belonging to the slow-growing Mycobacterium sp. In contrast, a culture enriched on pyrene at pH 7 from a slightly alkaline soil sampled at the same site was dominated by Pseudomonas putida and a fast-growing Mycobacterium sp. The M. montefiorense-related species dominating the pyrene-utilizing cultures enriched from the acidic soils was also the dominant Mycobacterium species in the acidic soils. Our data indicate that a slow-growing Mycobacterium species is involved in PAH degradation in that culture and show that bacteria able to degrade high-molecular-weight PAHs at low pH are present in acidic PAH-contaminated soil.

  17. Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment.

    PubMed

    Liu, Hongyan; Wang, Hongyu

    2016-07-01

    To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment.

  18. Using Culture beyond Its Borders: The Use of Content-Enriched Instruction and the Effects of Input Enhancement on Learning in High School French Classes

    ERIC Educational Resources Information Center

    Grim, Frédérique

    2014-01-01

    The American Council on the Teaching of Foreign Languages Standards emphasizes the integration of Communication, Cultures, Connections, Comparisons, and Communities within teaching. "Content-enriched instruction" aims at teaching linguistic forms within content and eases the implementation of the five Cs. The focus is at beginning levels…

  19. Characterization of bacterial diversity in an atrazine degrading enrichment culture and degradation of atrazine, cyanuric acid and biuret in industrial wastewater.

    PubMed

    Dutta, Anirban; Vasudevan, Venugopal; Nain, Lata; Singh, Neera

    2016-01-01

    An enrichment culture was used to study atrazine degradation in mineral salt medium (MSM) (T1), MSM+soil extract (1:1, v/v) (T2) and soil extract (T3). Results suggested that enrichment culture required soil extract to degrade atrazine, as after second sequential transfer only partial atrazine degradation was observed in T1 treatment while atrazine was completely degraded in T2 and T3 treatments even after fourth transfer. Culture independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique confirmed selective enrichment of genus Bacillus along with Pseudomonas and Burkholderia. Degradation of atrazine/metabolites in the industrial wastewater was studied at different initial concentrations of the contaminants [wastewater-water (v/v) ratio: T1, 1:9; T2, 2:8; T3, 3:7; T4, 5:5 and T5, undiluted effluent]. The initial concentrations of atrazine, cyanuric acid and biuret ranged between 5.32 and 53.92 µg mL(-1), 265.6 and 1805.2 µg mL(-1) and 1.85 and 16.12 µg mL(-1), respectively. The enrichment culture was able to completely degrade atrazine, cyanuric acid and biuret up to T4 treatment, while no appreciable degradation of contaminants was observed in the undiluted effluent (T5). Inability of enrichment culture to degrade atrazine/metabolites might be due to high concentrations of cyanuric acid. Therefore, a separate study on cyanuric acid degradation suggested: (i) no appreciable cyanuric acid degradation with accumulation of an unidentified metabolite in the medium where cyanuric acid was supplemented as the sole source of carbon and nitrogen; (ii) partial cyanuric acid degradation with accumulation of unidentified metabolite in the medium containing additional nitrogen source; and (iii) complete cyanuric acid degradation in the medium supplemented with an additional carbon source. This unidentified metabolite observed during cyanuric acid degradation and also detected in the enrichment culture inoculated wastewater samples

  20. Establishment of microbial eukaryotic enrichment cultures from a chemically stratified antarctic lake and assessment of carbon fixation potential.

    PubMed

    Dolhi, Jenna M; Ketchum, Nicholas; Morgan-Kiss, Rachael M

    2012-04-20

    Lake Bonney is one of numerous permanently ice-covered lakes located in the McMurdo Dry Valleys, Antarctica. The perennial ice cover maintains a chemically stratified water column and unlike other inland bodies of water, largely prevents external input of carbon and nutrients from streams. Biota are exposed to numerous environmental stresses, including year-round severe nutrient deficiency, low temperatures, extreme shade, hypersalinity, and 24-hour darkness during the winter (1). These extreme environmental conditions limit the biota in Lake Bonney almost exclusively to microorganisms (2). Single-celled microbial eukaryotes (called "protists") are important players in global biogeochemical cycling (3) and play important ecological roles in the cycling of carbon in the dry valley lakes, occupying both primary and tertiary roles in the aquatic food web. In the dry valley aquatic food web, protists that fix inorganic carbon (autotrophy) are the major producers of organic carbon for organotrophic organisms (4, 2). Phagotrophic or heterotrophic protists capable of ingesting bacteria and smaller protists act as the top predators in the food web (5). Last, an unknown proportion of the protist population is capable of combined mixotrophic metabolism (6, 7). Mixotrophy in protists involves the ability to combine photosynthetic capability with phagotrophic ingestion of prey microorganisms. This form of mixotrophy differs from mixotrophic metabolism in bacterial species, which generally involves uptake dissolved carbon molecules. There are currently very few protist isolates from permanently ice-capped polar lakes, and studies of protist diversity and ecology in this extreme environment have been limited (8, 4, 9, 10, 5). A better understanding of protist metabolic versatility in the simple dry valley lake food web will aid in the development of models for the role of protists in the global carbon cycle. We employed an enrichment culture approach to isolate potentially

  1. Isolation and Identification of Psychrophilic Species of Bacillus from Milk

    PubMed Central

    Shehata, T. E.; Collins, E. B.

    1971-01-01

    Forty isolates from 97 raw milk samples (heated to 80 C for 10 min and stored at 4 to 7 C for 3 to 4 weeks) were sporeforming, aerobic, gram-positive or gram-variable, rod-shaped bacteria. Fifteen isolates that were identified had characteristics similar to species of Bacillus, except that they had lower growth temperature ranges, were gram-variable, and were somewhat different in sugar fermentations. Four isolates grew well within 2 weeks at 0 C, but they grew faster at 20 to 25 C. These psychrophilic sporeforming bacteria, the importance of which is discussed, are considered to be variant strains of mesophilic bacilli adapted to low temperatures. PMID:5108104

  2. The metabolism of neonicotinoid insecticide thiamethoxam by soil enrichment cultures, and the bacterial diversity and plant growth-promoting properties of the cultured isolates.

    PubMed

    Zhou, Guang-Can; Wang, Ying; Ma, Yuan; Zhai, Shan; Zhou, Ling-Yan; Dai, Yi-Jun; Yuan, Sheng

    2014-01-01

    A soil enrichment culture (SEC) rapidly degraded 96% of 200 mg L(-1) neonicotinoid insecticide thiamethoxam (TMX) in MSM broth within 30 d; therefore, its metabolic pathway of TMX, bacterial diversity and plant growth-promoting rhizobacteria (PGPR) activities of the cultured isolates were studied. The SEC transformed TMX via the nitro reduction pathway to form nitrso, urea metabolites and via cleavage of the oxadiazine cycle to form a new metabolite, hydroxyl CLO-tri. In addition, 16S rRNA gene-denaturing gradient gel electrophoresis analysis revealed that uncultured rhizobacteria are predominant in the SEC broth and that 77.8% of the identified bacteria belonged to uncultured bacteria. A total of 31 cultured bacterial strains including six genera (Achromobacter, Agromyces, Ensifer, Mesorhizobium, Microbacterium and Pseudoxanthomonas) were isolated from the SEC broth. The 12 strains of Ensifer adhaerens have the ability to degrade TMX. All six selected bacteria showed PGPR activities. E. adhaerens TMX-23 and Agromyces mediolanus TMX-25 produced indole-3-acetic acid, whereas E. adhaerens TMX-23 and Mesorhizobium alhagi TMX-36 are N2-fixing bacteria. The six-isolated microbes were tolerant to 200 mg L(-1) TMX, and the growth of E. adhaerens was significantly enhanced by TMX, whereas that of Achromobacter sp. TMX-5 and Microbacterium sp.TMX-6 were enhanced slightly. The present study will help to explain the fate of TMX in the environment and its microbial degradation mechanism, as well as to facilitate future investigations of the mechanism through which TMX enhances plant vigor.

  3. Effect of nitrogen source on methanol oxidation and genetic diversity of methylotrophic mixed cultures enriched from pulp and paper mill biofilms.

    PubMed

    Babbitt, Callie W; Lindner, Angela S

    2011-04-01

    Methanol-oxidizing bacteria may play an important role in the development and use of biological treatment systems for the removal of methanol from industrial effluents. Optimization of methanol degradation potential in such systems is contingent on availability of nutrients, such as nitrogen, in the most favorable form and concentration. To that end, this study examined the variation in growth, methanol degradation, and bacterial diversity of two mixed methylotrophic cultures that were provided nitrogen either as ammonium or nitrate and in three different concentrations. Methanol-degrading cultures were enriched from biofilms sampled at a pulp and paper mill and grown in liquid batch culture with methanol as the only carbon source and either ammonium or nitrate as the only added nitrogen source. Results indicate that growth and methanol removal of the mixed cultures increase directly with increased nitrogen, added in either form. However, methanol removal and bacterial diversity, as observed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods, were higher when using nitrate as the nitrogen source for enrichment and growth, rather than ammonium. Based on results described here, nitrate may potentially be a better nitrogen source when enriching or working with mixed methylotrophic cultures, and possibly more effective when used as a nutrient addition to biofilters.

  4. Phylogenetic and Metabolic Diversity of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-transforming Bacteria in Strictly Anaerobic Mixed Cultures Enriched on RDX as Nitrogen Source

    DTIC Science & Technology

    2003-01-01

    International (Menlo Park, CA, USA). All other chemicals used were of reagent grade. The basic salts and vitamins medium were prepared as described...wastewater to methane (70% of the total gas released). The following compounds were added to the basic salts and vitamins medium to enrich bacteria using RDX...6 months. The ¢nal enrichment cultures did not show any growth in the basic salts media in the absence of RDX (Table 1). The enrichment cultures were

  5. Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part B--Nitrogen-, Sulfur-, and Oxygen-Containing Heterocyclic Aromatic Compounds.

    PubMed

    Oberoi, Akashdeep Singh; Philip, Ligy; Bhallamudi, S Murty

    2015-07-01

    Present study focused on the biodegradation of various heterocyclic nitrogen, sulfur, and oxygen (NSO) compounds using naphthalene-enriched culture. Target compounds in the study were pyridine, quinoline, benzothiophene, and benzofuran. Screening studies were carried out using different microbial consortia enriched with specific polycyclic aromatic hydrocarbon (PAH) and NSO compounds. Among different microbial consortia, naphthalene-enriched culture was the most efficient consortium based on high substrate degradation rate. Substrate degradation rate with naphthalene-enriched culture followed the order pyridine > quinoline > benzofuran > benzothiophene. Benzothiophene and benzofuran were found to be highly recalcitrant pollutants. Benzothiophene could not be biodegraded when concentration was above 50 mg/l. It was observed that 2-(1H)-quinolinone, benzothiophene-2-one, and benzofuran-2,3-dione were formed as metabolic intermediates during biodegradation of quinoline, benzothiophene, and benzofuran, respectively. Quinoline-N and pyridine-N were transformed into free ammonium ions during the biodegradation process. Biodegradation pathways for various NSO compounds are proposed. Monod inhibition model was able to simulate single substrate biodegradation kinetics satisfactorily. Benzothiophene and benzofuran biodegradation kinetics, in presence of acetone, was simulated using a generalized multi-substrate model.

  6. Rapid and Specific Enrichment of Culturable Gram Negative Bacteria Using Non-Lethal Copper-Free Click Chemistry Coupled with Magnetic Beads Separation

    PubMed Central

    Fugier, Emilie; Dumont, Audrey; Malleron, Annie; Poquet, Enora; Mas Pons, Jordi; Baron, Aurélie; Vauzeilles, Boris; Dukan, Sam

    2015-01-01

    Currently, identification of pathogenic bacteria present at very low concentration requires a preliminary culture-based enrichment step. Many research efforts focus on the possibility to shorten this pre-enrichment step which is needed to reach the minimal number of cells that allows efficient identification. Rapid microbiological controls are a real public health issue and are required in food processing, water quality assessment or clinical pathology. Thus, the development of new methods for faster detection and isolation of pathogenic culturable bacteria is necessary. Here we describe a specific enrichment technique for culturable Gram negative bacteria, based on non-lethal click chemistry and the use of magnetic beads that allows fast detection and isolation. The assimilation and incorporation of an analog of Kdo, an essential component of lipopolysaccharides, possessing a bio-orthogonal azido function (Kdo-N3), allow functionalization of almost all Gram negative bacteria at the membrane level. Detection can be realized through strain-promoted azide-cyclooctyne cycloaddition, an example of click chemistry, which interestingly does not affect bacterial growth. Using E. coli as an example of Gram negative bacterium, we demonstrate the excellent specificity of the technique to detect culturable E. coli among bacterial mixtures also containing either dead E. coli, or live B. subtilis (as a model of microorganism not containing Kdo). Finally, in order to specifically isolate and concentrate culturable E. coli cells, we performed separation using magnetic beads in combination with click chemistry. This work highlights the efficiency of our technique to rapidly enrich and concentrate culturable Gram negative bacteria among other microorganisms that do not possess Kdo within their cell envelope. PMID:26061695

  7. Survival of a Psychrophilic Marine Vibrio Under Long-Term Nutrient Starvation 1

    PubMed Central

    Novitsky, James A.; Morita, Richard Y.

    1977-01-01

    Ant-300, a psychrophilic marine vibrio isolated from the surface water of the Antarctic convergence, was starved for periods of more than 1 year. During the first week of starvation, cell numbers increased from 100 to 800% of the initial number of cells. Fifty percent of the starved cells remained viable for 6 to 7 weeks while a portion of the population remained viable for more than 1 year. During the first 2 days of starvation, the endogenous respiration of the cells decreased over 80%. After 7 days, respiration had been reduced to 0.0071% total carbon respired per hour and remained constant thereafter. After 6 weeks of starvation, 46% of the cellular deoxyribonucleic acid had been degraded. Observation of the cellular deoxyribonucleic acid with Feulgen staining before starvation showed the average number of nuclear bodies per cell varied from 1.44 to 4.02 depending on the age of the culture. A linear relationship was found between the number of nuclear bodies per cell and the increase in cell numbers upon starvation. Our data suggest that Ant-300 is capable of surviving long periods of time with little or no nutrients and is therefore well adapted for the sparse nutrient conditions of the colder portions of the open ocean. PMID:16345219

  8. Glutathionylation of the iron superoxide dismutase from the psychrophilic eubacterium Pseudoalteromonas haloplanktis.

    PubMed

    Castellano, Immacolata; Ruocco, Maria Rosaria; Cecere, Francesca; Di Maro, Antimo; Chambery, Angela; Michniewicz, Andzelika; Parlato, Giuseppe; Masullo, Mariorosario; De Vendittis, Emmanuele

    2008-05-01

    Our previous work showed that the adduct between beta-mercaptoethanol and the single cysteine residue (Cys57) in superoxide dismutase from the psychrophilic eubacterium Pseudoalteromonas haloplanktis (PhSOD) reduces the enzyme inactivation by peroxynitrite. In this work, immunoblotting experiments prove that peroxynitrite inactivation of PhSOD involves formation of nitrotyrosine residue(s). In order to study the role of Cys57 as a redox-sensor residue modifiable by cellular thiols, a recombinant PhSOD and two Cys57 mutants were produced and characterized. Recombinant and mutant enzymes share similar activity and peroxynitrite inactivation, but different reactivity towards three glutathione forms. Indeed, oxidized glutathione and S-nitrosoglutathione, but reduced glutathione, lead to S-glutathionylation of recombinant PhSOD. This new covalent modification for a Fe-SOD does not occur in both Cys57 mutants, thus indicating that its target is Cys57. Moreover, mass spectrometry analysis confirmed that S-glutathionylation of Cys57 takes place also with endogenous PhSOD. Formation of this mixed disulfide in PhSOD protects the enzyme from tyrosine nitration and peroxynitrite inactivation. PhSOD undergoes S-glutathionylation during its overproduction in E. coli cells and in a growing culture of P. haloplanktis. In both cases the extent of glutathionylated PhSOD is enhanced upon cell exposure to oxidative agents. We suggest that S-glutathionylation of PhSOD could represent a further cold-adaptation strategy to improve the antioxidant cellular defence mechanism.

  9. Detection of Mycoplasma ovipneumoniae and M. arginini in bighorn sheep using enrichment culture coupled with genus- and species-specific polymerase chain reaction.

    PubMed

    Weiser, Glen C; Drew, Mark L; Cassirer, E Frances; Ward, Alton C S

    2012-04-01

    Mycoplasma species are of interest as possible primary pathogens in the pneumonia complex of bighorn sheep (Ovis canadensis). Previous investigations have not commonly detected low frequencies of Mycoplasma spp. from free-ranging bighorn sheep, possibly due to the fastidious and slow growth of these organisms. We developed a culture protocol that employed an average initial 3-day enrichment culture in liquid Hayflick broth in a CO(2)-enhanced atmosphere. The broth was plated to solid Hayflick medium and the cultures observed for growth for up to 30 days. Polymerase chain reaction (PCR) was performed on DNA isolated from the enrichment broth and on isolates obtained from culture using Mycoplasma genus-specific PCR assays and species-specific PCR assays for M. arginini and M. ovipneumoniae. Some cultures that grew on Hayflick plates were picked as single colonies but were mixed because two organisms may grow together and appear as a single colony. Culture and PCR tests produced similar results for M. arginini, but for M. ovipneumoniae, culture alone was less accurate than PCR. Use of genus-specific primers also may allow detection of other species in samples negative for M. arginini and M. ovipneumoniae. Two methods of transport from field to laboratory (Port-a-Cul™ tubes, cryoprotectant in liquid N(2) and Fisher Transport System) gave similar results under our study conditions.

  10. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures.

    PubMed

    Takishita, Kiyotaka; Yubuki, Naoji; Kakizoe, Natsuki; Inagaki, Yuji; Maruyama, Tadashi

    2007-07-01

    Recent culture-independent surveys of eukaryotic small-subunit ribosomal DNA (SSU rDNA) from many environments have unveiled unexpectedly high diversity of microbial eukaryotes (microeukaryotes) at various taxonomic levels. However, such surveys were most probably biased by various technical difficulties, resulting in underestimation of microeukaryotic diversity. In the present study on oxygen-depleted sediment from a deep-sea methane cold seep of Sagami Bay, Japan, we surveyed the diversity of eukaryotic rDNA in raw sediment samples and in two enrichment cultures. More than half of all clones recovered from the raw sediment samples were of the basidiomycetous fungus Cryptococcus curvatus. Among other clones, phylotypes of eukaryotic parasites, such as Apicomplexa, Ichthyosporea, and Phytomyxea, were identified. On the other hand, we observed a marked difference in phylotype composition in the enrichment samples. Several phylotypes belonging to heterotrophic stramenopiles were frequently found in one enrichment culture, while a phylotype of Excavata previously detected at a deep-sea hydrothermal vent dominated the other. We successfully established a clonal culture of this excavate flagellate. Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation step successfully found at least a fraction of the "hidden" microeukaryotic diversity in the environment examined.

  11. Enhanced enrichment of prostate cancer stem-like cells with miniaturized 3D culture in liquid core-hydrogel shell microcapsules

    PubMed Central

    Yu, Jianhua; Lu, Xiongbin; Zynger, Debra L.; He, Xiaoming

    2015-01-01

    Cancer stem-like cells (CSCs) are rare subpopulations of cancer cells that are reported to be responsible for cancer resistance and metastasis associated with conventional cancer therapies. Therefore, effective enrichment/culture of CSCs is of importance to both the understanding and treatment of cancer. However, it usually takes approximately 10 days for the widely used conventional approach to enrich CSCs through the formation of CSC-containing aggregates. Here we report the time can be shortened to 2 days while obtaining prostate CSC-containing aggregates with better quality based on the expression of surface receptor markers, dye exclusion, gene and protein expression, and in vivo tumorigenicity. This is achieved by encapsulating and culturing human prostate cancer cells in the miniaturized 3D liquid core of microcapsules with an alginate hydrogel shell. The miniaturized 3D culture in core–shell microcapsules is an effective strategy for enriching/culturing CSCs in vitro to facilitate cancer research and therapy development. PMID:24952981

  12. Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method.

    PubMed

    Dalmasso, Marion; Bolocan, Andrei Sorin; Hernandez, Marta; Kapetanakou, Anastasia E; Kuchta, Tomáš; Manios, Stavros G; Melero, Beatriz; Minarovičová, Jana; Muhterem, Meryem; Nicolau, Anca Ioana; Rovira, Jordi; Skandamis, Panagiotis N; Stessl, Beatrix; Wagner, Martin; Jordan, Kieran; Rodríguez-Lázaro, David

    2014-03-01

    Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is

  13. Changes in glucose fermentation pathways by an enriched bacterial culture in response to regulated dissolved H2 concentrations.

    PubMed

    Zheng, Hang; Zeng, Raymond J; Duke, Mikel C; O'Sullivan, Cathryn A; Clarke, William P

    2015-06-01

    It is well established that metabolic pathways in the fermentation of organic waste are primarily controlled by dissolved H2 concentrations, but there is no reported study that compares observed and predicted shifts in fermentation pathways induced by manipulating the dissolved H2 concentration. A perfusion system is presented that was developed to control dissolved H2 concentrations in the continuous fermentation of glucose by a culture highly enriched towards Thermoanaerobacterium thermosaccharolyticum (86 ± 9% relative abundance) from an originally diverse consortia in the leachate of a laboratory digester fed with municipal solid waste. Media from a 2.5 L CSTR was drawn through sintered steel membrane filters to retain biomass, allowing vigorous sparging in a separate chamber without cellular disruption. Through a combination of sparging and variations in glucose feeding rate from 0.8 to 0.2 g/L/d, a range of steady state fermentations were performed with dissolved H2 concentrations as low as an equivalent equilibrated H2 partial pressure of 3 kPa. Trends in product formation rates were simulated using a H2 regulation partitioning model. The model correctly predicted the direction of products redistribution in response to H2 concentration changes and the acetate and butyrate formation rates when H2 concentrations were less than 6 kPa. However, the model over-estimated acetate, ethanol and butanol productions at the expense of butyrate production at higher H2 concentrations. The H2 yield at the lowest dissolved H2 concentration was 2.67 ± 0.08 mol H2 /mol glucose, over 300% higher than the yield achieved in a CSTR operated without sparging.

  14. Isolation and culture of highly enriched populations of Leydig cells from guinea-pig (Cavia porcellus) testes.

    PubMed

    Kukucka, M A; Misra, H P

    1994-01-01

    Leydig cells were isolated from adult male guinea-pig testes using a multi-step procedure involving enzymatic dissociation and Percoll-gradient centrifugation. The following description is the first account of a successful isolation of adolescent guinea-pig Leydig cells. The enriched Leydig-cell preparation routinely isolated from six intact testicles yielded approximately 5.0 x 10(6) +/- 0.7 x 10(6) (+/- SEM) Leydig cells with a viability of 98.0 +/- 0.4% as determined using the trypan-blue exclusion method. The purity of the isolated cell population as assessed by 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD) staining averaged 82.5 +/- 0.8%. Under light microscopy, guinea-pig Leydig cells were polyhedral in shape with a large prominent nucleus and a distinct nucleolus. The acidophilic cytoplasm contained numerous lipid-filled vesicles. Ultrastructurally, guinea-pig Leydig cells displayed an eccentrically located ovoid nucleus with dark-staining peripheral heterochromatin. Large quantities of mitochondria, smooth endoplasmic reticulum and particulate-laden lipid droplets were also evident. The steroidogenic potential of the isolated Leydig cells was verified using a maximally stimulating dose of ovine LH (100 ng ml-1) and human CG (200 mIU ml-1). Leydig cells incubated in a shaking (120 cycles min-1) water bath for 3 h at 37 degrees C in capped polypropylene microcentrifuge tubes produced 233 +/- 21 ng and 223 +/- 18 ng testosterone per 1 x 10(6) cells when maximally stimulated with oLH or hCG, respectively. The inclusion of low (1-5 microM) levels of sodium ascorbate during culture enhanced significantly Leydig-cell viability vs. control values.

  15. Preparation of glycerol-enriched yeast culture and its effect on blood metabolites and ruminal fermentation in goats.

    PubMed

    Ye, Gengping; Zhu, Yongxing; Liu, Jin; Chen, Xingxiang; Huang, Kehe

    2014-01-01

    The aim of this study was to isolate a glycerol-producing yeast strain from nature to prepare glycerol-enriched yeast culture (GY), and preliminarily evaluate the effects of GY on blood metabolites and ruminal fermentation in goats. During the trial, six isolates were isolated from unprocessed honey, and only two isolates with higher glycerol yield were identified by analysis of 26S ribosomal DNA sequences. One of the two isolates was identified as Saccharomyces cerevisiae, a direct-fed microbe permitted by the FDA. This isolate was used to prepare GY. The fermentation parameters were optimized through single-factor and orthogonal design methods to maximize the glycerol yield and biomass. The final GY contained 38.7±0.6 g/L glycerol and 12.6±0.5 g/L biomass. In vivo, eight castrated male goats with ruminal fistula were used in a replicated 4×4 Latin square experiment with four consecutive periods of 15 d. Treatments were as follows: control, LGY, MGY, and HGY with 0, 100, 200, and 300 mL GY per goat per day, respectively. The GY was added in two equal portions at 08∶00 and 17∶00 through ruminal fistula. Samples of blood and ruminal fluid were collected on the last one and two days of each period, respectively. Results showed that the plasma concentrations of triglyceride and total cholesterol were not affected by the supplemented GY. Compared with the control, goats supplemented with MGY and HGY had significantly higher (P<0.05) concentrations of plasma glucose and total protein, ruminal volatile fatty acid and molar proportion of propionate, and significantly lower (P<0.05) ruminal pH and ammonia nitrogen. These parameters changed linearly with increasing GY supplementation level (P<0.05). In conclusion, GY has great potential to be developed as a feed additive with dual effects of glycerol and yeast for ruminants.

  16. Psychrophilic and Psychrotolerant Microbial Extremophiles in Polar Environments

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Pikuta, Elena V.

    2010-01-01

    The microbial extremophiles that inhabit the polar regions of our planet are of tremendous significance. The psychrophilic and psychrotolerant microorganisms, which inhabit all of the cold environments on Earth have important applications to Bioremediation, Medicine, Pharmaceuticals, and many other areas of Biotechnology. Until recently, most of the research on polar microorganisms was confined to studies of polar diatoms, yeast, fungi and cyanobacteria. However, within the past three decades, extensive studies have been conducted to understand the bacteria and archaea that inhabit the Arctic and Antarctic sea-ice, glaciers, ice sheets, permafrost and the cryptoendolithic, cryoconite and ice-bubble environments. These investigations have resulted in the discovery of many new genera and species of anaerobic and aerobic microbial extremophiles. Exotic enzymes, cold-shock proteins and pigments produced by some of the extremophiles from polar environments have the potential to be of great benefit to Mankind. Knowledge about microbial life in the polar regions is crucial to understanding the limitations and biodiversity of life on Earth and may provide valuable clues to the Origin of Life on Earth. The discovery of viable microorganisms in ancient ice from the Fox Tunnel, Alaska and the deep Vostok Ice has shown that microorganisms can remain alive while cryopreserved in ancient ice. The psychrophilic lithoautotrophic homoacetogen isolated from the deep anoxic trough of Lake Untersee is an ideal candidate for life that might inhabit comets or the polar caps of Mars. The spontaneous release of gas from within the Anuchin Glacier above Lake Untersee may provide clues to the ice geysers that erupt from the tiger stripe regions of Saturn s moon Enceladus. The methane productivity in the lower regimes of Lake Untersee may also provide insights into possible mechanisms for the recently discovered methane releases on Mars. Since most of the other water bearing bodies of our

  17. Photosynthetic and Respiratory Rates of Two Psychrophilic Diatoms 1

    PubMed Central

    Van Baalen, Chase

    1985-01-01

    The photosynthetic rates in two psychrophilic diatoms, Chaetoceros sp. strain K3-10 and Nitzschia sp. K3-3 for cells grown at 0°C were 8 to 10 microliters O2 evolved per milligram dry weight per hour, and 10-fold higher, about 80 for cells grown at 10°C. The respiration rates followed the same pattern, with a value of around 1 microliter dark uptake per milligram dry weight per hour for both organisms grown at 0°C, and 6 to 10 for cells grown at 10°C. When cells grown at 0°C were immediately shifted to 10°C or cells grown at 10°C were shifted to 0°C, the respiratory rates quickly adapted to values characteristic of cells grown at the shift temperature. On the other hand, the light-saturated rate of O2 evolution showed much less immediate adaptation, especially on the up shift, 0° to 10°C. The chlorophyll a content of 0°C grown cells was about 0.5% of dry weight, in 10°C grown cells 1.3% (strain K3-10) and 2.2% (strain K3-3). In addition to a diminished chlorophyll a content in 0°C grown cells, there seemed proportionally (by absorbance and calculation) less c to a than in 10°C grown cells. The relative fluorescence excitation spectra of 680-nm emission also showed a lower contribution by both chlorophyll c and fucoxanthin in 0°C grown cells of Chaetoceros sp. strain K3-10 as compared to 10°C grown cells. The data at hand suggest that in psychrophilic diatoms continuously growing at 0°C there may be problems associated with synthesis of an effective accessory pigment system, and as a working hypothesis it is suggested this is related to restriction of synthesis of one or several accessory pigment proteins. PMID:16664328

  18. Deep-sea oil plume enriches psychrophilic oil-degrading bacteria

    SciTech Connect

    Hazen, T.C.; Dubinsky, E.A.; DeSantis, T.Z.; Andersen, G.L.; Piceno, Y.M.; Singh, N.; Jansson, J.K.; Probst, A.; Borglin, S.E.; Fortney, J.L.; Stringfellow, W.T.; Bill, M.; Conrad, M.S.; Tom, L.M.; Chavarria, K.L.; Alusi, T.R.; Lamendella, R.; Joyner, D.C.; Spier, C.; Auer, M.; Zemla, M.L.; Chakraborty, R.; Sonnenthal, E.L.; D'haeseleer, P.; Holman, H.-Y. N.; Osman, S.; Lu, Z.; Van Nostrand, J.D.; Deng, Y.; Zhou, J.; Mason, O.U.

    2010-09-01

    The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous {gamma}-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5 C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.

  19. Psychrophilic yeasts in glacial environments of Alpine glaciers.

    PubMed

    Turchetti, Benedetta; Buzzini, Pietro; Goretti, Marta; Branda, Eva; Diolaiuti, Guglielmina; D'Agata, Carlo; Smiraglia, Claudio; Vaughan-Martini, Ann

    2008-01-01

    The presence of psychrophilic yeasts in supra- and subglacial sediments, ice and meltwater collected from two glaciers of the Italian Alps (Forni and Sforzellina-Ortles-Cevedale group) was investigated. After incubation at 4 degrees C, subglacial sediments contained from 1.3 x 10(3) to 9.6 x 10(3) CFU of yeasts g(-1). The number of yeast cells in supraglacial sediments was c. 10-100-fold lower. A significant proportion of isolated yeasts exhibited one or more extracellular enzymatic activities (starch-degrading, lipolytic, esterolytic, proteolytic and pectinolytic activity) at 4 degrees C. Selected isolates were able to grow at 2 degrees C under laboratory-simulated in situ conditions. In all, 106 isolated yeasts were identified by MSP-PCR fingerprinting and 26S rRNA gene sequencing of the D1/D2 region as belonging to 10 species: Aureobasidium pullulans, Cryptococcus gilvescens (over 50% of the total), Cryptococcus terricolus, Mrakia gelida, Naganishia globosa, Rhodotorula glacialis, Rhodotorula psychrophenolica, Rhodotorula bacarum, Rhodotorula creatinivora and Rhodotorula laryngis. Four strains, all belonging to a new yeast species, yet to be described, were also isolated.

  20. Characterization of psychrophilic alanine racemase from Bacillus psychrosaccharolyticus.

    PubMed

    Okubo, Y; Yokoigawa, K; Esaki, N; Soda, K; Kawai, H

    1999-03-16

    A psychrophilic alanine racemase gene from Bacillus psychrosaccharolyticus was cloned and expressed in Escherichia coli SOLR with a plasmid pYOK3. The gene starting with the unusual initiation codon GTG showed higher preference for codons ending in A or T. The enzyme purified to homogeneity showed the high catalytic activity even at 0 degrees C and was extremely labile over 35 degrees C. The enzyme was found to have a markedly large Km value (5.0 microM) for the pyridoxal 5'-phosphate (PLP) cofactor in comparison with other reported alanine racemases, and was stabilized up to 50 degrees C in the presence of excess amounts of PLP. The low affinity of the enzyme for PLP may be related to the thermolability, and may be related to the high catalytic activity, initiated by the transaldimination reaction, at low temperature. The enzyme has a distinguishing hydrophilic region around the residue no. 150 in the deduced amino acid sequence (383 residues), whereas the corresponding regions of other Bacillus alanine racemases are hydrophobic. The position of the region in the three dimensional structure of C atoms of the enzyme was predicted to be in a surface loop surrounding the active site. The region may interact with solvent and reduce the compactness of the active site.

  1. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H

    PubMed Central

    Harvilla, Paul B.; Wolcott, Holly N.

    2014-01-01

    Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth’s ecosystems are at temperatures ≤ 5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: 4O1W). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed. PMID:24727932

  2. High Frequency of Thermodesulfovibrio spp. and Anaerolineaceae in Association with Methanoculleus spp. in a Long-Term Incubation of n-Alkanes-Degrading Methanogenic Enrichment Culture

    PubMed Central

    Liang, Bo; Wang, Li-Ying; Zhou, Zhichao; Mbadinga, Serge M.; Zhou, Lei; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2016-01-01

    In the present study, the microbial community and functional gene composition of a long-term active alkane-degrading methanogenic culture was established after two successive enrichment culture transfers and incubated for a total period of 1750 days. Molecular analysis was conducted after the second transfer (incubated for 750 days) for both the active alkanes-degrading methanogenic enrichment cultures (T2-AE) and the background control (T2-BC). A net increase of methane as the end product was detected in the headspace of the enrichment cultures amended with long-chain n-alkanes and intermediate metabolites, including octadecanoate, hexadecanoate, isocaprylate, butyrate, isobutyrate, propionate, acetate, and formate were measured in the liquid cultures. The composition of microbial community shifted through the successive transfers over time of incubation. Sequences of bacterial and archaeal 16S rRNA gene (16S rDNA) and mcrA functional gene indicated that bacterial sequences affiliated to Thermodesulfovibrio spp. and Anaerolineaceae and archaeal sequences falling within the genus Methanoculleus were the most frequently encountered and thus represented the dominant members performing the anaerobic degradation of long-chain n-alkanes and methanogenesis. In addition, the presence of assA functional genes encoding the alkylsuccinate synthase α subunit indicated that fumarate addition mechanism could be considered as a possible initial activation step of n-alkanes in the present study. The succession pattern of microbial communities indicates that Thermodesulfovibrio spp. could be a generalist participating in the metabolism of intermediates, while Anaerolineaceae plays a key role in the initial activation of long-chain n-alkane biodegradation. PMID:27695441

  3. Psychrophilic and psychrotolerant fungi on bats and the presence of Geomyces spp. on bat wings prior to the arrival of white nose syndrome.

    PubMed

    Johnson, Lynnaun J A N; Miller, Andrew N; McCleery, Robert A; McClanahan, Rod; Kath, Joseph A; Lueschow, Shiloh; Porras-Alfaro, Andrea

    2013-09-01

    Since 2006, Geomyces destructans, the causative agent of white nose syndrome (WNS), has killed over 5.7 million bats in North America. The current hypothesis suggests that this novel fungus is an invasive species from Europe, but little is known about the diversity within the genus Geomyces and its distribution on bats in the United States. We documented the psychrophilic and psychrotolerant fungal flora of hibernating bats prior to the arrival of WNS using culture-based techniques. A total of 149 cultures, which were obtained from 30 bats in five bat hibernacula located in four caves and one mine, were sequenced for the entire internal transcribed spacer (ITS) nuclear ribosomal DNA (nrDNA) region. Approximately 53 operational taxonomic units (OTUs) at 97% similarity were recovered from bat wings, with the community dominated by fungi within the genera Cladosporium, Fusarium, Geomyces, Mortierella, Penicillium, and Trichosporon. Eleven Geomyces isolates were obtained and placed in at least seven distinct Geomyces clades based on maximum-likelihood phylogenetic analyses. Temperature experiments revealed that all Geomyces strains isolated are psychrotolerant, unlike G. destructans, which is a true psychrophile. Our results confirm that a large diversity of fungi, including several Geomyces isolates, occurs on bats prior to the arrival of WNS. Most of these isolates were obtained from damaged wings. Additional studies need to be conducted to determine potential ecological roles of these abundant Geomyces strains isolated from bats.

  4. Psychrophilic versus psychrotolerant bacteria--occurrence and significance in polar and temperate marine habitats.

    PubMed

    Helmke, E; Weyland, H

    2004-07-01

    The numerical dominance and ecological role of psychrophilic bacteria in bottom sediments, sea ice, surface water and melt pools of the polar oceans were investigated using isolates, colony forming units (CFU) and metabolic activities. All sediment samples of the Southern Ocean studied showed a clear numerical dominance of cold-loving bacteria. In Arctic sediments underlying the influence of cold polar water bodies psychrophiles prevailed also but they were less dominant in sediments influenced by the warm Atlantic Water. A predominance of psychrophiles was further found in consolidated Antarctic sea ice as well as in multiyear Arctic sea ice and in melt pools on top of Arctic ice floes. A less uniform adaptation response was, however, met in polar surface waters. In the very northern part of the Fram Strait (Arctic Ocean) we found bacterial counts and activities at 1 degree C exceeding those at 22 degrees C. In surface water of the Weddell Sea (Southern Ocean) psychrophiles also dominated numerically in early autumn but the dominance declined obviously with the onset of winter-water and a decrease of chlorphyll a. Otherwise in surface water of the Southern Ocean CFUs were higher at 22 degrees C than at 1 degree C while activities were vice versa indicating at least a functional dominance of psychrophiles. Even in the temperate sediments of the German Bight true psychrophiles were present and a clear shift towards cold adapted communities in winter observed. Among the polar bacteria a more pronounced cold adaptation of Antarctic in comparison with Arctic isolates was obtained. The results and literature data indicate that stenothermic cold adapted bacteria play a significant role in the global marine environment. On the basis of the temperature response of our isolates from different habitats it is suggested to expand the definition of Morita in order to meet the cold adaptation strategies of the bacteria in the various cold habitats.

  5. Overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism.

    PubMed

    Oswald, Victoria F; Chen, WeiTing; Harvilla, Paul B; Magyar, John S

    2014-02-01

    The psychrophilic, hydrocarbonoclastic microorganism Colwellia psychrerythraea is important in global nutrient cycling and bioremediation. In order to investigate how this organism can live so efficiently at low temperatures (~4°C), thermal denaturation studies of a small electron transfer protein from Colwellia were performed. Colwellia cytochrome c552 was overexpressed in Escherichia coli, isolated, purified, and characterized by UV-visible absorption spectroscopy. The melting temperature (Tm) and the van't Hoff enthalpy (ΔHvH) were determined. These values suggest an unexpectedly high stability for this psychrophilic cytochrome.

  6. Coliforms, Enterococci, Thermodurics, Thermophiles, and Psychrophiles in Untreated Farm Pond Waters

    PubMed Central

    Malaney, G. W.; Weiser, H. H.; Turner, R. O.; Van Horn, Marilyn

    1962-01-01

    Untreated waters from ten farm ponds located in central, north central, southeastern, and southwestern Ohio were examined for numbers of coliforms, enterococci, thermodurics, thermophiles, and psychrophiles. The median population densities per 100 ml water for all ponds were: coliforms, 23; enterococci, 3.6; thermodurics, 6,000; thermophiles, 450; psychrophiles, 1,000. The results indicate that these farm pond waters were only lightly polluted and suggest that farm ponds, properly maintained, are a source of raw water of high bacteriological quality, requiring a minimum of treatment to be made suitable for domestic and livestock purposes. PMID:14468809

  7. Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

    PubMed Central

    Fayolle-Guichard, Françoise; Lombard, Vincent; Hébert, Agnès; Coutinho, Pedro M.; Groppi, Alexis; Barre, Aurélien; Henrissat, Bernard

    2016-01-01

    Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity. PMID:27936240

  8. Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures.

    PubMed

    Heiss-Blanquet, Senta; Fayolle-Guichard, Françoise; Lombard, Vincent; Hébert, Agnès; Coutinho, Pedro M; Groppi, Alexis; Barre, Aurélien; Henrissat, Bernard

    2016-01-01

    Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.

  9. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

    PubMed Central

    McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  10. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures.

    PubMed

    McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  11. Enrichment of prostate cancer stem-like cells from human prostate cancer cell lines by culture in serum-free medium and chemoradiotherapy.

    PubMed

    Wang, Lei; Huang, Xing; Zheng, Xinmin; Wang, Xinghuan; Li, Shiwen; Zhang, Lin; Yang, Zhonghua; Xia, Zhiping

    2013-01-01

    The discovery of rare subpopulations of cancer stem cells (CSCs) has created a new focus in cancer research. As CSCs demonstrate resistance to chemoradiation therapy relative to other cancer cells, this allows the enrichment of CSC populations by killing apoptosis-susceptible cancer cells. In this study, three commonly used human prostate cancer (PCa) cell lines (DU145, PC-3 and LNCaP) were examined for their expression of the putative stem cell markers CD133 and CD44 via flow cytometric analysis. Under normal culture conditions, CD133(+)/CD44(+) cells were only present in the DU145 cell line, and comprised only a minor percentage (0.1% ± 0.01%) of the total population. However, the proportion of these CD133(+)/CD44(+) prostate CSCs could be increased in these cell lines via culture in serum-free medium (SFM), or through chemotherapy or radiotherapy. Indeed, after culture in SFM, the proportion of CD133(+)/CD44(+) cells in DU145 and PC-3 had increased to 10.3% and 3.0%, respectively. Moreover, the proportion had increased to 9.8% enriched by chemotherapy and 3.5% by radiotherapy in DU145. Colony-formation tests, cell invasion assays, and tumor xenografts in BALB/c nude mice were used to evaluate the stem cell properties of CD133(+)/CD44(+) PCa cells that were isolated via fluorescence-activated cell sorting (FACS). CD133(+)/CD44(+) cells had an enhanced colony-formation capability and invasive ability in vitro, and displayed greater tumorigenic properties in vivo. These results demonstrate the presence of CD133(+)/CD44(+) prostate CSCs in established PCa cell lines and that populations of these cells can be enriched by culture in SFM or chemoradiotherapy. Finding novel therapies to override chemoradiation resistance in the prostate CSCs is the key to improve long-term results in PCa management.

  12. The influence of IgM-enriched immunoglobulin therapy on neonatal mortality and hematological variables in newborn infants with blood culture-proven sepsis.

    PubMed

    Abbasoğlu, Aslıhan; Ecevit, Ayşe; Tuğcu, Ali Ulaş; Yapakçı, Ece; Tekindal, Mustafa Agah; Tarcan, Aylin; Ecevit, Zafer

    2014-01-01

    The aim of this study was to determine the effects of adjuvant immunoglobulin M (IgM)-enriched intravenous immunoglobulin (IVIG) therapy on mortality rate, hematological variables and length of hospital stay in newborn infants with blood culture-proven sepsis. Demographic and clinical features and outcome measures of 63 newborn infants with blood culture-proven sepsis were documented retrospectively from the medical records. The patients were divided into two groups according to their treatment history. The patients in Group 1 received antibiotic therapy only and the patients in Group 2 received both antibiotic and adjuvant IgMenriched IVIG. The study revealed that mortality rates were 28.1% and 12.9% in Group 1 and Group 2, respectively. The mortality rate was lower in Group 2, but the difference between the two groups was not statistically significant (p=0.21). Coagulase-negative Staphylococcus was the most common type of bacteria isolated from the blood culture in both groups. When changing laboratory results were compared between the two groups, hemoglobin, leukocyte count and C-reactive protein levels were different during the first three days of antibiotic treatment. Our study revealed that if diagnosed at an early stage and treated aggressively with appropriate and effective antibiotics, adjuvant IgM-enriched IVIG treatment has no additional benefits in neonatal sepsis.

  13. Bioconversion of H2/CO 2 by acetogen enriched cultures for acetate and ethanol production: the impact of pH.

    PubMed

    Xu, Shuyun; Fu, Bo; Zhang, Lijuan; Liu, He

    2015-06-01

    Syngas fermentation into ethanol and other bioproducts by mixed cultures is considered a promising biotechnology. Effects of pH on product generation and microbial community during H2/CO2 utilization by acetogen enrichment cultures were investigated in this work. The maximum acetate concentration reached 95.41 mmol L(-1) at pH 7, which was 71.7, 21.8 and 50.9% higher than at pH 5, 9 and 11, respectively. The maximum ethanol concentration at pH 7 was 45.7, 50, 72% higher than that at pH 5, 9 and 11, respectively. The CO dehydrogenase (CODH) gene copy number was highest at pH 7, indicating that metabolically active acetogens reached their highest level at pH 7. The CODH gene copy number at pH 9 was lower than at pH 7, but higher than at pH 5 and 11. Correspondingly, the enrichment cultures at pH 7 had the highest species richness and diversity, while those at pH 9 had the second highest diversity, and those at pH 5 and 11 had the lowest diversity. The shift in microbial community structure and the different active acetogen contents resulting from different pHs were responsible for the differences in acetate and ethanol production.

  14. Biosynthesis of highly enriched 13C-lycopene for human metabolic studies using repeated batch tomato cell culturing with 13C-glucose.

    PubMed

    Moran, Nancy Engelmann; Rogers, Randy B; Lu, Chi-Hua; Conlon, Lauren E; Lila, Mary Ann; Clinton, Steven K; Erdman, John W

    2013-08-15

    While putative disease-preventing lycopene metabolites are found in both tomato (Solanum lycopersicum) products and in their consumers, mammalian lycopene metabolism is poorly understood. Advances in tomato cell culturing techniques offer an economical tool for generation of highly-enriched (13)C-lycopene for human bioavailability and metabolism studies. To enhance the (13)C-enrichment and yields of labelled lycopene from the hp-1 tomato cell line, cultures were first grown in (13)C-glucose media for three serial batches and produced increasing proportions of uniformly labelled lycopene (14.3±1.2%, 39.6±0.5%, and 48.9±1.5%) with consistent yields (from 5.8 to 9 mg/L). An optimised 9-day-long (13)C-loading and 18-day-long labelling strategy developed based on glucose utilisation and lycopene yields, yielded (13)C-lycopene with 93% (13)C isotopic purity, and 55% of isotopomers were uniformly labelled. Furthermore, an optimised acetone and hexane extraction led to a fourfold increase in lycopene recovery from cultures compared to a standard extraction.

  15. Epidemiology of Salmonella sp. in California cull dairy cattle: prevalence of fecal shedding and diagnostic accuracy of pooled enriched broth culture of fecal samples

    PubMed Central

    Abu Aboud, Omran A.; Adaska, John M.; Williams, Deniece R.; Rossitto, Paul V.; Champagne, John D.; Lehenbauer, Terry W.; Atwill, Robert; Li, Xunde

    2016-01-01

    Background The primary objective of this cross-sectional study was to estimate the crude, seasonal and cull-reason stratified prevalence of Salmonella fecal shedding in cull dairy cattle on seven California dairies. A secondary objective was to estimate and compare the relative sensitivity (Se) and specificity (Sp) for pools of 5 and 10 enriched broth cultures of fecal samples for Salmonella sp. detection. Methods Seven dairy farms located in the San Joaquin Valley of California were identified and enrolled in the study as a convenience sample. Cull cows were identified for fecal sampling once during each season between 2014 and 2015, specifically during spring, summer, fall, and winter, and 10 cows were randomly selected for fecal sampling at the day of their sale. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous four month’s herd management. Fecal samples were frozen until testing for Salmonella. After overnight enrichment in liquid broth, pools of enrichment broth (EBP) were created for 5 and 10 samples. All individual and pooled broths were cultured on selective media with putative Salmonella colonies confirmed by biochemical testing before being serogrouped and serotyped. Results A total of 249 cull cows were enrolled into the study and their fecal samples tested for Salmonella. The survey-weighted period prevalence of fecal shedding of all Salmonella sp. in the cull cow samples across all study herds and the entire study period was 3.42% (N = 249; SE 1.07). The within herd prevalence of Salmonella shed in feces did not differ over the four study seasons (P = 0.074). The Se of culture of EBP of five samples was 62.5% (SE = 17.12), which was not statistically different from the Se of culture of EBP of 10 (37.5%, SE = 17.12, P = 0.48). The Sp of culture of EBP of five samples was 95.24% (SE = 3.29) and for pools of 10 samples was 100.00% (SE = 0). There was no statistical difference

  16. Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505

    PubMed Central

    Margolles, Abelardo; Gueimonde, Miguel

    2012-01-01

    Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from cyanobacterial mat samples, originally collected from ponds in McMurdo, Antarctica. This orange-pigmented bacterium grows at 4°C and may possess interesting enzymatic activities at low temperatures. Here we report the first genomic sequence of P. antarcticus DSM 14505. PMID:22843594

  17. Metabolic Influence of Psychrophilic Diatoms on Travertines at the Huanglong Natural Scenic District of China

    PubMed Central

    Sun, Shiyong; Dong, Faqin; Ehrlich, Hermann; Zhao, Xueqing; Liu, Mingxue; Dai, Qunwei; Li, Qiongfang; An, Dejun; Dong, Hailiang

    2014-01-01

    Diatoms are a highly diversified group of algae that are widely distributed in aquatic ecosystems, and various species have different nutrient and temperature requirements for optimal growth. Here, we describe unusual psychrophilic diatoms of Cymbella in a travertine deposition environment in southwestern China in winter season. Travertine surfaces are colonized by these psychrophilic diatoms, which form biofilms of extracellular polysaccharide substances (EPS) with active metabolic activities in extremely cold conditions. The travertine in Huanglong, is a typical single crystalline calcite with anisotropic lattice distortions of unit cell parameters along axes of a and c, and this structure is suggestive of some level of metabolic mediation on mineralization. Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) results further confirmed the occurrence of biogenic distortion of the crystal lattice of travertine calcite. Overall, our results imply that the metabolic influence of psychrophilic diatoms may be particularly important for promoting formation and dissolution of travertine in extremely cold environments of Huanglong. The EPS of psychrophilic diatoms will protect travertine from HCO3− etching and provide template for forming travertine when water re-flowing, in warm season. PMID:25522049

  18. Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample

    PubMed Central

    Lee, Jaejin; Kwon, Miye; Yang, Jae Young; Woo, Jusun; Lee, Hong Kum; Hong, Soon Gyu

    2016-01-01

    Psychrobacter alimentarius PAMC 27889, a Gram-negative, psychrophilic bacterium, was isolated from an Antarctic rock sample. Here, we report the complete genome of P. alimentarius PAMC 27889, which has the nonmevalonate methylerythritol phosphate pathway of terpenoid biosynthesis and a complete gene cluster for benzoate degradation. PMID:27445386

  19. Efficient aspartic acid production by a psychrophile-based simple biocatalyst.

    PubMed

    Tajima, Takahisa; Hamada, Mai; Nakashimada, Yutaka; Kato, Junichi

    2015-10-01

    We previously constructed a Psychrophile-based Simple bioCatalyst (PSCat) reaction system, in which psychrophilic metabolic enzymes are inactivated by heat treatment, and used it here to study the conversion of aspartic acid from fumaric acid mediated by the activity of aspartate ammonia-lyase (aspartase). In Escherichia coli, the biosynthesis of aspartic acid competes with that of L-malic acid produced from fumaric acid by fumarase. In this study, E. coli aspartase was expressed in psychrophilic Shewanella livingstonensis Ac10 heat treated at 50 °C for 15 min. The resultant PSCat could convert fumaric acid to aspartic acid without the formation of L-malic acid because of heat inactivation of psychrophilic fumarase activity. Furthermore, alginate-immobilized PSCat produced high yields of aspartic acid and could be re-used nine times. The results of our study suggest that PSCat can be applied in biotechnological production as a new approach to increase the yield of target compounds.

  20. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil.

    PubMed Central

    Rabus, R; Fukui, M; Wilkes, H; Widdle, F

    1996-01-01

    A mesophilic sulfate-reducing enrichment culture growing anaerobically on crude oil was used as a model system to study which nutritional types of sulfate-reducing bacteria may develop on original petroleum constituents in oil wells, tanks, and pipelines. Chemical analysis of oil hydrocarbons during growth revealed depletion of toluene and o-xylene within 1 month and of m-xylene, o-ethyltoluene, m-ethyltoluene, m-propyltoluene, and m-isopropyltoluene within approximately 2 months. In anaerobic counting series, the highest numbers of CFU (6 x 10(6) to 8 x 10(6) CFU ml-1) were obtained with toluene and benzoate. Almost the same numbers were obtained with lactate, a substrate often used for detection of the vibrio-shaped, incompletely oxidizing Desulfovibrio sp. In the present study, however, lactate yielded mostly colonies of oval to rod-shaped, completely oxidizing, sulfate-reducing bacteria which were able to grow slowly on toluene or crude oil. Desulfovibrio species were detected only at low numbers (3 x 10(5) CFU ml-1). In agreement with this finding, a fluorescently labeled, 16S rRNA-targeted oligonucleotide probe described in the literature as specific for members of the Desulfovibrionaceae (suggested family) hybridized only with a small portion (< 5%) of the cells in the enrichment culture. These results are consistent with the observation that known Desulfovibrio species do not utilize aromatic hydrocarbons, the predominant substrates in the enrichment culture. All known sulfate-reducing bacteria which utilize aromatic compounds belong to a separate branch, the Desulfobacteriaceae (suggested family). Most members of this family are complete oxidizers. For specific hybridization with members of this branch, the probe had to be modified by a nucleotide exchange. Indeed, this modified probe hybridized with more than 95% of the cells in the enrichment culture. The results show that completely oxidizing, alkylbenzene-utilizing sulfate-reducing bacteria rather than

  1. Relative binding and biochemical effects of heterodimeric and homodimeric isoforms of platelet-derived growth factor in osteoblast-enriched cultures from fetal rat bone

    SciTech Connect

    Centrella, M.; McCarthy, T.L.; Kusmik, W.F.; Canalis, E. )

    1991-06-01

    Platelet-derived growth factor (PDGF) exists as a homodimer or a heterodimer comprising either PDGF-A or PDGF-B subunits, and each isoform occurs in various tissues, including bone. Although the stimulatory effects of PDGF-BB have been studied in cultures of bone cells and intact bone fragments, the influence of other isoforms that may arise locally or systematically in vivo, has not been reported. Therefore recombinant human PDGF-BB, PDGF-AB, and PDGF-AA were evaluated in osteoblast-enriched cultures from fetal rat bone. Within 24 hours these factors produced a graded response in bone cell DNA and protein synthesis, with half-maximal effects at approximately 0.6, 2.1, and 4.8 nM PDGF-BB, PDGF-AB, and PDGF-AA, respectively. Increases in collagen and noncollagen protein synthesis were abrogated when DNA synthesis was blocked with hydroxyurea. Furthermore, each factor reduced alkaline phosphatase activity, PDGF-BB being the most inhibitory. Binding studies with 125I-PDGF-BB or 125I-PDGF-AA and each unlabeled PDGF isoform produced discrete ligand binding and displacement patterns: 125I-PDGF-BB binding was preferentially displaced by PDGF-BB (Ki approximately 0.7 nM), less by PDGF-AB (Ki approximately 2.3 nM) and poorly by PDGF-AA. In contrast, 125I-PDGF-AA binding was measurably reduced by PDGF-AA (Ki approximately 4.0 nM), but was more effectively displaced by PDGF-BB or PDGF-AB (each with Ki approximately 0.7 nM). These studies indicate that each PDGF isoform produces biochemical effects proportional to binding site occupancy and suggest that receptors that favor PDGF-B subunit binding preferentially mediate these results in osteoblast-enriched bone cell cultures.

  2. DENATURATION AND RENATURATION OF MALIC DEHYDROGENASE IN A CELL-FREE EXTRACT FROM A MARINE PSYCHROPHILE.

    PubMed

    BURTON, S D; MORITA, R Y

    1963-11-01

    Burton, Sheril D. (Oregon State University, Corvallis), and Richard Y. Morita. Denaturation and renaturation of malic dehydrogenase in a cell-free extract from a marine psychrophile. J. Bacteriol. 86:1019-1024. 1963.-Malic dehydrogenase from a marine psychrophilic vibrio (PS 207) was found to be heat-sensitive at 30 C, the maximal growth temperature for the organism. Initial denaturation was reversible, with maximal renaturation occurring when the denatured enzyme was slowly cooled in the presence of mercaptoethanol, reduced nicotinamide adenine dinucleotide, and malate. No renaturation occurred when these compounds were added after slow cooling, or when the renaturation mixture was rapidly cooled. Mercaptoethylamine, cysteine, glutathione, or mercaptoacetic acid could not replace mercaptoethanol. The kinetics of denaturation and renaturation suggest the presence of several malic isozymes each with different heat labilities, or that these processes are occurring in several distinct steps.

  3. Cloning and expression of phosphoglycerate mutase from the psychrophilic yeast, Glaciozyma antarctica PI12

    NASA Astrophysics Data System (ADS)

    Jaafar, Nardiah Rizwana; Bakar, Farah Diba Abu; Murad, Abdul Munir Abdul; Mahadi, Nor Muhammad

    2015-09-01

    The conversion of 3-phosphoglycerate to 2-phosphoglycerate during glycolysis and gluconeogenesis is catalyzed by phosphoglycerate mutase (PGM). Better understanding of metabolic reactions performed by this enzyme has been studied extensively in prokaryotes and eukaryotes. Here, we report a phosphoglycerate mutase from the psychrophilic yeast, Glaciozyma antarctica. cDNA encoding for PGM from G. antarctica PI12, a psychrophilic yeast isolated from sea ice at Casey Station, Antarctica was amplified. The gene was then cloned into a cloning vector and sequenced, which verified its identity as the gene putatively encoding for PGM. The recombinant protein was expressed in Escherichia coli BL21 (DE3) as inclusion bodies and this was confirmed by SDS-PAGE and Western blot.

  4. Dioszegia antarctica sp. nov. and Dioszegia cryoxerica sp. nov., psychrophilic basidiomycetous yeasts from polar desert soils in Antarctica

    USGS Publications Warehouse

    Rodriguez, Russell J.; Connell, L.; Redman, R.; Barrett, A.; Iszard, M.; Fonseca, A.

    2010-01-01

    During a survey of the culturable soil fungal population in samples collected in Taylor Valley, South Victoria Land, Antarctica, 13 basidiomycetous yeast strains with orange-coloured colonies were isolated. Phylogenetic analyses of internal transcribed spacer (ITS) and partial LSU rRNA gene sequences showed that the strains belong to the Dioszegia clade of the Tremellales (Tremellomycetes, Agaricomycotina), but did not correspond to any of the hitherto recognized species. Two novel species, Dioszegia antarctica sp. nov. (type strain ANT-03-116T =CBS 10920T =PYCC 5970T) and Dioszegia cryoxerica sp. nov. (type strain ANT-03-071T =CBS 10919T =PYCC 5967T), are described to accommodate ten and three of these strains, respectively. Analysis of ITS sequences demonstrated intrastrain sequence heterogeneity in D. cryoxerica. The latter species is also notable for producing true hyphae with clamp connections and haustoria. However, no sexual structures were observed. The two novel species can be considered obligate psychrophiles, since they failed to grow above 20 °C and grew best between 10 and 15 °C.

  5. Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture.

    PubMed

    Xu, Mouzhong; Schnorr, Jon; Keibler, Brandon; Simon, Holly M

    2012-04-01

    We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

  6. Protein enrichment of grain sorghum by submerged culture of the amylolytic yeastsSchwanniomyces occidentalis andLipomyces kononenkoae.

    PubMed

    Horn, C H; du Preez, J C; Kilian, S G

    1992-07-01

    Cultivation of aSchwanniomyces occidentalis derepressed mutant in a 10% (w/v) gelatinized grain sorghum slurry increased the crude protein content of the biomass from an initial value of 12% to 41% (dry) within 20 h, with no detectable residual starch. Co-cultivation ofCandida utilis with theS. occidentalis mutant improved the final crude protein content to 47% within 18 h, whereas a co-culture ofC. utilis with aLipomyces kononenkoae mutant resulted in a cultivation time of 50 h with a significantly lower protein content and a low final α-amylase activity. In a 15% (w/v) grain sorghum slurry aC. utilis/S. occidentalis co-culture increased the protein content to about 44% within 30 h. Yeast cultivation increased the lysine and threonine content of the final biomass considerably.

  7. Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway)--denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures.

    PubMed

    Wartiainen, Ingvild; Hestnes, Anne Grethe; Svenning, Mette M

    2003-10-01

    The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78 degrees N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 degrees C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated. The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon. Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere.

  8. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    NASA Astrophysics Data System (ADS)

    González-Toril, E.; Amils, R.; Delmas, R. J.; Petit, J.-R.; Komárek, J.; Elster, J.

    2009-01-01

    Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  9. Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

    PubMed Central

    2013-01-01

    Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30′ N, 64°40′ W), B (10°40′ N, 64°45′ W) and D (10°43’N, 64°32’W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin. PMID:23981583

  10. Endotoxin structures in the psychrophiles Psychromonas marina and Psychrobacter cryohalolentis contain distinctive acyl features.

    PubMed

    Sweet, Charles R; Alpuche, Giancarlo M; Landis, Corinne A; Sandman, Benjamin C

    2014-07-09

    Lipid A is the essential component of endotoxin (Gram-negative lipopolysaccharide), a potent immunostimulatory compound. As the outer surface of the outer membrane, the details of lipid A structure are crucial not only to bacterial pathogenesis but also to membrane integrity. This work characterizes the structure of lipid A in two psychrophiles, Psychromonas marina and Psychrobacter cryohalolentis, and also two mesophiles to which they are related using MALDI-TOF MS and fatty acid methyl ester (FAME) GC-MS. P. marina lipid A is strikingly similar to that of Escherichia coli in organization and total acyl size, but incorporates an unusual doubly unsaturated tetradecadienoyl acyl residue. P. cryohalolentis also shows structural organization similar to a closely related mesophile, Acinetobacter baumannii, however it has generally shorter acyl constituents and shows many acyl variants differing by single methylene (-CH2-) units, a characteristic it shares with the one previously reported psychrotolerant lipid A structure. This work is the first detailed structural characterization of lipid A from an obligate psychrophile and the second from a psychrotolerant species. It reveals distinctive structural features of psychrophilic lipid A in comparison to that of related mesophiles which suggest constitutive adaptations to maintain outer membrane fluidity in cold environments.

  11. Stable Carbon Isotope Fractionation During 1,2-Dichloropropane-to-Propene Transformation by an Enrichment Culture Containing Dehalogenimonas Strains and a dcpA Gene.

    PubMed

    Martín-González, L; Mortan, S Hatijah; Rosell, M; Parladé, E; Martínez-Alonso, M; Gaju, N; Caminal, G; Adrian, L; Marco-Urrea, E

    2015-07-21

    A stable enrichment culture derived from Besòs river estuary sediments stoichiometrically dechlorinated 1,2-dichloropropane (1,2-DCP) to propene. Sequential transfers in defined anaerobic medium with the inhibitor bromoethanesulfonate produced a sediment-free culture dechlorinating 1,2-DCP in the absence of methanogenesis. Application of previously published genus-specific primers targeting 16S rRNA gene sequences revealed the presence of a Dehalogenimonas strain, and no amplification was obtained with Dehalococcoides-specific primers. The partial sequence of the 16S rRNA amplicon was 100% identical with Dehalogenimonas alkenigignens strain IP3-3. Also, dcpA, a gene described to encode a corrinoid-containing 1,2-DCP reductive dehalogenase was detected. Resistance of the dehalogenating activity to vancomycin, exclusive conversion of vicinally chlorinated alkanes, and tolerance to short-term oxygen exposure is consistent with the hypothesis that a Dehalogenimonas strain is responsible for 1,2-DCP conversion in the culture. Quantitative PCR showed a positive correlation between the number of Dehalogenimonas 16S rRNA genes copies in the culture and consumption of 1,2-DCP. Compound specific isotope analysis revealed that the Dehalogenimonas-catalyzed carbon isotopic fractionation (εC(bulk)) of the 1,2-DCP-to-propene reaction was -15.0 ± 0.7‰ under both methanogenic and nonmethanogenic conditions. This study demonstrates that carbon isotope fractionation is a valuable approach for monitoring in situ 1,2-DCP reductive dechlorination by Dehalogenimonas strains.

  12. Short communication: Viability of culture organisms in honey-enriched acidophilus-bifidus-thermophilus (ABT)-type fermented camel milk.

    PubMed

    Varga, L; Süle, J; Nagy, P

    2014-11-01

    The aim of this research was to monitor the survival during refrigerated storage of Lactobacillus acidophilus LA-5 (A), Bifidobacterium animalis ssp. lactis BB-12 (B), and Streptococcus thermophilus CHCC 742/2130 (T) in cultured dairy foods made from camel and, for comparison, cow milks supplemented with black locust (Robinia pseudoacacia L.) honey and fermented by an acidophilus-bifidus-thermophilus (ABT)-type culture. Two liters of dromedary camel milk and 2 L of cow milk were heated to 90 °C and held for 10 min, then cooled to 40 °C. One half of both types of milk was fortified with black locust honey at the rate of 5.0% (wt/vol), whereas the other half was devoid of honey and served as a control. The camel and cow milks with and without honey were subsequently inoculated with ABT-5 culture and were fermented at 37 °C until a pH value of 4.6 was reached. Thereafter, the probiotic fermented milks were cooled to 15 °C in ice water and were each separated into 18 fractions that were transferred in sterile, tightly capped centrifuge tubes. After 24 h of cooling at 8 °C (d 0), the samples were stored at refrigeration temperature (4 °C). Three tubes of all 4 products (i.e., fermented camel and cow milks with and without honey) were taken at each sampling time (i.e., following 0, 7, 14, 21, 28, and 35 d of storage), and the counts of characteristic microorganisms and those of certain spoilage microbes (yeasts, molds, coliforms, Escherichia coli) were enumerated. The entire experimental program was repeated twice. The results showed that addition of black locust honey at 5% to heat-treated camel and cow milks did not influence the growth and survival of starter streptococci during production and subsequent refrigerated storage of fermented ABT milks. In contrast, honey improved retention of viability of B. animalis ssp. lactis BB-12 in the camel milk-based product during storage at 4 °C up to 5 wk. No spoilage organisms were detected in any of the samples tested

  13. Identification of in vivo HSP90-interacting proteins reveals modularity of HSP90 complexes is dependent on the environment in psychrophilic bacteria

    PubMed Central

    García-Descalzo, Laura; Alcazar, Alberto; Baquero, Fernando

    2010-01-01

    Heat shock protein 90 (HSP90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. In this paper, HSP90 complexes were investigated in γ-proteobacteria from mild (Shewanella oneidensis) and cold environments (Shewanella frigidimarina and Psychrobacter frigidicola), to determine changes in HSP90 interactions with client proteins in response to the adaptation to cold environments. HSP90 participation in cold adaptation was determined using the specific inhibitor 17-allylamino-geldanamycin. Then, HSP90 was immunoprecipitated from bacterial cultures, and the proteins in HSP90 complexes were analyzed by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. According to HSP90-associated protein analysis, only 15 common proteins were found in both species from the same genus, S. oneidensis and S. frigidimarina, whereas a significant higher number of common proteins were found in both psychrophilic species S. frigidimarina and P. frigidicola 21 (p < 0.001). Only two HSP90-interacting proteins, the chaperone proteins DnaK and GroEL, were common to the three species. Interestingly, some proteins related to energy metabolism (isocitrate lyase, succinyl-CoA synthetase, alcohol dehydrogenase, NAD(+) synthase, and malate dehydrogenase) and some translation factors only interacted with HSP90 in psychrophilic bacteria. We can conclude that HSP90 and HSP90-associated proteins might take part in the mechanism of adaptation to cold environments, and interestingly, organisms living in similar environments conserve similar potential HSP90 interactors in opposition to phylogenetically closely related organisms of the same genus but from different environments. PMID:20890740

  14. Biodegradation of 1,2,3- and 1,2,4-Trichlorobenzene in Soil and in Liquid Enrichment Culture

    PubMed Central

    Marinucci, A. C.; Bartha, R.

    1979-01-01

    The biodegradation of radiochemically pure (99%) 1,2,3- and 1,2,4-trichlorobenzene (TCB) in soil was investigated. Experimental difficulties posed by the high volatility and slow biodegradation rate of the TCBs were partially overcome by using a specially designed incubation and trapping apparatus. Evolution of 14CO2 from active versus poisoned soil dosed with 50 μg of the individual TCBs per g gave conclusive proof that both isomers are biodegradable. At 20°C, 1,2,4-TCB was mineralized at an approximate rate of 1 nmol/day per 20 g of soil sample, and 1,2,3-TCB was mineralized at one-half to one-third that rate. Mineral fertilizers or cosubstrates failed to increase TCB mineralization rates in soil. Anaerobic conditions had a negative effect on mineralization, and increased temperatures had a positive effect. With increasing 1,2,4-TCB concentrations, 14CO2 evolution exhibited saturation kinetics with an apparent Km of 55.5 nmol per g of soil. Recovery of total radioactivity was good from soil containing high organic matter concentrations. From low-organic-matter soil, some of the radioactivity was recovered only on combustion, and overall recovery was lower. In soil-inoculated liquid culture, the cosubstrates glucose and benzene caused a slight stimulation of 1,2,4-TCB mineralization. Cochromatography of known standards with the extracts of soil pretreated with [14C]TCBs indicated that 3,4,5-trichlorophenol, 2,6-dichlorophenol and, to a lesser degree, 2,3-dichlorophenol were present in soils incubated with 1,2,3-TCB. 2,4-, 2,5-, and 3,4-dichlorophenol were present in soils incubated with 1,2,4-TCB. PMID:120698

  15. The social cost of coastal erosion. Using cultural theory to enrich the interpretation of stated preference data.

    NASA Astrophysics Data System (ADS)

    Kontogianni, A.; Tourkolias, C.; Vousdoukas, M.; Skourtos, M.

    2012-04-01

    Natural coastal processes are to a great extent modified by proximity to man-made structures. Engineered interventions, port facilities, housing and industrial infrastructure, all can increase the coastline fluctuations significantly relative to those along a long unobstructed coastline. As a consequence, coastlines are increasingly exposed to coastal erosion, a phenomenon defined as the encroachment of land by the sea after averaging over a period, which is sufficiently long to eliminate the impacts of weather, storm events and local sediment dynamics. In order to provide cost effective management of coastal erosion it is crucial to estimate both the benefits and costs associated with various management alternatives. The initiatives on Integrated Coastal Zone Manegment in Europe, but also the upcoming Marine Strategy Framwork Directive would benefit greatly from a proliferation of socioeconomic information to assist decision makers who must weigh the impacts of various types of coastal improvement and the cost of beach protection/restoration. In that spirit, the objective of the present research is to report the results of a survey undertaken in two resort beaches on the island of Lesvos (Greece), designed to estimate public preferences for avoiding coastal erosion. A mixed methodological approach is employed by combining an open-ended contingent valuation survey with cultural theory of risk perception. The empirical models to analyze individual choices of erosion control programs and the associated welfare measures are presented, followed by the discussion of model specification and estimation issues, and the results of the data analysis. Some concluding remarks are then presented. By choosing this approach we aim at improving our understanding of preference structure for avoiding public risk, accepted level of risk and perceptions thereof. The framework can also be used for assessing the social cost of extreme weather events such as storm surges in the coastal

  16. Structural and chemical modification of Fe-rich smectite associated with microbial Fe-respiration by psychrophilic bacteria in King George Island, West Antarctica

    NASA Astrophysics Data System (ADS)

    Jung, J.; Kim, J. Y.; Lim, H. S.; Lee, Y. K.; Kim, O. S.; Park, K.; Lee, J.; Yoon, H.; Kim, J. W.

    2015-12-01

    Biotic/abiotic redox reaction is a ubiquitous process in a mineral alteration and an elemental cycling in the sediments/ocean. The role of psychrophiles in clay mineral alteration was tested in the soil for the seven sites from the coast to the inland at Barton Peninsula. Batch experiments of microbe-mineral interaction under the various temperatures (4 ℃, 15 ℃) that mimics the Antarctic condition were performed to understand the mechanism of biogeochemical alteration of clay minerals. After 12 months incubation of the bulk surface soil samples in the M1 minimal medium, the extent of Fe reduction was reached up to 49 and 42 % at 4 ℃ and 15 ℃. The increase in CEC corresponds to the extent of Fe reduction. Moreover, precipitations of secondary phase mineral such as vivianite were observed only in 12 months enrichment samples at 4 ℃ and 15 ℃. Sulfate reducing bacteria and Fe-reducing bacteria capable of reducing Fe were identified by 16S rRNA pyrosequencing. The Fe reduction coupled to oxidation of organic matter might be enhanced by cooperation of a consortium of Sulfate reducing bacteria and Fe-reducing bacteria. Moreover, Nitrate reducing bacteria which have an ability to oxidize ferrous iron anaerobically with nitrate reduction were identified at 15 ℃. The lower values observed in the extent of Fe reduction at 15 ℃ may be associated with Fe-oxidation induced by nitrate reduction.In order to verify the mechanism of microbial Fe reduction in clay minerals at low temperatures (4 and 15 ℃), Fe-rich Nontronite (NAu-1) and Psychrophilic bacteria were incubated for 4 months in anaerobic condition. Total structural Fe in NAu-1 is 16.4 % and 99.6 % of the total Fe is ferric. The extent of Fe reduction in nontronite was reached up to 11.5 % and 11 % at 4 ℃ and 15 ℃, respectively. The structural modification of biologically Fe-reduced nontronite was observed in the (001) peak shift to the lower 2 theta indicating the layer collapse associated with K

  17. Combined extrinsic and intrinsic manipulations exert complementary neuronal enrichment in embryonic rat neural precursor cultures: an in vitro and in vivo analysis.

    PubMed

    Furmanski, Orion; Gajavelli, Shyam; Lee, Jeung Woon; Collado, Maria E; Jergova, Stanislava; Sagen, Jacqueline

    2009-07-01

    Numerous central nervous system (CNS) disorders share a common pathology in dysregulation of gamma-aminobutyric acid (GABA) inhibitory signaling. Transplantation of GABA-releasing cells at the site of disinhibition holds promise for alleviating disease symptoms with fewer side effects than traditional drug therapies. We manipulated fibroblast growth factor (FGF)-2 deprivation and mammalian achaete-scute homolog (MASH)1 transcription factor levels in an attempt to amplify the default GABAergic neuronal fate in cultured rat embryonic neural precursor cells (NPCs) for use in transplantation studies. Naïve and MASH1 lentivirus-transduced NPCs were maintained in FGF-2 or deprived of FGF-2 for varying lengths of time. Immunostaining and quantitative analysis showed that GABA- and beta-III-tubulin-immunoreactive cells generally decreased through successive passages, suggesting a loss of neurogenic potential in rat neurospheres expanded in vitro. However, FGF-2 deprivation resulted in a small, but significantly increased population of GABAergic cells derived from passaged neurospheres. In contrast to naïve and GFP lentivirus-transduced clones, MASH1 transduction resulted in increased bromodeoxyuridine (BrdU) incorporation and clonal colony size. Western blotting showed that MASH1 overexpression and FGF-2 deprivation additively increased beta-III-tubulin and decreased cyclic nucleotide phosphodiesterase (CNPase) expression, whereas FGF-2 deprivation alone attenuated glial fibrillary acidic protein (GFAP) expression. These results suggest that low FGF-2 signaling and MASH1 activity can operate in concert to enrich NPC cultures for a GABA neuronal phenotype. When transplanted into the adult rat spinal cord, this combination also yielded GABAergic neurons. These findings indicate that, even for successful utilization of the default GABAergic neuronal precursor fate, a combination of both extrinsic and intrinsic manipulations will likely be necessary to realize the full

  18. [Distribution of psychrophilic microorganisms in terrestrial biotopes of the Antarctic Region].

    PubMed

    Romanovskaia, V A; Tashirev, A B; Shilin, S O; Gladka, G V

    2012-01-01

    It is shown that the total number of chemoorganotrophic aerobic microorganisms in the Antarctic Region revealed at 1 degree C and 5 degrees C made from 10(4) up to 10(6) cells/g of plant-soil sample of biotopes: grass Deschampcia antarctica, grass Colobanthus, green mosses, crustose black lichens and a biofilm of accretion on vertical rocks. From 10(6) up to 10(8) cells/g of samples were revealed in the same Antarctic samples at 30 degrees C. At 42 degrees C thermotolerant bacteria were either absent, or their quantity was less than 10(4) cells/g of samples. Thus the fraction (part) of the Antarctic microorganisms, which grow at different temperatures, varied: at 1-5 degrees C their part made from 5 to 15%, and at 30 degrees C--from 10 to 45%. At 15-20 degrees C the growth of both psychrophilic/psychrotolerant, and mesophilic microorganisms was observed. When comparing the results of plating of samples from different climatic zones (the Antarctic Region and Ukraine), it is shown that in the Antarctic biotopes in comparison with biotopes of the zone with temperate climate: (1) the total number of microorganisms is lower, (2) quantity of psychrophilic/psychrotolerant bacteria is higher, (3) quantity of mesophilic microorganisms is less, (4) as a result the part psychrophilic/psychrotolerant microorganisms in the total number of microorganisms is much higher. It is evident, that low temperatures, and also daily cycles of freezing and thawing are factors which limit microbial colonization ofAntarctic biotopes.

  19. DNA stable-isotope probing of oil sands tailings pond enrichment cultures reveals different key players for toluene degradation under methanogenic and sulfidogenic conditions.

    PubMed

    Laban, Nidal Abu; Dao, Anh; Foght, Julia

    2015-05-01

    Oil sands tailings ponds are anaerobic repositories of fluid wastes produced by extraction of bitumen from oil sands ores. Diverse indigenous microbiota biodegrade hydrocarbons (including toluene) in situ, producing methane, carbon dioxide and/or hydrogen sulfide, depending on electron acceptor availability. Stable-isotope probing of cultures enriched from tailings associated specific taxa and functional genes to (13)C6- and (12)C7-toluene degradation under methanogenic and sulfate-reducing conditions. Total DNA was subjected to isopycnic ultracentrifugation followed by gradient fraction analysis using terminal restriction fragment length polymorphism (T-RFLP) and construction of 16S rRNA, benzylsuccinate synthase (bssA) and dissimilatory sulfite reductase (dsrB) gene clone libraries. T-RFLP analysis plus sequencing and in silico digestion of cloned taxonomic and functional genes revealed that Clostridiales, particularly Desulfosporosinus (136 bp T-RF) contained bssA genes and were key toluene degraders during methanogenesis dominated by Methanosaeta. Deltaproteobacterial Desulfobulbaceae (157 bp T-RF) became dominant under sulfidogenic conditions, likely because the Desulfosporosinus T-RF 136 apparently lacks dsrB and therefore, unlike its close relatives, is presumed incapable of dissimilatory sulfate reduction. We infer incomplete oxidation of toluene by Desulfosporosinus in syntrophic association with Methanosaeta under methanogenic conditions, and complete toluene oxidation by Desulfobulbaceae during sulfate reduction.

  20. Isolation and characterization of a mesophilic heavy-metals-tolerant sulfate-reducing bacterium Desulfomicrobium sp. from an enrichment culture using phosphogypsum as a sulfate source.

    PubMed

    Azabou, Samia; Mechichi, Tahar; Patel, Bharat K C; Sayadi, Sami

    2007-02-09

    A sulfate-reducing bacterium, was isolated from a 6 month trained enrichment culture in an anaerobic media containing phosphogypsum as a sulfate source, and, designated strain SA2. Cells of strain SA2 were rod-shaped, did not form spores and stained Gram-negative. Phylogenetic analysis of the 16S rRNA gene sequence of the isolate revealed that it was related to members of the genus Desulfomicrobium (average sequence similarity of 98%) with Desulfomicrobium baculatum being the most closely related (sequence similarity of 99%). Strain SA2 used thiosulfate, sulfate, sulfite and elemental sulfur as electron acceptors and produced sulfide. Strain SA2 reduced sulfate contained in 1-20g/L phosphogypsum to sulfide with reduction of sulfate contained in 2g/L phosphogypsum being the optimum concentration. Strain SA2 grew with metalloid, halogenated and non-metal ions present in phosphogypsum and with added high concentrations of heavy metals (125ppm Zn and 100ppm Ni, W, Li and Al). The relative order for the inhibitory metal concentrations, based on the IC(50) values, was Cu, Te>Cd>Fe, Co, Mn>F, Se>Ni, Al, Li>Zn.

  1. DNRA and Denitrification Coexist over a Broad Range of Acetate/N-NO3− Ratios, in a Chemostat Enrichment Culture

    PubMed Central

    van den Berg, Eveline M.; Boleij, Marissa; Kuenen, J. Gijs; Kleerebezem, Robbert; van Loosdrecht, Mark C. M.

    2016-01-01

    Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) compete for nitrate in natural and engineered environments. A known important factor in this microbial competition is the ratio of available electron donor and elector acceptor, here expressed as Ac/N ratio (acetate/nitrate-nitrogen). We studied the impact of the Ac/N ratio on the nitrate reduction pathways in chemostat enrichment cultures, grown on acetate mineral medium. Stepwise, conditions were changed from nitrate limitation to nitrate excess in the system by applying a variable Ac/N ratio in the feed. We observed a clear correlation between Ac/N ratio and DNRA activity and the DNRA population in our reactor. The DNRA bacteria dominated under nitrate limiting conditions in the reactor and were outcompeted by denitrifiers under limitation of acetate. Interestingly, in a broad range of Ac/N ratios a dual limitation of acetate and nitrate occurred with co-occurrence of DNRA bacteria and denitrifiers. To explain these observations, the system was described using a kinetic model. The model illustrates that the Ac/N effect and concomitant broad dual limitation range related to the difference in stoichiometry between both processes, as well as the differences in electron donor and acceptor affinities. Population analysis showed that the presumed DRNA-performing bacteria were the same under nitrate limitation and under dual limiting conditions, whereas the presumed denitrifying population changed under single and dual limitation conditions. PMID:27933040

  2. Vibrio psychroerythrus sp. n.: Classification of the Psychrophilic Marine Bacterium, NRC 1004

    PubMed Central

    D'aoust, J. Y.; Kushner, D. J.

    1972-01-01

    A red-pigmented organism, formerly known as marine psychrophile NRC 1004, has been classified as Vibrio psychroerythrus sp. n. Classification was mainly based on morphology, the ability of the organism to oxidize and ferment glucose, its sensitivity to vibriostat 0/129, and its deoxyribonucleic acid base composition of 40.0 moles% guanine plus cytosine, determined by thermal denaturation. The organism gave positive reactions for catalase, oxidase, and starch hydrolysis and produced acid from maltose and dextrin but not from arabinose. It was indole- and citrate-negative and reduced nitrate to nitrite without producing gas. PMID:5053463

  3. Enrichment of the Cancer Stem Phenotype in Sphere Cultures of Prostate Cancer Cell Lines Occurs through Activation of Developmental Pathways Mediated by the Transcriptional Regulator ΔNp63α

    PubMed Central

    Portillo-Lara, Roberto; Alvarez, Mario Moisés

    2015-01-01

    Background Cancer stem cells (CSC) drive prostate cancer tumor survival and metastasis. Nevertheless, the development of specific therapies against CSCs is hindered by the scarcity of these cells in prostate tissues. Suspension culture systems have been reported to enrich CSCs in primary cultures and cell lines. However, the molecular mechanisms underlying this phenomenon have not been fully explored. Methodology/Principal Findings We describe a prostasphere assay for the enrichment of CD133+ CSCs in four commercial PCa cell lines: 22Rv1, DU145, LNCaP, and PC3. Overexpression of CD133, as determined by flow cytometric analysis, correlated with an increased clonogenic, chemoresistant, and invasive potential in vitro. This phenotype is concordant to that of CSCs in vivo. Gene expression profiling was then carried out using the Cancer Reference panel and the nCounter system from NanoString Technologies. This analysis revealed several upregulated transcripts that can be further explored as potential diagnostic markers or therapeutic targets. Furthermore, functional annotation analysis suggests that ΔNp63α modulates the activation of developmental pathways responsible for the increased stem identity of cells growing in suspension cultures. Conclusions/Significance We conclude that profiling the genetic mechanisms involved in CSC enrichment will help us to better understand the molecular pathways that underlie CSC pathophysiology. This platform can be readily adapted to enrich and assay actual patient samples, in order to design patient-specific therapies that are aimed particularly against CSCs. PMID:26110651

  4. UV Radiation and Visible Light Induce hsp70 Gene Expression in the Antarctic Psychrophilic Ciliate Euplotes focardii.

    PubMed

    Fulgentini, Lorenzo; Passini, Valerio; Colombetti, Giuliano; Miceli, Cristina; La Terza, Antonietta; Marangoni, Roberto

    2015-08-01

    The psychrophilic ciliate Euplotes focardii inhabits the shallow marine coastal sediments of Antarctica, where, over millions of years of evolution, it has reached a strict molecular adaptation to such a constant-temperature environment (about -2 °C). This long evolution at sub-zero temperatures has made E. focardii unable to respond to heat stress with the activation of its heat shock protein (hsp) 70 genes. These genes can, however, be expressed in response to other stresses, like the oxidative one, thus indicating that the molecular adaptation has exclusively altered the heat stress signaling pathways, while it has preserved hsp70 gene activation in response to other environmental stressors. Since radiative stress has proved to be affine to oxidative stress in several organisms, we investigated the capability of UV radiation to induce hsp70 transcription. E. focardii cell cultures were exposed to several different irradiation regimes, ranging from visible only to a mixture of visible, UV-A and UV-B. The irradiation values of each spectral band have been set to be comparable with those recorded in a typical Antarctic spring. Using Northern blot analysis, we measured the expression level of hsp70 immediately after irradiation (0-h-labeled samples), 1 h, and 2 h from the end of the irradiation. Surprisingly, our results showed that besides UV radiation, the visible light was also able to induce hsp70 expression in E. focardii. Moreover, spectrophotometric measurements have revealed no detectable endogenous pigments in E. focardii, making it difficult to propose a possible explanation for the visible light induction of its hsp70 genes. Further research is needed to conclusively clarify this point.

  5. Microbial diversity in methanogenic hydrocarbon-degrading enrichment cultures isolated from a water-flooded oil reservoir (Dagang oil field, China)

    NASA Astrophysics Data System (ADS)

    Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans H.; Krüger, Martin

    2015-04-01

    Microbial transformation of oil to methane is one of the main degradation processes taking place in oil reservoirs, and it has important consequences as it negatively affects the quality and economic value of the oil. Nevertheless, methane could constitute a recovery method of carbon from exhausted reservoirs. Previous studies combining geochemical and isotopic analysis with molecular methods showed evidence for in situ methanogenic oil degradation in the Dagang oil field, China (Jiménez et al., 2012). However, the main key microbial players and the underlying mechanisms are still relatively unknown. In order to better characterize these processes and identify the main microorganisms involved, laboratory biodegradation experiments under methanogenic conditions were performed. Microcosms were inoculated with production and injection waters from the reservoir, and oil or 13C-labelled single hydrocarbons (e.g. n-hexadecane or 2-methylnaphthalene) were added as sole substrates. Indigenous microbiota were able to extensively degrade oil within months, depleting most of the n-alkanes in 200 days, and producing methane at a rate of 76 ± 6 µmol day-1 g-1 oil added. They could also produce heavy methane from 13C-labeled 2-methylnaphthalene, suggesting that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. Microbial communities from oil and 2-methyl-naphthalene enrichment cultures were slightly different. Although, in both cases Deltaproteobacteria, mainly belonging to Syntrophobacterales (e.g. Syntrophobacter, Smithella or Syntrophus) and Clostridia, mostly Clostridiales, were among the most represented taxa, Gammaproteobacteria could be only identified in oil-degrading cultures. The proportion of Chloroflexi, exclusively belonging to Anaerolineales (e.g. Leptolinea, Bellilinea) was considerably higher in 2-methyl-naphthalene degrading cultures. Archaeal communities consisted almost exclusively of representatives of

  6. Feeding glycerol-enriched yeast culture improves performance, energy status, and heat shock protein gene expression of lactating Holstein cows under heat stress.

    PubMed

    Liu, J; Ye, G; Zhou, Y; Liu, Y; Zhao, L; Liu, Y; Chen, X; Huang, D; Liao, S F; Huang, K

    2014-06-01

    This study was conducted to evaluate the effects of supplemental common yeast culture (CY) and glycerol-enriched yeast culture (GY) on performance, plasma metabolites, antioxidant status, and heat shock protein 70 (HSP70) mRNA expression in lactating Holstein cows under heat stress. During summer months, 30 healthy multiparous lactating cows (parity 3.25 ± 0.48; 60 ± 13 d in milk [DIM]; 648 ± 57 kg BW; an average milk yield of 33.8 ± 1.6 kg/d) were blocked by parity, previous milk yield, and DIM and randomly allocated to 3 dietary treatments: no supplemental yeast culture (Control), 1 L/d of CY (33.1 g yeast) per cow, and 2 L/d of GY (153.2 g glycerol and 31.6 g yeast) per cow. During the 60-d experiment, values of air temperature and relative humidity inside the barn were recorded hourly every 3 d to calculate temperature-humidity index (THI). Weekly rectal temperatures (RT) and respiration rates and daily DMI and milk yield were recorded for all cows. Milk and blood samples were taken twice monthly, and BW and BCS were obtained on d 0 and 60. In this experiment, THI values indicated cows experienced a moderate heat stress. Cows supplemented with CY and GY had greater yields of milk, energy-corrected milk and milk fat, and milk fat percent but lower HSP70 mRNA expression in peripheral blood lymphocytes than Control cows (P < 0.05). Supplementing CY and GY tended (P < 0.15) to decrease RT at 1400 h, increase milk protein yield and erythrocyte glutathione, and reduce plasma urea nitrogen compared with Control. Lower plasma NEFA concentration and HSP70 mRNA expression in peripheral blood lymphocytes (P < 0.05) and tendencies towards greater plasma glucose concentration (P = 0.11) but less BW loss (P = 0.14) were observed in GY relative to CY cows. In conclusion, either CY or GY supplementation partially mitigated the negative effects of heat stress on performance and HSP70 mRNA expression of lactating cows, and GY supplementation provided additional improvements

  7. Structural thermal adaptation of β-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii.

    PubMed

    Chiappori, Federica; Pucciarelli, Sandra; Merelli, Ivan; Ballarini, Patrizia; Miceli, Cristina; Milanesi, Luciano

    2012-04-01

    Tubulin dimers of psychrophilic eukaryotes can polymerize into microtubules at 4°C, a temperature at which microtubules from mesophiles disassemble. This unique capability requires changes in the primary structure and/or in post-translational modifications of the tubulin subunits. To contribute to the understanding of mechanisms responsible for microtubule cold stability, here we present a computational structural analysis based on molecular dynamics (MD) and experimental data of three β-tubulin isotypes, named EFBT2, EFBT3, and EFBT4, from the Antarctic protozoon Euplotes focardii that optimal temperature for growth and reproduction is 4°C. In comparison to the β-tubulin from E. crassus, a mesophilic Euplotes species, EFBT2, EFBT3, and EFBT4 possess unique amino acid substitutions that confer different flexible properties of the polypeptide, as well as an increased hydrophobicity of the regions involved in microtubule interdimeric contacts that may overcome the microtubule destabilizing effect of cold temperatures. The structural analysis based on MD indicated that all isotypes display different flexibility properties in the regions involved in the formation of longitudinal and lateral contacts during microtubule polymerization. We also investigated the role of E. focardii β-tubulin isotypes during the process of cilia formation. The unique characteristics of the primary and tertiary structures of psychrophilic β-tubulin isotypes seem responsible for the formation of microtubules with distinct dynamic and functional properties.

  8. Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica.

    PubMed

    de Menezes, Graciéle C A; Godinho, Valéria M; Porto, Bárbara A; Gonçalves, Vívian N; Rosa, Luiz H

    2017-03-01

    In the present study, we have identified and characterised a new snow resident ascomycete blue stain fungus from Antarctica named Antarctomyces pellizariae sp. nov. Menezes, Godinho, Porto, Gonçalves and Rosa, using polyphasic taxonomy techniques. This fungal species was recovered from the seasonal snow of the Antarctic Peninsula. Antarctomyces pellizariae displayed different macro- and micromorphology when compared with A. psychrotrophicus Stchigel and Guarro, the only other Antarctomyces species reported until date. Antarctomyces pellizariae showed psychrophilic behavior and very low growth rate at 22-25 °C, quite different from A. psychrotrophicus that has a higher growth rate at mesophilic temperatures. In addition, micromorphological characteristics and the analysis of the nuclear rDNA internal transcribed spacer, β-tubulin, and RNA polymerase II regions revealed that A. pellizariae is a new species that is related to A. psychrotrophicus and Thelebolus species. Since the Antarctic Peninsula is reported to be one of the main regions of the earth experiencing the effects of global change in climate, species, such as A. pellizariae, might provide information about these effects on the endemic Antarctic biota. In addition, A. pellizariae displayed psychrophilic behavior and might be a source of interesting anti-freeze compounds that might prove useful in biotechnological processes.

  9. Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.

    PubMed

    Lonhienne, T; Baise, E; Feller, G; Bouriotis, V; Gerday, C

    2001-02-09

    Isothermal titration calorimetry has been applied to the determination of the kinetic parameters of chitinases (EC 3.2.1.14) by monitoring the heat released during the hydrolysis of chitin glycosidic bonds. Experiments were carried out using two different macromolecular substrates: a soluble polymer of N-acetylglucosamine and the insoluble chitin from crab shells. Different experimental temperatures were used in order to compare the thermodependence of the activity of two chitinases from the psychrophile Arthrobacter sp. TAD20 and of chitinase A from the mesophile Serratia marcescens. The method allowed to determine unequivocally the catalytic rate constant k(cat), the activation energy (E(a)) and the thermodynamic activation parameters (DeltaG(#), DeltaH(#), DeltaS(#)) of the chitinolytic reaction on the soluble substrate. The catalytic activity has also been determined on insoluble chitin, which displays an effect of substrate saturation by chitinases. On both substrates, the thermodependence of the activity of the psychrophilic chitinases was lower than that observed with the mesophilic counterpart.

  10. Purification and characterization of cold-adapted beta-agarase from an Antarctic psychrophilic strain

    PubMed Central

    Li, Jiang; Hu, Qiushi; Li, Yuquan; Xu, Yuan

    2015-01-01

    An extracellular β-agarase was purified from Pseudoalteromonas sp. NJ21, a Psychrophilic agar-degrading bacterium isolated from Antarctic Prydz Bay sediments. The purified agarase (Aga21) revealed a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, with an apparent molecular weight of 80 kDa. The optimum pH and temperature of the agarase were 8.0 and 30 °C, respectively. However, it maintained as much as 85% of the maximum activities at 10 °C. Significant activation of the agarase was observed in the presence of Mg2+, Mn2+, K+; Ca2+, Na+, Ba2+, Zn2+, Cu2+, Co2+, Fe2+, Sr2+ and EDTA inhibited the enzyme activity. The enzymatic hydrolyzed product of agar was characterized as neoagarobiose. Furthermore, this work is the first evidence of cold-adapted agarase in Antarctic psychrophilic bacteria and these results indicate the potential for the Antarctic agarase as a catalyst in medicine, food and cosmetic industries. PMID:26413048

  11. INFLUENCE OF MODERATE TEMPERATURE ON GROWTH AND MALIC DEHYDROGENASE ACTIVITY OF A MARINE PSYCHROPHILE.

    PubMed

    MORITA, R Y; BURTON, S D

    1963-11-01

    Morita, Richard Y. (Oregon State University, Corvallis), and Sheril D. Burton. Influence of moderate temperature on growth and malic dehydrogenase activity of a marine psychrophile. J. Bacteriol. 86:1025-1029. 1963.-The maximal and optimal growth temperatures for a marine psychrophilic vibrio (PS 207) were determined to be 30 and 24.5 C, respectively. Malic dehydrogenase was found to be functioning in whole cells at about 1/20 of its observed maximum. Incubation of the cells, prior to or during the assay, at temperatures above the maximal growth temperature permitted the malic dehydrogenase to operate nearer its maximum, but this also inactivated the intracellular enzyme. The heating of whole cells gave an apparent effect of increasing malic dehydrogenase activity. Lysis of the cells permitted the enzyme to function at its full potential but rendered the enzyme more sensitive to heat denaturation. Lysis of the cells also caused the enzyme to lose approximately one-half of its malic dehydrogenase activity with each 10 C drop in temperature, whereas whole cells only lose approximately 1/5 of their enzyme activity at low temperatures with each 10 C drop.

  12. Temperature-Sensitive Salmonella enterica Serovar Enteritidis PT13a Expressing Essential Proteins of Psychrophilic Bacteria

    PubMed Central

    Duplantis, Barry N.; Puckett, Stephanie M.; Rosey, Everett L.; Ameiss, Keith A.; Hartman, Angela D.; Pearce, Stephanie C.

    2015-01-01

    Synthetic genes based on deduced amino acid sequences of the NAD-dependent DNA ligase (ligA) and CTP synthetase (pyrG) of psychrophilic bacteria were substituted for their native homologues in the genome of Salmonella enterica serovar Enteritidis phage type 13a (PT13a). The resulting strains were rendered temperature sensitive (TS) and did not revert to temperature resistance at a detectable level. At permissive temperatures, TS strains grew like the parental strain in broth medium and in macrophage-like cells, but their growth was slowed or stopped when they were shifted to a restrictive temperature. When injected into BALB/c mice at the base of the tail, representing a cool site of the body, the strains with restrictive temperatures of 37, 38.5, and 39°C persisted for less than 1 day, 4 to 7 days, and 20 to 28 days, respectively. The wild-type strain persisted at the site of inoculation for at least 28 days. The wild-type strain, but not the TS strains, was also found in spleen-plus-liver homogenates within 1 day of inoculation of the tail and was detectable in these organs for at least 28 days. Intramuscular vaccination of White Leghorn chickens with the PT13a strain carrying the psychrophilic pyrG gene provided some protection against colonization of the reproductive tract and induced an anti-S. enterica antibody response. PMID:26187965

  13. Project ENRICH.

    ERIC Educational Resources Information Center

    Gwaley, Elizabeth; And Others

    Project ENRICH was conceived in Beaver County, Pennsylvania, to: (1) identify preschool children with learning disabilities, and (2) to develop a program geared to the remediation of the learning disabilities within a school year, while allowing the child to be enrolled in a regular class situation for the following school year. Through…

  14. Draft genome of Cryobacterium sp. MLB-32, an obligate psychrophile from glacier cryoconite holes of high Arctic.

    PubMed

    Singh, Purnima; Kapse, Neelam; Arora, Preeti; Singh, Shiv Mohan; Dhakephalkar, Prashant K

    2015-06-01

    Obligate psychrophilic, Cryobacterium sp. MLB-32, was isolated from cryoconite holes of high Arctic glaciers. Here, we report the first draft genome sequence of the putative novel species of the genus Cryobacterium, providing opportunities for biotechnological and agricultural exploitation of its genome features.

  15. [NO3-/NO2- inhibits sulfate-reducing activity of the enrichment culture of sulfate-reducing prokaryotes from an off-shore oil reservoir at Bohai Bay, China].

    PubMed

    Liu, Hong-Yu; Shi, Rong-Jiu; Zhang, Ying; Shi, Zhen-Guo; Zhang, Ying-Yue; Yu, Liang; Zhang, Xiao-Bo; Tan, Tao

    2014-08-01

    Long-term injection of sulfate-rich water into oil reservoirs stimulates the proliferation of sulfate-reducing prokaryotes (SRP) therein and results in production of a great amount of H2S, leading to souring in oil reservoirs and related environmental problems. In this study, we first, using modified API RP 38 medium, enriched SRP present in production water from a producing well at Bohai Bay, China, and then examined the inhibitory effects of nitrate or nitrite on sulfate reduction activity of the SRP. Results showed that the enriched SRP culture exhibited a high sulfate reduction activity as indicated by a sulfate-reducing rate of 10.4 mmol SO4(2-) x d(-1) x g(-1) dry cell. In presence of 0.4, 0.8, 1.8, and 4.2 mmol x L(-1) nitrate, sulfate reduction was inhibited for 5, 9, 20, and over 35 days, respectively. With the addition of 0.6, 0.9, 1.4, 2.6 and 4.6 mmol x L(-1) of nitrite, the inhibitory period lasted 3, 12, 22, and over 39 days, respectively. The SRP enrichment culture could dissimilatorily reduce nitrate to ammonium. When sulfate, nitrate and nitrite coexisted, nitrate or nitrite was preferentially used over sulfate as electron acceptor by the enriched SRP. This competitive use of electron acceptor and the strong inhibitory effect of nitrite possibly accounted for the suppression of nitrate and nitrite on the sulfate-reducing activity of the enriched SRP cultures from offshore oil reservoir at Bohai Bay.

  16. Feeding glycerol-enriched yeast culture improves lactation performance, energy status, and hepatic gluconeogenic enzyme expression of dairy cows during the transition period.

    PubMed

    Ye, G; Liu, J; Liu, Y; Chen, X; Liao, S F; Huang, D; Huang, K

    2016-06-01

    This study aimed to evaluate the effects of feeding glycerol-enriched yeast culture (GY) on feed intake, lactation performance, blood metabolites, and expression of some key hepatic gluconeogenic enzymes in dairy cows during the transition period. Forty-four multiparous transition Holstein cows were blocked by parity, previous 305-d mature equivalent milk yield, and expected calving date and randomly allocated to 4 dietary treatments: Control (no additive), 2 L/d of GY (75.8 g/L glycerol and 15.3 g/L yeast), 150 g/d of glycerol (G; 0.998 g/g glycerol), and 1 L/d of yeast culture (Y; 31.1 g/L yeast). All additives were top-dressed and hand mixed into the upper one-third of the total mixed ration in the morning from -14 to +28 d relative to calving. Results indicated that the DMI, NE intake, change of BCS, and milk yields were not affected by the treatments ( > 0.05). Supplementation of GY or Y increased milk fat percentages, milk protein percentages, and milk protein yields relative to the Control or G group ( < 0.05). Cows fed GY or G had higher glucose levels and lower β-hydroxybutyric acid (BHBA) and NEFA levels in plasma than cows fed the Control ( < 0.05) and had lower NEFA levels than cows fed Y ( < 0.05). On 14 d postpartum, cows fed GY or G had higher enzyme activities, mRNA, and protein expression of cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C; < 0.05); higher enzyme activities ( < 0.05) and a tendency toward higher mRNA expression ( < 0.10) of glycerol kinase (GK); and a tendency toward higher enzyme activities of pyruvate carboxylase (PC) in the liver ( < 0.10) when compared with cows fed Control or Y. The enzyme activities, mRNA, and protein expression of PEPCK-C, PC, and GK did not differ between cows fed GY and G ( > 0.10). In conclusion, dietary GY or Y supplementation increased the milk fat and protein content of the cows in early lactation and GY or G supplementation improved the energy status as indicated by greater plasma glucose and

  17. The effects of co-contaminants and native wetland sediments on the activity and dominant transformation mechanisms of a 1,1,2,2-tetrachloroethane (TeCA)-degrading enrichment culture

    USGS Publications Warehouse

    Lorah, Michelle M.; Schiffmacher, Emily N.; Becker, Jennifer G.; Voytek, Mary A.

    2016-01-01

    Bioremediation strategies, including bioaugmentation with chlorinated ethene-degrading enrichment cultures, have been successfully applied in the cleanup of subsurface environments contaminated with tetrachloroethene (PCE) and/or trichloroethene (TCE). However, these compounds are frequently found in the environment as components of mixtures that may also contain chlorinated ethanes and methanes. Under these conditions, the implementation of bioremediation may be complicated by inhibition effects, particularly when multiple dehalorespirers are present. We investigated the ability of the 1,1,2,2-tetrachloroethane (TeCA)-dechlorinating culture WBC-2 to biotransform TeCA alone, or a mixture of TeCA plus PCE and carbon tetrachloride (CT), in microcosms. The microcosms contained electron donors provided to biostimulate the added culture and sediment collected from a wetland where numerous “hotspots” of contamination with chlorinated solvent mixtures exist. The dominant TeCA biodegradation mechanism mediated by the WBC-2 culture in the microcosms was different in the presence of these wetland sediments than in the sediment-free enrichment culture or in previous WBC-2 bioaugmented microcosms and column tests conducted with wetland sediment collected at nearby sites. The co-contaminants and their daughter products also inhibited TeCA biodegradation by WBC-2. These results highlight the need to conduct biodegradability assays at new sites, particularly when multiple contaminants and dehalorespiring populations are present.

  18. A study of psychrophilic organisms isolated from the manufacture and assembly areas of spacecraft to be used in the Viking mission

    NASA Technical Reports Server (NTRS)

    Foster, T. L.; Winans, L., Jr.

    1973-01-01

    The sampling of soils from the manufacture and assembly areas of the Viking spacecraft is reported and the methodology employed in the analysis of these samples for psychrophilic microorganisms, and temperature studies on these organisms is outlined. Results showing the major types of organisms and the percentage of obligate psychrophiles in each sample are given and discussed. Emphasis in all areas is toward application of these results to the objectives of the planetary quarantine program.

  19. In silico analysis of the thermodynamic stability changes of psychrophilic and mesophilic alpha-amylases upon exhaustive single-site mutations.

    PubMed

    Gilis, Dimitri

    2006-01-01

    Identifying sequence modifications that distinguish psychrophilic from mesophilic proteins is important for designing enzymes with different thermodynamic stabilities and to understand the underlying mechanisms. The PoPMuSiC algorithm is used to introduce, in silico, all the single-site mutations in four mesophilic and one psychrophilic chloride-dependent alpha-amylases and to evaluate the changes in thermodynamic stability. The analysis of the distribution of the sequence positions that could be stabilized upon mutation shows a clear difference between the three domains of psychrophilic and mesophilic alpha-amylases. Most of the mutations stabilizing the psychrophilic enzyme are found in domains B and C, contrary to the mesophilic proteins where they are preferentially situated in the catalytic domain A. Moreover, the calculations show that the environment of some residues responsible for the activity of the psychrophilic protein has evolved to reinforce favorable interactions with these residues. In the second part, these results are exploited to propose rationally designed mutations that are predicted to confer to the psychrophilic enzyme mesophilic-like thermodynamic properties. Interestingly, most of the mutations found in domain C strengthen the interactions with domain A, in agreement with suggestions made on the basis of structural analyses. Although this study focuses on single-site mutations, the thermodynamic effects of the recommended mutations should be additive if the mutated residues are not close in space.

  20. Isolation and characterization of marine psychrophilic phage-host systems from Arctic sea ice.

    PubMed

    Borriss, Michael; Helmke, Elisabeth; Hanschke, Renate; Schweder, Thomas

    2003-10-01

    Phage-host systems from extreme cold environments have rarely been surveyed. This study is concerned with the isolation and characterization of three different phage-host systems from Arctic sea ice and melt pond samples collected north-west of Svalbard (Arctic). On the basis of 16S rDNA sequences, the three bacterial phage hosts exhibited the greatest similarity to the species Shewanella frigidimarina (96.0%), Flavobacterium hibernum (94.0%), and Colwellia psychrerythraea (98.4%), respectively. The host bacteria are psychrophilic with good growth at 0 degrees C, resulting in a rapid formation of visible colonies at this temperature. The phages showed an even more pronounced adaptation to cold temperatures than the bacteria, with growth maxima below 14 degrees C and good plaque formation at 0 degrees C. Transmission electron microscopy (TEM) examinations revealed that the bacteriophages belonged to the tailed, double-stranded DNA phage families Siphoviridae and Myoviridae. All three phages were host-specific.

  1. Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent alpha-amylases.

    PubMed

    Cipolla, Alexandre; Delbrassine, François; Da Lage, Jean-Luc; Feller, Georges

    2012-09-01

    The functional and structural adaptations to temperature have been addressed in homologous chloride-dependent α-amylases from a psychrophilic Antarctic bacterium, the ectothermic fruit fly, the homeothermic pig and from a thermophilic actinomycete. This series covers nearly all temperatures encountered by living organisms. We report a striking continuum in the functional properties of these enzymes coupled to their structural stability and related to the thermal regime of the source organism. In particular, thermal stability recorded by intrinsic fluorescence, circular dichroism and differential scanning calorimetry appears to be a compromise between the requirement for a stable native state and the proper structural dynamics to sustain the function at the environmental/physiological temperatures. The thermodependence of activity, the kinetic parameters, the activations parameters and fluorescence quenching support these activity-stability relationships in the investigated α-amylases.

  2. Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax.

    PubMed

    Ciok, Anna; Dziewit, Lukasz; Grzesiak, Jakub; Budzik, Karol; Gorniak, Dorota; Zdanowski, Marek K; Bartosik, Dariusz

    2016-04-01

    The Svalbard archipelago (Spitsbergen Island) is the northernmost landmass in the European Arctic and has a variety of small- and medium-sized glaciers. The plasmidome of eleven psychrophilic strains of Variovorax spp. isolated from the ice surface of Hans and Werenskiold Glaciers of Spitsbergen Island, was defined. This analysis revealed the presence of six plasmids whose nucleotide sequences have been determined. Four of them, exhibiting high reciprocal sequence similarity, possess unique structures, since their genomes lack any recognized genes. These miniature replicons, not exceeding 1 kb in size, include pHW69V1 (746 bp), which is the smallest autonomous replicon so far identified in free-living bacteria. The miniature plasmids share no similarity with known sequences present in the databases. In silico and experimental analyses identified conserved DNA regions essential for the initiation of replication of these replicons.

  3. Dry-heat resistance of selected psychrophiles. [Viking lander in spacecraft sterilization

    NASA Technical Reports Server (NTRS)

    Winans, L.; Pflug, I. J.; Foster, T. L.

    1977-01-01

    The dry-heat resistance characteristics of spores of psychrophilic organisms isolated from soil samples from the Viking spacecraft assembly areas at Cape Kennedy Space Flight Center, Cape Canaveral, Fla., were studied. Spore suspensions were produced, and dry-heat D values were determined for the microorganisms that demonstrated growth or survival under a simulated Martian environment. The dry-heat tests were carried out by using the planchet-boat-hot plate system at 110 and 125 C with an ambient relative humidity of 50% at 22 C. The spores evaluated had a relatively low resistance to dry heat. D (110 C) values ranged from 7.5 to 122 min, whereas the D (125 C) values ranged from less than 1.0 to 9.8 min.

  4. Paenibacillus tibetensis sp. nov., a psychrophilic bacterium isolated from alpine swamp meadow soil.

    PubMed

    Han, Li-Li; He, Ji-Zheng; Zheng, Yuan-Ming; Zeng, Jun; Zhang, Li-Mei

    2015-05-01

    A novel psychrophilic strain, SSB001(T), was isolated from an alpine swamp meadow soil in Tibet, China, and identified as a representative of a novel phylogenetic subclade in the genus Paenibacillus , with Paenibacillus antarcticus (96.2%), Paenibacillus macquariensis (96.53%) and Paenibacillus glacialis (96.2%) as the most closely related species on the basis of 16S rRNA gene sequence analyses. The strain was distinguished from defined species of the genus Paenibacillus by further study of rpoB gene sequences, phenotypic characterization, cellular fatty acid composition, quinones, polar lipids and meso-diaminopimelic acid in the peptidoglycan. Based upon these results, we propose the strain as a representative of a novel species named Paenibacillus tibetensis sp. nov., with SSB001(T) ( =ACCC 19728(T) =DSM 29321(T)) as the type strain. The DNA G+C content (mol%) of strain SSB001(T) was 40.18 mol% (HPLC).

  5. Toward understanding life under subzero conditions: the significance of exploring psychrophilic "cold-shock" proteins.

    PubMed

    Kuhn, Emanuele

    2012-11-01

    Understanding the behavior of proteins under freezing conditions is vital for detecting and locating extraterrestrial life in cold environments, such as those found on Mars and the icy moons of Jupiter and Saturn. This review highlights the importance of studying psychrophilic "cold-shock" proteins, a topic that has yet to be explored. A strategy for analyzing the psychrophilic RNA helicase protein CsdA (Psyc_1082) from Psychrobacter arcticus 273-4 as a key protein for life under freezing temperatures is proposed. The experimental model presented here was developed based on previous data from investigations of Escherichia coli, P. arcticus 273-4, and RNA helicases. P. arcticus 273-4 is considered a model for life in freezing environments. It is capable of growing in temperatures as cold as -10°C by using physiological strategies to survive not only in freezing temperatures but also under low-water-activity and limited-nutrient-availability conditions. The analyses of its genome, transcriptome, and proteome revealed specific adaptations that allow it to inhabit freezing environments by adopting a slow metabolic strategy rather than a cellular dormancy state. During growth at subzero temperatures, P. arcticus 273-4 genes related to energy metabolism and carbon substrate incorporation are downregulated, and genes for maintenance of membranes, cell walls, and nucleic acid motion are upregulated. At -6°C, P. arcticus 273-4 does not upregulate the expression of either RNA or protein chaperones; however, it upregulates the expression of its cold-shock induced DEAD-box RNA helicase protein A (CsdA - Psyc_1082). CsdA - Psyc_1082 was investigated as a key helper protein for sustaining life in subzero conditions. Proving CsdA - Psyc_1082 to be functional as a key protein for life under freezing temperatures may extend the known minimum growth temperature of a mesophilic cell and provide key information about the mechanisms that underlie cold-induced biological systems in

  6. Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments

    PubMed Central

    Dziewit, Lukasz; Bartosik, Dariusz

    2014-01-01

    Extremely cold environments are a challenge for all organisms. They are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. Such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. Such “short-term” evolution is often enabled by plasmids—extrachromosomal replicons that represent major players in horizontal gene transfer. The genomic sequences of thousands of microorganisms, including those of many cold-active bacteria have been obtained over the last decade, but the collected data have yet to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the presence of numerous genes, which may increase the phenotypic flexibility of their host strains. These genes encode enzymes possibly involved in (i) protection against cold and ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v) utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy metals, metalloids and antibiotics. Some of the plasmids also contain type II restriction-modification systems, which are involved in both plasmid stabilization and protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic modules responsible for conjugal transfer or mobilization for transfer, which may facilitate the spread of these replicons among various bacteria, including across species

  7. Rapid identification of Salmonella serovars in feces by specific detection of virulence genes, invA and spvC, by an enrichment broth culture-multiplex PCR combination assay.

    PubMed Central

    Chiu, C H; Ou, J T

    1996-01-01

    In order to make a rapid and definite diagnosis of Salmonella enteritis in children, an enrichment broth culture-multiplex PCR combination assay was devised to identify Salmonella serovars directly from fecal samples. Two pairs of oligonucleotide primers were prepared according to the sequences of the chromosomal invA and plasmid spvC genes. PCR with these two primers would produce either one amplicon (from the invA gene) or two amplicons (from the invA and spvC genes), depending on whether or not the Salmonella bacteria contained a virulence plasmid. The fecal sample was diluted 10- to 20-fold into gram-negative enrichment broth and incubated to eliminate inhibitory compounds and also to allow selective enrichment of the bacteria. One or two amplicons were obtained, the expected result if Salmonella bacteria were present. The detection limit of this PCR was about 200 bacteria per reaction mixture. The primers were specific, as no amplification products were obtained with 18 species and 22 isolates of non-Salmonella bacteria tested which could be present in the feces or cause contamination. In contrast, when 23 commonly seen Salmonella serovars (38 isolates) were tested, all were shown to carry the invA gene and seven concomitantly harbored the spvC gene of the virulence plasmid. This assay was applied to the diagnosis of Salmonella enteritis in 57 children who were suffering from mucoid and/or bloody diarrhea. Of the 57 children, 38 were PCR positive and 22 were culture positive. There were two culture-positive samples that were not detected by PCR. Thus, this PCR assay showed an efficiency of 95% (38 of 40), which is much higher than the 60% (24 of 40) by culture alone. Not only is this method more sensitive, rapid, and efficient but it will cause only an incremental increase in the cost of stool processing, since enrichment cultivation of fecal samples from diarrheal patients using gram-negative enrichment broth is a routine practice for identification in many

  8. Accelerated methanogenesis from effluents of hydrogen-producing stage in anaerobic digestion by mixed cultures enriched with acetate and nano-sized magnetite particles.

    PubMed

    Yang, Zhiman; Xu, Xiaohui; Guo, Rongbo; Fan, Xiaolei; Zhao, Xiaoxian

    2015-08-01

    Potential for paddy soil enrichments obtained in the presence of nano-sized magnetite particles (named as PSEM) to promote methane production from effluents of hydrogen-producing stage in two-stage anaerobic digestion was investigated. The results showed that the addition of magnetite significantly accelerated methane production from acetate in a dose-independent manner. The results from high-throughput sequencing analysis revealed that Rhodocyclaceae-related species were selectively enriched, which were likely the key players for conversion of acetate to methane in PSEM. Compared to the paddy soil enrichments obtained in the absence of magnetite (named as PSEC), the maximum methane production rate in PSEM was significantly higher (1.5-5.5times higher for the artificial medium and 0.2-1.7times higher for the effluents). The accelerated methane production from the effluents indicated remarkably application potential of PSEM for improving performance of anaerobic digestion.

  9. Temperature Sensitivity Conferred by ligA Alleles from Psychrophilic Bacteria upon Substitution in Mesophilic Bacteria and a Yeast Species

    PubMed Central

    Pankowski, Jarosław A.; Puckett, Stephanie M.

    2016-01-01

    We have assembled a collection of 13 psychrophilic ligA alleles that can serve as genetic elements for engineering mesophiles to a temperature-sensitive (TS) phenotype. When these ligA alleles were substituted into Francisella novicida, they conferred a TS phenotype with restrictive temperatures between 33 and 39°C. When the F. novicida ligA hybrid strains were plated above their restrictive temperatures, eight of them generated temperature-resistant variants. For two alleles, the mutations that led to temperature resistance clustered near the 5′ end of the gene, and the mutations increased the predicted strength of the ribosome binding site at least 3-fold. Four F. novicida ligA hybrid strains generated no temperature-resistant variants at a detectable level. These results suggest that multiple mutations are needed to create temperature-resistant variants of these ligA gene products. One ligA allele was isolated from a Colwellia species that has a maximal growth temperature of 12°C, and this allele supported growth of F. novicida only as a hybrid between the psychrophilic and the F. novicida ligA genes. However, the full psychrophilic gene alone supported the growth of Salmonella enterica, imparting a restrictive temperature of 27°C. We also tested two ligA alleles from two Pseudoalteromonas strains for their ability to support the viability of a Saccharomyces cerevisiae strain that lacked its essential gene, CDC9, encoding an ATP-dependent DNA ligase. In both cases, the psychrophilic bacterial alleles supported yeast viability and their expression generated TS phenotypes. This collection of ligA alleles should be useful in engineering bacteria, and possibly eukaryotic microbes, to predictable TS phenotypes. PMID:26773080

  10. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG)

    PubMed Central

    Parkes, R John; Sellek, Gerard; Webster, Gordon; Martin, Derek; Anders, Erik; Weightman, Andrew J; Sass, Henrik

    2009-01-01

    Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use with subsurface gas hydrate sediments from the Indian Continental Shelf, Cascadia Margin and Gulf of Mexico. Generally, highest cell concentrations in enrichments occurred close to in situ pressures (14 MPa) in a variety of media, although growth continued up to at least 80 MPa. Predominant sequences in enrichments were Carnobacterium, Clostridium, Marinilactibacillus and Pseudomonas, plus Acetobacterium and Bacteroidetes in Indian samples, largely independent of media and pressures. Related 16S rRNA gene sequences for all of these Bacteria have been detected in deep, subsurface environments, although isolated strains were piezotolerant, being able to grow at atmospheric pressure. Only the Clostridium and Acetobacterium were obligate anaerobes. No Archaea were enriched. It may be that these sediment samples were not deep enough (total depth 1126–1527 m) to obtain obligate piezophiles. PMID:19694787

  11. THE ANAEROBIC BIODEGRADATION OF O-,M- AND P-CRESOL BY SULFATE-REDUCING BACTERIAL ENRICHMENT CULTURES OBTAINED FROM A SHALLOW ANOXIC AQUIFER

    EPA Science Inventory

    Sulfate-reducing bacterial enrichments were obtained from a shallow anoxic aquifer for their ability to metabolize either o-, m-, orp-cresol. GC/MS and simultaneous adaptation experiments suggested that the anaerobic decomposition of p-cresol proceeds ...

  12. Detection of psychrophilic and psychrotolerant Clostridium spp. in chilled fresh vacuum-packed meat using different PCR methods.

    PubMed

    Bonke, R; Drees, N; Gareis, M

    2016-01-01

    Since 1989, blown pack spoilage has been recognized as a special form of spoilage in vacuum-packed raw and cooked beef. However, only limited information concerning the occurrences of bacteria causing blown pack spoilage on chilled fresh meat is available. In this study, a total of 63 beef and 33 lamb commercially available samples from different countries and without any signs of spoilage were examined for contamination with psychrophilic and psychrotolerant Clostridium spp. using different PCR systems. In total, 34.4% of the chilled fresh vacuum-packed meats were PCR positive. A higher number of lamb samples were identified as PCR positive compared with beef. A geographical relationship between positive results and the origin of the samples could not be determined. PCR system described by Brightwell and Clemens (Development and validation of a real-time PCR assay specific for Clostridium estertheticum and C. estertheticum-like psychrotolerant bacteria. Meat Sci 2012;92:697-703) gave the highest number of positive detections compared with the Broda, Boerema and Bell PCR system (PCR detection of psychrophilic Clostridium spp. causing 'blown pack' spoilage of vacuum-packed chilled meats. J Appl Microbiol 2003;94:515-22). Eight clostridia isolates from two German beef and four Welsh lamb samples were isolated overall. Three of these clostridia isolates were identified as Clostridium estertheticum whereas five clostridia isolates remain unidentified. The study shows that psychrophilic and psychrotolerant Clostridium spp. are more prevalent in retail samples than previously suspected.

  13. Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila

    PubMed Central

    Su, Yao; Jiang, Xianzhi; Wu, Wenping; Wang, Manman; Hamid, M. Imran; Xiang, Meichun; Liu, Xingzhong

    2016-01-01

    Mrakia psychrophila is an obligate psychrophilic fungus. The cold adaptation mechanism of psychrophilic fungi remains unknown. Comparative genomics analysis indicated that M. psychrophila had a specific codon usage preference, especially for codons of Gly and Arg and its major facilitator superfamily (MFS) transporter gene family was expanded. Transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°, while genes involved in unfolded protein binding, protein processing in the endoplasmic reticulum, proteasome, spliceosome, and mRNA surveillance were upregulated at 20°. In addition, genes related to unfolded protein binding were alternatively spliced. Consistent with other psychrophiles, desaturase and glycerol 3-phosphate dehydrogenase, which are involved in biosynthesis of unsaturated fatty acid and glycerol respectively, were upregulated at 4°. Cold adaptation of M. psychrophila is mediated by synthesizing unsaturated fatty acids to maintain membrane fluidity and accumulating glycerol as a cryoprotectant. The proteomic analysis indicated that the correlations between the dynamic patterns between transcript level changes and protein level changes for some pathways were positive at 4°, but negative at 20°. The death of M. psychrophila above 20° might be caused by an unfolded protein response. PMID:27633791

  14. Improvement of sensitivity for Mycobacterium avium subsp. paratuberculosis (MAP) detection in bovine fecal samples by specific duplex F57/IC real-time and conventional IS900 PCRs after solid culture enrichment.

    PubMed

    Fawzy, Ahmad; Eisenberg, Tobias; El-Sayed, Amr; Zschöck, Michael

    2015-04-01

    Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne's disease in ruminants and a probable pathogen of Crohn's disease in humans. Accurate, cost-effective, and time-relevant diagnostics are the basis for efficient control programs. This study was conducted as an attempt to re-evaluate MAP detection improvement by coupling solid media enrichment to a more specific IS900 conventional PCR and a very specific F57/IC real-time PCR. In a spiking experiment, we investigated the improvement of molecular-based MAP detection in feces after a culture-based enrichment step into Herrold's egg yolk media with mycobactin J (HEYM-MJ) for different time intervals, when compared to traditional culture. Detection limit of culture was 0.33 × 10(4) bacteria × g(-1) (33 CFU g(-1)), while that of IS900 PCR when coupled with an enrichment step for 2, 4, and 6 weeks was 0.33 × 10(5) (0.33 × 10(3) CFU g(-1)), 0.33 × 10(4) (33 CFU g(-1)), and 33 (>3.3 CFU g(-1)) bacteria × g(-1), respectively. Whereas the detection limits of F57/IC real-time PCR after the enrichment step for the same time intervals were 0.33 × 10(5) (0.33 × 10(3) CFU g(-1)), 0.33 × 10(3) (3.3 CFU g(-1)), and 33 (>3.3 CFU g(-1)) bacteria × g(-1), respectively. Altogether, enrichment of bovine fecal samples into solid media increased the sensitivity of specific molecular detection of MAP using IS900 conventional PCR and duplex F57/IC real-time PCR and offers an expedited and accurate alternative for MAP detection in bovine feces. Validation of these results is further recommended using field bovine fecal samples.

  15. Multiplex Real-Time PCR Assays for Screening of Shiga Toxin 1 and 2 Genes, Including All Known Subtypes, and Escherichia coli O26-, O111-, and O157-Specific Genes in Beef and Sprout Enrichment Cultures.

    PubMed

    Harada, Tetsuya; Iguchi, Atsushi; Iyoda, Sunao; Seto, Kazuko; Taguchi, Masumi; Kumeda, Yuko

    2015-10-01

    Shiga toxin family members have recently been classified using a new nomenclature into three Stx1 subtypes (Stx1a, Stx1c, and Stx1d) and seven Stx2 subtypes (Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g). To develop screening methods for Stx genes, including all of these subtype genes, and Escherichia coli O26-, O111-, and O157-specific genes in laboratory investigations of Shiga toxin-producing E. coli (STEC) foodborne cases, we developed multiplex real-time PCR assays and evaluated their specificity and quantitative accuracy using STEC and non-STEC isolates, recombinant plasmids, and food enrichment cultures and by performing STEC spiking experiments with beef and sprout enrichment cultures. In addition, we evaluated the relationship between the recovery rates of the target strains by direct plating and immunomagnetic separation and the cycle threshold (CT) values of the real-time PCR assays for the Stx subtypes and STEC O26, O111, and O157 serogroups. All three stx1- and seven stx2-subtype genes were detected by real-time PCR with high sensitivity and specificity, and the quantitative accuracy of this assay was confirmed using control plasmids and STEC spiking experiments. The results of the STEC spiking experiments suggest that it is not routinely possible to isolate STEC from enrichment cultures with real-time PCR CT values greater than 30 by direct plating on MacConkey agar, although highly selective media and immunomagnetic beads were able to isolate the inoculated strains from the enrichment cultures. These data suggest that CT values obtained from the highly quantitative real-time PCR assays developed in this study provide useful information to develop effective isolation strategies for STEC from food samples. The real-time PCR assays developed here are expected to aid in investigations of infections or outbreaks caused by STEC harboring any of the stx-subtype genes in the new Stx nomenclature, as well as STEC O26, O111, and O157.

  16. Structural prediction and comparative docking studies of psychrophilic β- Galactosidase with lactose, ONPG and PNPG against its counter parts of mesophilic and thermophilic enzymes.

    PubMed

    Kumar, Ponnada Suresh; Pulicherla, Kk; Ghosh, Mrinmoy; Kumar, Anmol; Rao, Krs Sambasiva

    2011-01-01

    Enzymes from psychrophiles catalyze the reactions at low temperatures with higher specific activity. Among all the psychrophilic enzymes produced, cold active β-galactosidase from marine psychrophiles revalorizes a new arena in numerous areas at industrial level. The hydrolysis of lactose in to glucose and galactose by cold active β-galactosidase offers a new promising approach in removal of lactose from milk to overcome the problem of lactose intolerance. Herein we propose, a 3D structure of cold active β-galactosidase enzyme sourced from Pseudoalteromonas haloplanktis by using Modeler 9v8 and best model was developed having 88% of favourable region in ramachandran plot. Modelling was followed by docking studies with the help of Auto dock 4.0 against the three substrates lactose, ONPG and PNPG. In addition, comparative docking studies were also performed for the 3D model of psychrophilic β-galactosidase with mesophilic and thermophilic enzymes. Docking studies revealed that binding affinity of enzyme towards the three different substrates is more for psychrophilic enzyme when compared with mesophilic and thermophilic enzymes. It indicates that the enzyme has high specific activity at low temperature when compared with mesophilic and thermophilic enzymes.

  17. Anaerobic cultures from preserved tissues of baby mammoth

    NASA Astrophysics Data System (ADS)

    Pikuta, Elena V.; Fisher, Daniel; Hoover, Richard B.

    2011-10-01

    Microbiological analysis of several cold-preserved tissue samples from the Siberian baby mammoth known as Lyuba revealed a number of culturable bacterial strains that were grown on anaerobic media at 3 oC. Lactic acid produced by LAB (lactic acid bacteria) group, usually by members of the genera Carnobacterium and Lactosphera, appears to be a wonderful preservative that keeps other bacteria from colonizing a system. Permafrost and lactic acid preserved the body of this one month-old baby mammoth and kept it in exceptionally good condition, resulting in this mammoth being the most complete sample of the species ever recovered. The diversity of novel psychrophilic anaerobic isolates was expressed on morphological, physiological and phylogenetic levels. Here, we discuss the specifics of the isolation of new psychrophilic strains, differentiation from trivial contamination, and preliminary results for characterization of the cultures.

  18. Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core.

    PubMed

    Shen, Liang; Liu, Yongqin; Gu, Zhengquan; Xu, Baiqing; Wang, Ninglian; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang

    2015-07-01

    Strain B528-3(T), a Gram-stain-negative, rod-shaped, aerobic, facultatively psychrophilic bacterium with polar flagella, was isolated from an ice core drilled from Muztagh Glacier, Xinjiang, China. The novel isolate was classified into the genus Massilia. The 16S rRNA gene sequence of the novel isolate shares a pairwise similarity of less than 97% with those of all the type strains of the genus Massilia. The major fatty acids of strain B528-3(T) were summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) (57.31%), C16:0 (11.46%) and C18:1ω7c (14.72%). The predominant isoprenoid quinone was Q-8. The DNA G + C content was 62.2 mol% (Tm). The major polar lipids of this bacterium were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. From the genotypic and phenotypic data, it is evident that strain B528-3(T) represents a novel species of the genus Massilia, for which the name Massilia eurypsychrophila sp. nov. is proposed. The type strain is B528-3(T) ( = JCM 30074(T) = CGMCC 1.12828(T)).

  19. Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic.

    PubMed

    Zhang, De-Chao; Li, Hui-Rong; Xin, Yu-Hua; Chi, Zhen-Ming; Zhou, Pei-Jin; Yu, Yong

    2008-06-01

    Strain 20041(T) was isolated from sea-ice of the Canadian Basin (7 degrees 23' 14'' N 14 degrees 06' 55'' W). Phylogenetic analysis based on 16S rRNA gene homology showed that strain 20041(T) was related to members of the genus Marinobacter and had highest 16S rRNA gene sequence similarity with the type strain of Marinobacter maritimus. Cells were Gram-negative, rod-shaped, psychrophilic and motile. The temperature range for growth was 0-22 degrees C, with optimum growth occurring at 16-18 degrees C and at approximately pH 6.0-9.0. Strain 20041(T) had ubiquinone-9 as the major respiratory quinone and iso-C(15 : 0) 2OH and/or C(16 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c and C(12 : 0) 3OH as major fatty acids. The genomic DNA G+C content was 55.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain 20041(T) is considered to represent a novel species, for which the name Marinobacter psychrophilus sp. nov. is proposed. The type strain is 20041(T) (=CGMCC 1.6499(T)=JCM 14643(T)).

  20. Moritella dasanensis sp. nov., a psychrophilic bacterium isolated from the Arctic ocean.

    PubMed

    Kim, Hak Jun; Park, Soyoung; Lee, Jung Min; Park, Seungil; Jung, Woongsic; Kang, Jae-Shin; Joo, Hyung Min; Seo, Ki-Won; Kang, Sung-Ho

    2008-04-01

    An aerobic, motile, Gram-negative, ice-active substance-producing, rod-shaped psychrophile, designated strain ArB 0140T, was isolated from seawater collected from near a glacier in Kongsfjorden, Svalbard Archipelago, Norway. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain ArB 0140T showed a distinct phyletic line within the genus Moritella. Characteristic chemotaxonomic data [predominant isoprenoid quinone, Q8; major fatty acids, C14 : 0, C14 : 1, C16 : 0, C16 : 1 and C22 : 6 (docosahexaenoic acid; DHA)] also corroborated the affiliation of strain ArB 0140T to the genus Moritella. The maximal growth rate of the novel strain was observed at 9 degrees C, with a maximum temperature for growth of 18 degrees C. The genomic DNA G+C content was 46.9 mol%. Based on the data obtained from this polyphasic study, including DNA-DNA relatedness, physiological and biochemical tests and ice-controlling activity, strain ArB 0140T was found to be genetically and phenotypically different from other recognized species of the genus Moritella. Therefore strain ArB 0140T represents a novel species, for which the name Moritella dasanensis sp. nov. is proposed. The type strain is ArB 0140T (=KCTC 10814T=KCCM 42845T=JCM 14759T).

  1. Sporosarcina antarctica sp. nov., a psychrophilic bacterium isolated from the Antarctic.

    PubMed

    Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Sheng, Jun; Chi, Zhen-Ming; Zhou, Pei-Jin; Zhang, De-Chao

    2008-09-01

    A Gram-positive, psychrophilic, rod-shaped bacterium, designated strain N-05(T), was isolated from soil samples collected off King George Island, west Antarctica (6 degrees 13' 31'' S 5 degrees 57' 08'' W). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N-05(T) was related to members of the genus Sporosarcina and had highest 16S rRNA gene sequence similarity with the type strain of Sporosarcina macmurdoensis (98.0%). The temperature range for growth of strain N-05(T) was 0-23 degrees C, with optimum growth occurring at 17-18 degrees C and approximately pH 6.0-8.0. Strain N-05(T) had MK-7 as the major menaquinone and anteiso-C(15:0) and C(16:1)omega7c alcohol as major fatty acids. The genomic DNA G+C content was 39.2 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain N-05(T) is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina antarctica is proposed. The type strain is N-05(T) (=CGMCC 1.6503(T)=JCM 14646(T)).

  2. Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.

    PubMed

    Liu, Qing; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

    2013-08-01

    In this study, two psychrophilic bacterial strains were isolated from the China No. 1 glacier in Xinjiang, north-west China. Cells were Gram-positive rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus Cryobacterium. Phylogenetic analysis showed that they clustered together and are most closely related to Cryobacterium luteum CGMCC 1.11210(T), Cryobacterium flavum CGMCC 1.11215(T), Cryobacterium psychrophilum CGMCC 1.4292(T), Cryobacterium psychrotolerans CGMCC 1.5382(T) and Cryobacterium roopkundense CGMCC 1.10672(T). The major cellular fatty acids of the novel strains were anteiso-C15 : 0, anteiso-C15 : 1 A, iso-C16 : 0 and iso-C15 : 0. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in the cell membrane. The results of DNA-DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strains Hh34(T) and Hh28 from related species. However, their high DNA-DNA relatedness showed that they belong to the same novel species. Strain Hh34(T) (= NBRC 107883(T) = CGMCC 1.11211(T)) was selected as the type strain to represent this novel species, for which the name Cryobacterium levicorallinum sp. nov. is proposed.

  3. Expression, purification, and characterization of cold-adapted inorganic pyrophosphatase from psychrophilic Shewanella sp. AS-11.

    PubMed

    Ginting, Elvy Like; Iwasaki, Syouhei; Maeganeku, Chihiro; Motoshima, Hiroyuki; Watanabe, Keiichi

    2014-01-01

    In the presence of divalent cations, inorganic pyrophosphatase is activated to hydrolyze inorganic pyrophosphate to inorganic phosphate. Here, we clone, express, purify, and characterize inorganic pyrophosphatase from the psychrophilic Shewanella sp. AS-11 (Sh-PPase). The recombinant Sh-PPase was expressed in Escherichia coli BL21 (DE3) at 20°C using pET16b as an expression vector and purified from the cell extracts by a combination of ammonium sulfate fractionation and anion-exchange chromatography. Sh-PPase was found to be a family II PPase with a subunit molecular mass of 34 kD that preferentially utilizes Mn²⁺ over Mg²⁺ ions for activity. The functional characteristics of Sh-PPase, such as activity, temperature dependency, and thermal inactivation, were greatly influenced by manganese ions. Manganese ion activation increased the enzyme's activity at low temperatures; therefore, it was required to gain the cold-adapted characteristics of Sh-PPase.

  4. Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

    NASA Technical Reports Server (NTRS)

    Madigan, M. T.; Jung, D. O.; Woese, C. R.; Achenbach, L. A.

    2000-01-01

    A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

  5. Influence of hydraulic retention time on the psychrophilic hydrolysis/acidogenesis of proteins.

    PubMed

    Poirrier, Paola; Schiappacasse, María Cristina; Carballa, Marta; Lema, Juan M

    2016-11-01

    The influence of the hydraulic retention time (HRT) on the anaerobic hydrolysis of complex substrates has been studied under psychrophilic conditions. For this purpose, a continuous stirred tank reactor was operated at 15 °C and neutral pH and gelatin was considered as a model protein. Three HRTs have been tested: 12, 21 and 36 h. Gelatin hydrolysis was greatly dependent on HRT, increasing from 40% at 12 h-HRT to a maximum of 65% at 36 h-HRT. Molecular size distribution analyses of the effluent showed that hydrolysation of compounds larger than 10 kDa was poor at 12 h-HRT, whereas the fraction of 1-10 kDa was completely transformed into compounds smaller than 1 kDa. Higher HRT (36 h) improved the degradation of the recalcitrant fraction (>10 kDa), obtaining an effluent with around 95% of soluble molecules (<1 kDa). In that way, the use of membrane bioreactors for the treatment of this type of macromolecules could improve the degradation efficiencies by enabling to increase the residence time of the non-hydrolyzed molecules, with what would be possible to achieve higher organic loading rate operation.

  6. Biodegradation of isopropanol in a three phase fixed bed bioreactor: start up and acclimation using a previously-enriched microbial culture.

    PubMed

    Bustard, M T; Meeyoo, V; Wright, P C

    2001-10-01

    The aerobic biodegradation of high liquid phase concentrations of 2-propanol (IPA) by a previously enriched solvent-tolerant bacterial consortium within a 1.9 l fed-batch three phase fixed bed bioreactor was investigated. Solvent concentrations of up to 7.9 g l(-1) were investigated. Previously enriched solvent-tolerant bacterial cells were immobilised onto porous glass cylinders as a means obioprocess intensification. Bioreactor start-up and acclimation was studied anacetone concentration tracked as an indicator of IPA utilization, as the sole carbon source within a minimal salts medium (MSM). The initial batch treatment of IPA exhibited a biodegradation rate of 0.11 g l(-1) h(-1) prior to biofilm formation Biofilm growth during the second batch treatment was consistent with an increase in metabolic activity and an IPA biodegradation rate of 0.34 g l(-1), followed by a reduction of biodegradation rate to a constant value of 0.078 g l(-1) h(-1) after 650 h. A maximum acetone generation rate of 1.3 g l(-1) h(-1) was obtained during the fourth IPA addition although the maximum acetone biodegradation rate of 0.38 g l(-1) h(-1) was observed during the initial IPA addition. It is proposed that the metabolic lag resulting from switching from alcohol dehydrogenase to acetone carboxylase is a major rate-limiting step in the deep oxidation of IPA to acetone. The results demonstrate the potential of a previously enriched solvent-tolerant bacterial consortium in fixed bed bioreactor systems, for the aerobic treatment of concentrated solvent-containing wastestreams.

  7. Culture.

    ERIC Educational Resources Information Center

    1997

    Twelve conference papers on cultural aspects of second language instruction include: "Towards True Multiculturalism: Ideas for Teachers" (Brian McVeigh); Comparing Cultures Through Critical Thinking: Development and Interpretations of Meaningful Observations" (Laurel D. Kamada); "Authority and Individualism in Japan and the…

  8. Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens

    PubMed Central

    Horton, Rene' N; Apel, William A; Thompson, Vicki S; Sheridan, Peter P

    2006-01-01

    Background Chromium is a transition metal most commonly found in the environment in its trivalent [Cr(III)] and hexavalent [Cr(VI)] forms. The EPA maximum total chromium contaminant level for drinking water is 0.1 mg/l (0.1 ppm). Many water sources, especially underground sources, are at low temperatures (less than or equal to 15 Centigrade) year round. It is important to evaluate the possibility of microbial remediation of Cr(VI) contamination using microorganisms adapted to these low temperatures (psychrophiles). Results Core samples obtained from a Cr(VI) contaminated aquifer at the Hanford facility in Washington were enriched in Vogel Bonner medium at 10 Centigrade with 0, 25, 50, 100, 200, 400 and 1000 mg/l Cr(VI). The extent of Cr(VI) reduction was evaluated using the diphenyl carbazide assay. Resistance to Cr(VI) up to and including 1000 mg/l Cr(VI) was observed in the consortium experiments. Reduction was slow or not observed at and above 100 mg/l Cr(VI) using the enrichment consortium. Average time to complete reduction of Cr(VI) in the 30 and 60 mg/l Cr(VI) cultures of the consortium was 8 and 17 days, respectively at 10 Centigrade. Lyophilized consortium cells did not demonstrate adsorption of Cr(VI) over a 24 hour period. Successful isolation of a Cr(VI) reducing organism (designated P4) from the consortium was confirmed by 16S rDNA amplification and sequencing. Average time to complete reduction of Cr(VI) at 10 Centigrade in the 25 and 50 mg/l Cr(VI) cultures of the isolate P4 was 3 and 5 days, respectively. The 16S rDNA sequence from isolate P4 identified this organism as a strain of Arthrobacter aurescens, a species that has not previously been shown to be capable of low temperature Cr(VI) reduction. Conclusion A. aurescens, indigenous to the subsurface, has the potential to be a predominant metal reducer in enhanced, in situ subsurface bioremediation efforts involving Cr(VI) and possibly other heavy metals and radionuclides. PMID:16436214

  9. Quantitative ecology and dry-heat resistance of psychrophiles. M.S. Thesis; [in soil samples from Viking spacecraft manufacturing areas

    NASA Technical Reports Server (NTRS)

    Winans, L., Jr.

    1974-01-01

    Microorganisms capable of growth at 7 C were enumerated and isolated from soil samples from the manufacture area (Denver, Colorado) and assembly area (Cape Kennedy, Florida) of the Viking spacecraft. Temperature requirements were determined for these isolates, and those growing at 3 C, but not at 32 C were designated as obligate psychrophiles in this investigation. These were identified to major generic groups, and the population density of obligate psychrophiles from the various groups was determined. Dry heat D-values were found for those spores that demonstrated growth or survival under a simulated Martian environment.

  10. Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism.

    PubMed

    Feng, Shi; Powell, Shane M; Wilson, Richard; Bowman, John P

    2014-01-01

    Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755(T), associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44(T). Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism.

  11. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

    SciTech Connect

    Allen, Michele A; Lauro, Federico M; Williams, Timothy J; Burg, Dominic; Siddiqui, Khawar S; DeFrancisci, Davide; Chong, Kevin WY; Pilak, Oliver; Chew, Hwee H; DeMaere, Matthew Z; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R; Galperin, Michael Y.; Anderson, Iain; Ivanova, N; Dalin, Eileen; Martinez, Michele; Lapidus, Alla L.; Hauser, Loren John; Land, Miriam L; Thomas, Torsten; Cavicchioli, Ricardo

    2009-01-01

    Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from - and -Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they have an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it

  12. Cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241: structure, sequence, and complementation in the mesophile, Chlamydomonas reinhardtii.

    PubMed

    Gudynaite-Savitch, Loreta; Gretes, Michael; Morgan-Kiss, Rachael M; Savitch, Leonid V; Simmonds, John; Kohalmi, Susanne E; Hüner, Norman P A

    2006-04-01

    Although cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241, exhibits a lower apparent molecular mass (34 kD) than that of the mesophile C. reinhardtii (41 kD) based on SDS-PAGE, both proteins are comparable in calculated molecular mass and show 79% identity in amino acid sequence. The difference in apparent molecular mass was maintained after expression of petA from both Chlamydomonas species in either E. coli or a C. reinhardtii DeltapetA mutant and after substitution of a unique third cysteine-292 to phenylalanine in the psychrophilic cytochrome f. Moreover, the heme of the psychrophilic form of cytochrome f was less stable upon heating than that of the mesophile. In contrast to C. raudensis, a C. reinhardtii DeltapetA mutant transformed with petA from C. raudensis exhibited the ability to undergo state transitions and a capacity for intersystem electron transport comparable to that of C. reinhardtii wild type. However, the C. reinhardtii petA transformants accumulated lower levels of cytochrome b ( 6 ) /f complexes and exhibited lower light saturated rates of O(2) evolution than C. reinhardtii wild type. We show that the presence of an altered form of cytochrome f in C. raudensis does not account for its inability to undergo state transitions or its impaired capacity for intersystem electron transport as previously suggested. A combined survey of the apparent molecular mass, thermal stability and amino acid sequences of cytochrome f from a broad range of mesophilic species shows unequivocally that the observed differences in cytochrome f structure are not related to psychrophilly. Thus, caution must be exercised in relating differences in amino acid sequence and thermal stability to adaptation to cold environments.

  13. Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus

    PubMed Central

    Miao, Li-Li; Hou, Yan-Jie; Fan, Hong-Xia; Qu, Jie; Qi, Chao; Liu, Ying

    2016-01-01

    Psychrophilic enzymes play crucial roles in cold adaptation of microbes and provide useful models for studies of protein evolution, folding, and dynamic properties. We examined the crystal structure (2.2-Å resolution) of the psychrophilic β-glucosidase BglU, a member of the glycosyl hydrolase 1 (GH1) enzyme family found in the cold-adapted bacterium Micrococcus antarcticus. Structural comparison and sequence alignment between BglU and its mesophilic and thermophilic counterpart enzymes (BglB and GlyTn, respectively) revealed two notable features distinct to BglU: (i) a unique long-loop L3 (35 versus 7 amino acids in others) involved in substrate binding and (ii) a unique amino acid, His299 (Tyr in others), involved in the stabilization of an ordered water molecule chain. Shortening of loop L3 to 25 amino acids reduced low-temperature catalytic activity, substrate-binding ability, the optimal temperature, and the melting temperature (Tm). Mutation of His299 to Tyr increased the optimal temperature, the Tm, and the catalytic activity. Conversely, mutation of Tyr301 to His in BglB caused a reduction in catalytic activity, thermostability, and the optimal temperature (45 to 35°C). Loop L3 shortening and H299Y substitution jointly restored enzyme activity to the level of BglU, but at moderate temperatures. Our findings indicate that loop L3 controls the level of catalytic activity at low temperatures, residue His299 is responsible for thermolability (particularly heat lability of the active center), and long-loop L3 and His299 are jointly responsible for the psychrophilic properties. The described structural basis for the cold adaptedness of BglU will be helpful for structure-based engineering of new cold-adapted enzymes and for the production of mutants useful in a variety of industrial processes at different temperatures. PMID:26801571

  14. The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

    SciTech Connect

    Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

    2009-04-01

    Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the

  15. Phosphate-independent utilization of phosphonoacetic acid as sole phosphorus source by a psychrophilic strain of Geomyces pannorum P15.

    PubMed

    Klimek-Ochab, Magdalena

    2014-09-01

    A psychrophilic fungal strain of Geomyces pannorum P15 was screened for its ability to utilize a range of synthetic and natural organophosphonate compounds as the sole source of phosphorus, nitrogen, or carbon. Only phosphonoacetic acid served as a phosphorus source for microbial growth in phosphate-independent manner. Substrate metabolism did not lead to extracellular release of inorganic phosphate. No phosphonate metabolizing enzyme activity was detectable in cell-free extracts prepared from Geomyces biomass pregrown on 2 mmol/L phosphonoacetic acid.

  16. Complete genome sequence of the Sporosarcina psychrophila DSM 6497, a psychrophilic Bacillus strain that mediates the calcium carbonate precipitation.

    PubMed

    Yan, Wenkai; Xiao, Xiang; Zhang, Yu

    2016-05-20

    Sporosarcina psychrophila DSM 6497 is a gram positive, spore-formation psychrophilic bacterial strain, widely distributed in terrestrial and aquatic environments. Here we report its complete sequence including one circular chromosome of 4674191bp with a GC content of 40.3%. Genes encoding urease are predicted in the genome, which provide insight information on the microbiologically mediated urea hydrolysis process. This urea hydrolysis can further lead to an increase of carbonate anion and alkalinity in the environment, which promotes the microbiologically induced carbonate precipitation with various applications, such as the bioremediation of calcium rich wastewater and bio-reservation of architectural patrimony.

  17. Local entropy difference upon a substrate binding of a psychrophilic α-amylase and a mesophilic homologue

    NASA Astrophysics Data System (ADS)

    Kosugi, Takahiro; Hayashi, Shigehiko

    2011-01-01

    Psychrophilic α-amylase from the antarctic bacterium pseudoalteromonashaloplanktis (AHA) and its mesophilic homologue, porcine pancreatic α-amylase (PPA) are theoretically investigated with molecular dynamics (MD) simulations. We carried out 240-ns MD simulations for four systems, AHA and PPA with/without the bound substrate, and examined protein conformational entropy changes upon the substrate binding. We developed an analysis that decomposes the entropy changes into contributions of individual amino acids, and successfully identified protein regions responsible for the entropy changes. The results provide a molecular insight into the structural flexibilities of those enzymes related to the temperature dependences of the enzymatic activity.

  18. Enrichment of Secondary Wastewater Sludge for Production of Hydrogen from Crude Glycerol and Comparative Evaluation of Mono-, Co- and Mixed-Culture Systems

    PubMed Central

    Pachapur, Vinayak Laxman; Kutty, Prianka; Brar, Satinder Kaur; Ramirez, Antonio Avalos

    2016-01-01

    Anaerobic digestion using mixed-culture with broader choice of pretreatments for hydrogen (H2) production was investigated. Pretreatment of wastewater sludge by five methods, such as heat, acid, base, microwave and chloroform was conducted using crude glycerol (CG) as substrate. Results for heat treatment (100 °C for 15 min) showed the highest H2 production across the pretreatment methods with 15.18 ± 0.26 mmol/L of medium at 30 °C in absence of complex media and nutrient solution. The heat-pretreated inoculum eliminated H2 consuming bacteria and produced twice as much as H2 as compared to other pretreatment methods. The fermentation conditions, such as CG concentration (1.23 to 24 g/L), percentage of inoculum size (InS) (1.23% to 24% v/v) along with initial pH (2.98 to 8.02) was tested using central composite design (CCD) with H2 production as response parameter. The maximum H2 production of 29.43 ± 0.71 mmol/L obtained at optimum conditions of 20 g/L CG, 20% InS and pH 7. Symbiotic correlation of pH over CG and InS had a significant (p-value: 0.0011) contribution to H2 production. The mixed-culture possessed better natural acclimatization activity for degrading CG, at substrate inhibition concentration and provided efficient inoculum conditions in comparison to mono- and co-culture systems. The heat pretreatment step used across mixed-culture system is simple, cheap and industrially applicable in comparison to mono-/co-culture systems for H2 production. PMID:26771607

  19. Enrichment of Secondary Wastewater Sludge for Production of Hydrogen from Crude Glycerol and Comparative Evaluation of Mono-, Co- and Mixed-Culture Systems.

    PubMed

    Pachapur, Vinayak Laxman; Kutty, Prianka; Brar, Satinder Kaur; Ramirez, Antonio Avalos

    2016-01-13

    Anaerobic digestion using mixed-culture with broader choice of pretreatments for hydrogen (H₂) production was investigated. Pretreatment of wastewater sludge by five methods, such as heat, acid, base, microwave and chloroform was conducted using crude glycerol (CG) as substrate. Results for heat treatment (100 °C for 15 min) showed the highest H₂ production across the pretreatment methods with 15.18 ± 0.26 mmol/L of medium at 30 °C in absence of complex media and nutrient solution. The heat-pretreated inoculum eliminated H₂ consuming bacteria and produced twice as much as H₂ as compared to other pretreatment methods. The fermentation conditions, such as CG concentration (1.23 to 24 g/L), percentage of inoculum size (InS) (1.23% to 24% v/v) along with initial pH (2.98 to 8.02) was tested using central composite design (CCD) with H₂ production as response parameter. The maximum H₂ production of 29.43 ± 0.71 mmol/L obtained at optimum conditions of 20 g/L CG, 20% InS and pH 7. Symbiotic correlation of pH over CG and InS had a significant (p-value: 0.0011) contribution to H₂ production. The mixed-culture possessed better natural acclimatization activity for degrading CG, at substrate inhibition concentration and provided efficient inoculum conditions in comparison to mono- and co-culture systems. The heat pretreatment step used across mixed-culture system is simple, cheap and industrially applicable in comparison to mono-/co-culture systems for H₂ production.

  20. Effect of a Semi-Purified Oligosaccharide-Enriched Fraction from Caprine Milk on Barrier Integrity and Mucin Production of Co-Culture Models of the Small and Large Intestinal Epithelium

    PubMed Central

    Barnett, Alicia M.; Roy, Nicole C.; McNabb, Warren C.; Cookson, Adrian L.

    2016-01-01

    Caprine milk contains the highest amount of oligosaccharides among domestic animals, which are structurally similar to human milk oligosaccharides (HMOs). This suggests caprine milk oligosaccharides may offer similar protective and developmental effects to that of HMOs. However, to date, studies using oligosaccharides from caprine milk have been limited. Thus, this study aimed to examine the impact of a caprine milk oligosaccharide-enriched fraction (CMOF) on barrier function of epithelial cell co-cultures of absorptive enterocytes (Caco-2 cells) and mucus-secreting goblet cells (HT29-MTX cells), that more closely simulate the cell proportions found in the small (90:10) and large intestine (75:25). Treatment of epithelial co-cultures with 0.4, 1.0, 2.0 and 4.0 mg/mL of CMOF was shown to have no effect on metabolic activity but did enhance cell epithelial barrier integrity as measured by trans-epithelial electrical resistance (TEER), in a dose-dependent manner. The CMOF at the maximum concentration tested (4.0 mg/mL) enhanced TEER, mucin gene expression and mucin protein abundance of epithelial co-cultures, all of which are essential components of intestinal barrier function. PMID:27164134

  1. Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor.

    PubMed

    Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

    2017-01-01

    Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.

  2. Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor

    PubMed Central

    Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M.; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

    2017-01-01

    Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized. PMID:28220112

  3. Immunoaffinity enrichment and liquid chromatography-selected reaction monitoring mass spectrometry for quantitation of carbonic anhydrase 12 in cultured renal carcinoma cells

    PubMed Central

    Rafalko, Agnes; Iliopoulos, Othon; Fusaro, Vincent A.; Hancock, William; Hincapie, Marina

    2010-01-01

    Liquid chromatography-selected reaction monitoring (LC-SRM) is a highly specific and sensitive mass spectrometry (MS) technique that is widely being applied to selectively qualify and validate candidate markers within complex biological samples. However, in order for LC-SRM methods to take on these attributes, target-specific optimization of sample processing is required, in order to reduce analyte complexity, prior to LC-SRM. In this study, we have developed a targeted platform consisting of protein immunoaffinity enrichment on magnetic beads and LC-SRM for measuring carbonic anhydrase 12 (CA12) protein in a renal cell carcinoma (RCC) cell line (PRC3), a candidate biomarker for RCC whose expression at the protein level has not been previously reported. Sample processing and LC-SRM assay were optimized for signature peptides selected as surrogate markers of CA12 protein. Using LC-SRM coupled with stable isotope dilution, we achieved limits of quantitation in the low fmol range sufficient for measuring clinically relevant biomarkers with good intra- and inter-assay accuracy and precision (≤17%). Our results show that using a quantitative immunoaffinity capture approach provides specific, accurate, and robust assays amenable to high-throughput verification of potential biomarkers. PMID:20936840

  4. Cloning and in-silico analysis of beta-1,3-xylanase from psychrophilic yeast, Glaciozyma antarctica PI12

    NASA Astrophysics Data System (ADS)

    Nor, Nooraisyah Mohamad; Bakar, Farah Diba Abu; Mahadi, Nor Muhammad; Murad, Abdul Munir Abdul

    2015-09-01

    A beta-1,3-xylanase (EC 3.2.1.32) gene from psychrophilic yeast, Glaciozyma antarctica has been identified via genome data mining. The enzyme was grouped into GH26 family based on Carbohydrate Active Enzyme (CaZY) database. The molecular weight of this protein was predicted to be 42 kDa and is expected to be soluble for expression. The presence of signal peptide suggested that this enzyme may be released extracellularly into the marine environment of the host's habitat. This supports the theory that such enzymatic activity is required for degradation of nutrients of polysaccharide origins into simpler carbohydrates outside the environment before it could be taken up inside the cell. The sequence for this protein showed very little conservation (< 30%) with other beta-1,3-xylanases from available databases. Based on the phylogenetic analysis, this protein also showed distant relationship to other xylanases from eukaryotic origin. The protein may have undergone major substitution in its gene sequence order to adapt to the cold climate. This is the first report of beta-1,3-xylanase gene isolated from a psychrophilic yeast.

  5. A study of psychrophilic organisms isolated from the manufacture and assembly areas of spacecraft to be used in the Viking mission, 1 January - 30 June 1973

    NASA Technical Reports Server (NTRS)

    Foster, T. L.; Winans, L., Jr.

    1973-01-01

    Soil samples from the areas associated with the Viking spacecraft were analyzed for major generic groups of microorganisms and the percentage of obligate psychrophiles. Results are presented which show the distribution of organisms isolated at low temperatures and the methods employed for subjecting samples to simulated Martian conditions. Emphasis is placed on application of these results to the objectives of the quarantine program.

  6. Survival of the North American strain of viral hemorrhagic septicemia virus (VHSV) in filtered seawater and seawater containing ovarian fluid, crude oil and serum-enriched culture medium

    USGS Publications Warehouse

    Kocan, R.M.; Hershberger, P.K.; Elder, N.E.

    2001-01-01

     The North American strain of viral hemorrhagic septicemia virus (NA-VHSV) could be recovered for up to 40 h in natural filtered seawater (27 ppt) with a 50% loss of infectivity after approximately 10 h at 15°C. Addition of 10 ppb North Slope crude oil to the seawater had no effect on virus survival. However, when various concentrations of teleost ovarian fluid were added to seawater, virus could be recovered after 72 h at 0.01% ovarian fluid and after 96 h at 1.0%. When cell culture medium supplemented with 10% fetal bovine serum was added to the seawater, 100% of the virus could be recovered for the first 15 d and 60% of the virus remained after 36 d. These findings quantify NA-VHSV infectivity in natural seawater and demonstrate that ovarian fluid, which occurs naturally during spawning events, significantly prolongs the survival and infectivity of the virus. The extended stabilization of virus in culture medium supplemented with serum allows for low titer field samples to be collected and transported in an unfrozen state without significant loss of virus titer.

  7. Effect of CO sub 2 enrichment and high photosynthetic photon flux densities (PPFD) on rubisco and PEP-case activities of in vitro cultured strawberry plants

    SciTech Connect

    Desjardins, Y.; Beeson, R.; Gosselin, A. )

    1989-04-01

    Standard growing conditions in vitro (low light and CO{sub 2}) are not conducive to autotrophy. An experiment was conducted to improve photosynthesis in vitro in the hope of increasing survival in acclimatization. A factorial experiment was elaborated where CO{sub 2} and PPFD were supplied to in vitro cultured strawberry plants in the rooting stage. Activities of carboxylating enzymes were determined after 4 weeks of culture. The activities of non-activated and activated rubisco and PEP-Case were measured after extraction of the enzymes and a reaction with NaH{sup 14}CO{sub 3} followed by scintillation counting spectroscopy. High CO{sub 2} concentration significantly increased net assimilation rates (NAR) by 165% over the control for both 1650 and 3000 ppm CO{sub 2}. High PPFD only increased NAR by 12 and 35% for 150 and 250 {mu}mol{center dot}m{sup {minus}2}{center dot}s{sup {minus}1} respectively over the control. Plants grown at 3000 ppm CO{sub 2} had the highest level of chlorophyll/g FW with 97% more than the control. The activity of PEP-Case was the highest at high light levels and high CO{sub 2} with rates of 1.65 for 1650 ppm versus 1.22 mmol CO{sub 2} mg{sup {minus}1} chl. h{sup {minus}1} at 250 {mu}mol{center dot}m{sup {minus}2}{center dot}s{sup {minus}1}. There was no difference in PEP activity at low light levels. The rubisco activity was lower at 1650 and 3000 ppm CO{sub 2}. Increases in NAR correlate more closely to the PEP-Case than to Rubisco activity. Physiological significance of high activity of PEP-Case over rubisco will be discussed.

  8. Derived enriched uranium market

    SciTech Connect

    Rutkowski, E.

    1996-12-01

    The potential impact on the uranium market of highly enriched uranium from nuclear weapons dismantling in the Russian Federation and the USA is analyzed. Uranium supply, conversion, and enrichment factors are outlined for each country; inventories are also listed. The enrichment component and conversion components are expected to cause little disruption to uranium markets. The uranium component of Russian derived enriched uranium hexafluoride is unresolved; US legislation places constraints on its introduction into the US market.

  9. Differential cold-adaptation among protein components of the thioredoxin system in the psychrophilic eubacterium Pseudoalteromonas haloplanktis TAC 125.

    PubMed

    Cotugno, Roberta; Rosaria Ruocco, Maria; Marco, Salvatore; Falasca, Patrizia; Evangelista, Giovanna; Raimo, Gennaro; Chambery, Angela; Di Maro, Antimo; Masullo, Mariorosario; De Vendittis, Emmanuele

    2009-05-01

    Thioredoxin and thioredoxin reductase from the psychrophilic eubacterium Pseudoalteromonas haloplanktis were obtained as recombinant His-tagged proteins (rPhTrx and rPhTrxR, respectively). rPhTrxR is organised as a homodimeric flavoenzyme, whereas rPhTrx is a small monomeric protein, both containing a functional disulfide bridge. However, three additional cysteines are present as free thiols in purified rPhTrxR. When individually tested in specific assays, rPhTrxR and rPhTrx display a full activity at low temperatures, an indispensable requirement for cold-adapted proteins. In particular, rPhTrxR catalyses the NADPH dependent reduction of DTNB and rPhTrx provokes the insulin precipitation in the presence of DTT. The analysis of the effect of temperature on these reactions indicates that rPhTrxR is more cold-adapted than rPhTrx, having a higher psychrophilicity. The combined activity of rPhTrxR and rPhTrx, tested in a reconstituted assay containing NADPH as electrons donor and human insulin as the thioredoxin substrate, demonstrates a direct functional interaction between the purified recombinant components of the thioredoxin system of P. haloplanktis. Furthermore, the NADPH-dependent reduction of rPhTrx catalysed by rPhTrxR is fully reversible and allows the determination of its redox potential, whose value is in the range of other bacterial and archaeal thioredoxins. The analysis of the thermostability of rPhTrxR points to its discrete heat resistance. However, rPhTrx is much more heat resistant, with a half inactivation time of about 4 h at 95 degrees C. This exceptional heat resistance for a psychrophilic protein is significantly decreased by the reduction of the disulfide bridge of rPhTrx. Functionality, thermodependence and thermostability of the P. haloplanktis thioredoxin system point to the relevance of this key mechanism for the preservation of the reduced state of cytoplasmic proteins even in a cold-adapted source.

  10. Development of a rapid lateral flow immunoassay test for detection of exosomes previously enriched from cell culture medium and body fluids

    PubMed Central

    Oliveira-Rodríguez, Myriam; López-Cobo, Sheila; Reyburn, Hugh T.; Costa-García, Agustín; López-Martín, Soraya; Yáñez-Mó, María; Cernuda-Morollón, Eva; Paschen, Annette; Valés-Gómez, Mar; Blanco-López, Maria Carmen

    2016-01-01

    Exosomes are cell-secreted nanovesicles (40–200 nm) that represent a rich source of novel biomarkers in the diagnosis and prognosis of certain diseases. Despite the increasingly recognized relevance of these vesicles as biomarkers, their detection has been limited due in part to current technical challenges in the rapid isolation and analysis of exosomes. The complexity of the development of analytical platforms relies on the heterogeneous composition of the exosome membrane. One of the most attractive tests is the inmunochromatographic strips, which allow rapid detection by unskilled operators. We have successfully developed a novel lateral flow immunoassay (LFIA) for the detection of exosomes based on the use of tetraspanins as targets. We have applied this platform for the detection of exosomes purified from different sources: cell culture supernatants, human plasma and urine. As proof of concept, we explored the analytical potential of this LFIA platform to accurately quantify exosomes purified from a human metastatic melanoma cell line. The one-step assay can be completed in 15 min, with a limit of detection of 8.54×105 exosomes/µL when a blend of anti-CD9 and anti-CD81 were selected as capture antibodies and anti-CD63 labelled with gold nanoparticles as detection antibody. Based on our results, this platform could be well suited to be used as a rapid exosome quantification tool, with promising diagnostic applications, bearing in mind that the detection of exosomes from different sources may require adaptation of the analytical settings to their specific composition. PMID:27527605

  11. Development of a rapid lateral flow immunoassay test for detection of exosomes previously enriched from cell culture medium and body fluids.

    PubMed

    Oliveira-Rodríguez, Myriam; López-Cobo, Sheila; Reyburn, Hugh T; Costa-García, Agustín; López-Martín, Soraya; Yáñez-Mó, María; Cernuda-Morollón, Eva; Paschen, Annette; Valés-Gómez, Mar; Blanco-López, Maria Carmen

    2016-01-01

    Exosomes are cell-secreted nanovesicles (40-200 nm) that represent a rich source of novel biomarkers in the diagnosis and prognosis of certain diseases. Despite the increasingly recognized relevance of these vesicles as biomarkers, their detection has been limited due in part to current technical challenges in the rapid isolation and analysis of exosomes. The complexity of the development of analytical platforms relies on the heterogeneous composition of the exosome membrane. One of the most attractive tests is the inmunochromatographic strips, which allow rapid detection by unskilled operators. We have successfully developed a novel lateral flow immunoassay (LFIA) for the detection of exosomes based on the use of tetraspanins as targets. We have applied this platform for the detection of exosomes purified from different sources: cell culture supernatants, human plasma and urine. As proof of concept, we explored the analytical potential of this LFIA platform to accurately quantify exosomes purified from a human metastatic melanoma cell line. The one-step assay can be completed in 15 min, with a limit of detection of 8.54×10(5) exosomes/µL when a blend of anti-CD9 and anti-CD81 were selected as capture antibodies and anti-CD63 labelled with gold nanoparticles as detection antibody. Based on our results, this platform could be well suited to be used as a rapid exosome quantification tool, with promising diagnostic applications, bearing in mind that the detection of exosomes from different sources may require adaptation of the analytical settings to their specific composition.

  12. Dry anaerobic digestion of high solids content dairy manure at high organic loading rates in psychrophilic sequence batch reactor.

    PubMed

    Massé, Daniel I; Saady, Noori M Cata

    2015-05-01

    Cow manure with bedding is renewable organic biomass available around the year on dairy farms. Developing efficient and cost-effective psychrophilic dry anaerobic digestion (PDAD) processes could contribute to solving farm-related environmental, energy, and manure management problems in cold-climate regions. This study was to increase the organic loading rate (OLR), fed to a novel psychrophilic (20 °C) dry anaerobic digestion of 27% total solid dairy manure (cow feces and wheat straw) in sequence batch reactor (PDAD-SBR), by 133 to 160%. The PDAD-SBR process operated at treatment cycle length of 21 days and OLR of 7.0 and 8.0 g total chemical oxygen demand (TCOD) kg(-1) inoculum day(-1) (5.2 ± 0.1 and 5.8 ± 0.0 g volatile solids (VS) kg(-1) inoculum day(-1)) for four successive cycles (84 days) produced average specific methane yields (SMYs) of 147.1 ± 17.2 and 143.2 ± 11.7 normalized liters (NL) CH4 kg(-1) VS fed, respectively. PDAD of cow feces and wheat straw is possible with VS-based inoculum-to-substrate ratio of 1.45 at OLR of 8.0 g TCOD kg(-1) inoculum day(-1). Hydrolysis was the limiting step reaction. The VS removal averaged around 57.4 ± 0.5 and 60.5 ± 5.7% at OLR 7.0 and 8.0 g TCOD kg(-1) inoculum day(-1), respectively.

  13. Gravimetric enrichment of high lipid and starch accumulating microalgae.

    PubMed

    Hassanpour, Morteza; Abbasabadi, Mahsa; Ebrahimi, Sirous; Hosseini, Maryam; Sheikhbaglou, Ahmad

    2015-11-01

    This study presents gravimetric enrichment of mixed culture to screen starch and lipid producing species separately in a sequencing batch reactor. In the enriched starch-producing mixed culture photobioreactor, the starch content at the end of steady state batch became 3.42 times the beginning of depletion. Whereas in the enriched lipid-producing photobioreactor, the lipid content at the end of steady state batch became 3 times the beginning of famine phase. The obtained results revealed that the gravimetric enrichment is a suitable screening method for specific production of storage compounds in none-sterile large-scaled condition.

  14. A study of psychrophilic organisms isolated from the manufacture and assembly areas of spacecraft to be used in the Viking mission

    NASA Technical Reports Server (NTRS)

    Foster, T. L.

    1974-01-01

    The effect of storage of dry heat treated Teflon ribbons under nitrogen gas followed by high vacuum on the recovery of hardy organisms from the ribbons was studied. A similar experiment was performed on spore crops of hardy organisms recovered previously from Cape Canaveral. Hardy organisms have been inoculated onto slides and subjected to an artificial Martian environment in an attempt to demonstrate their growth in this environment. Additional experiments using the artificial Martian environment include response of soil samples from the VAB with both constant temperature and freeze-thaw cycles. These experiments were performed with dried soil and soil containing added water. Other investigations included the effect of heatshock on soil samples, psychrophilic counts of new soil samples from the manufacture area of the Viking spacecraft, effect of pour plate versus spread plate on psychrophilic counts, and preparation of spore crops of hardy organisms from Cape Canaveral.

  15. Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1

    SciTech Connect

    Fujii, Tomomi; Oikawa, Tadao; Muraoka, Ikuo; Soda, Kenji; Hata, Yasuo

    2007-11-01

    A psychrophilic malate dehydrogenase from the novel Antarctic bacterium F. frigidimaris KUC-1 was crystallized using the hanging-drop vapour-diffusion method. The crystals contained one tetrameric molecule per asymmetric unit. The best crystal diffracted to 1.8 Å resolution. Flavobacterium frigidimaris KUC-1 is a novel psychrotolerant bacterium isolated from Antarctic seawater. Malate dehydrogenase (MDH) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from F. frigidimaris KUC-1. In contrast to the already known dimeric form of MDH from the psychrophile Aquaspirillium arcticum, F. frigidimaris MDH exists as a tetramer. It was crystallized at 288 K by the hanging-drop vapour-diffusion method using ammonium sulfate as the precipitating agent. The crystal diffracted to a maximum resolution of 1.80 Å. It contains one tetrameric molecule in the asymmetric unit.

  16. Identity and physiology of a new psychrophilic eukaryotic green alga, Chlorella sp., strain BI, isolated from a transitory pond near Bratina Island, Antarctica

    USGS Publications Warehouse

    Morgan-Kiss, R. M.; Ivanov, A.G.; Modla, S.; Czymmek, K.; Huner, N.P.A.; Priscu, J.C.; Lisle, J.T.; Hanson, T.E.

    2008-01-01

    Permanently low temperature environments are one of the most abundant microbial habitats on earth. As in most ecosystems, photosynthetic organisms drive primary production in low temperature food webs. Many of these phototrophic microorganisms are psychrophilic; however, functioning of the photosynthetic processes of these enigmatic psychrophiles (the 'photopsychrophiles') in cold environments is not well understood. Here we describe a new chlorophyte isolated from a low temperature pond, on the Ross Ice Shelf near Bratina Island, Antarctica. Phylogenetic and morphological analyses place this strain in the Chlorella clade, and we have named this new chlorophyte Chlorella BI. Chlorella BI is a psychrophilic species, exhibiting optimum temperature for growth at around 10??C. However, psychrophily in the Antarctic Chlorella was not linked to high levels of membrane-associated poly-unsaturated fatty acids. Unlike the model Antarctic lake alga, Chlamydomonas raudensis UWO241, Chlorella BI has retained the ability for dynamic short term adjustment of light energy distribution between photosystem II (PS II) and photosystem I (PS I). In addition, Chlorella BI can grow under a variety of trophic modes, including heterotrophic growth in the dark. Thus, this newly isolated photopsychrophile has retained a higher versatility in response to environmental change than other well studied cold-adapted chlorophytes. ?? 2008 Springer.

  17. American Indian Enrichment Activities. Mini-Review.

    ERIC Educational Resources Information Center

    Kosnick, Sally

    Focusing on American Indians, this annotated bibliography covers a variety of resources for enriching multicultural education in the elementary classroom and includes limited information about Mexican Americans, Blacks, and other cultural groups. Each of the 26 entries provides a descriptive annotation and indicates where the material can be…

  18. Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008.

    PubMed

    Dedysh, Svetlana N; Kulichevskaya, Irina S; Serkebaeva, Yulia M; Mityaeva, Maria A; Sorokin, Vladimir V; Suzina, Natalia E; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe

    2012-03-01

    An aerobic, pink-pigmented, chemo-organotrophic bacterium, designated strain SN10(T), was isolated from a methanotrophic enrichment culture obtained from an acidic Sphagnum peat. This isolate was represented by Gram-negative, non-motile rods that multiply by normal cell division and form rosettes. Strain SN10(T) is an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.2-6.6 (with an optimum at pH 4.7-5.2) and at 6-32 °C (with an optimum at 20-24 °C). The preferred growth substrates are sugars and several heteropolysaccharides of plant and microbial origin, such as pectin, lichenan, fucoidan and gellan gum. While not being capable of growth on C(1) compounds, strain SN10(T) can develop in co-culture with exopolysaccharide-producing methanotrophs by utilization of their capsular material. The major fatty acids determined in strain SN10(T) using the conventional lipid extraction procedure are iso-C(15:0) and C(16:1)ω7c. Upon hydrolysis of total cell material, substantial amounts of the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (isodiabolic acid) were also detected. The polar lipids are two phosphohexoses, phosphatidylethanolamine, phosphatidylglycerol and several phospholipids of unknown structure. The major quinone is MK-8. Pigments are carotenoids. The G+C content of the DNA is 60.7 mol%. Strain SN10(T) forms a separate lineage within subdivision 1 of the phylum Acidobacteria and displays 94.0-95.4% 16S rRNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0-93.7% similarity to members of the genus Terriglobus and 92.2-92.3 % similarity to the type strains of Telmatobacter bradus and Acidobacterium capsulatum. Therefore, strain SN10(T) is classified within a novel genus and species, for which the name Bryocella elongata gen. nov., sp. nov. is proposed. Strain SN10(T) (=LMG 25276(T) =DSM 22489(T)) is the type strain of Bryocella elongata. An emended description of Edaphobacter

  19. Enrichment Activities for Geometry.

    ERIC Educational Resources Information Center

    Usiskin, Zalman

    1983-01-01

    Enrichment activities that teach about geometry as they instruct in geometry are given for some significant topics. The facets of geometry included are tessellations, round robin tournaments, geometric theorems on triangles, and connections between geometry and complex numbers. (MNS)

  20. Characterization of a salt-tolerant family 42 beta-galactosidase from a psychrophilic antarctic Planococcus isolate.

    PubMed

    Sheridan, P P; Brenchley, J E

    2000-06-01

    We isolated a gram-positive, halotolerant psychrophile from a hypersaline pond located on the McMurdo Ice Shelf in Antarctica. A phylogenetic analysis of the 16S rRNA gene sequence of this organism showed that it is a member of the genus Planococcus. This assignment is consistent with the morphology and physiological characteristics of the organism. A gene encoding a beta-galactosidase in this isolate was cloned in an Escherichia coli host. Sequence analysis of this gene placed it in glycosidase family 42 most closely related to an enzyme from Bacillus circulans. Even though an increasing number of family 42 glycosidase sequences are appearing in databases, little information about the biochemical features of these enzymes is available. Therefore, we purified and characterized this enzyme. The purified enzyme did not appear to have any metal requirement, had an optimum pH of 6.5 and an optimum temperature of activity at 42 degrees C, and was irreversibly inactivated within 10 min when it was incubated at 55 degrees C. The enzyme had an apparent K(m) of 4.9 micromol of o-nitrophenyl-beta-D-galactopyranoside, and the V(max) was 467 micromol of o-nitrophenol produced/min/mg of protein at 39 degrees C. Of special interest was the finding that the enzyme remained active at high salt concentrations, which makes it a possible reporter enzyme for halotolerant and halophilic organisms.

  1. Structure prediction of Fe(II) 2-oxoglutarate dioxygenase from a psychrophilic yeast Glaciozyma antarctica PI12

    NASA Astrophysics Data System (ADS)

    Yusof, Nik Yusnoraini; Bakar, Farah Diba Abu; Mahadi, Nor Muhammad; Raih, Mohd Firdaus; Murad, Abdul Munir Abdul

    2015-09-01

    A cDNA encoding Fe(II) 2-oxoglutarate (2OG) dependent dioxygenases was isolated from psychrophilic yeast, Glaciozyma antarctica PI12. We have successfully amplified 1,029 bp cDNA sequence that encodes 342 amino acid with predicted molecular weight 38 kDa. The prediction protein was analysed using various bioinformatics tools to explore the properties of the protein. Based on a BLAST search analysis, the Fe2OX amino acid sequence showed 61% identity to the sequence of oxoglutarate/iron-dependent oxygenase from Rhodosporidium toruloides NP11. SignalP prediction showed that the Fe2OX protein contains no putative signal peptide, which suggests that this enzyme most probably localised intracellularly.The structure of Fe2OX was predicted by homology modelling using MODELLER9v11. The model with the lowest objective function was selected from hundred models generated using MODELLER9v11. Analysis of the structure revealed the longer loop at Fe2OX from G.antarctica that might be responsible for the flexibility of the structure, which contributes to its adaptation to low temperatures. Fe2OX hold a highly conserved Fe(II) binding HXD/E…H triad motif. The binding site for 2-oxoglutarate was found conserved for Arg280 among reported studies, however the Phe268 was found to be different in Fe2OX.

  2. Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4.

    PubMed

    Casillo, Angela; Parrilli, Ermenegilda; Filomena, Sannino; Lindner, Buko; Lanzetta, Rosa; Parrilli, Michelangelo; Tutino, Maria Luisa; Corsaro, Maria Michela

    2015-07-22

    Psychrophilic microorganisms have successfully colonized all permanently cold environments from the deep sea to mountain and polar regions. The ability of an organism to survive and grow in cryoenviroments depends on a number of adaptive strategies aimed at maintaining vital cellular functions at subzero temperatures, which include the structural modifications of the membrane. To understand the role of the membrane in the adaptation, it is necessary to characterize the cell-wall components, such as the lipopolysaccharides, that represent the major constituent of the outer membrane. The aim of this study was to investigate the structure of the carbohydrate backbone of the lipooligosaccharide (LOS) isolated from the cold-adapted Psychrobacter arcticus 273-4. The strain, isolated from a 20,000-to-30,000-year-old continuously frozen permafrost in Siberia, was cultivated at 4 °C. The LOS was isolated from dry cells and analyzed by means of chemical methods. In particular, it was degraded either by mild acid hydrolysis or by hydrazinolysis and investigated in detail by (1)H and (13)C NMR spectroscopy and by ESI FT-ICR mass spectrometry. The oligosaccharide was characterized by the substitution of the heptose residue, usually linked to Kdo in the inner core, with a glucose, and for the unusual presence of N-acetylmuramic acid.

  3. Spectroscopic analyses of manganese ions effects on the conformational changes of inorganic pyrophosphatase from psychrophilic Shewanella sp. AS-11.

    PubMed

    Ginting, Elvy Like; Maeganeku, Chihiro; Motoshima, Hiroyuki; Watanabe, Keiichi

    2014-02-01

    Mn²⁺ ions influence the activity, temperature dependence, and thermostability of the psychrophilic Shewanella-PPase (Sh-PPase), and are required to function in cold environments. The functional characteristics of Sh-PPase on activation with Mn²⁺ ions are possibly related to conformational changes in the molecule. In this study, conformational changes of Sh-PPase on activation with Mn²⁺ ions were analyzed in solution by fluorescence spectroscopy analysis of intrinsic tryptophan residues, 1-anilino-8-naphthalene sulfonate fluorescence, and circular dichroism spectroscopy. For Sh-PPase, Mn²⁺ ions did not affect the flexibility of the tryptophan residues and secondary structure of the enzyme. However, the microenvironment of the tryptophan residues and surface area of Sh-PPase were more hydrophilic on activation with Mn²⁺ ions. These results indicate that activation with Mn²⁺ ions causes conformational changes around the aromatic amino acid residues and affects the hydrophobicity of the enzyme surface, which results in conformational changes. Substrate-induced conformational changes reflect that metal-free Sh-PPase in solution indicated an open structure and will be a close structure when binding substrate. In combination of our spectroscopic analyses on Sh-PPase, it can be concluded that activation with Mn²⁺ ions changes some conformation of Sh-PPase molecule in solution.

  4. Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard.

    PubMed

    Vandieken, Verona; Mussmann, Marc; Niemann, Helge; Jørgensen, Bo Barker

    2006-05-01

    Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed.

  5. Production of cryoprotectant extracellular polysaccharide substances (EPS) by the marine psychrophilic bacterium Colwellia psychrerythraea strain 34H under extreme conditions.

    PubMed

    Marx, Joseph G; Carpenter, Shelly D; Deming, Jody W

    2009-01-01

    Extracellular polysaccharide substances (EPS) play critical roles in microbial ecology, including the colonization of extreme environments in the ocean, from sea ice to the deep sea. After first developing a sugar-free growth medium, we examined the relative effects of temperature, pressure, and salinity on EPS production (on a per cell basis) by the obligately marine and psychrophilic gamma-proteobacterium, Colwellia psychrerythraea strain 34H. Over growth-permissive temperatures of approximately 10 to -4 degrees C, EPS production did not change, but from -8 to -14 degrees C when samples froze, EPS production rose dramatically. Similarly, at growth-permissive hydrostatic pressures of 1-200 atm (1 atm = 101.325 kPa) (at -1 and 8 degrees C), EPS production was unchanged, but at higher pressures of 400 and 600 atm EPS production rose markedly. In salinity tests at 10-100 parts per million (and -1 and 5 degrees C), EPS production increased at the freshest salinity tested. Extreme environmental conditions thus appear to stimulate EPS production by this strain. Furthermore, strain 34H recovered best from deep-freezing to -80 degrees C (not found for Earthly environments) if first supplemented with a preparation of its own EPS, rather than other cryoprotectants like glycerol, suggesting EPS production as both a survival strategy and source of compounds with potentially novel properties for biotechnological and other applications.

  6. In silico analysis of β-1,3-glucanase from a psychrophilic yeast, Glaciozyma antarctica PI12

    NASA Astrophysics Data System (ADS)

    Mohammadi, Salimeh; Bakar, Farah Diba Abu; Rabu, Amir; Murad, Abdul Munir Abdul

    2014-09-01

    1,3-beta-glucanase is an industrially important enzyme having wide range of applications especially in food industry. It is crucial to gain an understanding about the structure and functional aspects of various beta-1,3-glucanase produced from diverse sources. In this, study a cDNA encoding β-1,3-glucanase (GaExg55) was isolated from a psychrophilic yeast, Glaciozyma antarctica PI12. The cDNA sequence has been submitted to Genbank with an accession number (KJ436377). Subsequently, the perdition protein was analyzed using various bioinformatics tools to explore the properties of the protein. GaEXG55 is consisting of 1,440-bp nucleotides encoding 480 amino acid residues. Alignment of the deduced amino acid for GaExg55 with other exo-β-1,3-glucanase available at the NCBI database indicate that deduced amino acids shared a consensus motif NEP, which is signature pattern of GH5 hydrolases. Predicted molecular weight of GaExg55 is 53.66 kDa. GaExg55 sequences possesses signal peptide sequence and it is highly conserved with other fungal exo-beta-1,3 glucanase.

  7. 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

  8. Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4

    PubMed Central

    Casillo, Angela; Parrilli, Ermenegilda; Filomena, Sannino; Lindner, Buko; Lanzetta, Rosa; Parrilli, Michelangelo; Tutino, Maria Luisa; Corsaro, Maria Michela

    2015-01-01

    Psychrophilic microorganisms have successfully colonized all permanently cold environments from the deep sea to mountain and polar regions. The ability of an organism to survive and grow in cryoenviroments depends on a number of adaptive strategies aimed at maintaining vital cellular functions at subzero temperatures, which include the structural modifications of the membrane. To understand the role of the membrane in the adaptation, it is necessary to characterize the cell-wall components, such as the lipopolysaccharides, that represent the major constituent of the outer membrane. The aim of this study was to investigate the structure of the carbohydrate backbone of the lipooligosaccharide (LOS) isolated from the cold-adapted Psychrobacter arcticus 273-4. The strain, isolated from a 20,000-to-30,000-year-old continuously frozen permafrost in Siberia, was cultivated at 4 °C. The LOS was isolated from dry cells and analyzed by means of chemical methods. In particular, it was degraded either by mild acid hydrolysis or by hydrazinolysis and investigated in detail by 1H and 13C NMR spectroscopy and by ESI FT-ICR mass spectrometry. The oligosaccharide was characterized by the substitution of the heptose residue, usually linked to Kdo in the inner core, with a glucose, and for the unusual presence of N-acetylmuramic acid. PMID:26204948

  9. Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO2-Enriched Anoxic Atmospheres

    PubMed Central

    Ulrich, Richard; Berry, Bonnie J.; Nicholson, Wayne L.

    2013-01-01

    Abstract Twenty-six strains of 22 bacterial species were tested for growth on trypticase soy agar (TSA) or sea-salt agar (SSA) under hypobaric, psychrophilic, and anoxic conditions applied singly or in combination. As each factor was added to multi-parameter assays, the interactive stresses decreased the numbers of strains capable of growth and, in general, reduced the vigor of the strains observed to grow. Only Serratia liquefaciens strain ATCC 27592 exhibited growth at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres. To discriminate between the effects of desiccation and hypobaria, vegetative cells of Bacillus subtilis strain 168 and Escherichia coli strain K12 were grown on TSA surfaces and simultaneously in liquid Luria-Bertani (LB) broth media. Inhibition of growth under hypobaria for 168 and K12 decreased in similar ways for both TSA and LB assays as pressures were reduced from 100 to 25 mbar. Results for 168 and K12 on TSA and LB are interpreted to indicate a direct low-pressure effect on microbial growth with both species and do not support the hypothesis that desiccation alone on TSA was the cause of reduced growth at low pressures. The growth of S. liquefaciens at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres was surprising since S. liquefaciens is ecologically a generalist that occurs in terrestrial plant, fish, animal, and food niches. In contrast, two extremophiles tested in the assays, Deinococcus radiodurans strain R1 and Psychrobacter cryohalolentis strain K5, failed to grow under hypobaric (25 mbar; R1 only), psychrophilic (0°C; R1 only), or anoxic (<0.1% ppO2; both species) conditions. Key Words: Habitable zone—Hypobaria—Extremophiles—Special regions—Planetary protection. Astrobiology 13, 115–131. PMID:23289858

  10. Laser and gas centrifuge enrichment

    SciTech Connect

    Heinonen, Olli

    2014-05-09

    Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

  11. A Cultural Classroom Library

    ERIC Educational Resources Information Center

    Lawrence, Maria

    2007-01-01

    Native American and other cultural stories provide students with a broader perspective on the world. In addition, cultural stories connect science content and knowledge about the world to cultural interpretations and people's life ways. By implementing the ideas suggested in this article, you can select books that both enrich your science library…

  12. The Characterization of Psychrophilic Microorganisms and their potentially useful Cold-Active Glycosidases Final Progress Report

    SciTech Connect

    Brenchly, Jean E.

    2008-06-30

    Our studies of novel, cold-loving microorganisms have focused on two distinct extreme environments. The first is an ice core sample from a 120,000 year old Greenland glacier. The results of this study are particularly exciting and have been highlighted with press releases and additional coverage. The first press release in 2004 was based on our presentation at the General Meeting of the American Society for Microbiology and was augmented by coverage of our publication (Appl. Environ. Microbiol. 2005. Vol. 71:7806) in the Current Topics section of the ASM news journal, “Microbe.” Of special interest for this report was the isolation of numerous, phylogenetically distinct and potentially novel ultrasmall microorganisms. The detection and isolation of members of the ultrasmall population is significant because these cells pass through 0.2 micron pore filters that are generally used to trap microorganisms from environmental samples. Thus, analyses by other investigators that examined only cells captured on the filters would have missed a significant portion of this population. Only a few ultrasmall isolates had been obtained prior to our examination of the ice core samples. Our development of a filtration enrichment and subsequent cultivation of these organisms has added extensively to the collection of, and knowledge about, this important population in the microbial world.

  13. Capture of Arginine at Low Concentrations by a Marine Psychrophilic Bacterium †

    PubMed Central

    Geesey, Gill G.; Morita, Richard Y.

    1979-01-01

    The cells of the marine bacterium Ant-300 were found to take up arginine when this substrate was at low concentrations. The cells possessed an uptake system(s) that specifically transported l-arginine. The kinetic parameters for uptake appeared to differ when the cells were exposed to nanomolar and micromolar concentrations of the amino acid. Uptake over this concentration range functioned in the absence of an exogenous energy source, even after the cells had been preincubated in unsupplemented artificial seawater. Respiratory activity appeared to be a more important driving force for arginine uptake than adenosine 5′-triphosphate hydrolysis. The cells also exhibited chemotaxis toward l-arginine. The minimum arginine concentration needed to elicit a chemotactic response was between 10−5 and 10−6 M. It is proposed that the capture of arginine by cells of Ant-300 in nutrient-depleted waters, which are typical of the open ocean, proceeds via high-affinity active transport, whereas in substrate-enriched seawater, capture involves chemotaxis and an active transport mechanism with reduced affinity for the substrate. PMID:16345475

  14. Science Student Enrichment Opportunities.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Sacramento.

    This document was developed with the intention of increasing California public school students' awareness of and participation in science-related enrichment activities. Some of the activities are intended for participation by individuals, while others are meant for teams of students. These annual events are listed in chronological order for a…

  15. Enriching the Catalog

    ERIC Educational Resources Information Center

    Tennant, Roy

    2004-01-01

    After decades of costly and time-consuming effort, nearly all libraries have completed the retrospective conversion of their card catalogs to electronic form. However, bibliographic systems still are really not much more than card catalogs on wheels. Enriched content that Amazon.com takes for granted--such as digitized tables of contents, cover…

  16. Biodegradation of lindane, methyl parathion and carbofuran by various enriched bacterial isolates.

    PubMed

    Krishna, K Rama; Philip, Ligy

    2008-02-01

    In the present study, lindane (1,2,3,4,5,6-hexachlorocyclohexane), methyl parathion (O-dimethylO-(4-nitro-phenyl) phosphorothioate) and carbofuran (2,3-dihydro-2,2-dimethyl-7-benzofuranyl methylcarbamate) degradation potential of different enriched bacterial cultures were evaluated under various environmental conditions. Enriched cultures behaved differently with different pesticides. Degradation was more in a facultative anaerobic condition as compared to that in aerobic condition. A specific pesticide enriched culture showed maximum degradation of that pesticide irrespective of pesticides and environmental conditions. Lindane and endosulfan enriched cultures behaved almost similarly. Degradation of lindane by lindane enriched cultures was 75 +/- 3% in aerobic co-metabolic process whereas 78 +/- 5% of lindane degradation occurred in anaerobic co-metabolic process. Degradation of methyl parathion by methyl parathion enriched culture was 87 +/- 1% in facultative anaerobic condition. In almost all the cases, many intermediate metabolites were observed. However, many of these metabolites disappeared after 4-6 weeks of incubation. Mixed pesticide-enriched culture degraded all the three pesticides more effectively as compared to specific pesticide- enriched cultures. It can be inferred from the results that a bacterial consortium enriched with a mixture of all the possible pesticides that are present in the site seems to be a better option for the effective bioremediation of multi-pesticide contaminated site.

  17. Expression and characterization of a recombinant psychrophilic Cu/Zn superoxide dismutase from Deschampsia antarctica E. Desv. [Poaceae].

    PubMed

    Rojas-Contreras, Juan A; de la Rosa, Ana P Barba; De León-Rodríguez, Antonio

    2015-04-01

    We present here the structural modeling and biochemical characterization of a recombinant superoxide dismutase (SOD) from Deschampsia antarctica E. Desv. [Poaceae] produced in Escherichia coli. The recombinant protein was purified by affinity chromatography nickel-nitrilotriacetic acid (Ni-NTA), and its identity was demonstrated by immunoblotting and inhibition by H2O2 and KCN. Inductively coupled plasma optical emission spectroscopy (ICP-OES) analysis confirmed the presence of Cu and Zn. Modeling of the D. antarctica Cu/Zn-SOD (DaSOD) amino acid sequence using the SWISS-MODEL and 2Q2L_B monomer of the psychrophilic Cu/Zu-SOD from Potentilla atrosanguinea (PaSOD) as template produced a structure similar to that of the typical eukaryotic Cu/Zn-SODs. Activity assays using the p-nitro blue tetrazolium chloride (NBT) solution method showed that the purified DaSOD had a specific activity of 5818 U/mg at 25 °C and pH 7.2 and that it was active in a pH interval of 5-8 and a temperature interval of 0-40 °C. Furthermore, DaSOD was still active at -20 °C as observed by a zymogram assay. We found 100 % activity when it was heated at 80 °C for 60 min, indicating a high thermostability. DaSOD properties suggest that this enzyme could be useful for preventing the oxidation of refrigerated or frozen foods, as well as in the preparation of cosmetic and pharmaceutical products.

  18. The Antarctic Psychrophile Chlamydomonas sp. UWO 241 Preferentially Phosphorylates a Photosystem I-Cytochrome b6/f Supercomplex.

    PubMed

    Szyszka-Mroz, Beth; Pittock, Paula; Ivanov, Alexander G; Lajoie, Gilles; Hüner, Norman P A

    2015-09-01

    Chlamydomonas sp. UWO 241 (UWO 241) is a psychrophilic green alga isolated from Antarctica. A unique characteristic of this algal strain is its inability to undergo state transitions coupled with the absence of photosystem II (PSII) light-harvesting complex protein phosphorylation. We show that UWO 241 preferentially phosphorylates specific polypeptides associated with an approximately 1,000-kD pigment-protein supercomplex that contains components of both photosystem I (PSI) and the cytochrome b₆/f (Cyt b₆/f) complex. Liquid chromatography nano-tandem mass spectrometry was used to identify three major phosphorylated proteins associated with this PSI-Cyt b₆/f supercomplex, two 17-kD PSII subunit P-like proteins and a 70-kD ATP-dependent zinc metalloprotease, FtsH. The PSII subunit P-like protein sequence exhibited 70.6% similarity to the authentic PSII subunit P protein associated with the oxygen-evolving complex of PSII in Chlamydomonas reinhardtii. Tyrosine-146 was identified as a unique phosphorylation site on the UWO 241 PSII subunit P-like polypeptide. Assessment of PSI cyclic electron transport by in vivo P700 photooxidation and the dark relaxation kinetics of P700(+) indicated that UWO 241 exhibited PSI cyclic electron transport rates that were 3 times faster and more sensitive to antimycin A than the mesophile control, Chlamydomonas raudensis SAG 49.72. The stability of the PSI-Cyt b₆/f supercomplex was dependent upon the phosphorylation status of the PsbP-like protein and the zinc metalloprotease FtsH as well as the presence of high salt. We suggest that adaptation of UWO 241 to its unique low-temperature and high-salt environment favors the phosphorylation of a PSI-Cyt b₆/f supercomplex to regulate PSI cyclic electron transport rather than the regulation of state transitions through the phosphorylation of PSII light-harvesting complex proteins.

  19. Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat

    PubMed Central

    Baker, Jennifer M.; Riester, Carli J.; Skinner, Blair M.; Newell, Austin W.; Swingley, Wesley D.; Madigan, Michael T.; Jung, Deborah O.; Asao, Marie; Chen, Min; Loughlin, Patrick C.; Pan, Hao; Lin, Yuankui; Li, Yaqiong; Shaw, Jacob; Prado, Mindy; Sherman, Chris; Tang, Joseph Kuo-Hsiang; Blankenship, Robert E.; Zhao, Tingting; Touchman, Jeffrey W.; Sattley, W. Matthew

    2017-01-01

    Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment. PMID:28230808

  20. Motif enrichment tool.

    PubMed

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/.

  1. Evolution of Arginine Biosynthesis in the Bacterial Domain: Novel Gene-Enzyme Relationships from Psychrophilic Moritella Strains (Vibrionaceae) and Evolutionary Significance of N-α-Acetyl Ornithinase

    PubMed Central

    Xu, Ying; Liang, Ziyuan; Legrain, Christianne; Rüger, Hans J.; Glansdorff, Nicolas

    2000-01-01

    In the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of N-α-acetylornithine to glutamate (ornithine acetyltransferase [OATase]) (argJ encoded). Only two exceptions had been reported—the Enterobacteriaceae and Myxococcus xanthus (members of the γ and δ groups of the class Proteobacteria, respectively)—in which ornithine is produced from N-α-acetylornithine by a deacylase, acetylornithinase (AOase) (argE encoded). We have investigated the gene-enzyme relationship in the arginine regulons of two psychrophilic Moritella strains belonging to the Vibrionaceae, a family phylogenetically related to the Enterobacteriaceae. Most of the arg genes were found to be clustered in one continuous sequence divergently transcribed in two wings, argE and argCBFGH(A) [“H(A)” indicates that the argininosuccinase gene consists of a part homologous to known argH sequences and of a 3′ extension able to complement an Escherichia coli mutant deficient in the argA gene, encoding N-α-acetylglutamate synthetase, the first enzyme committed to the pathway]. Phylogenetic evidence suggests that this new clustering pattern arose in an ancestor common to Vibrionaceae and Enterobacteriaceae, where OATase was lost and replaced by a deacylase. The AOase and ornithine carbamoyltransferase of these psychrophilic strains both display distinctly cold-adapted activity profiles, providing the first cold-active examples of such enzymes. PMID:10692366

  2. Chromatin enrichment for proteomics

    PubMed Central

    Kustatscher, Georg; Wills, Karen L. H.; Furlan, Cristina; Rappsilber, Juri

    2015-01-01

    During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a simple biochemical procedure that enriches interphase chromatin in all its complexity. It enables researchers to take a ‘snapshot’ of chromatin and to isolate and identify even transiently bound factors. In ChEP, cells are fixed with formaldehyde; subsequently, DNA together with all cross-linked proteins is isolated by centrifugation under denaturing conditions. This approach enables the analysis of global chromatin composition and its changes, which is in contrast with existing chromatin enrichment procedures, which either focus on specific chromatin loci (e.g., affinity purification) or are limited in specificity, such as the analysis of the chromatin pellet (i.e., analysis of all insoluble nuclear material). ChEP takes half a day to complete and requires no specialized laboratory skills or equipment. ChEP enables the characterization of chromatin response to drug treatment or physiological processes. Beyond proteomics, ChEP may preclear chromatin for chromatin immunoprecipitation (ChIP) analyses. PMID:25101823

  3. Draft genome sequence of Paenisporosarcina sp. strain TG-14, a psychrophilic bacterium isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica.

    PubMed

    Koh, Hye Yeon; Lee, Sung Gu; Lee, Jun Hyuck; Doyle, Shawn; Christner, Brent C; Kim, Hak Jun

    2012-12-01

    The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments.

  4. Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica

    PubMed Central

    Koh, Hye Yeon; Lee, Sung Gu; Lee, Jun Hyuck; Doyle, Shawn; Christner, Brent C.

    2012-01-01

    The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments. PMID:23144403

  5. [Comparative studies of methods of salmonella enrichment (author's transl)].

    PubMed

    Pietzsch, O; Kretschmer, F J; Bulling, E

    1975-07-01

    Eight different methods of salmonella enrichment were compared in two series of experiments involving 100 samples of whole-egg powder and 80 samples of frozen whole liquid egg, respectively. 66 out of a total of 100 samples of whole-egg powder had been artificially infected with varying numbers of S. typhi-murium; 60 out of 80 samples of frozen whole liquid egg were found to be naturally infected with various salmonella species. 3 of the 8 methods (Table 1) were compared within an international collaborative study with 14 laboratories in 11 countries participating. A reduction of the pre-enrichment period from 18 to 6 hours and of volumes used in pre-enrichment and selective enrichment from 10 and 100 ml, respectively to 1 and 10 ml, respectively were found to have adverse influence upon the result of isolations, in particular in the case of weakly infected samples. In contrast, extended incubation over 48 hours as well as preparation of two sub-cultures on solid selective media following incubation of enrichment cultures over 18-24 hours and 42-48 hours, respectively always resulted in a certain increase of salmonella yield which, however, exhibited gradual differences for the individual methods examined. Preparation of a 2nd sub-culture meant, in particular, a decisive improvement of the result of isolations from artificially infected samples if selenite-cystine enrichment volumes were 10 and 100 ml, respectively. The best results could be obtained by means of the following methods of enrichment: Pre-enrichment of material in buffered peptone water at 37 degrees C over 18 hours; pipetting of 10 ml inoculated and incubated pre-enriched material into 100 ml selenite-cystine or tetrathionate enrichment medium according to MULLER-KAUFFMANN; onward incubation of the enrichment culture at 43 degrees C over 48 hours; and preparation of sub-cultures on solid selective media after 24 and 48 hours. The method using tetrathionate enrichment medium was found to be most

  6. Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix.

    PubMed

    Srinivas, T N R; Prasad, S; Manasa, P; Sailaja, B; Begum, Z; Shivaji, S

    2013-02-01

    A novel gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9a(T), was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9a(T) was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C(15 : 1) G (21.8 %), anteiso-C(15 : 0) (19.1 %), anteiso-C(15 : 1) A (18.6 %), iso-C(15 : 0) (13.8 %) and iso-C(16 : 1) H (6.4 %). Strain E4-9a(T) contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9a(T) were Lacinutrix copepodicola, L. algicola and L. mariniflava, with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9a(T) clustered with the type strain of L. copepodicola and with those of L. algicola and L. mariniflava at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA-DNA hybridization with L. copepodicola DJ3(T) showed 59 % relatedness with respect to strain E4-9a(T). The DNA G+C content of strain E4-9a(T) was 29 mol%. Based on the results of DNA-DNA hybridization and phenotypic data, it appears that strain E4-9a(T) represents a novel species of the genus Lacinutrix, for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9a(T) ( = CIP 110310(T)  = KCTC 23612(T)).

  7. Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.

    PubMed

    Dong, Danghong; Ihara, Tokuo; Motoshima, Hiroyuki; Watanabe, Keiichi

    2005-03-01

    The psychrophilic alkaline serine protease Apa1 secreted by the Antarctic psychrotroph Pseudoalteromonas sp. strain AS-11 consists of a subtilisin-like region (293 residues) and an additional insert region (148 residues) that does not show a sequence homology to any proteins in the RCSB Protein Data Bank. Apa1 inhibited with phenylmethanesulfonyl fluoride has been crystallized and X-ray diffraction data have been collected to 1.78 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 122.94, b = 138.48, c = 64.77 A, alpha = gamma = 90, beta = 97.5 degrees. A molecular-replacement solution has been found using the structure of the mesophilic counterpart subtilisin DY with 38% sequence identity to the catalytic domain of Apa1 as a search model. This is the first crystallographic study of a cold-adapted subtilisin-like protease.

  8. Thermal breeder fuel enrichment zoning

    DOEpatents

    Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

    1992-01-01

    A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

  9. Advanced Neutron Source enrichment study

    SciTech Connect

    Bari, R.A.; Ludewig, H.; Weeks, J.R.

    1994-12-31

    A study has been performed of the impact on performance of using low enriched uranium (20% {sup 235}U) or medium enriched uranium (35% {sup 235}U) as an alternative fuel for the Advanced Neutron Source, which is currently designed to use uranium enriched to 93% {sup 235}U. Higher fuel densities and larger volume cores were evaluated at the lower enrichments in terms of impact on neutron flux, safety, safeguards, technical feasibility, and cost. The feasibility of fabricating uranium silicide fuel at increasing material density was specifically addressed by a panel of international experts on research reactor fuels. The most viable alternative designs for the reactor at lower enrichments were identified and discussed. Several sensitivity analyses were performed to gain an understanding of the performance of the reactor at parametric values of power, fuel density, core volume, and enrichment that were interpolations between the boundary values imposed on the study or extrapolations from known technology.

  10. Characterization and comparative analysis of psychrophilic and mesophilic alpha-amylases from Euplotes species: a contribution to the understanding of enzyme thermal adaptation.

    PubMed

    Yang, Guang; Yang, Guang; Aprile, Lino; Turturo, Vincenzo; Pucciarelli, Sandra; Pucciarelli, Stefania; Miceli, Cristina

    2013-09-06

    The eukaryotic α-amylase isolated from the psychrophilic ciliated protozoon Euplotes focardii (EfAmy) was expressed in Escherichia coli and biochemically characterized. Its enzymatic activity was compared to that of the homologous protein from the mesophilic congeneric species Euplotes crassus (EcAmy). The comparison of the amino acid composition and the surface residue composition of the two enzymes indicated a preference for tiny residues and the avoidance of charged, aromatic and hydrophobic residues in EfAmy. Our comparative homology modeling study reveals a lack of surface salt bridges, a decreased number of the surface charged residues, decreased hydrogen bonds and bound ions, and a reduction of aromatic-sulfur interactions, cationic-π interactions and disulfide interactions in EfAmy. In contrast, sequence alignment and homology modeling showed five unconserved prolines located on the surface loops of EcAmy. By analyzing amylolytic activity towards soluble starch as the substrate, we determined the temperature and pH dependence, thermostability and kinetic parameters of these two enzymes. We demonstrated that EfAmy shows the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at low temperatures and high thermolability. In contrast, the EcAmy showed mesophilic characteristics with the highest activity at moderate temperatures and a more than 2-fold increased half-life at 50°C compared to EfAmy. The kcat and KM values of EfAmy were higher than those of the mesophilic EcAmy at all tested temperatures. Furthermore, both EfAmy and EcAmy showed maximum activities at pH 9 and maintained high activities in the presence of surfactants. These results suggest the potential applications of EfAmy and EcAmy as ingredients in detergents for industrial applications.

  11. 16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM ...

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

    16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM RECOVERY PROCESSED RELATIVELY PURE MATERIALS AND SOLUTIONS AND SOLID RESIDUES WITH RELATIVELY LOW URANIUM CONTENT. URANIUM RECOVERY INVOLVED BOTH SLOW AND FAST PROCESSES. (4/4/66) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO

  12. Fostering Earth Science Inquiry From Within a Native Hawaiian Cultural Framework In O`ahu (Hawai`i) Through A Multidisciplinary Place-Based High School Summer Enrichment Program

    NASA Astrophysics Data System (ADS)

    Moxey, L.; Dias, R.; Legaspi, E.

    2010-12-01

    During the summer of 2010, twenty-five public high school students from underrepresented communities and ethnicities (Hawaiian, part-Hawaiian, Sāmoan, Filipino, Pacific Islander) in O`ahu (Hawai`i) participated in the Mālama Ke Ahupua`a (protecting our watershed) program. This rigorous three-week hands-on, place-based multidisciplinary program provided students with the opportunity of visiting the Mānoa Valley watershed (O`ahu, Hawaii) for learning and experiencing the Earth Science System dynamics that comprises it, while simultaneously exploring the significance of the ahupua`a (watershed) as related to native Hawaiian history and culture. While earning Hawaii DOE-approved academic credit, students utilized GPS/GIS technology, quantitative water quality testing equipment, and environmental monitoring tools for performing a watershed survey and water quality study of Mānoa Stream (Mānoa Valley) from its inception in the mountains, its advance through Honolulu’s urbanized areas, and its convergence with the Pacific Ocean. Through this hands-on field-based study, students documented changes in the watershed’s environment as reflected in declining water quality induced by anthropogenic pollution sources and urbanization. Students also visited relevant native Hawaiian cultural sites in Mānoa, and explored their direct links with the historical sustainable usage of the watershed’s natural resources, both from a cultural and science-based perspective. Finally, traditional wa`a (native Hawaiian outrigger canoes) were used as both cultural resources for discussing ancient Polynesian exploration, as well as scientific research platforms for conducting near-shore reef surveys & assessments. This program served to promote not only Earth Science literacy and STEM skills, but also contributed to further environmental stewardship while fostering native Hawaiian & Polynesian cultural identities.

  13. Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils.

    PubMed

    França, Luís; Sannino, Ciro; Turchetti, Benedetta; Buzzini, Pietro; Margesin, Rosa

    2016-11-01

    The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545-2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.

  14. Successful enrichment of the ubiquitous freshwater acI Actinobacteria.

    PubMed

    Garcia, Sarahi L; McMahon, Katherine D; Grossart, Hans-Peter; Warnecke, Falk

    2014-02-01

    Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for > 50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acI Actinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.

  15. New generation enrichment monitoring technology for gas centrifuge enrichment plants

    SciTech Connect

    Ianakiev, Kiril D; Alexandrov, Boian S.; Boyer, Brian D.; Hill, Thomas R.; Macarthur, Duncan W.; Marks, Thomas; Moss, Calvin E.; Sheppard, Gregory A.; Swinhoe, Martyn T.

    2008-06-13

    The continuous enrichment monitor, developed and fielded in the 1990s by the International Atomic Energy Agency, provided a go-no-go capability to distinguish between UF{sub 6} containing low enriched (approximately 4% {sup 235}U) and highly enriched (above 20% {sup 235}U) uranium. This instrument used the 22-keV line from a {sup 109}Cd source as a transmission source to achieve a high sensitivity to the UF{sub 6} gas absorption. The 1.27-yr half-life required that the source be periodically replaced and the instrument recalibrated. The instrument's functionality and accuracy were limited by the fact that measured gas density and gas pressure were treated as confidential facility information. The modern safeguarding of a gas centrifuge enrichment plant producing low-enriched UF{sub 6} product aims toward a more quantitative flow and enrichment monitoring concept that sets new standards for accuracy stability, and confidence. An instrument must be accurate enough to detect the diversion of a significant quantity of material, have virtually zero false alarms, and protect the operator's proprietary process information. We discuss a new concept for advanced gas enrichment assay measurement technology. This design concept eliminates the need for the periodic replacement of a radioactive source as well as the need for maintenance by experts. Some initial experimental results will be presented.

  16. Hydrogen-enriched fuels

    SciTech Connect

    Roser, R.

    1998-08-01

    NRG Technologies, Inc. is attempting to develop hardware and infrastructure that will allow mixtures of hydrogen and conventional fuels to become viable alternatives to conventional fuels alone. This commercialization can be successful if the authors are able to achieve exhaust emission levels of less than 0.03 g/kw-hr NOx and CO; and 0.15 g/kw-hr NMHC at full engine power without the use of exhaust catalysts. The major barriers to achieving these goals are that the lean burn regimes required to meet exhaust emissions goals reduce engine output substantially and tend to exhibit higher-than-normal total hydrocarbon emissions. Also, hydrogen addition to conventional fuels increases fuel cost, and reduces both vehicle range and engine output power. Maintaining low emissions during transient driving cycles has not been demonstrated. A three year test plan has been developed to perform the investigations into the issues described above. During this initial year of funding research has progressed in the following areas: (a) a cost effective single-cylinder research platform was constructed; (b) exhaust gas speciation was performed to characterize the nature of hydrocarbon emissions from hydrogen-enriched natural gas fuels; (c) three H{sub 2}/CH{sub 4} fuel compositions were analyzed using spark timing and equivalence ratio sweeping procedures and finally; (d) a full size pick-up truck platform was converted to run on HCNG fuels. The testing performed in year one of the three year plan represents a baseline from which to assess options for overcoming the stated barriers to success.

  17. Communities of purple sulfur bacteria in a Baltic Sea coastal lagoon analyzed by puf LM gene libraries and the impact of temperature and NaCl concentration in experimental enrichment cultures.

    PubMed

    Tank, Marcus; Blümel, Martina; Imhoff, Johannes F

    2011-12-01

    Shallow coastal waters, where phototrophic purple sulfur bacteria (PSB) regularly form massive blooms, are subjected to massive diurnal and event-driven changes of physicochemical conditions including temperature and salinity. To analyze the ability of PSB to cope with these environmental factors and to compete in complex communities we have studied changes of the environmental community of PSB of a Baltic Sea lagoon under experimental enrichment conditions with controlled variation of temperature and NaCl concentration. For the first time, changes within a community of PSB were specifically analyzed using the photosynthetic reaction center genes pufL and M by RFLP and cloning experiments. The most abundant PSB phylotypes in the habitat were found along the NaCl gradient from freshwater conditions up to 7.5% NaCl. They were accompanied by smaller numbers of purple nonsulfur bacteria and aerobic anoxygenic phototrophic bacteria. Major components of the PSB community of the brackish lagoon were affiliated to PSB genera and species known as marine, halophilic or salt-tolerant, including species of M arichromatium, H alochromatium, T hiorhodococcus, A llochromatium, T hiocapsa, T hiorhodovibrio, and T hiohalocapsa. A dramatic shift occurred at elevated temperatures of 41 and 44°C when M arichromatium gracile became most prominent which was not detected at lower temperatures.

  18. Environmental enrichment for aquatic animals.

    PubMed

    Corcoran, Mike

    2015-05-01

    Aquatic animals are the most popular pets in the United States based on the number of owned pets. They are popular display animals and are increasingly used in research settings. Enrichment of captive animals is an important element of zoo and laboratory medicine. The importance of enrichment for aquatic animals has been slower in implementation. For a long time, there was debate over whether or not fish were able to experience pain or form long-term memories. As that debate has reduced and the consciousness of more aquatic animals is accepted, the need to discuss enrichment for these animals has increased.

  19. A Field-Suitable, Semisolid Aerobic Enrichment Medium for Isolation of Campylobacter jejuni in Small Numbers

    PubMed Central

    Jeffrey, J. S.; Hunter, A.; Atwill, E. R.

    2000-01-01

    The objective of this study was to produce an economical, easy to prepare, field-suitable enrichment medium for detection of Campylobacter jejuni in small numbers. A semisolid aerobic enrichment medium was developed. Rates of recovery from inoculated medium, sterile swabs, and mixed cultures of C. jejuni and coliform bacteria were tested. PMID:10747165

  20. Enrichment, amplification, and sequence-based typing of Salmonella enterica and other foodborne pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Detection and characterization of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture; this is ideally followed by strain typing which provides information critical to outbreak and source investigations. Pulsed-field gel e...

  1. Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

    PubMed Central

    Mühling, Martin; Poehlein, Anja; Stuhr, Anna; Voitel, Matthias; Daniel, Rolf; Schlömann, Michael

    2016-01-01

    Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus “Ferrovum” and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of “Ferrovum” and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis. PMID:28066396

  2. Enrichment and terminal differentiation of striated muscle progenitors in vitro

    SciTech Connect

    Becher, Ulrich M.; Breitbach, Martin; Sasse, Philipp; Garbe, Stephan; Ven, Peter F.M. van der; Fuerst, Dieter O.; Fleischmann, Bernd K.

    2009-10-01

    Enrichment and terminal differentiation of mammalian striated muscle cells is severely hampered by fibroblast overgrowth, de-differentiation and/or lack of functional differentiation. Herein we report a new, reproducible and simple method to enrich and terminally differentiate muscle stem cells and progenitors from mice and humans. We show that a single gamma irradiation of muscle cells induces their massive differentiation into structurally and functionally intact myotubes and cardiomyocytes and that these cells can be kept in culture for many weeks. Similar results are also obtained when treating skeletal muscle-derived stem cells and progenitors with Mitomycin C.

  3. Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica).

    PubMed

    Dziewit, Lukasz; Grzesiak, Jakub; Ciok, Anna; Nieckarz, Marta; Zdanowski, Marek K; Bartosik, Dariusz

    2013-09-01

    Pseudomonas sp. GLE121 (a psychrophilic Antarctic strain) carries three plasmids: pGLE121P1 (6899 bp), pGLE121P2 (8330 bp) and pGLE121P3 (39,583 bp). Plasmids pGLE121P1 and pGLE121P2 show significant sequence similarity to members of the IncP-9 and IncP-7 incompatibility groups, respectively, while the largest replicon, pGLE121P3, is highly related to plasmid pNCPPB880-40 of Pseudomonas syringae pathovar tomato NCPPB880. All three plasmids have a narrow host range, limited to members of the genus Pseudomonas. Plasmid pGLE121P3 encodes a conjugal transfer system, while pGLE121P1 carries only a putative MOB module, conserved in many mobilizable plasmids. Plasmid pGLE121P3 contains an additional load of genetic information, including a pair of genes with homology to the rulAB operon, responsible for ultraviolet radiation (UVR) tolerance. Given the increasing UV exposure in Antarctic regions, the expression of these genes is likely to be an important adaptive response.

  4. Transcriptome-wide analysis of DEAD-box RNA helicase gene family in an Antarctic psychrophilic alga Chlamydomonas sp. ICE-L.

    PubMed

    Liu, Chenlin; Huang, Xiaohang

    2015-09-01

    DEAD-box RNA helicase family proteins have been identified in almost all living organisms. Some of them play a crucial role in adaptation to environmental changes and stress response, especially in the low-temperature acclimation in different kinds of organisms. Compared with the full swing study in plants and bacteria, the characters and functions of DEAD-box family proteins had not been surveyed in algae. To identify genes critical for freezing acclimation in algae, we screened DEAD-box RNA helicase genes from the transcriptome sequences of a psychrophilic microalga Chlamydomonas sp. ICE-L which was isolated from Antarctic sea ice. Totally 39 DEAD-box RNA helicase genes had been identified. Most of the DEAD-box RNA helicase have 1:1 homologous relationships in Chlamydomonas reinhardtii and Chlamydomonas sp. ICE-L with several exceptions. The homologous proteins in ICE-L to the helicases critical for cold or freezing tolerance in Arabidopsis thaliana had been identified based on phylogenetic comparison studies. The response of these helicase genes is not always identical in the Chlamydomonas sp. ICE-L and Arabidopsis under the same low-temperature treatment. The expression of several DEAD-box RNA helicase genes including CiRH5, CiRH25, CiRH28, and CiRH55 were significantly up-regulated under freezing treatment of ICE-L and their function in freezing acclimation of ICE-L deserved further investigation.

  5. Impact of organic loading rate on the performance of psychrophilic dry anaerobic digestion of dairy manure and wheat straw: long-term operation.

    PubMed

    Saady, Noori M Cata; Massé, Daniel I

    2015-04-01

    Development of efficient processes for valorising animal wastes would be a major advancement in cold-climate regions. This paper reports the results of long term (315 days experiment) of novel psychrophilic (20°C) dry anaerobic digestion (PDAD) of cow feces and wheat straw in laboratory scale sequence batch reactor operated at increasing organic loading rate. The PDAD process fed with a mixture of feces and straw (TS of 27%) over a treatment cycle length of 21 days at organic loading rate (OLR) 4.0, 5.0 and 6.0 g TCOD kg(-1) inoculum d(-1) (of 2.9 ± 0.1, 3.7 ± 0.1, and 4.4 ± 0.1g VS kg(-1) inoculum d(-1), respectively) resulted in average specific methane yield (SMY) of 187.3 ± 18.1, 163.6 ± 39.5, 150.8 ± 32.9 N L CH4 kg(-1)VS fed, respectively. PDAD of cow feces and wheat straw is possible with VS-based inoculum-to-substrate ratio of 1.4 at OLR of 6.0 g TCOD kg(-1) inoculum d(-1). Hydrolysis was the limiting step reaction.

  6. Cow, sheep and llama manure at psychrophilic anaerobic co-digestion with low cost tubular digesters in cold climate and high altitude.

    PubMed

    Martí-Herrero, J; Alvarez, R; Cespedes, R; Rojas, M R; Conde, V; Aliaga, L; Balboa, M; Danov, S

    2015-04-01

    The aim of this research is to evaluate the co-digestion of cow and llama manure combined with sheep manure, in psychrophilic conditions and real field low cost tubular digesters adapted to cold climate. Four digesters were monitored in cold climate conditions; one fed with cow manure, a second one with llama manure, the third one with co-digestion of cow-sheep manure and the fourth one was fed with llama-sheep manure. The slurry had a mean temperature of 16.6 °C, the organic load rate was 0.44 kgvs m(-3) d(-1) and the hydraulic retention time was 80 days. After one hundred days biogas production was stable, as was the methane content and the pH of the effluent. The co-digestion of cow-sheep manure results in a biogas production increase of 100% compared to the mono-digestion of cow manure, while co-digestion of llama-sheep manure results in a decrease of 50% in biogas production with respect to mono-digestion of llama manure.

  7. Purification, characterization and preliminary X-ray diffraction analysis of a cold-active lipase (CpsLip) from the psychrophilic bacterium Colwellia psychrerythraea 34H.

    PubMed

    Do, Hackwon; Lee, Jun Hyuck; Kwon, Mi Hyun; Song, Hye Eun; An, Jun Yop; Eom, Soo Hyun; Lee, Sung Gu; Kim, Hak Jun

    2013-08-01

    The putative lipase CpsLip from the psychrophilic bacterium Colwellia psychrerythraea 34H encodes a 34,538 Da, 308-amino-acid protein. In this study, CpsLip (UniProtKB code Q486T5) was expressed as an N-terminal hexahistidine fusion protein in Escherichia coli and purified by affinity and size-exclusion chromatography. The expression and purification of CpsLip enabled characterization of the lipase enzymatic properties of the protein. The optimal activity temperature and pH of the recombinant protein were 298 K and pH 7, respectively. CpsLip maintained over 80% activity in the low-temperature range (278-288 K), thereby suggesting that CpsLip is a cold-active lipase. Substrate-specificity analysis demonstrated that CpsLip exhibits maximum activity towards the C12 acyl group. In addition, sequence-alignment results revealed that CpsLip has a highly conserved catalytic triad in the active site consisting of residues Ser111, Asp135 and His283. Moreover, purified CpsLip was successfully crystallized using the hanging-drop vapour-diffusion method and a complete diffraction data set was collected to 4.0 Å resolution using synchrotron radiation on the BL-5A beamline of the Photon Factory.

  8. Elucidation of stability determinants of cold-adapted monomeric isocitrate dehydrogenase from a psychrophilic bacterium, Colwellia maris, by construction of chimeric enzymes.

    PubMed

    Watanabe, Seiya; Yasutake, Yoshiaki; Tanaka, Isao; Takada, Yasuhiro

    2005-04-01

    To elucidate determinants of differences in thermostability between mesophilic and psychrophilic monomeric isocitrate dehydrogenases (IDHs) from Azotobacter vinelandii (AvIDH) and Colwellia maris (CmIDH), respectively, chimeric enzymes derived from the two IDHs were constructed based on the recently resolved three-dimensional structure of AvIDH, and several characteristics of the two wild-type and six chimeric IDHs were examined. These characteristics were then compared with those of dimeric IDH from Escherichia coli (EcIDH). All recombinant enzymes with a (His)(6)-tag attached to the N-terminal were overexpressed in the E. coli cells and purified by Ni(2+)-affinity chromatography. The catalytic activity (k(cat)) and catalytic efficiency (k(cat)/K(m)) of the wild-type AvIDH and CmIDH were higher than those of EcIDH, implying that an improved catalytic rate more than compensates for the loss of a catalytic site in the former two IDHs due to monomerization. Analyses of the thermostability and kinetic parameters of the chimeric enzymes indicated that region 2, corresponding to domain II, and particularly region 3 located in the C-terminal part of domain I, are involved in the thermolability of CmIDH, and that the corresponding two regions of AvIDH are important for exhibiting higher catalytic activity and affinity for isocitrate than CmIDH. The relationships between the stability, catalytic activity and structural characteristics of AvIDH and CmIDH are discussed.

  9. Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis.

    PubMed

    Ramli, Aizi Nor Mazila; Azhar, Mohd Akmal; Shamsir, Mohd Shahir; Rabu, Amir; Murad, Abdul Munir Abdul; Mahadi, Nor Muhammad; Illias, Rosli Md

    2013-08-01

    A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica PI12 has yet to be studied in detail. A 3D model of AmyPI12 was built using a homology modelling approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9.9. Analysis of the AmyPI12 model revealed the presence of binding sites for a conserved calcium ion (CaI), non-conserved calcium ions (CaII and CaIII) and a sodium ion (Na). Compared with its template-the thermostable α-amylase from Bacillus stearothermophilus (BSTA)-the binding of CaII, CaIII and Na ions in AmyPI12 was observed to be looser, which suggests that the low stability of AmyPI12 allows the protein to work at different temperature scales. The AmyPI12 amino acid sequence and model were compared with thermophilic α-amylases from Bacillus species that provided the highest structural similarities with AmyPI12. These comparative studies will enable identification of possible determinants of cold adaptation.

  10. Enrichment of light hydrocarbon mixture

    SciTech Connect

    Yang; Dali; Devlin, David; Barbero, Robert S.; Carrera, Martin E.; Colling, Craig W.

    2010-08-10

    Light hydrocarbon enrichment is accomplished using a vertically oriented distillation column having a plurality of vertically oriented, nonselective micro/mesoporous hollow fibers. Vapor having, for example, both propylene and propane is sent upward through the distillation column in between the hollow fibers. Vapor exits neat the top of the column and is condensed to form a liquid phase that is directed back downward through the lumen of the hollow fibers. As vapor continues to ascend and liquid continues to countercurrently descend, the liquid at the bottom of the column becomes enriched in a higher boiling point, light hydrocarbon (propane, for example) and the vapor at the top becomes enriched in a lower boiling point light hydrocarbon (propylene, for example). The hollow fiber becomes wetted with liquid during the process.

  11. Enrichment of light hydrocarbon mixture

    SciTech Connect

    Yang, Dali; Devlin, David; Barbero, Robert S; Carrera, Martin E; Colling, Craig W

    2011-11-29

    Light hydrocarbon enrichment is accomplished using a vertically oriented distillation column having a plurality of vertically oriented, nonselective micro/mesoporous hollow fibers. Vapor having, for example, both propylene and propane is sent upward through the distillation column in between the hollow fibers. Vapor exits neat the top of the column and is condensed to form a liquid phase that is directed back downward through the lumen of the hollow fibers. As vapor continues to ascend and liquid continues to countercurrently descend, the liquid at the bottom of the column becomes enriched in a higher boiling point, light hydrocarbon (propane, for example) and the vapor at the top becomes enriched in a lower boiling point light hydrocarbon (propylene, for example). The hollow fiber becomes wetted with liquid during the process.

  12. 31 CFR 540.316 - Uranium enrichment.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process...

  13. Building a Culture of Achievement

    ERIC Educational Resources Information Center

    Major, Marc R.

    2009-01-01

    Culture is the social and intergenerational glue that defines, connects, sustains, and enriches the members of successful communities--including schools and classrooms. A classroom culture is a psychological atmosphere that nurtures and shapes students' attitudes about their own identity, classes, school, and learning in general. Classroom culture…

  14. Musicals Enrich Middle School Programs

    ERIC Educational Resources Information Center

    Thomas, Douglas D.; North, Rita

    2005-01-01

    An enriching fine arts program has long been advocated as an essential element of an effective middle school program. The vocal music program at Pleasant Hill (Missouri) Middle School supports student growth and development beyond the regular classroom. It supports students' existing skills and talents and provides opportunities for them to…

  15. Enrichment Tours in Physical Education.

    ERIC Educational Resources Information Center

    McCarthy, Jean

    1980-01-01

    Enrichment tours designed to heighten interest and enhance the breadth and depth of learning a lifetime sport are encouraged. A tour of the Florida Keys and Bahama Islands for sailing and diving taken by students from Mankato State University is described. (JMF)

  16. Day Care Center Enrichment Program.

    ERIC Educational Resources Information Center

    West Virginia State Dept. of Welfare, Charleston.

    This guide to a West Virginia Department of Welfare project for upgrading the quality of day care centers throughout the state presents samples of the forms used in the program, accompanied by a brief description of the program's format, requirements and procedures. The Day Care Center Enrichment Program provides a monetary incentive for…

  17. Opportunistic pathogens enriched in showerhead biofilms

    PubMed Central

    Feazel, Leah M.; Baumgartner, Laura K.; Peterson, Kristen L.; Frank, Daniel N.; Harris, J. Kirk; Pace, Norman R.

    2009-01-01

    The environments we humans encounter daily are sources of exposure to diverse microbial communities, some of potential concern to human health. In this study, we used culture-independent technology to investigate the microbial composition of biofilms inside showerheads as ecological assemblages in the human indoor environment. Showers are an important interface for human interaction with microbes through inhalation of aerosols, and showerhead waters have been implicated in disease. Although opportunistic pathogens commonly are cultured from shower facilities, there is little knowledge of either their prevalence or the nature of other microorganisms that may be delivered during shower usage. To determine the composition of showerhead biofilms and waters, we analyzed rRNA gene sequences from 45 showerhead sites around the United States. We find that variable and complex, but specific, microbial assemblages occur inside showerheads. Particularly striking was the finding that sequences representative of non-tuberculous mycobacteria (NTM) and other opportunistic human pathogens are enriched to high levels in many showerhead biofilms, >100-fold above background water contents. We conclude that showerheads may present a significant potential exposure to aerosolized microbes, including documented opportunistic pathogens. The health risk associated with showerhead microbiota needs investigation in persons with compromised immune or pulmonary systems. PMID:19805310

  18. Psychrophilic (6--15 {degree}C) high-rate anaerobic treatment of malting wastewater in a two-module expanded granular sludge bed system

    SciTech Connect

    Rebac, S.; Lier, J.B. van; Lens, P.; Cappellen, J. van; Vermeulen, M.; Stams, A.J.M.; Lettinga, G.; Dekkers, F.; Swinkels, K.T.M.

    1998-11-01

    Psychrophilic (6--15 C) anaerobic treatment of malting wastewater was investigated. A two-module expanded granular sludge bed reactor system with a total volume of 140 dm{sup 3} was used to treat malting wastewater having a soluble and total chemical oxygen demand (COD) between 233 and 1778 mg dm{sup {minus}3} and between 317 and 4422 mg dm{sup {minus}3}, respectively. The removal efficiencies at 6 C were 47 and 71% of the soluble and volatile fatty acids (VFA) COD, at organic loading rates (OLR) ranging between 3.3 and 5.8 kg of COD m{sup {minus}3} day{sup {minus}1}. The removal efficiencies at 10--15 C were 67--78 and 90--96% of the soluble and VFA COD at an OLR between 2.8 and 12.3 kg of COD m{sup {minus}3} day{sup {minus}1}. The specific methanogenic activity of the sludge present in each module increased 2--3-fold during system operation for 400 days. The relatively high concentration of suspended solids in the influent (25% of the total COD) caused a deterioration of the sludge bed in the first reactor module. This was aggravated by excessive growth of acidifying biomass, which persisted in the first module sludge bed and resulted in granular sludge flotation. However, the second module could accommodate the increased OLR, this providing a very high effluent quality (soluble COD < 200 mg dm{sup {minus}3}) of the total system. The stability of module 1 concerning suspended solids could be restored by presettling the wastewater.

  19. Structural and Chemical Modification of Fe-Rich Smectite Associated with Microbial Fe-Respiration By Psychrophilic Bacteria in King George Island, West Antarctica

    NASA Astrophysics Data System (ADS)

    Jung, J.; Kim, J.; Lim, H. S.; Yoon, H.; Lee, Y. K.; Park, K.; Lee, J.; Kim, J. W.

    2014-12-01

    Surface soil samples were collected from Antarctic exploration (2010/2011, 2011/2012) at Barton Peninsula, King George Island, West Antarctica to determine the feasible biological alteration of clay minerals in Antarctica where the physical weathering is considered to be a major process. Seven areas (1226-1, 1226-2, 0101-4, 0105-1, 0105-2, 0107-2, 0107-3) from the coast toward the inland were investigated. The duration of exposure of soil samples to the air depending on the retraction of ice to the inland may affect the microbial activity resulting in the biogeochemical mineral alteration. The multiline of techniques for example, X-ray diffraction (XRD), Scanning Electron Microscope (SEM), wet chemistry analysis including the extent of Fe(III) reduction, and batch experiments of microbe-mineral interaction under the low temperature that mimics the Antarctic condition to understand the mechanism of biogeochemical alteration of clay minerals. Clay minerals of smectite, mica, chlorite and kaolinite were detected in the XRD profiles. The variation of relative amount of clay minerals in the regions indicated that the physical/biological alteration might be different depending on the duration of ice retraction. From the batch experiment using Nontronite (NAu-1), moreover, we confirm that Psychrophilic bacteria (Shewanella sp. isolated from King George Island) reduce structural Fe(III) of clay mineral, and occur structural change of smectite at low temperature (4℃ and 15℃). The present study, therefore, would present the feasibility of biological effects on chemical modification through the structural changes in clay mineral in cold environment and suggest a new pathway of Fe-supply into the Antarctic Ocean.

  20. Filter-based pathogen enrichment technology for detection of multiple viable foodborne pathogens in 1 day.

    PubMed

    Murakami, Taku

    2012-09-01

    Conventional foodborne pathogen assays currently used in the food industry often require long culture enrichments to increase pathogen levels so they can be detected. Even using sensitive real-time PCR assays, culture enrichment at least overnight is necessary especially for detection of pathogens with slow growth rates such as Listeria monocytogenes. To eliminate this cumbersome enrichment step and detect minute amounts of pathogens within 1 day, filter-based pathogen enrichment technology was developed utilizing a unique combination of glass fiber depth filter and porous filter aid materials to efficiently separate pathogens from food homogenates and avoid filter clogging by food particles. After pathogen immobilization in depth filters, only viable pathogens were selectively collected in a small volume of growth medium via microbial multiplication and migration; nonviable pathogens remained inside the filters. By assaying viable pathogens using real-time PCRs, multiple species of foodborne pathogens were detected, including L. monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, at around 1 CFU/ml or 1 CFU/g in various food samples. This filter-based pathogen enrichment technology is a unique bacterial enrichment alternative to the conventional culture enrichment step and can significantly shorten the time necessary to obtain assay results.

  1. Enriching tortoises: assessing color preference.

    PubMed

    Passos, Luiza F; Mello, Humberto Espirito Santo; Young, Robert John

    2014-01-01

    Environmental enrichment is a principle that is used to enhance the quality of care for nonhuman animals in captivity. To achieve this, it is necessary to understand the animal's needs. This study focused on color preference to provide food stimuli as a source of environmental enrichment for the tortoise, Chelonoidis denticulata. During this study, the stimuli green-, blue-, yellow-, and red-colored bananas and plaster blocks were randomly offered to the tortoises. Analysis of the data showed that the tortoises had a preference for the stimuli dyed with colors red and yellow over the other presented colors. It was possible to conclude that presenting food in different colors stimulated the animals to evaluate their environment and make choices in relation to their color preference. Thus, this experiment introduced an element of choice into their lives, beyond identifying color food preferences for the tortoises. The element of choice is known to be important to animal welfare.

  2. AN ENRICHMENT CULTURE THAT DEGRADES MTBE UNDER ANAEROBIC CONDITIONS

    EPA Science Inventory

    Biodegradation of MTBE in ground water may be a significant factor helping to reduce MTBE contamination from gasoline spills. Previously, decreases in MTBE concentrations in wells at release sites were thought to be due exclusively to dispersion and dilution. Researchers have i...

  3. People, Places, and Environments: Social Studies and Spanish Cultural Enrichment

    ERIC Educational Resources Information Center

    Helms, Ronald G.; Ankenbauer, Mary

    2009-01-01

    If the young people are to become effective participants in a democratic society, then social studies must be an essential part of the curriculum in the early childhood/elementary years. In a world that demands independent and cooperative problem solving to address complex social, economic, ethical, and personal concerns, the social studies are as…

  4. Cultural Enrichment: Connecting African American Elementary Children to Academic Achievement

    ERIC Educational Resources Information Center

    Winston, Deborah L.

    2011-01-01

    A large, growing number of mis-educated American citizens are being produced by America's public schools. Many of these students are being funneled into the penal system shortly after dropping out of high school. This phenomenon is especially prevalent among African American male students, many of whom have withdrawn academically years prior…

  5. Selective enrichment of a methanol-utilizing consortium using pulp & paper mill waste streams

    SciTech Connect

    Gregory R. Mockos; William A. Smith; Frank J. Loge; David N. Thompson

    2007-04-01

    Efficient utilization of carbon inputs is critical to the economic viability of the current forest products sector. Input carbon losses occur in various locations within a pulp mill, including losses as volatile organics and wastewater . Opportunities exist to capture this carbon in the form of value-added products such as biodegradable polymers. Waste activated sludge from a pulp mill wastewater facility was enriched for 80 days for a methanol-utilizing consortium with the goal of using this consortium to produce biopolymers from methanol-rich pulp mill waste streams. Five enrichment conditions were utilized: three high-methanol streams from the kraft mill foul condensate system, one methanol-amended stream from the mill wastewater plant, and one methanol-only enrichment. Enrichment reactors were operated aerobically in sequencing batch mode at neutral pH and 25°C with a hydraulic residence time and a solids retention time of four days. Non-enriched waste activated sludge did not consume methanol or reduce chemical oxygen demand. With enrichment, however, the chemical oxygen demand reduction over 24 hour feed/decant cycles ranged from 79 to 89 %, and methanol concentrations dropped below method detection limits. Neither the non-enriched waste activated sludge nor any of the enrichment cultures accumulated polyhydroxyalkanoates (PHAs) under conditions of nitrogen sufficiency. Similarly, the non-enriched waste activated sludge did not accumulate PHAs under nitrogen limited conditions. By contrast, enriched cultures accumulated PHAs to nearly 14% on a dry weight basis under nitrogen limited conditions. This indicates that selectively-enriched pulp mill waste activated sludge can serve as an inoculum for PHA production from methanol-rich pulp mill effluents.

  6. Selective Enrichment of a Methanol-Utilizing Consortium Using Pulp and Paper Mill Waste Streams

    NASA Astrophysics Data System (ADS)

    Mockos, Gregory R.; Smith, William A.; Loge, Frank J.; Thompson, David N.

    Efficient utilization of carbon inputs is critical to the economic viability of the current forest products sector. Input carbon losses occur in various locations within a pulp mill, including losses as volatile organics and wastewater. Opportunities exist to capture this carbon in the form of value-added products such as biodegradable polymers. Wasteactivated sludge from a pulp mill wastewater facility was enriched for 80 days for a methanol-utilizing consortium with the goal of using this consortium to produce biopolymers from methanol-rich pulp mill waste streams. Five enrichment conditions were utilized: three high-methanol streams from the kraft mill foul condensate system, one methanol-amended stream from the mill wastewater plant, and one methanol-only enrichment. Enrichment reactors were operated aerobically in sequencing batch mode at neutral pH and 25°C with a hydraulic residence time and a solids retention time of 4 days. Non-enriched waste activated sludge did not consume methanol or reduce chemical oxygen demand. With enrichment, however, the chemical oxygen demand reduction over 24-h feed/ decant cycles ranged from 79 to 89%, and methanol concentrations dropped below method detection limits. Neither the non-enriched waste-activated sludge nor any of the enrichment cultures accumulated polyhydroxyalkanoates (PHAs) under conditions of nitrogen sufficiency. Similarly, the non-enriched waste activated sludge did not accumulate PHAs under nitrogen-limited conditions. By contrast, enriched cultures accumulated PHAs to nearly 14% on a dry weight basis under nitrogen-limited conditions. This indicates that selectively enriched pulp mill waste activated sludge can serve as an inoculum for PHA production from methanol-rich pulp mill effluents.

  7. Cultural variant interaction in teaching and transmission.

    PubMed

    Abrams, Marshall

    2015-01-01

    Focus on the way in which cultural variants affect other variants' probabilities of transmission in modeling and empirical work can enrich Kline's conceptualization of teaching. For example, the problem of communicating complex cumulative culture is an adaptive problem; teaching methods that manage transmission so that acquisition of some cultural variants increases the probability of acquiring others, provide a partial solution.

  8. The small domain of cytochrome f from the psychrophile Chlamydomonas raudensis UWO 241 modulates the apparent molecular mass and decreases the accumulation of cytochrome f in the mesophile Chlamydomonas reinhardtii.

    PubMed

    Gudynaite-Savitch, Loreta; Loiselay, Christelle; Savitch, Leonid V; Simmonds, John; Kohalmi, Susanne E; Choquet, Yves; Hüner, Norman P A

    2007-10-01

    Cytochrome f from the psychrophile Chlamydomonas raudensis UWO 241 has a lower thermostability of its c-type heme and an apparent molecular mass that is 7 kDa lower than that of the model mesophilic green alga Chlamydomonas reinhardtii. We combined chloroplast transformation, site-directed mutagensis, and the creation of chimeric fusion constructs to assess the contribution of specific domains and (or) amino acids residues to the structure, stability, and accumulation of cytochrome f, as well as its function in photosynthetic intersystem electron transport. We demonstrate that differences in the amino acid sequence of the small domain and specific charged amino acids in the large domain of cytochrome f alter the physical properties of this protein but do not affect either the thermostability of the c-type heme, the apparent half-life of cytochrome f in the presence of the chloroplastic protein synthesis inhibitor chloramphenicol, or the capacity for photosynthetic intersystem electron transport, measured as e-/P700. However, pulse-labeling with [14C]acetate, combined with immunoblotting, indicated that the negative autoregulation of cytochrome f accumulation observed in mesophilic C. reinhardtii transformed with chimeric constructs from the psychrophile was likely the result of the defective association of the chimeric forms of cytochrome f with the other subunits of the cytochrome b6/f complex native to the C. reinhardtii wild type. These results are discussed in terms of the unique fatty acid composition of the thylakoid membranes of C. raudensis UWO 241 adapted to cold environments.

  9. Enrichment and characterization of sulfate reducing, naphthalene degrading microorganisms

    NASA Astrophysics Data System (ADS)

    Steffen, Kümmel; Florian-Alexander, Herbst; Márcia, Duarte; Dietmar, Pieper; Jana, Seifert; Bergen Martin, von; Hans-Hermann, Richnow; Carsten, Vogt

    2014-05-01

    Polycyclic aromatic hydrocarbons (PAH) are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. PAH are widely distributed in the environment by accidental discharges during the transport, use and disposal of petroleum products, and during forest and grass fires. Caused by their hydrophobic nature, PAH basically accumulate in sediments from where they are slowly released into the groundwater. Although generally limited by the low water solubility of PAH, microbial degradation is one of the major mechanisms leading to the complete clean-up of PAH-contaminated sites. Whereas organisms and biochemical pathways responsible for the aerobic breakdown of PAH are well known, anaerobic PAH biodegradation is less understood; only a few anaerobic PAH degrading cultures have been described. We studied the anaerobic PAH degradation in a microcosm approach to enrich anaerobic PAH degraders. Anoxic groundwater and sediment samples were used as inoculum. Groundwater samples were purchased from the erstwhile gas works facility and a former wood impregnation site. In contrast, sources of sediment samples were a former coal refining area and an old fuel depot. Samples were incubated in anoxic mineral salt medium with naphthalene as sole carbon source and sulfate as terminal electron acceptor. Grown cultures were characterized by feeding with 13C-labeled naphthalene, 16S rRNA gene sequencing using an Illumina® approach, and functional proteome analyses. Finally, six enrichment cultures able to degrade naphthalene under anoxic conditions were established. First results point to a dominance of identified sequences affiliated to the freshwater sulfate-reducing strain N47, which is a known anaerobic naphthalene degrader, in four out of the six enrichments. In those enrichments, peptides related to the pathway of anoxic naphthalene degradation in N47 were abundant. Overall the data underlines the importance of Desulfobacteria for natural

  10. Louis D. Brandeis High School, Demonstration Bilingual Enrichment College Preparatory Program. O.E.E. Evaluation Report, 1982-1983.

    ERIC Educational Resources Information Center

    Cochran, Effie Papatzikou; Collins, Carla

    The Enrichment College Preparatory Program, an Elementary and Secondary Education Act, Title VII bilingual demonstration project at a Manhattan, New York City, high school, completed the final year of a two-year funding cycle in June 1983. The program, which provided cultural enrichment and advanced academic experiences to 160 intellectually…

  11. Characterization of nitrate-reducing and amino acid-using bacteria prominent in nitrotoxin-enriched equine cecal populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the present study, populations of equine cecal microbes enriched for enhanced rates of 3-nitro-1-propionic acid (NPA) or nitrate metabolism were diluted and cultured for NPA-metabolizing bacteria on a basal enrichment medium (BEM) or tryptose soy agar (TSA) medium supplemented with either 5 mM NP...

  12. Thermotolerance and molecular chaperone function of an SGT1-like protein from the psychrophilic yeast, Glaciozyma antarctica.

    PubMed

    Yusof, Nur Athirah; Hashim, Noor Haza Fazlin; Beddoe, Travis; Mahadi, Nor Muhammad; Illias, Rosli Md; Bakar, Farah Diba Abu; Murad, Abdul Munir Abdul

    2016-07-01

    The ability of eukaryotes to adapt to an extreme range of temperatures is critically important for survival. Although adaptation to extreme high temperatures is well understood, reflecting the action of molecular chaperones, it is unclear whether these molecules play a role in survival at extremely low temperatures. The recent genome sequencing of the yeast Glaciozyma antarctica, isolated from Antarctic sea ice near Casey Station, provides an opportunity to investigate the role of molecular chaperones in adaptation to cold temperatures. We isolated a G. antarctica homologue of small heat shock protein 20 (HSP20), GaSGT1, and observed that the GaSGT1 mRNA expression in G. antarctica was markedly increased following culture exposure at low temperatures. Additionally, we demonstrated that GaSGT1 overexpression in Escherichia coli protected these bacteria from exposure to both high and low temperatures, which are lethal for growth. The recombinant GaSGT1 retained up to 60 % of its native luciferase activity after exposure to luciferase-denaturing temperatures. These results suggest that GaSGT1 promotes cell thermotolerance and employs molecular chaperone-like activity toward temperature assaults.

  13. Boron enrichment in martian clay.

    PubMed

    Stephenson, James D; Hallis, Lydia J; Nagashima, Kazuhide; Freeland, Stephen J

    2013-01-01

    We have detected a concentration of boron in martian clay far in excess of that in any previously reported extra-terrestrial object. This enrichment indicates that the chemistry necessary for the formation of ribose, a key component of RNA, could have existed on Mars since the formation of early clay deposits, contemporary to the emergence of life on Earth. Given the greater similarity of Earth and Mars early in their geological history, and the extensive disruption of Earth's earliest mineralogy by plate tectonics, we suggest that the conditions for prebiotic ribose synthesis may be better understood by further Mars exploration.

  14. Boron Enrichment in Martian Clay

    PubMed Central

    Nagashima, Kazuhide; Freeland, Stephen J.

    2013-01-01

    We have detected a concentration of boron in martian clay far in excess of that in any previously reported extra-terrestrial object. This enrichment indicates that the chemistry necessary for the formation of ribose, a key component of RNA, could have existed on Mars since the formation of early clay deposits, contemporary to the emergence of life on Earth. Given the greater similarity of Earth and Mars early in their geological history, and the extensive disruption of Earth's earliest mineralogy by plate tectonics, we suggest that the conditions for prebiotic ribose synthesis may be better understood by further Mars exploration. PMID:23762242

  15. Proteome-wide enrichment of proteins modified by lysine methylation

    PubMed Central

    Carlson, Scott M; Moore, Kaitlyn E; Green, Erin M; Martín, Glòria Mas; Gozani, Or

    2015-01-01

    We present a protocol for using the triple malignant brain tumor domains of L3MBTL1 (3×MBT), which bind to mono- and di-methylated lysine with minimal sequence specificity, in order to enrich for such methylated lysine from cell lysates. Cells in culture are grown with amino acids containing light or heavy stable isotopic labels. Methylated proteins are enriched by incubating cell lysates with 3×MBT, or with the binding-null D355N mutant as a negative control. Quantitative liquid chromatography and tandem mass spectrometry (LC-MS/MS) are then used to identify proteins that are specifically enriched by 3×MBT pull-down. The addition of a third isotopic label allows the comparison of protein lysine methylation between different biological conditions. Unlike most approaches, our strategy does not require a prior hypothesis of candidate methylated proteins, and it recognizes a wider range of methylated proteins than any available method using antibodies. Cells are prepared by growing in isotopic labeling medium for about 7 d; the process of enriching methylated proteins takes 3 d and analysis by LC-MS/MS takes another 1–2 d. PMID:24309976

  16. Environmental enrichment for primates in laboratories

    NASA Astrophysics Data System (ADS)

    Buchanan-Smith, H. M.

    2010-06-01

    Environmental enrichment is a critical component of Refinement, one of the 3Rs underlying humane experimentation on animals. In this paper I discuss why primates housed in laboratories, which often have constraints of space and study protocols, are a special case for enrichment. I outline a framework for categorising the different types of enrichment, using the marmoset as a case study, and summarise the methods used to determine what animals want/prefer. I briefly review the arguments that enrichment does not negatively affect experimental outcomes. Finally I focus on complexity and novelty, choice and control, the underlying features of enrichment that makes it successful, and how combined with a thorough understanding of natural history we can put effective enrichment into practice in laboratories. Throughout the paper I emphasise the need to evaluate enrichment to ensure it is having the desired effect.

  17. Application of Oxygen-Enriched Aeration in the Production of Bacitracin by Bacillus licheniformis

    PubMed Central

    Flickinger, M. C.; Perlman, D.

    1979-01-01

    The physiological effects of controlling the dissolved oxygen tension at 0.01, 0.02, and 0.05 atm by the use of oxygen-enriched aeration were investigated during growth and bacitracin production by Bacillus licheniformis ATCC 10716. Up to a 2.35-fold increase in the final antibiotic yield and a 4-fold increase in the rate of bacitracin synthesis were observed in response to O2-enriched aeration. The increase in antibiotic production was accompanied by increased respiratory activity and an increase in the specific productivity of the culture from 1.3 to 3.6 g of antibiotic per g of cell mass produced. Oxygen enrichment of the aeration decreased medium carbohydrate uptake and the maximum specific growth rate of B. licheniformis from 0.6 h−1 to as low as 0.15 h−1, depending upon the level of enrichment and the conditions of oxygen transfer rate (impeller speed). The response of this culture to O2 enrichment suggests that this method of controlling the dissolved oxygen tension for antibiotic-producing cultures may simulate conditions that would occur if the carbon source were fed slowly, as is often employed to optimize antibiotic production. Analysis of the biologically active bacitracins produced by B. licheniformis ATCC 10716 suggested that the ratio of biologically active peptides was not changed by O2 enrichment, nor were any new biologically active compounds formed. Images PMID:34361

  18. Bacterial diversity and bioprospecting for cold-active hydrolytic enzymes from culturable bacteria associated with sediment from Nella Fjord, Eastern Antarctica.

    PubMed

    Yu, Yong; Li, Hui-Rong; Zeng, Yin-Xin; Chen, Bo

    2011-01-31

    The diversity and cold-active hydrolytic enzymes of culturable bacteria associated with sandy sediment from Nella Fjord, Eastern Antarctica (69°22'6″ S, 76°21'45″ E) was investigated. A total of 33 aerobic heterotrophic bacterial strains were isolated at 4 °C. These bacterial isolates could be sorted into 18 phylotypes based on the 16S rRNA gene sequence belonging to four phyla, namely Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Only seven isolates were psychrophilic, 15 isolates were moderately psychrophilic, and 11 isolates were psychrotolerant. More than 72% of the isolates required sodium chloride to grow. Esterase, β-glucosidase and proteases activities at 4 °C were detected in more than 45% of the strains while approximately 21%, 15% and 12% of the strains possessed lipase, amylase and chitinase, respectively. These results indicate that a relatively high culturable bacterial diversity is present within marine sediment of Nella Fjord and it could serve as an ideal candidate region for bioprospecting.

  19. Manzanita Wood: A Sanitizable Enrichment Option for Nonhuman Primates

    PubMed Central

    Luchins, Kerith R; Baker, Kate C; Gilbert, Margaret H; Blanchard, James L; Bohm, Rudolf P

    2011-01-01

    Wooden objects are often used as nonhuman primate enrichment to provide variety and novelty, promote exploratory behavior, and supply an outlet for curiosity. However, concerns have been raised regarding the ability to sanitize wood by using conventional cage-wash procedures. To address this concern, we examined sanitation outcomes between soiled plastic toys and manzanita wooden manipulanda immediately after a cage-wash cycle. Both an ATP luminometer device, which is capable of providing an immediate assessment of sanitation levels, and traditional bacterial culture were used, with the secondary goal of comparing these methods for sanitation monitoring. Results showed that the wooden objects did not differ from plastic toys with respect to the overall efficacy of cage-wash sanitization. Therefore, manzanita wood can be used as nonhuman primate enrichment without risking pathogen transmission when items are rotated among animals. PMID:22330781

  20. Phytoremediation of shallow organically enriched marine sediments using benthic microalgae.

    PubMed

    Yamamoto, Tamiji; Goto, Ikue; Kawaguchi, Osamu; Minagawa, Kazuaki; Ariyoshi, Eiji; Matsuda, Osamu

    2008-01-01

    We examined whether replantation of benthic microalgae (BMA) can remediate shallow organically enriched sediment. Nitzschia sp., the dominant species in the tested area (Hiroshima Bay, Japan), was isolated and mass cultured, then replanted in the same area. Changes in the condition of the sediment were monitored for five months. During the study period, we observed an increase in redox potential (ORP) and a decrease in acid-volatile sulfide (AVS) in the experimental area, indicating that the sediment condition changed from reduced to oxic. Organic matter in the sediment, represented by chemical oxygen demand (COD), ignition loss (IL) and organic nitrogen (ON) decreased significantly, while inorganic nutrients (ammonia and phosphate) increased in the interstitial water. These changes imply that oxygen produced by the replanted BMA may have enhanced aerobic bacterial activity, accelerating the decomposition of organic matter. Thus, replantation of BMA shows potential as a novel and promising "phytoremediation" method for organically enriched sediment.

  1. Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water.

    PubMed

    Unal, Burcu; Perry, Verlin Ryan; Sheth, Mili; Gomez-Alvarez, Vicente; Chin, Kuk-Jeong; Nüsslein, Klaus

    2012-01-01

    Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R(2) = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community.

  2. Trace Elements Affect Methanogenic Activity and Diversity in Enrichments from Subsurface Coal Bed Produced Water

    PubMed Central

    Ünal, Burcu; Perry, Verlin Ryan; Sheth, Mili; Gomez-Alvarez, Vicente; Chin, Kuk-Jeong; Nüsslein, Klaus

    2012-01-01

    Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community. PMID

  3. Enrichment and characteristics of mixed methane-oxidizing bacteria from a Chinese coal mine.

    PubMed

    Jiang, Hao; Duan, Changhong; Luo, Mingfang; Xing, Xin-Hui

    2016-12-01

    In methane-rich environments, methane-oxidizing bacteria usually occur predominantly among consortia including other types of microorganisms. In this study, artificial coal bed gas and methane gas were used to enrich mixed methanotrophic cultures from the soil of a coal mine in China, respectively. The changes in microbial community structure and function during the enrichment were examined. The microbial diversity was reduced as the enrichment proceeded, while the capacity for methane oxidation was significantly enhanced by the increased abundance of methanotrophs. The proportion of type II methanotrophs increased greatly from 7.84 % in the sampled soil to about 50 % in the enrichment cultures, due to the increase of methane concentration. After the microbial community of the cultures got stable, Methylomonas and Methylocystis became the dominant type I and type II methanotrophs, while Methylophilus was the prevailing methylotroph. The sequences affiliated with pigment-producing strains, Methylomonas rubra, Hydrogenophaga sp. AH-24, and Flavobacterium cucumis, could explain the orange appearance of the cultures. Comparing the two cultures, the multi-carbon sources in the artificial coal bed gas caused more variety of non-methanotrophic bacteria, but did not help to maintain the diversity or to increase the quantity and activity of methanotrophs. The results could help to understand the succession and interaction of microbial community in a methane-driven ecosystem.

  4. Circulating tumor cells in pancreatic cancer patients: Enrichment and cultivation

    PubMed Central

    Bobek, Vladimir; Gurlich, Robert; Eliasova, Petra; Kolostova, Katarina

    2014-01-01

    AIM: To investigate the feasibility of separation and cultivation of circulating tumor cells (CTCs) in pancreatic cancer (PaC) using a filtration device. METHODS: In total, 24 PaC patients who were candidates for surgical treatment were enrolled into the study. Peripheral blood samples were collected before an indicated surgery. For each patient, approximately 8 mL of venous blood was drawn from the antecubital veins. A new size-based separation MetaCell® technology was used for enrichment and cultivation of CTCs in vitro. (Separated CTCs were cultured on a membrane in FBS enriched RPMI media and observed by inverted microscope. The cultured cells were analyzed by means of histochemistry and immunohistochemistry using the specific antibodies to identify the cell origin. RESULTS: CTCs were detected in 16 patients (66.7%) of the 24 evaluable patients. The CTC positivity did not reflect the disease stage, tumor size, or lymph node involvement. The same percentage of CTC positivity was observed in the metastatic and non-metastatic patients (66.7% vs 66.7%). We report a successful isolation of CTCs in PaC patients capturing proliferating cells. The cells were captured by a capillary action driven size-based filtration approach that enabled cells cultures from the viable CTCs to be unaffected by any antibodies or lysing solutions. The captured cancer cells displayed plasticity which enabled some cells to invade the separating membrane. Further, the cancer cells in the “bottom fraction”, may represent a more invasive CTC-fraction. The CTCs were cultured in vitro for further downstream applications. CONCLUSION: The presented size-based filtration method enables culture of CTCs in vitro for possible downstream applications. PMID:25493031

  5. Enriching the hot circumgalactic medium

    NASA Astrophysics Data System (ADS)

    Crain, Robert A.; McCarthy, Ian G.; Schaye, Joop; Theuns, Tom; Frenk, Carlos S.

    2013-07-01

    Simple models of galaxy formation in a cold dark matter universe predict that massive galaxies are surrounded by a hot, quasi-hydrostatic circumgalactic corona of slowly cooling gas, predominantly accreted from the intergalactic medium (IGM). This prediction is borne out by the recent cosmological hydrodynamical simulations of Crain et al., which reproduce observed scaling relations between the X-ray and optical properties of nearby disc galaxies. Such coronae are metal poor, but observations of the X-ray emitting circumgalactic medium (CGM) of local galaxies typically indicate enrichment to near-solar iron abundance, potentially signalling a shortcoming in current models of galaxy formation. We show here that, while the hot CGM of galaxies formed in the simulations is typically metal poor in a mass-weighted sense, its X-ray luminosity-weighted metallicity is often close to solar. This bias arises because the soft X-ray emissivity of a typical ˜0.1 keV corona is dominated by collisionally excited metal ions that are synthesized in stars and recycled into the hot CGM. We find that these metals are ejected primarily by stars that form in situ to the main progenitor of the galaxy, rather than in satellites or external galaxies. The enrichment of the hot CGM therefore proceeds in an `inside-out' fashion throughout the assembly of the galaxy: metals are transported from the central galaxy by supernova-driven winds and convection over several Gyr, establishing a strong negative radial metallicity gradient. Whilst metal ions synthesized by stars are necessary to produce the X-ray emissivity that enables the hot CGM of isolated galaxies to be detected with current instrumentation, the electrons that collisionally excite them are equally important. Since our simulations indicate that the electron density of hot coronae is dominated by the metal-poor gas accreted from the IGM, we infer that the hot CGM observed via X-ray emission is the outcome of both hierarchical

  6. Cultural Programs for the Community.

    ERIC Educational Resources Information Center

    Lorenzi, Paul

    Descriptions are provided of projects undertaken at three county colleges in New Jersey to improve the cultural enrichment opportunities of the surrounding communities. First, introductory material discusses the pluralistic components (i.e., federal, state, and local governments; philanthropic foundations; private patrons; business; and the market…

  7. Shenandoah elementary science enrichment program

    SciTech Connect

    Garrett, P.

    1994-12-31

    Shenandoah Elementary School is a rural educational facility located in the farmlands of Indiana. The Elementary Science Enrichment Program was established to create a learning atmosphere that encourages scientific thinking and problem-solving. Its inception was founded on the belief that the concepts and process skills inherent in the teaching of science are critical to the early intellectual development of elementary students. The program was established through speaking engagements at the local and state level which resulted in the necessary support to insure its continuation. All students in grades K-5 meet for weekly science activities in our elementary lab to investigate many exciting curricular areas including planaria regeneration, star life cycles, and acid rain telecommunications. This allows for in-depth exploration of the science process skills which culminate in a variety of products including student portfolios, hands-on assessments, simulations and global data communications. These activities are extended through family science and the modeling of science instructional techniques for classroom educators.

  8. Student science enrichment training program

    SciTech Connect

    Sandhu, S.S.

    1994-08-01

    This is a report on the Student Science Enrichment Training Program, with special emphasis on chemical and computer science fields. The residential summer session was held at the campus of Claflin College, Orangeburg, SC, for six weeks during 1993 summer, to run concomitantly with the college`s summer school. Fifty participants selected for this program, included high school sophomores, juniors and seniors. The students came from rural South Carolina and adjoining states which, presently, have limited science and computer science facilities. The program focused on high ability minority students, with high potential for science engineering and mathematical careers. The major objective was to increase the pool of well qualified college entering minority students who would elect to go into science, engineering and mathematical careers. The Division of Natural Sciences and Mathematics and engineering at Claflin College received major benefits from this program as it helped them to expand the Departments of Chemistry, Engineering, Mathematics and Computer Science as a result of additional enrollment. It also established an expanded pool of well qualified minority science and mathematics graduates, which were recruited by the federal agencies and private corporations, visiting Claflin College Campus. Department of Energy`s relationship with Claflin College increased the public awareness of energy related job opportunities in the public and private sectors.

  9. 21 CFR 137.350 - Enriched rice.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 2 2013-04-01 2013-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  10. 21 CFR 137.350 - Enriched rice.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 2 2014-04-01 2014-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  11. 21 CFR 137.350 - Enriched rice.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 2 2012-04-01 2012-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  12. 21 CFR 137.350 - Enriched rice.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  13. 21 CFR 137.350 - Enriched rice.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 2 2011-04-01 2011-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  14. Inoculation Stress Hypothesis of Environmental Enrichment

    PubMed Central

    Crofton, Elizabeth J.; Zhang, Yafang; Green, Thomas A.

    2014-01-01

    One hallmark of psychiatric conditions is the vast continuum of individual differences in susceptibility vs. resilience resulting from the interaction of genetic and environmental factors. The environmental enrichment paradigm is an animal model that is useful for studying a range of psychiatric conditions, including protective phenotypes in addiction and depression models. The major question is how environmental enrichment, a non-drug and non-surgical manipulation, can produce such robust individual differences in such a wide range of behaviors. This paper draws from a variety of published sources to outline a coherent hypothesis of inoculation stress as a factor producing the protective enrichment phenotypes. The basic tenet suggests that chronic mild stress from living in a complex environment and interacting non-aggressively with conspecifics can inoculate enriched rats against subsequent stressors and/or drugs of abuse. This paper reviews the enrichment phenotypes, mulls the fundamental nature of environmental enrichment vs. isolation, discusses the most appropriate control for environmental enrichment, and challenges the idea that cortisol/corticosterone equals stress. The intent of the inoculation stress hypothesis of environmental enrichment is to provide a scaffold with which to build testable hypotheses for the elucidation of the molecular mechanisms underlying these protective phenotypes and thus provide new therapeutic targets to treat psychiatric/neurological conditions. PMID:25449533

  15. 21 CFR 137.165 - Enriched flour.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Related Products § 137.165 Enriched flour. Enriched flour conforms to the definition and standard of... vitamins and minerals are maintained throughout the expected shelf life of the food under...

  16. The paradox of enrichment in metaecosystems.

    PubMed

    Gounand, Isabelle; Mouquet, Nicolas; Canard, Elsa; Guichard, Frédéric; Hauzy, Céline; Gravel, Dominique

    2014-12-01

    The paradox of enrichment has been studied almost exclusively within communities or metacommunities, without explicit nutrient dynamics. Yet local recycling of materials from enriched ecosystems may affect the stability of connected ecosystems. Here we study the effect of nutrient, detritus, producer, and consumer spatial flows-combined with changes in regional enrichment-on the stability of a metaecosystem model. We considered both spatially homogeneous and heterogeneous enrichment. We found that nutrient and detritus spatial flows are destabilizing, whereas producer or consumer spatial flows are either neutral or stabilizing. We noticed that detritus spatial flows have only a weak impact on stability. Our study reveals that heterogeneity no longer stabilizes well-connected systems when accounting for explicit representation of nutrient dynamics. We also found that intermediate consumer diffusion could lead to multiple equilibria in strongly enriched metaecosystems. Stability can emerge from a top-down control allowing the storage of materials into inorganic form, a mechanism never documented before. In conclusion, local enrichment can be stabilized if spatial flows are strong enough to efficiently redistribute the local excess of enrichment to unfertile ecosystems. However, high regional enrichment can be dampened only by intermediate consumer diffusion rates.

  17. 76 FR 387 - Atomic Safety and Licensing Board; AREVA Enrichment Services, LLC (Eagle Rock Enrichment Facility)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-04

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Atomic Safety and Licensing Board; AREVA Enrichment Services, LLC (Eagle Rock Enrichment Facility... Eagle Rock Enrichment Facility (EREF)--in Bonneville County, Idaho; and (2) the receipt, possession,...

  18. Effects of the antimicrobial sulfamethoxazole on groundwater bacterial enrichment

    USGS Publications Warehouse

    Underwood, J.C.; Harvey, R.W.; Metge, D.W.; Repert, D.A.; Baumgartner, L.K.; Smith, R.L.; Roane, T.M.; Barber, L.B.

    2011-01-01

    The effects of "trace" (environmentally relevant) concentrations of the antimicrobial agent sulfamethoxazole (SMX) on the growth, nitrate reduction activity, and bacterial composition of an enrichment culture prepared with groundwater from a pristine zone of a sandy drinking-water aquifer on Cape Cod, MA, were assessed by laboratory incubations. When the enrichments were grown under heterotrophic denitrifying conditions and exposed to SMX, noticeable differences from the control (no SMX) were observed. Exposure to SMX in concentrations as low as 0.005 ??M delayed the initiation of cell growth by up to 1 day and decreased nitrate reduction potential (total amount of nitrate reduced after 19 days) by 47% (p = 0.02). Exposure to 1 ??M SMX, a concentration below those prescribed for clinical applications but higher than concentrations typically detected in aqueous environments, resulted in additional inhibitions: reduced growth rates (p = 5 ?? 10-6), lower nitrate reduction rate potentials (p = 0.01), and decreased overall representation of 16S rRNA gene sequences belonging to the genus Pseudomonas. The reduced abundance of Pseudomonas sequences in the libraries was replaced by sequences representing the genus Variovorax. Results of these growth and nitrate reduction experiments collectively suggest that subtherapeutic concentrations of SMX altered the composition of the enriched nitrate-reducing microcosms and inhibited nitrate reduction capabilities. ?? 2011 American Chemical Society.

  19. Neuron enriched nuclear proteome isolated from human brain.

    PubMed

    Dammer, Eric B; Duong, Duc M; Diner, Ian; Gearing, Marla; Feng, Yue; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

    2013-07-05

    The brain consists of diverse cell types including neurons, astrocytes, oligodendrocytes, and microglia. The isolation of nuclei from these distinct cell populations provides an opportunity to identify cell-type-specific nuclear proteins, histone modifications, and regulation networks that are altered with normal brain aging or neurodegenerative disease. In this study, we used a method by which intact neuronal and non-neuronal nuclei were purified from human post-mortem brain employing a modification of fluorescence activated cell sorting (FACS) termed fluorescence activated nuclei sorting (FANS). An antibody against NeuN, a neuron specific splicing factor, was used to isolate neuronal nuclei. Utilizing mass spectrometry (MS) based label-free quantitative proteomics, we identified 1755 proteins from sorted NeuN-positive and negative nuclear extracts. Approximately 20% of these proteins were significantly enriched or depleted in neuronal versus non-neuronal populations. Immunoblots of primary cultured rat neuron, astrocyte, and oligodendrocyte extracts confirmed that distinct members of the major nucleocytoplasmic structural linkage complex (LINC), nesprin-1 and nesprin-3, were differentially enriched in neurons and astrocytes, respectively. These comparative proteomic data sets also reveal a number of transcription and splicing factors that are selectively enriched in a cell-type-specific manner in human brain.

  20. Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production.

    PubMed

    van de Vossenberg, Jack; Rattray, Jayne E; Geerts, Wim; Kartal, Boran; van Niftrik, Laura; van Donselaar, Elly G; Sinninghe Damsté, Jaap S; Strous, Marc; Jetten, Mike S M

    2008-11-01

    Microbiological investigation of anaerobic ammonium oxidizing (anammox) bacteria has until now been restricted to wastewater species. The present study describes the enrichment and characterization of two marine Scalindua species, the anammox genus that dominates almost all natural habitats investigated so far. The species were enriched from a marine sediment in the Gullmar Fjord (Sweden) using a medium based on Red Sea salt. Anammox cells comprised about 90% of the enrichment culture after 10 months. The enriched Scalindua bacteria displayed all typical features known for anammox bacteria, including turnover of hydrazine, the presence of ladderane lipids, and a compartmentalized cellular ultrastructure. The Scalindua species also showed a nitrate-dependent use of formate, acetate and propionate, and performed a formate-dependent reduction of nitrate, Fe(III) and Mn(IV). This versatile metabolism may be the basis for the global distribution and substantial contribution of the marine Scalindua anammox bacteria to the nitrogen loss from oxygen-limited marine ecosystems.

  1. Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments.

    PubMed

    Le Digabel, Yoann; Demanèche, Sandrine; Benoit, Yves; Fayolle-Guichard, Françoise; Vogel, Timothy M

    2014-08-30

    The ethyl tert-butyl ether (ETBE) degradation capacity and phylogenetic composition of five aerobic enrichment cultures with ETBE as the sole carbon and energy source were studied. In all cases, ETBE was entirely degraded to biomass and CO2. Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases. The two other enrichments have different microbiota with an abundance of Acidobacteria in one case, whereas the microbiota in the second was more diverse (majority of Actinobacteria, Chlorobi and Gemmatimonadetes). Actinobacteria were detected in all five enrichments. Several bacterial strains were isolated from the enrichments and five were capable of degrading ETBE and/or tert-butyl alcohol (TBA), a degradation intermediate. The five included three Rhodococcus sp. (IFP 2040, IFP 2041, IFP 2043), one Betaproteobacteria (IFP 2047) belonging to the Rubrivivax/Leptothrix/Ideonella branch, and one Pseudonocardia sp. (IFP 2050). Quantification of these five strains and two other strains, Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP2049, which had been previously isolated from one of the enrichments was carried out on the different enrichments based on quantitative PCR with specific 16S rRNA gene primers and the results were consistent with the hypothesized role of Actinobacteria and Betaproteobacteria in the degradation of ETBE and the possible role of Bradyrhizobium strains in the degradation of TBA.

  2. Stool Culture

    MedlinePlus

    ... products and services. Advertising & Sponsorship: Policy | Opportunities Stool Culture Share this page: Was this page helpful? Also known as: Bacterial Culture, stool; Feces Culture Formal name: Enteric Pathogens Culture, ...

  3. Fluxes in PHA-storing microbial communities during enrichment and biopolymer accumulation processes.

    PubMed

    Janarthanan, Om Murugan; Laycock, Bronwyn; Montano-Herrera, Liliana; Lu, Yang; Arcos-Hernandez, Monica V; Werker, Alan; Pratt, Steven

    2016-01-25

    The use of mixed microbial cultures for the production of polyhydroxyalkanoates (PHAs) is emerging as a viable technology. In this study, 16S rRNA gene amplicon pyrosequencing was used to analyse fluctuations in populations over a 63-day period within a PHA-storing mixed microbial community enriched on fermented whey permeate. This community was dominated by the genera Flavisolibacter and Zoogloea as well as an unidentified organism belonging to the phylum Bacteroidetes. The population was observed to cycle through an increase in Zoogloea followed by a return to a community composition similar to the initial one (highly enriched in Flavisolibacter). It was found that the PHA accumulation capacity of the community was robust to population flux during enrichment and even PHA accumulation, with final polymer composition dependent on the overall proportion of acetic to propionic acids in the feed. This community adaptation suggests that mixed culture PHA production is a robust process.

  4. Deuterium enrichment of interstellar dusts

    NASA Astrophysics Data System (ADS)

    Das, Ankan; Chakrabarti, Sandip Kumar; Majumdar, Liton; Sahu, Dipen

    2016-07-01

    High abundance of some abundant and simple interstellar species could be explained by considering the chemistry that occurs on interstellar dusts. Because of its simplicity, the rate equation method is widely used to study the surface chemistry. However, because the recombination efficiency for the formation of any surface species is highly dependent on various physical and chemical parameters, the Monte Carlo method is best suited for addressing the randomness of the processes. We carry out Monte-Carlo simulation to study deuterium enrichment of interstellar grain mantle under various physical conditions. Based on the physical properties, various types of clouds are considered. We find that in diffuse cloud regions, very strong radiation fields persists and hardly a few layers of surface species are formed. In translucent cloud regions with a moderate radiation field, significant number of layers would be produced and surface coverage is mainly dominated by photo-dissociation products such as, C, CH_3, CH_2D, OH and OD. In the intermediate dense cloud regions (having number density of total hydrogen nuclei in all forms ˜2 × 10^4 cm^{-3}), water and methanol along with their deuterated derivatives are efficiently formed. For much higher density regions (˜10^6 cm^{-3}), water and methanol productions are suppressed but surface coverage of CO, CO_2, O_2, O_3 are dramatically increased. We find a very high degree of fractionation of water and methanol. Observational results support a high fractionation of methanol but surprisingly water fractionation is found to be low. This is in contradiction with our model results indicating alternative routes for de-fractionation of water.

  5. Filter characteristics influencing circulating tumor cell enrichment from whole blood.

    PubMed

    Coumans, Frank A W; van Dalum, Guus; Beck, Markus; Terstappen, Leon W M M

    2013-01-01

    A variety of filters assays have been described to enrich circulating tumor cells (CTC) based on differences in physical characteristics of blood cells and CTC. In this study we evaluate different filter types to derive the properties of the ideal filter for CTC enrichment. Between 0.1 and 10 mL of whole blood spiked with cells from tumor cell lines were passed through silicon nitride microsieves, polymer track-etched filters and metal TEM grids with various pore sizes. The recovery and size of 9 different culture cell lines was determined and compared to the size of EpCAM+CK+CD45-DNA+ CTC from patients with metastatic breast, colorectal and prostate cancer. The 8 µm track-etched filter and the 5 µm microsieve had the best performance on MDA-231, PC3-9 and SKBR-3 cells, enriching >80% of cells from whole blood. TEM grids had poor recovery of ∼25%. Median diameter of cell lines ranged from 10.9-19.0 µm, compared to 13.1, 10.7, and 11.0 µm for breast, prostate and colorectal CTC, respectively. The 11.4 µm COLO-320 cell line had the lowest recovery of 17%. The ideal filter for CTC enrichment is constructed of a stiff, flat material, is inert to blood cells, has at least 100,000 regularly spaced 5 µm pores for 1 ml of blood with a ≤10% porosity. While cell size is an important factor in determining recovery, other factors must be involved as well. To evaluate a filtration procedure, cell lines with a median size of 11-13 µm should be used to challenge the system.

  6. Use of an Interculturally Enriched Collaboration Script in Computer-Supported Collaborative Learning in Higher Education

    ERIC Educational Resources Information Center

    Popov, Vitaliy; Biemans, Harm J. A.; Kuznetsov, Andrei N.; Mulder, Martin

    2014-01-01

    In this exploratory study, the authors introduced an interculturally enriched collaboration script (IECS) for working in culturally diverse groups within a computer-supported collaborative learning (CSCL) environment and then assessed student online collaborative behaviour, learning performance and experiences. The question was if and how these…

  7. Bacterial isolates from polysaccharide enrichments cluster by host origin for Firmicutes but not Bacteroidetes.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The intestinal microbiota allows mammals to recover energy stored in plant biomass through fermentation of plant cell walls, primarily cellulose and hemicellulose. Bacteria were isolated from 8 week continuous culture enrichments with cellulose and xylan/pectin from cow (C, n=4), goat (G, n=4), huma...

  8. An enrichment, amplification, and sequence-based typing (EAST) approach for foodborne pathogen detection and surveillance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: Detection of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture. This is typically followed by strain typing, which provides information critical to outbreak and source investigations. In the early 1990’s pul...

  9. Tissue culture: the unrealized potential

    PubMed Central

    2007-01-01

    Lack of differentiated functions of the tissue of origin in tissue culture thought to be due to dedifferentiation was shown to be due to selective overgrowth of fibroblasts. Enrichment culture techniques, (alternate animal and culture passage), designed to give the functionally differentiated cells selective advantage over the fibroblasts resulted in a large number of functionally differentiated clonal strains. Thus the dogma of dedifferentiation was destroyed. It is proposed to substitute the dedifferentiation hypothesis with the hypothesis that cells in culture accurately represent cells in vivo without the complex in vivo environment. With the development of hormonally defined media, combined with functionally differentiated clonal cell lines, the potential of tissue culture studies is greatly augmented. Hormonal responses and dependencies can be discovered in culture and the discovery of dependencies of cancer cells has led to a new rationale for therapy. PMID:19003154

  10. Enrichment of Acinetobacter spp. from food samples.

    PubMed

    Carvalheira, Ana; Ferreira, Vânia; Silva, Joana; Teixeira, Paula

    2016-05-01

    Relatively little is known about the role of foods in the chain of transmission of acinetobacters and the occurrence of different Acinetobacter spp. in foods. Currently, there is no standard procedure to recover acinetobacters from food in order to gain insight into the food-related ecology and epidemiology of acinetobacters. This study aimed to assess whether enrichment in Dijkshoorn enrichment medium followed by plating in CHROMagar™ Acinetobacter medium is a useful method for the isolation of Acinetobacter spp. from foods. Recovery of six Acinetobacter species from food spiked with these organisms was compared for two selective enrichment media (Baumann's enrichment and Dijkshoorn's enrichment). Significantly (p < 0.01) higher cell counts were obtained in Dijkshoorn's enrichment. Next, the Dijkshoorn's enrichment followed by direct plating on CHROMagar™ Acinetobacter was applied to detect Acinetobacter spp. in different foods. Fourteen different presumptive acinetobacters were recovered and assumed to represent nine different strains on the basis of REP-PCR typing. Eight of these strains were identified by rpoB gene analysis as belonging to the species Acinetobacter johnsonii, Acinetobacter calcoaceticus, Acinetobacter guillouiae and Acinetobacter gandensis. It was not possible to identify the species level of one strain which may suggests that it represents a distinct species.

  11. Nocturnal oxygen enrichment in sleep apnoea.

    PubMed

    Pokorski, M; Jernajczyk, U

    2000-01-01

    We hypothesized that a modest oxygen enrichment, rather than 100% oxygen supplementation as used in previous trials, could result in improvement in ventilatory and cardiac symptoms, in patients with obstructive sleep apnoea (OSA), without jeopardizing the chemostimulant ventilatory drive. This hypothesis was tested in five male patients with OSA in a single-blinded trial consisting of one night spent sleeping in control room air (control night), followed by one night spent sleeping while exposed to air with a 9% enriched oxygen content (oxygen-enriched night). Oxygen enrichment resulted in a significant shift in the oxygen saturation profile towards values of > or = 95% and to decrease desaturation dips throughout the night. The apnoea index decreased from the control night to the oxygen-enriched night from 52.7 +/- 10.4 to 38.9 +/- 9.3; the decrease being greatest for the longest apnoeas (> or = 30 s). Additionally, the cardiovascular status improved. No signs of depressed chemostimulant drive in the oxygen-enriched night were detected. We conclude that nocturnal oxygen enrichment merits consideration for therapeutic trial in the prevention of long apnoeic and desaturation episodes.

  12. Method for isotope enrichment by photoinduced chemiionization

    DOEpatents

    Dubrin, James W.

    1985-01-01

    Isotope enrichment, particularly .sup.235 U enrichment, is achieved by irradiating an isotopically mixed vapor feed with radiant energy at a wavelength or wavelengths chosen to selectively excite the species containing a desired isotope to a predetermined energy level. The vapor feed if simultaneously reacted with an atomic or molecular reactant species capable of preferentially transforming the excited species into an ionic product by a chemiionization reaction. The ionic product, enriched in the desired isotope, is electrostatically or electromagnetically extracted from the reaction system.

  13. Profile of World Uranium Enrichment Programs - 2007

    SciTech Connect

    Laughter, Mark D

    2007-11-01

    It is generally agreed that the most difficult step in building a nuclear weapon is acquiring weapons grade fissile material, either plutonium or highly enriched uranium (HEU). Plutonium is produced in a nuclear reactor, while HEU is produced using a uranium enrichment process. Enrichment is also an important step in the civil nuclear fuel cycle, in producing low enriched uranium (LEU) for use in fuel for nuclear reactors. However, the same equipment used to produce LEU for nuclear fuel can also be used to produce HEU for weapons. Safeguards at an enrichment plant are the array of assurances and verification techniques that ensure uranium is only enriched to LEU, no undeclared LEU is produced, and no uranium is enriched to HEU or secretly diverted. There are several techniques for enriching uranium. The two most prevalent are gaseous diffusion, which uses older technology and requires a lot of energy, and gas centrifuge separation, which uses more advanced technology and is more energy efficient. Gaseous diffusion plants (GDPs) provide about 40% of current world enrichment capacity, but are being phased out as newer gas centrifuge enrichment plants (GCEPs) are constructed. Estimates of current and future enrichment capacity are always approximate, due to the constant upgrades, expansions, and shutdowns occurring at enrichment plants, largely determined by economic interests. Currently, the world enrichment capacity is approximately 53 million kg-separative work units (SWU) per year, with 22 million in gaseous diffusion and 31 million in gas centrifuge plants. Another 23 million SWU/year of capacity are under construction or planned for the near future, almost entirely using gas centrifuge separation. Other less-efficient techniques have also been used in the past, including electromagnetic and aerodynamic separations, but these are considered obsolete, at least from a commercial perspective. Laser isotope separation shows promise as a possible enrichment technique

  14. Anaerobic Naphthalene Degradation by a Sulfate-Reducing Enrichment Culture†

    PubMed Central

    Meckenstock, Rainer U.; Annweiler, Eva; Michaelis, Walter; Richnow, Hans H.; Schink, Bernhard

    2000-01-01

    Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture was studied by substrate utilization tests and identification of metabolites by gas chromatography-mass spectrometry. In substrate utilization tests, the culture was able to oxidize naphthalene, 2-methylnaphthalene, 1- and 2-naphthoic acids, phenylacetic acid, benzoic acid, cyclohexanecarboxylic acid, and cyclohex-1-ene-carboxylic acid with sulfate as the electron acceptor. Neither hydroxylated 1- or 2-naphthoic acid derivatives and 1- or 2-naphthol nor the monoaromatic compounds ortho-phthalic acid, 2-carboxy-1-phenylacetic acid, and salicylic acid were utilized by the culture within 100 days. 2-Naphthoic acid accumulated in all naphthalene-grown cultures. Reduced 2-naphthoic acid derivatives could be identified by comparison of mass spectra and coelution with commercial reference compounds such as 1,2,3,4-tetrahydro-2-naphthoic acid and chemically synthesized decahydro-2-naphthoic acid. 5,6,7,8-Tetrahydro-2-naphthoic acid and octahydro-2-naphthoic acid were tentatively identified by their mass spectra. The metabolites identified suggest a stepwise reduction of the aromatic ring system before ring cleavage. In degradation experiments with [1-13C]naphthalene or deuterated D8-naphthalene, all metabolites mentioned derived from the introduced labeled naphthalene. When a [13C]bicarbonate-buffered growth medium was used in conjunction with unlabeled naphthalene, 13C incorporation into the carboxylic group of 2-naphthoic acid was shown, indicating that activation of naphthalene by carboxylation was the initial degradation step. No ring fission products were identified. PMID:10877763

  15. A Guide to Job Enrichment and Redesign.

    ERIC Educational Resources Information Center

    Cunningham, J. Barton; Eberle, Ted

    1990-01-01

    Describes job design alternatives--job enrichment, the job characteristics model, Japanese style management, and quality-of-worklife approaches. Focuses on the problems that human resources professionals may encounter when attempting to implement these approaches. (Author/JOW)

  16. Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen.

    PubMed

    Groudieva, Tatiana; Kambourova, Margarita; Yusef, Hoda; Royter, Maryna; Grote, Ralf; Trinks, Hauke; Antranikian, Garabed

    2004-12-01

    The diversity of culturable bacteria associated with sea ice from four permanently cold fjords of Spitzbergen, Arctic Ocean, was investigated. A total of 116 psychrophilic and psychrotolerant strains were isolated under aerobic conditions at 4 degrees C. The isolates were grouped using amplified rDNA restriction analysis fingerprinting and identified by partial sequencing of 16S rRNA gene. The bacterial isolates fell in five phylogenetic groups: subclasses alpha and gamma of Proteobacteria, the Bacillus-Clostridium group, the order Actinomycetales, and the Cytophaga-Flexibacter-Bacteroides (CFB) phylum. Over 70% of the isolates were affiliated with the Proteobacteria gamma subclass. Based on phylogenetic analysis (<98% sequence similarity), over 40% of Arctic isolates represent potentially novel species or genera. Most of the isolates were psychrotolerant and grew optimally between 20 and 25 degrees C. Only a few strains were psychrophilic, with an optimal growth at 10-15 degrees C. The majority of the bacterial strains were able to secrete a broad range of cold-active hydrolytic enzymes into the medium at a cultivation temperature of 4 degrees C. The isolates that are able to degrade proteins (skim milk, casein), lipids (olive oil), and polysaccharides (starch, pectin) account for, respectively, 56, 31, and 21% of sea-ice and seawater strains. The temperature dependences for enzyme production during growth and enzymatic activity were determined for two selected enzymes, alpha-amylase and beta-galactosidase. Interestingly, high levels of enzyme productions were measured at growth temperatures between 4 and 10 degrees C, and almost no production was detected at higher temperatures (20-30 degrees C). Catalytic activity was detected even below the freezing point of water (at -5 degrees C), demonstrating the unique properties of these enzymes.

  17. Comparative proteomic assessment of matrisome enrichment methodologies

    PubMed Central

    Krasny, Lukas; Paul, Angela; Wai, Patty; Howard, Beatrice A.; Natrajan, Rachael C.; Huang, Paul H.

    2016-01-01

    The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome. PMID:27589945

  18. Molecular and Kinetic Characterization of Planktonic Nitrospira spp. Selectively Enriched from Activated Sludge.

    PubMed

    Park, Mee-Rye; Park, Hongkeun; Chandran, Kartik

    2017-03-07

    Nitrospira spp. are chemolithoautotrophic nitrite-oxidizing bacteria (NOB), which are ubiquitous in natural and engineered environments. However, there exist few independent biokinetic studies on Nitrospira spp., likely because their isolation and selective enrichment from environmental consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 μm. On the basis of respirometric assays, estimated maximum specific growth rate (μmax), nitrite half saturation coefficient (KS), oxygen half saturation coefficient (KO), and biomass yield coefficient (Y) of the enriched cultures were 0.69 ± 0.10 d(-1), 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O2/L, and 0.14 ± 0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and thermodynamic parameters can help toward the development and application of energy-efficient biological nutrient removal processes through effective Nitrospira out-selection.

  19. Microfluidic droplet enrichment for targeted sequencing

    PubMed Central

    Eastburn, Dennis J.; Huang, Yong; Pellegrino, Maurizio; Sciambi, Adam; Ptáček, Louis J.; Abate, Adam R.

    2015-01-01

    Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications. PMID:25873629

  20. Conversion and enrichment in the Soviet Union

    SciTech Connect

    1991-04-01

    In the Soviet Union, just as in the West, the civilian nuclear industry emerged from research work undertaken for nuclear weapons development. At first, researchers tried various techniques for physical separation of uranium isotopes: electromagnetic and molecular-kinetic thermo-diffusion methods; gaseous diffusion; and centrifuge methods. All of those methods, which are based primarily on differences in the atomic mass of uranium isotopes, called for extensive research and the development of new, technically unprecedented equipment. Gradually gaseous diffusion and gas centrifuge technology became recognized as most feasible for industrial use, so research on other methods was terminated. Industrial-scale uranium enrichment in the Soviet Union began in 1949 using the gaseous diffusion method; by the early 1960s, centrifuge technology was in use on an industrial scale. All Soviet production of highly-enriched, weapons-grade uranium was halted in 1987. The Soviet Union now has four enrichment plants in operation (at classified locations), solely for civilian nuclear power needs. All four enrichment plants have centrifuge modules, and enrichment provided by gaseous diffusion accounts for less than 5% of their total output. Two of the four enrichment plants also incorporate facilities for conversion to uranium hexafluoride (UF{sub 6}).

  1. Toward a predictive theory for environmental enrichment.

    PubMed

    Watters, Jason V

    2009-11-01

    There have been many applications of and successes with environmental enrichment for captive animals. The theoretical spine upon which much enrichment work hangs largely describes why enrichment should work. Yet, there remains no clear understanding of how enrichment should be applied to achieve the most beneficial results. This lack of understanding may stem in part from the assumptions that underlie the application of enrichment by practitioners. These assumptions are derived from an understanding that giving animals choice and control in their environment stimulates their motivation to perform behaviors that may indicate a heightened state of well-being. Learning theory provides a means to question the manner in which these constructs are routinely applied, and converting learning theory's findings to optimality predictions suggests a particularly vexing paradox-that motivation to perform appears to be maintained best when acquiring a payoff for expressing the behavior is uncertain. This effect occurs even when the actual value of the payoff is the same for all schedules of certainty of payoff acquisition. The paradox can be resolved by invoking rewards of an alternative type, such as cognitive rewards, or through an understanding of how the average payoff changes with changes in the probability of reward. This model, with measures of the average change of the payoff, suggests testable scenarios by which practitioners can measure the quality of environmental uncertainty in enrichment programs.

  2. Dialogismo, lenguas extranjeras e identidad cultural (Dialogism, Foreign Languages, and Cultural Identity).

    ERIC Educational Resources Information Center

    Zoreda, Margaret Lee

    Foreign Language education will play an important role in the broadening and globalization of higher education for the 21st century. Where else will educators find the tools to "dialog" with--to engage--the "other" as part of the enriching process that accompanies cultural exchange, cultural broadening? This paper sheds light on these issues, and…

  3. Comparison of direct-plating and enrichment methods for isolation of Vibrio cholerae from diarrhea patients.

    PubMed Central

    Lesmana, M; Richie, E; Subekti, D; Simanjuntak, C; Walz, S E

    1997-01-01

    A direct-plating method on thiosulfate citrate bile salts sucrose agar (DIR-TCBS) in conjunction with enrichment in alkaline peptone water (APW) incubated for both 6 h and 24 h followed by subculture onto TCBS (APW6h-TCBS and APW24h-TCBS, respectively) was performed on 16,034 rectal swab samples for isolating Vibrio cholerae. A total of 2,932 (18.3%) rectal swab samples were positive for V. cholerae O1 biotype El Tor, with the Ogawa serotype constituting 99.2% of the isolates. There were no significant differences in V. cholerae O1 isolation rates between the three culture systems nor between the combinations of any two systems. However, direct plating plus enrichment demonstrated a significantly higher V. cholerae O1 isolation rate than DIR-TCBS alone (P < 0.02). Conversely, enrichment procedure, alone or in combination with DIR-TCBS, yielded significantly more (P < 0.0001) V. cholerae non-O1 isolates than DIR-TCBS alone. The length of incubation time of the enrichment broth, 6 h, offers no significant advantages over 24 h for the isolation of V. cholerae O1 and non-O1. A 24-h enrichment broth incubation period has the practical advantage of being easy to integrate into a normal laboratory workday, whereas 6-h broth enrichment, although more commonly recommended, requires that arrangements be made for after-hours subculture. PMID:9196208

  4. Development of a multi-pathogen enrichment broth for simultaneous growth of five common foodborne pathogens.

    PubMed

    Chen, Juan; Tang, Junni; Bhunia, Arun K; Tang, Cheng; Wang, Changting; Shi, Hui

    2015-01-01

    The objective of the present study was to formulate a multi-pathogen enrichment broth which could support the simultaneous growth of five common foodborne pathogens (Salmonella enterica, Staphylococcus aureus, Shigella flexneri, Listeria monocytogenes and Escherichia coli O157:H7). The formulated broth SSSLE was composed of potassium tellurite, bile salt, lithium chloride, and sodium chloride as growth-inhibitors; glucose, esculin, mannitol and sodium pyruvate as growth-promoters. Compared with the respective specific selective enrichment broths, the individual growth pattern of each target pathogen in SSSLE was equal, or even better, except in the case of S. flexneri. In mixed-culture experiments, the gram-negative bacteria showed higher growth capabilities than the gram-positive bacteria after 8-h enrichment; however, the cell numbers after 24-h enrichment indicated that SSSLE could support the concurrent growth of five target pathogens irrespective of whether pathogens were inoculated initially at equal or unequal levels. For natural food samples under the high background flora, the final cell numbers enriched in SSSLE for five targets were enough to be detected by multiplex PCR. In conclusion, SSSLE was capable of supporting the growth of five target pathogens concurrently. The new broth formulated in this study has the potential of saving time, efforts and costs in multi-pathogen enrichment procedures.

  5. Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion

    PubMed Central

    Kato, Souichiro; Goya, Eri; Tanaka, Michiko; Kitagawa, Wataru; Kikuchi, Yoshitomo; Asano, Kozo; Kamagata, Yoichi

    2016-01-01

    Interest in the interaction of microorganisms with cesium ions (Cs+) has arisen, especially in terms of their potent ability for radiocesium bioaccumulation and their important roles in biogeochemical cycling. Although high concentrations of Cs+ display toxic effects on microorganisms, there have been only limited reports for Cs+-tolerant microorganisms. Here we report enrichment and isolation of Cs+-tolerant microorganisms from soil microbiota. Microbial community analysis revealed that bacteria within the phylum Bacteroidetes, especially Flavobacterium spp., dominated in enrichment cultures in the medium supplemented with 50 or 200 mM Cs+, while Gammaproteobacteria was dominant in the control enrichment cultures (in the presence of 50 and 200 mM K+ instead of Cs+). The dominant Flavobacterium sp. was successfully isolated from the enrichment culture and was closely related to Flavobacterium chungbukense with 99.5% identity. Growth experiments clearly demonstrated that the isolate has significantly higher tolerance to Cs+ compared to its close relatives, suggesting the Cs+-tolerance is a specific trait of this strain, but not a universal trait in the genus Flavobacterium. Measurement of intracellular K+ and Cs+ concentrations of the Cs+-tolerant isolate and its close relatives suggested that the ability to maintain low intracellular Cs+ concentration confers the tolerance against high concentrations of external Cs+. PMID:26883718

  6. Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion.

    PubMed

    Kato, Souichiro; Goya, Eri; Tanaka, Michiko; Kitagawa, Wataru; Kikuchi, Yoshitomo; Asano, Kozo; Kamagata, Yoichi

    2016-02-17

    Interest in the interaction of microorganisms with cesium ions (Cs(+)) has arisen, especially in terms of their potent ability for radiocesium bioaccumulation and their important roles in biogeochemical cycling. Although high concentrations of Cs(+) display toxic effects on microorganisms, there have been only limited reports for Cs(+)-tolerant microorganisms. Here we report enrichment and isolation of Cs(+)-tolerant microorganisms from soil microbiota. Microbial community analysis revealed that bacteria within the phylum Bacteroidetes, especially Flavobacterium spp., dominated in enrichment cultures in the medium supplemented with 50 or 200 mM Cs(+), while Gammaproteobacteria was dominant in the control enrichment cultures (in the presence of 50 and 200 mM K(+) instead of Cs(+)). The dominant Flavobacterium sp. was successfully isolated from the enrichment culture and was closely related to Flavobacterium chungbukense with 99.5% identity. Growth experiments clearly demonstrated that the isolate has significantly higher tolerance to Cs(+) compared to its close relatives, suggesting the Cs(+)-tolerance is a specific trait of this strain, but not a universal trait in the genus Flavobacterium. Measurement of intracellular K(+) and Cs(+) concentrations of the Cs(+)-tolerant isolate and its close relatives suggested that the ability to maintain low intracellular Cs(+) concentration confers the tolerance against high concentrations of external Cs(+).

  7. Urine culture

    MedlinePlus

    Culture and sensitivity - urine ... when urinating. You also may have a urine culture after you have been treated for an infection. ... when bacteria or yeast are found in the culture. This likely means that you have a urinary ...

  8. Urine Culture

    MedlinePlus

    ... products and services. Advertising & Sponsorship: Policy | Opportunities Urine Culture Share this page: Was this page helpful? Also known as: Urine Culture and Sensitivity; Urine C and S Formal name: Culture, ...

  9. Safeguards Culture

    SciTech Connect

    Frazar, Sarah L.; Mladineo, Stephen V.

    2012-07-01

    The concepts of nuclear safety and security culture are well established; however, a common understanding of safeguards culture is not internationally recognized. Supported by the National Nuclear Security Administration, the authors prepared this report, an analysis of the concept of safeguards culture, and gauged its value to the safeguards community. The authors explored distinctions between safeguards culture, safeguards compliance, and safeguards performance, and evaluated synergies and differences between safeguards culture and safety/security culture. The report concludes with suggested next steps.

  10. Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Different Enrichment Conditions Influence Bioavailability and Selection of Phenanthrene-Degrading Isolates

    PubMed Central

    Grosser, Robert J.; Friedrich, Michael; Ward, David M.; Inskeep, William P.

    2000-01-01

    The sorption of organic contaminants by natural organic matter (NOM) often limits substrate bioavailability and is an important factor affecting microbial degradation rates in soils and sediments. We hypothesized that reduced substrate bioavailability might influence which microbial assemblages are responsible for contaminant degradation under enrichment culture conditions. Our primary goal was to characterize enrichments in which different model organic solid phases were used to establish a range of phenanthrene bioavailabilities for soil microorganisms. Phenanthrene sorption coefficients (expressed as log KD values) ranged from 3.0 liters kg−1 for Amberlite carboxylic acid cation-exchange resin (AMB) to 3.5 liters kg−1 for Biobeads polyacrylic resin (SM7) and 4.2 liters kg−1 for Biobeads divinyl benzene resin (SM2). Enrichment cultures were established for control (no sorptive phase), sand, AMB, SM7, and SM2 treatments by using two contaminated soils (from Dover, Ohio, and Libby, Mont.) as the initial inocula. The effects of sorption by model phases on the degradation of phenanthrene were evaluated for numerous transfers in order to obtain stable microbial assemblages representative of sorptive and nonsorptive enrichment cultures and to eliminate the effects of the NOM present in the initial inoculum. Phenanthrene degradation rates were similar for each soil inoculum and ranged from 4 to 5 μmol day−1 for control and sand treatments to approximately 0.4 μmol day−1 in the presence of the SM7 sorptive phase. The rates of phenanthrene degradation in the highly sorptive SM2 enrichment culture were insignificant; consequently, stable microbial populations could not be obtained. Bacterial isolates obtained from serial dilutions of enrichment culture samples exhibited significant differences in rates of phenanthrene degradation performed in the presence of SM7, suggesting that enrichments performed in the presence of a sorptive phase selected for different

  11. Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

    PubMed Central

    Daquigan, Ninalynn; Grim, Christopher J.; White, James R.; Hanes, Darcy E.; Jarvis, Karen G.

    2016-01-01

    Culture based methods are commonly employed to detect pathogens in food and environmental samples. These methods are time consuming and complex, requiring multiple non-selective and selective enrichment broths, and usually take at least 1 week to recover and identify pathogens. Improving pathogen detection in foods is a primary goal for regulatory agencies and industry. Salmonella detection in food relies on a series of culture steps in broth formulations optimized to resuscitate Salmonella and reduce the abundance of competitive bacteria. Examples of non-selective pre-enrichment broths used to isolate Salmonella from food include Lactose, Universal Pre-enrichment, BPW, and Trypticase Soy broths. Tetrathionate (TT) and Rappaport–Vassiliadis (RV) broths are employed after a 24-h non-selective enrichment to select for Salmonella and hamper the growth of competitive bacteria. In this study, we tested a new formulation of TT broth that lacks brilliant green dye and has lower levels of TT . We employed this TT broth formulation in conjunction with a 6-h non-selective pre-enrichment period and determined that Salmonella recovery was possible one day earlier than standard food culture methods. We tested the shortened culture method in different non-selective enrichment broths, enumerated Salmonella in the non-selective enrichments, and used 16S rRNA gene sequencing to determine the proportional abundances of Salmonella in the TT and RV selective enrichments. Together these data revealed that a 6-h non-selective pre-enrichment reduces the levels of competitive bacteria inoculated into the selective TT and RV broths, enabling the recovery of Salmonella 1 day earlier than standard culture enrichment methods. PMID:28082968

  12. Cultural Heritage Content Re-Use: An Aggregators's Point of View

    NASA Astrophysics Data System (ADS)

    Gavrilis, D.; Ioannides, M.; Theofanous, E.

    2015-08-01

    This paper introduces a use case of re-using aggregated and enriched metadata for the tourism creative industry. The MORe aggregation and enrichment framework is presented along with an example for enriching cultural heritage objects harvested from a number of Omeka repositories. The enriched content is then published both to the EU Digital Library Europeana (http://www.europeana.eu) and to an Elastic Search component that feeds a portal aimed at providing tourists with interesting information.

  13. Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters

    PubMed Central

    Berdugo-Clavijo, Carolina; Gieg, Lisa M.

    2014-01-01

    The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir. PMID:24829563

  14. Indices, multispecies and synthesis descriptors in benthic assessments: Intertidal organic enrichment from oyster farming

    NASA Astrophysics Data System (ADS)

    Quintino, Victor; Azevedo, Ana; Magalhães, Luísa; Sampaio, Leandro; Freitas, Rosa; Rodrigues, Ana Maria; Elliott, Michael

    2012-09-01

    Intertidal off-bottom oyster culture is shown to cause organic enrichment of the shore and although there are two stressors of interest (the presence of a structure, the trestles, and also the sediment and organic waste from the oysters), these can be separated and their relative impacts determined using an appropriate nested experimental design and data treatments. Although no artificial food sources are involved, the oysters feeding activity and intensity of culture enhances biodeposition and significantly increases the sediment fines content and total organic matter. This in general impoverished the benthic community in culture areas rather than a species succession with the installation of opportunists or a resulting increase in the abundance and biomass of benthic species; the findings can be a direct consequence of the intertidal situation which is less-amenable recruitment of species more common to the subtidal environment. Thus the most appropriate biological descriptors to diagnose the effects associated with the organic enrichment were the multispecies abundance data as well as the primary biological variables species richness and abundance. The effects were however spatially and statistically significantly confined to the area located directly underneath the culture bags compared to the corridors located between the trestles, which do not show such enrichment effects. Synthesis biotic indices were much less effective to diagnose the benthic alterations associated with this organic enrichment. These results show that special attention must be paid when using indices in areas where the organic enrichment induces an impoverishment of the benthic community but not necessarily a species replacement with the installation of opportunists.

  15. Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters.

    PubMed

    Berdugo-Clavijo, Carolina; Gieg, Lisa M

    2014-01-01

    The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir.

  16. Evaluation of different enrichment methods for pathogenic Yersinia species detection by real time PCR

    PubMed Central

    2014-01-01

    Background Yersiniosis is a zoonotic disease reported worldwide. Culture and PCR based protocols are the most common used methods for detection of pathogenic Yersinia species in animal samples. PCR sensitivity could be increased by an initial enrichment step. This step is particularly useful in surveillance programs, where PCR is applied to samples from asymptomatic animals. The aim of this study was to evaluate the improvement in pathogenic Yersinia species detection using a suitable enrichment method prior to the real time PCR (rtPCR). Nine different enrichment protocols were evaluated including six different broth mediums (CASO, ITC, PSB, PBS, PBSMSB and PBSSSB). Results The analysis of variance showed significant differences in Yersinia detection by rtPCR according to the enrichment protocol used. These differences were higher for Y. pseudotuberculosis than for Y. enterocolitica. In general, samples incubated at lower temperatures yielded the highest detection rates. The best results were obtained with PBSMSB and PBS2. Application of PBSMSB protocol to free-ranging wild board samples improved the detection of Y. enterocolitica by 21.2% when compared with direct rtPCR. Y. pseudotuberculosis detection was improved by 10.6% when results obtained by direct rtPCR and by PBSMSB enrichment before rtPCR were analyzed in combination. Conclusions The data obtained in the present study indicate a difference in Yersinia detection by rtPCR related to the enrichment protocol used, being PBSMSB enrichment during 15 days at 4°C and PBS during 7 days at 4°C the most efficient. The use of direct rtPCR in combination with PBSMSB enrichment prior to rtPCR resulted in an improvement in the detection rates of pathogenic Yersinia in wild boar and could be useful for application in other animal samples. PMID:25168886

  17. The enriched chromium neutrino source for GALLEX

    SciTech Connect

    Hartmann, F.X.; Hahn, R.L.

    1991-01-18

    The preparation and study of an intense source of neutrinos in the form of neutron irradiated materials which are enriched in Cr-50 for use in the GALLEX solar neutrino experiment are discussed. Chromyl fluoride gas is enriched in the Cr-50 isotope by gas centrifugation and subsequently converted to a very stable form of chromium oxide. The results of neutron activation analyses of such chromium samples indicate low levels of any long-lived activities, but show that short-lived activities, in particular Na-24, may be of concern. These results show that irradiating chromium oxide enriched in Cr-50 is preferable to irradiating either natural chromium or argon gas as a means of producing a neutrino source to calibrate the GALLEX detector. These results of the impurity level analysis of the enriched chromyl fluoride gas and its conversion to the oxide are also of interest to work in progress by other members of the Collaboration investigating an alternative conversion of the enriched gas to chromium metal. 35 refs., 12 figs., 5 tabs.

  18. Linking nutrient enrichment, sediment erodibility and biofilms

    NASA Astrophysics Data System (ADS)

    Conrad, B.; Mahon, R.; Sojka, S. L.

    2014-12-01

    Sediment movement in coastal lagoons affects nutrient flux and primary producer growth. Previous research has shown that sediment erodibility is affected by biofilm concentration and that growth of benthic organisms, which produce biofilm, is affected by nutrient enrichment. However, researchers have not examined possible links between nutrient addition and sediment erodibility. We manipulated nutrient levels in the water column of 16 microcosms filled with homogenized sediment from a shallow coastal lagoon and artificial seawater to determine the effects on biofilm growth, measured through chlorophyll a and colloidal carbohydrate concentrations. Erosion tests using a Gust microcosm were conducted to determine the relationship between sediment erodibility and biofilm concentration. Results show that carbohydrate levels decreased with increasing nutrient enrichment and were unrelated to chlorophyll concentrations and erodibility. The nutrient levels did not predictably affect the chlorophyll levels, with lower chlorophyll concentrations in the control and medium enrichment treatments than the low and high enrichment treatments. Controls on biofilm growth are still unclear and the assumed relationship between carbohydrates and erodibility may be invalid. Understanding how biofilms respond to nutrient enrichment and subsequent effects on sediment erodibility is essential for protecting and restoring shallow coastal systems.

  19. Profile of World Uranium Enrichment Programs-2009

    SciTech Connect

    Laughter, Mark D

    2009-04-01

    It is generally agreed that the most difficult step in building a nuclear weapon is acquiring fissile material, either plutonium or highly enriched uranium (HEU). Plutonium is produced in a nuclear reactor, whereas HEU is produced using a uranium enrichment process. Enrichment is also an important step in the civil nuclear fuel cycle, in producing low enriched uranium (LEU) for use as fuel for nuclear reactors to generate electricity. However, the same equipment used to produce LEU for nuclear reactor fuel can also be used to produce HEU for weapons. Safeguards at an enrichment plant are the array of assurances and verification techniques that ensure uranium is not diverted or enriched to HEU. There are several techniques for enriching uranium. The two most prevalent are gaseous diffusion, which uses older technology and requires a lot of energy, and gas centrifuge separation, which uses more advanced technology and is more energy efficient. Gaseous diffusion plants (GDPs) provide about 40% of current world enrichment capacity but are being phased out as newer gas centrifuge enrichment plants (GCEPs) are constructed. Estimates of current and future enrichment capacity are always approximate, due to the constant upgrades, expansions, and shutdowns occurring at enrichment plants, largely determined by economic interests. Currently, the world enrichment capacity is approximately 56 million kilogram separative work units (SWU) per year, with 22.5 million in gaseous diffusion and more than 33 million in gas centrifuge plants. Another 34 million SWU/year of capacity is under construction or planned for the near future, almost entirely using gas centrifuge separation. Other less-efficient techniques have also been used in the past, including electromagnetic and aerodynamic separations, but these are considered obsolete, at least from a commercial perspective. Laser isotope separation shows promise as a possible enrichment technique of the future but has yet to be

  20. 75 FR 52996 - Areva Enrichment Services, LLC (Eagle Rock Enrichment Facility); Notice of Atomic Safety and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-30

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Areva Enrichment Services, LLC (Eagle Rock Enrichment Facility); Notice of Atomic Safety and Licensing Board Reconstitution Pursuant to 10 CFR 2.313(c) and 2.321(b), the Atomic Safety and...

  1. 76 FR 11523 - Atomic Safety and Licensing Board; AREVA Enrichment Services, LLC (Eagle Rock Enrichment Facility...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-02

    ..., ID, 76 FR 9054 (Feb. 16, 2011). In accord with Atomic Energy Act (AEA) section 274l, 42 U.S.C. Sec... Rock Enrichment Facility), 74 FR 38,052, 38,055 (Jul. 30, 2009) (CLI-09- 15, 70 NRC 1, 10-11 (2009... of Enrichment Facility Licensing Proceeding), 75 FR 63,213 (Oct. 14, 2010), which was the subject...

  2. Uranium enrichment management review: summary of analysis

    SciTech Connect

    Not Available

    1981-01-01

    In May 1980, the Assistant Secretary for Resource Applications within the Department of Energy requested that a group of experienced business executives be assembled to review the operation, financing, and management of the uranium enrichment enterprise as a basis for advising the Secretary of Energy. After extensive investigation, analysis, and discussion, the review group presented its findings and recommendations in a report on December 2, 1980. The following pages contain background material on which that final report was based. This report is arranged in chapters that parallel those of the uranium enrichment management review final report - chapters that contain summaries of the review group's discussion and analyses in six areas: management of operations and construction; long-range planning; marketing of enrichment services; financial management; research and development; and general management. Further information, in-depth analysis, and discussion of suggested alternative management practices are provided in five appendices.

  3. Inhomogeneous chemical enrichment in the Galactic Halo

    NASA Astrophysics Data System (ADS)

    Kobayashi, Chiaki

    2015-08-01

    In a galaxy, chemical enrichment takes place in an inhomogeneous fashion, and the Galactic Halo is one of the places where the inhomogeneous effects are imprinted and can be constrained from observations. I show this using my chemodynamical simulations of Milky Way type galaxies. The scatter in the elemental abundances is originated from radial migration, merging/accretion of satellite galaxies, local variation of star formation and chemical enrichment, and intrinsic variation of nucleosynthesis yields. In the simulated galaxies, there is no strong age-metallicity relations. This means that the most metal poor stars are not always the oldest stars, and can be formed in chemically unevolved clouds at later times. The long-lifetime sources of chemical enrichment such as asymptotic giant blanch stars or neutron star mergers can contribute the abundance patterns of extremely metal-poor stars, which are in good agreement with observations.

  4. Nutrient Enrichment Increases Mortality of Mangroves

    PubMed Central

    Lovelock, Catherine E.; Ball, Marilyn C.; Martin, Katherine C.; C. Feller, Ilka

    2009-01-01

    Nutrient enrichment of the coastal zone places intense pressure on marine communities. Previous studies have shown that growth of intertidal mangrove forests is accelerated with enhanced nutrient availability. However, nutrient enrichment favours growth of shoots relative to roots, thus enhancing growth rates but increasing vulnerability to environmental stresses that adversely affect plant water relations. Two such stresses are high salinity and low humidity, both of which require greater investment in roots to meet the demands for water by the shoots. Here we present data from a global network of sites that documents enhanced mortality of mangroves with experimental nutrient enrichment at sites where high sediment salinity was coincident with low rainfall and low humidity. Thus the benefits of increased mangrove growth in response to coastal eutrophication is offset by the costs of decreased resilience due to mortality during drought, with mortality increasing with soil water salinity along climatic gradients. PMID:19440554

  5. Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results

    PubMed Central

    Isserlin, Ruth; Merico, Daniele; Voisin, Veronique; Bader, Gary D.

    2014-01-01

    High-throughput OMICs experiments generate signals for millions of entities (i.e. genes, proteins, metabolites or any measurable biological entity) in the cell. In an effort to summarize and explore these signals, expression results are examined in the context of known pathways and processes, through enrichment analysis to generate a set of pathways and processes that is significantly enriched. Due to the high redundancy in annotation resources this often results in hundreds of sets. To facilitate the analysis of these results, we have developed the Enrichment Map app to visualize enrichments as a network. We have updated Enrichment Map to support Cytoscape 3, and have added additional features including new data formats and command line access. PMID:25075306

  6. 21 CFR 136.115 - Enriched bread, rolls, and buns.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... thereof, including any wheat germ or partly defatted wheat germ in any enriched flour used, shall not be more than 5 percent of the flour ingredient. (5) Enriched flour may be used, in whole or in part, instead of flour. As used in this section, the term “enriched flour” includes enriched bromated flour....

  7. Status of gadolinium enrichment technology at LLNL

    SciTech Connect

    Haynam, C.; Comaskey, B.; Conway, J.; Eggert, J.; Glaser, J.; Ng, E.; Paisner, J.; Solarz, R.; Worden, E.

    1993-01-01

    A method based on,polarization selectivity and three step laser photoionization is presented for separation of the odd isotopes of gadolinium. Measurements of the spectroscopic parameters needed to quantify the excitation pathway are discussed. Model results are presented for the efficiency of photoionization. The vapor properties of electron beam vaporized gadolinium are presented which show dramatic cooling during the expansion of the hot dense vapor into a vacuum. This results in a significant increase in the efficiency of conversion of natural feed into enriched product in the AVLIS process. Production of enriched gadolinium for use in commercial power reactors appears to be economically viable using technology in use at LLNL.

  8. Fire extinguishment in oxygen enriched atmospheres

    NASA Technical Reports Server (NTRS)

    Robertson, A. F.; Rappaport, M. W.

    1973-01-01

    Current state-of-the-art of fire suppression and extinguishment techniques in oxygen enriched atmosphere is reviewed. Four classes of extinguishment action are considered: cooling, separation of reactants, dilution or removal of fuel, and use of chemically reactive agents. Current practice seems to show preference for very fast acting water spray applications to all interior surfaces of earth-based chambers. In space, reliance has been placed on fire prevention methods through the removal of ignition sources and use of nonflammable materials. Recommendations are made for further work related to fire suppression and extinguishment in oxygen enriched atmospheres, and an extensive bibliography is appended.

  9. 3D microfilter device for viable circulating tumor cell (CTC) enrichment from blood.

    PubMed

    Zheng, Siyang; Lin, Henry K; Lu, Bo; Williams, Anthony; Datar, Ram; Cote, Richard J; Tai, Yu-Chong

    2011-02-01

    Detection of circulating tumor cells has emerged as a promising minimally invasive diagnostic and prognostic tool for patients with metastatic cancers. We report a novel three dimensional microfilter device that can enrich viable circulating tumor cells from blood. This device consists of two layers of parylene membrane with pores and gap precisely defined with photolithography. The positions of the pores are shifted between the top and bottom membranes. The bottom membrane supports captured cells and minimize the stress concentration on cell membrane and sustain cell viability during filtration. Viable cell capture on device was investigated with scanning electron microscopy, confocal microscopy, and immunofluorescent staining using model systems of cultured tumor cells spiked in blood or saline. The paper presents and validates this new 3D microfiltration concept for circulation tumor cell enrichment application. The device provides a highly valuable tool for assessing and characterizing viable enriched circulating tumor cells in both research and clinical settings.

  10. Yersinia enterocolitica: its isolation by cold enrichment from patients and healthy subjects.

    PubMed Central

    Van Noyen, R; Vandepitte, J; Wauters, G; Selderslaghs, R

    1981-01-01

    Routine culture and cold enrichment were compared in a prospective study on the isolation of Yersinia enterocolitica from patients with intestinal disease. Healthy controls were examined with the cold enrichment method only. Y enterocolitica was isolated from 5.9% of 1635 patient stools, 3.4% of 206 appendices, and 4.0% of 555 control stools. Serotypes 0:3 and 0:9 were eight times more prevalent in patients than in controls. Other serotypes were twice as prevalent in controls than in patients. Cold enrichment did not significantly increase the recovery of serotypes 0:3 and 0:9 in acute enteritis, but it was responsible for all isolates of the other serotypes. Evidence is presented that the other serotypes are not pathogenic. In patient stools, Y enterocolitica was demonstrated less frequently than Salmonella (9.1%), and more often than Campylobacter jejuni (1.8%) and Shigella (0.1%). PMID:7024325

  11. Differential Response of High-Elevation Planktonic Bacterial Community Structure and Metabolism to Experimental Nutrient Enrichment

    PubMed Central

    Nelson, Craig E.; Carlson, Craig A.

    2011-01-01

    Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and

  12. 77 FR 13367 - General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-06

    ... COMMISSION General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...- Hitachi Global Laser Enrichment, LLC (GLE) Uranium Enrichment Facility. On June 26, 2009, GLE submitted a license application that proposes the construction, operation, and decommissioning of a...

  13. Global Nomads and the Search for Cultural Identity: Tips from the Classroom

    ERIC Educational Resources Information Center

    Al-Issa, Ahmad

    2004-01-01

    Understanding one's cultural system leads to greater skills in appreciating other cultures. When students and teachers from diverse cultural backgrounds come together, they bring diversity that can either improve or break down the process of learning and teaching. If handled properly, cultural diversity can enrich the classroom; if ignored,…

  14. CD8+ enriched “young” tumor infiltrating lymphocytes can mediate regression of metastatic melanoma

    PubMed Central

    Dudley, Mark E.; Gross, Colin A.; Langhan, Michelle M.; Garcia, Marcos R.; Sherry, Richard M.; Yang, James C.; Phan, Giao Q.; Kammula, Udai S.; Hughes, Marybeth S.; Citrin, Deborah E.; Restifo, Nicholas P.; Wunderlich, John; Prieto, Peter A.; Hong, Jenny J.; Langan, Russell C.; Zlott, Daniel A.; Morton, Kathleen E.; White, Donald E.; Laurencot, Carolyn; Rosenberg, Steven A.

    2010-01-01

    Purpose Tumor infiltrating lymphocytes (TIL) and interleukin (IL)-2 administered following lymphodepletion can cause the durable complete regression of bulky metastatic melanoma in patients refractory to approved treatments. However, the generation of a unique tumor-reactive TIL culture for each patient may be prohibitively difficult. We therefore investigated the clinical and immunological impact of unscreened, CD8+ enriched “young” TIL. Experimental Design Methods were developed for generating TIL that minimized the time in culture and eliminated the individualized tumor-reactivity screening step. Thirty-three patients were treated with these CD8+ enriched young TIL and IL-2 following non-myeloablative lymphodepletion (NMA). Twenty-three additional patients were treated with CD8+ enriched young TIL and IL-2 after lymphodepletion with NMA and 6Gy of total body irradiation (TBI). Results Young TIL cultures for therapy were successfully established from 83% of 122 consecutive melanoma patients. Nineteen of 33 patients (58%) treated with CD8+ enriched young TIL and NMA had an objective response (RECIST) including three complete responders. Eleven of 23 patients (48%) treated with TIL and 6Gy TBI had an objective response including two complete responders. At one month after TIL infusion the absolute CD8+ cell numbers in the periphery were highly correlated with response. Conclusion This study shows that a rapid and simplified method can be used to reliably generate CD8+ enriched young TIL for administration as an individualized therapy for advanced melanoma, and may allow this potentially effective treatment to be applied at other institutions and to reach additional patients. PMID:20668005

  15. Methods for Enhanced Culture Recovery of Francisella tularensis

    PubMed Central

    Petersen, Jeannine M.; Schriefer, Martin E.; Gage, Kenneth L.; Montenieri, John A.; Carter, Leon G.; Stanley, Miles; Chu, May C.

    2004-01-01

    Francisella tularensis is found in a wide variety of hosts and extrahost environments, making culture recovery a diagnostic challenge. Here we demonstrate improved recovery times and good sensitivity (90%) when cultures were inoculated on the site of an investigation using fresh tissues. For contaminated specimens, antibiotic supplementation of enriched cysteine heart agar blood culture medium improved recovery of F. tularensis by 81.1%. For transport of tissues, immediate freezing yielded culture recovery rates as high as 94%. PMID:15184180

  16. Enriching and Assessing Young Children's Multimodal Storytelling

    ERIC Educational Resources Information Center

    Wessel-Powell, Christy; Kargin, Tolga; Wohlwend, Karen E.

    2016-01-01

    This article provides primary teachers with assessment tools and curricular examples to expand writers' workshop by adding a multimodal storytelling unit on drama and filmmaking, allowing students to create engaging off-the-page stories through films and play performances that enrich writing. Too often, children's literacy abilities are assessed…

  17. Projects To Enrich School Mathematics. Level 3.

    ERIC Educational Resources Information Center

    Sachs, Leroy, Ed.

    This is a series of research projects that can be used for enrichment of the high school mathematics curriculum. It is suggested that the topics are either not found in the standard curriculum or represent a more indepth study of standard topics. The areas considered are: applications of the microcomputer in mathematics; the fourth dimension and…

  18. Implementing the Schoolwide Enrichment Model in Brazil

    ERIC Educational Resources Information Center

    de Souza Fleith, Denise; Soriano de Alencar, Eunice M. L.

    2010-01-01

    The Schoolwide Enrichment Model (SEM) has been one of the most widely used models in the education of the gifted in Brazil. It has inspired the political and pedagogical project of the Centers of Activities of High Abilities/Giftedness recently implemented in 27 Brazilian states by the Ministry of Education. In this article, our experience in…

  19. Projects To Enrich School Mathematics. Level 2.

    ERIC Educational Resources Information Center

    Sachs, Leroy, Ed.

    This is a series of research projects that can be used for enrichment of the middle school mathematics curriculum. It is suggested that the topics are either not found in the standard curriculum or represent a more indepth study of standard topics. The areas considered are: microcomputer programs; divisibility; magic squares; pentominoes; the…

  20. Parents as Partners in Art Education Enrichment

    ERIC Educational Resources Information Center

    Hansen, Laurie

    2008-01-01

    The author describes a parent art program, how it works, and ways to implement it. She emphasizes the strengths of parent programs as a way to support and enrich existing arts education, not as a replacement. Hansen describes the art kit--the adult's teaching resource--and the basic four-part process: presentation, demonstration, an art activity,…

  1. Enriching Science and Math through Engineering

    ERIC Educational Resources Information Center

    Redmond, Adrienne; Thomas, Julie; High, Karen; Scott, Margaret; Jordan, Pat; Dockers, Jean

    2011-01-01

    This case study reviewed the collaborative efforts of university engineers, teacher educators, and middle school teachers to advance sixth- and seventh-grade students' learning through a series of project-based engineering activities. This two-year project enriched regular school curricula by introducing real-world applications of science and…

  2. National 4-H School Enrichment Survey.

    ERIC Educational Resources Information Center

    Diem, Keith G.

    2001-01-01

    A survey of 4-H school enrichment programs (813 responses) found that they reach large numbers of diverse youth and develop credibility with community and schools. Long-term programs such as 4-H clubs have proven effective in helping youth develop life skills, but Extension must carefully consider the purpose and consequences of diverting…

  3. Enriching a Child's Literacy Environment (ECLE).

    ERIC Educational Resources Information Center

    Reid, Ethna R.

    The Enriching a Child's Literacy Environment (ECLE) program was designed to establish a model for teaching parents, teachers, and other care providers how to develop the oral language, thinking abilities and motor skills of young children (ages six months to three years). ECLE trainers instruct the parents or other care providers by first modeling…

  4. Method for laser induced isotope enrichment

    DOEpatents

    Pronko, Peter P.; Vanrompay, Paul A.; Zhang, Zhiyu

    2004-09-07

    Methods for separating isotopes or chemical species of an element and causing enrichment of a desired isotope or chemical species of an element utilizing laser ablation plasmas to modify or fabricate a material containing such isotopes or chemical species are provided. This invention may be used for a wide variety of materials which contain elements having different isotopes or chemical species.

  5. Teaching Mathematical Modelling: Demonstrating Enrichment and Elaboration

    ERIC Educational Resources Information Center

    Warwick, Jon

    2015-01-01

    This paper uses a series of models to illustrate one of the fundamental processes of model building--that of enrichment and elaboration. The paper describes how a problem context is given which allows a series of models to be developed from a simple initial model using a queuing theory framework. The process encourages students to think about the…

  6. Research Related to the Enrichment Triad Model.

    ERIC Educational Resources Information Center

    Gubbins, E. Jean, Ed.

    This report highlights four research studies related to the Enrichment Triad Model, which encourages problem finding and problem solving in gifted students. The first study, "Academic Underachievement among the Gifted: Reversing School Failure" by Linda J. Emerick, identified six factors which influenced the reversal of the…

  7. Enrichment Education: Key to NCLEX Success.

    ERIC Educational Resources Information Center

    Wolahan, Caryle G. Hussey; Wieczorek, Rita Reis

    1991-01-01

    A concomitant decrease in test scores and major change in the composition of the student body was dealt with by the College of Nursing at the State University of New York through the Nursing Education Success Plan. The plan addresses student preparation for the National Council Licensure Exam (NCLEX), curriculum revision, remediation/enrichment,…

  8. ParentSource: A Practice in Enrichment

    ERIC Educational Resources Information Center

    Blackwell, Patricia

    2005-01-01

    Community-based parenting education programs have a unique role to play in the promotion of infant mental health. In contrast to classes that seek to accelerate child development, the author describes enrichment programs that promote parent-child bonding and healthy social and emotional development. The ParentSource program was developed on the…

  9. 21 CFR 137.305 - Enriched farina.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 2 2014-04-01 2014-04-01 false Enriched farina. 137.305 Section 137.305 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION CEREAL FLOURS AND RELATED PRODUCTS Requirements for Specific Standardized Cereal Flours...

  10. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture.

  11. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

    PubMed Central

    Russell, Joseph A.; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolate